The DOI matches its Crossref record; 254 of the 254 references it cites were found in a registry or an index; 10 of the 253 sources its claims cite were checked for support.
PROTAC targeted protein degraders: the past is prologue
Open accessAbstract
Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin–proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered ‘undruggable’. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology. Targeted protein degradation with proteolysis-targeting chimeras (PROTACs) has the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. This article summarizes the first two decades of PROTAC discovery and discusses key areas for the future of this therapeutic modality, including establishing the target classes for which it is most suitable and extending its application beyond oncology.
Overview
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Written from the paper’s full text.
TL;DR
This review summarizes 20 years of PROTAC targeted protein degradation, from the first small-molecule PROTAC in 2001 to clinical proof-of-concept in 2020 and a growing industry pipeline. It argues that TPD is poised to expand beyond oncology, to new E3 ligases, and to previously undrugged targets.
Key findings
- The first fully synthetic PROTAC, Protac-1, was reported in 2001 and targeted METAP2 via β-TRCP; the field then moved from peptide-based bioPROTACs to fully synthetic small molecules, with the first heterobifunctional degraders ARV-110 and ARV-471 entering phase I trials in 2019.
- In 2020, ARV-110 (AR degrader) was well tolerated up to 420 mg, showed target degradation in tumours and early antitumour activity, and began phase II ARDENT in October 2020 at 420 mg; ARV-471 (ER degrader) showed a manageable tolerability profile and a 42% clinical benefit rate in a heavily pretreated population, with better ER degradation than fulvestrant and other clinical-stage SERDs at the same stage.
- By the end of 2021, at least 15 targeted protein degraders had entered the clinic, including heterobifunctional PROTACs and molecular glues; most early clinical PROTACs recruit CRBN, with DT2216 as a notable VHL-recruiting exception.
- The review identifies future inflection points: defining target classes best served by degradation over inhibition, expanding the E3 ligase landscape beyond CRBN/VHL (with more than 600 human E3 ligases), extending TPD beyond oncology, and validating modalities beyond IMiDs and PROTACs.
Methods
- Narrative review, not a systematic review, synthesizing the first two decades of PROTAC/TPD discovery and the current clinical landscape with a focus on industry activity.
- Data sources are published literature, clinical trial registries/company disclosures, and tables of clinical-stage heterobifunctional PROTACs and molecular glues (Tables 1 and 2).
- Main analysis is qualitative synthesis of mechanism, target selection, E3 ligase biology, clinical proof-of-concept, and future directions; no meta-analysis or primary experimental data are reported.
Limitations
- The paper does not state a formal limitations section. Evident from the text: it is a narrative review without a systematic search strategy or quantitative synthesis.
- Clinical data cited are early/interim phase I/II results and rapidly evolving; several compounds in Table 1 have undisclosed E3 ligases or are only in IND-enabling studies, limiting conclusions about the full clinical landscape.
- The future outlook is explicitly author-perspective (“in our opinion”), so forward-looking statements are not evidence-based predictions.
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Claims the paper makes
134 Not checked yet · 58 Own interpretation · 25 No basis given · 4 Partly supported · 1 Supported · 1 Supported so far · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Currently there are limited methods to selectively covalently bind to a protein56–58”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Partly supportedcites [56] Sletten, E. M. & Bertozzi, C. R. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem. Int. Ed. Engl. 48, 6974–6998 (2009). sourceExperimental — accuracy not yet measured
Section 3, “Achieving Bioorthogonality with Unique Amino Acid Sequences,” says single-site protein modification is difficult to achieve, supporting a limitation on highly selective covalent modification. But Section 2.1 describes routine protein conjugation and multiple selective residue-modification methods, so the paper does not establish that methods for selectively covalently modifying proteins are generally limited. Page numbers were not available in our copy. (LLM, conf=0.82)
- Not checked yetcites [57] Ray, S. & Murkin, A. S. New electrophiles and strategies for mechanism-based and targeted covalent inhibitor design. Biochemistry 58, 5234–5244 (2019). source
- Not checked yetcites [58] Lossouarn, A., Renard, P. Y. & Sabot, C. Tailored bioorthogonal and bioconjugate chemistry: a source of inspiration for developing kinetic target-guided synthesis strategies. Bioconjug Chem. 32, 63–72 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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- Partly supported
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In the paper
“Examples here include the approved IMiD class, which relies on CRBN to degrade IKZF1/IKZF3 (refs4,5) via a molecular glue mechanism”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Partly supportedcites [4] Kronke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014). sourceExperimental — accuracy not yet measured
The paper reports that lenalidomide promotes CRBN binding to IKZF1 and IKZF3, leading to their ubiquitination and degradation—a mechanism consistent with the citing sentence’s description of a molecular glue (Abstract, page not provided). It also reports that thalidomide binds CRBN and regulates IKZF1/IKZF3 levels, but does not establish the degradation mechanism for the entire approved IMiD class. (LLM, conf=0.83)
- Supportedcites [5] Kronke, J. et al. Lenalidomide induces ubiquitination and degradation of CK1alpha in del(5q) MDS. Nature 523, 183–188 (2015). source
The Discussion states that thalidomide, lenalidomide, and pomalidomide bind CRBN and induce CRL4CRBN-mediated degradation of IKZF1 and IKZF3. The Species-specific effects section describes IMiD binding as creating a site for substrate interactions, supporting the molecular-glue characterization. Page numbers are unavailable in our copy. (LLM, conf=0.90)
plaindirect- Asserted: passes — The authors put it forward as true.
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- Partly supported
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In the paper
“several central nervous system (CNS)-specific E3 ligases have emerged, such as RNF182 (ref.148) and tripartite motif-containing protein 9 (TRIM9)149”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Partly supportedcites [148] Liu, Q. Y., Lei, J. X., Sikorska, M. & Liu, R. A novel brain-enriched E3 ubiquitin ligase RNF182 is up regulated in the brains of Alzheimer’s patients and targets ATP6V0C for degradation. Mol. Neurodegener. 3, 4 (2008). sourceExperimental — accuracy not yet measured
The Results (‘The expression patterns of RNF182’; page not provided) report RNF182 expression in the tested CNS tissues but not in four tested non-CNS tissues, and the paper calls it ‘brain-enriched.’ The Results also demonstrate that RNF182 functions as an E3 ligase. This supports RNF182 as the example cited to this paper, but ‘CNS-specific’ is stronger than the tissue evidence establishes; TRIM9 has a separate citation in the citing sentence. (LLM, conf=0.83)
- Partly supportedcites [149] Menon, S. et al. The TRIM9/TRIM67 neuronal interactome reveals novel activators of morphogenesis. Mol. Biol. Cell 32, 314–330 (2021). sourceExperimental — accuracy not yet measured
The Results section describes TRIM9 as enriched in neurons, and the Introduction identifies TRIM proteins as E3 ubiquitin ligases. That supports the TRIM9 example, but enrichment does not establish the stronger claim that TRIM9 is CNS-specific. The separate RNF182 citation is not being judged here. (LLM, conf=0.83)
plain- Asserted: passes — The authors put it forward as true.
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- Partly supported
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered ‘undruggable’.”
- Also stated in: § Introduction · plain
“in 2020, these trials provided the first clinical proof-of-concept for the modality against two well-established cancer targets: the oestrogen receptor (ER) and the androgen receptor (AR).”
§ PROTAC targeted protein degraders: the past is prologue > Abstract
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- Also stated in: § Introduction · plain
None of the sources cited for this claim have been checked yet.
In the paper
“The subsequent discovery of a peptide from hypoxia-inducible factor 1 subunit-α (HIF1α) that bound the E3 ligase von Hippel–Lindau tumour suppressor (VHL)18,19 led to the design of cell-penetrating PROTACs that degraded a range of POIs.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [18] Hon, W. C. et al. Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. Nature 417, 975–978 (2002). source
- Not checked yetcites [19] Min, J. H. et al. Structure of an HIF-1alpha-pVHL complex: hydroxyproline recognition in signaling. Science 296, 1886–1889 (2002). source
plaindirect- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In 2019, the first PROTAC molecules entered clinical testing; in 2020, these trials provided the first clinical proof-of-concept for the modality against two well-established cancer targets: the oestrogen receptor (ER) and the androgen receptor (AR).”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Protac-1 acted as a tether between METAP2 and β-TRCP, enabling the ligase to ubiquitylate METAP2 in extracts from unfertilized Xenopus laevis eggs.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [9] Sakamoto, K. M. et al. Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl Acad. Sci. USA 98, 8554–8559 (2001). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In parallel with the development of these early PROTAC molecules, the E3 ligase cereblon (CRBN) was identified as the target of thalidomide and its analogues lenalidomide and pomalidomide6, which are known as immunomodulatory imide drugs (IMiDs) in the context of cancer therapy.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [6] Ito, T. et al. Identification of a primary target of thalidomide teratogenicity. Science 327, 1345–1350 (2010). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In this pathway, proteins are targeted for degradation by the proteasome in a three-step process involving ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2) and, finally, ubiquitin–protein ligases (E3), which coordinate the transfer of ubiquitin molecules to the target protein (substrate)14.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [14] Ciechanover, A., Orian, A. & Schwartz, A. L. Ubiquitin-mediated proteolysis: biological regulation via destruction. Bioessays 22, 442–451 (2000). source
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The concept of harnessing this natural degradation system for therapeutic purposes was inspired by early studies of viruses and plants (Box 2), which highlighted the possibility of deliberately designing small molecules that co-opt E3 ligases and recruit them for degradation of a POI.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“One involved using ligase-recruiting ligands to probe the biology and phenotype of a POI as an alternative to targeted inhibition, gene knockout or gene knockdown.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Auxin acts by stabilizing the interaction between Aux/IAA proteins and the plant E3 ligase transport inhibitor response 1 (Tir1)239,240.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [239] Dharmasiri, N., Dharmasiri, S. & Estelle, M. The F-box protein TIR1 is an auxin receptor. Nature 435, 441–445 (2005). source
- Not checked yetcites [240] Kepinski, S. & Leyser, O. Auxin-induced SCFTIR1-Aux/IAA interaction involves stable modification of the SCFTIR1 complex. Proc. Natl Acad. Sci. USA 101, 12381–12386 (2004). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“More recently, targeted discovery of degrader compounds against oncoproteins in a cell-based system has enabled the discovery of novel cereblon (CRBN)-dependent and CRBN-independent IKAROS family zinc finger 1 (IKZF1) degraders235, suggesting that screening for degraders against a target of choice is a strategy that can yield a bounty of phenotypically relevant degrader molecules.”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
What the sources say
- Not checked yetcites [235] Koduri, V. et al. Targeting oncoproteins with a positive selection assay for protein degraders. Sci. Adv. 7, eabd6263 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In vitro proof of concept for the first fully synthetic PROTAC, dubbed Protac-1, was reported in 2001 (ref.9).”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [9] Sakamoto, K. M. et al. Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl Acad. Sci. USA 98, 8554–8559 (2001). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The first rational discovery of molecular glues between a ligase and a substrate involved a series of compounds that restored binding affinity between the β-TRCP ligase and its mutated phospho-degron, discovered in a biochemical screen234.”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
What the sources say
- Not checked yetcites [234] Simonetta, K. R. et al. Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction. Nat. Commun. 10, 1402 (2019). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The ER in breast cancer38,39 and the AR in prostate cancer33 are the leading examples of such targets.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Target selection for degraders
What the sources say
- Not checked yetcites [38] McDonnell, D. P., Wardell, S. E. & Norris, J. D. Oral selective estrogen receptor downregulators (SERDs), a breakthrough endocrine therapy for breast cancer. J. Med. Chem. 58, 4883–4887 (2015). source
- Not checked yetcites [39] Ariazi, E. A., Ariazi, J. L., Cordera, F. & Jordan, V. C. Estrogen receptors as therapeutic targets in breast cancer. Curr. Top. Med. Chem. 6, 181–202 (2006). source
- Not checked yetcites [33] Salami, J. et al. Androgen receptor degradation by the proteolysis-targeting chimera ARCC-4 outperforms enzalutamide in cellular models of prostate cancer drug resistance. Commun. Biol. 1, 100 (2018). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“and ideally have an unstructured region that can be threaded into the proteasome.”
- Also stated in: § Targets best suited for degradation · plain
“and ideally, an unstructured region to thread into the proteasome46,47.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [46] Guharoy, M., Bhowmick, P., Sallam, M. & Tompa, P. Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system. Nat. Commun. 7, 10239 (2016). source
- Not checked yetcites [47] Davis, C., Spaller, B. L. & Matouschek, A. Mechanisms of substrate recognition by the 26S proteasome. Curr. Opin. Struct. Biol. 67, 161–169 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Also stated in: § Targets best suited for degradation · plain
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“ATTECs link a POI warhead to a ligand that binds to the autophagy protein LC3 (microtubule-associated protein 1 light chain 3α) glue, thereby bypassing the ubiquitin pathways by directly tethering the POI to the autophagosome.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD
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In the paper
“Twenty years after its theoretical conception, at least 15 targeted protein degraders, among them heterobifunctional PROTACs and molecular glues, had entered the clinic by the end of 2021 (ref.30) (Tables 1,2), and many more are expected to follow.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [30] Mullard, A. Targeted protein degraders crowd into the clinic. Nat. Rev. Drug Discov. 20, 247–250 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The success of proteolysis-targeting chimeras (PROTACs) in hijacking the ubiquitin–proteasome system (UPS) for targeted protein degradation (TPD) has motivated research into other classes of heterobifunctional molecules that depend on non-UPS pathways to degrade a protein of interest (POI)246,247.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD
What the sources say
- Not checked yetcites [246] Ding, Y., Fei, Y. & Lu, B. Emerging new concepts of degrader technologies. Trends Pharmacol. Sci. 41, 464–474 (2020). source
- Not checked yetcites [247] Kastl, J. M., Davies, G., Godsman, E. & Holdgate, G. A. Small-molecule degraders beyond PROTACs-challenges and opportunities. SLAS Discov. 26, 524–533 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Although this has been a highly effective approach, it has left potential drug targets undrugged or underdrugged45.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [45] Hopkins, A. L. & Groom, C. R. The druggable genome. Nat. Rev. Drug Discov. 1, 727–730 (2002). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The data also demonstrated ARV-110-mediated degradation of the protein target in tumours — the first such evidence for a PROTAC molecule in humans — and revealed early signs of antitumour activity, as measured by reductions in levels of prostate specific antigen (PSA) and/or by RECIST (Response Evaluation Criteria in Solid Tumors).”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [40] Petrylak, D. P. et al. First-in-human phase I study of ARV-110, an androgen receptor (AR) PROTAC degrader in patients (pts) with metastatic castrate-resistant prostate cancer (mCRPC) following enzalutamide (ENZ) and/or abiraterone (ABI). J. Clin. Oncol. 38, 3500–3500 (2020). source
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The interim data for ARV-471 revealed a manageable tolerability profile with robust signals of clinical efficacy41, a 42% clinical benefit rate in a heavily pretreated population and evidence of better ER degradation than fulvestrant and other clinical-stage selective ER degraders (SERDs) when compared at the same stage of development.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [41] Snyder, L. B. et al. The discovery of ARV-471, an orally bioavailable estrogen receptor degrading PROTAC for the treatment of patients with breast cancer. In Proc. 112th Annual Meeting of the American Association for Cancer Research 1116 (AACR, 2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In 2020, initial positive data reported from the phase I trials of ARV-110 and ARV-471 answered all four foundational questions in the affirmative — not just for the compounds themselves but for the entire TPD field.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The interim data for ARV-471 revealed a manageable tolerability profile with robust signals of clinical efficacy41, a 42% clinical benefit rate in a heavily pretreated population and evidence of better ER degradation than fulvestrant and other clinical-stage selective ER degraders (SERDs) when compared at the same stage of development.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [41] Snyder, L. B. et al. The discovery of ARV-471, an orally bioavailable estrogen receptor degrading PROTAC for the treatment of patients with breast cancer. In Proc. 112th Annual Meeting of the American Association for Cancer Research 1116 (AACR, 2021). source
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Proteolysis-targeting chimeras (PROTACs) bring the protein degrader function to the target; they do not need to bind within a biologically functional active site.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
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In the paper
“AbTACs are bispecific antibodies that recruit membrane-bound E3 ligases to a membrane POI for degradation by the lysosome degradation pathway.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD
plaindirect- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Although not heterobifunctional, these new-generation CRBN modulators have been engineered with therapeutic targets in mind (IKZF1/IKZF3 and G1 to S phase transition 1 (GSPT1)), which are recruited by the compounds in a molecular glue mechanism to target them for degradation (Box 1).”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD
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In the paper
“The data also demonstrated ARV-110-mediated degradation of the protein target in tumours — the first such evidence for a PROTAC molecule in humans — and revealed early signs of antitumour activity, as measured by reductions in levels of prostate specific antigen (PSA) and/or by RECIST (Response Evaluation Criteria in Solid Tumors).”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [40] Petrylak, D. P. et al. First-in-human phase I study of ARV-110, an androgen receptor (AR) PROTAC degrader in patients (pts) with metastatic castrate-resistant prostate cancer (mCRPC) following enzalutamide (ENZ) and/or abiraterone (ABI). J. Clin. Oncol. 38, 3500–3500 (2020). source
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In the paper
“From a structural perspective, PROTAC targets need a small-molecule binding surface that is approachable by an E3 ligase”
- Also stated in: § Targets best suited for degradation · plain
“Although ‘PROTACable’ POIs do not need an enzyme active site, they do need a small-molecule binding site that is approachable by an E3 ligase.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
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In the paper
“The era of rationally designed targeted protein degraders as potential human therapeutics began in 2019 with the entry of two heterobifunctional degraders into first-in-human trials (Fig. 3): the PROTACs ARV-110 (NCT03888612) and ARV-471 (NCT04072952), targeting the AR and the ER, respectively.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD
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In the paper
“Proteins that may be best suited to therapeutic intervention by targeted protein degradation instead of stoichiometric inhibition include proteins with disease-causing gain of function owing to mutation, overexpression, aggregation or the differential expression or localization of protein isoforms.”
- Also stated in: § Targets best suited for degradation · plain
“a change away from the natural state, via overexpression, mutation, aggregation, isoform expression or localization, that results in a disease-causing gain of function”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
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In the paper
“So, the initial wave of heterobifunctional degraders in the clinic (Table 1) has focused on proteins with a combination of well-characterized biological and biochemical properties, clinically validated roles in diseases with clear unmet medical need, and previously established clinical efficacy for their inhibition.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Target selection for degraders
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- Rests on an assumption: For any new therapeutic modality, selecting well-known targets is important for establishing proof of concept because it introduces just one variable (the modality), not two.
In the paper
“In MDA-MB-231 cells, AC-1 induced the degradation of PDL1 via an RNF43- and lysosomal-dependent mechanism.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD
What the sources say
- Not checked yetcites [251] Cotton, A. D., Nguyen, D. P., Gramespacher, J. A., Seiple, I. B. & Wells, J. A. Development of antibody-based PROTACs for the degradation of the cell-surface immune checkpoint protein PD-L1. J. Am. Chem. Soc. 143, 593–598 (2021). source
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In the paper
“Initial trial data showed that ARV-110 was well tolerated at doses up to 420 mg.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [40] Petrylak, D. P. et al. First-in-human phase I study of ARV-110, an androgen receptor (AR) PROTAC degrader in patients (pts) with metastatic castrate-resistant prostate cancer (mCRPC) following enzalutamide (ENZ) and/or abiraterone (ABI). J. Clin. Oncol. 38, 3500–3500 (2020). source
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In the paper
“AUTACs link a warhead for the POI to a guanine derivative that tags the protein for degradation by the autophagy machinery.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD
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In the paper
“LYTACs bind a membrane-bound POI and the extracellular domains of a lysosome-shuttling receptor, which then drags the POI into the lysosome for degradation.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD
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In the paper
“Bensimon et al.52 challenged this view by showing that multi-transmembrane proteins from the solute carrier (SLC) transporter family could be degraded using the dTAG technology53.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [52] Bensimon, A. et al. Targeted degradation of SLC transporters reveals amenability of multi-pass transmembrane proteins to ligand-induced proteolysis. Cell Chem. Biol. 27, 728–739 e729 (2020). source
- Not checked yetcites [53] Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018). source
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In the paper
“PROTACs that covalently bind the POI lose the ability to turn over and act iteratively55”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [55] Bond, M. J., Chu, L., Nalawansha, D. A., Li, K. & Crews, C. M. Targeted degradation of oncogenic KRAS(G12C) by VHL-recruiting PROTACs. ACS Cent. Sci. 6, 1367–1375 (2020). source
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In the paper
“Recently, it was disclosed that both ARV-110 and ARV-471 use CRBN as the E3 ligase that is recruited to their respective targets, AR and ER, to catalyse their ubiquitylation and proteasomal degradation41,71.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [41] Snyder, L. B. et al. The discovery of ARV-471, an orally bioavailable estrogen receptor degrading PROTAC for the treatment of patients with breast cancer. In Proc. 112th Annual Meeting of the American Association for Cancer Research 1116 (AACR, 2021). source
- Not checked yetcites [71] Snyder, L. B. et al. Discovery of ARV-110, a first in class androgen receptor degrading PROTAC for the treatment of men with metastatic castration resistant prostate cancer. In Proc. 112th Annual Meeting of the American Association for Cancer Research 1115 (AACR, 2021).
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“CRBN appears to be emerging as a preferred E3 ligase for the first wave of TPD therapeutics in clinical trials.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [3] Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014). source
- Not checked yetcites [4] Kronke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014). source
- Not checked yetcites [72] Chamberlain, P. P. & Cathers, B. E. Cereblon modulators: low molecular weight inducers of protein degradation. Drug Discov. Today Technol. 31, 29–34 (2019). source
- Not checked yetcites [73] Matyskiela, M. E. et al. A cereblon modulator (CC-220) with improved degradation of Ikaros and Aiolos. J. Med. Chem. 61, 535–542 (2018). source
- Not checked yetcites [74] Petzold, G., Fischer, E. S. & Thoma, N. H. Structural basis of lenalidomide-induced CK1alpha degradation by the CRL4(CRBN) ubiquitin ligase. Nature 532, 127–130 (2016). source
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In the paper
“In general, PROTAC physicochemical property space falls beyond the ‘rule of 5’ (refs59,60) owing to the bifunctional nature of the molecules.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [59] Lipinski, C. A., Lombardo, F., Dominy, B. W. & Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46, 3–26 (2001). source
- Not checked yetcites [60] Doak, B. C., Over, B., Giordanetto, F. & Kihlberg, J. Oral druggable space beyond the rule of 5: insights from drugs and clinical candidates. Chem. Biol. 21, 1115–1142 (2014). source
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In the paper
“However, several orally bioavailable compounds have been developed that fall outside the rule of 5 parameters.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
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In the paper
“Short linkers can be used to modulate PROTAC molecular weights67 and properties65”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [67] Troup, R. I., Fallan, C. & Baud, M. G. J. Current strategies for the design of PROTAC linkers: a critical review. Explor. Target. Antitumor Ther. 1, 273–312 (2020). source
- Not checked yetcites [65] Han, X. et al. Strategies toward discovery of potent and orally bioavailable proteolysis targeting chimera degraders of androgen receptor for the treatment of prostate cancer. J. Med. Chem. 64, 12831–12854 (2021). source
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Selection of the ligand-binding site is particularly important in the case of scaffolding proteins, where the POI may only be partially exposed within a given complex.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
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In the paper
“More recently, Wang et al.54 showed that programmed cell death ligand 1 (PDL1) — an immune checkpoint protein that resides on the cell surface to carry out its natural function but circulates between the surface and the cytoplasm — could be degraded using a CRBN-based PROTAC linked to the BMS-37 PDL1 warhead in MC-38 cells.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [54] Wang, Y. et al. In vitro and in vivo degradation of programmed cell death ligand 1 (PD-L1) by a proteolysis targeting chimera (PROTAC). Bioorg. Chem. 111, 104833 (2021). source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“PROTACs may also benefit from cooperative PPIs between the E3 ligase and the POI. This can have the advantages of improved potency49 and selectivity50.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [49] Bondeson, D. P. et al. Lessons in PROTAC design from selective degradation with a promiscuous warhead. Cell Chem. Biol. 25, 78–87 e75 (2018). source
- Not checked yetcites [50] Alabi, S. et al. Mutant-selective degradation by BRAF-targeting PROTACs. Nat. Commun. 12, 920 (2021).
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In the paper
“Schneider et al.70 have provided the first systematic assessment of drug targets according to their ability to be degraded by PROTAC molecules.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [70] Schneider, M. et al. The PROTACtable genome. Nat. Rev. Drug Discov. 20, 789–797 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Accordingly, it has become routine to generate and characterize a new degrader in cell culture experiments and animal models of disease, using either VHL or CRBN as a recruiting ligase93.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [93] Wang, Y., Jiang, X., Feng, F., Liu, W. & Sun, H. Degradation of proteins by PROTACs and other strategies. Acta Pharm. Sin. B 10, 207–238 (2020). source
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In the paper
“In fact, not only CR8, but four separate classes of compounds, each discovered by a different screening method, were found to have molecular glue-like properties in potentiating the interaction of DDB1 and CDK12, resulting in CCNK degradation84–87.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [84] Lv, L. et al. Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation. eLife 9, e59994 (2020).
- Not checked yetcites [85] Slabicki, M. et al. The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature 585, 293–297 (2020). source
- Not checked yetcites [86] Mayor-Ruiz, C. et al. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat. Chem. Biol. 16, 1199–1207 (2020). source
- Not checked yetcites [87] Dieter, S. M. et al. Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer. Cell Rep. 36, 109394 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“a unique class of cyclin-dependent kinase 12 (CDK12) inhibitors, exemplified by CR8, which, unexpectedly, has been shown to directly co-opt DDB1 as an E3 ligase for the degradation of cyclin K (CCNK)84–86.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [84] Lv, L. et al. Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation. eLife 9, e59994 (2020).
- Not checked yetcites [85] Slabicki, M. et al. The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature 585, 293–297 (2020). source
- Not checked yetcites [86] Mayor-Ruiz, C. et al. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat. Chem. Biol. 16, 1199–1207 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“and can potentially enable the employment of E3 ligases with unique characteristics that could offer advantages against a particular target or in a given therapeutic setting.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“The modular nature of such PROTACs could allow ‘ligase-hopping’ — the ability to swap ligase ‘handles’ that offer the most potent degradation and the best physicochemical properties”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“HaloPROTACs, dTAGs and other degradation proof-of-concept strategies, such as the AID system, have been reviewed extensively elsewhere96,97 and now serve as crucial target validation tools when approaching a new therapeutic POI.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [96] Roth, S., Fulcher, L. J. & Sapkota, G. P. Advances in targeted degradation of endogenous proteins. Cell Mol. Life Sci. 76, 2761–2777 (2019). source
- Not checked yetcites [97] Prozzillo, Y. et al. Targeted protein degradation tools: overview and future perspectives. Biology (Basel) 9, 421 (2020).
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“These findings suggest that many more compounds, including those approved or already in the clinic, could have a hitherto overlooked degrader contribution to their mechanism of action.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“With more than 600 human ubiquitin E3 ligases79,80 to potentially explore”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [79] Oh, E., Akopian, D. & Rape, M. Principles of ubiquitin-dependent signaling. Annu. Rev. Cell Dev. Biol. 34, 137–162 (2018). source
- Not checked yetcites [80] Schapira, M., Calabrese, M. F., Bullock, A. N. & Crews, C. M. Targeted protein degradation: expanding the toolbox. Nat. Rev. Drug. Discov. 18, 949–963 (2019). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“this creates concerns that tumour cells could mutate to evade degraders that rely on non-essential ligases, such as CRBN and VHL, whose genomic loss or deletion results in no discernible effect on cellular viability or phenotype as defined by CERES scores in DepMap98, for example.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [98] Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021).
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although the generation of VHL- and CRBN-based PROTAC molecules as research tools has become routine, their preclinical and clinical development can still pose challenges.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“sulfonamides previously in clinical trials81,82 that have since been shown to use DCAF15 to degrade RBM39 (refs25,27,29), also via a molecular glue mechanism”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [25] Han, T. et al. Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science 356, eaal3755 (2017). source
- Not checked yetcites [27] Uehara, T. et al. Selective degradation of splicing factor CAPERalpha by anticancer sulfonamides. Nat. Chem. Biol. 13, 675–680 (2017). source
- Not checked yetcites [29] Ting, T. C. et al. Aryl sulfonamides degrade RBM39 and RBM23 by recruitment to CRL4-DCAF15. Cell Rep. 29, 1499–1510 e1496 (2019). source
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although use of small-molecule PROTACs in an endogenous setting is limited to protein targets that have ligands available”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In fact, preclinical studies of degraders that use CRBN or VHL to target multiple protein classes have detected emerging resistance that occurs via mutation and/or downregulation of components of the ubiquitin ligase machinery99–101.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [99] Shirasaki, R. et al. Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins. Cell Rep. 34, 108532 (2021). source
- Not checked yetcites [100] Zhang, L., Riley-Gillis, B., Vijay, P. & Shen, Y. Acquired resistance to BET-PROTACs (proteolysis-targeting chimeras) caused by genomic alterations in core components of E3 ligase complexes. Mol. Cancer Ther. 18, 1302–1311 (2019). source
- Not checked yetcites [101] Ottis, P. et al. Cellular resistance mechanisms to targeted protein degradation converge toward impairment of the engaged ubiquitin transfer pathway. ACS Chem. Biol. 14, 2215–2223 (2019).
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In the paper
“Similarly, in the clinical setting in multiple myeloma, resistance to IMiDs such as pomalidomide and lenalidomide has been shown to include genomic alterations in both the target protein (IKZF1/IKZF3) and components of the CRBN ligase machinery102,103.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [102] Gooding, S. et al. Multiple cereblon genetic changes are associated with acquired resistance to lenalidomide or pomalidomide in multiple myeloma. Blood 137, 232–237 (2021). source
- Not checked yetcites [103] Barrio, S. et al. IKZF1/3 and CRL4(CRBN) E3 ubiquitin ligase mutations and resistance to immunomodulatory drugs in multiple myeloma. Haematologica 105, e237–e241 (2020). source
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In the paper
“Buckley et al.94 have developed a tagging system based on HaloTag fusions that can be targeted by HaloPROTACs”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [94] Buckley, D. L. et al. HaloPROTACS: use of small molecule PROTACs to induce degradation of halotag fusion proteins. ACS Chem. Biol. 10, 1831–1837 (2015). source
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In the paper
“a few additional ‘generic’ E3 ligases have been shown to be exploitable by PROTACs, using small-molecule covalent tools that specifically recruit the ligases to degrade the prototypical TPD substrate, BRD4; these ligases include ring finger protein 4 (RNF4)132, RNF114 (refs133–135), KEAP1 (refs136,137) and most recently, fem-1 homologue B (FEM1B)138.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [132] Ward, C. C. et al. Covalent ligand screening uncovers a RNF4 E3 ligase recruiter for targeted protein degradation applications. ACS Chem. Biol. 14, 2430–2440 (2019). source
- Not checked yetcites [133] Spradlin, J. N. et al. Harnessing the anti-cancer natural product nimbolide for targeted protein degradation. Nat. Chem. Biol. 15, 747–755 (2019). source
- Not checked yetcites [134] Luo, M. et al. Chemoproteomics-enabled discovery of covalent RNF114-based degraders that mimic natural product function. Cell Chem. Biol. 28, 559–566 (2021). source
- Not checked yetcites [135] Tong, B. et al. A nimbolide-based kinase degrader preferentially degrades oncogenic BCR-ABL. ACS Chem. Biol. 15, 1788–1794 (2020). source
- Not checked yetcites [136] Tong, B. et al. Bardoxolone conjugation enables targeted protein degradation of BRD4. Sci. Rep. 10, 15543 (2020).
- Not checked yetcites [137] Wei, J. et al. Harnessing the E3 Ligase KEAP1 for targeted protein degradation. J. Am. Chem. Soc. 143, 15073–15083 (2021). source
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In the paper
“Zeng et al.124 initially developed a covalent PROTAC (XY-4-88) based on ARS-1620, a KRAS(G12C)-binding covalent warhead, and thalidomide as the CRBN-recruiting ligand124.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [124] Zeng, M. et al. Exploring targeted degradation strategy for oncogenic KRAS(G12C). Cell Chem. Biol. 27, 19–31 e16 (2020). source
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In the paper
“a nuclear E3 ligase, DCAF16, has been shown to restrict target degradation to the nucleus131.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [131] Zhang, X., Crowley, V. M., Wucherpfennig, T. G., Dix, M. M. & Cravatt, B. F. Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16. Nat. Chem. Biol. 15, 737–746 (2019). source
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In the paper
“the pairing of VHL versus CRBN for a given target can result in different degradation efficiencies49, as was first observed when targeting the fusion oncogene BCR–ABL by PROTACs118.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [49] Bondeson, D. P. et al. Lessons in PROTAC design from selective degradation with a promiscuous warhead. Cell Chem. Biol. 25, 78–87 e75 (2018). source
- Not checked yetcites [118] Lai, A. C. et al. Modular PROTAC design for the degradation of oncogenic BCR-ABL. Angew. Chem. Int. Ed. Engl. 55, 807–810 (2016). source
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In the paper
“The different outcomes of these two studies could arise from the different KRAS warheads, the linker between the POI and E3 ligase warheads, and/or the choice of E3 ligase.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“It is therefore possible that one ligase in particular may be better than others for degrading a certain target.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“Currently, all PROTACs to date use just a handful of these non-specialized ligases, collated in an online database: PROTAC-DB92.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [92] Weng, G. et al. PROTAC-DB: an online database of PROTACs. Nucleic Acids Res. 49, D1381–D1387 (2021). source
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In the paper
“Bond et al.55 developed a covalent VHL–KRAS(G12C) PROTAC (LC-2), based on the MRTX849 KRAS(G12C)-targeting warhead and a VHL ligand.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [55] Bond, M. J., Chu, L., Nalawansha, D. A., Li, K. & Crews, C. M. Targeted degradation of oncogenic KRAS(G12C) by VHL-recruiting PROTACs. ACS Cent. Sci. 6, 1367–1375 (2020). source
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In the paper
“A remarkable example is the low expression of VHL in platelets”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [152] Khan, S. et al. A selective BCL-XL PROTAC degrader achieves safe and potent antitumor activity. Nat. Med. 25, 1938–1947 (2019). source
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In the paper
“these are of high interest in tackling targets in neuronal diseases, as discussed below, where CNS-specific therapeutic targeting is desirable to avoid systemic off-target and toxicity effects.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“several recent reviews have analysed and categorized publicly available datasets — such as GTEx, The Cancer Genome Atlas (TCGA), ProteinAtlas and others — for ligase expression in healthy and diseased states, to highlight ligases with clear and distinct expression profiles80,99,143,144.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [80] Schapira, M., Calabrese, M. F., Bullock, A. N. & Crews, C. M. Targeted protein degradation: expanding the toolbox. Nat. Rev. Drug. Discov. 18, 949–963 (2019). source
- Not checked yetcites [99] Shirasaki, R. et al. Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins. Cell Rep. 34, 108532 (2021). source
- Not checked yetcites [143] Khan, S. et al. PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics. Oncogene 39, 4909–4924 (2020). source
- Not checked yetcites [144] He, Y. et al. Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies. J. Hematol. Oncol. 13, 103 (2020). source
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In the paper
“the definition of low-hanging fruit with respect to structural enablement of ligases has recently been redefined with the ground-breaking publication of artificial intelligence (AI)-driven tertiary structure prediction models from Google/DeepMind141 and RoseTTAFold142.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [141] Tunyasuvunakool, K. et al. Highly accurate protein structure prediction for the human proteome. Nature 596, 590–596 (2021). source
- Not checked yetcites [142] Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021). source
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In the paper
“DT2216 is in phase I trials30”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [30] Mullard, A. Targeted protein degraders crowd into the clinic. Nat. Rev. Drug Discov. 20, 247–250 (2021). source
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In the paper
“some ligases exhibit ‘reverse specificity’ — low expression in some tissue or cell types — that may also be advantageous for protein degraders.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“which has been shown to occur for some CRBN- and VHL-recruiting PROTACs, as discussed previously.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [99] Shirasaki, R. et al. Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins. Cell Rep. 34, 108532 (2021). source
- Not checked yetcites [100] Zhang, L., Riley-Gillis, B., Vijay, P. & Shen, Y. Acquired resistance to BET-PROTACs (proteolysis-targeting chimeras) caused by genomic alterations in core components of E3 ligase complexes. Mol. Cancer Ther. 18, 1302–1311 (2019). source
- Not checked yetcites [101] Ottis, P. et al. Cellular resistance mechanisms to targeted protein degradation converge toward impairment of the engaged ubiquitin transfer pathway. ACS Chem. Biol. 14, 2215–2223 (2019).
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In the paper
“there are several other ubiquitin ligases, enabled by structural and/or validated substrate information, that present a path for the development of small molecules that can ultimately be converted into PROTACs, yet await development as potential PROTACable ligases.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Finally, cancer-testis antigens (CTAs) also comprise ubiquitin ligases that have restricted expression in the normal testis but are highly overexpressed across multiple cancer types154,155.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [154] Wei, R. et al. Cancer testis antigens in sarcoma: expression, function and immunotherapeutic application. Cancer Lett. 479, 54–60 (2020). source
- Not checked yetcites [155] Weon, J. L. & Potts, P. R. The MAGE protein family and cancer. Curr. Opin. Cell Biol. 37, 1–8 (2015). source
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In the paper
“The advantage of ligases with these profiles is that tumour cells would be less able to develop ligase-based resistance to PROTACs”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“These correlations can be drawn and have been shown by analysing CERES scores in DepMap98 of E3 ligases across multiple tumour cell lines.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [98] Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021).
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In the paper
“Often, but not always, tumour enrichment of an E3 ligase coincides with the dependence of the tumour on expression of that ligase.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“This has allowed the identification of E3 ligases and other UPS genes — some better-characterized than others, such as cell division cycle 20 (CDC20), cytosolic iron–sulfur assembly component 1 (CIAO1) and WD repeat-containing protein 82 (WDR82) — that exhibit high tumour essentiality across many different cancer cell types99.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [99] Shirasaki, R. et al. Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins. Cell Rep. 34, 108532 (2021). source
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In the paper
“Although not all MAGE E3 ligases are tumour specific159”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [159] Tacer, K. F. & Potts, P. R. Cellular and disease functions of the Prader-Willi syndrome gene MAGEL2. Biochem. J. 474, 2177–2190 (2017). source
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In the paper
“Among the clearest examples of ligases with tissue-specific expression are kelch-like family member 40 (KLHL40) and KLHL41 in skeletal muscle145”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [145] Ehrlich, K. C., Baribault, C. & Ehrlich, M. Epigenetics of muscle- and brain-specific expression of KLHL family genes. Int. J. Mol. Sci. 21, 8394 (2020). source
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In the paper
“The exact mechanism of ubiquitylation for MRLs is not as well understood as the mechanism for CRLs, for which substrate recruitment by multiple adaptors and the molecular details of Ub transfer from E2–Ub to the target has been extensively characterized at the atomic level of an entire CRL1 complex106,117.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [106] Baek, K. et al. NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly. Nature 578, 461–466 (2020). source
- Not checked yetcites [117] Horn-Ghetko, D. et al. Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Nature 590, 671–676 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“ligases have other key characteristics, such as tissue and cell-type specificity, tumour enrichment and tumour essentiality (Fig. 6), that can offer opportunities for ‘niche’ ligase degrader development.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“FBXO44 and other tissue- or cell-enriched ligases nonetheless have exciting potential for TPD, because the affinity of their ligands could be tuned to engineer in the specificity towards the tissue of choice, even though some basal level of ligase expression exists ubiquitously.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“a concept originally proposed in the landmark PROTAC paper by Sakamoto et al.9 20 years ago.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [9] Sakamoto, K. M. et al. Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl Acad. Sci. USA 98, 8554–8559 (2001). source
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In the paper
“Although these antibody–PROTAC conjugates obviously lose the clear advantages of oral bioavailability and tunable dosing schedule of small-molecule PROTACs”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“Particularly for IRAK4, its scaffolding role in Toll-like receptor (TLR) signalling around the myddosome is established165,172”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [165] Zarrin, A. A., Bao, K., Lupardus, P. & Vucic, D. Kinase inhibition in autoimmunity and inflammation. Nat. Rev. Drug Discov. 20, 39–63 (2021). source
- Not checked yetcites [172] Qin, J., Jiang, Z., Qian, Y., Casanova, J. L. & Li, X. IRAK4 kinase activity is redundant for interleukin-1 (IL-1) receptor-associated kinase phosphorylation and IL-1 responsiveness. J. Biol. Chem. 279, 26748–26753 (2004). source
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In the paper
“Of these, KT-474 from Kymera Therapeutics is the first to enter clinical trials (Table 1).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites Table 1
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“and has been the subject of intense PROTAC molecule experimentation across academia and industry166–168”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [166] Schiemer, J. et al. Snapshots and ensembles of BTK and cIAP1 protein degrader ternary complexes. Nat. Chem. Biol. 17, 152–160 (2021). source
- Not checked yetcites [167] Zorba, A. et al. Delineating the role of cooperativity in the design of potent PROTACs for BTK. Proc. Natl Acad. Sci. USA 115, E7285–E7292 (2018). source
- Not checked yetcites [168] Tinworth, C. P. et al. PROTAC-mediated degradation of bruton’s tyrosine kinase is inhibited by covalent binding. ACS Chem. Biol. 14, 342–347 (2019). source
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In the paper
“Herein lies one of the great advantages of PROTACs: owing to their event-driven (versus occupancy-driven) pharmacology, PROTACs may overcome insensitivity to such resistance mutations through catalytic degradation of the target.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
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In the paper
“but given that PROTACs can comparatively achieve greater specificity with respect to off-target effects of some kinase inhibitors126,181”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [126] Donovan, K. A. et al. Mapping the degradable kinome provides a resource for expedited degrader development. Cell 183, 1714–1731 e1710 (2020). source
- Not checked yetcites [181] Burslem, G. M. et al. The advantages of targeted protein degradation over inhibition: an RTK case study. Cell Chem. Biol. 25, 67–77 e63 (2018). source
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In the paper
“and may only be addressable by PROTAC degraders, many of which have been described to date173–175.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [173] Zhang, J. et al. Assessing IRAK4 functions in ABC DLBCL by IRAK4 kinase inhibition and protein degradation. Cell Chem. Biol. 27, 1500–1509 e1513 (2020). source
- Not checked yetcites [174] Nunes, J. et al. Targeting IRAK4 for degradation with PROTACs. ACS Med. Chem. Lett. 10, 1081–1085 (2019). source
- Not checked yetcites [175] Chen, Y. et al. Design, synthesis, and biological evaluation of IRAK4-targeting PROTACs. ACS Med. Chem. Lett. 12, 82–87 (2021). source
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In the paper
“the ADC approach can be valuable for potent and robust degraders that have poor physicochemical properties for parenteral administration.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“Dragovic et al.160–162 at Genentech have pushed this modality forward and successfully demonstrated tumour-specific targeting in two different cancer types with ADCs involving VHL–BRD4 PROTACs.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [160] Pillow, T. H. et al. Antibody conjugation of a chimeric BET degrader enables in vivo activity. ChemMedChem 15, 17–25 (2020). source
- Not checked yetcites [161] Dragovich, P. S. et al. Antibody-mediated delivery of chimeric BRD4 degraders. Part 2: improvement of in vitro antiproliferation activity and in vivo antitumor efficacy. J. Med. Chem. 64, 2576–2607 (2021). source
- Not checked yetcites [162] Dragovich, P. S. et al. Antibody-mediated delivery of chimeric BRD4 degraders. Part 1: exploration of antibody linker, payload loading, and payload molecular properties. J. Med. Chem. 64, 2534–2575 (2021). source
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In the paper
“Most recently, PROTACs that target mitogen-activated protein kinase kinase kinase kinase 1 (MAP4K1; also known as HPK1) have been described with promising preclinical activity180”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [180] Si, J. et al. Hematopoietic progenitor kinase1 (HPK1) mediates T cell dysfunction and is a druggable target for T cell-based immunotherapies. Cancer Cell 38, 551–566 e511 (2020). source
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In the paper
“Here, the potential scaffolding role of IRAK4 is especially intriguing as a target, as inhibitors of its kinase function may not fully address the role of IRAK4 in these conditions.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
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In the paper
“particularly because of emergence of the C481S resistance mutation in BTK that renders first-generation BTK inhibitors less effective169,170.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [169] Buhimschi, A. D. et al. Targeting the C481S ibrutinib-resistance mutation in Bruton’s tyrosine kinase using PROTAC-mediated degradation. Biochemistry 57, 3564–3575 (2018). source
- Not checked yetcites [170] Sun, Y. et al. PROTAC-induced BTK degradation as a novel therapy for mutated BTK C481S induced ibrutinib-resistant B-cell malignancies. Cell Res. 28, 779–781 (2018). source
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In the paper
“Degrader drugs currently on the market (the IMiD class) and the overwhelming majority of newly developed PROTACs and molecular glue compounds currently in clinical trials (Tables 1,2) target various types of cancer30,163.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [30] Mullard, A. Targeted protein degraders crowd into the clinic. Nat. Rev. Drug Discov. 20, 247–250 (2021). source
- Not checked yetcites [163] Jan, M., Sperling, A. S. & Ebert, B. L. Cancer therapies based on targeted protein degradation — lessons learned with lenalidomide. Nat. Rev. Clin. Oncol. 18, 401–417 (2021). source
- Not checked yetcites Tables 1,2
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In the paper
“A BTK degrader (NX-5948) and an IRAK4 degrader (KT-474) in phase I clinical trials (Table 1), from Nurix Therapeutics and Kymera Therapeutics, respectively, could treat patients with various immuno-inflammatory diseases, such as rheumatoid arthritis.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites Table 1
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In the paper
“PROTACs have the potential to be first-in-class medicines in immuno-oncology as small-molecule drugs that target immune cell activation to phenocopy PD1/PDL1-directed agents178,179.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [178] Wang, Y., Deng, S. & Xu, J. Proteasomal and lysosomal degradation for specific and durable suppression of immunotherapeutic targets. Cancer Biol. Med. 17, 583–598 (2020). source
- Not checked yetcites [179] Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators of immune function. Cell 175, 1958–1971 e1915 (2018). source
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In the paper
“Although PROTACs are poised to become an important modality for certain target classes, there are POIs that do not have the small-molecule binding sites needed for this approach.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
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In the paper
“In fact, in preclinical models, decreasing tau protein levels via ASO strategies185,186 and recently by engineered zinc-finger transcription factors187 was shown to be durable and to reverse tau pathology.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [185] DeVos, S. L. et al. Tau reduction prevents neuronal loss and reverses pathological tau deposition and seeding in mice with tauopathy. Sci. Transl. Med. 9, eaag0481 (2017). source
- Not checked yetcites [186] Yiannopoulou, K. G. & Papageorgiou, S. G. Current and future treatments in Alzheimer disease: an update. J. Cent. Nerv. Syst. Dis. 12, 1179573520907397 (2020). source
- Not checked yetcites [187] Wegmann, S. et al. Persistent repression of tau in the brain using engineered zinc finger protein transcription factors. Sci. Adv. 7, eabe1611 (2021). source
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In the paper
“but bioPROTACs and hybrid PROTACs are unlikely to be oral drugs owing to their peptide components.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
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In the paper
“as clearance of mHTT via the UPS pathway is thought to be beneficial for disease progression195.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [195] Sap, K. A. & Reits, E. A. Strategies to investigate ubiquitination in Huntington’s disease. Front. Chem. 8, 485 (2020). source
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In the paper
“but SARS-CoV-2 catalytic virulence factors, such as its two proteases, Mpro and PLpro201, and the RNA-dependent RNA polymerase (Rdrp), which is the target of remdesivir202, are potentially targetable by a PROTAC.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [201] Ghosh, A. K., Brindisi, M., Shahabi, D., Chapman, M. E. & Mesecar, A. D. Drug development and medicinal chemistry efforts toward SARS-coronavirus and Covid-19 therapeutics. ChemMedChem 15, 907–932 (2020). source
- Not checked yetcites [202] Yin, W. et al. Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science 368, 1499–1504 (2020). source
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In the paper
“Zhou et al.210 described some of the earliest chimeric bioPROTACs, including a fusion consisting of full-length β-TRCP protein and an N-terminal peptide of the E7 protein of human papillomavirus type 16 (HPV-16) that degraded retinoblastoma protein (RB1) in a human osteosarcoma cell line.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [210] Zhou, P., Bogacki, R., McReynolds, L. & Howley, P. M. Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins. Mol. Cell 6, 751–756 (2000). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Indeed, bioPROTACs would most likely be delivered as mRNA or DNA constructs via a viral vector gene delivery system204–206 or in a nanoparticle207–209.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [204] De Haan, P., Van Diemen, F. R. & Toscano, M. G. Viral gene delivery vectors: the next generation medicines for immune-related diseases. Hum. Vaccin. Immunother. 17, 14–21 (2021). source
- Not checked yetcites [205] Sung, Y. K. & Kim, S. W. Recent advances in the development of gene delivery systems. Biomater. Res. 23, 8 (2019).
- Not checked yetcites [206] Ghosh, S., Brown, A. M., Jenkins, C. & Campbell, K. Viral vector systems for gene therapy: a comprehensive literature review of progress and biosafety challenges. Appl. Biosaf. 25, 7–18 (2020). source
- Not checked yetcites [207] Yang, K. C. et al. Nanotechnology advances in pathogen- and host-targeted antiviral delivery: multipronged therapeutic intervention for pandemic control. Drug Deliv. Transl. Res. 11, 1420–1437 (2021). source
- Not checked yetcites [208] Steinhauff, D. & Ghandehari, H. Matrix mediated viral gene delivery: a review. Bioconjug Chem. 30, 384–399 (2019). source
- Not checked yetcites [209] Editorial. Let’s talk about lipid nanoparticles. Nat. Rev. Mater. 6, 99 (2021). source
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In the paper
“As ARV-110 and ARV-471 have demonstrated, PROTACs can be developed as oral therapeutics”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites ARV-110
- Not checked yetcites ARV-471
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In the paper
“Additionally, PROTACs have inspired the exploration of other classes of heterobifunctional molecules that harness non-UPS machinery to degrade POIs (Box 3), each of which offer features that sets it apart from the other TPD modalities and from small-molecule inhibitors (Table 3).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites Table 3
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In the paper
“This attribute makes targets for several neurodegenerative diseases involving toxic build-up of proteins, such as tau, α-synuclein, mutant huntingtin (mHTT), TAR RNA-binding protein (TARDBP; also known as TDP43) and FUS RNA-binding protein (FUS), potentially addressable with the PROTAC modality.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
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In the paper
“The feasibility of antiviral PROTACs was first established with the degradation of the hepatitis C virus (HCV) NS3/4A protease in cell-based assays by an HCV inhibitor linked to CRBN198”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [198] de Wispelaere, M. et al. Small molecule degraders of the hepatitis C virus protease reduce susceptibility to resistance mutations. Nat. Commun. 10, 3468 (2019). source
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In the paper
“The TRAFTAC system has been used to degrade NF-κB and brachyury (T-box transcription factor T; TBXT) in human cell lines in a UPS-dependent manner that was specific to the dsDNA sequence and E3 ligase43.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [43] Samarasinghe, K. T. G. et al. Targeted degradation of transcription factors by TRAFTACs: TRAnscription Factor TArgeting Chimeras. Cell Chem. Biol. https://doi.org/10.1016/j.chembiol.2021.03.011 (2021). source
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In the paper
“For example, after demonstrating that their GFP-degrading bioPROTACs also degraded a GFP-tagged proliferating cell nuclear antigen (PCNA), Partridge and colleagues219 replaced the GFP-binding domain in one of those bioPROTACs with the 16-amino-acid Con1 peptide, which contains the conserved PIP sequence common to PCNA binding partners, to generate a Con1–SPOP bioPROTAC.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [219] Lim, S. et al. Exquisitely specific anti-KRAS biodegraders inform on the cellular prevalence of nucleotide-loaded states. ACS Cent. Sci. 7, 274–291 (2021). source
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In the paper
“TRAFTACs consist of a HaloPROTAC that bridges an E3 ligase and a dCas9–HT7 fusion protein, then binds a bifunctional dsDNA–CRISPR-RNA to form a transcription factor-recruiting complex.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [43] Samarasinghe, K. T. G. et al. Targeted degradation of transcription factors by TRAFTACs: TRAnscription Factor TArgeting Chimeras. Cell Chem. Biol. https://doi.org/10.1016/j.chembiol.2021.03.011 (2021). source
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In the paper
“Such constructs have been shown to reduce levels of the RBP LIN28A and the transcription factors ETS transcription factor (ERG) and lymphoid enhancer-binding factor 1 (LEF1) in various human cancer cell lines.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [220] Ghidini, A., Clery, A., Halloy, F., Allain, F. H. T. & Hall, J. RNA-PROTACs: Degraders of RNA-binding proteins. Angew. Chem. Int. Ed. Engl. 60, 3163–3169 (2021). source
- Not checked yetcites [221] Shao, J. et al. Destruction of DNA-binding proteins by programmable O’PROTAC: oligonucleotide-based PROTAC. bioRxiv https://doi.org/10.1101/2021.03.08.434493 (2021). source
- Not checked yetcites [222] Liu, J. et al. TF-PROTACs enable targeted degradation of transcription factors. J. Am. Chem. Soc. 143, 8902–8910 (2021). source
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In the paper
“These studies demonstrated that the SCF E3 ligase could be redirected to degrade non-SCF targets.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [210] Zhou, P., Bogacki, R., McReynolds, L. & Howley, P. M. Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins. Mol. Cell 6, 751–756 (2000). source
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In the paper
“Similarly, O’PROTACs221 and transcription factor PROTACs222 use a double-stranded DNA (dsDNA) consensus sequence as the transcription factor-binding warhead, linked to an E3 ligase-recruiting ligand.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [221] Shao, J. et al. Destruction of DNA-binding proteins by programmable O’PROTAC: oligonucleotide-based PROTAC. bioRxiv https://doi.org/10.1101/2021.03.08.434493 (2021). source
- Not checked yetcites [222] Liu, J. et al. TF-PROTACs enable targeted degradation of transcription factors. J. Am. Chem. Soc. 143, 8902–8910 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“RNA-PROTACs use an RNA consensus sequence as the RBP-binding warhead, linked to an E3 ligase-binding element220.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [220] Ghidini, A., Clery, A., Halloy, F., Allain, F. H. T. & Hall, J. RNA-PROTACs: Degraders of RNA-binding proteins. Angew. Chem. Int. Ed. Engl. 60, 3163–3169 (2021). source
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In the paper
“Additionally, multiple groups have described a range of pepTACs that harness SKP1/SCF F-box, VHL, KEAP1 and other E3 ligases to degrade tau or α-synuclein in primary neurons and other cell lines188,193,213”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [188] Lu, M. et al. Discovery of a Keap1-dependent peptide PROTAC to knockdown Tau by ubiquitination-proteasome degradation pathway. Eur. J. Med. Chem. 146, 251–259 (2018). source
- Not checked yetcites [193] Qu, J. et al. Specific knockdown of alpha-synuclein by peptide-directed proteasome degradation rescued its associated neurotoxicity. Cell Chem. Biol. 27, 763 (2020). source
- Not checked yetcites [213] Chu, T. T. et al. Specific knockdown of endogenous tau protein by peptide-directed ubiquitin-proteasome degradation. Cell Chem. Biol. 23, 453–461 (2016). source
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In the paper
“The platform has been used to generate GFP-degrading bioPROTACs based on various E3 ligases: the CUL1 ligases β-TRCP, F-box and WD repeat domain-containing 7 (FBW7) and SKP2; the CUL2 ligase VHL; the CUL3 ligase speckle type BTB/POZ protein (SPOP); the CUL5 ligases suppressor of cytokine signalling 2 (SOCS2) and ankyrin repeat and SOCS box-containing 1 (ASB1); and the U-box E3 ligase CHIP.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [214] Lim, S. et al. bioPROTACs as versatile modulators of intracellular therapeutic targets including proliferating cell nuclear antigen (PCNA). Proc. Natl Acad. Sci. USA 117, 5791–5800 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Given the progress in the past two decades and the recent level of interest and investment from both academia and industry, it is clear that targeted protein degradation could become a key therapeutic modality.”
§ PROTAC targeted protein degraders: the past is prologue > Conclusion
boostedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: unclear — It is unclear whether it could be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 58
- Probably not a substantial claim. 48
- The quote only partly states this claim. 1
Every source the paper cites for this claim was checked and supports it.
In the paper
“These drugs co-opt CRBN to target IKAROS family zinc finger 1 (IKZF1) and IKZF3 for degradation3,4,24, and are now considered as pioneering examples of molecular glues.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Supportedcites [3] Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014). source
The paper’s Abstract states that lenalidomide-bound cereblon targets IKZF1 and IKZF3 for proteasomal degradation. The citation is attached to that mechanism, before the sentence’s separate characterization of these drugs as pioneering molecular glues. (LLM, conf=0.94)
- Supportedcites [4] Kronke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014). source
The citation is attached to the degradation claim, not the subsequent characterization as pioneering molecular glues. The Abstract reports that lenalidomide increases IKZF1 and IKZF3 binding to CRBN and promotes their ubiquitination and degradation; it also identifies both proteins among those regulated by thalidomide. (LLM, conf=0.91)
- Supportedcites [24] Gandhi, A. K. et al. Immunomodulatory agents lenalidomide and pomalidomide co-stimulate T cells by inducing degradation of T cell repressors Ikaros and Aiolos via modulation of the E3 ubiquitin ligase complex CRL4(CRBN). Br. J. Haematol. 164, 811–821 (2014). source
The citation is attached to the claim that these drugs use CRBN to target IKZF1 and IKZF3 for degradation, not to the citing authors’ later molecular-glue characterization. The Abstract identifies Ikaros and Aiolos as encoded by IKZF1 and IKZF3, respectively; the Results show drug-dependent binding to Cereblon and CRBN-dependent degradation. Page numbers are not provided in our copy. (LLM, conf=0.94)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“RBR ligases use a hybrid between the RING and HECT ligation strategies114,115.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [114] Yuan, L., Lv, Z., Atkison, J. H. & Olsen, S. K. Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI. Nat. Commun. 8, 211 (2017).
- Supportedcites [115] Dove, K. K. et al. Structural studies of HHARI/UbcH7~Ub reveal unique E2~Ub conformational restriction by RBR RING1. Structure 25, 890–900 e895 (2017). source
The Introduction (page not provided) says RBR E3s have an E2-binding RING1 domain structurally similar to canonical RING domains. It also says RBR and HECT E3s share a two-step ubiquitin-transfer mechanism, supporting the description of RBR ligases as a hybrid of the two strategies. (LLM, conf=0.92)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“α-Synuclein and tau are both intrinsically disordered proteins with distinct conformations that probably drive their respective pathologies and for which induced proteolytic degradation could be disease-modifying184.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Partly supportedcites [184] Chang, C. W., Shao, E. & Mucke, L. Tau: enabler of diverse brain disorders and target of rapidly evolving therapeutic strategies. Science 371, eabb8255 (2021). sourceExperimental — accuracy not yet measured
The Introduction identifies tau as intrinsically disordered, and Therapeutic approaches describes targeted proteolytic degradation of tau as a promising strategy under preclinical evaluation. Pathogenic mechanisms of abnormal tau reports disease-specific tau structures but says whether they causally contribute to disease remains undetermined. The paper mentions α-synuclein in Interactions with other pathogenic factors, but does not establish that it is intrinsically disordered or that targeted degradation of it could be disease-modifying. Page numbers were not available in our copy. (LLM, conf=0.88)
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
In the paper
“This construct rapidly degraded PCNA and maintained low levels of PCNA for the 10 days of doxycycline dosing.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [219] Lim, S. et al. Exquisitely specific anti-KRAS biodegraders inform on the cellular prevalence of nucleotide-loaded states. ACS Cent. Sci. 7, 274–291 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“However, in mice bearing xenograft pancreatic tumours, orthotopic injection of the Vif-based degrader was more efficacious than intraperitoneal injection, highlighting the need for better delivery methods to advance bioPROTACs from laboratory tools to therapeutics.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [212] Pan, T. et al. A recombinant chimeric protein specifically induces mutant KRAS degradation and potently inhibits pancreatic tumor growth. Oncotarget 7, 44299–44309 (2016). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“These are heterobifunctional small molecules consisting of two ligands joined by a linker: one ligand recruits and binds a protein of interest (POI) while the other recruits and binds an E3 ubiquitin ligase.”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Molecular glues, based on the serendipitous discovery that thalidomide and its analogues act as degrader molecules, constitute another important therapeutic class1–8.”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
What the sources say
- Not checked yetcites [1] Surka, C. et al. CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Blood 137, 661–677 (2021). source
- Not checked yetcites [2] Hansen, J. D. et al. Discovery of CRBN E3 ligase modulator CC-92480 for the treatment of relapsed and refractory multiple myeloma. J. Med. Chem. 63, 6648–6676 (2020). source
- Not checked yetcites [3] Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014). source
- Not checked yetcites [4] Kronke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014). source
- Not checked yetcites [5] Kronke, J. et al. Lenalidomide induces ubiquitination and degradation of CK1alpha in del(5q) MDS. Nature 523, 183–188 (2015). source
- Not checked yetcites [6] Ito, T. et al. Identification of a primary target of thalidomide teratogenicity. Science 327, 1345–1350 (2010). source
- Not checked yetcites [7] Fischer, E. S. et al. Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512, 49–53 (2014). source
- Not checked yetcites [8] Chamberlain, P. P. & Hamann, L. G. Development of targeted protein degradation therapeutics. Nat. Chem. Biol. 15, 937–944 (2019). source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Simultaneous binding of the POI and ligase by the PROTAC induces ubiquitylation of the POI and its subsequent degradation by the ubiquitin–proteasome system (UPS), after which the PROTAC is recycled to target another copy of the POI (Fig. 1).”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules.”
§ PROTAC targeted protein degraders: the past is prologue > Abstract
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- Rests on an assumption: Many disease-causing proteins are difficult to target with conventional small molecules because their active sites are broad, shallow pockets or their surfaces are smooth with few binding sites.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“It is this catalytic-type mechanism of action (MoA) and event-driven pharmacology that distinguishes PROTACs from classical inhibitors, which have a one-to-one relationship with the POI and whose pharmacology is driven by stoichiometry and, usually, by interactions with a catalytic site.”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin–proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development.”
§ PROTAC targeted protein degraders: the past is prologue > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In the same time frame, TPD molecules have progressed from being based on peptides to fully synthetic, rationally designed small molecules.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Over the past two decades, evidence for the broad therapeutic potential of PROTACs and other TPD molecules has moved from studies in cell lysates and cell culture to studies in animals and animal models of disease.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Human immunodeficiency virus 1 (HIV-1) deploys its viral proteins Vpr and Vpx, to recruit DDB1 and CUL4-associated factor 1 (DCAF1) to target several different human proteins, including DNA repair proteins, for ubiquitylation237,238.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [237] Planelles, V. & Barker, E. Roles of Vpr and Vpx in modulating the virus-host cell relationship. Mol. Asp. Med. 31, 398–406 (2010). source
- Not checked yetcites [238] Yan, J. et al. HIV-1 Vpr reprograms CLR4(DCAF1) E3 ubiquitin ligase to antagonize exonuclease 1-mediated restriction of HIV-1 infection. mBio 9, e01732-18 (2018).
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“The discovery of small-molecule mimetics of the HIF1α peptide20,21 opened the door to the rational design of PROTACs based wholly on small molecular structures — for example, the first PROTACs based on the bromodomain protein inhibitor JQ1 that recruited VHL to degrade bromodomain-containing protein 4 (BRD4)22,23.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [20] Buckley, D. L. et al. Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1alpha. Angew. Chem. Int. Ed. Engl. 51, 11463–11467 (2012). source
- Not checked yetcites [21] Buckley, D. L. et al. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1alpha interaction. J. Am. Chem. Soc. 134, 4465–4468 (2012). source
- Not checked yetcites [22] Bondeson, D. P. et al. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat. Chem. Biol. 11, 611–617 (2015). source
- Not checked yetcites [23] Zengerle, M., Chan, K. H. & Ciulli, A. Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem. Biol. 10, 1770–1777 (2015). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“At least two dozen viruses are known to hijack the human ubiquitin–proteasome system (UPS) to promote their own survival and replication10.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [10] Verma, R., Mohl, D. & Deshaies, R. J. Harnessing the power of proteolysis for targeted protein inactivation. Mol. Cell 77, 446–460 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Ubiquitin-dependent proteolysis is a major pathway that degrades intracellular proteins as part of normal cellular maintenance processes.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [14] Ciechanover, A., Orian, A. & Schwartz, A. L. Ubiquitin-mediated proteolysis: biological regulation via destruction. Bioessays 22, 442–451 (2000). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“For example, the E6 protein of human papillomavirus type 16 (HPV-16) and type 18 (HPV-18) recruits the human E3 ligase, ubiquitin–protein ligase E3A (UBE3A; also known as E6AP) to ubiquitylate p53, resulting in its degradation236.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [236] Lou, Z. & Wang, S. E3 ubiquitin ligases and human papillomavirus-induced carcinogenesis. J. Int. Med. Res. 42, 247–260 (2014). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The human genome is estimated to encode more than 600 E3 ligases15, each with specificity for a different subset of proteins.”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
What the sources say
- Not checked yetcites [15] Burslem, G. M. & Crews, C. M. Proteolysis-targeting chimeras as therapeutics and tools for biological discovery. Cell 181, 102–114 (2020). source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Although not heterobifunctional in the manner of PROTAC molecules, molecular glues promote ubiquitylation of a POI by enhancing a protein–protein interaction (PPI) between a ligase and a potential substrate (Fig. 2; Box 1).”
§ PROTAC targeted protein degraders: the past is prologue > Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This expands the accessible targets well beyond those that are druggable by traditional stoichiometric inhibition and provides novel ways to achieve selectivity.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“To date, traditional small-molecule drug discovery research for intracellular targets has often focused on developing high-affinity inhibitors that target either the active site or an allosteric site on an enzyme to shut down the function of the POI (occupancy-driven pharmacology).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“By incorporating the ligand into a PROTAC, which often acts in an iterative or ‘pseudo-catalytic’ fashion by binding and facilitating the interaction of its ligase and POI targets, the POI can be degraded without requiring a large excess of drug, thereby resulting in more complete target blockade and a wider therapeutic window22,48.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [22] Bondeson, D. P. et al. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat. Chem. Biol. 11, 611–617 (2015). source
- Not checked yetcites [48] Mares, A. et al. Extended pharmacodynamic responses observed upon PROTAC-mediated degradation of RIPK2. Commun. Biol. 3, 140 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The interim data for ARV-471 revealed a manageable tolerability profile with robust signals of clinical efficacy41, a 42% clinical benefit rate in a heavily pretreated population and evidence of better ER degradation than fulvestrant and other clinical-stage selective ER degraders (SERDs) when compared at the same stage of development.”
§ PROTAC targeted protein degraders: the past is prologue > Status of clinical translation of TPD > Clinical proof of concept for PROTACs
What the sources say
- Not checked yetcites [41] Snyder, L. B. et al. The discovery of ARV-471, an orally bioavailable estrogen receptor degrading PROTAC for the treatment of patients with breast cancer. In Proc. 112th Annual Meeting of the American Association for Cancer Research 1116 (AACR, 2021). source
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“PROTACs bring the degradation function to the target (event-driven pharmacology), negating the need for an active site and redefining undruggable targets as simply undrugged.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: Many disease-causing proteins are difficult to target with conventional small molecules because their active sites are broad, shallow pockets or their surfaces are smooth with few binding sites.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Proteins that have evolved resistance mutations to targeted therapies, proteins with scaffolding functions and proteins that are considered ‘undruggable’ with other modalities can also be highly suitable PROTAC targets.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The linker can contribute to the PROTAC solution conformation68 and degradation efficiency (DC50/Dmax)69, and influence the E3 ligase–POI interactions and presentation of the POI within the zone of ubiquitylation (Fig. 5).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“They based their analysis on several aspects of protein degradation mentioned here, such as availability of a small-molecule binder against the target, information on the endogenous ubiquitylation status of the target and target protein half-life.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [70] Schneider, M. et al. The PROTACtable genome. Nat. Rev. Drug Discov. 20, 789–797 (2021). source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“whereas PROTACs that covalently bind an E3 ligase would reduce the three-body assembly kinetics into a two-body problem and enhance the catalytic efficiency.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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It may state two separate claims as one.
In the paper
“Furthermore, they developed d9A-2, a pomalidomide-based PROTAC that degraded SLC family 9 member A1 (SLC9A1) — and, to a lesser extent, other SLC9 family members — leading to impaired pH homeostasis and cytotoxicity in multiple cancer cell lines, via a mechanism consistent with UPS-dependent TPD52.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
What the sources say
- Not checked yetcites [52] Bensimon, A. et al. Targeted degradation of SLC transporters reveals amenability of multi-pass transmembrane proteins to ligand-induced proteolysis. Cell Chem. Biol. 27, 728–739 e729 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“A notable exception is a BCL-xL degrader known as DT2216 developed by Dialectic Therapeutics that uses VHL as the recruiting ligase77,78, which is in phase I trials (Table 1).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [77] He, Y. et al. DT2216-a Bcl-xL-specific degrader is highly active against Bcl-xL-dependent T cell lymphomas. J. Hematol. Oncol. 13, 95 (2020). source
- Not checked yetcites [78] Zhang, X. et al. Utilizing PROTAC technology to address the on-target platelet toxicity associated with inhibition of BCL-XL. Chem. Commun. 55, 14765–14768 (2019). source
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“To take full advantage of favourable PROTAC-induced E3–POI interactions a wider set of PROTACable E3 ligases will be needed, as discussed in the next section.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Targets best suited for degradation
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As noted earlier, degrader discovery has converged upon two main paths for discovering molecules that result in specific target degradation (Fig. 2; Box 1).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plain- Asserted: passes — The authors put it forward as true.
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The quote only partly states this claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Nabet et al.53,95 have developed a heterologous tagging platform, dTAG, that allows validation of unliganded or yet-to-be-liganded proteins as degradation targets and is enabled for both VHL and CRBN.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [53] Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018). source
- Not checked yetcites [95] Nabet, B. et al. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat. Commun. 11, 4687 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The modular nature of the modality and its ability to achieve near-immediate degradation of a wide range of target proteins allows rapid evaluation of such basic degraders and characterization of their functions in cells through acute protein loss.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We would argue that the opportunity is ripe to tap into unexplored E3 ligases for protein degradation.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These and other challenges leave the door open to opportunities for identifying and developing alternative E3 ligases.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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Probably not a substantial claim. It may be too vague to check against evidence.
None of the sources cited for this claim have been checked yet.
In the paper
“ubiquitin E3 ligases serve as scaffolds between a target protein and an activated ubiquitin E2 conjugating enzyme charged with a ubiquitin molecule (E2–Ub), by binding both molecules, then catalysing the transfer of ubiquitin from the active site cysteine of the E2 onto a lysine side chain of a target protein104–107.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [104] Zimmerman, E. S., Schulman, B. A. & Zheng, N. Structural assembly of cullin-RING ubiquitin ligase complexes. Curr. Opin. Struct. Biol. 20, 714–721 (2010). source
- Not checked yetcites [105] Duda, D. M. et al. Structural regulation of cullin-RING ubiquitin ligase complexes. Curr. Opin. Struct. Biol. 21, 257–264 (2011). source
- Not checked yetcites [106] Baek, K. et al. NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly. Nature 578, 461–466 (2020). source
- Not checked yetcites [107] Baek, K., Scott, D. C. & Schulman, B. A. NEDD8 and ubiquitin ligation by cullin-RING E3 ligases. Curr. Opin. Struct. Biol. 67, 101–109 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Its proximity to the membrane and the large size of the Cullin 4A (CUL4A)–DDB1–CRBN–E2–Ub complex relative to the smaller CUL2–elongin B (ELOB)–ELOC–VHL–E2–Ub complex (Fig. 5) could be a contributing factor.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedgedconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“CRBN and VHL, for example, are substrate receptor proteins that pair with CRL4 and CRL2, respectively.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Cooperativity of the ternary complex, which is a measure of ternary complex formation in a heterobifunctional system, may be positive or negative between a ligase and a target enabled by a PROTAC molecule128 and has been shown to lead to degradation in both cases.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [128] Hughes, S. J. & Ciulli, A. Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders. Essays Biochem. 61, 505–516 (2017). source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Collectively, these findings demonstrate that KRAS(G12C) is specifically targetable via the PROTAC mechanism, but that targetability depends on the choice of E3 ligase”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
boosteddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“LC-2 was able to engage endogenous KRAS(G12C), induce its poly-ubiquitylation and degrade it via the 20S proteasome.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [55] Bond, M. J., Chu, L., Nalawansha, D. A., Li, K. & Crews, C. M. Targeted degradation of oncogenic KRAS(G12C) by VHL-recruiting PROTACs. ACS Cent. Sci. 6, 1367–1375 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“the more than 600 E3 ligases in the human genome fall into different classes, depending on which ubiquitin ligation strategy they use (reviewed in refs80,108–110).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [80] Schapira, M., Calabrese, M. F., Bullock, A. N. & Crews, C. M. Targeted protein degradation: expanding the toolbox. Nat. Rev. Drug. Discov. 18, 949–963 (2019). source
- Not checked yetcites [108] Yau, R. & Rape, M. The increasing complexity of the ubiquitin code. Nat. Cell Biol. 18, 579–586 (2016). source
- Not checked yetcites [109] Komander, D. & Rape, M. The ubiquitin code. Annu. Rev. Biochem. 81, 203–229 (2012). source
- Not checked yetcites [110] Zheng, N. & Shabek, N. Ubiquitin ligases: structure, function, and regulation. Annu. Rev. Biochem. 86, 129–157 (2017). source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“The second class, HECT ligases, bind the target then use an intermediate strategy of transferring ubiquitin onto themselves before transferring ubiquitin to the target112,113.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [112] Zhang, W. et al. System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes. Mol. Cell 62, 121–136 (2016). source
- Not checked yetcites [113] Kamadurai, H. B. et al. Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. eLife 2, e00828 (2013). source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Cooperativity plays a role in the efficiency of the VHL–BRD4 degrader MZ1 (ref.129), but is dispensable for CRBN–BRD4 degraders130.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [129] Gadd, M. S. et al. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat. Chem. Biol. 13, 514–521 (2017). source
- Not checked yetcites [130] Nowak, R. P. et al. Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat. Chem. Biol. 14, 706–714 (2018). source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“the degree of ternary complex formation may differ from substrate to substrate127; that is, a ternary complex that forms too efficiently and remains tightly bound will not lead to efficient degradation.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [127] Rodriguez-Rivera, F. P. & Levi, S. M. Unifying catalysis framework to dissect proteasomal degradation paradigms. ACS Cent. Sci. 7, 1117–1125 (2021). source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“Although XY-4-88 was able to degrade a GFP–KRAS(G12C) fusion protein, albeit in a non-catalytic manner because it covalently bound the target, it could not degrade untagged, endogenous KRAS(G12C).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [124] Zeng, M. et al. Exploring targeted degradation strategy for oncogenic KRAS(G12C). Cell Chem. Biol. 27, 19–31 e16 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Subsequent studies revealed that XY-4-88 induced the CRBN–KRAS(G12C) complex, but not its poly-ubiquitylation.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“RING and RBR ligases have recently been shown to work in unison to mediate substrate ubiquitylation in a site-specific manner116,117.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [116] Scott, D. C. et al. Two distinct types of E3 ligases work in unison to regulate substrate ubiquitylation. Cell 166, 1198–1214 e1124 (2016). source
- Not checked yetcites [117] Horn-Ghetko, D. et al. Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Nature 590, 671–676 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“a recent massive kinase degradation study using various kinase inhibitors as warheads has revealed the ‘degradable kinome’ and a diversity of kinase-degrading profiles among E3 ligases”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [126] Donovan, K. A. et al. Mapping the degradable kinome provides a resource for expedited degrader development. Cell 183, 1714–1731 e1710 (2020). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“KRAS is a small protein (189 amino acids) and, when farnesylated, it is localized to the plasma membrane.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“F-box protein 44 (FBXO44)150 that is enriched in some tissues but not specific to any151.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [150] Kumanomidou, T. et al. The structural differences between a glycoprotein specific F-box protein Fbs1 and its homologous protein FBG3. PLoS ONE 10, e0140366 (2015). source
- Not checked yetcites [151] Glenn, K. A., Nelson, R. F., Wen, H. M., Mallinger, A. J. & Paulson, H. L. Diversity in tissue expression, substrate binding, and SCF complex formation for a lectin family of ubiquitin ligases. J. Biol. Chem. 283, 12717–12729 (2008). source
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“One caveat for this group of ligases is that tumour enrichment provides only a potential window of opportunity for PROTACs, which may not translate to a greatly expanded therapeutic index for pleiotropically toxic inhibitors that are converted into tumour-specific PROTACs.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The intersection between the practical and aspirational attributes of these niche ligases with respect to novel degrader development is often minimal at best, thus offering high risk/high reward scenarios for PROTAC discovery and development of degraders that recruit such specialized ligases.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Alphafold from DeepMind has made available all their high-quality predicted models across the proteome (https://alphafold.ebi.ac.uk/) and now serves as a major stepping stone in potentially enabling computer-aided drug discovery for many hitherto unreachable targets and ligases.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [141] Tunyasuvunakool, K. et al. Highly accurate protein structure prediction for the human proteome. Nature 596, 590–596 (2021). source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“PROTACs based on these ligases might therefore exhibit toxicities associated with classical chemotherapeutic agents, but this remains to be tested.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The TPD field has now matured to the point that strides are being taken to realize such specificity goals and enable precision TPD (pTPD).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“degradation of BCL-xL by the VHL-recruiting PROTAC DT2216 (ref.152) was spared in platelets, thus resulting in reduced platelet-driven toxicity and an improved therapeutic index compared with a BCL-xL inhibitor78,153.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [152] Khan, S. et al. A selective BCL-XL PROTAC degrader achieves safe and potent antitumor activity. Nat. Med. 25, 1938–1947 (2019). source
- Not checked yetcites [78] Zhang, X. et al. Utilizing PROTAC technology to address the on-target platelet toxicity associated with inhibition of BCL-XL. Chem. Commun. 55, 14765–14768 (2019). source
- Not checked yetcites [153] Zhang, X. et al. Discovery of PROTAC BCL-XL degraders as potent anticancer agents with low on-target platelet toxicity. Eur. J. Med. Chem. 192, 112186 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, as many E3 ligases are multisubunit complexes, analysing expression levels of a single subunit is only part of the whole picture.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Another new frontier to explore for pTPD is specific targeting of a PROTAC molecule by tumour cells over adjacent, non-cancerous tissue or uptake by a given type of tumour-initiating cell, which may be achieved by targeting tumour-specific or tumour-enriched E3 ligases.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“An example of such a family of ligases are the MAGE (melanoma antigen genes) family of ubiquitin E3 ligases, often referred to as the MAGE-RING ligases (MRLs), which comprise proteins that serve as substrate-recruitment modules for other RING E3 ligases156,157, adding to and/or altering the substrate specificity of their co-E3 ligases (reviewed elsewhere155,158).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [156] Yang, S. W. et al. A cancer-specific ubiquitin ligase drives mRNA alternative polyadenylation by ubiquitinating the mRNA 3′ end processing complex. Mol. Cell 77, 1206–1221 e1207 (2020). source
- Not checked yetcites [157] Pineda, C. T. et al. Degradation of AMPK by a cancer-specific ubiquitin ligase. Cell 160, 715–728 (2015). source
- Not checked yetcites [155] Weon, J. L. & Potts, P. R. The MAGE protein family and cancer. Curr. Opin. Cell Biol. 37, 1–8 (2015). source
- Not checked yetcites [158] Lee, A. K. & Potts, P. R. A comprehensive guide to the MAGE family of ubiquitin ligases. J. Mol. Biol. 429, 1114–1142 (2017). source
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In the paper
“A second caveat is that highly tumour-enriched and tumour-dependent E3 ligases and ligase adaptors tend to be associated with the cell cycle — for example, CDC20 or S-phase kinase-associated protein 2 (SKP2) and others — and are likely to have similar profiles in tumours and rapidly dividing non-cancerous cells in the human body, such as in the bone marrow.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
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In the paper
“which have a documented role in the biology of nemaline myopathy146,147.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Expanding the ligase landscape
What the sources say
- Not checked yetcites [146] Gupta, V. A. et al. Identification of KLHL41 mutations implicates BTB-kelch-mediated ubiquitination as an alternate pathway to myofibrillar disruption in nemaline myopathy. Am. J. Hum. Genet. 93, 1108–1117 (2013). source
- Not checked yetcites [147] Garg, A. et al. KLHL40 deficiency destabilizes thin filament proteins and promotes nemaline myopathy. J. Clin. Invest. 124, 3529–3539 (2014). source
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In the paper
“Another advantage of PROTAC degraders is their ability to degrade the target completely, instead of only inhibiting its enzymatic function, which would not affect any scaffolding role that a target may have.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
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In the paper
“BTK is a well-established target in inflammation, as well as in oncology, with approved drugs in the clinic164,165”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [164] Dobrovolsky, D. et al. Bruton tyrosine kinase degradation as a therapeutic strategy for cancer. Blood 133, 952–961 (2019). source
- Not checked yetcites [165] Zarrin, A. A., Bao, K., Lupardus, P. & Vucic, D. Kinase inhibition in autoimmunity and inflammation. Nat. Rev. Drug Discov. 20, 39–63 (2021). source
boosted- Asserted: passes — The authors put it forward as true.
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In the paper
“However, given its potential to degrade any target of choice, the reach of TPD is extending further than oncology.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
plaindirect- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: TPD has the potential to degrade any target of choice.
In the paper
“A BTK PROTAC from Nurix Therapeutics that targets haematological malignancies (NX-2127) is currently in a phase I trial (Table 1).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites Table 1
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In the paper
“but the role of IRAK4 in inflammatory conditions, as well as in B cell lymphomas, is well established, and several inhibitors are currently in clinical trials in autoimmune indications165,171.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [165] Zarrin, A. A., Bao, K., Lupardus, P. & Vucic, D. Kinase inhibition in autoimmunity and inflammation. Nat. Rev. Drug Discov. 20, 39–63 (2021). source
- Not checked yetcites [171] Wiese, M. D., Manning-Bennett, A. T. & Abuhelwa, A. Y. Investigational IRAK-4 inhibitors for the treatment of rheumatoid arthritis. Expert Opin. Investig. Drugs 29, 475–482 (2020). source
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In the paper
“Following in the footsteps of immunotherapy, small-molecule-mediated activation of the immune response against tumours is a rich area of drug development176,177.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [176] van der Zanden, S. Y., Luimstra, J. J., Neefjes, J., Borst, J. & Ovaa, H. Opportunities for small molecules in cancer immunotherapy. Trends Immunol. 41, 493–511 (2020). source
- Not checked yetcites [177] Kerr, W. G. & Chisholm, J. D. The next generation of immunotherapy for cancer: small molecules could make big waves. J. Immunol. 202, 11–19 (2019). source
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In the paper
“In fact, two small-molecule TPD strategies have been reported to lower mHTT levels: a small-molecule glue approach inducing the proximity between mHTT and microtubule-associated protein 1 light chain 3α (MAP1LC3α; also known as LC3) to target it to the autophagy pathway for degradation196; and small-molecule PROTACs that recruit mHTT aggregates to E3 ligases from the IAP family, causing the protea”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [196] Li, Z. et al. Allele-selective lowering of mutant HTT protein by HTT-LC3 linker compounds. Nature 575, 203–209 (2019). source
- Not checked yetcites [197] Tomoshige, S., Nomura, S., Ohgane, K., Hashimoto, Y. & Ishikawa, M. Discovery of small molecules that induce the degradation of huntingtin. Angew. Chem. Int. Ed. Engl. 56, 11530–11533 (2017). source
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In the paper
“A large PPI study in SARS-CoV-2-infected cells revealed several potential druggable pathways and proteins that may be exploited by repurposing inhibitors199, and that could potentially be addressed by SARS-CoV-2-targeting PROTAC molecules.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [199] Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459–468 (2020). source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“a PROTAC approach may result in a cleaner inhibitory phenotype and better tolerability as a therapeutic agent.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“However, small-molecule probes against tau oligomeric species, such as 18F-T807, have been developed and are currently in use as clinical tau PET tracers190.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [190] Chien, D. T. et al. Early clinical PET imaging results with the novel PHF-tau radioligand [F-18]-T807. J. Alzheimers Dis. 34, 457–468 (2013). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“These antiviral inhibitors could provide starting points for the development of antiviral PROTACs that target SARS-CoV-2.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
hedgedconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Even so, these targets are still susceptible to degradation by alternative PROTAC approaches, including bioPROTACs and hybrid PROTACs.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper may give no reason why it holds.
In the paper
“A peptide-based α-synuclein degrader (see below) has been reported and was shown to protect neurons from α-synuclein overexpression-induced toxicity193.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [193] Qu, J. et al. Specific knockdown of alpha-synuclein by peptide-directed proteasome degradation rescued its associated neurotoxicity. Cell Chem. Biol. 27, 763 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Importantly, Pfizer initiated a phase I trial of its orally bioavailable SARS-CoV-2 Mpro inhibitor, PF-07321332 (NCT04756531) in healthy individuals in February 2021, followed by a phase II/III study, in which the first patient was dosed in September 2021 (NCT04960202).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites NCT04756531
- Not checked yetcites NCT04960202
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“In Huntington disease, poly-glutamine-expanded mHTT aggregates and accumulates194”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [194] MacDonald, M. E. et al. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell 72, 971–983 (1993). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Tauopathies include neurological disorders, such as Alzheimer disease, frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP)182, in which pathology is heavily associated with toxic accumulation of aberrant tau species, leading tau to aggregate into paired helical filaments and ultimately into neurofibrillary tangles that result in neuronal cell death183.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“With the recent discontinuation of the phase III trial of tominersen, an HTT-lowering ASO that it was hoped could become the first disease-modifying therapy for Huntington disease, the PROTAC modality could provide a useful alternative route to pursue this key target.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
hedgedconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“A key PROTAC property is the ability to degrade proteins that are not classically targetable by small-molecule inhibitors because they lack active sites.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper may give no reason why it holds.
In the paper
“Other targets in neurology where a PROTAC modality may offer clear advantages over current therapeutic agents include α-synuclein, a protein that can accumulate in the neurons of patients with Parkinson disease192.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [192] Kotzbauer, P. T., Trojanowsk, J. Q. & Lee, V. M. Lewy body pathology in Alzheimer’s disease. J. Mol. Neurosci. 17, 225–232 (2001). source
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Tau in its monomeric form is an intrinsically disordered protein without clearly defined small-molecule binding pockets, which has made development of small-molecule inhibitors challenging.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In fact, one strategy has utilized such PET tracers by turning them into tool PROTAC molecules that target tau by recruiting CRBN, and these were shown to cause degradation of tau species in cell-based models of tauopathy191.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [191] Silva, M. C. et al. Targeted degradation of aberrant tau in frontotemporal dementia patient-derived neuronal cell models. eLife 8, e45457 (2019). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Pfizer has also developed an Mpro inhibitor prodrug, PF-07304814 (ref.203), which is given intravenously and which entered clinical trials in hospitalized patients with COVID-19 in 2020 (NCT04535167).”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [203] Boras, B. et al. Discovery of a novel inhibitor of coronavirus 3CL protease as a clinical candidate for the potential treatment of COVID-19. bioRxiv https://doi.org/10.1101/2020.09.12.293498 (2020). source
- Not checked yetcites NCT04535167
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Importantly, induced turnover of tau by the UPS, and the degradability of tau species, has been demonstrated by a tau–kelch-like ECH-associated protein 1 (KEAP1) chimeric peptide PROTAC molecule188, as well as by a VHL–tau PROTAC189.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Therapeutic areas beyond oncology
What the sources say
- Not checked yetcites [188] Lu, M. et al. Discovery of a Keap1-dependent peptide PROTAC to knockdown Tau by ubiquitination-proteasome degradation pathway. Eur. J. Med. Chem. 146, 251–259 (2018). source
- Not checked yetcites [189] Wang, W. et al. A novel small-molecule PROTAC selectively promotes tau clearance to improve cognitive functions in Alzheimer-like models. Theranostics 11, 5279–5295 (2021). source
boosteddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the near term, bioPROTACs will be used as tool molecules to drive small-molecule PROTAC drug development.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Continued advances in nanoparticle drug delivery methods and viral vector gene delivery systems will play a major part in bringing these novel modalities to patients.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Since then, other groups have reported fusion bioPROTACs that degraded the cancer targets human epidermal growth factor receptor 2 (HER2), MYC and KRAS and demonstrated therapeutically relevant effects in human cancer cell lines and mouse xenograft tumour models overexpressing these POIs16,17,211,212.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
What the sources say
- Not checked yetcites [16] Ma, Y. et al. Targeted degradation of KRAS by an engineered ubiquitin ligase suppresses pancreatic cancer cell growth in vitro and in vivo. Mol. Cancer Ther. 12, 286–294 (2013). source
- Not checked yetcites [17] Hatakeyama, S., Watanabe, M., Fujii, Y. & Nakayama, K. I. Targeted destruction of c-Myc by an engineered ubiquitin ligase suppresses cell transformation and tumor formation. Cancer Res. 65, 7874–7879 (2005). source
- Not checked yetcites [211] Li, X. et al. Degradation of HER2 by Cbl-based chimeric ubiquitin ligases. Cancer Res. 67, 8716–8724 (2007). source
- Not checked yetcites [212] Pan, T. et al. A recombinant chimeric protein specifically induces mutant KRAS degradation and potently inhibits pancreatic tumor growth. Oncotarget 7, 44299–44309 (2016). source
boosteddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Chimeric bioPROTACs can potentially be delivered as gene products and intracellular levels controlled by finely tuned promoters.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
hedgedconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Small-molecule PROTACs have the potential for oral delivery, and cellular levels can be controlled by dosing.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plainconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although bioPROTACs, O’PROTACs and TRAFTACs have the potential to become therapeutic agents, delivery and dosing are key hurdles to overcome.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“and we believe this modality has the potential to offer patients new treatment options across diverse indications.”
§ PROTAC targeted protein degraders: the past is prologue > Conclusion
hedgedconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may be too vague to check against evidence. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For undrugged targets for which small-molecule ligands have not yet been discovered or productive small-molecule binding sites do not exist, bioPROTACs have an advantage: undrugged targets often form PPIs that are difficult to block with traditional drugs, but their protein-binding domains offer starting points for assembling bioPROTACs to initiate the drug discovery process.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plaindirect- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Like small-molecule PROTACs, bioPROTACs can be rapidly assembled to identify potent degraders if the warheads are known.”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, bioPROTACs can be used for the following: to determine the biological benefit of complete inhibition of a protein via degradation versus partial inhibition with a small molecule; to compare the biological effect of post-expression degradation versus silencing expression with RNA interference; and to determine which face of the target protein is approachable by the E3 ligase and leads to”
§ PROTAC targeted protein degraders: the past is prologue > Outlook for the next 20 years of TPD > Alternative PROTAC modalities
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
The paper relies on this without support.
Many disease-causing proteins are difficult to target with conventional small molecules because their active sites are broad, shallow pockets or their surfaces are smooth with few binding sites.
“Some have been intractable because their active sites are broad, shallow pockets that are difficult to bridge with small molecules; others have ‘smooth’ surfaces that offer few sites for a small molecule to bind.”
The paper relies on this without support.
For any new therapeutic modality, selecting well-known targets is important for establishing proof of concept because it introduces just one variable (the modality), not two.
“For any new therapeutic modality, the selection of well-known targets is important for establishing proof of concept because it introduces just one variable (the modality), not two (the modality and a novel target) into the equation.”
The paper relies on this without support.
Moderate affinity (≥1–500 nM) is typically needed for a ligand to be used in a PROTAC.
“Using these sites does not require a high-affinity ligand if coupled to the right E3 ligand, but moderate affinity (≥1–500 nM) is typically needed”
The paper relies on this without support.
Access to the POI surface near the binding site by a recruited E3 ligase is essential.
“and access to the POI surface near the binding site by a recruited E3 ligase is essential.”
The paper relies on this without support.
An ideal E3 ligase ligand would be a potent binder with a slow off-rate.
“an ideal E3 ligase ligand would be a potent binder with a slow off-rate.”
The paper relies on this without support.
Short linkers limit the number of ways the E3 ligase and POI come together and how the POI fits into the full E3–E2–ubiquitin complex.
“However, short linkers limit the number of ways the E3 ligase and POI come together and, ultimately, how the POI fits into the full E3–E2–ubiquitin complex.”
The paper relies on this without support.
Ternary complex formation is a necessary step in the action of a PROTAC molecule.
“Ternary complex formation is a necessary step in the action of a PROTAC molecule”
The paper relies on this without support.
Several ligases exist in an off state and are auto-inhibited in the absence of an activating post-translational modification or presence of a binding partner.
“Several ligases exist in an ‘off’ state and are auto-inhibited in the absence of an activating post-translational modification or presence of a binding partner.”
The paper relies on this without support.
TPD has the potential to degrade any target of choice.
“given its potential to degrade any target of choice”
The paper relies on this without support.
Some MAGE E3 ligases do not degrade their targets.
“as some do not degrade their targets”
The paper relies on this without support.
There are currently no approved IRAK4-targeting therapies.
“By contrast, there are currently no approved IRAK4-targeting therapies”
The paper relies on this without support.
HPK1 inhibitors are equally effective as HPK1-targeting PROTACs.
“although HPK1 inhibitors were shown to be equally effective”
The paper relies on this without support.
Transcription factors and RNA-binding proteins have largely remained undrugged because many lack ligand-binding sites.
“Despite much effort, these POIs have largely remained undrugged as many of them lack ligand-binding sites.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“Targeted protein degradation (TPD), including molecular glues and PROTACs, has emerged as a promising strategy to target proteins previously considered undruggable53.”
From Harnessing artificial intelligence to identify Bufalin as a molecular glue degrader of estrogen receptor alpha (2025) · cites this paper as [53]
The cited source says what the claim attributes to it.
In the citing paper
“Proteolysis-targeting chimeras (PROTACs) offer a powerful strategy for antitumor drug discovery40.”
From An HDAC4-specific PROTAC degrader achieves radiation sensitization by enhancing ferroptosis in lung cancer (2026) · cites this paper as [40]
The cited source says what the claim attributes to it.
In the citing paper
“The composition and length of linkers can affect the efficiency of degraders40,41.”
From An HDAC4-specific PROTAC degrader achieves radiation sensitization by enhancing ferroptosis in lung cancer (2026) · cites this paper as [40]
In the citing paper
“Indeed, this exciting technology is currently transitioning to the clinic, with several PROTACs now in clinical trials.16,31”
From Chasing molecular glue degraders: screening approaches (2022) · cites this paper as [16]
In the citing paper
“Chemical diversification of known glue degraders, especially IMiDs, has delivered derivatives that are even approaching the clinic.16,31”
From Chasing molecular glue degraders: screening approaches (2022) · cites this paper as [16]
In the citing paper
“The Helios glue degrader DKY709 (Fig. 8) from Novartis is in Phase I for solid cancers (currently tested as monotherapy and in combination with spartalizumab, an anti-PD-1).16,31”
From Chasing molecular glue degraders: screening approaches (2022) · cites this paper as [16]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
“The Vpr protein of HIV-1 (ref.244) and the E6 protein of hepatitis B virus (HBV)245 act as bispecific antibody mimics”
§ PROTAC targeted protein degraders: the past is prologue > Foundations of TPD
“the E6 protein of human papillomavirus type 16 (HPV-16) and type 18 (HPV-18) recruits the human E3 ligase, ubiquitin–protein ligase E3A (UBE3A; also known as E6AP) to ubiquitylate p53, resulting in its degradation236.”
Citations
Cites
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Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature · doi:10.1038/s41586-020-2286-9 · Cited by 4,405
Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes
Liu, J., Farmer, J. D., Lane, W. S., Friedman, J., Weissman, I., & Schreiber, S. L. (1991) · Cell · doi:10.1016/0092-8674(91)90124-h · Cited by 4,116
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Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality
Sletten, E. M., & Bertozzi, C. R. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200900942 · Cited by 3,165
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025
Sakamoto, K. M., Kim, K. B., Kumagai, A., Mercurio, F., Crews, C. M., & Deshaies, R. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.141230798 · Cited by 2,609
Self-citation
Research works printed but not linked: 1
- Snyder, L. B. et al. Discovery of ARV-110, a first in class androgen receptor degrading PROTAC for the treatment of men with metastatic castration resistant prostate cancer. In Proc. 112th Annual Meeting of the American Association for Cancer Research 1115 (AACR, 2021).
Cited by
Sorted by citations
PROTACs: past, present and future
Li, K., & Crews, C. M. (2022) · Chemical Society Reviews · doi:10.1039/d2cs00193d · Cited by 869
Self-citationExploring the next generation of antibody–drug conjugates
Tsuchikama, K., Anami, Y., Ha, S. Y. Y., & Yamazaki, C. M. (2024) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00850-2 · Cited by 659
Protein degraders enter the clinic — a new approach to cancer therapy
Chirnomas, D., Hornberger, K. R., & Crews, C. M. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00736-3 · Cited by 658
Self-citationMolecular targeted therapy for anticancer treatment
Min, H.-Y., & Lee, H.-Y. (2022) · Experimental & Molecular Medicine · doi:10.1038/s12276-022-00864-3 · Cited by 569
Chemistries of bifunctional PROTAC degraders
Cao, C., He, M., Wang, L., He, Y., & Rao, Y. (2022) · Chemical Society Reviews · doi:10.1039/d2cs00220e · Cited by 313
Metadata
- Authors
- Békés, M., Langley, D. R., & Crews, C. M.
- Affiliations
- Arvinas (United States) (US)
- Yale University (US)
- Corresponding author
- Békés, Miklós
- Langley, David R.
- Crews, Craig M.
- Venue
- Nature Reviews Drug Discovery
- Published
- 2022-01-18
- Volume
- 21
- Issue
- 3
- Pages
- 181-200
- ISSN
- 1474-1776 (ISSN-L)
- 1474-1784
- PMC
- PMC8765495
- OpenAlex
- W4205379795
- Semantic Scholar
- 4f8ace44d3e56b048f0dd996990cee73fed98aeb
- Cited by
- 3,395
- References
- 254
- Citations by year
- 2026: 841 · 2025: 965 · 2024: 798 · 2023: 550 · 2022: 240
- FWCI
- 67.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Reviews Drug Discovery (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (R35CA197589)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Keywords
- PROTACs, targeted protein degradation, ubiquitin-proteasome system, ubiquitin ligase, undruggable targets, cancer therapeutics, precision medicine, drug discovery, pharmaceutical industry development
- MeSH terms
- Humans, Proteins, Proteasome Endopeptidase Complex, Proteolysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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