PROTAC targeted protein degraders: the past is prologue

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.”

What the sources say

• Supported

  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)

  cites [3] Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014). source
• Supported

  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)

  cites [4] Kronke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014). source
• Supported

  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)

  cites [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

In the paper

“RBR ligases use a hybrid between the RING and HECT ligation strategies114,115.”

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).
• Supported

  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)

  cites [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

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.”

What the sources say

• Partly supported

  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)

  cites [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

In the paper

“This construct rapidly degraded PCNA and maintained low levels of PCNA for the 10 days of doxycycline dosing.”

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

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.”

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

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.”

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.”

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

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).”

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.”

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.”

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.”

In the paper

“In the same time frame, TPD molecules have progressed from being based on peptides to fully synthetic, rationally designed small molecules.”

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.”

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.”

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).

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.”

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

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.”

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

In the paper

“Ubiquitin-dependent proteolysis is a major pathway that degrades intracellular proteins as part of normal cellular maintenance processes.”

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

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.”

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

In the paper

“The human genome is estimated to encode more than 600 E3 ligases15, each with specificity for a different subset of proteins.”

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

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).”

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.”

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).”

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.”

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

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.”

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

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.”

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.”

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).”

What the sources say

• Not checked yetcites [68] Atilaw, Y. et al. Solution conformations shed light on PROTAC cell permeability. ACS Med. Chem. Lett. 12, 107–114 (2021). source
• Not checked yetcites [69] Cyrus, K. et al. Impact of linker length on the activity of PROTACs. Mol. Biosyst. 7, 359–364 (2011). source

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.”

What the sources say

• Not checked yetcites [70] Schneider, M. et al. The PROTACtable genome. Nat. Rev. Drug Discov. 20, 789–797 (2021). source

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.”

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.”

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

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).”

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

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.”

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).”

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.”

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

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.”

In the paper

“We would argue that the opportunity is ripe to tap into unexplored E3 ligases for protein degradation.”

In the paper

“These and other challenges leave the door open to opportunities for identifying and developing alternative E3 ligases.”

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.”

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

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.”

In the paper

“CRBN and VHL, for example, are substrate receptor proteins that pair with CRL4 and CRL2, respectively.”

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.”

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

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”

In the paper

“LC-2 was able to engage endogenous KRAS(G12C), induce its poly-ubiquitylation and degrade it via the 20S proteasome.”

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

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).”

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

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.”

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

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.”

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

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.”

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

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).”

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

In the paper

“Subsequent studies revealed that XY-4-88 induced the CRBN–KRAS(G12C) complex, but not its poly-ubiquitylation.”

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.”

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

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”

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

In the paper

“KRAS is a small protein (189 amino acids) and, when farnesylated, it is localized to the plasma membrane.”

In the paper

“F-box protein 44 (FBXO44)150 that is enriched in some tissues but not specific to any151.”

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

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.”

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.”

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.”

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

In the paper

“PROTACs based on these ligases might therefore exhibit toxicities associated with classical chemotherapeutic agents, but this remains to be tested.”

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).”

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.”

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

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.”

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.”

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).”

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

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.”

In the paper

“which have a documented role in the biology of nemaline myopathy146,147.”

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

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.”

In the paper

“BTK is a well-established target in inflammation, as well as in oncology, with approved drugs in the clinic164,165”

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

In the paper

“However, given its potential to degrade any target of choice, the reach of TPD is extending further than oncology.”

In the paper

“A BTK PROTAC from Nurix Therapeutics that targets haematological malignancies (NX-2127) is currently in a phase I trial (Table 1).”

What the sources say

• Not checked yetcites Table 1

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.”

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

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.”

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

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”

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

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.”

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

In the paper

“a PROTAC approach may result in a cleaner inhibitory phenotype and better tolerability as a therapeutic agent.”

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.”

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

In the paper

“These antiviral inhibitors could provide starting points for the development of antiviral PROTACs that target SARS-CoV-2.”

In the paper

“Even so, these targets are still susceptible to degradation by alternative PROTAC approaches, including bioPROTACs and hybrid PROTACs.”

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.”

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

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).”

What the sources say

• Not checked yetcites NCT04756531
• Not checked yetcites NCT04960202

In the paper

“In Huntington disease, poly-glutamine-expanded mHTT aggregates and accumulates194”

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

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.”

What the sources say

• Not checked yetcites [182] Wang, Y. & Mandelkow, E. Tau in physiology and pathology. Nat. Rev. Neurosci. 17, 5–21 (2016). source
• Not checked yetcites [183] Goedert, M. Tau protein and neurodegeneration. Semin. Cell Dev. Biol. 15, 45–49 (2004). source

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.”

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.”

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.”

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

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.”

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.”

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

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).”

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

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.”

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

In the paper

“In the near term, bioPROTACs will be used as tool molecules to drive small-molecule PROTAC drug development.”

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.”

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.”

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

In the paper

“Chimeric bioPROTACs can potentially be delivered as gene products and intracellular levels controlled by finely tuned promoters.”

In the paper

“Small-molecule PROTACs have the potential for oral delivery, and cellular levels can be controlled by dosing.”

In the paper

“Although bioPROTACs, O’PROTACs and TRAFTACs have the potential to become therapeutic agents, delivery and dosing are key hurdles to overcome.”

In the paper

“and we believe this modality has the potential to offer patients new treatment options across diverse indications.”

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.”

In the paper

“Like small-molecule PROTACs, bioPROTACs can be rapidly assembled to identify potent degraders if the warheads are known.”

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”