Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders
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Molecular glues and bivalent inducers of protein degradation (also known as PROTACs) represent a fascinating new modality in pharmacotherapeutics: the potential to knockdown previously thought ‘undruggable’ targets at sub-stoichiometric concentrations in ways not possible using conventional inhibitors. Mounting evidence suggests these chemical agents, in concert with their target proteins, can be modelled as three-body binding equilibria that can exhibit significant cooperativity as a result of specific ligand-induced molecular recognition. Despite this, many existing drug design and optimization regimens still fixate on binary target engagement, in part due to limited structural data on ternary complexes. Recent crystal structures of protein complexes mediated by degrader molecules, including the first PROTAC ternary complex, underscore the importance of protein–protein interactions and intramolecular contacts to the mode of action of this class of compounds. These discoveries have opened the door to a new paradigm for structure-guided drug design: borrowing surface area and molecular recognition from nature to elicit cellular signalling.
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Molecular glue-based degraders have potentially lower molecular weight than linker-based bifunctional molecules such as PROTACs, a possible advantage for increased bioavailability and improved pharmacokinetic profiles.
“Molecular glue-based degraders, as exemplified by the IMiD-family of immunomodulatory drugs including thalidomide, are notable for their potentially lower molecular weight as compared to linker-based bifunctional molecules (e.g. PROTACS), a possible advantage for increased bioavailability and improved pharmacokinetic profiles 4.”
From Manumycin polyketides act as molecular glues between UBR7 and P53 (2020) · cites this paper as [4]
Degradation of SALL4 leads to teratogenic effects while degradation of Ikaros is a proven chemotherapeutic strategy.
“Paradoxically, degradation of the former leads to teratogenic effects while degradation of the latter is a proven chemotherapeutic strategy4,6.”
From Manumycin polyketides act as molecular glues between UBR7 and P53 (2020) · cites this paper as [4]
Cooperativity of the ternary complex may be positive or negative and has been shown to lead to degradation in both cases.
“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.”
From PROTAC targeted protein degraders: the past is prologue (2022) · cites this paper as [128]
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- Authors
- Hughes, S. J., & Ciulli, A.
- Affiliations
- University of Dundee (GB)
- Corresponding author
- Ciulli, Alessio
- Venue
- Essays in Biochemistry
- Publisher
- Portland Press Ltd.
- Published
- 2017-11-08
- Volume
- 61
- Issue
- 5
- Pages
- 505-516
- ISSN
- 0071-1365 (ISSN-L)
- 1744-1358
- PMC
- PMC5869862
- OpenAlex
- W2767966404
- Cited by
- 240
- References
- 66
- Citations by year
- 2026: 26 · 2025: 22 · 2024: 24 · 2023: 25 · 2022: 24 · 2021: 44 · 2020: 33 · 2019: 33 · 2018: 8 · 2017: 1
- FWCI
- 1.92
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Essays in Biochemistry (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (100476, 100476/Z/12/Z)
- European Commission
- FP7 Ideas: European Research Council (311460)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- PROTACs, molecular glues, bivalent ligands, protein degradation, ternary complex, structure-based drug design, protein-protein interaction, intramolecular contacts, undruggable targets
- MeSH terms
- Lenalidomide, Binding Sites, Humans, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Proteins, Structure-Activity Relationship, Thalidomide, Drug Design, Protein Engineering, Crystallography, X-Ray, Small Molecule Libraries, Drug Discovery, Proteolysis
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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.
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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