Cited by 240Protein Degradation and InhibitorsComputational Drug Discovery MethodsChemical Synthesis and Analysis

Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders

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Hughes, Scott J., Ciulli, Alessio·2017·Essays in Biochemistry

Abstract

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.”
  • 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.”
  • 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
Published
2017-11-08
Volume
61
Issue
5
Pages
505-516
ISSN
  • 0071-1365 (ISSN-L)
  • 1744-1358
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
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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