Therapeutic Targeting the Allosteric Cysteinome of RAS and Kinase Families
Open accessAbstract
Allosteric mechanisms are pervasive in nature, but human-designed allosteric perturbagens are rare. The history of KRAS G12C inhibitor development suggests that covalent chemistry may be a key to expanding the armamentarium of allosteric inhibitors. In that effort, irreversible targeting of a cysteine converted a non-deal allosteric binding pocket and low affinity ligands into a tractable drugging strategy. Here we examine the feasibility of expanding this approach to other allosteric pockets of RAS and kinase family members, given that both protein families are regulators of vital cellular processes that are often dysregulated in cancer and other human diseases. Moreover, these heavily studied families are the subject of numerous drug development campaigns that have resulted, sometimes serendipitously, in the discovery of allosteric inhibitors. We consequently conducted a comprehensive search for cysteines, a commonly targeted amino acid for covalent drugs, using AlphaFold-generated structures of those families. This new analysis presents potential opportunities for allosteric targeting of validated and understudied drug targets, with an emphasis on cancer therapy.
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Allosteric drugs have higher specificity and lower toxicity due to targeting nonconserved allosteric sites.
“Due to its higher specificity and consequently lower toxicity, which results from targeting nonconserved allosteric sites, allostery also increasingly features in allosteric drugs.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [125]
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A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1
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Self-citationThe small molecule BI-2852 induces a nonfunctional dimer of KRAS
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Structure-based discovery of cellular-active allosteric inhibitors of FAK
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KRAS Switch Mutants D33E and A59G Crystallize in the State 1 Conformation
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Interaction of a Novel GDP Exchange Inhibitor with the Ras Protein
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Molecular basis of Tousled-Like Kinase 2 activation
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A resource for exploring the understudied human kinome for research and therapeutic opportunitiesPreprint
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Structural basis of the atypical activation mechanism of KRASV14I
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Self-citationDisplacement Assay for the Detection of Stabilizers of Inactive Kinase Conformations
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New Insights in Protein Kinase Conformational Dynamics
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Protein Allostery in Drug Discovery
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Design, synthesis and biological evaluation of novel glucokinase activators
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GTP hydrolysis is modulated by Arg34 in the RASopathy‐associated KRASP34R
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Self-citationStructural dataset for the fast-exchanging KRAS G13D
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Self-citationFirst-in-Human Study of JNJ-74699157 in Participants With Tumors Harboring the KRAS G12C Mutation
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A Study of LY3499446 in Participants With Advanced Solid Tumors With KRAS G12C Mutation
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Flagged first, then by citations
4 of the 145 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
AlphaFold, Artificial Intelligence (AI), and Allostery
Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works
Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design
Berezovsky, I. N., & Nussinov, R. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167751 · Cited by 36 · see citing works
Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins
Parise, A., Cresca, S., & Magistrato, A. (2024) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2024.2387856 · Cited by 27 · see citing works
Computer-Aided Drug Design Boosts RAS Inhibitor Discovery
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Covalent binding of withanolides to cysteines of protein targets
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An in-depth review of AI-powered advancements in cancer drug discovery
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AlphaFold for a medicinal chemist: tool or toy?
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Redox, cysteines, and kinases—A triad sustaining myeloid leukemia
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Self-citationHarnessing AI to decode protein kinases: Structural, functional, and therapeutic design perspectives
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Bunney, T. D., Nyvall, H. G., Macrae, C., Lalović, D., Gregory, A., Huray, K. I. P. L., Harvey, N., Pinotsis, N., Kalli, A. C., Waudby, C. A., et al. (2025) · Biochemical Journal · doi:10.1042/bcj20253358
- Authors
- Li, L., Meyer, C., Zhou, Z.-W., Elmezayen, A., & Westover, K.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- Corresponding author
- Westover, Kenneth
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2022-09
- Volume
- 434
- Issue
- 17
- Pages
- 167626
- ISSN
- 0022-2836 (ISSN-L)
- PMC
- PMC9590303
- OpenAlex
- W4280544989
- Cited by
- 14
- References
- 145
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 6 · 2022: 3
- FWCI
- 0.34
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (am, 351 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Journal of Molecular Biology (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Astellas Pharma US
- Cancer Prevention and Research Institute of Texas (RP220145)
- National Institutes of Health
- Revolution Medicines
- American Cancer Society (RSG-18-039-01)
- Welch Foundation (I1829)
- National Cancer Institute (R01 CA244341, P30CA142543)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Keywords
- allosteric inhibitors, Ras, kinases, covalent inhibitors, irreversible inhibition, AlphaFold structures, cancer therapy, drug target identification
- MeSH terms
- Antineoplastic Agents, Cysteine, Humans, Neoplasms, Protein Kinases, ras Proteins, Protein Kinase Inhibitors, Molecular Targeted Therapy
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