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Chemical acylation of an acquired serine suppresses oncogenic signaling of K-Ras(G12S). Nat Chem Biol 2022; 18:1177-1183. [PMID: 35864332 DOI: 10.1038/s41589-022-01065-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022]
Abstract
Drugs that directly impede the function of driver oncogenes offer exceptional efficacy and a therapeutic window. The recently approved mutant selective small-molecule cysteine-reactive covalent inhibitor of the G12C mutant of K-Ras, sotorasib, provides a case in point. KRAS is the most frequently mutated proto-oncogene in human cancer, yet despite success targeting the G12C allele, targeted therapy for other hotspot mutants of KRAS has not been described. Here we report the discovery of small molecules that covalently target a G12S somatic mutation in K-Ras and suppress its oncogenic signaling. We show that these molecules are active in cells expressing K-Ras(G12S) but spare the wild-type protein. Our results provide a path to targeting a second somatic mutation in the oncogene KRAS by overcoming the weak nucleophilicity of an acquired serine residue. The chemistry we describe may serve as a basis for the selective targeting of other unactivated serines.
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Zhang Z, Gao R, Hu Q, Peacock H, Peacock DM, Dai S, Shokat KM, Suga H. GTP-State-Selective Cyclic Peptide Ligands of K-Ras(G12D) Block Its Interaction with Raf. ACS CENTRAL SCIENCE 2020; 6:1753-1761. [PMID: 33145412 PMCID: PMC7596874 DOI: 10.1021/acscentsci.0c00514] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Indexed: 05/08/2023]
Abstract
We report the identification of three cyclic peptide ligands of K-Ras(G12D) using an integrated in vitro translation-mRNA display selection platform. These cyclic peptides show preferential binding to the GTP-bound state of K-Ras(G12D) over the GDP-bound state and block Ras-Raf interaction. A co-crystal structure of peptide KD2 with K-Ras(G12D)·GppNHp reveals that this peptide binds in the Switch II groove region with concomitant opening of the Switch II loop and a 40° rotation of the α2 helix, and that a threonine residue (Thr10) on KD2 has direct access to the mutant aspartate (Asp12) on K-Ras. Replacing this threonine with non-natural amino acids afforded peptides with improved potency at inhibiting the interaction between Raf1-RBD and K-Ras(G12D) but not wildtype K-Ras. The union of G12D over wildtype selectivity and GTP state/GDP state selectivity is particularly desirable, considering that oncogenic K-Ras(G12D) exists predominantly in the GTP state in cancer cells, and wildtype K-Ras signaling is important for the maintenance of healthy cells.
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Affiliation(s)
- Ziyang Zhang
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Rong Gao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Qi Hu
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Hayden Peacock
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - D. Matthew Peacock
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Shizhong Dai
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Zhang Z, Shokat KM. Bifunctional Small-Molecule Ligands of K-Ras Induce Its Association with Immunophilin Proteins. Angew Chem Int Ed Engl 2019; 58:16314-16319. [PMID: 31557383 PMCID: PMC6980260 DOI: 10.1002/anie.201910124] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Indexed: 12/20/2022]
Abstract
Here we report the design, synthesis, and characterization of bifunctional chemical ligands that induce the association of Ras with ubiquitously expressed immunophilin proteins such as FKBP12 and cyclophilin A. We show this approach is applicable to two distinct Ras ligand scaffolds, and that both the identity of the immunophilin ligand and the linker chemistry affect compound efficacy in biochemical and cellular contexts. These ligands bind to Ras in an immunophilin-dependent fashion and mediate the formation of tripartite complexes of Ras, immunophilin, and the ligand. The recruitment of cyclophilin A to GTP-bound Ras blocks its interaction with B-Raf in biochemical assays. Our study demonstrates the feasibility of ligand-induced association of Ras with intracellular proteins and suggests it as a promising therapeutic strategy for Ras-driven cancers.
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Affiliation(s)
- Ziyang Zhang
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94143, USA
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94143, USA
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Zhang Z, Shokat KM. Bifunctional Small‐Molecule Ligands of K‐Ras Induce Its Association with Immunophilin Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ziyang Zhang
- Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California, San Francisco 600 16th Street San Francisco CA 94143 USA
| | - Kevan M. Shokat
- Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California, San Francisco 600 16th Street San Francisco CA 94143 USA
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Niebel B, Wosnitza CI, Famulok M. RNA-aptamers that modulate the RhoGEF activity of Tiam1. Bioorg Med Chem 2013; 21:6239-46. [PMID: 23757206 DOI: 10.1016/j.bmc.2013.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/26/2013] [Accepted: 05/14/2013] [Indexed: 11/25/2022]
Abstract
Rho GTPases regulate the actin cytoskeleton and thereby control cell migration, cell morphology, cell motility, and other cellular functions. The gene product of the oncogene Tiam1 acts as a guanine nucleotide exchange factor (GEF) for the Rho GTPase Rac. Like other RhoGEFs, Tiam1 is involved in cancer progression, but it also counteracts invasion in different cancer cell types. Hence, further investigations are required to unravel the functions of Tiam1 in the context of cancer initiation and progression, which appear to be cell specific. Although RhoGEFs in general seem to be attractive therapeutic targets, not many inhibitors have been described, yet. Here we report the identification and characterization of inhibitory RNA aptamers that specifically target Tiam1. After 16 selection rounds three aptamers sharing a 15 nucleotides consensus motif were identified. The clones K91 and K11 inhibited the Tiam1-mediated activation of the GTPase Rac2 in vitro. The tightest binder K91 neither bound the Rho GEF Vav1 nor the Arf GEF Cytohesin-2. In the presence of Rac1, the binding of K91 to Tiam1 was impaired indicating that the binding motif on Tiam1 overlaps with the GTPase binding site. K91 and K11 are the first reported inhibitory molecules targeting the GEF function of Tiam1. Due to their specificity over related GEF proteins they may represent promising tools for further elucidation of the biological functions of Tiam1. We anticipated that these aptamers will prove useful in validating the ambiguous roles of Tiam1 in cancer biology.
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Affiliation(s)
- Björn Niebel
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Str 1, 53121 Bonn, Germany
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