Directly targeting oncogenic V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-Ras) with small-molecule inhibitors has historically been considered prohibitively challenging. Recent reports of compounds that bind directly to the K-Ras G12C muta ...
Directly targeting oncogenic V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-Ras) with small-molecule inhibitors has historically been considered prohibitively challenging. Recent reports of compounds that bind directly to the K-Ras G12C mutant suggest avenues to overcome key obstacles that stand in the way of developing such compounds. We aim to target the guanine nucleotide (GN)-binding pocket because the natural contents of this pocket dictate the signaling state of K-Ras. Here, we characterize the irreversible inhibitor SML-8-73-1 (SML), which targets the GN-binding pocket of K-Ras G12C. We report a high-resolution X-ray crystal structure of G12C K-Ras bound to SML, revealing that the compound binds in a manner similar to GDP, forming a covalent linkage with Cys-12. The resulting conformation renders K-Ras in the open, inactive conformation, which is not predicted to associate productively with or activate downstream effectors. Conservation analysis of the Ras family GN-binding pocket reveals variability in the side chains surrounding the active site and adjacent regions, especially in the switch I region. This variability may enable building specificity into new iterations of Ras and other GTPase inhibitors. High-resolution in situ chemical proteomic profiling of SML confirms that SML effectively discriminates between K-Ras G12C and other cellular GTP-binding proteins. A biochemical assay provides additional evidence that SML is able to compete with millimolar concentrations of GTP and GDP for the GN-binding site.
Organizational Affiliation:
Departments of Biochemistry and Radiation Oncology and.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.,Department of Cancer Biology andBlais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115;,Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390.,Department of Cancer Biology andDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; and.,Department of Cancer Biology andDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; andDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.,Departments of Biochemistry and Radiation Oncology and kenneth.westover@utsouthwestern.edu.
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