Binding modes of the KRAS(G12C) inhibitors GDC-6036 and LY3537982 revealed by all atom molecular dynamics simulations

27 March 2025, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Over 100 co-crystal structures of KRAS switch-II pocket (SII-P) targeting inhibitors are currently available in the RCSB Protein Data Bank. These publicly available structures are invaluable tools that have led to a more in-depth understanding of KRAS SII-P pocket, which is crucial for targeted drug design efforts. The binding modes (co-crystal structures) of two KRAS(G12C) inhibitors that have advanced to the clinical trials, GDC-6036 (divarasib) and LY3537982 (olomorasib), are currently unavailable. Here, we reveal the putative binding modes of these two G12C inhibitors by utilizing the available structural data of analogous compounds and molecular dynamics (MD) simulations (total simulation time of 200 us). Our biochemical assays reveal remarkably high affinity for both inhibitors towards KRAS(G12C), which is, however, compromised by a co-mutation at Tyr96 (GDC-6036, LY3537982) or His95 (GDC-6036). While both inhibitors display low activity towards KRAS(WT), LY3537982 maintains high activity against other RAS isoforms with G12C mutation. As the simulation predictions align with the experimental results, our findings indicate that microsecond timescale simulations can be a valuable tool for predicting binding modes.

Keywords

KRAS
KRAS(G12C) inhibitors
molecular dynamics simulations
drug design
WaterMap
nucleotide exchange
chemical stability
thermal stability

Supplementary materials

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Supporting Information
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Supplementary Figures S1–S10; Supplementary Table S1.
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Representative binding mode of GDC-6036
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PyMOL session of the representative binding mode of GDC-6036 derived from the simulations
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Representative binding mode of LY3537982
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PyMOL session of the representative binding mode of LY3537982 derived from the simulations
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Representative binding mode of GDC-6036 (pdb)
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PDB-file of the representative binding mode of GDC-6036 with water molecules removed
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Representative binding mode of LY3537982 (pdb)
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PDB-file of the representative binding mode of LY3537982 with water molecules removed
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SMILES
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SMILES with assay IC50 values
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Simulation starting configuration of LY3537982 (pdb)
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PDB-file of the MD simulation starting configuration of LY3537982 with all waters and ions
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Simulation starting configuration of GDC-6036 (pdb)
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PDB-file of the MD simulation starting configuration of GDC-6036 with all waters and ions.
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