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