Decoding KRAS dynamics: Exploring the impact of mutations and inhibitor binding

KRAS (Kirsten rat sarcoma viral oncogene homologue), the most common mutated protein in human cancers, is the leading cause of morbidity and mortality. Before Sotorasib (AMG-510) was approved for non-small cell lung cancer treatment in 2020, the oncogenic KRAS mutations were believed to be non-druggable. High-resolution X-ray crystal structures of GDP-bound KRAS mutants with and without inhibitor are resolved and deposited in the Protein Data Bank (PDB). Nevertheless, to develop inhibitors targeting oncogenic KRAS mutants, understanding the dynamics of protein conformations and respective binding sites is crucial. In the present study, multiple molecular dynamics (MD) simulations were conducted on wild-type and mutant KRAS structures to understand how G12C or G12D mutations lead to the stabilization of the active state and how KRAS inhibitors lock the mutated conformations in their inactive state. The study found that the guanosine diphosphate (GDP)-bound KRAS mutants, G12C and G12D, were locked in the inactive state, in terms of stability, when the KRAS inhibitors, AMG-510 and MRTX1133, respectively, bind to the respective Switch-II (S-II) pocket. Covalent inhibitor AMG-510 locked the inactive GDP-bound KRAS^G12C mutant more efficiently when compared to the non-covalent inhibitor MRTX1133. The Cα atom distance between key highly dynamic amino acids from P-loop, Switch-I, and Switch-II domains, lying within 4 Å of the inhibitor, were stable in the KRAS mutant with bound inhibitors (AMG-510 or MRTX1133), but were varying largely in the absence of any inhibitor throughout the microsecond simulation. According to the per-residue energy decomposition results, S-II amino acids in inhibitor-free KRAS^G12C and KRAS^G12D mutants showed larger variations in energy values as compared to AMG-510-bound KRAS^G12C and MRTX1133-bound KRAS^G12D, respectively. For example, the inhibitor-free KRAS^G12C exhibited larger variations in energy values in the S-II residues, namely, Thr58, Gln61, Glu63, and Arg68, as compared to the AMG-510-bound KRAS^G12C. The study found that the higher stability of AMG-510 in torsion angles was due to its covalent nature of binding to the KRAS^G12C mutant. The S-II amino acids, namely, Thr58, Glu63, and Arg68 remained stable in AMG-510-bound KRAS^G12C. The study showed that AMG-510 binding significantly stabilizes the amino acids surrounding it, surpassing that of MRTX1133. The insights gained in the present study is expected to be useful in the design and development of new KRAS-targeted drugs.