Structural insights into non-hotspot KRAS mutations and their potential as targets for effective cancer therapies

Abstract

Kirsten rat sarcoma virus protein (KRAS) is a protein that plays a central role in signal transduction using extracellular signal regulated kinase (ERK) and mitogen activated protein kinase (MAPK) cellular signaling pathway. KRAS is a frequently mutated oncogene and plays a pivotal role in tumor initiation and progression. Hotspot mutations on codon 12, 13 and 61 in KRAS are well-known for their role in drug resistance and non-hotspot mutations also play a significant part in contributing to resistance mechanisms. The understanding of how these non-hotspot mutations might affect the signal transduction of KRAS and their contribution towards drug resistance is understudied. Here we provide structural insights into the interaction of non-hotspot KRAS mutants with GTP (the native ligand) using a molecular docking and molecular dynamics simulation approach. Extensive molecular docking and simulation studies suggest that non-hotspot mutations (E31D and E63K) show stable interaction with native ligand using all five trajectories, as evidenced by root mean square of distance (RMSD), root mean square of fluctuation (RMSF), radius of gyration (RoG), coulomb short-range energy and MMGBSA analysis. These results suggest that non-hotspot mutations do not undermine the oncogenic nature of KRAS. This observation is consistent with previous findings where overexpressing E31D and E63K mutations share phenotypic features with G12D and G13D transfected cells, including increased proliferative capacity, actin cytoskeleton organization, and migration rates. We further test whether FDA-approved KRAS inhibitors sotorasib and adagrasib successfully inhibit the E31D and E63K mutants. Results suggest that these two non-hotspot mutants can be inhibited by both drugs with following trend of structural stability (E31D > E63K > wild-KRAS > Q61H > G12C). Based on sharp coherence in trajectories between wild KRAS and non-hotspot mutants, it is suggested that these novel mutants do not contribute to drug resistance mechanism. Overall, we provide a comprehensive understanding of the impact of non-hotspot mutations on KRAS and their potential as targets for effective cancer therapies.

Communicated by Ramaswamy H. Sarma

Keywords:

• KRAS and G12C
• KRAS mutant
• drug resistance
• sotorasib
• adagrasib
• non-hotspot mutation

Authors’ contributions

C.D. and G.W. conceived the idea and contributed to the main analysis. W.Z. wrote the primary draft. Y.M. Software and perform critical revision. J.M. supervises the project and provides the resources for this study. All the authors read and approve the final draft for submission and publication.

Consent for publication

All the authors of this manuscript gave the consent for the publication of this paper by corresponding author.

Disclosure statement

The authors declare no competing interests.

Data availability statement

The authors acknowledge that the data presented in this study must be deposited and made publicly available in an acceptable repository before publication. The authenticity of this article has been validated by uploading the key raw data onto the Research Data Deposit platform (www.researchdata.org.cn), with the approval RDD number as RDDB2024514524.

Additional information

Funding

This study was supported by grants from the National Natural Science Foundation of China (81930072), Cancer Innovative Research Program of Sun Yat-sen University Cancer Center (CIRP-SYSUCC-0005).