Study on the mechanism of KRAS R68G secondary mutation-induced resistance to KRASG12D-targeted inhibitor MRTX1133

doi:10.3969/j.issn.1674-8115.2025.06.005

Abstract

Abstract:

Objective ·To explore the mechanism at the atomic level by which the KRAS^G12D/R68G mutation induces tumor cell resistance to MRTX1133. Methods ·The crystal structure data of the KRAS^G12D-MRTX1133 complex were obtained from the RCSB Protein Data Bank (PDB). PyMOL software was used to mutate arginine at position 68 of KRAS to glycine (R68G), constructing the initial conformations of the KRAS^G12D-MRTX1133 and KRAS^G12D/R68G-MRTX1133 complexes. The LEaP module was used to build simulation systems under periodic boundary conditions. The ff19SB force field was applied to standard amino acids in KRAS, GAFF (general AMBER force field) to MRTX1133, and TIP3P (intermolecular potential three point) to water molecules. Energy minimization was performed using the Amber software suite. The systems were then heated to 300 K, followed by NVT (constant volume and temperature) equilibration and NPT (constant pressure and temperature) production. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), principal component analysis (PCA) and solvent-accessible surface area (SASA) of MRTX1133 and GDP were analyzed using cpptraj. The number of hydrogen bonds between regions and the dynamic cross-correlation matrix (DCCM) of amino acid movements were also calculated. Results ·RMSD analysis showed greater structural variation in KRAS in the KRAS^G12D/R68G system compared to the KRAS^G12D system. RMSF analysis revealed significantly higher fluctuations in the Switch Ⅰ and Switch Ⅱ regions of the KRAS^G12D/R68G system. PCA indicated that Switch Ⅰ and Switch Ⅱ in the KRAS^G12D/R68G system were more frequently in an open conformation. The distances between Switch Ⅰ and the P-loop, and between Switch Ⅱ and the P-loop, were larger in the KRAS^G12D/R68G system, indicating an expanded binding pocket for GDP and MRTX1133 compared to the KRAS^G12D system. SASA analysis indicated that both GDP and MRTX1133 had increased solvent exposure in the KRAS^G12D/R68G system. DCCM analysis revealed more decoupled movements among the Switch Ⅰ, Switch Ⅱ and P-loop regions in the KRAS^G12D/R68G system. Conclusion ·The KRAS^G12D/R68G mutation disrupts the interactions between the Switch Ⅰ and Switch Ⅱ regions, leading to their separation and the opening of the MRTX1133 binding pocket. This increases the solvent exposure of MRTX1133, accelerates its dissociation, and ultimately results in KRAS^G12D/R68G resistance to MRTX1133.

Key words: MRTX1133, KRAS secondary mutation, molecular dynamics simulation, resistance mechanism

CLC Number:

WANG Gaoming, CUI Ran, LI Yanjing, LIU Yingbin. Study on the mechanism of KRAS R68G secondary mutation-induced resistance to KRAS^G12D-targeted inhibitor MRTX1133[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2025, 45(6): 705-716.

Figures/Tables 6

Fig 1 MRTX1133 and its binding pocket in KRAS, and associated resistance mutations

Fig 2 Conformational dynamics of KRASG12D and KRASG12D/R68G

Fig 3 Global conformational changes of the KRAS protein

Fig 4 Conformational landscape and representative conformations of the KRAS protein

Fig 5 SASAs of MRTX1133 and GDP

Fig 6 Dynamic relationship between Switch Ⅰ and Switch Ⅱ regions

TrendMD

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