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<p>The oncogenic KRas protein is a crucial therapeutic target for cancer, but the efficacy of inhibitors against its variants remains complex. Using steered molecular simulations we quantified the binding free energies (ΔG<sub>bind</sub>) of GDP to wild-type (WT) KRas and its key oncogenic mutants <sup>G12C, G12D, G12R, and G12V,</sup> with and without MRTX1133 a potential inhibitor of the KRas G12D variant. In this study we highlighted the cooperative effect of GDP on holo KRas and KRas-bound MRTX1133, including variants. In comparison to the WT’s baseline of KRas, the ΔG<sub>bind</sub> of GDP was found to be -49 ± 3.3&#xa0;kJ/mol. The ΔG<sub>bind</sub> increases significantly against variants G12C, G12D, G12R, and G12V, ranging from − 99.2 ± 12.3 to -154.8 ± 5.05&#xa0;kJ/mol), respectively, resulting in higher effectiveness two to three times more against halo KRas variants. Furthermore, the ΔGbind of GDP against WT, KRas complexed with MRTX1133, was found to be -100.5&#xa0;kJ/mol, whereas the ΔGbind against variants G12C, G12D, G12R, and G12V ranges from 110.6 ± 14.4 to -113.2 ± 2.7&#xa0;kJ/mol, respectively. The binding affinities confirmed that GDP is a fundamental driver of oncogenicity. This reveals a significant cooperative effect where the presence of MRTX1133 paradoxically strengthened subsequent GDP binding in all systems. These findings provide a molecular-level explanation for the aggressiveness of KRas mutants. More importantly, this study reveals a potentially counterproductive mechanism for the G12R and G12V variants, where the inhibitor may inadvertently hyper-stabilize the active oncogenic state. This study highlights the critical need for mutation-specific strategies in designing Pan-KRas inhibitors.</p>

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Exploring the GDP binding to KRas WT, G12C, G12D, G12R, and G12V and bound with MRTX1133 using steered molecular dynamics

  • 期刊论文

  • 发表日期：

    2026年2月4日

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  • Abdulaziz Alamri,
  • Showkat Ahmad Mir,
  • Shahnawaz Khan,
  • Irshad Ahmad,
  • Jamoliddin Razzokov,
  • Binata Nayak

摘要

The oncogenic KRas protein is a crucial therapeutic target for cancer, but the efficacy of inhibitors against its variants remains complex. Using steered molecular simulations we quantified the binding free energies (ΔGbind) of GDP to wild-type (WT) KRas and its key oncogenic mutants G12C, G12D, G12R, and G12V, with and without MRTX1133 a potential inhibitor of the KRas G12D variant. In this study we highlighted the cooperative effect of GDP on holo KRas and KRas-bound MRTX1133, including variants. In comparison to the WT’s baseline of KRas, the ΔGbind of GDP was found to be -49 ± 3.3 kJ/mol. The ΔGbind increases significantly against variants G12C, G12D, G12R, and G12V, ranging from − 99.2 ± 12.3 to -154.8 ± 5.05 kJ/mol), respectively, resulting in higher effectiveness two to three times more against halo KRas variants. Furthermore, the ΔGbind of GDP against WT, KRas complexed with MRTX1133, was found to be -100.5 kJ/mol, whereas the ΔGbind against variants G12C, G12D, G12R, and G12V ranges from 110.6 ± 14.4 to -113.2 ± 2.7 kJ/mol, respectively. The binding affinities confirmed that GDP is a fundamental driver of oncogenicity. This reveals a significant cooperative effect where the presence of MRTX1133 paradoxically strengthened subsequent GDP binding in all systems. These findings provide a molecular-level explanation for the aggressiveness of KRas mutants. More importantly, this study reveals a potentially counterproductive mechanism for the G12R and G12V variants, where the inhibitor may inadvertently hyper-stabilize the active oncogenic state. This study highlights the critical need for mutation-specific strategies in designing Pan-KRas inhibitors.