Structural and molecular investigation of the impact of S30L and D88N substitutions in G9R protein on coupling with E4R from Monkeypox virus (MPXV)

Abstract

Understanding the pathogenesis mechanism of the Monkeypox virus (MPXV) is essential to guide therapeutic development against the Monkeypox virus. In the current study, we investigated the impact of the only two reported substitutions, S30L, D88N, and S30L-D88N on the G9R of the replication complex in 2022 with E4R using structural modeling, simulation, and free energy calculation methods. From the molecular docking and dissociation constant (K_D) results, it was observed that the binding affinity did not increase in the mutants, but the interaction paradigm was altered by these substitutions. Molecular simulation data revealed that these mutations are responsible for destabilization, changes in protein packing, and internal residue fluctuations, which can cause functional variance. Additionally, hydrogen bonding analysis revealed that the estimated number of hydrogen bonds are almost equal among the wild-type G9R and each mutant. The total binding free energy for the wild-type G9R with E4R was −85.00 kcal/mol while for the mutants the TBE was −42.75 kcal/mol, −43.68 kcal/mol, and −48.65 kcal/mol respectively. This shows that there is no direct impact of these two reported mutations on the binding with E4R, or it may affect the whole replication complex or any other mechanism involved in pathogenesis. To explore these variations further, we conducted PCA and FEL analyses. Based on our findings, we speculate that within the context of interaction with E4R, the mutations in the G9R protein might be benign, potentially leading to functional diversity associated with other proteins.

Communicated by Ramaswamy H. Sarma

Keywords:

• Monkeypox virus
• replication complex
• resistance
• protein–protein interaction
• molecular simulation

Acknowledgments

The computations were partially performed at the Center for High-Performance Computing of Shanghai Jiao Tong University and Pengcheng Lab.

Disclosure statement

No potential conflict of interest was reported by the authors.

Authors contribution

Conceptualization, Yifan Jin, Syed Asad Gillani, Farah Batool, Fahad M Alshabrmi, Eid Alatawi, Yasir Waheed*, Anwar Mohammad, Abbas Khan and Dongqing Wei; Data curation, Farah Batool, Eid Alatawi and Anwar Mohammad; Formal analysis, Yifan Jin, Syed Asad Gillani, Fahad M Alshabrmi, Eid Alatawi and Abbas Khan; Funding acquisition, Dongqing Wei; Investigation, Eid Alatawi, Yasir Waheed* and Anwar Mohammad; Methodology, Yifan Jin, Farah Batool, Yasir Waheed* and Anwar Mohammad; Project administration, Dongqing Wei; Resources, Fahad M Alshabrmi, Eid Alatawi and Anwar Mohammad; Software, Yifan Jin; Validation, Syed Asad Gillani, Farah Batool, Fahad M Alshabrmi and Yasir Waheed*; Visualization, Yasir Waheed* and Abbas Khan; Writing—original draft, Abbas Khan and Dongqing Wei; Writing—review & editing, Abbas Khan and Dongqing Wei.

Additional information

Funding

This work was supported by the National Key R&D Program of China (Grant No. 2021YFA0911500) and the Shanghai Pujiang Program (Grant No. 21PJ1405100). Dong-Qing Wei was supported by the National Science Foundation of China (Grant No. 32070662, 61832019, 32030063), the Science and Technology Commission of Shanghai Municipality (No. 19430750600), as well as SJTU JiRLMDS Joint Research Fund and Joint Research Funds for Medical and Engineering and Scientific Research at Shanghai Jiao Tong University (YG2021ZD02). Yifan Jin was supported by the China Postdoctoral Science Foundation (2022M722100).