Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM.

Md Fulbabu Sk,Nisha Amarnath Jonniya,Parimal Kar,Rajarshi Roy,Sayan Poddar

doi:10.3389/fmolb.2020.590165

Abstract

Recently, a highly contagious novel coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has emerged, posing a global threat to public health. Identifying a potential target and developing vaccines or antiviral drugs is an urgent demand in the absence of approved therapeutic agents. The 5′-capping mechanism of eukaryotic mRNA and some viruses such as coronaviruses (CoVs) are essential for maintaining the RNA stability and protein translation in the virus. SARS-CoV-2 encodes S-adenosyl-L-methionine (SAM) dependent methyltransferase (MTase) enzyme characterized by nsp16 (2′-O-MTase) for generating the capped structure. The present study highlights the binding mechanism of nsp16 and nsp10 to identify the role of nsp10 in MTase activity. Furthermore, we investigated the conformational dynamics and energetics behind the binding of SAM to nsp16 and nsp16/nsp10 heterodimer by employing molecular dynamics simulations in conjunction with the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) method. We observed from our simulations that the presence of nsp10 increases the favorable van der Waals and electrostatic interactions between SAM and nsp16. Thus, nsp10 acts as a stimulator for the strong binding of SAM to nsp16. The hydrophobic interactions were predominately identified for the nsp16-nsp10 interactions. Also, the stable hydrogen bonds between Ala83 (nsp16) and Tyr96 (nsp10), and between Gln87 (nsp16) and Leu45 (nsp10) play a vital role in the dimerization of nsp16 and nsp10. Besides, Computational Alanine Scanning (CAS) mutagenesis was performed, which revealed hotspot mutants, namely I40A, V104A, and R86A for the dimer association. Hence, the dimer interface of nsp16/nsp10 could also be a potential target in retarding the 2′-O-MTase activity in SARS-CoV-2. Overall, our study provides a comprehensive understanding of the dynamic and thermodynamic process of binding nsp16 and nsp10 that will contribute to the novel design of peptide inhibitors based on nsp16.

Highlights

Coronaviruses (CoVs) are considered as an etiological agent for causing severe acute respiratory syndrome (SARS) in humans
Our molecular dynamics (MD)/MMPBSA calculations suggested that SAM binds strongly to the nsp16/nsp10 heterodimer and fails to bind to the nsp16 monomer
Our study revealed that the binding of nsp10 stabilizes the complex structure

Summary

INTRODUCTION

Coronaviruses (CoVs) are considered as an etiological agent for causing severe acute respiratory syndrome (SARS) in humans. It is further methylated at the 2′-O position of mRNA by 2′-O- methyltransferase (2′-O-MTase) and generates the cap-1 (m7GpppNm) and cap-2 (m7GpppNmNm) structures This mimicking of the eukaryotic mRNA capping mechanism helps the virus evade the host innate immune system (Furuichi and Shatkin, 2000; Wang et al, 2015). Both the MTase uses S-adenosyl-L-methionine (SAM or AdoMet) as a donor. The conformational changes in nsp and nsp due to their association were investigated

MATERIALS AND METHODS

CONCLUSIONS

Findings

DATA AVAILABILITY STATEMENT