J Biomol Struct Dyn . Structure-based Virtual Screening and Molecular Dynamics Simulation of SARS-CoV-2 Guanine-N7 Methyltransferase (nsp14) for Identifying Antiviral Inhibitors Against COVID-19

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J Biomol Struct Dyn


. 2020 Jun 22;1-12.
doi: 10.1080/07391102.2020.1778535. Online ahead of print.
Structure-based Virtual Screening and Molecular Dynamics Simulation of SARS-CoV-2 Guanine-N7 Methyltransferase (nsp14) for Identifying Antiviral Inhibitors Against COVID-19


Chandrabose Selvaraj ¹ , Dhurvas Chandrasekaran Dinesh ² , Umesh Panwar ¹ , Rajaram Abhirami ¹ , Evzen Boura ² , Sanjeev Kumar Singh ¹



Affiliations

• PMID: 32567979
• DOI: 10.1080/07391102.2020.1778535

Abstract

The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) calls the whole world into a medical emergency. For tackling Coronavirus Disease 2019 (COVID-19), researchers from around the world are swiftly working on designing and identifying inhibitors against all possible viral key protein targets. One of the attractive drug targets is guanine-N7 methyltransferase which plays the main role in capping the 5'-ends of viral genomic RNA and sub genomic RNAs, to escape the host's innate immunity. We performed homology modeling and molecular dynamic (MD) simulation, in order to understand the molecular architecture of Guanosine-P3-Adenosine-5',5'-Triphosphate (G3A) binding with C-terminal N7-MTase domain of nsp14 from SARS-CoV-2. The residue Asn388 is highly conserved in present both in N7-MTase from SARS-CoV and SARS-CoV-2 and displays a unique function in G3A binding. For an in-depth understanding of these substrate specificities, we tried to screen and identify inhibitors from the Traditional Chinese Medicine (TCM) database. The combination of several computational approaches, including screening, MM/GBSA, MD simulations, and PCA calculations, provides the screened compounds that readily interact with the G3A binding site of homology modeled N7-MTase domain. Compounds from this screening will have strong potency towards inhibiting the substrate-binding and efficiently hinder the viral 5'-end RNA capping mechanism. We strongly believe the final compounds can become COVID-19 therapeutics, with huge international support.Communicated by Ramaswamy H. Sarma.

Keywords: COVID-19; Methyltransferase; N7-MTase; RNA capping; SARS-CoV-2; TCM; ensemble sampling; molecular dynamics; natural products; nsp14.