Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19

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.

The focus of this study is to screen for antiviral inhibitors blocking guanine-N7 methyltransferase (N7-MTase), one of the key drug targets involved in the first methylation step of the SARS-CoV-2 RNA capping mechanism. Compounds binding the substrate-binding site can interfere with enzyme catalysis and impede 5’-end cap formation, which is crucial to mimic host RNA and evade host cellular immune responses. Therefore, our study proposes the top hit compounds from the Traditional Chinese Medicine (TCM) database using a combination of several computational approaches.

Communicated by Ramaswamy H. Sarma.

Keywords:

• SARS-CoV-2
• nsp14
• N7-MTase
• RNA capping
• Methyltransferase
• COVID-19
• TCM
• natural products
• molecular dynamics
• ensemble sampling

Acknowledgements

Special thanks to Marisol Vierra and Dr. Satish Selvaraj Venkatesh (Prufer, India) for proofreading the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

CS and SKS thankfully acknowledge RUSA-Phase 2.0 Policy (TNmulti-Gen), Dept. of Edn, Govt. of India (Grant No: F.24-51/2014-U). DCD and EB acknowledge European Regional Development Fund; OP RDE; Project: “Chemical biology for drugging undruggable targets (ChemBioDrug)” (No. CZ.02.1.01/0.0/0.0/16_019/0000729), Czech Academy of Sciences Post-doctoral Fellowship (No. L200551951 Programu podpory perspektivních lidských zdrojů - postdoktorandů) and the Academy of Sciences of Czech Republic (RVO: 61388963). UP thank to Indian Council of Medical Research (ISRM/11/(19)/2017, dated:09.08.2018) for providing ICMR-SRF (Senior Research Fellowship).