Combining SARS-CoV-2 Proofreading Exonuclease and RNA-Dependent RNA Polymerase Inhibitors as a Strategy to Combat COVID-19: A High-Throughput in silico Screening

Shradha Khater; Pawan Kumar; Nandini Dasgupta; Gautam Das; Shashikant Ray; Amresh Prakash

doi:10.3389/fmicb.2021.647693

Combining SARS-CoV-2 Proofreading Exonuclease and RNA-Dependent RNA Polymerase Inhibitors as a Strategy to Combat COVID-19: A High-Throughput in silico Screening

Front Microbiol. 2021 Jul 20:12:647693. doi: 10.3389/fmicb.2021.647693. eCollection 2021.

Authors

Shradha Khater^{1

2}, Pawan Kumar³, Nandini Dasgupta², Gautam Das², Shashikant Ray⁴, Amresh Prakash⁵

Affiliations

¹ Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
² miBiome Therapeutics LLP, Mumbai, India.
³ National Institute of Immunology, New Delhi, India.
⁴ Department of Biotechnology, Mahatma Gandhi Central University, Motihari, India.
⁵ Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people worldwide. Currently, many clinical trials in search of effective COVID-19 drugs are underway. Viral RNA-dependent RNA polymerase (RdRp) remains the target of choice for prophylactic or curative treatment of COVID-19. Nucleoside analogs are the most promising RdRp inhibitors and have shown effectiveness in vitro, as well as in clinical settings. One limitation of such RdRp inhibitors is the removal of incorporated nucleoside analogs by SARS-CoV-2 exonuclease (ExoN). Thus, ExoN proofreading activity accomplishes resistance to many of the RdRp inhibitors. We hypothesize that in the absence of highly efficient antivirals to treat COVID-19, combinatorial drug therapy with RdRp and ExoN inhibitors will be a promising strategy to combat the disease. To repurpose drugs for COVID-19 treatment, 10,397 conformers of 2,240 approved drugs were screened against the ExoN domain of nsp14 using AutoDock VINA. The molecular docking approach and detailed study of interactions helped us to identify dexamethasone metasulfobenzoate, conivaptan, hesperidin, and glycyrrhizic acid as potential inhibitors of ExoN activity. The results were further confirmed using molecular dynamics (MD) simulations and molecular mechanics combined with generalized Born model and solvent accessibility method (MM-GBSA) calculations. Furthermore, the binding free energy of conivaptan and hesperidin, estimated using MM-GBSA, was -85.86 ± 0.68 and 119.07 ± 0.69 kcal/mol, respectively. Based on docking, MD simulations and known antiviral activities, and conivaptan and hesperidin were identified as potential SARS-CoV-2 ExoN inhibitors. We recommend further investigation of this combinational therapy using RdRp inhibitors with a repurposed ExoN inhibitor as a potential COVID-19 treatment.

Keywords: SARS-CoV-2; combinatorial therapy; drug repurposing; exonuclease inhibitor; molecular docking and MD simulation; nucleoside analog.