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,Amresh Prakash,Gautam Das,Nandini Dasgupta,Pawan Kumar,Shashikant Ray

doi:10.3389/fmicb.2021.647693

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.

Highlights

On December 31, 2019, the World Health Organization (WHO) office in China was informed that cases of pneumonia of an unknown cause were detected in Wuhan City, in the Hubei Province of China
We propose that combinatorial therapy with one drug from favipiravir/remdesivir/ribavirin/galidesivir and an inhibitor of ExoN would be effective in increasing the efficacy of the RNA-dependent RNA polymerase (RdRp) inhibitors (Figure 1)
Binding energy estimation using molecular mechanics combined with generalized Born model and solvent accessibility method (MM-GBSA) studies estimated binding free energies of conivaptan and hesperidin as −85.86 ± 0.68 and 119.07 ± 0.69 kcal/mol, respectively

Summary

Introduction

On December 31, 2019, the World Health Organization (WHO) office in China was informed that cases of pneumonia of an unknown cause were detected in Wuhan City, in the Hubei Province of China. Remdesivir and favipiravir have shown promise in different countries These drugs being nucleoside analogs act either by introducing mutations in the viral RNA or by chain termination during replication. The action of these drugs on viruses that do not have proofreading enzymes is good (Warren et al, 2016). ExoN is capable of excising incorporated nucleoside analogs by virtue of its 3 –5 exonuclease proofreading activity This results in negating the action of these drugs, to varying extents, and depending on the type of nucleoside analog chemistry [ribavirin, 5-fluorouracil (5FU), and remdesivir] (Figure 1; Smith et al, 2013; Ferron et al, 2018). The delicate balance between incorporation and excision properties of nucleoside analogs by RdRp and ExoN respectively, decides the fate of the action of RdRp-based antivirals

Methods

Results

Conclusion