A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease.

Jorge E Hernández González,Dieter Willbold,Mônika A Coronado,Raphael J Eberle

doi:10.3389/fmolb.2021.816166

Abstract

The SARS-CoV-2 main protease, also known as 3-chymotrypsin-like protease (3CLpro), is a cysteine protease responsible for the cleavage of viral polyproteins pp1a and pp1ab, at least, at eleven conserved sites, which leads to the formation of mature nonstructural proteins essential for the replication of the virus. Due to its essential role, numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat Covid-19 and have reported a vast number of inhibitors and their co-crystal structures. Despite all the ongoing efforts, D-peptides, which possess key advantages over L-peptides as therapeutic agents, have not been explored as potential drug candidates against 3CLpro. The current work fills this gap by reporting an in silico approach for the discovery of D-peptides capable of inhibiting 3CLpro that involves structure-based virtual screening (SBVS) of an in-house library of D-tripeptides and D-tetrapeptides into the protease active site and subsequent rescoring steps, including Molecular Mechanics Generalized-Born Surface Area (MM-GBSA) free energy calculations and molecular dynamics (MD) simulations. In vitro enzymatic assays conducted for the four top-scoring D-tetrapeptides at 20 μM showed that all of them caused 55–85% inhibition of 3CLpro activity, thus highlighting the suitability of the devised approach. Overall, our results present a promising computational strategy to identify D-peptides capable of inhibiting 3CLpro, with broader application in problems involving protein inhibition.

Highlights

Covid-19 is a pandemic disease caused by the novel acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
The subsequent rescoring steps aimed to correct this bias and enrich selected D-peptides’ lists with accurate hits. It can be observed from the sequence logos, shown in Figure 2, that even though TRP was still prevalent at different positions of the D-peptides, other residues became progressively more abundant throughout the workflow steps, which was apparent for D-tetrapeptides, in which HIS and PRO were found to be predominant in positions 1 to 3 after completing the workflow (Figure 2)
This work reports the in silico identification and in vitro validation of promising D-peptide inhibitors of SARS-CoV-2 3chymotrypsin-like protease (3CLpro)

Summary

Introduction

Covid-19 is a pandemic disease caused by the novel acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2, together with SARS-CoV and Middle East Respiratory Syndrome (MERS) coronaviruses responsible for two significant outbreaks during the current century, are enveloped and single-stranded RNA viruses (Payne, 2017; Wu F. et al, 2020; Wang et al, 2020) During their replication, coronaviruses encode several accessory proteins and two replicase polyproteins (pp1a and pp1ab) (Marra et al, 2003; Rota et al, 2003; Ziebuhr, 2005; Wu F. et al, 2020; Yan and Wu, 2021), which are proteolytically processed by two cysteine proteases, i.e., the papain-. Numerous potent orthosteric inhibitors of 3CLpro, most of them of peptide-based or peptidomimetic nature, have been reported so far (Amin et al, 2021; Chia et al, 2021; Sabbah et al, 2021; Yan and Gao, 2021) These compounds have shown significant inhibitory activity, against the protease and against the viral replication in cell cultures. All these results underscore the importance of 3CLpro as an attractive drug target to combat Covid-19

Methods

Results

Conclusion