Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition

Aleix Gimeno, Júlia Mestres-Truyol, María José Ojeda-Montes, Guillem Macip, Bryan Saldivar-Espinoza, Adrià Cereto-Massagué, Gerard Pujadas, Santiago Garcia-Vallvé

10.3390/ijms21113793

Research curated

Abstract

Since the outbreak of the COVID-19 pandemic in December 2019 and its rapid spread worldwide, the scientific community has been under pressure to react and make progress in the development of an effective treatment against the virus responsible for the disease. Here, we implement an original virtual screening (VS) protocol for repositioning approved drugs in order to predict which of them could inhibit the main protease of the virus (M-pro), a key target for antiviral drugs given its essential role in the virus’ replication. Two different libraries of approved drugs were docked against the structure of M-pro using Glide, FRED and AutoDock Vina, and only the equivalent high affinity binding modes predicted simultaneously by the three docking programs were considered to correspond to bioactive poses. In this way, we took advantage of the three sampling algorithms to generate hypothetic binding modes without relying on a single scoring function to rank the results. Seven possible SARS-CoV-2 M-pro inhibitors were predicted using this approach: Perampanel, Carprofen, Celecoxib, Alprazolam, Trovafloxacin, Sarafloxacin and ethyl biscoumacetate. Carprofen and Celecoxib have been selected by the COVID Moonshot initiative for in vitro testing; they show 3.97 and 11.90% M-pro inhibition at 50 µM, respectively.

Source: PubMed

Related molecules

Name	Synonyms	Genes
Carprofen
Alprazolam
Trovafloxacin
Sarafloxacin
Ethyl biscoumacetate	Ethyldicoumarol, Tromexan, Bis(4-hydroxy-2-oxo-2H-chromen-3-yl)-essigsäureethylester, Ethyl-2,2-bis(4-hydroxy-2-oxo-2H-chromen-3-yl)acetat
Perampanel
Celecoxib
3C-like protease	3CLpro, Mpro, SARS coronavirus main peptidase, 3CLpro-SARS-CoV-2	rep, ORF1a-1b

Related interactions

Target	Drug	Type	Result
3C-like protease	Carprofen	Computational	positive
3C-like protease	Alprazolam	Computational	positive
3C-like protease	Trovafloxacin	Computational	positive
3C-like protease	Sarafloxacin	Computational	positive
3C-like protease	Ethyl biscoumacetate	Computational	positive
3C-like protease	Carprofen	In vitro	positive
3C-like protease	Celecoxib	In vitro	positive
3C-like protease	Perampanel	Computational	positive