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Open AccessArticle

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

1
Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain
2
Escoles Universitàries Gimbernat i Tomàs Cerdà, 08174 Sant Cugat del Vallès, Barcelona, Catalonia, Spain
3
EURECAT, TECNIO, CEICS, Avinguda Universitat 1, 43204 Reus Catalonia, Spain
*
Authors to whom correspondence should be addressed.
Both authors contributed equally to this study.
Int. J. Mol. Sci. 2020, 21(11), 3793; https://doi.org/10.3390/ijms21113793
Received: 14 April 2020 / Revised: 16 May 2020 / Accepted: 22 May 2020 / Published: 27 May 2020
(This article belongs to the Special Issue New Avenues in Molecular Docking for Drug Design 2020)
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. View Full-Text
Keywords: SARS coronavirus; COVID-19; SARS-CoV-2; 3CL-pro; M-pro; chymotrypsin-like protease; 2019-nCov SARS coronavirus; COVID-19; SARS-CoV-2; 3CL-pro; M-pro; chymotrypsin-like protease; 2019-nCov
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Gimeno, A.; Mestres-Truyol, J.; Ojeda-Montes, M.J.; Macip, G.; Saldivar-Espinoza, B.; Cereto-Massagué, A.; Pujadas, G.; Garcia-Vallvé, S. Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition. Int. J. Mol. Sci. 2020, 21, 3793.

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