Drug repurposing screening validated by experimental assays identifies two clinical drugs targeting SARS-CoV-2 main protease

DENIS N. PRADA GORI; SANTIAGO RUATTA; MARTÍN FLÓ; LUCAS N. ALBERCA; CAROLINA L. BELLERA; SOONJU PARK; JINYEONG HEO; HONGGUN LEE; KYU-HO PAUL PARK; OTTO PRITSCH; DAVID SHUM; MARCELO A. COMINI; ALAN TALEVI

Frontiers in Drug Discovery

Frontiers

Año: 2023 vol. 2 p. 1082065 - 1082078

2674-0338

The COVID-19 pandemic prompted several drug repositioning initiatives withthe aim to rapidly deliver pharmacological candidates able to reduce SARSCoV-2 dissemination and mortality. A major issue shared by many of the in silicostudies addressing the discovery of compounds or drugs targeting SARS-CoV-2 molecules is that they lacked experimental validation of the results. Here wepresent a computer-aided drug-repositioning campaign against theindispensable SARS-CoV-2 main protease (MPro or 3CLPro) that involvedthe development of ligand-based ensemble models and the experimentaltesting of a small subset of the identified hits. The search method exploredrandom subspaces of molecular descriptors to obtain linear classifiers. The bestmodels were then combined by selective ensemble learning to improve theirpredictive power. Both the individual models and the ensembles were validatedby retrospective screening, and later used to screen the DrugBank, DrugRepurposing Hub and Sweetlead libraries for potential inhibitors of MPro.From the 4 in silico hits assayed, atpenin and tinostamustine inhibited MPro(IC50 1 μM and 4 μM, respectively) but not the papain-like protease of SARSCoV-2 (drugs tested at 25 μM). Preliminary kinetic characterization suggeststhat tinostamustine and atpenin inhibit MPro by an irreversible and acompetitivemechanisms, respectively. Both drugs failed to inhibit the proliferation of SARSCoV-2 in VERO cells. The virtual screening method reported here may be apowerful tool to further extent the identification of novel MPro inhibitors.Furthermore, the confirmed MPro hits may be subjected to optimization orretrospective search strategies to improve their molecular target and anti-viralpotency.