Identification of a dual acting SARS-CoV-2 proteases inhibitor through in silico design and step-by-step biological characterization

https://doi.org/10.1016/j.ejmech.2021.113863Get rights and content

Highlights

  • Indole based compounds were designed in-silico as SARS-CoV-2 main protease inhibitors.

  • Step-by-step optimization of the cognate compounds was performed by in-vitro assays.

  • Different compounds showed low μM potencies when challenged in SARS-CoV-2 transfected Vero cells.

  • Further investigations were performed over different SARS-CoV-2 targets.

  • A dual Mpro/PLpro inhibitor and a selective SP inhibitor were disclosed.

Abstract

COVID-19 pandemic, starting from the latest 2019, and caused by SARS-CoV-2 pathogen, led to the hardest health-socio-economic disaster in the last century. Despite the tremendous scientific efforts, mainly focused on the development of vaccines, identification of potent and efficient anti-SARS-CoV-2 therapeutics still represents an unmet need. Remdesivir, an anti-Ebola drug selected from a repurposing campaign, is the only drug approved, so far, for the treatment of the infection. Nevertheless, WHO in later 2020 has recommended against its use in COVID-19. In the present paper, we describe a step-by-step in silico design of a small library of compounds as main protease (Mpro) inhibitors. All the molecules were screened by an enzymatic assay on Mpro and, then, cellular activity was evaluated using Vero cells viral infection model. The cellular screening disclosed compounds 29 and 34 as in-vitro SARS-CoV-2 replication inhibitors at non-toxic concentrations (0.32 < EC50 < 5.98 μM). To rationalize these results, additional in-vitro assays were performed, focusing on papain like protease (PLpro) and spike protein (SP) as potential targets for the synthesized molecules. This pharmacological workflow allowed the identification of compound 29, as a dual acting SARS-CoV-2 proteases inhibitor featuring micromolar inhibitory potency versus Mpro (IC50 = 1.72 μM) and submicromolar potency versus PLpro (IC50 = 0.67 μM), and of compound 34 as a selective SP inhibitor (IC50 = 3.26 μM).

Keywords

In-silico design
SARS-CoV-2 proteases dual inhibitor
Enzymatic assays
Biophysical assays
Cellular characterization

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1

These authors contributed equally to this work.

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