Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2
Coronaviruses
SARS-CoV-2
Medicinal & Biomolecular Chemistry
610
COVID-19
Coronavirus Papain-Like Proteases
Computation Theory and Mathematics
Antiviral Agents
3. Good health
Molecular Docking Simulation
Medicinal and Biomolecular Chemistry
Infectious Diseases
Emerging Infectious Diseases
Theoretical and Computational Chemistry
Theoretical and computational chemistry
Chemical Sciences
Papain
Medicinal and biomolecular chemistry
Humans
Protease Inhibitors
Infection
Coronavirus 3C Proteases
Naphthoquinones
DOI:
10.1021/acs.jcim.2c00693
Publication Date:
2022-08-12T17:03:06Z
AUTHORS (21)
ABSTRACT
AbstractThe worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 µM and 66 µM. In addition, eight compounds inhibited PLpro with IC50 ranging from 1.7 µM to 46 µM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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