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Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling.

ABSTRACT: We have applied a computational strategy, using a combination of virtual screening, docking and molecular dynamics techniques, aimed at identifying possible lead compounds for the non-covalent inhibition of the main protease 3CLpro of the SARS-CoV2 Coronavirus. Based on the X-ray structure (PDB code: 6LU7), ligands were generated using a multimodal structure-based design and then docked to the monomer in the active state. Docking calculations show that ligand-binding is strikingly similar in SARS-CoV and SARS-CoV2 main proteases. The most potent docked ligands are found to share a common binding pattern with aromatic moieties connected by rotatable bonds in a pseudo-linear arrangement.

SUBMITTER: Macchiagodena M

PROVIDER: S-EPMC7165110 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling.

Macchiagodena Marina M Pagliai Marco M Procacci Piero P

Chemical physics letters 20200418

We have applied a computational strategy, using a combination of virtual screening, docking and molecular dynamics techniques, aimed at identifying possible lead compounds for the non-covalent inhibition of the main protease 3CLpro of the SARS-CoV2 Coronavirus. Based on the X-ray structure (PDB code: 6LU7), ligands were generated using a multimodal structure-based design and then docked to the monomer in the active state. Docking calculations show that ligand-binding is strikingly sim ...[more]

PMID: 32313296

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