7JKV image
Deposition Date 2020-07-29
Release Date 2020-09-23
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7JKV
Title:
Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.25 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:3C-like proteinase
Gene (Uniprot):rep
Chain IDs:A, B
Chain Length:307
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Primary Citation
A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.
Nat Commun 12 668 668 (2021)
PMID: 33510133 DOI: 10.1038/s41467-021-20900-6

Abstact

Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (Mpro). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC50 values of 15 ± 4 and 4.2 ± 0.7 μM for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with Mpro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead Mpro inhibitor for the development of therapeutics for SARS-CoV-2 infection.

Legend

Protein

Chemical

Disease

Primary Citation of related structures