SARS-CoV-2 papain-like protease PLpro in complex with natural compounds reveal allosteric sites for antiviral drug design
Abstract
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to aid coronaviruses in evading the host’s innate immune responses. We established a high-throughput X-ray screening to identify inhibitors by elucidating the native PLpro structure refined to 1.42 Å and performing co-crystallization utilizing a diverse library of selected natural compounds. We identified three phenolic compounds as potential inhibitors. Crystal structures of PLpro inhibitor complexes, obtained to resolutions between 1.7-1.9 Å, show that all three compounds bind at the ISG15/Ub-S2 allosteric binding site, preventing the essential ISG15-PLpro molecular interactions. All compounds demonstrate clear inhibition in a deISGylation assay, two exhibit distinct antiviral activity and one inhibited a cytopathic effect in a non-cytotoxic concentration range. These results highlight the druggability of the rarely explored ISG15/Ub-S2 PLpro allosteric binding site to identify new and effective antiviral compounds. Importantly, in the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
Competing Interest Statement
The authors have declared no competing interest.
Subject Area
- Biochemistry (11760)
- Bioengineering (8760)
- Bioinformatics (29211)
- Biophysics (14985)
- Cancer Biology (12104)
- Cell Biology (17417)
- Clinical Trials (138)
- Developmental Biology (9426)
- Ecology (14189)
- Epidemiology (2067)
- Evolutionary Biology (18314)
- Genetics (12246)
- Genomics (16807)
- Immunology (11874)
- Microbiology (28106)
- Molecular Biology (11607)
- Neuroscience (61013)
- Paleontology (452)
- Pathology (1872)
- Pharmacology and Toxicology (3238)
- Physiology (4964)
- Plant Biology (10429)
- Synthetic Biology (2888)
- Systems Biology (7341)
- Zoology (1651)