RT Journal Article
SR Electronic
T1 SARS-CoV-2 papain-like protease PLpro in complex with natural compounds reveal allosteric sites for antiviral drug design
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.11.17.468943
DO 10.1101/2021.11.17.468943
A1 Vasundara Srinivasan
A1 Hévila Brognaro
A1 Prince R. Prabhu
A1 Edmarcia Elisa de Souza
A1 Sebastian Günther
A1 Patrick Y. A. Reinke
A1 Thomas J. Lane
A1 Helen Ginn
A1 Huijong Han
A1 Wiebke Ewert
A1 Janina Sprenger
A1 Faisal H. M. Koua
A1 Sven Falke
A1 Nadine Werner
A1 Hina Andaleeb
A1 Najeeb Ullah
A1 Bruno Alves Franca
A1 Mengying Wang
A1 Angélica Luana C Barra
A1 Markus Perbandt
A1 Martin Schwinzer
A1 Christina Schmidt
A1 Lea Brings
A1 Kristina Lorenzen
A1 Robin Schubert
A1 Rafael Rahal Guaragna Machado
A1 Erika Donizette Candido
A1 Danielle Bruna Leal Oliveira
A1 Edison Luiz Durigon
A1 Oleksandr Yefanov
A1 Julia Lieske
A1 Luca Gelisio
A1 Martin Domaracky
A1 Philipp Middendorf
A1 Michael Groessler
A1 Fabian Trost
A1 Marina Galchenkova
A1 Sofiane Saouane
A1 Johanna Hakanpää
A1 Markus Wolf
A1 Dusan Turk
A1 Arwen R. Pearson
A1 Henry N. Chapman
A1 Winfried Hinrichs
A1 Carsten Wrenger
A1 Alke Meents
A1 Christian Betzel
YR 2021
UL http://biorxiv.org/content/early/2021/11/22/2021.11.17.468943.abstract
AB 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 StatementThe authors have declared no competing interest.