Binding of SARS-CoV Covalent Non-Covalent Inhibitors to the SARS-CoV-2 Papain-Like Protease and Ovarian Tumor Domain Deubiquitinases.

Dakshinamurthy Sivakumar,Matthias Stein

doi:10.3390/biom11060802

Dakshinamurthy Sivakumar, Matthias Stein

Open Access

https://doi.org/10.3390/biom11060802

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Abstract

The urgent need for novel and effective drugs against the SARS-CoV-2 coronavirus pandemic has stimulated research worldwide. The Papain-like protease (PLpro), which is essential for viral replication, shares a similar active site structural architecture to other cysteine proteases. Here, we have used representatives of the Ovarian Tumor Domain deubiquitinase family OTUB1 and OTUB2 along with the PLpro of SARS-CoV-2 to validate and rationalize the binding of inhibitors from previous SARS-CoV candidate compounds. By forming a new chemical bond with the cysteine residue of the catalytic triad, covalent inhibitors irreversibly suppress the protein’s activity. Modeling covalent inhibitor binding requires detailed knowledge about the compounds’ reactivities and binding. Molecular Dynamics refinement simulations of top poses reveal detailed ligand-protein interactions and show their stability over time. The recently discovered selective OTUB2 covalent inhibitors were used to establish and validate the computational protocol. Structural parameters and ligand dynamics are in excellent agreement with the ligand-bound OTUB2 crystal structures. For SARS-CoV-2 PLpro, recent covalent peptidomimetic inhibitors were simulated and reveal that the ligand-protein interaction is very dynamic. The covalent and non-covalent docking plus subsequent MD refinement of known SARS-CoV inhibitors into DUBs and the SARS-CoV-2 PLpro point out a possible approach to target the PLpro cysteine protease from SARS-CoV-2. The results show that such an approach gives insight into ligand-protein interactions, their dynamic character, and indicates a path for selective ligand design.

Highlights

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A total of 11 reported selective covalent inhibitors for OTUB2 were co-crystallized by high throughput crystallization (PDB entries from 5QIP to 5QIZ (Table S1)) and selected for MD refinement studies to validate our molecular dynamics protocol
Deubiquitinating enzymes have recently received attention as drug targets in cancer, autoimmune diseases, chronic inflammation, and neurodegeneration, but the functionally related papain-like protease Papain-like protease (PLpro) may be a viable target against SARSCoV-2

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. The most recent pandemic, the SARS-CoV-2 coronavirus outbreak, is one of the largest threats to the human population worldwide and still significantly increasing in absolute numbers. According to WHO reports, it is one of the worst pandemics seen during recent times. The SARS-CoV-2 genome encodes for 29 proteins, of which 4 are structurally encoding and make up the virus’s actual structure. The spike (S) protein and the main protease MLpro have received the most attention in drug design. The X-ray crystal structure of the six-helical bundle (6-HB) core of the HR1 and HR2 domains in the SARS-CoV-2 spike protein S2 subunit was released [1].

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