Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals

Daniel W. Kneller; Stephanie Galanie; Gwyndalyn Phillips; Hugh M. O'Neill; Leighton Coates; Andrey Kovalevsky

doi:10.1016/j.str.2020.10.007

Malleability of the SARS-CoV-2 3CL M^pro Active-Site Cavity Facilitates Binding of Clinical Antivirals

Daniel W. Kneller, Stephanie Galanie, Gwyndalyn Phillips, Hugh M. O'Neill, Leighton Coates, Andrey Kovalevsky

Research output: Contribution to journal › Article › peer-review

98 Scopus citations

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 requires rapid development of specific therapeutics and vaccines. The main protease of SARS-CoV-2, 3CL M^pro, is an established drug target for the design of inhibitors to stop the virus replication. Repurposing existing clinical drugs can offer a faster route to treatments. Here, we report on the binding mode and inhibition properties of several inhibitors using room temperature X-ray crystallography and in vitro enzyme kinetics. The enzyme active-site cavity reveals a high degree of malleability, allowing aldehyde leupeptin and hepatitis C clinical protease inhibitors (telaprevir, narlaprevir, and boceprevir) to bind and inhibit SARS-CoV-2 3CL M^pro. Narlaprevir, boceprevir, and telaprevir are low-micromolar inhibitors, whereas the binding affinity of leupeptin is substantially weaker. Repurposing hepatitis C clinical drugs as COVID-19 treatments may be a useful option to pursue. The observed malleability of the enzyme active-site cavity should be considered for the successful design of specific protease inhibitors.

Original language	English
Pages (from-to)	1313-1320.e3
Journal	Structure
Volume	28
Issue number	12
DOIs	https://doi.org/10.1016/j.str.2020.10.007
State	Published - Dec 1 2020

Funding

This research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory , a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act . This research used resources at the Spallation Neutron Source and the High Flux Isotope Reactor, which are DOE Office of Science User Facilities operated by the Oak Ridge National Laboratory. The Office of Biological and Environmental Research supported research at ORNL's Center for Structural Molecular Biology , a DOE Office of Science User Facility. This research used resources at the Second Target Station, which is a DOE Office of Science User Facilities Construction Project at Oak Ridge National Laboratory. This research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act. This research used resources at the Spallation Neutron Source and the High Flux Isotope Reactor, which are DOE Office of Science User Facilities operated by the Oak Ridge National Laboratory. The Office of Biological and Environmental Research supported research at ORNL's Center for Structural Molecular Biology, a DOE Office of Science User Facility. This research used resources at the Second Target Station, which is a DOE Office of Science User Facilities Construction Project at Oak Ridge National Laboratory. Conceptualization, D.W.K. L.C. and A.K.; Methodology, D.W.K. S.G. G.P. and H.M.O'N.; Software, S.G. and L.C.; Validation, D.W.K. S.G. L.C. and A.K.; Formal Analysis, D.W.K. S.G. L.C. and A.K.; Investigation, D.W.K. and A.K.; Resources, G.P. and H.M.O'N.; Data Curation, S.G. and L.C.; Writing ? Original Draft, D.W.K. L.C. and A.K.; Writing ? Review & Editing, D.W.K. S.G. H.M.O'N. L.C. and A.K.; Visualization, D.W.K. and A.K.; Supervision, L.C. and A.K.; Project Administration, A.K.; Funding Acquisition, H.M.O'N. L.C. and A.K. The authors declare no competing interests.

Funders	Funder number
National Virtual Biotechnology Laboratory
Office of Biological and Environmental Research
U.S. Department of Energy
Office of Science
Biological and Environmental Research
Oak Ridge National Laboratory

Keywords

3CL M
3CL main protease
SARS-CoV-2
drug design
enzyme kinetics
hepatitis C clinical drugs
protease inhibitor
repurposing clinical drugs
room temperature X-ray crystallography

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.str.2020.10.007

Cite this

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title = "Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals",

abstract = "The COVID-19 pandemic caused by SARS-CoV-2 requires rapid development of specific therapeutics and vaccines. The main protease of SARS-CoV-2, 3CL Mpro, is an established drug target for the design of inhibitors to stop the virus replication. Repurposing existing clinical drugs can offer a faster route to treatments. Here, we report on the binding mode and inhibition properties of several inhibitors using room temperature X-ray crystallography and in vitro enzyme kinetics. The enzyme active-site cavity reveals a high degree of malleability, allowing aldehyde leupeptin and hepatitis C clinical protease inhibitors (telaprevir, narlaprevir, and boceprevir) to bind and inhibit SARS-CoV-2 3CL Mpro. Narlaprevir, boceprevir, and telaprevir are low-micromolar inhibitors, whereas the binding affinity of leupeptin is substantially weaker. Repurposing hepatitis C clinical drugs as COVID-19 treatments may be a useful option to pursue. The observed malleability of the enzyme active-site cavity should be considered for the successful design of specific protease inhibitors.",

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