6XQT

Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Narlaprevir

Summary for 6XQT

• Entry DOI: 10.2210/pdb6xqt/pdb
• Descriptor: 3C-like proteinase, (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (3 entities in total)
• Functional Keywords: 3c like proteinase, viral protein, viral protein-hydrolase complex, viral protein/hydrolase
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)
• Total number of polymer chains: 2
• Total formula weight: 69071.05

Authors

Kneller, D.W.,Kovalevsky, A.,Coates, L. (deposition date: 2020-07-10, release date: 2020-07-22, Last modification date: 2024-10-09)

Primary citation

Kneller, D.W.,Galanie, S.,Phillips, G.,O'Neill, H.M.,Coates, L.,Kovalevsky, A.
Malleability of the SARS-CoV-2 3CL M pro Active-Site Cavity Facilitates Binding of Clinical Antivirals.
Structure, 28:1313-, 2020

PubMed 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, 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. 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.

PubMed: 33152262
DOI: 10.1016/j.str.2020.10.007

Experimental method

X-RAY DIFFRACTION (2.3 Å)