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Research Highlight

Neutrons Help Design Inhibitors of SARS-CoV-2 Main Protease

Neutrons Help Design Inhibitors of SARS-CoV-2 Main Protease
Image shows how hybrid inhibitor BBH-1 was designed from boceprevir (hepatitis C protease inhibitor) and GC-376 (SARS-CoV-1 inhibitor) and its neutron structure with SARS-CoV-2 Mpro. Inset shows nuclear density of BBH-1 revealing deprotonated negatively charged oxyanion (red arrow).

Scientific Achievement

SARS-CoV-2 main protease (Mpro) enzyme is indispensable for virus replication and is an essential drug target for the design and development of small-molecule antivirals to treat COVID-19. Neutron crystallography was used to help design and characterize covalent hybrid protease inhibitors (BBH-1, BBH-2 and NBH-2) created by splicing components of known hepatitis C and SARS-CoV-1 protease inhibitors. These inhibitors demonstrated efficient inhibition of SARS-CoV-2 in cell-based assays, paving the way for further design of improved antivirals.


Significance and Impact

Hydrogen atoms are crucial players in drug binding, their locations determine protonation states and electric charges of ionizable residues. Knowledge of hydrogen atom positions provides unique information for drug design and was used to design potent (nanomolar) inhibitors of SARS-CoV-2 Mpro, map essential hydrogen bonding interactions between inhibitors and enzyme, and evaluated antiviral properties. Comparison with the FDA-approved nirmatrelvir from Pfizer indicated how inhibitor design can be further improved.


Research Details

  • Neutron structure of Mpro/BBH-1 complex visualized critical hydrogen atoms and hydrogen bonds for the inhibitor binding; X-ray structures of Mpro in complexes with BBH-2, NBH-2, and nirmatrelvir were determined.
  • Thermodynamics of inhibitor binding to Mpro evaluated by isothermal titration calorimetry.
  • Antiviral properties of the inhibitors were evaluated in cell-based assays.

D.W. Kneller, H. Li, G. Phillips, K.L Weiss, Q. Zhang, M.A. Arnould, C.B. Jonsson, S. Surendranathan, J. Parvathareddy, M.P. Blakeley, L. Coates, J.M. Louis, P.V. Bonnesen, A. Kovalevsky, Nat. Commun. 13 2268 (2022). DOI: 10.1038/s41467-022-29915-z.