Abstract
Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.
| Original language | English |
|---|---|
| Article number | 2268 |
| Journal | Nature Communications |
| Volume | 13 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 2022 |
Funding
This research used resources at the Center for Nanophase Materials Sciences, 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 (CSMB), a DOE Office of Science User Facility. This research used resources of the Spallation Neutron Source Second Target Station Project at Oak Ridge National Laboratory (ORNL). ORNL is managed by UT-Battelle LLC for DOE?s Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The authors thank the Institut Laue Langevin (beamline LADI-DALI) for awarded neutron beamtime. We thank Dr. Hugh M. O?Neill from ORNL for assistance during the expression of the partially deuterated protein. We thank Annie Aniana from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) for excellent technical assistance. This work was also supported by the Intramural Research Program of NIDDK, NIH. This research used resources at the Center for Nanophase Materials Sciences, 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 (CSMB), a DOE Office of Science User Facility. This research used resources of the Spallation Neutron Source Second Target Station Project at Oak Ridge National Laboratory (ORNL). ORNL is managed by UT-Battelle LLC for DOE’s Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The authors thank the Institut Laue Langevin (beamline LADI-DALI) for awarded neutron beamtime. We thank Dr. Hugh M. O’Neill from ORNL for assistance during the expression of the partially deuterated protein. We thank Annie Aniana from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) for excellent technical assistance. This work was also supported by the Intramural Research Program of NIDDK, NIH.
