9BPF

Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor

Summary for 9BPF

• Entry DOI: 10.2210/pdb9bpf/pdb
• Related: 6WTM
• Descriptor: 3C-like proteinase nsp5, N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide (3 entities in total)
• Functional Keywords: sars-cov-2, main protease, inhibitor, inhibitory activity, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 2
• Total formula weight: 68634.10

Authors

Chen, P.,Arutyunova, E.,Lemieux, M.J. (deposition date: 2024-05-07, release date: 2024-08-07, Last modification date: 2024-11-20)

Primary citation

Chen, P.,Van Oers, T.J.,Arutyunova, E.,Fischer, C.,Wang, C.,Lamer, T.,van Belkum, M.J.,Young, H.S.,Vederas, J.C.,Lemieux, M.J.
A Structural Comparison of Oral SARS-CoV-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (M pro ) of SARS-CoV-2 and MERS-CoV.
Jacs Au, 4:3217-3227, 2024

PubMed Abstract: Ibuzatrelvir (1) was recently disclosed and patented by Pfizer for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has received fast-track status from the USA Food and Drug Administration (FDA) and has entered phase III clinical trials as a possible replacement for Paxlovid. Like nirmatrelvir (2) in Paxlovid, this orally active drug candidate is designed to target viral main proteases (M) through reversible covalent interaction of its nitrile warhead with the active site thiol of the chymotrypsin-like cysteine protease (3CL protease). Inhibition of M hinders the processing of the proteins essential for viral replication . However, ibuzatrelvir apparently does not require ritonavir (3), which is coadministered in Paxlovid to block human oxidative metabolism of nirmatrelvir. Here, we report the crystal structure of the complex of ibuzatrelvir with the active site of SARS-CoV-2 M at 2.0 Å resolution. In addition, we show that ibuzatrelvir also potently inhibits the M of Middle East respiratory syndrome-related coronavirus (MERS-CoV), which is fortunately not widespread but can be dangerously lethal (∼36% mortality). Co-crystal structures show that the binding mode of the drug to both active sites is similar and that the trifluoromethyl group of the inhibitor fits precisely into a critical S2 substrate binding pocket of the main proteases. However, our results also provide a rationale for the differences in potency of ibuzatrelvir for these two proteases due to minor differences in the substrate preferences leading to a weaker H-bond network in MERS-CoV M. In addition, we examined the reversibility of compound binding to both proteases, which is an important parameter in reducing off-target effects as well as the potential immunogenicity. The crystal structures of the ibuzatrelvir complexes with M of SARS-CoV-2 and of MERS-CoV will further assist drug design for coronaviral infections in humans and animals.

PubMed: 39211604
DOI: 10.1021/jacsau.4c00508

Experimental method

X-RAY DIFFRACTION (2 Å)