8UH5

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-272

Summary for 8UH5

• Entry DOI: 10.2210/pdb8uh5/pdb
• Descriptor: 3C-like proteinase nsp5, (1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: sars-cov-2 main protease, 3c-like proteinase, viral protein, sars-cov-2
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 34587.37

Authors

Bulut, H.,Hayashi, H.,Kuwata, N.,Tsuji, K.,Das, D.,Tamamura, H.,Mitsuya, H. (deposition date: 2023-10-06, release date: 2023-12-13, Last modification date: 2025-02-19)

Primary citation

Higashi-Kuwata, N.,Bulut, H.,Hayashi, H.,Tsuji, K.,Ogata-Aoki, H.,Kiso, M.,Takamune, N.,Kishimoto, N.,Hattori, S.I.,Ishii, T.,Kobayakawa, T.,Nakano, K.,Shimizu, Y.,Das, D.,Saruwatari, J.,Hasegawa, K.,Murayama, K.,Sukenaga, Y.,Takamatsu, Y.,Yoshimura, K.,Aoki, M.,Furusawa, Y.,Okamura, T.,Yamayoshi, S.,Kawaoka, Y.,Misumi, S.,Tamamura, H.,Mitsuya, H.
An orally available P1'-5-fluorinated M pro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier.
Pnas Nexus, 4:pgae578-pgae578, 2025

PubMed Abstract: We identified a 5-fluoro-benzothiazole-containing small molecule, TKB272, through fluorine-scanning of the benzothiazole moiety, which more potently inhibits the enzymatic activity of SARS-CoV-2's main protease (M) and more effectively blocks the infectivity and replication of all SARS-CoV-2 strains examined including Omicron variants such as SARS-CoV-2 and SARS-CoV-2 than two M inhibitors: nirmatrelvir and ensitrelvir. Notably, the administration of ritonavir-boosted nirmatrelvir and ensitrelvir causes drug-drug interactions warranting cautions due to their CYP3A4 inhibition, thereby limiting their clinical utility. When orally administered, TKB272 blocked SARS-CoV-2 replication without ritonavir in B6.Cg-Tg(K18-hACE2)2-Prlmn/J-transgenic mice, comparably as did ritonavir-boosted nirmatrelvir. When the ancestral SARS-CoV-2 was propagated with nirmatrelvir in vitro, a highly nirmatrelvir-resistant E166V-carrying variant (SARS-CoV-2) readily emerged by passage 14; however, when propagated with TKB272, no variants emerged by passage 25. SARS-CoV-2 showed some cross-resistance to TKB272 but was substantially sensitive to the compound. X-ray structural analyses and mass-spectrometric data showed that the E166V substitution disrupts the critical dimerization-initiating Ser1'-E166 interactions, thereby limiting nirmatrelvir's M inhibition but that TKB272 nevertheless forms a tight binding with M's catalytic active sight even in the presence of the E166V substitution. TKB272 shows no apparent genotoxicity as tested in the micro-Ames test. Highly potent TKB272 may serve as a COVID-19 therapeutic, overcome resistance to existing M inhibitors.

PubMed: 39831159
DOI: 10.1093/pnasnexus/pgae578

Experimental method

X-RAY DIFFRACTION (1.74 Å)