8UH9 | pdb_00008uh9

Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272

• PDB DOI: https://doi.org/10.2210/pdb8UH9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-07 Released: 2023-12-20 
• Deposition Author(s): Bulut, H., Hayashi, H., Kuwata, N., Tsuji, K., Das, D., Tamamura, H., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.240 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

An orally available P1'-5-fluorinated M pro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier.

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.

(2025) PNAS Nexus 4: pgae578-pgae578

• PubMed: 39831159 
• DOI: https://doi.org/10.1093/pnasnexus/pgae578
• Primary Citation Related Structures: 
  8UH5, 8UH8, 8UH9


• 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 ^pro ) and more effectively blocks the infectivity and replication of all SARS-CoV-2 strains examined including Omicron variants such as SARS-CoV-2 ^XBB1.5 and SARS-CoV-2 ^EG.5.1 than two M ^pro 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 ^XBB1.5 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 ^E166V-P14 ) readily emerged by passage 14; however, when propagated with TKB272, no variants emerged by passage 25. SARS-CoV-2 _E166V 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 ^pro inhibition but that TKB272 nevertheless forms a tight binding with M ^pro '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 ^pro inhibitors.

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Organizational Affiliation: 
• Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
Department of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Aoba-ku, Sendai 980-8575, Japan.
Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan.
Department of Clinical Sciences, Kumamoto University Hospital, Chuo-ku, Kumamoto 860-8556, Japan.
Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection & Graduate School of Medical Sciences, Kumamoto University, Chuo-ku, Kumamoto 860-0811, Japan.
Division of Virology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
Department of Laboratory Animal Medicine, National Center for Global Health and Medicine Research Institute, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan.
Structural Biology Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.
Graduate School of Biomedical Engineering, Tohoku University, Miyagi 980-8579, Japan.
Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo 169-0073, Japan.
Department of Medical Technology, Kumamoto Health Science University, 325 Izumimachi, Kita-ku, Kumamoto 861-5598, Japan.
The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI 53711, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.56 kDa 
• Atom Count: 2,421 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WOK (Subject of Investigation/LOI)	B [auth A]	(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 C30 H37 F4 N5 O5 S AVAISVNJDSSFQV-UDQBHXPNSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.240 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.673	α = 90
b = 53.09	β = 101.96
c = 45.774	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Bulut, H., Hayashi, H., Kuwata, N., Tsuji, K., Das, D., Tamamura, H., Mitsuya, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-02-19
  Changes: Database references