8DOX | pdb_00008dox

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245

• PDB DOI: https://doi.org/10.2210/pdb8DOX/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-14 Released: 2022-09-21 
• Deposition Author(s): Bulut, H., Hayashi, H., Tsuji, K., Kuwata, N., 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: 1.46 Å
• R-Value Free: 
  0.229 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2.

Higashi-Kuwata, N., Tsuji, K., Hayashi, H., Bulut, H., Kiso, M., Imai, M., Ogata-Aoki, H., Ishii, T., Kobayakawa, T., Nakano, K., Takamune, N., Kishimoto, N., Hattori, S.I., Das, D., Uemura, Y., Shimizu, Y., Aoki, M., Hasegawa, K., Suzuki, S., Nishiyama, A., Saruwatari, J., Shimizu, Y., Sukenaga, Y., Takamatsu, Y., Tsuchiya, K., Maeda, K., Yoshimura, K., Iida, S., Ozono, S., Suzuki, T., Okamura, T., Misumi, S., Kawaoka, Y., Tamamura, H., Mitsuya, H.

(2023) Nat Commun 14: 1076-1076

• PubMed: 36841831 
• DOI: https://doi.org/10.1038/s41467-023-36729-0
• Primary Citation Related Structures: 
  8DOX, 8DPR


• PubMed Abstract: 
  

  COVID-19 caused by SARS-CoV-2 has continually been serious threat to public health worldwide. While a few anti-SARS-CoV-2 therapeutics are currently available, their antiviral potency is not sufficient. Here, we identify two orally available 4-fluoro-benzothiazole-containing small molecules, TKB245 and TKB248, which specifically inhibit the enzymatic activity of main protease (M ^pro ) of SARS-CoV-2 and significantly more potently block the infectivity and replication of various SARS-CoV-2 strains than nirmatrelvir, molnupiravir, and ensitrelvir in cell-based assays employing various target cells. Both compounds also block the replication of Delta and Omicron variants in human-ACE2-knocked-in mice. Native mass spectrometric analysis reveals that both compounds bind to dimer M ^pro , apparently promoting M ^pro dimerization. X-ray crystallographic analysis shows that both compounds bind to M ^pro 's active-site cavity, forming a covalent bond with the catalytic amino acid Cys-145 with the 4-fluorine of the benzothiazole moiety pointed to solvent. The data suggest that TKB245 and TKB248 might serve as potential therapeutics for COVID-19 and shed light upon further optimization to develop more potent and safer anti-SARS-CoV-2 therapeutics.

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Organizational Affiliation: 
• Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan.
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA.
Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan.
Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.
Department of Infectious Diseases, Tohoku University Graduate School of Medicine, Miyagi, Japan.
Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan.
Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan. [e-mail].
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA. [e-mail].
Kumamoto University Hospital, Kumamoto, Japan. [e-mail].

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: 34.14 kDa 
• Atom Count: 2,505 
• Modeled Residue Count: 303 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	303	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
T2L (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-{(1S,2S)-1-(4-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 HZJVVPOOURAASY-SWSSSNQJSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.229 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.333	α = 90
b = 52.913	β = 103.74
c = 45.604	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
MOLREP	phasing
xia2	data reduction
DIALS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Bulut, H., Hayashi, H., Tsuji, K., Kuwata, N., 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: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references
• Version 1.2: 2023-10-18
  Changes: Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary