7DDC

Crystal structure of SARS-CoV-2 main protease in complex with Tafenoquine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Tafenoquine and its derivatives as inhibitors for the severe acute respiratory syndrome coronavirus 2.

Chen, Y.Yang, W.H.Chen, H.F.Huang, L.M.Gao, J.Y.Lin, C.W.Wang, Y.C.Yang, C.S.Liu, Y.L.Hou, M.H.Tsai, C.L.Chou, Y.Z.Huang, B.Y.Hung, C.F.Hung, Y.L.Wang, W.J.Su, W.C.Kumar, V.Wu, Y.C.Chao, S.W.Chang, C.S.Chen, J.S.Chiang, Y.P.Cho, D.Y.Jeng, L.B.Tsai, C.H.Hung, M.C.

(2022) J Biol Chem 298: 101658-101658

  • DOI: https://doi.org/10.1016/j.jbc.2022.101658
  • Primary Citation of Related Structures:  
    7DDC

  • PubMed Abstract: 

    The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely affected human lives around the world as well as the global economy. Therefore, effective treatments against COVID-19 are urgently needed. Here, we screened a library containing Food and Drug Administration (FDA)-approved compounds to identify drugs that could target the SARS-CoV-2 main protease (M pro ), which is indispensable for viral protein maturation and regard as an important therapeutic target. We identified antimalarial drug tafenoquine (TFQ), which is approved for radical cure of Plasmodium vivax and malaria prophylaxis, as a top candidate to inhibit M pro protease activity. The crystal structure of SARS-CoV-2 M pro in complex with TFQ revealed that TFQ noncovalently bound to and reshaped the substrate-binding pocket of M pro by altering the loop region (residues 139-144) near the catalytic Cys145, which could block the catalysis of its peptide substrates. We also found that TFQ inhibited human transmembrane protease serine 2 (TMPRSS2). Furthermore, one TFQ derivative, compound 7, showed a better therapeutic index than TFQ on TMPRSS2 and may therefore inhibit the infectibility of SARS-CoV-2, including that of several mutant variants. These results suggest new potential strategies to block infection of SARS-CoV-2 and rising variants.


  • Organizational Affiliation

    Institute of New Drug Development, China Medical University, Taichung, Taiwan; Drug Development Center, China Medical University, Taichung, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, Taiwan. Electronic address: bluecrystalprotein@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase307Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H3F (Subject of Investigation/LOI)
Query on H3F

Download Ideal Coordinates CCD File 
B [auth A]Tafenoquine
C24 H28 F3 N3 O3
LBHLFPGPEGDCJG-HNNXBMFYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.294α = 90
b = 54.675β = 100.861
c = 44.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2311-B241-001
Ministry of Science and Technology (MoST, Taiwan)Taiwan109-2311-B241-001

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description