8C3D

Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.

Reinke, P.Y.A.de Souza, E.E.Gunther, S.Falke, S.Lieske, J.Ewert, W.Loboda, J.Herrmann, A.Rahmani Mashhour, A.Karnicar, K.Usenik, A.Lindic, N.Sekirnik, A.Botosso, V.F.Santelli, G.M.M.Kapronezai, J.de Araujo, M.V.Silva-Pereira, T.T.Filho, A.F.S.Tavares, M.S.Florez-Alvarez, L.de Oliveira, D.B.L.Durigon, E.L.Giaretta, P.R.Heinemann, M.B.Hauser, M.Seychell, B.Bohler, H.Rut, W.Drag, M.Beck, T.Cox, R.Chapman, H.N.Betzel, C.Brehm, W.Hinrichs, W.Ebert, G.Latham, S.L.Guimaraes, A.M.S.Turk, D.Wrenger, C.Meents, A.

(2023) Commun Biol 6: 1058-1058

  • DOI: https://doi.org/10.1038/s42003-023-05317-9
  • Primary Citation of Related Structures:  
    7QGW, 7QKA, 7QKB, 7QKC, 7Z3T, 7Z3U, 7Z58, 8C3D

  • PubMed Abstract: 

    Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (M pro ), its moderate activity in M pro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.


  • Organizational Affiliation

    Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLEB [auth LIG]3synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.63α = 90
b = 41.62β = 121.01
c = 65.66γ = 90
Software Package:
Software NamePurpose
MAINrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySlovenia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 2.0: 2023-11-01
    Changes: Atomic model, Database references
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection