7QKB | pdb_00007qkb

Crystal structure of human Cathepsin L in complex with covalently bound GC376

• PDB DOI: https://doi.org/10.2210/pdb7QKB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2021-12-17 Released: 2022-12-28 
• Deposition Author(s): Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.
• Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research, Slovenian Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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

• PubMed: 37853179 
• DOI: https://doi.org/10.1038/s42003-023-05317-9
• Primary Citation 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.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
Jožef Stefan International Postgraduate School, Jamova 39, Ljubljana, Slovenia.
Institute of Virology, Helmholtz Munich, Munich, Germany.
Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia.
Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil.
Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil.
Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4474 TAMU, School Station, TX, USA.
Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany.
Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany.
Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Universität Hamburg, 22607, Hamburg, Germany.
Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
Institute of Virology, Technical University of Munich, Munich, Germany.
The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, Australia.
St Vincent's Hospital Clinical School, UNSW, Sydney, NSW, Australia.
Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia. [e-mail].
Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia. [e-mail].
Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil. [e-mail].
Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.92 kDa 
• Atom Count: 7,279 
• Modeled Residue Count: 867 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L	A, B, C, D	220	Homo sapiens	Mutation(s): 1  Gene Names: CTSL, CTSL1 EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711  Go to UniProtKB:  P07711
PHAROS:  P07711 GTEx:  ENSG00000135047

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UED (Subject of Investigation/LOI)	J [auth A], P [auth B], U [auth C], X [auth D]	N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide C21 H31 N3 O5 JUCVXDDMQHPCKT-BZSNNMDCSA-N
P6G	W [auth D]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	T [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	G [auth A], O [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	E [auth A], I [auth A], K [auth B], L [auth B], M [auth B], Q [auth C], R [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], N [auth B], S [auth C], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.29	α = 105.306
b = 62.45	β = 93.523
c = 67.82	γ = 115.929

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	FISCOV
Helmholtz Association	Germany	SFragX
German Federal Ministry for Education and Research	Germany	16GW0277
German Federal Ministry for Education and Research	Germany	031B0405
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Author supporting evidence, Data collection, Database references
• Version 1.2: 2024-01-31
  Changes: Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary