7QGW | pdb_00007qgw

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

PDB DOI: https://doi.org/10.2210/pdb7QGW/pdb

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

Deposited: 2021-12-10 Released: 2022-12-21
Deposition Author(s): Loboda, J., Karnicar, K., Lindic, N., Usenik, A., Lieske, J., Meents, A., Guenther, S., Reinke, P.Y.A., Falke, S., Ewert, W., Turk, D.
Funding Organization(s): Slovenian Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.196 (Depositor), 0.174 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 37853179 Search on PubMed Search on PubMed Central
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.

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. dusan.turk@ijs.si.

Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia. dusan.turk@ijs.si.

Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil. cwrenger@icb.usp.br.

Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany. alke.meents@desy.de.

Macromolecule Content

Total Structure Weight: 50.19 kDa
Atom Count: 4,293
Modeled Residue Count: 442
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L2	A, B	221	Homo sapiens	Mutation(s): 2 Gene Names: CTSV, CATL2, CTSL2, CTSU, UNQ268/PRO305 EC: 3.4.22.43
UniProt & NIH Common Fund Data Resources
Find proteins for O60911 (Homo sapiens) Explore O60911 Go to UniProtKB: O60911
PHAROS: O60911 GTEx: ENSG00000136943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60911
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RN2 Query on RN2 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B]	K [auth A], U [auth B]	Calpeptin C₂₀ H₃₂ N₂ O₄ JDNZSBPOIODDLU-ROUUACIJSA-N		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain S [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth B] mmCIF format, chain L [auth B]	F [auth A], J [auth A], L [auth B], O [auth B], S [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B]	G [auth A] I [auth A] N [auth B] P [auth B] Q [auth B] G [auth A], I [auth A], N [auth B], P [auth B], Q [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth B]	C [auth A] D [auth A] E [auth A] H [auth A] M [auth B] C [auth A], D [auth A], E [auth A], H [auth A], M [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth B]