8CD9 | pdb_00008cd9

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 6

• PDB DOI: https://doi.org/10.2210/pdb8CD9/pdb

• Classification: HYDROLASE
• Organism(s): Schistosoma mansoni
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-01-30 Released: 2024-02-21 
• Deposition Author(s): Rubesova, P., Brynda, J., Fanfrlik, J., Gerwick, W.H., Mares, M.
• Funding Organization(s): Other government, Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.216 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Nature-Inspired Gallinamides Are Potent Antischistosomal Agents: Inhibition of the Cathepsin B1 Protease Target and Binding Mode Analysis.

Spiwokova, P., Horn, M., Fanfrlik, J., Jilkova, A., Fajtova, P., Leontovyc, A., Houstecka, R., Bielikova, L., Brynda, J., Chanova, M., Mertlikova-Kaiserova, H., Caro-Diaz, E.J.E., Almaliti, J., El-Sakkary, N., Gerwick, W.H., Caffrey, C.R., Mares, M.

(2024) ACS Infect Dis 10: 1935-1948

• PubMed: 38757505 
• DOI: https://doi.org/10.1021/acsinfecdis.3c00589
• Primary Citation Related Structures: 
  8CC2, 8CCU, 8CD9


• PubMed Abstract: 
  

  Schistosomiasis, caused by a parasitic blood fluke of the genus Schistosoma, is a global health problem for which new chemotherapeutic options are needed. We explored the scaffold of gallinamide A, a natural peptidic metabolite of marine cyanobacteria that has previously been shown to inhibit cathepsin L-type proteases. We screened a library of 19 synthetic gallinamide A analogs and identified nanomolar inhibitors of the cathepsin B-type protease SmCB1, which is a drug target for the treatment of schistosomiasis mansoni. Against cultured S. mansoni schistosomula and adult worms, many of the gallinamides generated a range of deleterious phenotypic responses. Imaging with a fluorescent-activity-based probe derived from gallinamide A demonstrated that SmCB1 is the primary target for gallinamides in the parasite. Furthermore, we solved the high-resolution crystal structures of SmCB1 in complex with gallinamide A and its two analogs and describe the acrylamide covalent warhead and binding mode in the active site. Quantum chemical calculations evaluated the contribution of individual positions in the peptidomimetic scaffold to the inhibition of the target and demonstrated the importance of the P1' and P2 positions. Our study introduces gallinamides as a powerful chemotype that can be exploited for the development of novel antischistosomal chemotherapeutics.

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Organizational Affiliation: 
• Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.
Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 5, Prague 6 16628, Czech Republic.
Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States.
First Faculty of Medicine, Charles University, Kateřinská 32, Praha 2 12108, Czech Republic.
Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2028/7, Prague 2 12800, Czech Republic.
Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 29.3 kDa 
• Atom Count: 2,368 
• Modeled Residue Count: 254 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B-like peptidase (C01 family)	A [auth AAA]	254	Schistosoma mansoni	Mutation(s): 2  Gene Names: cb1.1, Smp_103610
UniProt
Find proteins for Q8MNY2 (Schistosoma mansoni) Explore Q8MNY2  Go to UniProtKB:  Q8MNY2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UA9 (Subject of Investigation/LOI)	B [auth AAA]	[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-5-[(2~{S})-3-methoxy-5-oxidanylidene-2-(phenylmethyl)-2~{H}-pyrrol-1-yl]-5-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl] (2~{S})-2-(dimethylamino)-3-phenyl-propanoate C40 H56 N4 O7 WESAHNJMKCXPAC-WEHFJZMFSA-N
EDO	C [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.216 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.062	α = 90
b = 78.87	β = 90
c = 90.139	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Rubesova, P., Brynda, J., Fanfrlik, J., Gerwick, W.H., Mares, M.

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Funding Organization	Location	Grant Number
Other government		NV18-05-00345
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LTAUSA19109

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release
  
• Version 1.1: 2024-08-07
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Structure summary