8CD9

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsinfecdis.3c00589
  • Primary Citation of 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.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin B-like peptidase (C01 family)A [auth AAA]254Schistosoma mansoniMutation(s): 2 
Gene Names: cb1.1Smp_103610
UniProt
Find proteins for Q8MNY2 (Schistosoma mansoni)
Explore Q8MNY2 
Go to UniProtKB:  Q8MNY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8MNY2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UA9 (Subject of Investigation/LOI)
Query on UA9

Download Ideal Coordinates CCD File 
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
Query on EDO

Download Ideal Coordinates CCD File 
C [auth AAA]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.062α = 90
b = 78.87β = 90
c = 90.139γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentNV18-05-00345
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLTAUSA19109

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references