7JMT | pdb_00007jmt

Crystal structure of schistosome BCL-2 bound to ABT-737

• PDB DOI: https://doi.org/10.2210/pdb7JMT/pdb

• Classification: APOPTOSIS
• Organism(s): Schistosoma japonicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-02 Released: 2021-02-17 
• Deposition Author(s): Smith, N.A., Smith, B.J., Lee, E.F., Colman, P.M., Fairlie, W.D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Optimization of Benzothiazole and Thiazole Hydrazones as Inhibitors of Schistosome BCL-2.

Nguyen, W., Lee, E.F., Evangelista, M., Lee, M., Harris, T.J., Colman, P.M., Smith, N.A., Williams, L.B., Jarman, K.E., Lowes, K.N., Haeberli, C., Keiser, J., Smith, B.J., Fairlie, W.D., Sleebs, B.E.

(2021) ACS Infect Dis 7: 1143-1163

• PubMed: 33523649 
• DOI: https://doi.org/10.1021/acsinfecdis.0c00700
• Primary Citation Related Structures: 
  7JGV, 7JGW, 7JMT


• PubMed Abstract: 
  

  Limited therapeutic options are available for the treatment of human schistosomiasis caused by the parasitic Schistosoma flatworm. The B cell lymphoma-2 (BCL-2)-regulated apoptotic cell death pathway in schistosomes was recently characterized and shown to share similarities with the intrinsic apoptosis pathway in humans. Here, we exploit structural differences in the human and schistosome BCL-2 (sBCL-2) pro-survival proteins toward a novel treatment strategy for schistosomiasis. The benzothiazole hydrazone scaffold previously employed to target human BCL-XL was repurposed as a starting point to target sBCL-2. We utilized X-ray structural data to inform optimization and then applied a scaffold-hop strategy to identify the 5-carboxamide thiazole hydrazone scaffold ( 43 ) with potent sBCL-2 activity (IC ₅₀ 30 nM). Human BCL-XL potency (IC ₅₀ 13 nM) was inadvertently preserved during the optimization process. The lead analogues from this study exhibit on-target activity in model fibroblast cell lines dependent on either sBCL-2 or human BCL-XL for survival. Further optimization of the thiazole hydrazone class is required to exhibit activity in schistosomes and enhance the potential of this strategy for treating schistosomiasis.

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Organizational Affiliation: 
• The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.
Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.
La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia.
Olivia Newton-John Cancer Research Institute, Heidelberg 3084, Australia.
School of Cancer Medicine, La Trobe University, Melbourne 3086, Australia.
Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, Switzerland.
University of Basel, Basel 4001, Switzerland.
Department of Veterinary Biosciences, The University of Melbourne, Parkville 3010, Australia.

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.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 145.38 kDa 
• Atom Count: 7,819 
• Modeled Residue Count: 955 
• Deposited Residue Count: 1,260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2 protein	A, B, C, D, E, F	210	Schistosoma japonicum	Mutation(s): 0
UniProt
Find proteins for A0A4Z2CSJ3 (Schistosoma japonicum) Explore A0A4Z2CSJ3  Go to UniProtKB:  A0A4Z2CSJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N3C (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE C42 H45 Cl N6 O5 S2 HPLNQCPCUACXLM-PGUFJCEWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.021	α = 90
b = 67.789	β = 118.793
c = 100.907	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Smith, N.A., Smith, B.J., Lee, E.F., Colman, P.M., Fairlie, W.D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1135421
National Health and Medical Research Council (NHMRC, Australia)	Australia	1143974
National Health and Medical Research Council (NHMRC, Australia)	Australia	1002227

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description