8T0T | pdb_00008t0t

Structure of Compound 4 bound to human ALDH1A1

• PDB DOI: https://doi.org/10.2210/pdb8T0T/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-01 Released: 2024-05-01 
• Deposition Author(s): Hurley, T.D.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.240 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Development of substituted benzimidazoles as inhibitors of human aldehyde dehydrogenase 1A isoenzymes.

Takahashi, C., Chtcherbinine, M., Huddle, B.C., Wilson, M.W., Emmel, T., Hohlman, R.M., McGonigal, S., Buckanovich, R.J., Larsen, S.D., Hurley, T.D.

(2024) Chem Biol Interact 391: 110910-110910

• PubMed: 38364885 
• DOI: https://doi.org/10.1016/j.cbi.2024.110910
• Primary Citation Related Structures: 
  8T0N, 8T0T


• PubMed Abstract: 
  

  Aldehyde dehydrogenase 1A (ALDH1A) isoforms may be a useful target for overcoming chemotherapy resistance in high-grade serous ovarian cancer (HGSOC) and other solid tumor cancers. However, as different cancers express different ALDH1A isoforms, isoform selective inhibitors may have a limited therapeutic scope. Furthermore, resistance to an ALDH1A isoform selective inhibitor could arise via induction of expression of other ALDH1A isoforms. As such, we have focused on the development of pan-ALDH1A inhibitors, rather than on ALDH1A isoform selective compounds. Herein, we report the development of a new group of pan-ALDH1A inhibitors to assess whether broad spectrum ALDH1A inhibition is an effective adjunct to chemotherapy in HGSOC. Optimization of the CM10 scaffold, aided by ALDH1A1 crystal structures, led to improved biochemical potencies, improved cellular efficacy as demonstrated by reduction in ALDEFLUOR signal in HGSOC cells, and substantial improvements in liver microsomal stability. Based on this work we identified two compounds 17 and 25 suitable for future in vivo proof of concept experiments.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA.
Department of Obstetrics, Gynecology, and Reproductive Sciences, the Magee-Women's Research Institute, Pittsburgh, PA 15213, USA.
Department of Obstetrics, Gynecology, and Reproductive Sciences, the Magee-Women's Research Institute, Pittsburgh, PA 15213, USA; Division of Hematology-Oncology, Departments of Internal Medicine and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh Medical Center and the Magee-Women's Research Institute, Pittsburgh, PA, 15213, USA.
Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 55.61 kDa 
• Atom Count: 4,172 
• Modeled Residue Count: 494 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase 1A1	A	501	Homo sapiens	Mutation(s): 0  Gene Names: ALDH1A1, ALDC, ALDH1, PUMB1 EC: 1.2.1 (PDB Primary Data), 1.2.1.36 (PDB Primary Data), 1.2.1.19 (UniProt), 1.2.1.28 (UniProt), 1.2.1.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00352 (Homo sapiens) Explore P00352  Go to UniProtKB:  P00352
PHAROS:  P00352 GTEx:  ENSG00000165092

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y6E (Subject of Investigation/LOI)	C [auth A]	1-(4-{6-fluoro-3-[4-(methanesulfonyl)piperazine-1-carbonyl]quinolin-4-yl}phenyl)cyclopropane-1-carbonitrile C25 H23 F N4 O3 S WIXZFNIBMHEUJH-UHFFFAOYSA-N
YB	B [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.240 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.236	α = 90
b = 109.236	β = 90
c = 83.245	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Hurley, T.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA214567

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release