7JWV

Crystal structure of human ALDH1A1 bound to compound (R)-28

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


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Literature

Development of 2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one inhibitors of aldehyde dehydrogenase 1A (ALDH1A) as potential adjuncts to ovarian cancer chemotherapy.

Huddle, B.C., Grimley, E., Chtcherbinine, M., Buchman, C.D., Takahashi, C., Debnath, B., McGonigal, S.C., Mao, S., Li, S., Felton, J., Pan, S., Wen, B., Sun, D., Neamati, N., Buckanovich, R.J., Hurley, T.D., Larsen, S.D.

(2020) Eur J Med Chem 211: 113060-113060

  • DOI: https://doi.org/10.1016/j.ejmech.2020.113060
  • Primary Citation of Related Structures:  
    7JWS, 7JWT, 7JWU, 7JWV, 7JWW

  • PubMed Abstract: 

    • There is strong evidence that inhibition of one or more Aldehyde Dehydrogenase 1A (ALDH1A) isoforms may be beneficial in chemotherapy-resistant ovarian cancer and other tumor types. While many previous efforts have focused on development of ALDH1A1 selective inhibitors, the most deadly ovarian cancer subtype, high-grade serous (HGSOC), exhibits elevated expression of ALDH1A3 ...

    There is strong evidence that inhibition of one or more Aldehyde Dehydrogenase 1A (ALDH1A) isoforms may be beneficial in chemotherapy-resistant ovarian cancer and other tumor types. While many previous efforts have focused on development of ALDH1A1 selective inhibitors, the most deadly ovarian cancer subtype, high-grade serous (HGSOC), exhibits elevated expression of ALDH1A3. Herein, we report continued development of pan-ALDH1A inhibitors to assess whether broad spectrum ALDH1A inhibition is an effective adjunct to chemotherapy in this critical tumor subtype. Optimization of the CM39 scaffold, aided by metabolite ID and several new ALDH1A1 crystal structures, led to improved biochemical potencies, improved cellular ALDH inhibition in HGSOC cell lines, and substantial improvements in microsomal stability culminating in orally bioavailable compounds. We demonstrate that two compounds 68 and 69 are able to synergize with chemotherapy in a resistant cell line and patient-derived HGSOC tumor spheroids, indicating their suitability for future in vivo proof of concept experiments.

    Organizational Affiliation: 

    Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA. Electronic address: sdlarsen@med.umich.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinal dehydrogenase 1501Homo sapiensMutation(s): 1 
Gene Names: ALDH1A1, ALDC, ALDH1, PUMB1
EC: 1.2.1.19 (UniProt), 1.2.1.28 (UniProt), 1.2.1.3 (UniProt), 1.2.1.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00352 (Homo sapiens)
Explore P00352 
Go to UniProtKB:  P00352
PHAROS:  P00352
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00352
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VMJ (Subject of Investigation/LOI)
Query on VMJ
Download Ideal Coordinates CCD File 
C [auth A]5-[4-(hydroxymethyl)phenyl]-1-methyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
C21 H20 N4 O2 S
CXENUIKHQIZUDG-CQSZACIVSA-N		 Ligand Interaction
YB
Query on YB
Download Ideal Coordinates CCD File 
B [auth A]YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
VMJ Binding MOAD:  7JWV IC50: 600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.194α = 90
b = 109.194β = 90
c = 83.174γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214567

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release