9i3q

From Proteopedia

Crystal structure of DNPH1 bound by compound 2.

Structural highlights

9i3q is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.597Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNPH1_HUMAN Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases (By similarity).[HAMAP-Rule:MF_03036]

Publication Abstract from PubMed

DNPH1 is a nucleotide pool sanitizer that cleaves 5-hydroxymethyl-2-deoxyuridine-5-monophosphate (hmdUMP), preventing incorporation of the correspondent non-natural nucleotide into DNA. Recent findings have demonstrated that loss of DNPH1 could potentiate the sensitivity of PARP inhibitors in homologous recombination repair (HRR)-deficient cancers. We report the optimization of a non-nucleoside-based series of DNPH1 inhibitors. Starting from a weak compound 1 (binding affinity pIC(50) 4.7), we identified compound 38 as a very potent inhibitor of DNPH1 (pIC(50) 9.3) using DNPH1 X-ray structure-guided drug design. Compound 38 demonstrated target engagement of DNPH1 in the SUM149PT cell line (pIC(50) 7.2). Using this tool compound, we then report the in vitro pharmacology of a DNPH1 inhibitor in the BRCA1 mutant SUM149PT cell line.

Discovery and Optimization of a Non-Nucleoside-Based Series of Inhibitors of 2'-Deoxynucleoside 5'-Monophosphate Glycosidase (DNPH1).,Barlaam B, Alonso-Crisostomo L, Anderson NA, Argyrou A, Astles PC, Cadogan EB, Carlino L, Collie GW, Davies NL, Hall J, Kitching L, Li X, Michopoulos F, Milbradt AG, Nikkila J, Northall S, O'Connor MJ, Pei X, Shaw J, Slade D, Southgate H, Stead D, Stubbs CJ, Whitehurst BC, Xing B, Yuan Y, Zhou J J Med Chem. 2025 Nov 5. doi: 10.1021/acs.jmedchem.5c02356. PMID:41194588^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Barlaam B, Alonso-Crisostomo L, Anderson NA, Argyrou A, Astles PC, Cadogan EB, Carlino L, Collie GW, Davies NL, Hall J, Kitching L, Li X, Michopoulos F, Milbradt AG, Nikkilä J, Northall S, O'Connor MJ, Pei X, Shaw J, Slade D, Southgate H, Stead D, Stubbs CJ, Whitehurst BC, Xing B, Yuan Y, Zhou J. Discovery and Optimization of a Non-Nucleoside-Based Series of Inhibitors of 2'-Deoxynucleoside 5'-Monophosphate Glycosidase (DNPH1). J Med Chem. 2025 Nov 5. PMID:41194588 doi:10.1021/acs.jmedchem.5c02356