Structural Basis for the Selective Binding of Inhibitors to 6‑Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli

• Published in: Journal of medicinal chemistry Vol. 59; no. 11; pp. 5248 - 5263
• Main Authors: Dennis, Matthew L, Pitcher, Noel P, Lee, Michael D, DeBono, Aaron J, Wang, Zhong-Chang, Harjani, Jitendra R, Rahmani, Raphaël, Cleary, Ben, Peat, Thomas S, Baell, Jonathan B, Swarbrick, James D
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 09.06.2016; Amer Chemical Soc
• Subjects: Binding Sites - drug effects; Chemistry, Medicinal; Crystallography, X-Ray; Diphosphotransferases - antagonists & inhibitors; Diphosphotransferases - metabolism; Dose-Response Relationship, Drug; Enzyme Inhibitors - chemical synthesis; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Escherichia coli - enzymology; Life Sciences & Biomedicine; Models, Molecular; Molecular Structure; Pharmacology & Pharmacy; Science & Technology; Staphylococcus aureus - enzymology; Structure-Activity Relationship; ANTIBACTERIAL DRUG DISCOVERY; TRIMETHOPRIM RESISTANCE; TERNARY COMPLEX; BIOSYNTHESIS PATHWAY; CRYSTAL-STRUCTURE; DIHYDROFOLATE-REDUCTASE; INFECTION; DIHYDROPTEROATE SYNTHASE; BISUBSTRATE ANALOG INHIBITORS; STRUCTURE-BASED DESIGN
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.6b00002

6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a member of the folate biosynthesis pathway found in prokaryotes and lower eukaryotes that catalyzes the pyrophosphoryl transfer from the ATP cofactor to a 6-hydroxymethyl-7,8-dihydropterin substrate. We report the chemical synthesis of a series of S-functionalized 8-mercaptoguanine (8MG) analogues as substrate site inhibitors of HPPK and quantify binding against the E. coli and S. aureus enzymes (EcHPPK and SaHPPK). The results demonstrate that analogues incorporating acetophenone-based substituents have comparable affinities for both enzymes. Preferential binding of benzyl-substituted 8MG derivatives to SaHPPK was reconciled when a cryptic pocket unique to SaHPPK was revealed by X-ray crystallography. Differential chemical shift perturbation analysis confirmed this to be a common mode of binding for this series to SaHPPK. One compound (41) displayed binding affinities of 120 nM and 1.76 μM for SaHPPK and EcHPPK, respectively, and represents a lead for the development of more potent and selective inhibitors of SaHPPK.