3KQW

Crystal Structure of hPNMT in Complex AdoHcy and 5-Chlorobenzimidazole

Summary for 3KQW

• Entry DOI: 10.2210/pdb3kqw/pdb
• Related: 3KPJ 3KPU 3KPV 3KPW 3KPY 3KQM 3KQO 3KQP 3KQQ 3KQS 3KQT 3KQV 3KQY 3KR0 3KR1 3KR2
• Descriptor: Phenylethanolamine N-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, 5-chloro-1H-benzimidazole, ... (4 entities in total)
• Functional Keywords: methyltransferase, fragment screening, catecholamine biosynthesis, s-adenosyl-l-methionine, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 64765.92

Authors

Drinkwater, N.,Martin, J.L. (deposition date: 2009-11-17, release date: 2010-09-29, Last modification date: 2023-09-06)

Primary citation

Drinkwater, N.,Vu, H.,Lovell, K.M.,Criscione, K.R.,Collins, B.M.,Prisinzano, T.E.,Poulsen, S.A.,McLeish, M.J.,Grunewald, G.L.,Martin, J.L.
Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors.
Biochem.J., 431:51-61, 2010

PubMed Abstract: CNS (central nervous system) adrenaline (epinephrine) is implicated in a wide range of physiological and pathological conditions. PNMT (phenylethanolamine N-methyltransferase) catalyses the final step in the biosynthesis of adrenaline, the conversion of noradrenaline (norepinephrine) to adrenaline by methylation. To help elucidate the role of CNS adrenaline, and to develop potential drug leads, potent, selective and CNS-active inhibitors are required. The fragment screening approach has advantages over other lead discovery methods including high hit rates, more efficient hits and the ability to sample chemical diversity more easily. In the present study we applied fragment-based screening approaches to the enzyme PNMT. We used crystallography as the primary screen and identified 12 hits from a small commercial library of 384 drug-like fragments. The hits include nine chemicals with two fused rings and three single-ring chemical systems. Eight of the hits come from three chemical classes: benzimidazoles (a known class of PNMT inhibitor), purines and quinolines. Nine of the hits have measurable binding affinities (~5-700 μM) as determined by isothermal titration calorimetry and all nine have ligand efficiencies of 0.39 kcal/mol per heavy atom or better (1 kcal≈4.184 kJ). We synthesized five elaborated benzimidazole compounds and characterized their binding to PNMT, showing for the first time how this class of inhibitors interact with the noradrenaline-binding site. Finally, we performed a pilot study with PNMT for fragment-based screening by MS showing that this approach could be used as a fast and efficient first-pass screening method prior to characterization of binding mode and affinity of hits.

PubMed: 20642456
DOI: 10.1042/BJ20100651

Experimental method

X-RAY DIFFRACTION (2.486 Å)