7TEV

Human Ornithine Aminotransferase cocrystallized with its inhibitor, (3S,4R)-3-amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylate

Summary for 7TEV

• Entry DOI: 10.2210/pdb7tev/pdb
• Descriptor: Ornithine aminotransferase, mitochondrial, (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid (3 entities in total)
• Functional Keywords: human ornithine aminotransferase, hoat, oat, mechanism-based inhibitor, mbi, irreversible inhibitor, inactivator, transferase, transferase-inhibitor complex, transferase/inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 135745.89

Authors

Butrin, A.,Zhu, W.,Silverman, R.,Liu, D. (deposition date: 2022-01-05, release date: 2022-04-06, Last modification date: 2023-10-18)

Primary citation

Zhu, W.,Butrin, A.,Melani, R.D.,Doubleday, P.F.,Ferreira, G.M.,Tavares, M.T.,Habeeb Mohammad, T.S.,Beaupre, B.A.,Kelleher, N.L.,Moran, G.R.,Liu, D.,Silverman, R.B.
Rational Design, Synthesis, and Mechanism of (3 S ,4 R )-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase.
J.Am.Chem.Soc., 144:5629-5642, 2022

PubMed Abstract: Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that contains a similar active site to that of γ-aminobutyric acid aminotransferase (GABA-AT). Recently, pharmacological inhibition of hOAT was recognized as a potential therapeutic approach for hepatocellular carcinoma. In this work, we first studied the inactivation mechanisms of hOAT by two well-known GABA-AT inactivators ( and ). Inspired by the inactivation mechanistic difference between these two aminotransferases, a series of analogues were designed and synthesized, leading to the discovery of analogue as a highly selective and potent hOAT inhibitor. Intact protein mass spectrometry, protein crystallography, and dialysis experiments indicated that was converted to an irreversible tight-binding adduct () in the active site of hOAT, as was the unsaturated analogue (). The comparison of kinetic studies between and suggested that the active intermediate () was only generated in hOAT and not in GABA-AT. Molecular docking studies and p computational calculations highlighted the importance of chirality and the endocyclic double bond for inhibitory activity. The turnover mechanism of was supported by mass spectrometric analysis of dissociable products and fluoride ion release experiments. Notably, the stopped-flow experiments were highly consistent with the proposed mechanism, suggesting a relatively slow hydrolysis rate for hOAT. The novel second-deprotonation mechanism of contributes to its high potency and significantly enhanced selectivity for hOAT inhibition.

PubMed: 35293728
DOI: 10.1021/jacs.2c00924

Experimental method

X-RAY DIFFRACTION (1.91 Å)