54896-75-2Relevant academic research and scientific papers
Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors
Korczynska, Magdalena,Le, Daniel D.,Younger, Noah,Gregori-Puigjané, Elisabet,Tumber, Anthony,Krojer, Tobias,Velupillai, Srikannathasan,Gileadi, Carina,Nowak, Rados?aw P.,Iwasa, Eriko,Pollock, Samuel B.,Ortiz Torres, Idelisse,Oppermann, Udo,Shoichet, Brian K.,Fujimori, Danica Galoni?
, p. 1580 - 1598 (2016)
Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600a€ˉ000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ～3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.
Mechanism of Asymmetric Production of D-Amino Acids from the Corresponding Hydantoins by Pseudomonas sp.
Yokozeki, Kenzo,Kubota, Koji
, p. 721 - 728 (2007/10/02)
The mechanism of asymmetric production of D-amino acids from the corresponding hydantoins by Pseudomonas sp.AJ-11220 was examined by investigating the properties of the enzymes involved in the hydrolysis of DL-5-substituted hydantoins.The enzymatic production of D-amino acids from the corresponding hydantoins by Pseudomonas sp.AJ-11220 involved the following two successive reactions; the D-isomer specific hydrolysis, i.e., the ring opening of D-5-substituted hydantoins to D-form N-carbamyl amino acids by an enzyme, D-hydantoin hydrolase (D-HYD hydrolase), followed by the D-isomer specific hydrolysis, i.e., the cleavage of N-carbamyl-D-amino acids to D-amino acids by an enzyme, N-carbamyl-D-amino acid hydrolase (D-NCA hydrolase).L-5-Substituted hydantoins not hydrolyzed by D-HYD hydrolase were converted to D-form 5-substituted hydantoins through spontaneous racemization under the enzymatic reaction conditions.It was proposed that almost all of the DL-5-substituted hydantoins were stoichiometrically and directly converted to the corresponding D-amino acids through the successive reactions of D-HYD hydrolase and D-NCA hydrolase in parallel with the spontaneous racemization of L-5-substituted hydantoins to those of DL-form.
Mechanism of Asymmetric Production of L-Aromatic Amino Acids from the Corresponding Hydantoins by Flavobacterium sp.
Yokozeki, Kenzo,Hirose, Yoshiteru,Kubota, Koji
, p. 737 - 746 (2007/10/02)
The mechanism of asymmetric production of L-aromatic amino acids from the corresponding hydantoins by Flavobacterium sp.AJ-3912 was examined by investigating the properties of the enzymes involved in the hydrolysis of 5-substituted hydantoins corresponding to aromatic amino acids (AAH).The enzymatic hydrolysis of AAH by Flavobacterium sp.AJ-3912 consisted of the following two successive reactions; a hydrolytic ring opening reaction of DL-AAH to L- and D-form N-carbamyl aromatic amino acids (NCA), involving an enzyme (hydantoin hydrolase) followed by a hydrolytic cleaving reaction of the L-form NCA to L-aromatic amino acids involving another enzyme (N-carbamyl-L-aromatic amino acid hydrolase, abbreviated as L-NCA hydrolase).The ring opening reaction involving hydantoin hydrolase was not stereospecific, but the NCA cleaving reaction involving L-NCA hydrolase was completely L-specific.The pathway for the conversion of the by-produced D-form NCA to L-aromatic amino acids was as follows; conversion of D-form NCA to D-AAH through the reverse reaction of hydantoin hydrolase, and then conversion of the D-AAH to L-AAH through spontaneous racemization, followed by the successive hydrolysis of the L-AAH to L-aromatic amino acids by hydantoin hydrolase and L-NCA hydrolase.
