Takayoshi Kinoshita

Inhibitor-induced structural change of the active site of human poly(ADP-ribose) polymerase

The crystal structure of human recombinant poly(ADP‐ribose) polymerase (PARP) complexed with a potent inhibitor, FR257517, was solved at 3.0 Å resolution. The fluorophenyl part of the inhibitor induces an amazing conformational change in the active site of PARP by motion of the side chain of the amino acid, Arg878, which forms the bottom of the active site. Consequently, a corn‐shaped hydrophobic subsite, which consists of the side chains of Leu769, Ile879, Pro881, and the methylene chain of Arg878, newly emerges from the well‐known active site.

Discovery of quinazolinone and quinoxaline derivatives as potent and selective poly(ADP-ribose) polymerase-1/2 inhibitors.

Two classes of quinazolinone derivatives and quinoxaline derivatives were identified as potent and selective poly(ADP‐ribose) polymerase‐1 and 2 (PARP‐1) and (PARP‐2) inhibitors, respectively. In PARP enzyme assays using recombinant PARP‐1 and PARP‐2, quinazolinone derivatives displayed relatively high selectivity for PARP‐1 and quinoxaline derivatives showed superior selectivity for PARP‐2. SBDD analysis via a combination of X‐ray structural study and homology modeling suggested distinct interactions of inhibitors with PARP‐1 and PARP‐2. These findings provide a new structural framework for the design of selective inhibitors for PARP‐1 and PARP‐2.

Structure-based design of novel potent protein kinase CK2 (CK2) inhibitors with phenyl-azole scaffolds.

Protein kinase CK2 (CK2) is a ubiquitous serine/threonine protein kinase for hundreds of endogenous substrates. CK2 has been considered to be involved in many diseases, including cancers. Herein we report the discovery of a novel ATP-competitive CK2 inhibitor. Virtual screening of a compound library led to the identification of a hit 2-phenyl-1,3,4-thiadiazole compound. Subsequent structural optimization resulted in the identification of a promising 4-(thiazol-5-yl)benzoic acid derivative.

Crystallization and preliminary X-ray diffraction studies of catalase-peroxidase from Synechococcus PCC 7942

The recombinant catalase-peroxidase of Synechococcus PCC 7942 overexpressed in Escherichia coli was purified and crystallized by the hanging-drop vapour-diffusion method using sodium formate as a precipitant. The crystals belonged to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 109.3, c = 202.0 A. The calculated V(M) value based on a dimer in the asymmetric unit was 1.9 A(3) Da(-1). A native data set was collected to 2.3 A resolution from a frozen crystal using synchrotron radiation at SPring-8.

Discovery of FR166124, a novel water-soluble pyrazolo-[1,5-a]pyridine adenosine A1 receptor antagonist

Novel 3-(2-cycloalkyl and cycloalkenyl-3-oxo-2,3-dihydropyridazin-6-yl)-2-phenylpyrazo lo [1,5-a]-pyridines were synthesized and evaluated for their adenosine A1 receptor binding activities. In this series, FR166124 (3) was found to be the most potent and selective adenosine A1 receptor antagonist, and the double bond of the cyclohexenyl acetic acid group was essential for selectivity of A1 receptor binding. Furthermore, the solubility in water of the sodium salt of FR 166124 was high.

Crystal structure of human mono-phosphorylated ERK1 at Tyr204

Extracellular signal-regulated kinase (ERK) is a member of the MAP kinase family, and can regulate several cellular responses. The isoforms ERK1 and ERK2 have markedly similar amino acid sequences, but exhibit distinctive physiological functions. As well as ERK2, ERK1 was auto- and mono-phosphorylated at Tyr204 in the activation loop during Escherichia coli production, resulting in basal level activity, approximately 500-fold less compared with fully-active ERK1 dual-phosphorylated at Thr202 and Tyr204. Crystal structure demonstrated that the mono-phosphorylated ERK1 kinase possessed a novel conformation distinguishable from the un-phosphorylated (inactive) and the dual-phosphorylated (full-active) forms. The characteristic structural features in both the C-helix and the activation loop likely contribute to the basal activity of the mono-phosphorylated ERK1. The structural dissection of ERK1 compared to ERK2 suggests that the structural differences in the D-motif binding site and in the backside binding site are putative targets for development of selective ERK1/ERK2 inhibitors.

Asymmetric synthesis of FR165914: A novel β3-adrenergic agonist with a benzocycloheptene structure

Abstract The asymmetric synthesis of a novel β3-adrenergic agonist FR165194 is described. The critical steps involve preparation of an optically active amine via stereoselective reduction of a chiral imine prepared from α-methylbenzylamine and synthesis of a chiral epoxide via the Sharpless asymmetric dihydroxylation.

Palladium-Catalyzed asymmetric reduction of allylic esters with a new chiral monodentate ligand, 8-diphenylphosphino-8′-methoxy-1,1′-binaphthyl

Abstract A new chiral monodentate ligand, 8-diphenylphosphino-8′-methoxy-1,1′-binaphthyl (8-MeO-MOP), was used for palladium-catalyzed reduction of allylic carbonates with formic acid. Various methylcarbonates of 3,3′-disubstituted allylic alcohols were converted to the corresponding optically active 1-olefins with this ligand.

Structural insight into human CK2α in complex with the potent inhibitor ellagic acid

We determined the 2.35-A crystal structure of a human CK2 catalytic subunit (referred to as CK2alpha complexed with the ATP-competitive, potent CK2 inhibitor ellagic acid. The inhibitor binds to CK2alpha with a novel binding mode, including water-mediated hydrogen bonds. This structural information may support discovery of potent CK2 inhibitors.

Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method

Crystals of human triosephosphate isomerase with two crystal morphologies were obtained using the normal vapour-diffusion technique with identical crystallization conditions. One had a disordered plate shape and the crystals were hollow (crystal form 1). As a result, this form was very fragile, diffracted to 2.8 A resolution and had similar crystallographic parameters to those of the structure 1hti in the Protein Data Bank. The other had a fine needle shape (crystal form 2) and was formed more abundantly than crystal form 1, but was unsuitable for structure analysis. Since the normal vapour-diffusion method could not control the crystal morphology, gel-tube methods, both on earth and under microgravity, were applied for crystallization in order to control and improve the crystal quality. Whereas crystal form 1 was only slightly improved using this method, crystal form 2 was greatly improved and diffracted to 2.2 A resolution. Crystal form 2 contained a homodimer in the asymmetric unit, which was biologically essential. Its overall structure was similar to that of 1hti except for the flexible loop, which was located at the active centre Lys13.