Department of Pharmaceutical Sciences Lecturer
Last Updated :2023/12/05

Researcher Information


J-Global ID

Research Interests

  • 物理化学   フラグメント分子軌道法   計算化学   SBDD   分子設計   分子動力学   構造活性相関   

Research Areas

  • Life sciences / Pharmaceuticals - analytical and physicochemistry / Computational Chemistry

Academic & Professional Experience

  • 2018/04 - Today  Kindai UniversityFaculty of Pharmacy講師
  • 2013/04 - 2018/03  Kindai UniversityFaculty of Pharmacy助教
  • 2008/04 - 2013/03  Kindai UniversityFaculty of Pharmacy助手
  • 2007/04 - 2008/03  株式会社菱化システム計算科学部

Published Papers

  • Keiji Nishiwaki; Shinya Nakamura; Kenji Yoshioka; Eri Nakagawa; Shiori Nakatani; Masato Tsuyuguchi; Takayoshi Kinoshita; Isao Nakanishi
    Chemical and Pharmaceutical Bulletin Pharmaceutical Society of Japan 71 (7) 558 - 565 0009-2363 2023/07 [Refereed]
  • Tatsuo Akaki; Shinya Nakamura; Keiji Nishiwaki; Isao Nakanishi
    Chemical and Pharmaceutical Bulletin Pharmaceutical Society of Japan 71 (4) 299 - 306 0009-2363 2023/02 [Refereed]
  • Shinya Nakamura; Tatsuo Akaki; Keiji Nishiwaki; Midori Nakatani; Yuji Kawase; Yuki Takahashi; Isao Nakanishi
    Journal of Computational Chemistry Wiley 44 (7) 824 - 831 0192-8651 2022/11 [Refereed]
  • Asaka Ikeda; Masato Tsuyuguchi; Daisuke Kitagawa; Masaaki Sawa; Shinya Nakamura; Isao Nakanishi; Takayoshi Kinoshita
    Biochemical and biophysical research communications 630 30 - 35 2022/11 
    Casein kinase 2 (CK2) is a vital protein kinase that consists of two catalytic subunits (CK2α1 and/or CK2α2) and two regulatory subunits (CK2β). CK2α1 is a drug target for nephritis and cancers, while CK2α2 is a serious off-target because its inhibition causes testicular toxicity. High similarity between the isozymes CK2α1 and CK2α2 make it difficult to design CK2α1-specific inhibitors. Herein, the crystal structures of CK2α1 and CK2α2 complexed with a 3-amino-pyrazole inhibitor revealed the remarkable differences in the protein-inhibitor interaction modes. This inhibitor bound to the ATP binding sites of both isozymes in apparently distinct orientations. In addition, another molecule of this inhibitor bound to CK2α1, but not to CK2α2, at the CK2β protein-protein interface. Binding energy calculations and biochemical experiments suggested that this inhibitor possesses the conventional ATP-competitive characteristics with moderate allosteric function in a molecular glue mechanism. These results will assist the potential design of potent and selective CK2α1 inhibitors.
  • Katsuki Takashima; Mika Sakano; Eri Kinouchi; Shinya Nakamura; Shinsuke Marumoto; Fumihiro Ishikawa; Kiyofumi Ninomiya; Isao Nakanishi; Toshio Morikawa; Genzoh Tanabe
    Bioorganic & medicinal chemistry letters 33 127751 - 127751 2021/02 
    Four chain-extended analogs (12a-12d) and two related de-O-sulfonated analogs (13a and 13c) by introducing alkyl groups (a: R = C3H7, b R = C6H13, c: R = C8H17, d: R = C10H21) to the side chains of salacinol (1), a natural α-glucosidase inhibitor from Ayurvedic traditional medicine "Salacia", were synthesized. The α-glucosidase inhibitory activities of all the synthesized analogs were evaluated in vitro. Against human intestinal maltase, the inhibitory activities of 12a and 13a with seven-carbon side chain were equal to that of 1. In contrast, analogs (12b-12d, and 13c) exhibited higher level of inhibitory activity against the same enzyme than 1 and had equal or higher potency than those of the clinically used anti-diabetics, voglibose, acarbose, and miglitol. Thus, elongation of the side chains of 1 was effective for specifically increasing the inhibitory activity against human intestinal maltase.
  • Fumihiro Ishikawa; Aiko Hirano; Yuuto Yoshimori; Kana Nishida; Shinya Nakamura; Katsuki Takashima; Shinsuke Marumoto; Kiyofumi Ninomiya; Isao Nakanishi; Weijia Xie; Toshio Morikawa; Osamu Muraoka; Genzoh Tanabe
    RSC Advances Royal Society of Chemistry ({RSC}) 11 (6) 3221 - 3225 2046-2069 2021 

    Salacinol-type α-glucosidase inhibitors are ligand-compatible with the GH 31 family. Salacinol and its 3′-O-benzylated analogs inhibit human lysosomal α-glucosidase at submicromolar levels.

  • Fumihiro Ishikawa; Hinano Kitayama; Shinya Nakamura; Katsuki Takashima; Isao Nakanishi; Genzoh Tanabe
    Chemical & pharmaceutical bulletin 69 (2) 222 - 225 2021 
    The gatekeeping adenylation (A) domain of the non-ribosomal peptide synthetase (NRPS) selectively incorporates specific proteinogenic/non-proteinogenic amino acid into a growing peptide chain. The EntE of the enterobactin NRPS is a discrete aryl acid A-domain with 2,3-dihydroxybenzoic acid (DHB) substrate specificity. Reprogrammed EntE N235G variant possesses an enlarged substrate recognition site, and is capable of accepting non-native aryl acids. Biochemical characterization of this unique substrate recognition site should provide a better understanding of activi-site microenvironments. Here, we synthesized a non-hydrolysable adenylate analogue with 2-aminobenzoic acid (2-ABA), 3-aminobenzoic acid (3-ABA), and 4-aminobenzoic acid (4-ABA) and used them to calculate the apparent inhibition constants (Kiapp.). Dose-response experiments using 3-ABA-sulfamoyladenosine (AMS) provided Kiapp. values of 596 nM for wild-type EntE and 2.4 nM for the N235G variants. These results suggest that 3-amino group of benzoic acid plays an important role in substrate recognition by the N235G variant. These findings would help designing aryl acid substrates with substituents at the 2- and 3-positions.
  • Fumihiro Ishikawa; Maya Nohara; Shinya Nakamura; Isao Nakanishi; Genzoh Tanabe
    Biochemistry 59 (4) 351 - 363 2020/01 [Refereed]
    Aryl acids are most commonly found in iron-scavenging siderophores but are not limited to them. The nonribosomal peptide synthetase (NRPS) codes of aryl acids remain poorly elucidated relative to those of amino acids. Here, we defined more precisely the role of active-site residues in aryl acid adenylation domains (A-domains) by gradually grafting the NRPS codes used for salicylic acid (Sal) into an archetypal aryl acid A-domain, EntE [specific for the substrate 2,3-dihydroxybenzoic acid (DHB)]. Enzyme kinetics and modeling studies of these EntE variants demonstrated that the NRPS code residues at positions 236, 240, and 339 collectively regulate the substrate specificity toward DHB and Sal. Furthermore, the EntE variants exhibited the ability to activate the non-native aryl acids 3-hydroxybenzoic acid, 3-aminobenzoic acid, 3-fluorobenzoic acid, and 3-chlorobenzoic acid. These studies enhance our knowledge of the NRPS codes of aryl acids and could be exploited to reprogram aryl acid A-domains for non-native aryl acids.
  • Fumihiro Ishikawa; Akimasa Miyanaga; Hinano Kitayama; Shinya Nakamura; Isao Nakanishi; Fumitaka Kudo; Tadashi Eguchi; Genzoh Tanabe
    Angewandte Chemie Wiley 131 (21) 6980  2019/05 [Refereed]
  • Ishikawa F; Miyanaga A; Kitayama H; Nakamura S; Nakanishi I; Kudo F; Eguchi T; Tanabe G
    Angewandte Chemie (International ed. in English) 58 (21) 6906 - 6910 1433-7851 2019/04 [Refereed]
    Adenylation (A) domains act as the gatekeepers of non-ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron-chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A-domains. We show that a single asparagine-to-glycine mutation in an aryl acid A-domain leads to an enzyme that tolerates a wide range of non-native aryl acids. The engineered catalyst is capable of activating non-native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild-type enzyme was observed toward these substrates. Co-crystal structures with non-hydrolysable aryl-AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.
  • Nishiwaki K; Ohigashi K; Deguchi T; Murata K; Nakamura S; Matsuda H; Nakanishi I
    Chemical & pharmaceutical bulletin 66 (7) 741 - 747 0009-2363 2018/07 [Refereed]
    Hydroxychavicol (HC), which is obtained from the leaves of Piper betle LINN. (Piperaceae), inhibits xanthine oxidase (XO) with an IC50 value of 16.7 µM, making it more potent than the clinically used allopurinol (IC50=30.7 µM). Herein, a structure-activity relationship analysis of the polar part analogs of HC was conducted and an inhibitor was discovered with a potency 13 times that of HC. Kinetic studies have revealed that HC and its active analog inhibit XO in an uncompetitive manner. The binding structure prediction of these inhibitor molecules to the XO complex with xanthine suggested that both compounds (HC and its analog) could simultaneously form hydrogen bonds with xanthine and XO.
  • Miyagawa Takashi; Inuki Shinsuke; Honda Maho; Nakamura Shinya; Nakanishi Isao; Fujii Nobutaka; Oishi Shinya; Ohno Hiroaki
    TETRAHEDRON 74 (15) 1802 - 1809 0040-4020 2018/04 [Refereed]
  • Nakamura S; Kitayoshi H; Nakanishi I
    Journal of Computer Aided Chemistry Division of Chemical Information and Computer Sciences The Chemical Society of Japan 18 149 - 158 2017/10 [Refereed]
    Solvent dipole ordering virtual screening (SDO-VS) is a virtual screening method that focuses on the shape of the SDO region at the binding site of the protein. In SDO-VS, pseudo molecules (PMs) are generated to reproduce the shape of the SDO region. Compounds that have shapes (or volumes) similar to those of the PMs are then screened from a 3D structure database. The original implementation of SDO-VS involved PMs with only sp3-hybridized carbon atoms. However, utilization of sp2- and sp-hybridized atoms and/or small molecular fragments, in addition to sp3-hybridized atoms, is expected to provide more efficient screening. To this end, this study investigated the effect of sp3-, sp2-, and sp-hybridized atoms and phenyl rings as fragments for PM generation in the SDO-VS method. The screening efficiencies were compared with the original method for several drug target proteins. Overall, this new method improved screening efficiencies, as measured by the area under the curve of the corresponding receiver operating characteristic plots.
  • Shinya Nakamura; Rie Ohmura; Isao Nakanishi
    Chem-Bio Informatics Journal Chem-Bio Informatics Society 17 93 - 102 1347-0442 2017/09 [Refereed]
    In peptide vaccine therapy, a peptide with high affinity for human leukocyte antigen (HLA), is important to stimulate the immune system to kill cancer cells. Several methods to predict HLA–peptide binding have been reported, but most of them rely on informatics to analyze the amino acid sequence of the peptide. Although intermolecular-interaction-based analysis is expected to improve prediction accuracy, such a method generally involves a high computational cost. Therefore, comparative binding energy (COMBINE) analysis, a 3D-quantitative structure–activity relationship method, combined with a rapidly implemented protein modeling method, was applied to solve this problem. The new method enabled quick evaluation of peptide affinity predictions with accuracy beyond a statistical method. In addition, several amino acid residues of HLA, which are known to be important for peptide binding, could be identified.
  • Nakamura S; Shimada K; Tanabe G; Muraoka O; Nakanishi I
    Open Journal of Medicinal Chemistry 7 (2) 19 - 28 2017/06 [Refereed]
  • Hiroaki Ohno; Maho Honda; Naoka Hamada; Jun Miyagaki; Akira Iwata; Kazuhiro Otsuki; Toru Maruyama; Shinya Nakamura; Isao Nakanishi; Shinsuke Inuki; Nobutaka Fujii; Shinya Oishi
    BIOORGANIC & MEDICINAL CHEMISTRY PERGAMON-ELSEVIER SCIENCE LTD 25 (12) 3046 - 3052 0968-0896 2017/06 [Refereed]
    We recently reported that 4-epi-jaspine B exhibits potent inhibitory activity towards sphingosine kinases (SphKs). In this study, we investigated the effects of modifying the 2-alkyl group, as well as the functional groups on the THE ring of 4-epi-jaspine B using a diversity-oriented synthesis approach based on a late stage cross metathesis reaction. The introduction of a p-phenylene tether to the alkyl group was favored in most cases, whereas the replacement of a carbon atom with an oxygen atom led to a decrease in the inhibitory activity. Furthermore, the introduction of a bulky alkyl group at the terminus led to a slight increase in the inhibitory activity of this series towards SphKs compared with 4-epi-jaspine B (the Q values of compound 13 for SphK1 and SphK2 were 0.2 and 0.4, respectively). Based on this study, we identified two isoform selective inhibitors, including the m-phenylene derivative 4 [IC50 (SphK1) >= 30 mu M; IC50 (SphK2) = 2.2 mu M] and the methyl ether derivative 22 [IC50 (SphK1) = 4.0 mu M; IC50 (SphK2) >= 30 mu m]. (C) 2017 Elsevier Ltd. All rights reserved.
  • Chanikarn Chantarasrivong; Akiharu Ueki; Ryutaro Ohyama; Johan Unga; Shinya Nakamura; Isao Nakanishi; Yuriko Higuchi; Shigeru Kawakami; Hiromune Ando; Akihiro Imamura; Hideharu Ishida; Fumiyoshi Yamashita; Makoto Kiso; Mitsuru Hashida
    MOLECULAR PHARMACEUTICS AMER CHEMICAL SOC 14 (5) 1528 - 1537 1543-8384 2017/05 [Refereed]
    Sialyl LewisX (sLeX) is a natural ligand of E-selectin that is overexpressed by inflamed and tumor endothelium. Although sLeX is a potential ligand for drug targeting, synthesis of the tetrasaccharide is complicated with many reaction steps. In this study, structurally simplified novel sLeX analogues were designed and linked with 1,2-distearoylsn-glycero-3-phosphoethanolamine-polyethylene glycol-2000 (DSPE-PEG) for E-selectin-mediated liposomal delivery. The sLeX structural simplification strategies include (1) replacement of the Gal-G1cNAc disaccharide unit with lactose to reduce many initial steps and (2) substitution of neuraminic acid with a negatively charged group, i.e., 3'-sulfo, 3'-carboxymethyl (3'-CM), or 3'-(1-carboxy)ethyl (3'-CE). While all the liposomes developed were similar in particle size and charge, the 3'-CE sLeX mimic liposome demonstrated the highest uptake in inflammatory cytokine-treated human umbilical vein endothelial cells (HUVECs), being even more potent than native sLeX-decorated liposomes. Inhibition studies using antiselectin antibodies revealed that their uptake was mediated primarily by overexpressed E-sdectin on inflamed HUVECs. Molecular dynamics simulations were performed to gain mechanistic insight into the E-selectin binding differences among native and mimic sLeX. The terminally branched methyl group of the 3'-CE sLeX mimic oriented and faced the bulk hydrophilic solution during. E-selectin binding. Since this state is entropically unfavorable, the 3'-CE sLeX mimic molecule might be pushed toward the binding, pocket of E-selectin by a hydrophobic effect, leading to a higher probability of hydrogen-bond' formation than native sLeX and the 3'-CM sLeX mimic. This corresponded with the fact that the 3'-CE sLeX mimic liposome exhibited much greater uptake than the 3'-CM sLeX mimic liposome.
  • Genzoh Tanabe; Weijia Xie; Gorre Balakishan; Mumen F. A. Amer; Nozomi Tsutsui; Haruka Takemura; Shinya Nakamura; Junji Akaki; Kiyofumi Ninomiya; Toshio Morikawa; Isao Nakanishi; Osamu Muraoka
    BIOORGANIC & MEDICINAL CHEMISTRY PERGAMON-ELSEVIER SCIENCE LTD 24 (16) 3705 - 3715 0968-0896 2016/08 [Refereed]
    Using an in silico method, seven analogs bearing hydrophobic substituents (8a: Me, 8b: Et, 8c: n-Pent, 8d: n-Hept, 8e: n-Tridec, 8f: isoBu and 8g: neoPent) at the 3'-O-position in salacinol (1), a highly potent natural alpha-glucosidase inhibitor from Ayurvedic traditional medicine 'Salacia', were designed and synthesized. In order to verify the computational SAR assessments, their alpha-glucosidase inhibitory activities were evaluated in vitro. All analogs (8a-8g) exhibited an equal or considerably higher level of inhibitory activity against rat small intestinal alpha-glucosidases compared with the original sulfonate (1), and were as potent as or higher in potency than the clinically used anti-diabetics, voglibose, acarbose or miglitol. Their activities against human maltase exhibited good relationships to the results obtained with enzymes of rat origin. Among the designed compounds, the one with a 3'-O-neopentyl moiety (8g) was most potent, with an approximately ten fold increase in activity against human maltase compared to 1. (C) 2016 Elsevier Ltd. All rights reserved.
  • Hiroaki Ohno; Daiki Minamiguchi; Shinya Nakamura; Keito Shu; Shiho Okazaki; Maho Honda; Ryosuke Misu; Hirotomo Moriwaki; Shinsuke Nakanishi; Shinya Oishi; Takayoshi Kinoshita; Isao Nakanishi; Nobutaka Fujii
    BIOORGANIC & MEDICINAL CHEMISTRY PERGAMON-ELSEVIER SCIENCE LTD 24 (5) 1136 - 1141 0968-0896 2016/03 [Refereed]
    Two classes of modified analogs of 4-(thiazol-5-yl)benzoic acid-type CK2 inhibitors were designed. The azabenzene analogs, pyridine-and pyridazine-carboxylic acid derivatives, showed potent protein kinase CK2 inhibitory activities [IC50 (CK2 alpha) = 0.014-0.017 mu M; IC50 (CK2 alpha') = 0.0046-0.010 mu M]. Introduction of a 2-halo- or 2-methoxy-benzyloxy group at the 3-position of the benzoic acid moiety maintained the potent CK2 inhibitory activities [IC50 (CK2 alpha) = 0.014-0.016 mu M; IC50 (CK2 alpha') = 0.0088-0.014 mu M] and led to antiproliferative activities [CC50 (A549) = 1.5-3.3 mu M] three to six times higher than those of the parent compound. (C) 2016 Elsevier Ltd. All rights reserved.
  • Hiromasa Kaneko; Shinya Nakamura; Norihito Kawahsita
  • 中村真也
    CICSJ Bulletin (Web) 公益社団法人 日本化学会・情報化学部会 34 (1) 17‐20(J‐STAGE) - 17 1347-2283 2016 [Refereed]
  • N. Kawashita; H. Yamasaki; T. Miyano; K. Kawai; Y. Sakae; T. Ishikawa; K. Mori; S. Nakamura; H. Kaneko
    J. Comput. Aided Chem. Division of Chemical Information and Computer Sciences The Chemical Society of Japan 16 15 - 29 1345-8647 2015/10 [Refereed]
    We have reviewed chemoinformatics approaches for drug discovery such as aromatic interactions, aromatic clusters, structure generation, virtual screening, de novo design, evolutionary algorithm, inverse-QSPR/QSAR, Monte Carlo, molecular dynamics, fragment molecular orbital method and matched molecular pair analysis from the viewpoint of young researchers. We intend to introduce various fields of chemoinformatics for non-expert researchers. The structure of this review is given as follows: 1. Introduction, 2. Analysis of Aromatic Interactions, 2.1 Aromatic Interactions, 2.2 Aromatic Clusters, 3. Ligand Based Structure Generation, 3.1 Virtual Screening, 3.2 De Novo Ligand Design, 3.3 Combinatorial Explosion, 3.4 Inverse-QSPR/QSAR, 4. Trends in Chemoinformatics-Based De Novo Drug Design, 5. Conformational Search Method Using Genetic Crossover for Bimolecular Systems, 6. Interaction Analysis using Fragment Molecular Orbital Method for Drug Discovery, 7. Matched Molecular Pair Analysis and SAR Analysis by Fragment Molecular Orbital Method, 8. Chemoinformatics Approach in Pharmaceutical Processes, 9. Conclusion.
  • Isao Nakanishi; Katsumi Murata; Naoya Nagata; Masakuni Kurono; Takayoshi Kinoshita; Misato Yasue; Takako Miyazaki; Yoshinori Takei; Shinya Nakamura; Atsushi Sakurai; Nobuko Iwamoto; Keiji Nishiwaki; Tetsuko Nakaniwa; Yusuke Sekiguchi; Akira Hirasawa; Gozoh Tsujimoto; Kazuo Kitaura
    Novel protein kinase CK2 inhibitors were identified using the solvent dipole ordering virtual screening method. A total of 26 compounds categorized in 15 distinct scaffold classes inhibited greater than 50% of enzyme activity at 50 mu M, and eight exhibited IC50 values less than 10 mu M. Most of the identified compounds are lead-like and dissimilar to known inhibitors. The crystal structures of two of the CK2 complexes revealed the high accuracy of the predicted binding modes. (C) 2015 Elsevier Masson SAS. All rights reserved.
  • Tomoki Takeuchi; Shinya Oishi; Masato Kaneda; Ryosuke Misu; Hiroaki Ohno; Jun-ichi Sawada; Akira Asai; Shinya Nakamura; Isao Nakanishi; Nobutaka Fujii
    BIOORGANIC & MEDICINAL CHEMISTRY PERGAMON-ELSEVIER SCIENCE LTD 22 (12) 3171 - 3179 0968-0896 2014/06 [Refereed]
    Structure-activity relationship studies of diaryl amine-type KSP inhibitors were carried out. Diaryl amine derivatives with a pyridine ring or urea group were less active when compared with the parent carboline and carbazole derivatives. Optimization studies of a lactam-fused diphenylamine-type KSP inhibitor revealed that the aniline NH group and 3-CF3 phenyl group were indispensable for potent KSP inhibition. Modification with a seven-membered lactam-fused phenyl group and a 4-(trifluoromethyl)pyridin-2-yl group improved aqueous solubility while maintaining potent KSP inhibitory activity. From these studies, we identified novel diaryl amine-type KSP inhibitors with a favorable balance of potency and solubility. (C) 2014 Elsevier Ltd. All rights reserved.
  • Tomoki Takeuchi; Shinya Oishi; Masato Kaneda; Hiroaki Ohno; Shinya Nakamura; Isao Nakanishi; Masayoshi Yamane; Jun-ichi Sawada; Akira Asai; Nobutaka Fujii
    ACS MEDICINAL CHEMISTRY LETTERS AMER CHEMICAL SOC 5 (5) 566 - 571 1948-5875 2014/05 [Refereed]
    Diaryl amine derivatives have been designed and synthesized as novel kinesin spindle protein (KSP) inhibitors based on planar carbazole-type KSP inhibitors with poor aqueous solubility. The new generation of inhibitors was found to show comparable inhibitory activity and high selectivity for KSP, and this was accompanied with improved solubility. Kinetic analysis and molecular modeling studies suggested that these inhibitors work in an ATP-competitive manner via binding to the secondary allosteric site formed by alpha 4 and alpha 6 helices of KSP. Comparative structural investigations on a series of compounds revealed that the higher solubility of diaryl amine-type inhibitors was attributed to fewer van der Waals interactions in the crystal packing and the hydrogen-bond acceptor nitrogen of the aniline moiety for favorable solvation.
  • Kengo Miyamoto; Fumihiro Ishikawa; Shinya Nakamura; Yutaka Hayashi; Isao Nakanishi; Hideaki Kakeya
    BIOORGANIC & MEDICINAL CHEMISTRY PERGAMON-ELSEVIER SCIENCE LTD 22 (8) 2517 - 2528 0968-0896 2014/04 [Refereed]
    A putative 7-dimethylallyl tryptophan synthase (DMATS) gene from a fungal Neosartorya sp. was cloned and overexpressed as a soluble His(6)-fusion protein in Escherichia coli. The enzyme was found to catalyze the prenylation of L-tryptophan at the C7 position of the indole moiety in the presence of dimethylallyl diphosphate; thus, it functions as a 7-DMATS. In this study, we describe the biochemical characterization of 7-DMATS from Neosartorya sp., referred to as 7-DMATS(Neo), and the structural basis of the regioselective prenylation of L-tryptophan at the C7 position by comparison of the three-dimensional structural models of 7-DMATS(Neo) with FgaPT2 (4-DMATS) from Aspergillus fumigatus. (C) 2014 Elsevier Ltd. All rights reserved.
  • Takayoshi Kinoshita; Tetsuko Nakaniwa; Yusuke Sekiguchi; Yuri Sogabe; Atsushi Sakurai; Shinya Nakamura; Isao Nakanishi
    JOURNAL OF SYNCHROTRON RADIATION WILEY-BLACKWELL 20 (Pt 6) 974 - 979 0909-0495 2013/11 [Refereed]
    The Ser/Thr kinase CK2 consists of two catalytic subunits (CK2 alpha) and a dimer of the regulatory subunits (CK2 beta), and is a ubiquitous enzyme that regulates growth, proliferation and the survival of cells. CK2 is a remarkable drug target for potentially treating a wide variety of tumours and glomerulonephritis. The purified CK2 alpha protein was crystallized using ethylene glycol as a precipitant. The crystal structure of CK2 alpha with 21 loci of alternative conformations, including a niacin, 19 ethylene glycols and 346 waters, was determined at 1.06 angstrom resolution to an R-work of 14.0% (R-free = 16.5%). The alternative ensemble in the internal hydrophobic core underpins the plasticity of the alpha D-helix responsible for the regulation of ATP/GTP binding. The clear density map indicates that a niacin molecule, contained in the Escherichia coli culture medium, binds to the ATP binding site. An ethylene glycol molecule binds in the hydrophobic pocket lateral to the alpha D-helix forming the rim of the active site. The other ethylene glycol molecules occupy physiologically significant sites, including the CK2 beta binding interface and substrate binding site, as well as the gap in the crystal packing. Together with water molecules in the active site, these structural insights should facilitate drug discovery.
  • Genzoh Tanabe; Kanjyun Matsuoka; Masahiro Yoshinaga; Weijia Xie; Nozomi Tsutsui; Mumen F. A. Amer; Shinya Nakamura; Isao Nakanishi; Xiaoming Wu; Masayuki Yoshikawa; Osamu Muraoka
    BIOORGANIC & MEDICINAL CHEMISTRY PERGAMON-ELSEVIER SCIENCE LTD 20 (21) 6321 - 6334 0968-0896 2012/11 [Refereed]
    To examine the role of the side chain of kotalanol (2), a potent natural alpha-glucosidase inhibitor isolated from Salacia reticulata, on inhibitory activity, four diastereomers (11a-11d) with reversed configuration (S) at the C-4' position in the side chain were synthesized and evaluated. Two of the four (11b and 11d) significantly lost their inhibitory activity against both maltase and sucrase, while the other two (11a and 11c) sustained the inhibitory activity to a considerable extent, showing distinct activity in response to the change of stereochemistry of the hydroxyls at the 5' and 6' positions. Different activities were rationalized with reference to in silico docking studies on these inhibitors with hNtMGAM. Against isomaltase, all four analogs showed potent inhibitory activity as well as 2, and 11b and 11d exhibited enzyme selectivity. (C) 2012 Elsevier Ltd. All rights reserved.
  • Nakamura S; Takahira K; Tanabe G; Muraoka O; Nakanishi I
    Open Journal of Medicinal Chemistry 2 (3) 50 - 60 2012/09
  • Zengye Hou; Isao Nakanishi; Takayoshi Kinoshita; Yoshinori Takei; Misato Yasue; Ryosuke Misu; Yamato Suzuki; Shinya Nakamura; Tatsuhide Kure; Hiroald Ohno; Katsumi Murata; Kazuo Kitaura; Akira Hirasawa; Gozoh Tsujimoto; Shinya Oishi; Nobutaka Fujii
    JOURNAL OF MEDICINAL CHEMISTRY AMER CHEMICAL SOC 55 (6) 2899 - 2903 0022-2623 2012/03 [Refereed]
    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.
  • Tanabe Genzoh; Yoshikawa Masayuki; Muraoka Osamu; Nakamura Shinya; Yoshinaga Masahiro; Tsutsui Nozomi; Balakishan Gorre; Akaki Junji; Morikawa Toshio; Ninomiya Kiyofumi; Nakanishi Isao
    Symposium on the Chemistry of Natural Products, symposium papers 天然有機化合物討論会実行委員会 54 (0) 285 - 290 2012 
    To develop more potent α-glucosidase inhibitors whose seed-compound is salacinol (1), a potent natural α-glucosidase inhibitor isolated from Salacia reticulata of Ayurvedic traditional medicine, a series of 3'-O-benzylated analogs of 1 were designed with the aid of in silico method. Intensive docking studies proposed several promising compounds. To verify the computational SAR assessments, designed derivatives were synthesized and evaluated in vitro. Their α-glucosidase inhibitory activities against rat intestinal α-glucosidases were so potent as were expected by the docking studies, and all the compounds showed superior inhibitory activities to the original sulfonium sulfate (1). Among the sulfonium salts designed, one with 3'-O-(ortho-nitrobenzyl) moiety (8k) was found to be the most potent, and ca. forty times as potent as 1, the compound being the strongest inhibitor among the sulfonium type inhibitors synthesized so far. [chemical formula]
  • Genzoh Tanabe; Shinya Nakamura; Nozomi Tsutsui; Gorre Balakishan; Weijia Xie; Satoshi Tsuchiya; Junji Akaki; Toshio Morikawa; Kiyofumi Ninomiya; Isao Nakanishi; Masayuki Yoshikawa; Osamu Muraoka
    CHEMICAL COMMUNICATIONS ROYAL SOC CHEMISTRY 48 (69) 8646 - 8648 1359-7345 2012 [Refereed]
    With the aid of an in silico method, alpha-glucosidase inhibitors with far more potent activities than salacinol (1), a potent natural alpha-glucosidase inhibitor isolated from an Ayurvedic traditional medicine Salacia reticulata, have been developed.
  • Takayoshi Kinoshita; Yusuke Sekiguchi; Harumi Fukada; Tetsuko Nakaniwa; Toshiji Tada; Shinya Nakamura; Kazuo Kitaura; Hiroaki Ohno; Yamato Suzuki; Akira Hirasawa; Isao Nakanishi; Gozoh Tsujimoto
    MOLECULAR AND CELLULAR BIOCHEMISTRY SPRINGER 356 (1-2) 97 - 105 0300-8177 2011/10 [Refereed]
    The detailed understanding of the molecular features of a ligand binding to a target protein, facilitates the successful design of potent and selective inhibitors. We present a case study of ATP-competitive kinase inhibitors that include a pyradine moiety. These compounds have similar chemical structure, except for distinct terminal hydrophobic cyclopentyl or isopropyl groups, and block kinase activity of casein kinase 2 subunit alpha (CK2 alpha), which is a target for several diseases, such as cancer and glomerulonephritis. Although these compounds display similar inhibitory potency against CK2 alpha, the crystal structures reveal that the cyclopentyl derivative gains more favorable interactions compared with the isopropyl derivative, because of the additional ethylene moiety. The structural observations and biological data are consistent with the thermodynamic profiles of these inhibitors in binding to CK2 alpha, revealing that the enthalpic advantage of the cyclopentyl derivative is accompanied with a lower entropic loss. Computational analyses indicated that the relative enthalpic gain of the cyclopentyl derivative arises from an enhancement of a wide range of van der Waals interactions from the whole complex. Conversely, the relative entropy loss of the cyclopentyl derivative arises from a decrease in the molecular fluctuation and higher conformational restriction in the active site of CK2 alpha. These structural insights, in combination with thermodynamic and computational observations, should be helpful in developing potent and selective CK2 alpha inhibitors.
  • G. Tanabe; K. Matsuoka; M. Yoshinaga; W. Xie; N. Tsutsui; M. F. A. Amer; S. Nakamura; I. Nakanishi; X. Wu; M. Yoshikawa; O. Muraoka
    Bioorg. Med. Chem. 19 2252 - 2262 2011/04 [Refereed]
  • Nagamatsu Kazuhiko; Nakamura Shinya; Kinoshita Takayoshi; Hirasawa Akira; Tsujimoto Gozoh; Nakanishi Isao
    Symposium on Chemical Information and Computer Sciences The Chemical Society of Japan 2011 P2 - P2 2011 
    Casein kinase II (CK2), a serine-threonine protein kinase, is distributed ubiquitously in human body. It exists as a tetramer composed of two catalytic subunits (α and α') and two control subunits (β). Amino acid sequence homology between the catalytic subunit α and α' is very high, 83%. Inhibitors of this enzyme have been explored for cancer, virus infection and glomerulonephritis therapies, and several highly potent compounds have been reported as ATP competitive inhibitors. On the other hand, hematein, a natural compound isolated from Caesalpinia sappan, inhibits CK2α in an ATP uncompetitive manner, whereas it inhibits CK2α' in a competitive manner. We have investigated the binding mode of hematein to both isozymes using docking studies followed by the binding energy analysis with the MM/PBSA method and the simulated annealing simulation. The results suggested that hematein could bind to the ATP binding site of the both isozymes. In addition, it might bind to the allosteric site and the substrate binding site of CK2α.
  • Nakao Yoshihito; Nakamura Shinya; Nakanishi Isao
    Symposium on Chemical Information and Computer Sciences The Chemical Society of Japan 2011 P20 - P20 2011 
    Binding free energy ΔGbind of a ligand to the target protein is a physicochemical quantity which closely relates to a drug activity, and prediction of ΔGbind with accuracy leads to an efficient drug design. As a method to calculate ΔΔGbind, difference of ΔGbind between two ligands, FEP (free energy perturbation) and TI (thermodynamic integration) methods are well known. Theoretically, application of these methods are limited to the system where an energy difference is small, ~2 kcal/mol. Recently, Jorgensen et al. have applied these methods to a lead optimization study of HIV reverse transcriptase inhibitors, and succeeded in obtaining a qualitative relationship between the predicted and experimental values. However, it is desirable to establish an appropriate calculation procedure of these methods which reproduces experimental ΔΔGbind quantitatively. In this study, we applied the FEP/TI methods to the FXa (activated blood coagulation factor X) inhibitors, where one hydrogen atom on an inhibitor molecule was replaced with a chlorine atom. Several calculation procedures have been tested.
  • Shinya Nakamura; Kazunori Takahira; Genzoh Tanabe; Toshio Morikawa; Mika Sakano; Kiyofumi Ninomiya; Masayuki Yoshikawa; Osamu Muraoka; Isao Nakanishi
    Salacinol is a potent alpha-glucosidase inhibitor isolated from Salacia reticulata, and a good lead compound for an antidiabetic drug. It is essential to clarify the binding state of salacinol to alpha-glucosidase for efficient optimization study using structure-based drug design. Redocking simulations of two inhibitors, acarbose and casuarine whose complex structures are known, were performed to assure the appropriate docking pose prediction. The simulation reproduced both experimental binding states with accuracy. Then, using the same simulation protocol, the binding mode of salacinol and its derivatives has been predicted. Salacinol bound to the protein with a similar binding mode as casuarine, and the predicted structures could explain most of the structure-activity relationships of salacinol derivatives. (C) 2010 Elsevier Ltd. All rights reserved.
  • Shinya Nakamura; Isao Nakanishi; Kazuo Kitaura
    Comparative binding energy (COMBINE) analysis method is one of the QSAR techniques for the prediction of biological activities of inhibitors based on interaction energies between ligands and proteins decomposed into each amino acid residue. We supposed that the predictive ability of the COMBINE method does not depend essentially on the molecular frameworks of ligands. To verify this idea, we performed the COMBINE analysis of non-peptide inhibitors of HIV-1 protease (HIVp), where the prediction model was constructed using inhibitors with a peptide scaffold as a training set. The predictive performance of the AMBER and CHARMm force fields was very high and at the same level (q(2) = 0.75, 0.67, SDEPcv = 0.76, 0.89, and SDEPex = 0.92, 0.66, respectively). The high predictive ability of the COMBINE method for the distinct scaffold compounds is due to the informative description of the interaction energies for compounds that are located at the binding site. This result suggests that COMBINE analysis may be applied not only to the lead optimization stage but also to the lead evolution stages. (c) 2006 Elsevier Ltd. All rights reserved.

Books etc

Conference Activities & Talks

  • Improvement of Pseudo-molecule Generation on Solvent Dipole Ordering Virtual Screening (SDO-VS)  [Not invited]
    Shinya Nakamura
    The 11th China-Japan Joint Symposium on Drug Design and Development  2018/06
  • 計算化学初心者のための分子動力学計算講習会 ~WindowsPCで行うMD計算の環境作りと失敗しないための考え方~  [Invited]
    第8回ケモインフォマティクス入門講座  2017/11
  • Practical research of Solvent Dipole Ordering for Drug Discovery  [Not invited]
    Shinya Nakamura; Shotaku KIMURA; Hayao KITAYOSHI; Isao; NAKANISHI
    第10回分子科学討論会2016神戸  2016/09
  • 計算化学初心者のための分子動力学計算講習会 ~計算環境の構築と失敗しないための考え方~  [Invited]
    第3回ケモインフォマティクス入門講座  2016/05
  • サラシア属植物由来化合物を起源とする計算化学による高活性化合物探索研究  [Invited]
    第6回サラシア属植物シンポジウム  2013/09
  • サラシノール由来新規α-グルコシダーゼ阻害剤創出のためのMOEを用いたドラッグデザイン  [Invited]
    MOEフォーラム2013  2013/09
  • COMBINE解析法の応用とその可能性  [Invited]
    2010年度第2回CACフォーラムセミナー  2011/03
  • MOEによるフラグメント分子軌道計算支援環境の開発  [Not invited]
    中村 真也; 仲西 功
    日本コンピュータ化学会 年会:2010秋季年会  2010/10  新潟  日本コンピュータ化学会 年会:2010秋季年会
    計算機資源の向上と計算手法の発達により、従来では困難であった高精度な分子軌道計算による相互作用解析が、タンパク質-薬物複合体などの巨大分子系においても一般化しつつある。これらの知見は、構造に基づくドラッグデザインに大きな知見をもたらすと期待がされており、特に古典的な力場計算では考慮していなかった、CH-O相互作用やCl-pi相互作用などが結合に寄与することが重要視されてきている。巨大分子系の分子軌道計算は、近似計算の方のひとつであるフラグメント分子軌道法(FMO法)によって行われることが多い。FMO法の利点は、単純に計算時間が短縮できるという点だけではなく、リガンドと各アミノ酸残基との相互作用など通常の分子軌道計算では求めることが困難な要素を得ることが可能であり、それにより力場法で行っていたことに近い感覚で解析が可能であるという点が挙げられる。 すでにFMO法に関するインターフェースはABINIT-MPなどいくつか存在し
  • Binding mode prediction and analysis for salacinol derivatives as alpha-glucosidase inhibitors.  [Not invited]
    中村 真也; 仲西 功; 田邉 元三; 森川 敏生; 二宮 清文; 村岡 修; 高平和典; 坂野実加; 吉川雅之
    18th European QSAR symposium 2010  2010/09  Rhodes (Greece)  18th European QSAR symposium 2010
  • MOEを用いたGAMESS/FMO解析支援ツールの開発  [Invited]
    中村 真也; 仲西 功
    MOEフォーラム2010  2010/07  東京  MOEフォーラム2010
    計算機資源の向上に伴い、タンパク質-薬物複合体などの巨大分子系においても高精度な分子軌道計算による相互作用解析が浸透しつつある。それにより、従来の古典的な力場計算では考慮していなかった、CH-O相互作用やCL-π相互作用などによる結合への寄与が明らかになってきている。しかし巨大分子系の分子軌道計算は、通常の計算方法では現実的な計算時間で解析を行うことが困難なため、近似計算の方のひとつであるフラグメント分子軌道法(FMO法)によって行われることが多い。FMO法の利点は、単純な計算時間の短縮できるという点だけではなく、アミノ酸残基ごとの相互作用など通常の分子軌道計算では求めることが困難な要素を得ることが可能であり、それにより力場法で行っていたことに近い感覚で解析が可能であるという点が挙げられる。 現在FMO法による計算が可能なツールとしてはGAMESSやABINIT-MP, PAICSなどが存在しており、GAMESS/FMOではFMO法の開発者らによる最新の
  • CK2阻害剤結合時の熱力学的プロファイル差に関する計算化学的考察  [Not invited]
    中村 真也; 仲西 功; 金光政幸; 仲庭哲津子; 木下誉富; 深田はるみ; 北浦和夫; 大野浩章; 鈴木大和; 平澤明; 辻本豪三
    日本薬学会第130年会  2010/03  岡山  日本薬学会第130年会
    【目的】新規に阻害剤を設計する際には、阻害剤の結合自由エネルギーを予測することが重要となる。本研究で用いたCK2阻害剤であるCC4791およびCC4820の結合自由エネルギーはほぼ同等であるが、小さな置換基変化(イソプロピル基とシクロペンチル基)にも関わらず、熱力学的プロファイル(エンタルピー・エントロピーの寄与度)が異なることが熱測定により観測されている。構造の差がどのような要因で熱力学的な差を生じさせているのか、計算化学的に考察を行った。 【方法】それぞれの複合体に対し、阻害剤の周囲25?に対し水分子を発生させた系で分子動力学(MD)計算を行い、このトラジェクトリーに対し溶媒効果を含めた相互作用計算を行った。また、阻害剤の結合状態と水中との運動性の差を解析するため、阻害剤を半径25?の球状の水分子クラスター中に配置した系でもMD計算を行い、置換基の二面角を中心に運動性を検討した。 【結果と考察】相互作用計算の結果、CC4
  • salacia 属植物有効成分のα グルコシダーゼ結合様式の推定  [Not invited]
    高平和典; 中村 真也; 田邉 元三; 村岡 修; 仲西 功
    日本薬学会第130年会  2010/03  岡山  日本薬学会第130年会
    【目的】インドやスリランカの伝統医学アーユルヴェーダでは、Salacia属植物が糖尿病の特効薬として用いられている。本植物から単離されるチオ糖スルホニウム硫酸分子内塩構造を持つsalacinolやkotalanolは、?グルコシダーゼを阻害することによる糖吸収抑制作用を有しており、同メカニズムに基づく抗糖尿病薬であるacarboseやvogliboseに匹敵する?グルコシダーゼ阻害活性を有している。本研究では、これらの化合物のタンパク質結合構造をもとに新規阻害剤の設計をするために、両化合物のドッキングシミュレーションを実施した。 【方法】まず、?グルコシダーゼの1つであるマルターゼグルコアミラーゼのN末端側触媒ドメインとacarbose及びcasuarineとの複合体構造(PDBID:2QMJおよび3CTT)を再現できるドッキングシミュレーション条件を探索した。次にそのシミュレーション条件を用いて、salacinol及びkotalanolの結合様式を推定した。 【結果】結合シミュレーションの結果、salacinol及び
  • サラシア属植物含有成分salacinolのαグルコシダーゼへの結合シミュレーション  [Not invited]
    仲西 功; 中村 真也; 高平和典
    第3回食品薬学シンポジウム  2009/11  大阪  第3回食品薬学シンポジウム
  • 新規αグルコシダーゼ阻害剤探索へ向けたsalacinolの結合様式推定  [Not invited]
    仲西 功; 中村 真也; 高平和典
    第59回日本薬学会近畿支部大会  2009/10  大阪  第59回日本薬学会近畿支部大会
  • α-グルコシダーゼと阻害剤との複合体の結晶化  [Not invited]
    仲西 功; 中村 真也; 大迫久晃; 山口亜佐子; 木下誉富; 多田俊治
    第3回食品薬学シンポジウム  2009/10  大阪  第3回食品薬学シンポジウム
  • An approach for producing a CK2alpha inhibitor using X-ray, calculation and ITC.  [Not invited]
    関口雄介; 深田はるみ; 仲庭哲津子; 木下誉富; 多田俊治; 仲西 功; 中村 真也; 北浦和夫; 大野浩明; 鈴木大和; 平澤明; 辻本豪三
    25th European Crystallographic Meeting  2009/08  Istanbul (Turkey)  25th European Crystallographic Meeting
  • The effect of the electron correlation to the structure optimization by Fragment MO method  [Not invited]
    井上 雄貴; 中村 真也; 仲西 功; 北浦 和夫
    日本薬学会第129年会  2009/03  京都  日本薬学会第129年会
    【目的】タンパク質と低分子との結合親和力を高精度に計算することは、ターゲットの構造に基づく薬物設計を行うために最も重要な要素のひとつである。定量性に最も優れた非経験的分子軌道法を、タンパク質などの大きな系に適用する計算手法として、Fragment MO(FMO)法が開発されている。タンパク質のFMO法による計算はすでに浸透しつつあるが、一般的に、タンパク質と低分子との相互作用には分散力が大きく寄与することが、MP2レベルなどの電子相関を考慮したFMO法のエネルギー計算から明らかとなってきている。しかし相互作用を精密に計算する前段階である構造最適化は、計算コストの問題から電子相関を考慮しないHFレベルで計算されているのが現状である。本研究ではMP2レベルの計算が構造に与える影響について検討を行った。 【方法】GAMESS/FMOを用いて、FK506 Binding Protein(FKBP)とその4つの阻害剤との各複合体をFMO-MP2/6-31Gレベル、および比較のためにFMO-HF/3-21Gレベルで構造最
  • An approach for producing a potent CK2? inhibitor using X-ray and calorimetry analyses.  [Not invited]
    関口雄介; 深田はるみ; 仲庭哲津子; 木下誉富; 多田俊治; 仲西 功; 中村 真也; 北浦和夫; 大野浩明; 鈴木大和; 平澤明; 辻本豪三
    第38回構造活性相関シンポジウム  2008/11  神戸  第38回構造活性相関シンポジウム
  • Docking-pose prediction by a receptor-based tailor-made scoring function  [Not invited]
    中村 真也; 仲西 功; 北浦 和夫
    8th China-Japan symposium on drug design and development  2008/10  Kobe (Japan)  8th China-Japan symposium on drug design and development
    バーチャルスクリーニングの高精度化のため、COMBINE解析法を応用した受容体特異的なスコア関数を考案した。バーチャルスクリーニングでは化合物の活性値予測と結合様式予測の両者が重要となるが、今回はその検証の一つとして、後者の結合様式予測に関して、HIV ptorease およびAdenosine deaminaseとその阻害薬を用いて予測が可能か検討した。 (英文)


Awards & Honors

  • 2017/11 サラシア属植物普及協会 サラシア属植物普及協会会長賞
    受賞者: 中村真也
  • 2016/09 日本化学会情報化学部会 Journal of Computer Aided Chemistry論文賞
     A Mini-review on Chemoinformatics Approaches for Drug Discovery 
    受賞者: 川下 理日人;山崎 広之;宮尾 知幸;河合 健太;榮 慶丈;石川 岳志;森 健一;中村 真也;金子弘昌
  • 2005/09 日本薬学会構造活性相関部会 SAR Promotion Award
    受賞者: 中村真也

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