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Items: 45

1.

Structure-based virtual screening for novel chymase inhibitors by in silico fragment mapping.

Ozawa SI, Takahashi M, Yamaotsu N, Hirono S.

J Mol Graph Model. 2019 Mar 12;89:102-108. doi: 10.1016/j.jmgm.2019.03.011. [Epub ahead of print]

PMID:
30884446
2.

[Identifying Inhibitors of USP7-HDM2 Protein-Protein Interaction (PPI) by the in silico Fragment-Mapping Method].

Misawa K, Ozawa SI, Yoshida T, Nakagome I, Yamaotsu N, Hirono S.

Yakugaku Zasshi. 2019 Mar 5. doi: 10.1248/yakushi.19-00006. [Epub ahead of print] Japanese.

3.

Design of a New α-1-C-Alkyl-DAB Derivative Acting as a Pharmacological Chaperone for β-Glucocerebrosidase Using Ligand Docking and Molecular Dynamics Simulation.

Nakagome I, Kato A, Yamaotsu N, Yoshida T, Ozawa SI, Adachi I, Hirono S.

Molecules. 2018 Oct 18;23(10). pii: E2683. doi: 10.3390/molecules23102683.

4.

In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery.

Yamaotsu N, Hirono S.

J Comput Aided Mol Des. 2018 Nov;32(11):1229-1245. doi: 10.1007/s10822-018-0160-8. Epub 2018 Sep 8.

PMID:
30196523
6.

Validation of molecular force field parameters for peptides including isomerized amino acids.

Oda A, Nakayoshi T, Fukuyoshi S, Kurimoto E, Yamaotsu N, Hirono S, Takahashi O.

Chirality. 2018 Apr;30(4):332-341. doi: 10.1002/chir.22821. Epub 2018 Feb 2.

PMID:
29393985
8.

In silico analyses of the effects of a point mutation and a pharmacological chaperone on the thermal fluctuation of phenylalanine hydroxylase.

Hayakawa D, Yamaotsu N, Nakagome I, Ozawa SI, Yoshida T, Hirono S.

Biophys Chem. 2017 Sep;228:47-54. doi: 10.1016/j.bpc.2017.06.014. Epub 2017 Jun 30.

PMID:
28697448
9.

Long chain fatty acids alter the interactive binding of ligands to the two principal drug binding sites of human serum albumin.

Yamasaki K, Hyodo S, Taguchi K, Nishi K, Yamaotsu N, Hirono S, Chuang VTG, Seo H, Maruyama T, Otagiri M.

PLoS One. 2017 Jun 29;12(6):e0180404. doi: 10.1371/journal.pone.0180404. eCollection 2017.

10.

Investigation of substrate recognition for cytochrome P450 1A2 mediated by water molecules using docking and molecular dynamics simulations.

Watanabe Y, Fukuyoshi S, Kato K, Hiratsuka M, Yamaotsu N, Hirono S, Gouda H, Oda A.

J Mol Graph Model. 2017 Jun;74:326-336. doi: 10.1016/j.jmgm.2017.04.006. Epub 2017 Apr 13.

PMID:
28475969
11.

Precise prediction of activators for the human constitutive androstane receptor using structure-based three-dimensional quantitative structure-activity relationship methods.

Kato H, Yamaotsu N, Iwazaki N, Okamura S, Kume T, Hirono S.

Drug Metab Pharmacokinet. 2017 Jun;32(3):179-188. doi: 10.1016/j.dmpk.2017.02.001. Epub 2017 Feb 9.

PMID:
28412023
12.

Multi-step virtual screening to develop selective DYRK1A inhibitors.

Koyama T, Yamaotsu N, Nakagome I, Ozawa SI, Yoshida T, Hayakawa D, Hirono S.

J Mol Graph Model. 2017 Mar;72:229-239. doi: 10.1016/j.jmgm.2017.01.014. Epub 2017 Jan 15.

PMID:
28129593
13.

Prediction of three-dimensional structures and structural flexibilities of wild-type and mutant cytochrome P450 1A2 using molecular dynamics simulations.

Watanabe Y, Fukuyoshi S, Hiratsuka M, Yamaotsu N, Hirono S, Takahashi O, Oda A.

J Mol Graph Model. 2016 Jul;68:48-56. doi: 10.1016/j.jmgm.2016.06.006. Epub 2016 Jun 16.

PMID:
27371932
14.

Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62.

Fukuyoshi S, Kometani M, Watanabe Y, Hiratsuka M, Yamaotsu N, Hirono S, Manabe N, Takahashi O, Oda A.

PLoS One. 2016 Apr 5;11(4):e0152946. doi: 10.1371/journal.pone.0152946. eCollection 2016.

15.

Identification of Novel D-Aspartate Oxidase Inhibitors by in Silico Screening and Their Functional and Structural Characterization in Vitro.

Katane M, Yamada S, Kawaguchi G, Chinen M, Matsumura M, Ando T, Doi I, Nakayama K, Kaneko Y, Matsuda S, Saitoh Y, Miyamoto T, Sekine M, Yamaotsu N, Hirono S, Homma H.

J Med Chem. 2015 Sep 24;58(18):7328-40. doi: 10.1021/acs.jmedchem.5b00871. Epub 2015 Sep 4.

PMID:
26322531
16.
17.

Synthesis of a novel universal opioid receptor agonist with the 1,3,5-trioxazatriquinane skeleton and its pharmacologies.

Hirayama S, Wada N, Kuroda N, Iwai T, Yamaotsu N, Hirono S, Fujii H, Nagase H.

Bioorg Med Chem Lett. 2014 Oct 15;24(20):4895-8. doi: 10.1016/j.bmcl.2014.08.012. Epub 2014 Aug 12.

PMID:
25248680
18.

Evaluation of influence of single nucleotide polymorphisms in cytochrome P450 2B6 on substrate recognition using computational docking and molecular dynamics simulation.

Kobayashi K, Takahashi O, Hiratsuka M, Yamaotsu N, Hirono S, Watanabe Y, Oda A.

PLoS One. 2014 May 5;9(5):e96789. doi: 10.1371/journal.pone.0096789. eCollection 2014.

19.

Differential effects of methoxy group on the interaction of curcuminoids with two major ligand binding sites of human serum albumin.

Sato H, Chuang VT, Yamasaki K, Yamaotsu N, Watanabe H, Nagumo K, Anraku M, Kadowaki D, Ishima Y, Hirono S, Otagiri M, Maruyama T.

PLoS One. 2014 Feb 3;9(2):e87919. doi: 10.1371/journal.pone.0087919. eCollection 2014.

20.

In silico study on the inhibitory interaction of drugs with wild-type CYP2D6.1 and the natural variant CYP2D6.17.

Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S.

Drug Metab Pharmacokinet. 2014;29(1):52-60. Epub 2013 Jul 16.

21.

Three-dimensional quantitative structure-activity relationship analysis of inhibitors of human and rat cytochrome P4503A enzymes.

Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S.

Drug Metab Pharmacokinet. 2013;28(4):345-55. Epub 2013 Jan 29.

22.

Essential structure of opioid κ receptor agonist nalfurafine for binding to κ receptor 1: synthesis of decahydroisoquinoline derivatives and their pharmacologies.

Nagase H, Imaide S, Yamada T, Hirayama S, Nemoto T, Yamaotsu N, Hirono S, Fujii H.

Chem Pharm Bull (Tokyo). 2012;60(8):945-8.

23.

Quantitative structure-activity relationship (QSAR) analysis to predict drug-drug interactions of ABC transporter ABCG2.

Ishikawa T, Hirano H, Saito H, Sano K, Ikegami Y, Yamaotsu N, Hirono S.

Mini Rev Med Chem. 2012 Jun;12(6):505-14.

PMID:
22587765
24.

AMF-26, a novel inhibitor of the Golgi system, targeting ADP-ribosylation factor 1 (Arf1) with potential for cancer therapy.

Ohashi Y, Iijima H, Yamaotsu N, Yamazaki K, Sato S, Okamura M, Sugimoto K, Dan S, Hirono S, Yamori T.

J Biol Chem. 2012 Feb 3;287(6):3885-97. doi: 10.1074/jbc.M111.316125. Epub 2011 Dec 9.

25.
26.

Brazilian propolis-derived components inhibit TNF-α-mediated downregulation of adiponectin expression via different mechanisms in 3T3-L1 adipocytes.

Ikeda R, Yanagisawa M, Takahashi N, Kawada T, Kumazawa S, Yamaotsu N, Nakagome I, Hirono S, Tsuda T.

Biochim Biophys Acta. 2011 Jul;1810(7):695-703. doi: 10.1016/j.bbagen.2011.04.007. Epub 2011 Apr 29.

PMID:
21554928
27.

NMR spectroscopy and computational analysis of interaction between Serratia marcescens chitinase B and a dipeptide derived from natural-product cyclopentapeptide chitinase inhibitor argifin.

Gouda H, Sunazuka T, Hirose T, Iguchi K, Yamaotsu N, Sugawara A, Noguchi Y, Saito Y, Yamamoto T, Watanabe T, Shiomi K, Omura S, Hirono S.

Bioorg Med Chem. 2010 Aug 15;18(16):5835-44. doi: 10.1016/j.bmc.2010.06.093. Epub 2010 Jul 1.

PMID:
20667742
28.

Identification of the three-dimensional pharmacophore of kappa-opioid receptor agonists.

Yamaotsu N, Fujii H, Nagase H, Hirono S.

Bioorg Med Chem. 2010 Jun 15;18(12):4446-52. doi: 10.1016/j.bmc.2010.04.069. Epub 2010 Apr 28.

PMID:
20478711
29.

Drug design and synthesis of a novel kappa opioid receptor agonist with an oxabicyclo[2.2.2]octane skeleton and its pharmacology.

Nagase H, Watanabe A, Nemoto T, Yamaotsu N, Hayashida K, Nakajima M, Hasebe K, Nakao K, Mochizuki H, Hirono S, Fujii H.

Bioorg Med Chem Lett. 2010 Jan 1;20(1):121-4. doi: 10.1016/j.bmcl.2009.11.027. Epub 2009 Nov 13.

PMID:
19962305
30.

Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection.

Oda A, Yamaotsu N, Hirono S.

J Comput Chem. 2009 Dec;30(16):2728-37. doi: 10.1002/jcc.21299.

PMID:
19399761
31.

Structure-based CoMFA as a predictive model - CYP2C9 inhibitors as a test case.

Yasuo K, Yamaotsu N, Gouda H, Tsujishita H, Hirono S.

J Chem Inf Model. 2009 Apr;49(4):853-64. doi: 10.1021/ci800313h.

PMID:
19391630
32.

Brownian dynamics simulations of a wild type and mutants of bovine pancreatic trypsin inhibitors.

Oda A, Yamaotsu N, Hirono S, Takahashi O.

Biol Pharm Bull. 2008 Dec;31(12):2182-6.

33.

Determination of ligand-binding sites on proteins using long-range hydrophobic potential.

Yamaotsu N, Oda A, Hirono S.

Biol Pharm Bull. 2008 Aug;31(8):1552-8.

34.

In silico multi-filter screening approaches for developing novel beta-secretase inhibitors.

Fujimoto T, Matsushita Y, Gouda H, Yamaotsu N, Hirono S.

Bioorg Med Chem Lett. 2008 May 1;18(9):2771-5. doi: 10.1016/j.bmcl.2008.04.011. Epub 2008 Apr 10.

PMID:
18434150
35.

Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes.

Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S.

J Chem Inf Model. 2006 Jan-Feb;46(1):380-91.

PMID:
16426072
36.

Hydrolysis of angiotensin II receptor blocker prodrug olmesartan medoxomil by human serum albumin and identification of its catalytic active sites.

Ma SF, Anraku M, Iwao Y, Yamasaki K, Kragh-Hansen U, Yamaotsu N, Hirono S, Ikeda T, Otagiri M.

Drug Metab Dispos. 2005 Dec;33(12):1911-9. Epub 2005 Sep 23.

PMID:
16183779
37.
39.

Use of photoaffinity labeling and site-directed mutagenesis for identification of the key residue responsible for extraordinarily high affinity binding of UCN-01 in human alpha1-acid glycoprotein.

Katsuki M, Chuang VT, Nishi K, Kawahara K, Nakayama H, Yamaotsu N, Hirono S, Otagiri M.

J Biol Chem. 2005 Jan 14;280(2):1384-91. Epub 2004 Oct 27.

40.

Esterase-like activity of serum albumin: characterization of its structural chemistry using p-nitrophenyl esters as substrates.

Sakurai Y, Ma SF, Watanabe H, Yamaotsu N, Hirono S, Kurono Y, Kragh-Hansen U, Otagiri M.

Pharm Res. 2004 Feb;21(2):285-92.

PMID:
15032310
41.

Rational procedure for 3D-QSAR analysis using TRNOE experiments and computational methods: application to thermolysin inhibitors.

Radwan AA, Gouda H, Yamaotsu N, Torigoe H, Hirono S.

Drug Des Discov. 2001;17(3):265-81.

PMID:
11469756
42.

Molecular dynamics simulation of the calmodulin-trifluoperazine complex in aqueous solution.

Yamaotsu N, Suga M, Hirono S.

Biopolymers. 2001 Apr 5;58(4):410-21.

PMID:
11180054
43.

Analysis of affinities of penicillins for a class C beta-lactamase by molecular dynamics simulations.

Tsuchida K, Yamaotsu N, Hirono S.

Drug Des Discov. 1999 Aug;16(2):145-53.

PMID:
10533810
44.
45.

Molecular dynamics study of the stability of staphylococcal nuclease mutants: component analysis of the free energy difference of denaturation.

Yamaotsu N, Moriguchi I, Kollman PA, Hirono S.

Biochim Biophys Acta. 1993 Apr 21;1163(1):81-8.

PMID:
8476933

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