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Volumn 18, Issue 1, 2012, Pages 203-212

Computer-aided de novo ligand design and docking/molecular dynamics study of Vitamin D receptor agonists

Author keywords

De novo design; Molecular docking; Molecular dynamics; VDR agonist; Vitamin D

Indexed keywords

BENZENE; COLECALCIFEROL; DIAMINE DERIVATIVE; LIGAND; NAPHTHALENE; PYRIMIDINE DERIVATIVE; UNCLASSIFIED DRUG; VITAMIN D; VITAMIN D RECEPTOR; VITAMIN D RECEPTOR AGONIST;

EID: 84856240651     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1066-8     Document Type: Article
Times cited : (24)

References (49)
  • 1
    • 0028988403 scopus 로고
    • Structure-function relationships in the vitamin D endocrine system
    • 1:CAS:528:DyaK2MXmtFWisrg%3D
    • Bouillon R, Okamura WH, Norman AW (1995) Structure-function relationships in the vitamin D endocrine system. Endocr Rev 16:200-257
    • (1995) Endocr Rev , vol.16 , pp. 200-257
    • Bouillon, R.1    Okamura, W.H.2    Norman, A.W.3
  • 2
    • 0019302750 scopus 로고
    • Vitamin D deficiency inhibits pancreatic secretion of insulin
    • Norman AW, Frankel JB, Heldt AM, Grodsky GM (1980) Vitamin D deficiency inhibits pancreatic secretion of insulin. Science 209:823-825 (Pubitemid 10017495)
    • (1980) Science , vol.209 , Issue.4458 , pp. 823-825
    • Norman, A.W.1    Frankel, B.J.2    Heldt, A.M.3    Grodsky, G.M.4
  • 5
    • 0023913120 scopus 로고
    • The steroid and thyroid hormone receptor superfamily
    • 10.1126/science.3283939 1:CAS:528:DyaL1cXktVSqsr4%3D
    • Evans RM (1988) The steroid and thyroid hormone receptor superfamily. Science 240:889-895
    • (1988) Science , vol.240 , pp. 889-895
    • Evans, R.M.1
  • 6
    • 1542678306 scopus 로고    scopus 로고
    • Vitamin D analogs as modulators of vitamin D receptor action
    • 10.2174/1568026033451691 1:CAS:528:DC%2BD3sXotFKlsbc%3D
    • Peleg S, Posner GH (2003) Vitamin D analogs as modulators of vitamin D receptor action. Curr Top Med Chem 3:1555-1572
    • (2003) Curr Top Med Chem , vol.3 , pp. 1555-1572
    • Peleg, S.1    Posner, G.H.2
  • 7
    • 0034957480 scopus 로고    scopus 로고
    • Nuclear hormone receptors and gene expression
    • Aranda A, Pascual A (2001) Nuclear hormone receptors and gene expression. Physiol Rev 81:1269-1304 (Pubitemid 32606670)
    • (2001) Physiological Reviews , vol.81 , Issue.3 , pp. 1269-1304
    • Aranda, A.1    Pascual, A.2
  • 8
    • 0034122224 scopus 로고    scopus 로고
    • Mechanisms for the selective actions of vitamin D analogues
    • 10.2174/1381612003400416 1:CAS:528:DC%2BD3cXjvFGgtb0%3D
    • Brown AJ (2000) Mechanisms for the selective actions of vitamin D analogues. Curr Pharm Des 6:701-706
    • (2000) Curr Pharm des , vol.6 , pp. 701-706
    • Brown, A.J.1
  • 9
    • 0037705849 scopus 로고    scopus 로고
    • Vitamin D analogs-drug design based on proteins involved in vitamin D signal transduction
    • 10.2174/1568008033340315 1:CAS:528:DC%2BD3sXhtlClsr4%3D
    • Masuda S, Jones G (2003) Vitamin D analogs-drug design based on proteins involved in vitamin D signal transduction. Curr Drug Targets Immune Endocr Metab Disord 3:43-66
    • (2003) Curr Drug Targets Immune Endocr Metab Disord , vol.3 , pp. 43-66
    • Masuda, S.1    Jones, G.2
  • 12
    • 0024455377 scopus 로고
    • 3 analogues: Stereoselective preparation of 6β-vitamin D vinylallenes and a concise enynol synthesis for preparing the A-ring
    • 3 analogues: stereoselective preparation of 6β-Vitamin D vinylallenes and a concise enynol synthesis for preparing the A-ring. J Org Chem 54:4072-4083 (Pubitemid 19217352)
    • (1989) Journal of Organic Chemistry , vol.54 , Issue.17 , pp. 4072-4083
    • Okamura, W.H.1    Aurrecoechea, J.M.2    Gibbs, R.A.3    Norman, A.W.4
  • 14
    • 34547113990 scopus 로고    scopus 로고
    • Synthesis and conformational analysis of 17α,21-cyclo-22- unsaturated analogues of calcitriol
    • DOI 10.1021/jo0625195
    • Riveiros R, Rumbo A, Sarandeses LA, Mouriño A (2007) Synthesis and Conformational Analysis of 17α,21-Cyclo-22-Unsaturated Analogues of Calcitriol. J Org Chem 72:5477-5485 (Pubitemid 47104648)
    • (2007) Journal of Organic Chemistry , vol.72 , Issue.15 , pp. 5477-5485
    • Riveiros, R.1    Rumbo, A.2    Sarandeses, L.A.3    Mourino, A.4
  • 15
    • 0032560137 scopus 로고    scopus 로고
    • Conformation-function relationship of vitamin D: Conformational analysis predicts potential side-chain structure
    • DOI 10.1021/jm970761l
    • Yamada S, Yamamoto K, Masuno H, Ohta M (1998) Conformation-function relationship of vitamin D: conformational analysis predicts potential side-chain structure. J Med Chem 41:1467-1475 (Pubitemid 28198976)
    • (1998) Journal of Medicinal Chemistry , vol.41 , Issue.9 , pp. 1467-1475
    • Yamada, S.1    Yamamoto, K.2    Masuno, H.3    Ohta, M.4
  • 16
    • 34247231581 scopus 로고    scopus 로고
    • Practical synthesis of a heterocyclic immunosuppressive vitamin D analogue
    • 10.1021/op060130d 1:CAS:528:DC%2BD2sXhtVOmsbk%3D
    • Westermann J, Schneider M, Platzek J, Petrov O (2007) Practical synthesis of a heterocyclic immunosuppressive vitamin D analogue. Org Process Res Dev 11:200-205
    • (2007) Org Process Res Dev , vol.11 , pp. 200-205
    • Westermann, J.1    Schneider, M.2    Platzek, J.3    Petrov, O.4
  • 18
    • 64349090025 scopus 로고    scopus 로고
    • A new class of vitamin D analogues that induce structural rearrangement of the ligand-binding pocket of the receptor
    • 10.1021/jm8014348 1:CAS:528:DC%2BD1MXhsFWgtLc%3D
    • Inaba Y, Yoshimoto N, Sakamaki Y, Nakabayashi M, Ikura T, Tamamura H, Ito N, Shimizu M, Yamamoto K (2009) A new class of vitamin D analogues that induce structural rearrangement of the ligand-binding pocket of the receptor. J Med Chem 52:1438-1449
    • (2009) J Med Chem , vol.52 , pp. 1438-1449
    • Inaba, Y.1    Yoshimoto, N.2    Sakamaki, Y.3    Nakabayashi, M.4    Ikura, T.5    Tamamura, H.6    Ito, N.7    Shimizu, M.8    Yamamoto, K.9
  • 20
    • 33745604630 scopus 로고    scopus 로고
    • Ligands with a 3,3-diphenylpentane skeleton for nuclear vitamin D and androgen receptors: Dual activities and metabolic activation
    • DOI 10.1016/j.bmc.2006.04.039, PII S0968089606003403
    • Hosoda S, Tanatani A, Wakabayashi K, Makishima M, Imai K, Miyachi H, Nagasawad K, Hashimoto Y (2006) Ligands with a 3,3-diphenylpentane skeleton for nuclear vitamin D and androgen receptors: dual activities and metabolic activation. Bioorg Med Chem 14:5489-5502 (Pubitemid 43994477)
    • (2006) Bioorganic and Medicinal Chemistry , vol.14 , Issue.16 , pp. 5489-5502
    • Hosoda, S.1    Tanatani, A.2    Wakabayashi, K.-i.3    Makishima, M.4    Imai, K.5    Miyachi, H.6    Nagasawa, K.7    Hashimoto, Y.8
  • 21
    • 0032589797 scopus 로고    scopus 로고
    • 3-26,23-lactone analogs antagonize differentiation of human leukemia cells (HL-60 cells) but not of human acute promyelocytic leukemia cells (NB4 cells)
    • DOI 10.1016/S0014-5793(99)01347-2, PII S0014579399013472
    • 3-26,23-lactone analogs antagonize differentiation of human leukemia cells (HL-60 cells) but not of human acute promyelocytic leukemia cells (NB4 cells). FEBS Lett 460:297-302 (Pubitemid 29495958)
    • (1999) FEBS Letters , vol.460 , Issue.2 , pp. 297-302
    • Miura, D.1    Manabe, K.2    Gao, Q.3    Norman, A.W.4    Ishizuka, S.5
  • 22
    • 0033794692 scopus 로고    scopus 로고
    • Structure activity relationship of carboxylic ester antagonists of the vitamin D(3) receptor
    • 1:CAS:528:DC%2BD3cXnslKgt7g%3D
    • Bury Y, Steinmeyer A, Carlberg C (2000) Structure activity relationship of carboxylic ester antagonists of the vitamin D(3) receptor. Mol Pharmacol 58:1067-1074
    • (2000) Mol Pharmacol , vol.58 , pp. 1067-1074
    • Bury, Y.1    Steinmeyer, A.2    Carlberg, C.3
  • 23
    • 33644764283 scopus 로고    scopus 로고
    • The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors
    • DOI 10.1007/s00894-005-0063-1
    • García-Sosa AT, Mancera RL (2006) The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors. J Mol Model 12:422-431 (Pubitemid 43337181)
    • (2006) Journal of Molecular Modeling , vol.12 , Issue.4 , pp. 422-431
    • Garcia-Sosa, A.T.1    Mancera, R.L.2
  • 24
    • 42249114709 scopus 로고    scopus 로고
    • Design of Benzene-1,2-diamines as selective inducible nitric oxide synthase inhibitors: A combined de novo design and docking analysis
    • 10.1007/s00894-007-0263-y 1:CAS:528:DC%2BD1cXksFWntrc%3D
    • Francis SM, Mittal A, Sharma M, Bharatam PV (2008) Design of Benzene-1,2-diamines as selective inducible nitric oxide synthase inhibitors: a combined de novo design and docking analysis. J Mol Model 14:215-224
    • (2008) J Mol Model , vol.14 , pp. 215-224
    • Francis, S.M.1    Mittal, A.2    Sharma, M.3    Bharatam, P.V.4
  • 25
    • 0028522983 scopus 로고
    • On the use of LUDI to search the fine chemicals directory for ligands of proteins of known three-dimensional structure
    • 10.1007/BF00123669
    • Böhm HJ (1994) On the use of LUDI to search the fine chemicals directory for ligands of proteins of known three-dimensional structure. J Comput Aid Mol Des 8:623-632
    • (1994) J Comput Aided Mol des , vol.8 , pp. 623-632
    • Böhm, H.J.1
  • 26
    • 56349166106 scopus 로고    scopus 로고
    • An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus
    • 10.1016/j.bbrc.2008.10.148 1:CAS:528:DC%2BD1cXhsVGhu7vK
    • Huang RB, Du QS, Wang CH, Chou KC (2008) An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem Biophys Res Commun 377:1243-1247
    • (2008) Biochem Biophys Res Commun , vol.377 , pp. 1243-1247
    • Huang, R.B.1    Du, Q.S.2    Wang, C.H.3    Chou, K.C.4
  • 27
    • 67349139888 scopus 로고    scopus 로고
    • Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus
    • 10.1016/j.jtbi.2009.03.003 1:CAS:528:DC%2BD1MXmtlCiu7o%3D
    • Du QS, Huang RB, Wang CH, Li XM, Chou KC (2009) Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus. J Theor Biol 259:159-164
    • (2009) J Theor Biol , vol.259 , pp. 159-164
    • Du, Q.S.1    Huang, R.B.2    Wang, C.H.3    Li, X.M.4    Chou, K.C.5
  • 28
    • 33846617350 scopus 로고    scopus 로고
    • Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases
    • DOI 10.1016/j.bbrc.2006.12.235, PII S0006291X0602835X
    • Wang SQ, Du QS, Chou KC (2007) Study of drug resistance of chicken influenza a virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem Biophys Res Commun 354:634-640 (Pubitemid 46186231)
    • (2007) Biochemical and Biophysical Research Communications , vol.354 , Issue.3 , pp. 634-640
    • Wang, S.-Q.1    Du, Q.-S.2    Chou, K.-C.3
  • 29
    • 67650069265 scopus 로고    scopus 로고
    • Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus
    • 10.1016/j.bbrc.2009.06.016 1:CAS:528:DC%2BD1MXosVyit74%3D
    • Wang SQ, Du QS, Huang RB, Zhang DW, Chou KC (2009) Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus. Biochem Biophys Res Commun 386:432-436
    • (2009) Biochem Biophys Res Commun , vol.386 , pp. 432-436
    • Wang, S.Q.1    Du, Q.S.2    Huang, R.B.3    Zhang, D.W.4    Chou, K.C.5
  • 30
    • 0015208126 scopus 로고
    • 1,25-Dihydroxycholecalciferol: Identification of the proposed active form of vitamin D3 in the intestine
    • 10.1126/science.173.3991.51 1:CAS:528:DyaE3MXkvVGks78%3D
    • Norman AW, Myrtle JF, Miogett RJ, Nowicki HG, Williams V, Popjaák G (1971) 1,25-Dihydroxycholecalciferol: identification of the proposed active form of vitamin D3 in the intestine. Science 173:51-54
    • (1971) Science , vol.173 , pp. 51-54
    • Norman, A.W.1    Myrtle, J.F.2    Miogett, R.J.3    Nowicki, H.G.4    Williams, V.5    Popjaák, G.6
  • 32
    • 0003473269 scopus 로고    scopus 로고
    • Seocalcitol (EB 1089): A vitamin D analogue of anti-cancer potential. Background, design, synthesis, pre-clinical and clinical evaluation
    • Hansen CM, Hamberg KJ, Binderup E, Binderup L (2000) Seocalcitol (EB 1089) A vitamin D analogue of anti-cancer potential. Background, design, synthesis, pre-clinical and clinical evaluation. Curr Pharm Des 26:803-828 (Pubitemid 30396417)
    • (2000) Current Pharmaceutical Design , vol.6 , Issue.7 , pp. 803-828
    • Mork Hansen, C.1    Hamberg, K.J.2    Binderup, E.3    Binderup, L.4
  • 33
    • 0035871888 scopus 로고    scopus 로고
    • 3, that modulates cell growth, differentiation, apoptosis, cell cycle, and induction of PTEN in leukemic cells
    • DOI 10.1182/blood.V97.8.2427
    • 3, that modulates cell growth, differentiation, apoptosis, cell cycle, and induction of PTEN in leukemic cells. Blood 97:2427-2433 (Pubitemid 32291490)
    • (2001) Blood , vol.97 , Issue.8 , pp. 2427-2433
    • Hisatake, J.-I.1    O'Kelly, J.2    Uskokovic, M.R.3    Tomoyasu, S.4    Koeffler, H.P.5
  • 34
    • 0025856045 scopus 로고
    • Calcipotriol (MC 903): Pharmacokinetics in rats and biological activities of metabolites. A comparative study with 1,25(OH)2D3
    • 10.1016/0006-2952(91)90160-7 1:CAS:528:DyaK3MXkt1Wmurk%3D
    • Kissmeyer AM, Binderup L (1991) Calcipotriol (MC 903): pharmacokinetics in rats and biological activities of metabolites. A comparative study with 1,25(OH)2D3. Biochem Pharmacol 41:1601-1606
    • (1991) Biochem Pharmacol , vol.41 , pp. 1601-1606
    • Kissmeyer, A.M.1    Binderup, L.2
  • 35
    • 33947716119 scopus 로고    scopus 로고
    • Software news and update a semiempirical free energy force field with charge-based desolvation
    • DOI 10.1002/jcc.20634
    • Huey R, Morris GM, Olson AJ, Goodsell DS (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28:1145-1152 (Pubitemid 46506716)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.6 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 37
    • 2942532422 scopus 로고    scopus 로고
    • Development and testing of a general amber force field
    • 10.1002/jcc.20035 1:CAS:528:DC%2BD2cXksFakurc%3D
    • Wang JM, Wolf RM, Caldwell JW, Kollamn PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157-1174
    • (2004) J Comput Chem , vol.25 , pp. 1157-1174
    • Wang, J.M.1    Wolf, R.M.2    Caldwell, J.W.3    Kollamn, P.A.4    Case, D.A.5
  • 38
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • 10.1016/0021-9991(77)90098-5 1:CAS:528:DyaE2sXktVGhsL4%3D
    • Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327-341
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 39
    • 33846823909 scopus 로고
    • Particle mesh ewald: An N-log(N) method for ewald sums in large systems
    • 10.1063/1.464397 1:CAS:528:DyaK3sXks1Ohsr0%3D
    • Darden T, York D, Pedersen L (1993) Particle mesh ewald: an N-log(N) method for ewald sums in large systems. J Chem Phys 98:10089-10092
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 40
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • 10.1126/science.7761829 1:CAS:528:DyaK2MXlvVyqsrY%3D
    • Honig B, Nicholls A (1995) Classical electrostatics in biology and chemistry. Science 268:1144-1149
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 41
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • DOI 10.1021/ar000033j
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889-897 (Pubitemid 32056774)
    • (2000) Accounts of Chemical Research , vol.33 , Issue.12 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10    Donini, O.11
  • 42
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and continuum solvent approach (MM- PBSA/GBSA) to predict ligand binding
    • DOI 10.1023/A:1008763014207
    • Massova I, Kollman PA (2000) Combined molecular mechanical and continuum solvent approach (MM PBSA/GBSA) to predict ligand binding. Perspect Drug Discov Des 18:113-135 (Pubitemid 30191024)
    • (2000) Perspectives in Drug Discovery and Design , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 43
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • DOI 10.1002/prot.20033
    • Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55:383-394 (Pubitemid 38437495)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 44
    • 29144436035 scopus 로고    scopus 로고
    • Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase
    • DOI 10.1021/ja053973d
    • Zhou ZG, Madrid M, Evanseck JD, Madura JD (2005) Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase. J Am Chem Soc 127:17253-17260 (Pubitemid 41794061)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.49 , pp. 17253-17260
    • Zhou, Z.1    Madrid, M.2    Evanseck, J.D.3    Madura, J.D.4
  • 45
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
    • DOI 10.1021/jm001044l
    • Bissantz C, Folkers G, Rognan D (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 43:4759-4767 (Pubitemid 32002687)
    • (2000) Journal of Medicinal Chemistry , vol.43 , Issue.25 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 46
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • DOI 10.1021/jm0203783
    • Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46:2287-2303 (Pubitemid 36637914)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.12 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 49
    • 77954762254 scopus 로고    scopus 로고
    • 3 and residues in the ligand-binding pocket of the vitamin D receptor: A correlated fragment molecular orbital study
    • 10.1016/j.jsbmb.2010.03.028
    • 3 and residues in the ligand-binding pocket of the vitamin D receptor: a correlated fragment molecular orbital study. J Steroid Biochem 121:63-67
    • (2010) J Steroid Biochem , vol.121 , pp. 63-67
    • Yamagishia, K.1    Tokiwaa, H.2    Makishimac, M.3    Yamada, S.4


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