메뉴 건너뛰기




Volumn 914, Issue , 2012, Pages 271-284

Predicting the biological activities through QSAR analysis and docking-based scoring

Author keywords

Comparative molecular field analysis (CoMFA); Comparative molecular similarity index analysis (CoMSIA); G protein coupled receptors (GPCRs); Ligand based drug discovery; Molecular Docking; Multiple linear regression (MLR); Partial least square (PLS) regression; Quantitative structure activity relationships (QSAR); Structure based drug discovery

Indexed keywords

BETA 2 ADRENERGIC RECEPTOR; G PROTEIN COUPLED RECEPTOR;

EID: 84934443969     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-23-6_16     Document Type: Article
Times cited : (39)

References (53)
  • 1
    • 77949370572 scopus 로고    scopus 로고
    • The impact of GPCR structures on pharmacology and structure-based drug design
    • Congreve M, Marshall F (2010) The impact of GPCR structures on pharmacology and structure-based drug design. Br J Pharmacol 159:986-996
    • (2010) Br J Pharmacol , vol.159 , pp. 986-996
    • Congreve, M.1    Marshall, F.2
  • 2
    • 59149097144 scopus 로고    scopus 로고
    • Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery
    • Vilar S, Cozza G, Moro S (2008) Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery. Curr Top Med Chem 8:1555-1572
    • (2008) Curr Top Med Chem , vol.8 , pp. 1555-1572
    • Vilar, S.1    Cozza, G.2    Moro, S.3
  • 3
    • 72849148589 scopus 로고    scopus 로고
    • Ligand and structurebased methodologies for the prediction of the activity of G protein-coupled receptor ligands
    • Costanzi S, Tikhonova IG, Harden TK, Jacobson KA (2009) Ligand and structurebased methodologies for the prediction of the activity of G protein-coupled receptor ligands. J Comput Aided Mol Des 23:747-754
    • (2009) J Comput Aided Mol des , vol.23 , pp. 747-754
    • Costanzi, S.1    Tikhonova, I.G.2    Harden, T.K.3    Jacobson, K.A.4
  • 5
    • 76249121106 scopus 로고    scopus 로고
    • Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: Development and application to the b 2 -adrenergic receptor
    • Vilar S, Karpiak J, Costanzi S (2010) Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: Development and application to the b 2 -adrenergic receptor. J Comput Chem 31:707-720
    • (2010) J Comput Chem , vol.31 , pp. 707-720
    • Vilar, S.1    Karpiak, J.2    Costanzi, S.3
  • 6
    • 54049156024 scopus 로고    scopus 로고
    • Principles for 3D/4D QSAR classification of drugs
    • Potemkin V, Grishina M (2008) Principles for 3D/4D QSAR classification of drugs. Drug Discov Today 13:952-959
    • (2008) Drug Discov Today , vol.13 , pp. 952-959
    • Potemkin, V.1    Grishina, M.2
  • 7
    • 42449097683 scopus 로고    scopus 로고
    • How the parts organize in the whole? A top-down view of molecular descriptors and properties for QSAR and drug design
    • Estrada E (2008) How the parts organize in the whole? A top-down view of molecular descriptors and properties for QSAR and drug design. Mini Rev Med Chem 8:213-221
    • (2008) Mini Rev Med Chem , vol.8 , pp. 213-221
    • Estrada, E.1
  • 8
    • 0023751431 scopus 로고
    • Comparative Molecular-Field Analysis (CoMFA).1. Effect of Shape on Binding of Steroids to Carrier Proteins
    • Cramer RD, Patterson DE, Bunce JD (1988) Comparative Molecular-Field Analysis (CoMFA).1. Effect of Shape on Binding of Steroids to Carrier Proteins. J Am Chem Soc 110:5959-5967
    • (1988) J Am Chem Soc , vol.110 , pp. 5959-5967
    • Cramer, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 9
    • 0027944195 scopus 로고
    • Molecular Similarity Indexes in A Comparative-Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological-Activity
    • Klebe G, Abraham U, Mietzner T (1994) Molecular Similarity Indexes in A Comparative-Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological-Activity. J Med Chem 37:4130-4146
    • (1994) J Med Chem , vol.37 , pp. 4130-4146
    • Klebe, G.1    Abraham, U.2    Mietzner, T.3
  • 10
    • 0000220431 scopus 로고
    • Modeling data tables by principal components and PLSclass patterns and quantitative predictive relations
    • Wold S, Albano C, Dunn WJ, Esbensen K, Hellberg S, Johansson E et al (1984) Modeling data tables by principal components and PLSclass patterns and quantitative predictive relations. Analusis 12:477-485
    • (1984) Analusis , vol.12 , pp. 477-485
    • Wold, S.1    Albano, C.2    Dunn, W.J.3    Esbensen, K.4    Hellberg, S.5    Johansson, E.6
  • 11
    • 11144325691 scopus 로고
    • Partial leastsquares regression: A tutorial
    • Geladi P, Kowalski BR (1986) Partial leastsquares regression: a tutorial. Anal Chim Acta 185:1-17
    • (1986) Anal Chim Acta , vol.185 , pp. 1-17
    • Geladi, P.1    Kowalski, B.R.2
  • 12
    • 16844364506 scopus 로고    scopus 로고
    • Autocorrelation of molecular electrostatic potential surface properties combined with partial least squares analysis as alternative attractive tool to generate ligand-based 3D-QSARs
    • Moro S, Bacilieri M, Ferrari C, Spalluto G (2005) Autocorrelation of molecular electrostatic potential surface properties combined with partial least squares analysis as alternative attractive tool to generate ligand-based 3D-QSARs. Curr Drug Discov Technol 2:13-21
    • (2005) Curr Drug Discov Technol , vol.2 , pp. 13-21
    • Moro, S.1    Bacilieri, M.2    Ferrari, C.3    Spalluto, G.4
  • 13
    • 24744444738 scopus 로고    scopus 로고
    • Autocorrelation of molecular electrostatic potential surface properties combined with partial least squares analysis as new strategy for the prediction of the activity of human A 3 adenosine receptor antagonists
    • Moro S, Bacilieri M, Cacciari B, Spalluto G (2005) Autocorrelation of molecular electrostatic potential surface properties combined with partial least squares analysis as new strategy for the prediction of the activity of human A 3 adenosine receptor antagonists. J Med Chem 48:5698-5704
    • (2005) J Med Chem , vol.48 , pp. 5698-5704
    • Moro, S.1    Bacilieri, M.2    Cacciari, B.3    Spalluto, G.4
  • 14
    • 0034710718 scopus 로고    scopus 로고
    • GRid-INdependent descriptors (GRIND): A novel class of alignment-independent three-dimensional molecular descriptors
    • Pastor M, Cruciani G, McLay I, Pickett S, Clementi S (2000) GRid-INdependent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors. J Med Chem 43:3233-3243
    • (2000) J Med Chem , vol.43 , pp. 3233-3243
    • Pastor, M.1    Cruciani, G.2    McLay, I.3    Pickett, S.4    Clementi, S.5
  • 15
    • 2942604990 scopus 로고    scopus 로고
    • GRIND/ALMOND investigations on CysLT1 receptor antagonists of the quinolinyl(bridged)aryl type
    • Benedetti P, Mannhold R, Cruciani G, Ottaviani G (2004) GRIND/ALMOND investigations on CysLT1 receptor antagonists of the quinolinyl(bridged)aryl type. Bioorg Med Chem 12:3607-3617
    • (2004) Bioorg Med Chem , vol.12 , pp. 3607-3617
    • Benedetti, P.1    Mannhold, R.2    Cruciani, G.3    Ottaviani, G.4
  • 16
    • 71749083052 scopus 로고    scopus 로고
    • Rhodopsin and the others: A historical perspective on structural studies of G protein-coupled receptor
    • Costanzi S, Siegel J, Tikhonova IG, Jacobson KA (2009) Rhodopsin and the others: a historical perspective on structural studies of G protein-coupled receptor. Curr Pharm Des 15:3994-4002
    • (2009) Curr Pharm des , vol.15 , pp. 3994-4002
    • Costanzi, S.1    Siegel, J.2    Tikhonova, I.G.3    Jacobson, K.A.4
  • 17
    • 58149203324 scopus 로고    scopus 로고
    • Discovery of new GPCR biology: One receptor structure at a time
    • Hanson MA, Stevens RC (2009) Discovery of new GPCR biology: one receptor structure at a time. Structure 17:8-14
    • (2009) Structure , vol.17 , pp. 8-14
    • Hanson, M.A.1    Stevens, R.C.2
  • 18
    • 43949095157 scopus 로고    scopus 로고
    • On the applicability of GPCR homology models to computer-aided drug discovery: A comparison between in silico and crystal structures of the beta2-adrenergic receptor
    • Costanzi S (2008) On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta2-adrenergic receptor. J Med Chem 51:2907-2914
    • (2008) J Med Chem , vol.51 , pp. 2907-2914
    • Costanzi, S.1
  • 20
    • 67349088738 scopus 로고    scopus 로고
    • Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
    • Dixon J.S., Moult J., Stevens R.C. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat. Rev. Drug Discov. 8, 455-463
    • (2009) Nat. Rev. Drug Discov. , vol.8 , pp. 455-463
    • Dixon, J.S.1    Moult, J.2    Stevens, R.C.3
  • 21
    • 77955113796 scopus 로고    scopus 로고
    • Modeling G protein-coupled receptors: A concrete possibility
    • Costanzi S (2010) Modeling G protein-coupled receptors: a concrete possibility. Chimica Oggi-Chemistry Today 28:26-31
    • (2010) Chimica Oggi-Chemistry Today , vol.28 , pp. 26-31
    • Costanzi, S.1
  • 22
    • 33644532518 scopus 로고    scopus 로고
    • Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
    • Chipot C, Rozanska X, Dixit SB (2005) Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des 19:765-770
    • (2005) J Comput Aided Mol des , vol.19 , pp. 765-770
    • Chipot, C.1    Rozanska, X.2    Dixit, S.B.3
  • 23
    • 33845335781 scopus 로고    scopus 로고
    • Towards predictive ligand design with free-energy based computational methods?
    • Foloppe N, Hubbard R (2006) Towards predictive ligand design with free-energy based computational methods? Curr Med Chem 13:3583-3608
    • (2006) Curr Med Chem , vol.13 , pp. 3583-3608
    • Foloppe, N.1    Hubbard, R.2
  • 25
    • 50249156843 scopus 로고    scopus 로고
    • Selective structure-based virtual screening for full and partial agonists of the b 2-adrenergic receptor
    • de Graaf C, Rognan D (2008) Selective structure-based virtual screening for full and partial agonists of the b 2-adrenergic receptor. J Med Chem 51:4978-4985
    • (2008) J Med Chem , vol.51 , pp. 4978-4985
    • De Graaf, C.1    Rognan, D.2
  • 26
    • 65049089399 scopus 로고    scopus 로고
    • Identifying conformational changes of the b 2 -adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators
    • Reynolds KA, Katritch V, Abagyan R (2009) Identifying conformational changes of the b 2 -adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J Comput Aided Mol Des 23:273-288
    • (2009) J Comput Aided Mol des , vol.23 , pp. 273-288
    • Reynolds, K.A.1    Katritch, V.2    Abagyan, R.3
  • 27
    • 77649196223 scopus 로고    scopus 로고
    • GPCR 3D homology models for ligand screening: Lessons learned from blind predictions of adenosine A 2A receptor complex
    • Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R (2010) GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A 2A receptor complex. Proteins 78:197-211
    • (2010) Proteins , vol.78 , pp. 197-211
    • Katritch, V.1    Rueda, M.2    Lam, P.C.3    Yeager, M.4    Abagyan, R.5
  • 28
    • 77950823494 scopus 로고    scopus 로고
    • Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor
    • Bhattacharya S, Vaidehi N (2010) Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor. J Am Chem Soc 132:5205-5214
    • (2010) J Am Chem Soc , vol.132 , pp. 5205-5214
    • Bhattacharya, S.1    Vaidehi, N.2
  • 29
    • 79751525956 scopus 로고    scopus 로고
    • Dockingbased virtual screening for ligands of G proteincoupled receptors: Not only crystal structures but also in silico models
    • Submitted for publication
    • Vilar S, Ferino G, Sharangdhar SP, Berk B, Cavasotto CN, Costanzi S (2011) Dockingbased virtual screening for ligands of G proteincoupled receptors: not only crystal structures but also in silico models. J. Mol. Graph. Model 29, 614-623. Submitted for publication.
    • (2011) J. Mol. Graph. Model , vol.29 , pp. 614-623
    • Vilar, S.1    Ferino, G.2    Sharangdhar, S.P.3    Berk, B.4    Cavasotto, C.N.5    Costanzi, S.6
  • 30
    • 39849101195 scopus 로고    scopus 로고
    • Use of the X-ray structure of the b 2 -adrenergic receptor for drug discovery
    • Topiol S, Sabio M (2008) Use of the X-ray structure of the b 2 -adrenergic receptor for drug discovery. Bioorg Med Chem Lett 18:1598-1602
    • (2008) Bioorg Med Chem Lett , vol.18 , pp. 1598-1602
    • Topiol, S.1    Sabio, M.2
  • 33
    • 77649204282 scopus 로고    scopus 로고
    • Structure-based discovery of novel chemotypes for adenosine A 2A receptor antagonists
    • Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M et al (2010) Structure-based discovery of novel chemotypes for adenosine A 2A receptor antagonists. J Med Chem 53: 1799-1809
    • (2010) J Med Chem , vol.53 , pp. 1799-1809
    • Katritch, V.1    Jaakola, V.P.2    Lane, J.R.3    Lin, J.4    Ijzerman, A.P.5    Yeager, M.6
  • 34
    • 33748747498 scopus 로고    scopus 로고
    • Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation
    • Vaidehi N, Schlyer S, Trabanino RJ, Floriano WB, Abrol R, Sharma S et al (2006) Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation. J Biol Chem 281:27613-27620
    • (2006) J Biol Chem , vol.281 , pp. 27613-27620
    • Vaidehi, N.1    Schlyer, S.2    Trabanino, R.J.3    Floriano, W.B.4    Abrol, R.5    Sharma, S.6
  • 35
    • 42149139028 scopus 로고    scopus 로고
    • A virtual screen for diverse ligands: Discovery of selective G protein-coupled receptor antagonists
    • Engel S, Skoumbourdis AP, Childress J, Neumann S, Deschamps JR, Thomas CJ et al (2008) A virtual screen for diverse ligands: Discovery of selective G protein-coupled receptor antagonists. J Am Chem Soc 130:5115-5123
    • (2008) J Am Chem Soc , vol.130 , pp. 5115-5123
    • Engel, S.1    Skoumbourdis, A.P.2    Childress, J.3    Neumann, S.4    Deschamps, J.R.5    Thomas, C.J.6
  • 36
    • 39149097541 scopus 로고    scopus 로고
    • Discovery of novel agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening
    • Tikhonova IG, Sum CS, Neumann S, Engel S, Raaka BM, Costanzi S et al (2008) Discovery of novel agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening. J Med Chem 51:625-633
    • (2008) J Med Chem , vol.51 , pp. 625-633
    • Tikhonova, I.G.1    Sum, C.S.2    Neumann, S.3    Engel, S.4    Raaka, B.M.5    Costanzi, S.6
  • 37
    • 39149107126 scopus 로고    scopus 로고
    • Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening
    • Cavasotto CN, Orry AJ, Murgolo NJ, Czarniecki MF, Kocsi SA et al (2008) Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J Med Chem 51:581-588
    • (2008) J Med Chem , vol.51 , pp. 581-588
    • Cavasotto, C.N.1    Orry, A.J.2    Murgolo, N.J.3    Czarniecki, M.F.4    Kocsi, S.A.5
  • 39
    • 84880534055 scopus 로고    scopus 로고
    • E-Dragon, Virtual Computational Chemistry Laboratory, www.vcclab.org
    • Dragon, Talete, SRL, www.talete.mi.it ; E-Dragon, Virtual Computational Chemistry Laboratory, www.vcclab.org .
    • Dragon, Talete, SRL
  • 40
    • 84880569194 scopus 로고    scopus 로고
    • The CODESSA PRO project
    • The CODESSA PRO project, www.codessa-pro. com .
  • 41
    • 84880532082 scopus 로고    scopus 로고
    • MOE Chemical Computing Group Inc.
    • MOE, Chemical Computing Group, Inc., www.chemcomp.com .
  • 42
    • 84880516510 scopus 로고    scopus 로고
    • Schrödinger LLC
    • Schrödinger, LLC, www.schrodinger.com .
  • 43
    • 84880558822 scopus 로고    scopus 로고
    • ICM MolSoft LLC
    • ICM, MolSoft, LLC, www.molsoft.com .
  • 44
    • 84880550634 scopus 로고    scopus 로고
    • SYBYL Tripos Inc.
    • SYBYL, Tripos, Inc., www.tripos.com .
  • 45
    • 84880542411 scopus 로고    scopus 로고
    • GOLD Cambridge Crystallographic Data Centre
    • GOLD, Cambridge Crystallographic Data Centre, www.ccdc.cam.ac.uk/ products/life- sciences/gold .
  • 47
    • 84880518439 scopus 로고    scopus 로고
    • STATISTICA StatSoft, Inc.
    • STATISTICA, StatSoft, Inc., www.statsoft. com .
  • 48
    • 38549164272 scopus 로고    scopus 로고
    • GLIDA: GPCR-ligand database for chemical genomics drug discovery-database and tools update
    • Okuno Y, Tamon A, Yabuuchi H, Niijima S, Minowa Y, Tonomura K et al (2008) GLIDA: GPCR-ligand database for chemical genomics drug discovery-database and tools update. Nucleic Acids Res 36:D907-D912
    • (2008) Nucleic Acids Res , vol.36
    • Okuno, Y.1    Tamon, A.2    Yabuuchi, H.3    Niijima, S.4    Minowa, Y.5    Tonomura, K.6
  • 49
    • 34447508092 scopus 로고    scopus 로고
    • P2Y 1 antagonists: Combining receptor-based modeling and QSAR for a quantitative prediction of the biological activity based on consensus scoring
    • Costanzi S, Tikhonova IG, Ohno M, Roh EJ, Joshi BV, Colson AO et al (2007) P2Y 1 antagonists: Combining receptor-based modeling and QSAR for a quantitative prediction of the biological activity based on consensus scoring. J Med Chem 50:3229-3241
    • (2007) J Med Chem , vol.50 , pp. 3229-3241
    • Costanzi, S.1    Tikhonova, I.G.2    Ohno, M.3    Roh, E.J.4    Joshi, B.V.5    Colson, A.O.6
  • 51
    • 34047144922 scopus 로고    scopus 로고
    • Design of early validation trials of biomarkers
    • Normolle D, Ruffin MT, Brenner D (2005) Design of early validation trials of biomarkers. Cancer Inform 1:25-31
    • (2005) Cancer Inform , vol.1 , pp. 25-31
    • Normolle, D.1    Ruffin, M.T.2    Brenner, D.3
  • 52
    • 0029584326 scopus 로고
    • Importance of events per independent variable in proportional hazards analysis I. Background, goals, and general strategy
    • Concato J, Peduzzi P, Holford TR, Feinstein AR (1995) Importance of events per independent variable in proportional hazards analysis I. Background, goals, and general strategy. J Clin Epidemiol 48:1495-1501
    • (1995) J Clin Epidemiol , vol.48 , pp. 1495-1501
    • Concato, J.1    Peduzzi, P.2    Holford, T.R.3    Feinstein, A.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.