메뉴 건너뛰기




Volumn 503, Issue 1-2, 2000, Pages 31-50

Structure-based 3D-QSAR - Merging the accuracy of structure-based alignments with the computational efficiency of ligand-based methods

Author keywords

3D QSAR; Drug design

Indexed keywords

BENZYLPIPERAZINE DERIVATIVE; BENZYLPIPERIDINE DERIVATIVE; CHOLINESTERASE INHIBITOR; DECAMETHONIUM; DIETHYLSTILBESTROL; EDROPHONIUM; ESTROGEN RECEPTOR; HUPERZINE A; LIGAND; MINAPRINE; MORPHOLINE DERIVATIVE; PCS 1050; PIPERIDINE DERIVATIVE; TACRINE; TETRAHYDROISOQUINOLINE DERIVATIVE; UNCLASSIFIED DRUG;

EID: 0342368665     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-1280(99)00361-9     Document Type: Article
Times cited : (41)

References (58)
  • 2
    • 0030771347 scopus 로고    scopus 로고
    • QSAR and 3D-QSAR in drug design
    • Kubinyi H. QSAR and 3D-QSAR in drug design. Drug Discovery Today. 2:1997;457-467.
    • (1997) Drug Discovery Today , vol.2 , pp. 457-467
    • Kubinyi, H.1
  • 3
    • 0023751431 scopus 로고
    • Comparative molecular field analysis (CoMFA) 1. Effect of shape on binding of steroids to carrier proteins
    • Cramer R.D. III, Patterson D.E., Bunce J.D. Comparative molecular field analysis (CoMFA) 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 110:1988;5959-5967.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 5959-5967
    • Cramer R.D. III1    Patterson, D.E.2    Bunce, J.D.3
  • 5
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz J.D. Structure-based strategies for drug design and discovery. Science. 257:1992;1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, J.D.1
  • 6
    • 0027551285 scopus 로고
    • Non-linear dependencies in CoMFA
    • Kim K. Non-linear dependencies in CoMFA. J. Comput. Aided Mol. Des. 7:1993;71-82.
    • (1993) J. Comput. Aided Mol. Des. , vol.7 , pp. 71-82
    • Kim, K.1
  • 8
    • 0027397374 scopus 로고
    • On the prediction of binding properties of drug molecules by comparative molecular field analysis
    • Klebe G., Abraham U. On the prediction of binding properties of drug molecules by comparative molecular field analysis. J. Med. Chem. 36:1993;70-80.
    • (1993) J. Med. Chem. , vol.36 , pp. 70-80
    • Klebe, G.1    Abraham, U.2
  • 11
    • 0031296686 scopus 로고    scopus 로고
    • CASP2 Experiences with docking flexible ligands using FlexX
    • Kramer B., Rarey M., Lengauer T. CASP2 Experiences with docking flexible ligands using FlexX. Proteins, Suppl. 1:1997;221-225.
    • (1997) Proteins, Suppl. , vol.1 , pp. 221-225
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 13
    • 0029062909 scopus 로고
    • Ligand-protein docking and rational drug design
    • Lybrand T.P. Ligand-protein docking and rational drug design. Curr. Opin. Struct. Biol. 5:1995;224-228.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 224-228
    • Lybrand, T.P.1
  • 14
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng E., Shoichet B.K., Kuntz I.D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 13:1992;505-524.
    • (1992) J. Comput. Chem. , vol.13 , pp. 505-524
    • Meng, E.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 15
    • 0032993815 scopus 로고    scopus 로고
    • Scoring functions: A view from the bench
    • Tame J.R.H. Scoring functions: a view from the bench. J. Comput. Aided Mol. Des. 13:1999;99-108.
    • (1999) J. Comput. Aided Mol. Des. , vol.13 , pp. 99-108
    • Tame, J.R.H.1
  • 16
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de-novo design or 3D database search programs
    • Böhm H.J. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de-novo design or 3D database search programs. J. Comput. Aided Mol. Des. 12:1998;309-323.
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 309-323
    • Böhm, H.J.1
  • 17
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm H.J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8:1994;243-256.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 18
    • 0032488013 scopus 로고    scopus 로고
    • FLEXS: A method for fast flexible ligand superposition
    • Lemmen C., Lengauer T., Klebe G. FLEXS: a method for fast flexible ligand superposition. J. Med. Chem. 41:1998;4502-4520.
    • (1998) J. Med. Chem. , vol.41 , pp. 4502-4520
    • Lemmen, C.1    Lengauer, T.2    Klebe, G.3
  • 19
    • 0027762073 scopus 로고
    • Three-dimensional QSAR of human immunodeficiency virus (i) protease inhibitors. 1. A CoMFA study employing experimentally-determined alignment rules
    • Waller C.L., Oprea T.I., Giolitti A., Marshall G.R. Three-dimensional QSAR of human immunodeficiency virus (i) protease inhibitors. 1. A CoMFA study employing experimentally-determined alignment rules. J. Med. Chem. 36:1993;4152-4160.
    • (1993) J. Med. Chem. , vol.36 , pp. 4152-4160
    • Waller, C.L.1    Oprea, T.I.2    Giolitti, A.3    Marshall, G.R.4
  • 20
    • 0027183015 scopus 로고
    • 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: A comparison of COMFA models based on deduced and experimentally determined active-site geometries
    • De Priest S.A., Mayer D., Naylor C.B., Marshall G.R. 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: a comparison of COMFA models based on deduced and experimentally determined active-site geometries. J. Am. Chem. Soc. 115:1993;5372-5384.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 5372-5384
    • De Priest, S.A.1    Mayer, D.2    Naylor, C.B.3    Marshall, G.R.4
  • 21
    • 0000261607 scopus 로고    scopus 로고
    • Structure-based alignment and comparative molecular field analysis of acetylcholinesterase inhibitors
    • Cho S.J., Garsia M.L., Bier J., Tropsha A. Structure-based alignment and comparative molecular field analysis of acetylcholinesterase inhibitors. J. Med. Chem. 39:1996;5064-5071.
    • (1996) J. Med. Chem. , vol.39 , pp. 5064-5071
    • Cho, S.J.1    Garsia, M.L.2    Bier, J.3    Tropsha, A.4
  • 22
    • 0031442549 scopus 로고    scopus 로고
    • A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantiative structure-activity relationship analysis
    • Pastor M., Cruciani G., Watson K. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantiative structure-activity relationship analysis. J. Med. Chem. 40:1997;4089-4102.
    • (1997) J. Med. Chem. , vol.40 , pp. 4089-4102
    • Pastor, M.1    Cruciani, G.2    Watson, K.3
  • 23
    • 0032015246 scopus 로고    scopus 로고
    • Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxyl]phenyl]-3-(7-amidino-2- naphtyl)-propanoic acid hydrochloride and some analogs to factor Xa using a comparative molecular field analysis
    • Vaz R.J., McLean L.R., Pelton J.T. Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxyl]phenyl]-3-(7-amidino-2- naphtyl)-propanoic acid hydrochloride and some analogs to factor Xa using a comparative molecular field analysis. J. Comput. Aided Mol. Des. 12:1998;99-110.
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 99-110
    • Vaz, R.J.1    McLean, L.R.2    Pelton, J.T.3
  • 24
    • 0023913120 scopus 로고
    • The Steroid and thyroid hormone receptor superfamily
    • Evans R.M. The Steroid and thyroid hormone receptor superfamily. Science. 240:1988;889-895.
    • (1988) Science , vol.240 , pp. 889-895
    • Evans, R.M.1
  • 27
    • 0031059270 scopus 로고    scopus 로고
    • The estradiol pharmacophore: Ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site
    • Anstead G.M., Carlson K.E., Katzenellenbogen J.A. The estradiol pharmacophore: ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site. Steroids. 62:1996;268-303.
    • (1996) Steroids , vol.62 , pp. 268-303
    • Anstead, G.M.1    Carlson, K.E.2    Katzenellenbogen, J.A.3
  • 28
    • 0027252571 scopus 로고
    • A molecular modelling study on the hormone binding site of the estrogen receptor
    • Höltje H.-D., Dall N. A molecular modelling study on the hormone binding site of the estrogen receptor. Pharmazie. 48:1993;243-246.
    • (1993) Pharmazie , vol.48 , pp. 243-246
    • Höltje, H.-D.1    Dall, N.2
  • 29
    • 0028843084 scopus 로고
    • Molecular modeling of the human estrogen receptor and ligand interaction based on site-directed mutagenesis and amino acid sequence homology
    • Lewis D.F.V., Parker M.G., King R.J.B. Molecular modeling of the human estrogen receptor and ligand interaction based on site-directed mutagenesis and amino acid sequence homology. J. Steroid. Biochem. Mol. Biol. 52:1995;55-65.
    • (1995) J. Steroid. Biochem. Mol. Biol. , vol.52 , pp. 55-65
    • Lewis, D.F.V.1    Parker, M.G.2    King, R.J.B.3
  • 31
    • 0026524715 scopus 로고
    • A Model for the determination of the 3d-spatial distribution of the functions of the hormone-binding domain of receptor that bind 3-keto-4-ene steroids
    • Lemesle-Varloot L., Ojasoo T., Mornon J.P., Raynaud J.P. A Model for the determination of the 3d-spatial distribution of the functions of the hormone-binding domain of receptor that bind 3-keto-4-ene steroids. J. Steroid Bicohem. Mol. Biol. 41:1992;369-388.
    • (1992) J. Steroid Bicohem. Mol. Biol. , vol.41 , pp. 369-388
    • Lemesle-Varloot, L.1    Ojasoo, T.2    Mornon, J.P.3    Raynaud, J.P.4
  • 32
    • 0032554879 scopus 로고    scopus 로고
    • Three-dimensional models of estrogen receptor ligand binding domain complexes, based on related crystal structures and mutational and structure-activity relationships data
    • Wurtz J.M., Egner U., Heinrich N., Moras D., Mueller-Fahrnow A. Three-dimensional models of estrogen receptor ligand binding domain complexes, based on related crystal structures and mutational and structure-activity relationships data. J. Med. Chem. 41:1998;1803-1814.
    • (1998) J. Med. Chem. , vol.41 , pp. 1803-1814
    • Wurtz, J.M.1    Egner, U.2    Heinrich, N.3    Moras, D.4    Mueller-Fahrnow, A.5
  • 35
    • 0032446607 scopus 로고    scopus 로고
    • The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
    • Shiau A.K., Barstad D., Loria P.M., Cheng L., Kushner P.J., Agard D.A., Greene G.L. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell. 95:1998;927-937.
    • (1998) Cell , vol.95 , pp. 927-937
    • Shiau, A.K.1    Barstad, D.2    Loria, P.M.3    Cheng, L.4    Kushner, P.J.5    Agard, D.A.6    Greene, G.L.7
  • 36
    • 0029705324 scopus 로고    scopus 로고
    • Automated docking of flexible ligands: Applications of AUTODOCK
    • Goodsell D.S., Morris G.M., Olson A.J. Automated docking of flexible ligands: applications of AUTODOCK. J. Mol. Recognit. 9:1996;1-5.
    • (1996) J. Mol. Recognit. , vol.9 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 37
    • 0033081482 scopus 로고    scopus 로고
    • Modelling of factor Xa-inhibitor complexes: A computational flexible docking approach
    • Rao M.J., Olson A.J. Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach. Prot. Struct. Funct. Gen. 34:1999;173-183.
    • (1999) Prot. Struct. Funct. Gen. , vol.34 , pp. 173-183
    • Rao, M.J.1    Olson, A.J.2
  • 38
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favourable binding sites on biologically important macromolecules
    • Goodford P.J. A computational procedure for determining energetically favourable binding sites on biologically important macromolecules. J. Med. Chem. 28:1985;849-857.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 39
    • 0025158237 scopus 로고
    • A new force field for modelling metalloproteins
    • Vedani A., Huhta D.W. A new force field for modelling metalloproteins. J. Am. Chem. Soc. 112:1990;269-280.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 269-280
    • Vedani, A.1    Huhta, D.W.2
  • 40
    • 0022358609 scopus 로고
    • Lone-pair directionality of H-bond potential functions for molecular mechanics calculations: The inhibition of human carbonic anhydrase II by sulfonamides
    • Vedani A., Dunitz J.D. Lone-pair directionality of H-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides. J. Am. Chem. Soc. 107:1985;7653-7658.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 7653-7658
    • Vedani, A.1    Dunitz, J.D.2
  • 41
    • 0030157593 scopus 로고    scopus 로고
    • A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase
    • Taylor N.R., von Itzstein M. A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase. J. Comput. Aided Mol. Des. 10:1996;233-246.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 233-246
    • Taylor, N.R.1    Von Itzstein, M.2
  • 42
    • 0030828455 scopus 로고    scopus 로고
    • Molecular modelling and 3D-QSAR studies on the interaction mechanism of tripeptidyl thrombin inhibitors with human α-thrombin
    • Jiang H., Chen K., Tang Y., Chen J., Li Q., Wang Q., Ji R. Molecular modelling and 3D-QSAR studies on the interaction mechanism of tripeptidyl thrombin inhibitors with human α-thrombin. J. Med. Chem. 40:1997;3085-3090.
    • (1997) J. Med. Chem. , vol.40 , pp. 3085-3090
    • Jiang, H.1    Chen, K.2    Tang, Y.3    Chen, J.4    Li, Q.5    Wang, Q.6    Ji, R.7
  • 43
    • 13344282748 scopus 로고    scopus 로고
    • An approach to rapid estimation of relative binding affinities of enzyme inhibitors: Application to peptidomimetic inhibitors of the human immunodeficiency virus type I protease
    • Viswanadhan V.N., Reddy M.R., Wlodawer A., Varney M.D., Weinstein J. An approach to rapid estimation of relative binding affinities of enzyme inhibitors: application to peptidomimetic inhibitors of the human immunodeficiency virus type I protease. J. Med. Chem. 39:1996;705-712.
    • (1996) J. Med. Chem. , vol.39 , pp. 705-712
    • Viswanadhan, V.N.1    Reddy, M.R.2    Wlodawer, A.3    Varney, M.D.4    Weinstein, J.5
  • 45
    • 0028101464 scopus 로고
    • Comparative molecular field analysis using GRID force field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b
    • Cruciani G., Watson K. Comparative molecular field analysis using GRID force field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b. J. Med. Chem. 37:1994;2589-2601.
    • (1994) J. Med. Chem. , vol.37 , pp. 2589-2601
    • Cruciani, G.1    Watson, K.2
  • 46
    • 0030159247 scopus 로고    scopus 로고
    • Three-dimensional quantitative structure activity relationships of steroid aromatase inhibitors
    • Oprea T.I., Garcia A.E. Three-dimensional quantitative structure activity relationships of steroid aromatase inhibitors. J. Comput. Aided Mol. Des. 10:1996;186-200.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 186-200
    • Oprea, T.I.1    Garcia, A.E.2
  • 47
    • 0343811524 scopus 로고    scopus 로고
    • Receptor-based three-dimensional quantitative structure-activity relationships of estrogen receptor ligands
    • submitted for publication
    • W. Sippl, Receptor-based three-dimensional quantitative structure-activity relationships of estrogen receptor ligands, J. Comput. Aided. Mol. Des., submitted for publication, 1999.
    • (1999) J. Comput. Aided. Mol. Des.
    • Sippl, W.1
  • 49
    • 0030976004 scopus 로고    scopus 로고
    • Cognitive enhancement therapy for Alzheimer's disease. The way forward
    • Parnetti L., Senin U., Mecocci P. Cognitive enhancement therapy for Alzheimer's disease. The way forward. Drugs Future. 53:1997;752-768.
    • (1997) Drugs Future , vol.53 , pp. 752-768
    • Parnetti, L.1    Senin, U.2    Mecocci, P.3
  • 50
    • 0030763602 scopus 로고    scopus 로고
    • From molecular structure to alzheimer therapy
    • Giacobini E. From molecular structure to alzheimer therapy. Jpn. J. Pharmacol. 74:1997;225-241.
    • (1997) Jpn. J. Pharmacol. , vol.74 , pp. 225-241
    • Giacobini, E.1
  • 52
    • 0027273657 scopus 로고
    • Aminopyridazines - An alternative route to potent muscarinic agonists with noccholinergic syndrome
    • Wermuth C.G. Aminopyridazines - an alternative route to potent muscarinic agonists with noccholinergic syndrome. Farmaco, Ed. Sci. 48:1993;253-274.
    • (1993) Farmaco, Ed. Sci. , vol.48 , pp. 253-274
    • Wermuth, C.G.1
  • 56
    • 0025778840 scopus 로고
    • Atomic structure of acetylcholinesterase from torpedo californica: A prototypic acetylcholine-binding protein
    • Sussman J.L., Silman I. Atomic structure of acetylcholinesterase from torpedo californica: a prototypic acetylcholine-binding protein. Science. 253:1991;872-879.
    • (1991) Science , vol.253 , pp. 872-879
    • Sussman, J.L.1    Silman, I.2
  • 57
    • 0027368530 scopus 로고
    • Quaternary ligand binding to aromatic residues in the active site gorge of acetylcholinesterase
    • Harel M., Sussman J.L. Quaternary ligand binding to aromatic residues in the active site gorge of acetylcholinesterase. Proc. Natl. Acad. Sci. USA. 90:1993;9031-9035.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 9031-9035
    • Harel, M.1    Sussman, J.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.