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Volumn 72, Issue 1, 2008, Pages 65-78

Proteochemometric modeling of the inhibition complexes of matrix metalloproteinases with N-hydroxy-2-[(phenylsulfonyl)amino]acetamide derivatives using topological autocorrelation interaction matrix and model ensemble averaging

Author keywords

Bayesian regularized genetic neural networks; Genetic algorithm; MMP inhibitors; QSAR analysis

Indexed keywords

COLLAGENASE 3; GELATINASE A; GELATINASE B; INTERSTITIAL COLLAGENASE; LIGAND; MATRIX METALLOPROTEINASE INHIBITOR; N HYDROXY 2 [(PHENYLSULFONYL)AMINO] ACETAMIDE DERIVATIVE; STROMELYSIN;

EID: 45449097699     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2008.00675.x     Document Type: Article
Times cited : (8)

References (54)
  • 1
    • 0029150795 scopus 로고
    • Proteolytic remodeling of the extracellular matrix
    • Birkedal-Hansen H. (1995) Proteolytic remodeling of the extracellular matrix. Curr Opin Cell Biol 7: 728 735.
    • (1995) Curr Opin Cell Biol , vol.7 , pp. 728-735
    • Birkedal-Hansen, H.1
  • 2
    • 0036800192 scopus 로고    scopus 로고
    • Metalloproteinase inhibitors: Biological actions and therapeutic opportunities
    • Baker A.H., Edwards D.R., Murphy G. (2002) Metalloproteinase inhibitors: biological actions and therapeutic opportunities. J Cell Sci 115: 3719 3727.
    • (2002) J Cell Sci , vol.115 , pp. 3719-3727
    • Baker, A.H.1    Edwards, D.R.2    Murphy, G.3
  • 3
    • 0034628448 scopus 로고    scopus 로고
    • Protease inhibitors: Current status and future prospects
    • Leung D., Abbenante G., Fairlie D.P. (2000) Protease inhibitors: current status and future prospects. J Med Chem 43: 305 341.
    • (2000) J Med Chem , vol.43 , pp. 305-341
    • Leung, D.1    Abbenante, G.2    Fairlie, D.P.3
  • 5
    • 15644374838 scopus 로고    scopus 로고
    • Discovery of CGS
    • 27023A, a non-peptide, potent, and orally active stromelysin inhibitor that blocks cartilage degradation in rabbits.
    • MacPherson L.J., Bayburt E.K., Capparelli M.P., Carroll B.J., Goldstein R., Justice M.R., Zhu L. et al. (1997) Discovery of CGS 27023A, a non-peptide, potent, and orally active stromelysin inhibitor that blocks cartilage degradation in rabbits. J Med Chem 40: 2525 2532.
    • (1997) J Med Chem , vol.40 , pp. 2525-2532
    • MacPherson, L.J.1    Bayburt, E.K.2    Capparelli, M.P.3    Carroll, B.J.4    Goldstein, R.5    Justice, M.R.6    Zhu, L.7
  • 8
    • 0035855834 scopus 로고    scopus 로고
    • Design and synthesis of matrix metalloproteinase inhibitors guided by molecular modeling. Picking the S1 pocket using conformationally constrained inhibitors
    • Hanessian S., MacKay D.B., Moitessier N. (2001) Design and synthesis of matrix metalloproteinase inhibitors guided by molecular modeling. Picking the S1 pocket using conformationally constrained inhibitors. J Med Chem 44: 3074 3082.
    • (2001) J Med Chem , vol.44 , pp. 3074-3082
    • Hanessian, S.1    MacKay, D.B.2    Moitessier, N.3
  • 9
    • 0035571790 scopus 로고    scopus 로고
    • A comparative docking study and the design of potentially selective MMP inhibitors
    • Hanessian S., Moitessier N., Therrien E. (2001) A comparative docking study and the design of potentially selective MMP inhibitors. J Comput Aided Mol Des 15: 873 881.
    • (2001) J Comput Aided Mol des , vol.15 , pp. 873-881
    • Hanessian, S.1    Moitessier, N.2    Therrien, E.3
  • 10
    • 0037294719 scopus 로고    scopus 로고
    • A quantitative structure-activity relationship study on some matrix metalloproteinase and collagenase inhibitors
    • Kumar D., Gupta S.P. (2003) A quantitative structure-activity relationship study on some matrix metalloproteinase and collagenase inhibitors. Bioorg Med Chem 11: 421 426.
    • (2003) Bioorg Med Chem , vol.11 , pp. 421-426
    • Kumar, D.1    Gupta, S.P.2
  • 11
    • 33846906016 scopus 로고    scopus 로고
    • Matrix metalloproteinases (MMPs): Chemical-biological functions and (Q)SARs
    • Verma R.P., Hansch C. (2007) Matrix metalloproteinases (MMPs): chemical-biological functions and (Q)SARs. Bioorg Med Chem 15: 2223 2268.
    • (2007) Bioorg Med Chem , vol.15 , pp. 2223-2268
    • Verma, R.P.1    Hansch, C.2
  • 12
    • 33646186011 scopus 로고    scopus 로고
    • Linear and nonlinear QSAR study of N-hydroxy-2-[(phenylsulfonyl)amino] acetamide derivatives as matrix metalloproteinase inhibitors
    • Fernández M., Caballero J., Tundidor-Camba A. (2006) Linear and nonlinear QSAR study of N-hydroxy-2-[(phenylsulfonyl)amino] acetamide derivatives as matrix metalloproteinase inhibitors. Bioorg Med Chem 14: 4137 4150.
    • (2006) Bioorg Med Chem , vol.14 , pp. 4137-4150
    • Fernández, M.1    Caballero, J.2    Tundidor-Camba, A.3
  • 13
    • 34547093412 scopus 로고    scopus 로고
    • QSAR modeling of matrix metalloproteinase inhibition by N-hydroxy-alpha-phenylsulfonylacetamide derivatives
    • Fernández M., Caballero J. (2007) QSAR modeling of matrix metalloproteinase inhibition by N-hydroxy-alpha-phenylsulfonylacetamide derivatives. Bioorg Med Chem 15: 6298 6310.
    • (2007) Bioorg Med Chem , vol.15 , pp. 6298-6310
    • Fernández, M.1    Caballero, J.2
  • 14
    • 84954206661 scopus 로고    scopus 로고
    • Proteochemometrics: A tool for modeling the molecular interaction space
    • In: Kubinyi, H., Müller, G., editors. Weinheim: Wiley-VCH. p.
    • Wikberg S.J.E., Lapinsh M., Prusis P. (2004) Proteochemometrics: a tool for modeling the molecular interaction space. In: Kubinyi H., Müller G., editors. Chemogenomics in Drug Discovery: A Medicinal Chemistry Perspective. Weinheim: Wiley-VCH p. 289 309.
    • (2004) Chemogenomics in Drug Discovery: A Medicinal Chemistry Perspective. , pp. 289-309
    • Wikberg, S.J.E.1    Lapinsh, M.2    Prusis, P.3
  • 15
    • 33745380521 scopus 로고    scopus 로고
    • Amino acid sequence autocorrelation vectors and ensembles of Bayesian-regularized genetic neural networks for prediction of conformational stability of human lysozyme mutants
    • Caballero J., Fernández L., Abreu J.I., Fernández M. (2006) Amino acid sequence autocorrelation vectors and ensembles of Bayesian-regularized genetic neural networks for prediction of conformational stability of human lysozyme mutants. J Chem Inf Model 46: 1255 1268.
    • (2006) J Chem Inf Model , vol.46 , pp. 1255-1268
    • Caballero, J.1    Fernández, L.2    Abreu, J.I.3    Fernández, M.4
  • 16
    • 34250845013 scopus 로고    scopus 로고
    • Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines
    • Caballero J., Fernández L., Gariga M., Abreu J.I., Collina S., Fernández M. (2007) Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines. J Mol Graph Model 26: 166 178.
    • (2007) J Mol Graph Model , vol.26 , pp. 166-178
    • Caballero, J.1    Fernández, L.2    Gariga, M.3    Abreu, J.I.4    Collina, S.5    Fernández, M.6
  • 17
    • 34248549553 scopus 로고    scopus 로고
    • Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: Gene V protein mutants
    • Fernández L., Caballero J., Abreu J.I., Fernández M. (2007) Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants. Proteins 67: 834 852.
    • (2007) Proteins , vol.67 , pp. 834-852
    • Fernández, L.1    Caballero, J.2    Abreu, J.I.3    Fernández, M.4
  • 18
    • 36248942933 scopus 로고    scopus 로고
    • Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants using amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesian-regularized genetic neural networks
    • Fernández M., Abreu J.I., Caballero J., Gariga M., Fernández L. (2007) Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants using amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesian-regularized genetic neural networks. Mol Simul 33: 1045 1056.
    • (2007) Mol Simul , vol.33 , pp. 1045-1056
    • Fernández, M.1    Abreu, J.I.2    Caballero, J.3    Gariga, M.4    Fernández, L.5
  • 19
    • 0000412029 scopus 로고
    • Optimization of parameters for semi-empirical methods
    • Stewart J.J.P. (1989) Optimization of parameters for semi-empirical methods. J Comput Chem 10: 210 220.
    • (1989) J Comput Chem , vol.10 , pp. 210-220
    • Stewart, J.J.P.1
  • 21
    • 0030278229 scopus 로고    scopus 로고
    • Locating biologically active compounds in medium-sized heterogeneous datasets by topological autocorrelation vectors: Dopamine and benzodiazepine agonists
    • Bauknecht H., Zell A., Bayer H., Levi P., Wagener M., Sadowski J., Gasteiger J. (1996) Locating biologically active compounds in medium-sized heterogeneous datasets by topological autocorrelation vectors: dopamine and benzodiazepine agonists. J Chem Inf Comput Sci 36: 1205 1213.
    • (1996) J Chem Inf Comput Sci , vol.36 , pp. 1205-1213
    • Bauknecht, H.1    Zell, A.2    Bayer, H.3    Levi, P.4    Wagener, M.5    Sadowski, J.6    Gasteiger, J.7
  • 22
    • 0001057103 scopus 로고
    • Autocorrelation of a topological structure: A new molecular descriptor
    • Moreau G., Broto P. (1980) Autocorrelation of a topological structure: a new molecular descriptor. Nouv J Chim 4: 359 360.
    • (1980) Nouv J Chim , vol.4 , pp. 359-360
    • Moreau, G.1    Broto, P.2
  • 23
  • 24
    • 0001025418 scopus 로고
    • Bayesian interpolation
    • Mackay D.J.C. (1992) Bayesian interpolation. Neural Comput 4: 415 447.
    • (1992) Neural Comput , vol.4 , pp. 415-447
    • MacKay, D.J.C.1
  • 25
    • 0002704818 scopus 로고
    • A practical Bayesian framework for backprop networks
    • Mackay D.J.C. (1992) A practical Bayesian framework for backprop networks. Neural Comput 4: 448 472.
    • (1992) Neural Comput , vol.4 , pp. 448-472
    • MacKay, D.J.C.1
  • 26
    • 30744458142 scopus 로고    scopus 로고
    • Linear and nonlinear modeling of antifungal activity of some heterocyclic ring derivatives using multiple linear regression and Bayesian-regulated neural networks
    • Caballero J., Fernández M. (2006) Linear and nonlinear modeling of antifungal activity of some heterocyclic ring derivatives using multiple linear regression and Bayesian-regulated neural networks. J Mol Model 12: 168 181.
    • (2006) J Mol Model , vol.12 , pp. 168-181
    • Caballero, J.1    Fernández, M.2
  • 27
    • 33846815342 scopus 로고    scopus 로고
    • i) of some cruzain ketone-based inhibitors using 2D spatial autocorrelation vectors and data-diverse ensembles of Bayesian-regularized geneticneural networks
    • i) of some cruzain ketone-based inhibitors using 2D spatial autocorrelation vectors and data-diverse ensembles of Bayesian-regularized geneticneural networks. QSAR Comb Sci 26: 27 40.
    • (2007) QSAR Comb Sci , vol.26 , pp. 27-40
    • Caballero, J.1    Tundidor-Camba, A.2    Fernández, M.3
  • 28
    • 0029970338 scopus 로고    scopus 로고
    • Evolutionary optimization in quantitative structure-activity relationship: An application of genetic neural network
    • So S., Karplus M. (1996) Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural network. J Med Chem 39: 1521 1530.
    • (1996) J Med Chem , vol.39 , pp. 1521-1530
    • So, S.1    Karplus, M.2
  • 29
    • 0033549850 scopus 로고    scopus 로고
    • Robust QSAR models using Bayesian regularized neural networks
    • Burden F.R., Winkler D.A. (1999) Robust QSAR models using Bayesian regularized neural networks. J Med Chem 42: 3183 3187.
    • (1999) J Med Chem , vol.42 , pp. 3183-3187
    • Burden, F.R.1    Winkler, D.A.2
  • 30
    • 12444281776 scopus 로고    scopus 로고
    • Bayesian neural nets for modeling in drug discovery
    • Winkler D.A., Burden F.R. (2004) Bayesian neural nets for modeling in drug discovery. Biosilico 2: 104 111.
    • (2004) Biosilico , vol.2 , pp. 104-111
    • Winkler, D.A.1    Burden, F.R.2
  • 31
    • 28944449555 scopus 로고    scopus 로고
    • Modeling of cyclin-dependent kinase inhibition by 1H-pyrazolo [3,4-d] pyrimidine derivatives using artificial neural networks ensembles
    • Fernández M., Tundidor-Camba A., Caballero J. (2005) Modeling of cyclin-dependent kinase inhibition by 1H-pyrazolo [3,4-d] pyrimidine derivatives using artificial neural networks ensembles. J Chem Inf Model 45: 1884 1895.
    • (2005) J Chem Inf Model , vol.45 , pp. 1884-1895
    • Fernández, M.1    Tundidor-Camba, A.2    Caballero, J.3
  • 32
    • 27744456972 scopus 로고    scopus 로고
    • Modeling of farnesyltransferase inhibition by some thiol and non-thiol peptidomimetic inhibitors using genetic neural networks and RDF approaches
    • González M.P., Caballero J., Tundidor-Camba A., Helguera A.M., Fernández M. (2006) Modeling of farnesyltransferase inhibition by some thiol and non-thiol peptidomimetic inhibitors using genetic neural networks and RDF approaches. Bioorg Med Chem 14: 200 213.
    • (2006) Bioorg Med Chem , vol.14 , pp. 200-213
    • González, M.P.1    Caballero, J.2    Tundidor-Camba, A.3    Helguera, A.M.4    Fernández, M.5
  • 33
    • 27744524965 scopus 로고    scopus 로고
    • Modeling of activity of cyclic urea HIV-1 protease inhibitors using regularized-artificial neural networks
    • Fernández M., Caballero J. (2006) Modeling of activity of cyclic urea HIV-1 protease inhibitors using regularized-artificial neural networks. Bioorg Med Chem 14: 280 294.
    • (2006) Bioorg Med Chem , vol.14 , pp. 280-294
    • Fernández, M.1    Caballero, J.2
  • 34
    • 33750495370 scopus 로고    scopus 로고
    • Bayesian-regularized genetic neural networks applied to the modeling of non-peptide antagonists for the human luteinizing hormone-releasing hormone receptor
    • Fernández M., Caballero J. (2006) Bayesian-regularized genetic neural networks applied to the modeling of non-peptide antagonists for the human luteinizing hormone-releasing hormone receptor. J Mol Graph Model 25: 410 422.
    • (2006) J Mol Graph Model , vol.25 , pp. 410-422
    • Fernández, M.1    Caballero, J.2
  • 35
    • 33845769362 scopus 로고    scopus 로고
    • Modeling of acetylcholinesterase inhibition by tacrine analogues using Bayesian-regularized genetic neural networks and ensemble averaging
    • Fernández M., Carreiras M.C., Marco J.L., Caballero J. (2006) Modeling of acetylcholinesterase inhibition by tacrine analogues using Bayesian-regularized genetic neural networks and ensemble averaging. J Enzyme Inhib Med Chem 21: 647 661.
    • (2006) J Enzyme Inhib Med Chem , vol.21 , pp. 647-661
    • Fernández, M.1    Carreiras, M.C.2    Marco, J.L.3    Caballero, J.4
  • 36
    • 33947168866 scopus 로고    scopus 로고
    • QSAR models for predicting the activity of non-peptide luteinizing hormone-releasing hormone (LHRH) antagonists derived from erythromycin a using quantum chemical properties
    • Fernández M., Caballero J. (2007) QSAR models for predicting the activity of non-peptide luteinizing hormone-releasing hormone (LHRH) antagonists derived from erythromycin A using quantum chemical properties. J Mol Model 13: 465 476.
    • (2007) J Mol Model , vol.13 , pp. 465-476
    • Fernández, M.1    Caballero, J.2
  • 38
    • 0001447184 scopus 로고
    • Neural network studies. 1. Comparison of overfitting and overtraining
    • Tetko I., Livingstone D.J., Luik A.I. (1995) Neural network studies. 1. Comparison of overfitting and overtraining. J Chem Inf Comput Sci 35: 826 833.
    • (1995) J Chem Inf Comput Sci , vol.35 , pp. 826-833
    • Tetko, I.1    Livingstone, D.J.2    Luik, A.I.3
  • 40
    • 28444497469 scopus 로고    scopus 로고
    • Chance correlation in variable subset regression: Influence of the objective function, the selection mechanism, and ensemble averaging
    • Baumann K. (2005) Chance correlation in variable subset regression: influence of the objective function, the selection mechanism, and ensemble averaging. QSAR Comb Sci 24: 1033 1046.
    • (2005) QSAR Comb Sci , vol.24 , pp. 1033-1046
    • Baumann, K.1
  • 42
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • Kohonen T. (1982) Self-organized formation of topologically correct feature maps. Biol Cybern 43: 59 69.
    • (1982) Biol Cybern , vol.43 , pp. 59-69
    • Kohonen, T.1
  • 45
    • 1642380461 scopus 로고    scopus 로고
    • The problem of overfitting
    • Hawkins D.M. (2004) The problem of overfitting. J Chem Inf Comput Sci 44: 1 12.
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 1-12
    • Hawkins, D.M.1
  • 46
    • 23844539732 scopus 로고    scopus 로고
    • Interpreting computational neural network QSAR models: A detailed interpretation of the weights and biases
    • Guha R., Stanton D.T., Jurs P.C. (2005) Interpreting computational neural network QSAR models: a detailed interpretation of the weights and biases. J Chem Inf Model 45: 1109 1121.
    • (2005) J Chem Inf Model , vol.45 , pp. 1109-1121
    • Guha, R.1    Stanton, D.T.2    Jurs, P.C.3
  • 47
    • 0141890762 scopus 로고    scopus 로고
    • On the physical interpretation of QSAR models
    • Stanton D.T. (2003) On the physical interpretation of QSAR models. J Chem Inf Comput Sci 43: 1423 1433.
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 1423-1433
    • Stanton, D.T.1
  • 48
    • 0029666453 scopus 로고    scopus 로고
    • Understanding the P1′ specificity of the matrix metalloproteinases: Effect of S1′ pocket mutations in matrilysin and stromelysin-1
    • Welch A.R., Holman C.M., Huber M., Brenner M.C., Browner M.F., Van Wart H.E. (1996) Understanding the P1′ specificity of the matrix metalloproteinases: effect of S1′ pocket mutations in matrilysin and stromelysin-1. Biochemistry 35: 10103 10109.
    • (1996) Biochemistry , vol.35 , pp. 10103-10109
    • Welch, A.R.1    Holman, C.M.2    Huber, M.3    Brenner, M.C.4    Browner, M.F.5    Van Wart, H.E.6
  • 49
    • 0032712582 scopus 로고    scopus 로고
    • Crystal structure of the stromelysin catalytic domain at 2.0 a resolution: Inhibitor-induced conformational changes
    • Chen L., Rydel T.J., Gu F., Dunaway C.M., Pikul S., Dunham K.M., Barnett B.L. (1999) Crystal structure of the stromelysin catalytic domain at 2.0 A resolution: inhibitor-induced conformational changes. J Mol Biol 293: 545 557.
    • (1999) J Mol Biol , vol.293 , pp. 545-557
    • Chen, L.1    Rydel, T.J.2    Gu, F.3    Dunaway, C.M.4    Pikul, S.5    Dunham, K.M.6    Barnett, B.L.7
  • 52
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall T.A. (1999) BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95 98.
    • (1999) Nucleic Acids Symp Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 53
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673 4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 54
    • 34547838174 scopus 로고    scopus 로고
    • Insight into the structural determinants for selective inhibition of matrix metalloproteinases
    • Pirard B. (2007) Insight into the structural determinants for selective inhibition of matrix metalloproteinases. Drug Discov Today 12: 640 646.
    • (2007) Drug Discov Today , vol.12 , pp. 640-646
    • Pirard, B.1


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