메뉴 건너뛰기




Volumn 685, Issue , 2011, Pages 135-152

Combinatorial Library Design from Reagent Pharmacophore Fingerprints

Author keywords

combinatorial library design; genetic algorithm; multi objective optimisation; pharmacophore fingerprint; ProSAR; Shannon entropy; topological pharmacophore

Indexed keywords

AMINE; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS;

EID: 79952197171     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-931-4_7     Document Type: Chapter
Times cited : (2)

References (63)
  • 2
    • 33746931581 scopus 로고    scopus 로고
    • On outliers and activity cliffs – why QSAR often disappoints
    • Maggiora, G. M. (2006) On outliers and activity cliffs – why QSAR often disappoints. J Chem Inf Model 46, 1535.
    • (2006) J Chem Inf Model , vol.46 , pp. 1535
    • Maggiora, G.M.1
  • 3
    • 70350507116 scopus 로고    scopus 로고
    • Structural interpretation of activity cliffs revealed by systematic analysis of structure−activity relationships in analog series
    • Sisay, M. H., Peltason, L., Bajorath, J. (2009) Structural interpretation of activity cliffs revealed by systematic analysis of structure−activity relationships in analog series. J Chem Inf Model 49, 2179–2189.
    • (2009) J Chem Inf Model , vol.49 , pp. 2179-2189
    • Sisay, M.H.1    Peltason, L.2    Bajorath, J.3
  • 4
    • 33750981540 scopus 로고    scopus 로고
    • Do structurally similar ligands bind in a similar fashion?
    • Boström, J., Hogner, A., Schmitt, S. (2006) Do structurally similar ligands bind in a similar fashion? J Med Chem 49, 6716–6725.
    • (2006) J Med Chem , vol.49 , pp. 6716-6725
    • Boström, J.1    Hogner, A.2    Schmitt, S.3
  • 5
    • 0000864593 scopus 로고    scopus 로고
    • Recent developments in molecular diversity: Computational approaches to combinatorial chemistry
    • Spellmeyer, D. C., Grootenhuis, P. D. J. (1999) Recent developments in molecular diversity: computational approaches to combinatorial chemistry. Annu Rep Med Chem Rev 34, 287–296.
    • (1999) Annu Rep Med Chem Rev , vol.34 , pp. 287-296
    • Spellmeyer, D.C.1    Grootenhuis, P.D.J.2
  • 6
    • 0001073278 scopus 로고    scopus 로고
    • The design of combinatorial libraries using properties and 3D pharmacophore fingerprints
    • Beno, B. R., Mason, J. S. (2001) The design of combinatorial libraries using properties and 3D pharmacophore fingerprints. Drug Discovery Today 6, 251–258.
    • (2001) Drug Discovery Today , vol.6 , pp. 251-258
    • Beno, B.R.1    Mason, J.S.2
  • 7
    • 0033968062 scopus 로고    scopus 로고
    • Chemoinformatics – similarity and diversity in chemical libraries
    • Willett, P. (2000) Chemoinformatics – similarity and diversity in chemical libraries. Curr Opin Biotechnol 11, 85–88.
    • (2000) Curr Opin Biotechnol , vol.11 , pp. 85-88
    • Willett, P.1
  • 8
    • 0029894013 scopus 로고    scopus 로고
    • The properties of known drugs. 1. Molecular frameworks
    • Bemis, G. W., Murcko, M. A. (1996) The properties of known drugs. 1. Molecular frameworks. J Med Chem 39, 2887–2893.
    • (1996) J Med Chem , vol.39 , pp. 2887-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 9
    • 0036662353 scopus 로고    scopus 로고
    • Using molecular equivalence numbers to visually explore structural features that distinguish chemical libraries
    • Xu, Y. J., Johnson, M. (2002) Using molecular equivalence numbers to visually explore structural features that distinguish chemical libraries. J Chem Inf Comp Sci 42, 912–926.
    • (2002) J Chem Inf Comp Sci , vol.42 , pp. 912-926
    • Xu, Y.J.1    Johnson, M.2
  • 10
  • 11
    • 0029348572 scopus 로고
    • Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors
    • Good, A. C., Kuntz, I. D. (1995) Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors. J Mol Comput Aided Mol Des 9, 373–379.
    • (1995) J Mol Comput Aided Mol Des , vol.9 , pp. 373-379
    • Good, A.C.1    Kuntz, I.D.2
  • 12
    • 0033606988 scopus 로고    scopus 로고
    • New 4-point pharmaophore method for molecular similarity and diversity applications: Overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures
    • Mason, J. S., Morize, I., Menard, P. R., Cheney, D. L., Hulme, C., Labaudiniere, R. F. (1999) New 4-point pharmaophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J Med Chem 42, 3251–3264.
    • (1999) J Med Chem , vol.42 , pp. 3251-3264
    • Mason, J.S.1    Morize, I.2    Menard, P.R.3    Cheney, D.L.4    Hulme, C.5    Labaudiniere, R.F.6
  • 13
    • 85139077077 scopus 로고    scopus 로고
    • Santa Clara, CA 95051, USA
    • Symyx, 2.5; Symyx Technologies Inc., Santa Clara, CA 95051, USA.
  • 14
    • 0033127029 scopus 로고    scopus 로고
    • Pharmacophore fingerprinting. 1. Application to QSAR and focused library design
    • McGregor, M. J., Muskal, S. M. (1999) Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J Chem Inf Comput Sci 39, 569–574.
    • (1999) J Chem Inf Comput Sci , vol.39 , pp. 569-574
    • McGregor, M.J.1    Muskal, S.M.2
  • 15
    • 0000465937 scopus 로고    scopus 로고
    • Diversity profiling and design using 3D pharmacophore: Pharmacophore-derived queries (PDQ)
    • Pickett, S. D., Mason, J. S., Mclay, I. M. (1996) Diversity profiling and design using 3D pharmacophore: pharmacophore-derived queries (PDQ). J Chem Inf Comput Sci 36, 1214–1223.
    • (1996) J Chem Inf Comput Sci , vol.36 , pp. 1214-1223
    • Pickett, S.D.1    Mason, J.S.2    McLay, I.M.3
  • 16
    • 0034351497 scopus 로고    scopus 로고
    • Library design using BCUT chemistry-space descriptors and multiple four-point pharmacophore fingerprints: Simultaneous optimization and structure-based diversity
    • Mason, J. S., Beno, B. R. (2000) Library design using BCUT chemistry-space descriptors and multiple four-point pharmacophore fingerprints: simultaneous optimization and structure-based diversity. J Mol Graph Mod 18, 438–451.
    • (2000) J Mol Graph Mod , vol.18 , pp. 438-451
    • Mason, J.S.1    Beno, B.R.2
  • 17
    • 0344236539 scopus 로고    scopus 로고
    • Exploring pharmacophores with Chem-X
    • Güner, O., ed.), International University Line, La Jolla, CA
    • Cato, S. J. (2000) Exploring pharmacophores with Chem-X, in (Güner, O., ed.) Pharmacophore Perception, Development, and Use in Drug Designer. International University Line, La Jolla, CA, pp. 107–125.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Designer , pp. 107-125
    • Cato, S.J.1
  • 18
    • 0030831365 scopus 로고    scopus 로고
    • New methodology for profiling combinatorial libraries and screening sets: Cleaning up the design process with HARPick
    • Good, A. C., Lewis, R. A. (1997) New methodology for profiling combinatorial libraries and screening sets: cleaning up the design process with HARPick. J. Med Chem 40, 3926–3936.
    • (1997) J. Med Chem , vol.40 , pp. 3926-3936
    • Good, A.C.1    Lewis, R.A.2
  • 19
    • 0000128084 scopus 로고    scopus 로고
    • Recursive partitioning analysis of a large structure-activity data set using three-dimensional descriptors
    • Chen. X., Rusinko, A., III, Young, S. S. (1998) Recursive partitioning analysis of a large structure-activity data set using three-dimensional descriptors. J Chem Inf Comput Sci 38, 1054–1062.
    • (1998) J Chem Inf Comput Sci , vol.38 , pp. 1054-1062
    • Chen, X.1    Rusinko, A.2    Young, S.S.3
  • 20
    • 0001027028 scopus 로고    scopus 로고
    • Comparing 3D pharmacophore triplets and 2D fingerprints for selecting diverse compound subsets
    • Matter, H., Pötter, T. (1999) Comparing 3D pharmacophore triplets and 2D fingerprints for selecting diverse compound subsets. J Chem Inf Comput Sci 39, 1211–1225.
    • (1999) J Chem Inf Comput Sci , vol.39 , pp. 1211-1225
    • Matter, H.1    Pötter, T.2
  • 22
    • 0345530242 scopus 로고    scopus 로고
    • Pharmacophore-based approaches to combinatorial library design
    • Ghose, A. K., Viswanadhan, V. N., eds.), Marcel Dekker, New York
    • Good. A. C., Masson, J. S., Green, D. V. S., Leach, A. R. (2001) Pharmacophore-based approaches to combinatorial library design„ in (Ghose, A. K., Viswanadhan, V. N., eds.) Combinatorial Library Design and Evaluation. Marcel Dekker, New York, pp. 399–428.
    • (2001) Combinatorial Library Design and Evaluation , pp. 399-428
    • Good, A.C.1    Masson, J.S.2    Green, D.V.S.3    Leach, A.R.4
  • 23
    • 0033630852 scopus 로고    scopus 로고
    • Pharmacophore fingerprinting. 2. Application to primary library design
    • McGregor, M. J., Muskal, S. M. (2000) Pharmacophore fingerprinting. 2. Application to primary library design. J Chem Inf Comput Sci 40, 117–125.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 117-125
    • McGregor, M.J.1    Muskal, S.M.2
  • 24
    • 85139024978 scopus 로고
    • S. Hanley Rd., St. Louis, MO 63144, USA
    • SYBYL Pharmacophore triplet is distributed by Tripos, Inc., 1699 S. Hanley Rd., St. Louis, MO 63144, USA.
    • (1699)
  • 25
  • 26
    • 0002647926 scopus 로고    scopus 로고
    • Rapid quantification of molecular diversity for selective database acquisition
    • Turner, D. B., Tyrrell, S. M., Willett, P. (1997) Rapid quantification of molecular diversity for selective database acquisition. J Chem Inf Comput Sci 37, 18–22.
    • (1997) J Chem Inf Comput Sci , vol.37 , pp. 18-22
    • Turner, D.B.1    Tyrrell, S.M.2    Willett, P.3
  • 27
    • 0038198874 scopus 로고    scopus 로고
    • Reagent-based and product-based computational approaches in library design
    • Jamois, E. A. (2003) Reagent-based and product-based computational approaches in library design. Curr Opin Chem Biol 7, 326–330.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 326-330
    • Jamois, E.A.1
  • 28
    • 0032509984 scopus 로고    scopus 로고
    • Random or rational design? Evaluation of diverse compound subsets from chemical structure databases
    • Potter, T., Matter, H. (1998) Random or rational design? Evaluation of diverse compound subsets from chemical structure databases. J Med Chem 41, 478–488.
    • (1998) J Med Chem , vol.41 , pp. 478-488
    • Potter, T.1    Matter, H.2
  • 29
    • 0033630852 scopus 로고    scopus 로고
    • Pharmacophore fingerprinting. 2. Application to primary library design
    • McGregor, M. J., Muskal, S. M. (2000) Pharmacophore fingerprinting. 2. Application to primary library design. J Chem Inf Comput Sci 40, 117–125.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 117-125
    • McGregor, M.J.1    Muskal, S.M.2
  • 30
    • 0032011973 scopus 로고    scopus 로고
    • Rational combinatorial library design. 1. Focus-2D: A new approach to targeted combinatorial chemical libraries
    • Zheng, W., Cho, S. J., Tropsha, A. (1998) Rational combinatorial library design. 1. Focus-2D: a new approach to targeted combinatorial chemical libraries. J Chem Inf Comput Sci 38, 572–584.
    • (1998) J Chem Inf Comput Sci , vol.38 , pp. 572-584
    • Zheng, W.1    Cho, S.J.2    Tropsha, A.3
  • 31
    • 0034263171 scopus 로고    scopus 로고
    • Where are the gaps? A rational approach to monomer acquisition and selection
    • Leach, A. R., Green, D. V. S., Hann, M. M., Judd, D. B., Good, A. C. (2000) Where are the gaps? A rational approach to monomer acquisition and selection. J Chem Inf Comput Sci 40, 1262–1269.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 1262-1269
    • Leach, A.R.1    Green, D.V.S.2    Hann, M.M.3    Judd, D.B.4    Good, A.C.5
  • 32
    • 0000528756 scopus 로고    scopus 로고
    • The effectiveness of reactant pools for generating structurally diverse combinatorial libraries
    • Gillet, V. J., Willett, P., Bradshaw, J. (1997) The effectiveness of reactant pools for generating structurally diverse combinatorial libraries. J Chem Inf Comput Sci 37, 731–740.
    • (1997) J Chem Inf Comput Sci , vol.37 , pp. 731-740
    • Gillet, V.J.1    Willett, P.2    Bradshaw, J.3
  • 34
    • 33745686155 scopus 로고    scopus 로고
    • Multifingerprint based similarity searches for targeted class compound selection
    • Kogej, T., Engkvist, O., Blomberg, N., Muresan, S. (2006) Multifingerprint based similarity searches for targeted class compound selection. J Chem Inf Model 46, 1201–1213.
    • (2006) J Chem Inf Model , vol.46 , pp. 1201-1213
    • Kogej, T.1    Engkvist, O.2    Blomberg, N.3    Muresan, S.4
  • 35
    • 0141792684 scopus 로고    scopus 로고
    • Informative library design as an efficient strategy to identify and optimize leads: Application to cyclin-dependant kinase 2 antagonists
    • Bradley, E. K., Miller, J. L., Saiah, E., Grootenhuis, P. D. J. (2003) Informative library design as an efficient strategy to identify and optimize leads: application to cyclin-dependant kinase 2 antagonists. J Med Chem 46, 4360–4364.
    • (2003) J Med Chem , vol.46 , pp. 4360-4364
    • Bradley, E.K.1    Miller, J.L.2    Saiah, E.3    Grootenhuis, P.D.J.4
  • 38
    • 85139024504 scopus 로고    scopus 로고
    • Daylight Theory Manual; Daylight Chemical Information Systems, Inc. http://www.daylight.com/dayhtml/doc/theory/
  • 39
    • 85139061080 scopus 로고    scopus 로고
    • Symyx Technologies, Inc., Santa Clara, CA 95051, USA
    • MDL Available Chemicals Directory database 2007, Symyx Technologies, Inc., Santa Clara, CA 95051, USA.
    • (2007)
  • 40
    • 85139056818 scopus 로고    scopus 로고
    • Hyderabad 500016, India
    • GVKBio Medchem database 2007, GVK Biosciences Private Ltd., Hyderabad 500016, India.
    • (2007) GVK Biosciences Private Ltd
  • 42
    • 0000228805 scopus 로고    scopus 로고
    • Variabilities of molecular descriptors in compound databases revealed by Shannon entropy calculations
    • Godden, J. W., Stahura, F. L., Bajorath, J. (2000) Variabilities of molecular descriptors in compound databases revealed by Shannon entropy calculations. J Chem Inf Comput Sci 40, 796–800.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 796-800
    • Godden, J.W.1    Stahura, F.L.2    Bajorath, J.3
  • 44
    • 0037208266 scopus 로고    scopus 로고
    • Luddite: An information-theoretic library design tool
    • Miller, J. L., Bradley, E. K., Teig, S. L. (2003) Luddite: an information-theoretic library design tool. J Chem Inf Comput Sci 43, 47–54.
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 47-54
    • Miller, J.L.1    Bradley, E.K.2    Teig, S.L.3
  • 45
    • 0030066573 scopus 로고    scopus 로고
    • Molecular genetic insights into cardiovascular disease
    • Keating, M. T., Sanguinetti, M. C. (1996) Molecular genetic insights into cardiovascular disease. Science 272, 681–685.
    • (1996) Science , vol.272 , pp. 681-685
    • Keating, M.T.1    Sanguinetti, M.C.2
  • 46
    • 0037194634 scopus 로고    scopus 로고
    • Toward a pharmacophore for drugs including the long QT syndrome: Insights from a CoMFA study of HERG K(+) channel blockers
    • Cavalli, A., Poluzzi, E., De Ponti, F., Recanatini, M. (2002) Toward a pharmacophore for drugs including the long QT syndrome: insights from a CoMFA study of HERG K(+) channel blockers. J Med Chem 45, 3844–3853.
    • (2002) J Med Chem , vol.45 , pp. 3844-3853
    • Cavalli, A.1    Poluzzi, E.2    de Ponti, F.3    Recanatini, M.4
  • 48
    • 34447556847 scopus 로고    scopus 로고
    • Solubility prediction of drugs in water-cosolvent mixtures using Abraham solvation parameters
    • Jouyban, A., Soltanpour, S., Soltani, S., Chan, H. K., Acree, W. E. (2007) Solubility prediction of drugs in water-cosolvent mixtures using Abraham solvation parameters. J Pharm Sci 10, 263–277.
    • (2007) J Pharm Sci , vol.10 , pp. 263-277
    • Jouyban, A.1    Soltanpour, S.2    Soltani, S.3    Chan, H.K.4    Acree, W.E.5
  • 49
    • 0034687231 scopus 로고    scopus 로고
    • Prediction of drug absorption using multivariate statistics
    • Eagan, W. J., Merz, K. M., Baldwin, J. J. (2000) Prediction of drug absorption using multivariate statistics. J Med Chem 43, 3867–3877.
    • (2000) J Med Chem , vol.43 , pp. 3867-3877
    • Eagan, W.J.1    Merz, K.M.2    Baldwin, J.J.3
  • 50
    • 0034150327 scopus 로고    scopus 로고
    • Diversity measures for enhancing ADME admissibility of combinatorial libraries
    • Darvas, F., Dorman, G., Papp, A. (2000) Diversity measures for enhancing ADME admissibility of combinatorial libraries. J Chem Inf Comput Sci 40, 314–322.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 314-322
    • Darvas, F.1    Dorman, G.2    Papp, A.3
  • 51
    • 0035526164 scopus 로고    scopus 로고
    • Search for predictive generic model of aqueous solubility using Bayesian neural nets
    • Bruneau, P. (2001) Search for predictive generic model of aqueous solubility using Bayesian neural nets. J Chem Inf Comput Sci 41, 1605–1616.
    • (2001) J Chem Inf Comput Sci , vol.41 , pp. 1605-1616
    • Bruneau, P.1
  • 52
    • 34047134980 scopus 로고    scopus 로고
    • Development, interpretation and temporal evaluation of a global QSAR of hERG electrophys-iology screening data
    • Gavaghan, C. L., Arnby, C. H., Blomberg, N., Strandlund, G., Boyer, S. (2007) Development, interpretation and temporal evaluation of a global QSAR of hERG electrophys-iology screening data. J Comput Aided Mol Des 21, 189–206.
    • (2007) J Comput Aided Mol Des , vol.21 , pp. 189-206
    • Gavaghan, C.L.1    Arnby, C.H.2    Blomberg, N.3    Strandlund, G.4    Boyer, S.5
  • 53
    • 0035438391 scopus 로고    scopus 로고
    • Is there a difference between leads and drugs? A historical perspective
    • Oprea, T. I., Davis, A. M., Teague, S. J., Leeson, P. D. (2001) Is there a difference between leads and drugs? A historical perspective. J Chem Inf Comput Sci 41, 1308–1335.
    • (2001) J Chem Inf Comput Sci , vol.41 , pp. 1308-1335
    • Oprea, T.I.1    Davis, A.M.2    Teague, S.J.3    Leeson, P.D.4
  • 54
    • 0036589285 scopus 로고    scopus 로고
    • Current trends in lead discovery: Are we looking for the appropriate properties?
    • Oprea, T. I. (2002) Current trends in lead discovery: are we looking for the appropriate properties? J Comp Aided Mol Des 16, 325.
    • (2002) J Comp Aided Mol Des , vol.16 , pp. 325
    • Oprea, T.I.1
  • 56
    • 0033630524 scopus 로고    scopus 로고
    • Evaluation of reagent-based and product-based strategies in the design of combinatorial library subsets
    • Jamois, E. J., Hassan, M., Waldman, M. (2000) Evaluation of reagent-based and product-based strategies in the design of combinatorial library subsets. J Chem Inf Comput Sci 40, 63–70.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 63-70
    • Jamois, E.J.1    Hassan, M.2    Waldman, M.3
  • 58
    • 85138993152 scopus 로고    scopus 로고
    • US6271232B1; Campbell, D. A., Look, G. C., Szardenings, A. K., Patel, P. V. (1999) US5932579A; Campbell, D. A., Look, G. C., Szardenings, A. K., Patel, P. V. (1997) WO97/48685A1
    • Campbell, D. A., Look, G. C., Szardenings, A. K., Patel, P. V. (2001) US6271232B1; Campbell, D. A., Look, G. C., Szardenings, A. K., Patel, P. V. (1999) US5932579A; Campbell, D. A., Look, G. C., Szardenings, A. K., Patel, P. V. (1997) WO97/48685A1.
    • (2001)
    • Campbell, D.A.1    Look, G.C.2    Szardenings, A.K.3    Patel, P.V.4
  • 59
    • 0032543517 scopus 로고    scopus 로고
    • Rational design and combinatorial evaluation of enzyme inhibitor scaffolds: Identification of novel inhibitors of matrix metelloproteinases
    • Szardenings, A. K., Harris, D., Lam, S., Shi, L., Tien, D., Wang, Y., Patel, D. V., Navre, M., Campbell, D. A. (1998) Rational design and combinatorial evaluation of enzyme inhibitor scaffolds: identification of novel inhibitors of matrix metelloproteinases. J Med Chem 41, 2194–2200.
    • (1998) J Med Chem , vol.41 , pp. 2194-2200
    • Szardenings, A.K.1    Harris, D.2    Lam, S.3    Shi, L.4    Tien, D.5    Wang, Y.6    Patel, D.V.7    Navre, M.8    Campbell, D.A.9
  • 60
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • Martin, Y. C., Kofron, J. L., Traphagen, L. M. (2002) Do structurally similar molecules have similar biological activity? J Med Chem 45, 4350–4358.
    • (2002) J Med Chem , vol.45 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 61
    • 0000819953 scopus 로고    scopus 로고
    • Enhancing the hit-to-lead properties of lead optimization libraries
    • Pickett, S. D, McLay I. M., Clark, D. E. (2000) Enhancing the hit-to-lead properties of lead optimization libraries. J Chem Inf Comput Sci 40, 263–272.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 263-272
    • Pickett, S.D.1    McLay, I.M.2    Clark, D.E.3
  • 63
    • 0034351502 scopus 로고    scopus 로고
    • Combinatorial library design for diversity, cost efficiency, and drug-like character
    • Brown, R. D., Hassan, M., Waldman, M. (2000) Combinatorial library design for diversity, cost efficiency, and drug-like character. J Mol Graph Model 18, 427–437.
    • (2000) J Mol Graph Model , vol.18 , pp. 427-437
    • Brown, R.D.1    Hassan, M.2    Waldman, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.