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Volumn 1, Issue 1, 2009, Pages 213-218

Self-organizing molecular fingerprints: A ligand-based view on drug-like chemical space and off-target prediction

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEINASE INHIBITOR;

EID: 77952664105     PISSN: 17568919     EISSN: None     Source Type: Journal    
DOI: 10.4155/fmc.09.11     Document Type: Article
Times cited : (27)

References (51)
  • 1
    • 33846574259 scopus 로고    scopus 로고
    • Fragments, network biology and designing multiple ligands
    • Morphy R, Rankovic Z. Fragments, network biology and designing multiple ligands. Drug Discov. Today 12(3-4), 156-160 (2007).
    • (2007) Drug Discov. Today , vol.12 , Issue.3-4 , pp. 156-160
    • Morphy, R.1    Rankovic, Z.2
  • 3
    • 0033523672 scopus 로고    scopus 로고
    • "Scaffold-hopping" by topological pharmacophore search: A contribution to virtual screening
    • Schneider G, Neidhart W, Giller T, Schmid G. "Scaffold-hopping" by topological pharmacophore search: a contribution to virtual screening. Angew. Chem. Int. Ed. 38(19), 2894-2896 (1999).
    • (1999) Angew. Chem. Int. Ed. , vol.38 , Issue.19 , pp. 2894-2896
    • Schneider, G.1    Neidhart, W.2    Giller, T.3    Schmid, G.4
  • 4
    • 33846013232 scopus 로고    scopus 로고
    • Scaffold-hopping: How far can you jump?
    • Schneider G, Schneider P, Renner S. Scaffold-hopping: how far can you jump? QSAR Comb. Sci. 25(12), 1162-1171 (2006)
    • (2006) QSAR Comb Sci , vol.25 , Issue.12 , pp. 1162-1171
    • Schneider, G.1    Schneider, P.2    Renner, S.3
  • 5
    • 33846694819 scopus 로고    scopus 로고
    • Scaffold selection and scaffold hopping in lead generation: A medicinal chemistry perspective
    • Zhao H. Scaffold selection and scaffold hopping in lead generation: a medicinal chemistry perspective. Drug Discov. Today 12(3-4), 149-155 (2007).
    • (2007) Drug Discov. Today , vol.12 , Issue.3-4 , pp. 149-155
    • Zhao, H.1
  • 6
    • 42449144314 scopus 로고    scopus 로고
    • Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative crossreactivity
    • Kupas K, Ultsch A, Klebe G. Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative crossreactivity. Proteins 71(3), 1288-1306 (2008).
    • (2008) Proteins , vol.71 , Issue.3 , pp. 1288-1306
    • Kupas, K.1    Ultsch, A.2    Klebe, G.3
  • 7
    • 29144482496 scopus 로고    scopus 로고
    • Comprehensive identification of "druggable" protein ligand binding sites
    • An J, Totrov M, Abagyan R. Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform. 15(2), 31-41 (2004).
    • (2004) Genome Inform , vol.15 , Issue.2 , pp. 31-41
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 8
    • 30144443247 scopus 로고    scopus 로고
    • Similarity networks of protein binding sites
    • Zhang Z, Grigorov MG. Similarity networks of protein binding sites. Proteins 62(2), 470-478 (2006).
    • (2006) Proteins , vol.62 , Issue.2 , pp. 470-478
    • Zhang, Z.1    Grigorov, M.G.2
  • 9
    • 37649009919 scopus 로고    scopus 로고
    • Molecule-pharmacophore superpositioning and pattern matching in computational drug design
    • Wolber G, Seidel T, Bendix F, Langer T. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug Discov. Today 13(1-2), 23-29 (2008).
    • (2008) Drug Discov. Today , vol.13 , Issue.1-2 , pp. 23-29
    • Wolber, G.1    Seidel, T.2    Bendix, F.3    Langer, T.4
  • 10
    • 0032149905 scopus 로고    scopus 로고
    • Feature trees: A new molecular similarity measure based on tree matching
    • Rarey M, Dixon JS. Feature trees: a new molecular similarity measure based on tree matching. J. Comput. Aided Mol. Des. 12(5), 471-490 (1998).
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , Issue.5 , pp. 471-490
    • Rarey, M.1    Dixon, J.S.2
  • 11
    • 21044451732 scopus 로고    scopus 로고
    • GPCR antitarget modeling: Pharmacophore models for biogenic amine binding GPCRs to avoid GPCR-mediated side effects
    • Klabunde T, Evers A. GPCR antitarget modeling: pharmacophore models for biogenic amine binding GPCRs to avoid GPCR-mediated side effects. ChemBioChem 6(5), 876-889 (2005).
    • (2005) Chem Bio Chem , vol.6 , Issue.5 , pp. 876-889
    • Klabunde, T.1    Evers, A.2
  • 12
    • 61949313682 scopus 로고    scopus 로고
    • Self-organizing maps in drug discovery: Library design, scaffold-hopping, repurposing
    • Schneider P, Tanrikulu Y, Schneider G. Self-organizing maps in drug discovery: library design, scaffold-hopping, repurposing. Curr. Med. Chem. 16(3), 285-1266(2009).
    • (2009) Curr. Med. Chem. , vol.16 , Issue.3 , pp. 285-1266
    • Schneider, P.1    Tanrikulu, Y.2    Schneider, G.3
  • 14
    • 41149103365 scopus 로고    scopus 로고
    • Binding similarity network of ligand
    • Park K, Kim D. Binding similarity network of ligand. Proteins 71(2), 960-971 (2008).
    • (2008) Proteins , vol.71 , Issue.2 , pp. 960-971
    • Park, K.1    Kim, D.2
  • 15
    • 43949145741 scopus 로고    scopus 로고
    • Computational analysis of ligand relationships within target families
    • Bajorath J. Computational analysis of ligand relationships within target families. Curr. Opin. Chem. Biol. 12(3), 352-358 (2008).
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , Issue.3 , pp. 352-358
    • Bajorath, J.1
  • 16
    • 1542327276 scopus 로고    scopus 로고
    • Predicting undesirable drug interactions with promiscuous proteins in silico
    • Ekins S. Predicting undesirable drug interactions with promiscuous proteins in silico. Drug Discov. Today. 9(6), 276-285 (2004).
    • (2004) Drug Discov. Today. , vol.9 , Issue.6 , pp. 276-285
    • Ekins, S.1
  • 17
    • 33750357203 scopus 로고    scopus 로고
    • Predicting compound selectivity by self-organizing maps: Cross-activities of metabotropic glutamate receptor antagonists
    • Noeske T, Sasse BC, Stark H, Parsons CG, Weil T, Schneider G. Predicting compound selectivity by self-organizing maps: cross-activities of metabotropic glutamate receptor antagonists. ChemMedChem 1(10), 1066-1068 (2006).
    • (2006) Chem Med Chem , vol.1 , Issue.10 , pp. 1066-1068
    • Noeske, T.1    Sasse, B.C.2    Stark, H.3    Parsons, C.G.4    Weil, T.5    Schneider, G.6
  • 18
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • Kohonen T. Self-organized formation of topologically correct feature maps. Biol. Cybern. 43, 59-69 (1982).
    • (1982) Biol. Cybern. , vol.43 , pp. 59-69
    • Kohonen, T.1
  • 19
    • 0242467732 scopus 로고    scopus 로고
    • Collection of bioactive compounds for focused library design
    • Schneider P, Schneider G. Collection of bioactive compounds for focused library design. QSAR Comb. Sci. 22(7), 713-718 (2003).
    • (2003) QSAR Comb. Sci. , vol.22 , Issue.7 , pp. 713-718
    • Schneider, P.1    Schneider, G.2
  • 20
    • 0030339936 scopus 로고    scopus 로고
    • The comparison of geometric and electronic properties of molecular surfaces by neural networks: Application to the analysis of corticosteroid- binding globulin activity of steroids
    • Anzali S, Barnickel G, Krug M et al. The comparison of geometric and electronic properties of molecular surfaces by neural networks: application to the analysis of corticosteroid-binding globulin activity of steroids. J. Comput. Aided. Mol. Des. 10(6), 521-534 (1996).
    • (1996) J. Comput. Aided. Mol. Des. , vol.10 , Issue.6 , pp. 521-534
    • Anzali, S.1    Barnickel, G.2    Krug, M.3
  • 21
    • 34447567401 scopus 로고    scopus 로고
    • Searching for drug scaffolds with 3D pharmacophores and neural network ensembles
    • Renner S, Hechenberger M, Noeske T et al. Searching for drug scaffolds with 3D pharmacophores and neural network ensembles. Angew. Chem. Int. Ed. 46(28), 5336-5339 (2007).
    • (2007) Angew. Chem. Int. Ed. , vol.46 , Issue.28 , pp. 5336-5339
    • Renner, S.1    Hechenberger, M.2    Noeske, T.3
  • 22
    • 38049165680 scopus 로고    scopus 로고
    • Processing and classification of chemical data inspired by insect olfaction
    • Schmuker M, Schneider G. Processing and classification of chemical data inspired by insect olfaction. Proc. Natl Acad. Sci. USA 104(51), 20285-20289 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , Issue.51 , pp. 20285-20289
    • Schmuker, M.1    Schneider, G.2
  • 23
    • 33845760580 scopus 로고    scopus 로고
    • Applications of selforganizing neural networks in virtual screening and diversity selection
    • Selzer P, Ertl P. Applications of selforganizing neural networks in virtual screening and diversity selection. J. Chem. Inf. Model. 46(6), 2319-2323 (2006).
    • (2006) J. Chem. Inf. Model. , vol.46 , Issue.6 , pp. 2319-2323
    • Selzer, P.1    Ertl, P.2
  • 24
    • 8544276588 scopus 로고    scopus 로고
    • Optimization of a pharmacophore-based correlation vector descriptor
    • Fechner U, Schneider G. Optimization of a pharmacophore-based correlation vector descriptor. QSAR Comb. Sci. 23(1), 19-22 (2004).
    • (2004) QSAR Comb. Sci. , vol.23 , Issue.1 , pp. 19-22
    • Fechner, U.1    Schneider, G.2
  • 26
    • 0031735526 scopus 로고    scopus 로고
    • Artificial neural networks for computer-based molecular design
    • Schneider G, Wrede P. Artificial neural networks for computer-based molecular design. Prog. Biophys. Mol. Biol. 70(3), 175-222 (1998).
    • (1998) Prog. Biophys. Mol. Biol. , vol.70 , Issue.3 , pp. 175-222
    • Schneider, G.1    Wrede, P.2
  • 27
    • 84954240819 scopus 로고    scopus 로고
    • Navigation in chemical space: Ligand-based design of focused compound libraries
    • Kubinyi H, Müller H (Eds). Wiley-VCH, Weinheim, Germany
    • Schneider G, Schneider P. Navigation in chemical space: ligand-based design of focused compound libraries. In: Chemogenomics in Drug Discovery. Kubinyi H, Müller H (Eds). Wiley-VCH, Weinheim, Germany 341-376 (2004).
    • (2004) Chemogenomics in Drug Discovery , pp. 341-376
    • Schneider, G.1    Schneider, P.2
  • 30
    • 4444257019 scopus 로고    scopus 로고
    • Progress in the development of synthetic thrombin inhibitors as new orally active anticoagulants
    • Steinmetzer T, Stürzebecher J. Progress in the development of synthetic thrombin inhibitors as new orally active anticoagulants. Curr. Med. Chem. 11(17), 2297-2321 (2004).
    • (2004) Curr. Med. Chem. , vol.11 , Issue.17 , pp. 2297-2321
    • Steinmetzer, T.1    Stürzebecher, J.2
  • 31
    • 84969528333 scopus 로고    scopus 로고
    • Principles of enzyme-inhibitor design
    • Böhm HJ, Schneider G (Eds). Wiley-VCH, Weinheim, Germany
    • Banner D. Principles of enzyme-inhibitor design. In: Protein-Ligand Interactions. Böhm HJ, Schneider G (Eds). Wiley-VCH, Weinheim, Germany 163-186 (2003).
    • (2003) Protein-Ligand Interactions , pp. 163-186
    • Banner, D.1
  • 32
    • 0141563645 scopus 로고    scopus 로고
    • Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using selforganizing maps
    • Schneider G, Nettekoven M. Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using selforganizing maps. J. Comb. Chem. 5(3), 233-237 (2003).
    • (2003) J. Comb. Chem. , vol.5 , Issue.3 , pp. 233-237
    • Schneider, G.1    Nettekoven, M.2
  • 33
    • 58549112609 scopus 로고    scopus 로고
    • From molecular shape to potent bioactive agents I: Bioisosteric replacement of molecular fragments
    • Proschak E, Zettl H, Tanrikulu Y et al. From molecular shape to potent bioactive agents I: bioisosteric replacement of molecular fragments. ChemMedChem 4(1), 45-48 (2009).
    • (2009) Chem Med Chem , vol.4 , Issue.1 , pp. 45-48
    • Proschak, E.1    Zettl, H.2    Tanrikulu, Y.3
  • 34
    • 0029061685 scopus 로고
    • Neutral endopeptidase can hydrolyze b-amyloid(1-40) but shows no effect on b-amyloid precursor protein metabolism
    • Howell S, Nalbantoglu J, Crine P. Neutral endopeptidase can hydrolyze b-amyloid(1-40) but shows no effect on b-amyloid precursor protein metabolism. Peptides 16(4), 647-652 (1995).
    • (1995) Peptides , vol.16 , Issue.4 , pp. 647-652
    • Howell, S.1    Nalbantoglu, J.2    Crine, P.3
  • 35
    • 0029731345 scopus 로고    scopus 로고
    • Processing of b-amyloid precursor protein by cathepsin D
    • Higaki J, Catalano R, Guzzetta AW et al. Processing of b-amyloid precursor protein by cathepsin D. J. Biol. Chem. 271(50), 31885-31893 (1996).
    • (1996) J. Biol. Chem. , vol.271 , Issue.50 , pp. 31885-31893
    • Higaki, J.1    Catalano, R.2    Guzzetta, A.W.3
  • 36
    • 0141994826 scopus 로고    scopus 로고
    • Intramembranecleaving aspartic proteases and disease: Presenilins, signal peptide peptidase and their homologs
    • Martoglio B, Golde TE. Intramembranecleaving aspartic proteases and disease: presenilins, signal peptide peptidase and their homologs. Hum. Mol. Genet. 12(2), 201-206 (2003)
    • (2003) Hum. Mol. Genet. , vol.12 , Issue.2 , pp. 201-206
    • Martoglio, B.1    Golde, T.E.2
  • 37
    • 49449089299 scopus 로고    scopus 로고
    • Molecular docking of cathepsin l inhibitors in the binding site of papain
    • Beavers M, Myers M, Shah P et al. Molecular docking of cathepsin l inhibitors in the binding site of papain. J. Chem. Inf. Model. 48(7), 1464-1472 (2008).
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.7 , pp. 1464-1472
    • Beavers, M.1    Myers, M.2    Shah, P.3
  • 39
    • 0027163740 scopus 로고
    • Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus
    • Hijikata M, Mizushima H, Akagi T et al. Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus. J. Virol. 67(8), 4665-4675 (1993).
    • (1993) J. Virol. , vol.67 , Issue.8 , pp. 4665-4675
    • Hijikata, M.1    Mizushima, H.2    Akagi, T.3
  • 40
    • 33747452685 scopus 로고    scopus 로고
    • Structure of the catalytic domain of the hepatitis C virus NS2-3 protease
    • Lorenz IC, Marcotrigiano J, Dentzer TG, Rice CM. Structure of the catalytic domain of the hepatitis C virus NS2-3 protease. Nature 442(7104), 831-835 (2006).
    • (2006) Nature , vol.442 , Issue.7104 , pp. 831-835
    • Lorenz, I.C.1    Marcotrigiano, J.2    Dentzer, T.G.3    Rice, C.M.4
  • 41
    • 33846424965 scopus 로고    scopus 로고
    • The hepatitis C virus NS2/3 protease
    • Welbourn S, Pause A. The hepatitis C virus NS2/3 protease. Curr. Issues Mol. Biol. 9(1), 63-69 (2007).
    • (2007) Curr. Issues Mol. Biol. , vol.9 , Issue.1 , pp. 63-69
    • Welbourn, S.1    Pause, A.2
  • 42
    • 16044364658 scopus 로고    scopus 로고
    • Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide
    • Kim JL, Morgenstern KA, Lin C et al. Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87(2), 343-355 (1996).
    • (1996) Cell , vol.87 , Issue.2 , pp. 343-355
    • Kim, J.L.1    Morgenstern, K.A.2    Lin, C.3
  • 43
    • 0028290389 scopus 로고
    • Processing in the hepatitis C virus E2-NS2 region: Identification of p7 and two distinct E2-specific products with different C termini
    • Lin C, Lindenbach BD, Pragai BM, McCourt DW, Rice CM. Processing in the hepatitis C virus E2-NS2 region: identification of p7 and two distinct E2-specific products with different C termini. J. Virol. 68(8), 5063-5073 (1994).
    • (1994) J. Virol. , vol.68 , Issue.8 , pp. 5063-5073
    • Lin, C.1    Lindenbach, B.D.2    Pragai, B.M.3    McCourt, D.W.4    Rice, C.M.5
  • 44
    • 0029813908 scopus 로고    scopus 로고
    • Processing pathways of the hepatitis C virus proteins
    • Lohmann V, Koch JO, Bartenschlager R. Processing pathways of the hepatitis C virus proteins. J. Hepatol. 24(Suppl. 2), 11-19 (1996).
    • (1996) J. Hepatol. , vol.24 , Issue.SUPPL. 2 , pp. 11-19
    • Lohmann, V.1    Koch, J.O.2    Bartenschlager, R.3
  • 45
    • 33744457959 scopus 로고    scopus 로고
    • Discovery and development of VX-950, a novel, covalent, and reversible inhibitor of hepatitis C virus NS3.4A serine protease
    • Lin C, Kwong AD, Perni RB. Discovery and development of VX-950, a novel, covalent, and reversible inhibitor of hepatitis C virus NS3.4A serine protease. Infect. Disord. Drug Targets 6(1), 3-16 (2006).
    • (2006) Infect. Disord. Drug Targets , vol.6 , Issue.1 , pp. 3-16
    • Lin, C.1    Kwong, A.D.2    Perni, R.B.3
  • 46
    • 70349464514 scopus 로고    scopus 로고
    • Distance phenomena in high-dimensional chemical descriptor spaces: Consequences for similarity-based approaches
    • DOI: 10.1002/jcc.21218 Epub ahead of print
    • Rupp M, Schneider P, Schneider G. Distance phenomena in high-dimensional chemical descriptor spaces: consequences for similarity-based approaches. J. Comput. Chem. DOI: 10.1002/jcc.21218 (2009) (Epub ahead of print).
    • (2009) J. Comput. Chem.
    • Rupp, M.1    Schneider, P.2    Schneider, G.3
  • 47
    • 60349119258 scopus 로고    scopus 로고
    • Form follows function: Shape analysis of protein cavities for receptor-based drug design
    • Weisel M, Proschak E, Kriegl JM, Schneider G. Form follows function: shape analysis of protein cavities for receptor-based drug design. Proteomics 9(2), 451-459 (2009).
    • (2009) Proteomics , vol.9 , Issue.2 , pp. 451-459
    • Weisel, M.1    Proschak, E.2    Kriegl, J.M.3    Schneider, G.4
  • 48
    • 0037499669 scopus 로고    scopus 로고
    • How to acquire new biological activities in old compounds by computer prediction
    • Poroikov VV, Filimonov DA. How to acquire new biological activities in old compounds by computer prediction. J. Comput. Aided Mol. Des. 16(11), 819-824 (2002).
    • (2002) J. Comput. Aided Mol. Des. , vol.16 , Issue.11 , pp. 819-824
    • Poroikov, V.V.1    Filimonov, D.A.2
  • 50
    • 33750994920 scopus 로고    scopus 로고
    • Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors
    • Nettles JH, Jenkins JL, Bender A, Deng Z, Davies JW, Glick M. Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. J. Med. Chem. 49(23), 6802-6810 (2006).
    • (2006) J. Med. Chem. , vol.49 , Issue.23 , pp. 6802-6810
    • Nettles, J.H.1    Jenkins, J.L.2    Bender, A.3    Deng, Z.4    Davies, J.W.5    Glick, M.6
  • 51
    • 2342565108 scopus 로고    scopus 로고
    • Prediction of biological targets using probabilistic neural networks and atom-type descriptors
    • Niwa T. Prediction of biological targets using probabilistic neural networks and atom-type descriptors. J. Med. Chem. 47(10), 2645-2650 (2004).
    • (2004) J. Med. Chem. , vol.47 , Issue.10 , pp. 2645-2650
    • Niwa, T.1


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