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Volumn 8, Issue 14, 2016, Pages 1753-1767

On the origins of three-dimensionality in drug-like molecules

Author keywords

drug like molecules; library enumeration; molecular shape; molecular three dimensionality; plane of best fit; principal moments of inertia; scaffolds; ternary density plots

Indexed keywords

HYDROGEN; MOLECULAR SCAFFOLD; DRUG; MOLECULAR LIBRARY;

EID: 84986253756     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc-2016-0095     Document Type: Article
Times cited : (75)

References (38)
  • 1
    • 84879221884 scopus 로고    scopus 로고
    • Multi-objective optimization methods in drug design
    • Nicolaou CA, Brown N. Multi-objective optimization methods in drug design. Drug Discov. Today Technol. 10(3), e427-e435 (2013).
    • (2013) Drug Discov. Today Technol. , vol.10 , Issue.3 , pp. e427-e435
    • Nicolaou, C.A.1    Brown, N.2
  • 2
    • 84870401411 scopus 로고    scopus 로고
    • Fragment based drug design: From experimental to computational approaches
    • Kumar A, Voet A, Zhang KYJ. Fragment based drug design: from experimental to computational approaches. Curr. Med. Chem. 19(30), 5128-5147 (2012).
    • (2012) Curr. Med. Chem. , vol.19 , Issue.30 , pp. 5128-5147
    • Kumar, A.1    Voet, A.2    Zhang, K.Y.J.3
  • 3
    • 84889100044 scopus 로고    scopus 로고
    • Fragmentbased hit identification: Thinking in 3D
    • Morley AD, Pugliese A, Birchall K et al. Fragmentbased hit identification: thinking in 3D. Drug Discov. Today. 18(23-24), 1221-1227 (2013).
    • (2013) Drug Discov. Today , vol.18 , Issue.23-24 , pp. 1221-1227
    • Morley, A.D.1    Pugliese, A.2    Birchall, K.3
  • 4
    • 84893344225 scopus 로고    scopus 로고
    • Increasing the coverage of medicinal chemistry-relevant space in commercial fragments screening
    • Mok NY, Brenk R, Brown N. Increasing the coverage of medicinal chemistry-relevant space in commercial fragments screening. J. Chem. Inf. Model. 54(1), 79-85 (2014).
    • (2014) J. Chem. Inf. Model , vol.54 , Issue.1 , pp. 79-85
    • Mok, N.Y.1    Brenk, R.2    Brown, N.3
  • 6
    • 84874436407 scopus 로고    scopus 로고
    • 3D molecular descriptors important for clinical success
    • Kombo DC, Tallapragada K, Jain R et al. 3D molecular descriptors important for clinical success. J. Chem. Inf. Model. 53(2), 327-342 (2013).
    • (2013) J. Chem. Inf. Model , vol.53 , Issue.2 , pp. 327-342
    • Kombo, D.C.1    Tallapragada, K.2    Jain, R.3
  • 7
    • 71049126548 scopus 로고    scopus 로고
    • Escape from flatland: Increasing saturation as an approach to improving clinical success
    • Lovering F, Bikker J, Humblet C. Escape from flatland: increasing saturation as an approach to improving clinical success. J. Med. Chem. 52(21), 6752-6756 (2009).
    • (2009) J. Med. Chem. , vol.52 , Issue.21 , pp. 6752-6756
    • Lovering, F.1    Bikker, J.2    Humblet, C.3
  • 8
    • 84874464077 scopus 로고    scopus 로고
    • Escape from flatland 2: Complexity and promiscuity
    • Lovering F. Escape from flatland 2: complexity and promiscuity. MedChemComm 4(3), 515-519 (2013).
    • (2013) MedChemComm , vol.4 , Issue.3 , pp. 515-519
    • Lovering, F.1
  • 9
    • 61349117968 scopus 로고    scopus 로고
    • The importance of discerning shape in molecular pharmacology
    • Kortagere S, Krasowski MD, Ekins S. The importance of discerning shape in molecular pharmacology. Trends Pharmacol. Sci. 30(3), 138-147 (2009).
    • (2009) Trends Pharmacol. Sci. , vol.30 , Issue.3 , pp. 138-147
    • Kortagere, S.1    Krasowski, M.D.2    Ekins, S.3
  • 10
    • 84871599677 scopus 로고    scopus 로고
    • Natural-product-derived fragments for fragment-based ligand discovery
    • Over B, Wetzel S, Grütter C et al. Natural-product-derived fragments for fragment-based ligand discovery. Nat. Chem. 5(1), 21-28 (2013).
    • (2013) Nat. Chem. , vol.5 , Issue.1 , pp. 21-28
    • Over, B.1    Wetzel, S.2    Grütter, C.3
  • 11
    • 80053924872 scopus 로고    scopus 로고
    • 3,5-Dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands
    • Hewings DS, Wang M, Philpott M et al. 3,5-Dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands. J. Med. Chem. 54(19), 6761-6770 (2011).
    • (2011) J. Med. Chem. , vol.54 , Issue.19 , pp. 6761-6770
    • Hewings, D.S.1    Wang, M.2    Philpott, M.3
  • 12
    • 77952553431 scopus 로고    scopus 로고
    • Rational design of smallmolecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication
    • Christ F, Voet A, Marchand A et al. Rational design of smallmolecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat. Chem. Biol. 6(6), 442-448 (2010).
    • (2010) Nat. Chem. Biol. , vol.6 , Issue.6 , pp. 442-448
    • Christ, F.1    Voet, A.2    Marchand, A.3
  • 13
    • 84860508708 scopus 로고    scopus 로고
    • Bcl-2 inhibitors: Emerging drugs in cancer therapy
    • Bodur C, Basaga H. Bcl-2 inhibitors: emerging drugs in cancer therapy. Curr. Med. Chem. 19(12), 1804-1820 (2012).
    • (2012) Curr. Med. Chem. , vol.19 , Issue.12 , pp. 1804-1820
    • Bodur, C.1    Basaga, H.2
  • 14
    • 84922813362 scopus 로고    scopus 로고
    • Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 inhibitors) in clinical trials for cancer treatment
    • Zhao Y, Aguilar A, Bernard D, Wang S. Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 inhibitors) in clinical trials for cancer treatment. J. Med. Chem. 58(3), 1038-1052 (2015).
    • (2015) J. Med. Chem. , vol.58 , Issue.3 , pp. 1038-1052
    • Zhao, Y.1    Aguilar, A.2    Bernard, D.3    Wang, S.4
  • 15
    • 84860267055 scopus 로고    scopus 로고
    • Beyond size, ionization state, and lipophilicity: Influence of molecular topology on absorption, distribution, metabolism, excretion, and toxicity for druglike compounds
    • Yang Y, Engkvist O, Llinàs A, Chen H. Beyond size, ionization state, and lipophilicity: influence of molecular topology on absorption, distribution, metabolism, excretion, and toxicity for druglike compounds. J. Med. Chem. 55(8), 3667-3677 (2012).
    • (2012) J. Med. Chem. , vol.55 , Issue.8 , pp. 3667-3677
    • Yang, Y.1    Engkvist, O.2    Llinàs, A.3    Chen, H.4
  • 16
    • 79952804851 scopus 로고    scopus 로고
    • Improvement in aqueous solubility in small molecule drug discovery programs by disruption of molecular planarity and symmetry
    • Ishikawa M, Hashimoto Y. Improvement in aqueous solubility in small molecule drug discovery programs by disruption of molecular planarity and symmetry. J. Med. Chem. 54(6), 1539-1554 (2011).
    • (2011) J. Med. Chem. , vol.54 , Issue.6 , pp. 1539-1554
    • Ishikawa, M.1    Hashimoto, Y.2
  • 18
    • 0038512037 scopus 로고    scopus 로고
    • Molecular shape diversity of combinatorial libraries: A prerequisite for broad bioactivity
    • Sauer W, Schwarz MK. Molecular shape diversity of combinatorial libraries: a prerequisite for broad bioactivity. J. Chem. Inf. Comput. Sci. 43(3), 987-1003 (2003).
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , Issue.3 , pp. 987-1003
    • Sauer, W.1    Schwarz, M.K.2
  • 19
    • 84867774202 scopus 로고    scopus 로고
    • Plane of best fit: A novel method to characterize the three-dimensionality of molecules
    • Firth NC, Brown N, Blagg J. Plane of best fit: a novel method to characterize the three-dimensionality of molecules. J. Chem. Inf. Model. 52(10), 2516-2525 (2012).
    • (2012) J. Chem. Inf. Model , vol.52 , Issue.10 , pp. 2516-2525
    • Firth, N.C.1    Brown, N.2    Blagg, J.3
  • 20
    • 84862192766 scopus 로고    scopus 로고
    • ChEMBL: A largescale bioactivity database for drug discovery
    • Gaulton A, Bellis LJ, Bento AP et al. ChEMBL: a largescale bioactivity database for drug discovery. Nucl. Acids Res. 40(D1), D1100-D1107 (2011).
    • (2011) Nucl. Acids Res. , vol.40 , Issue.D1 , pp. D1100-D1107
    • Gaulton, A.1    Bellis, L.J.2    Bento, A.P.3
  • 21
    • 33846871027 scopus 로고    scopus 로고
    • The scaffold tree - Visualization of the scaffold universe by hierarchical scaffold classification
    • Schuffenhauer A, Ertl P, Roggo S, Wetzel S, Koch MA, Waldmann H. The scaffold tree - visualization of the scaffold universe by hierarchical scaffold classification. J. Chem. Inf. Model. 47(1), 47-58 (2007).
    • (2007) J. Chem. Inf. Model , vol.47 , Issue.1 , pp. 47-58
    • Schuffenhauer, A.1    Ertl, P.2    Roggo, S.3    Wetzel, S.4    Koch, M.A.5    Waldmann, H.6
  • 22
    • 84934980568 scopus 로고    scopus 로고
    • MOARF, an integrated workflow for multiobjective optimization: Implementation, synthesis, and biological evaluation
    • Firth NC, Atrash B, Brown N, Blagg J. MOARF, an integrated workflow for multiobjective optimization: implementation, synthesis, and biological evaluation. J. Chem. Inf. Model. 55(6), 1169-1180 (2015).
    • (2015) J. Chem. Inf. Model , vol.55 , Issue.6 , pp. 1169-1180
    • Firth, N.C.1    Atrash, B.2    Brown, N.3    Blagg, J.4
  • 23
    • 78650727351 scopus 로고    scopus 로고
    • Conformations and 3D pharmacophore searching
    • Schwab CH. Conformations and 3D pharmacophore searching. Drug Discov. Today Technol. 7(4), e245-e253 (2010).
    • (2010) Drug Discov. Today Technol. , vol.7 , Issue.4 , pp. e245-e253
    • Schwab, C.H.1
  • 24
    • 2342586724 scopus 로고    scopus 로고
    • Conformational analysis of druglike molecules bound to proteins: An extensive study of ligand reorganization upon binding
    • Perola E, Charifson PS. Conformational analysis of druglike molecules bound to proteins: an extensive study of ligand reorganization upon binding. J. Med. Chem. 47(10), 2499-2510 (2004).
    • (2004) J. Med. Chem. , vol.47 , Issue.10 , pp. 2499-2510
    • Perola, E.1    Charifson, P.S.2
  • 25
    • 0028466540 scopus 로고
    • Comparison of automatic three-dimensional model builders using 639 x-ray structures
    • Sadowski J, Gasteiger J, Klebe G. Comparison of automatic three-dimensional model builders using 639 x-ray structures. J. Chem. Inf. Model. 34(4), 1000-1008 (1994).
    • (1994) J. Chem. Inf. Model , vol.34 , Issue.4 , pp. 1000-1008
    • Sadowski, J.1    Gasteiger, J.2    Klebe, G.3
  • 26
    • 84986314259 scopus 로고    scopus 로고
    • ChEMBL v21. www.ebi.ac.uk/chembl/downloads
  • 27
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23(1-3), 3-25 (1997).
    • (1997) Adv. Drug Deliv. Rev. , vol.23 , Issue.1-3 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 28
    • 84864679725 scopus 로고    scopus 로고
    • Macrocycles in new drug discovery
    • Mallinson J, Collins I. Macrocycles in new drug discovery. Future Med. Chem. 4(11), 1409-1438 (2012).
    • (2012) Future Med. Chem. , vol.4 , Issue.11 , pp. 1409-1438
    • Mallinson, J.1    Collins, I.2
  • 30
    • 84986314591 scopus 로고    scopus 로고
    • Molecular Networks GmbH: Erlangen, Germany
    • CORINA, version 3.4, Molecular Networks GmbH: Erlangen, Germany (2013).
    • (2013) CORINA, Version 3.4
  • 31
    • 31444452744 scopus 로고
    • Automatic generation of 3D-atomic coordinates for organic molecules
    • Gasteiger J, Rudolph C, Sadowski J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Computer Methodology 3(6), 537-547 (1990).
    • (1990) Tetrahedron Computer Methodology , vol.3 , Issue.6 , pp. 537-547
    • Gasteiger, J.1    Rudolph, C.2    Sadowski, J.3
  • 34
    • 84880922581 scopus 로고    scopus 로고
    • Protein pocket and ligand shape comparison and its application in virtual screening
    • Wirth M, Volkamer A, Zoete V et al. Protein pocket and ligand shape comparison and its application in virtual screening. J. Comput. Aided Mol. Des. 27(6), 511-524 (2013).
    • (2013) J. Comput. Aided Mol. Des. , vol.27 , Issue.6 , pp. 511-524
    • Wirth, M.1    Volkamer, A.2    Zoete, V.3
  • 36
    • 84969617464 scopus 로고    scopus 로고
    • Analysis of past and present synthetic methodologies on medicinal chemistry: Where have all the new reactions gone?
    • Brown DG, Boström J. Analysis of past and present synthetic methodologies on medicinal chemistry: where have all the new reactions gone? J. Med. Chem. 59(10), 4443-4458 (2016).
    • (2016) J. Med. Chem. , vol.59 , Issue.10 , pp. 4443-4458
    • Brown, D.G.1    Boström, J.2
  • 37
    • 80053322606 scopus 로고    scopus 로고
    • Scaffold diversity of exemplified medicinal chemistry space
    • Langdon SR, Brown N, Blagg J. Scaffold diversity of exemplified medicinal chemistry space. J. Chem. Inf. Model. 51(9), 2174-2185 (2011).
    • (2011) J. Chem. Inf. Model , vol.51 , Issue.9 , pp. 2174-2185
    • Langdon, S.R.1    Brown, N.2    Blagg, J.3
  • 38
    • 0035324944 scopus 로고    scopus 로고
    • Molecular complexity and its impact on the probability of finding leads for drug discovery
    • Hann MM, Leach AR, Harper G. Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. Sci. 41(3), 856-864 (2001).
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , Issue.3 , pp. 856-864
    • Hann, M.M.1    Leach, A.R.2    Harper, G.3


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