De novo design - Hop(p)ing against hope

Drug Discovery Today: Technologies

Volumn 10, Issue 4, 2013, Pages

  Schneider, Gisbert ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER ANALYSIS; DRUG DESIGN; MATHEMATICAL MODEL; PHARMACOPHORE; STRUCTURE ACTIVITY RELATION;

DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84886310564     PISSN: None     EISSN: 17406749     Source Type: Journal    
DOI: 10.1016/j.ddtec.2012.06.001     Document Type: Review

References (62)

1. G. Schneider Virtual screening: an endless staircase? Nat Rev. Drug Discov. 9 2010 273 276
2. Sheng, C. and Zhang, W. (2012) Fragment informatics and computational fragment-based drug design: an overview and update. Med. Res. Rev. doi:10.1002/med.21255 (in press)
3. R. Law The multiple roles of computational chemistry in fragment-based drug design J. Comput. Aided Mol. Des. 23 2009 459 473
4. P.J. Hajduk, and J. Greer A decade of fragment-based drug design: strategic advances and lessons learned Nat. Rev. Drug Discov. 6 2007 211 219
5. R. Garcia-Serna, and J. Mestres Anticipating drug side effects by comparative pharmacology Expert Opin. Drug Metab. Toxicol. 6 2010 1253 1263
6. A. Merino Drug profiling: knowing where it hits Drug Discov. Today 15 2010 749 756
7. M.P. Gleeson Probing the links between in vitro potency, ADMET and physicochemical parameters Nat. Rev. Drug Discov. 10 2011 197 208
8. J.T. Metz, and P.J. Hajduk Rational approaches to targeted polypharmacology: creating and navigating protein-ligand interaction networks Curr. Opin. Chem. Biol. 14 2010 498 504
9. M. Hartenfeller, and G. Schneider Enabling future drug discovery by de novo design WIREs Comp. Mol. Sci. 1 2011 742 759
10. J.B. Moon, and W.J. Howe Computer design of bioactive molecules: a method for receptor-based de novo ligand design Proteins 11 1991 314 328
11. G. Schneider, and U. Fechner Computer-based de novo design of drug-like molecules Nat. Rev. Drug Discov. 4 2005 649 663
12. M. Hartenfeller, and G. Schneider De novo drug design Methods Mol. Biol. 672 2011 299 323
13. G. Schneider 'Scaffold-hopping' by topological pharmacophore search: a contribution to virtual screening Angew. Chem. Int. Ed. 38 1999 2894 2896
14. G. Schneider Designing the molecular future J. Comput. Aided Mol. Des. 26 2012 115 120
15. S.R. Langdon Bioisosteric replacement and scaffold hopping in lead generation and optimization Mol. Inform. 29 2010 366 385
16. M. Rarey, and M. Stahl Similarity searching in large combinatorial chemistry spaces J. Comput. Aided Mol. Des. 15 2001 497 520
17. G. Schneider Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors Future Med. Chem. 3 2011 415 424
18. P.J. Hajduk Fragment-based drug design: how big is too big? J. Med. Chem. 49 2006 6972 6976
19. O. Ichihara Compound design by fragment-linking Mol. Inform. 30 2011 298 306
20. K. Babaoglu, and B.K. Shoichet Deconstructing fragment-based inhibitor discovery Nat. Chem. Biol. 2 2006 720 723
21. C.W. Murray, and M.L. Verdonk The consequences of translational and rotational entropy lost by small molecules on binding to proteins J. Comput. Aided Mol. Des. 16 2002 741 753
22. R.E. Hubbard Informatics and modeling challenges in fragment-based drug discovery Curr. Opin. Drug Discov. Dev. 10 2007 289 297
23. M. Hartenfeller DOGS: reaction-driven de novo design of bioactive compounds PLoS Comput. Biol. 8 2012 e1002380
24. G. Schneider Voyages to the (un)known: adaptive design of bioactive compounds Trends Biotechnol. 27 2009 18 26
25. J.A. Hiss Concepts and applications of natural computing techniques in de novo drug and peptide design Curr. Pharm. Des. 16 2010 1656 1665
26. V.J. Gillett SPROUT, HIPPO and CAESA: tools for de novo structure generation and estimation of synthetic accessibility Perspect. Drug Discov. Des. 3 1995 34 50
27. A. Zaliani Second-generation de novo design: a view from a medicinal chemist perspective J. Comput. Aided Mol. Des. 23 2009 593 602
28. J. Law Route designer: a retrosynthetic analysis tool utilizing automated retrosynthetic rule generation J. Chem. Inform. Model. 49 2009 593 602
29. B.A. Krueger Scaffold-hopping potential of fragment-based de novo design: the chances and limits of variation Comb. Chem. High Throughput Screen. 12 2009 383 396
30. U. Fechner, and G. Schneider Flux (1): a virtual synthesis scheme for fragment-based de novo design J. Chem. Inform. Model. 46 2006 699 707
31. U. Fechner, and G. Schneider Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design J. Chem. Inform. Model. 47 2007 656 667
32. X.Q. Lewell RECAP - retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry J. Chem. Inform. Comput. Sci. 38 1998 511 522
33. V. Svetnik Random forest: a classification and regression tool for compound classification and QSAR modeling J. Chem. Inform. Comput. Sci. 43 2003 1947 1958
34. M.F. Schmidt, and J. Rademann Dynamic template-assisted strategies in fragment-based drug discovery Trends Biotechnol. 27 2009 512 521
35. W.L. Jorgensen Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase Bioorg. Med. Chem. Lett. 16 2006 663 667
36. S. Renner, and G. Schneider Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening J. Med. Chem. 47 2004 4653 4664
37. J.D. Holliday Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision J. Cheminform. 3 2011 29
38. A. Spoerri Authority and ranking effects in data fusion J. Am. Soc. Inform. Sci. Technol. 59 2008 450 460
39. G. Schneider, and S.S. So Adaptive Systems in Drug Design 2001 Landes Bioscience
40. R. Guha The ups and downs of structure-activity landscapes Methods Mol. Biol. 672 2011 101 117
41. J. Hussain, and C. Rea Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets J. Chem. Inform. Model. 50 2010 339 348
42. K. Müller The power of MMPA and a teaching lesson in medicinal chemistry J. Med. Chem. 55 2012 1815 1816
43. E. Griffen Matched molecular pairs as a medicinal chemistry tool J. Med. Chem. 54 2011 7739 7750
44. Nicolaou, C.A. et al. (2012) Multi-objective optimization methods in de novo drug design. Mini Rev. Med. Chem. (in press)
45. M. Reutlinger, and G. Schneider Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery J. Mol. Graphics Modell. 34 2012 108 117
46. M. Reutlinger Neighborhood-preserving visualization of adaptive structure-activity landscapes and application to drug discovery Angew. Chem. Int. Ed. 50 2011 11633 11636
47. D. Dimova Design of multitarget activity landscapes that capture hierarchical activity cliff distributions J. Chem. Inform. Model. 51 2011 258 266
48. J.L. Medina-Franco Multitarget structure-activity relationships characterized by activity-difference maps and consensus similarity measure J. Chem. Inform.Inform. Model. 51 2011 2427 2439
49. Stouch, T.R. (ed.) (2012) The Next 25 Years. J. Comput-Aided Mol. Des. 26
50. H. Mauser, and W. Guba Recent developments in de novo design and scaffold hopping Curr. Opin. Drug Discov. Dev. 11 2008 365 374
51. M.J. Keiser Relating protein pharmacology by ligand chemistry Nat. Biotechnol. 25 2007 197 206
52. J.J. Irwin, and B.K. Shoichet ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inform. Model. 45 2005 177 182
53. R.L. Mancera Molecular modeling of hydration in drug design Curr. Opin. Drug Discov. Dev. 10 2007 275 280
54. D.G. Lloyd The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models J. Comput. Aided Mol. Des. 18 2004 89 100
55. A.T. García-Sosa, and R.L. Mancera The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors J. Mol. Model. 12 2006 422 431
56. J. Blaney A very short history of structure-based design: how did we get here and where do we need to go? J Comput. Aided Mol. Des. 26 2012 13 14
57. M.P. Mazanetz Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method J. Cheminform. 3 2011 2
58. M. Nazaré Fragment deconstruction of small, potent factor Xa inhibitors: exploring the superadditivity energetics of fragment linking in protein-ligand complexes Angew. Chem. Int. Ed. 51 2012 905 911
59. S. Keppner Identification and validation of a potent type II inhibitor of inactive polo-like kinase 1 ChemMedChem 4 2009 1806 1809
60. Y. Tanrikulu Scaffold hopping by fuzzy pharmacophores and its application to RNA targets Chembiochem 8 2007 1932 1936
61. P. Schneider, and G. Schneider Collection of bioactive reference compounds for focused library design QSAR Comb. Sci. 22 2003 713 718
62. G. Hinton, and S. Roweis Stochastic neighbor embedding Adv. Neural Inform. Proc. Syst. 15 2002 833 840