Home LiteratureArticle Details
PMID: 16524830 Published · ppublish English Journal Article Review

Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery.

Blundell TL, Sibanda BL, Montalvão RW, Brewerton S, Chelliah V, Worth CL, Harmer NJ, Davies O, Burke D

Abstract

Impressive progress in genome sequencing, protein expression and high-throughput crystallography and NMR has radically transformed the opportunities to use protein three-dimensional structures to accelerate drug discovery, but the quantity and complexity of the data have ensured a central place for informatics. Structural biology and bioinformatics have assisted in lead optimization and target identification where they have well established roles; they can now contribute to lead discovery, exploiting high-throughput methods of structure determination that provide powerful approaches to screening of fragment binding.

MeSH Terms
Computational Biology Drug Design Drug Evaluation, Preclinical Humans Protein Conformation Substrate Specificity
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Blundell Tom L
Department of Biochemistry, University of Cambridge 80 Tennis Court Road, Cambridge CB2 1GA, UK. tom@cryst.bioc.cam.ac.uk
Sibanda Bancinyane L
Montalvão Rinaldo Wander
Brewerton Suzanne
Chelliah Vijayalakshmi
Worth Catherine L
Harmer Nicholas J
Davies Owen
Burke David
References (77)
77 references, click to expand
  1. Protein clefts in molecular recognition and function.
    Protein Sci. 1996 Dec;5(12):2438-52 PMID: 8976552
  2. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.
    J Mol Biol. 1997 Apr 11;267(4):1026-38 PMID: 9135128
  3. Sequence and structure conservation in a protein core.
    Proteins. 1998 Nov 15;33(3):358-66 PMID: 9829695
  4. The PROSITE database, its status in 1999.
    Nucleic Acids Res. 1999 Jan 1;27(1):215-9 PMID: 9847184
  5. Three-dimensional structure analysis of PROSITE patterns.
    J Mol Biol. 1999 Mar 12;286(5):1673-91 PMID: 10064723
  6. Science, art and drug discovery: a personal perspective.
    Clin Sci (Lond). 2000 Oct;99(4):255-60 PMID: 10995589
  7. Fragment-based lead discovery.
    Nat Rev Drug Discov. 2004 Aug;3(8):660-72 PMID: 15286733
  8. Virtual screening in lead discovery and optimization.
    Curr Opin Drug Discov Devel. 2004 Jul;7(4):396-403 PMID: 15338948
  9. Comprehensive survey of combinatorial library synthesis: 2003.
    J Comb Chem. 2004 Sep-Oct;6(5):623-79 PMID: 15360197
  10. Distinguishing structural and functional restraints in evolution in order to identify interaction sites.
    J Mol Biol. 2004 Oct 1;342(5):1487-504 PMID: 15364576
  11. The role of the medicinal chemist in drug discovery--then and now.
    Nat Rev Drug Discov. 2004 Oct;3(10):853-62 PMID: 15459676
  12. Compounds designed to fit a site of known structure in human haemoglobin.
    Br J Pharmacol. 1976 Jun;57(2):201-9 PMID: 938794
  13. The interaction of human haemoglobin with allosteric effectors as a model for drug-receptor interactions.
    Br J Pharmacol. 1980 Apr;68(4):741-8 PMID: 7378645
  14. Three-dimensional structure, specificity and catalytic mechanism of renin.
    Nature. 1983 Jul 21-27;304(5923):273-5 PMID: 6346109
  15. A structural model for the retroviral proteases.
    Nature. 1987 Sep 24-30;329(6137):351-4 PMID: 3306411
  16. Prediction of protein secondary structure and active sites using the alignment of homologous sequences.
    J Mol Biol. 1987 Jun 20;195(4):957-61 PMID: 3656439
  17. 18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design.
    Eur J Biochem. 1988 Mar 15;172(3):513-20 PMID: 3280310
  18. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures.
    Protein Eng. 1987 Oct-Nov;1(5):377-84 PMID: 3508286
  19. High-throughput screening of historic collections: observations on file size, biological targets, and file diversity.
    Biotechnol Bioeng. 1998 Winter;61(1):61-7 PMID: 10099497
  20. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences.
    J Mol Biol. 1999 Apr 9;287(4):797-815 PMID: 10191147
  21. Mapping of protein-protein interactions within the DNA-dependent protein kinase complex.
    Nucleic Acids Res. 1999 Sep 1;27(17):3494-502 PMID: 10446239
  22. Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding.
    Proteins. 1999 Oct 1;37(1):44-55 PMID: 10451549
  23. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery.
    Chem Biol. 1999 Oct;6(10):755-69 PMID: 10508679
  24. Model building by comparison at CASP3: using expert knowledge and computer automation.
    Proteins. 1999;Suppl 3:47-54 PMID: 10526351
  25. Docking and scoring in virtual screening for drug discovery: methods and applications.
    Nat Rev Drug Discov. 2004 Nov;3(11):935-49 PMID: 15520816
  26. Fragment-based lead discovery using X-ray crystallography.
    J Med Chem. 2005 Jan 27;48(2):403-13 PMID: 15658854
  27. Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation.
    J Med Chem. 2005 Jan 27;48(2):414-26 PMID: 15658855
  28. Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition.
    Proteins. 2005 Dec 1;61(4):722-31 PMID: 16193489
  29. Comparative protein modelling by satisfaction of spatial restraints.
    J Mol Biol. 1993 Dec 5;234(3):779-815 PMID: 8254673
  30. Identification of related proteins on family, superfamily and fold level.
    J Mol Biol. 2000 Jan 21;295(3):613-25 PMID: 10623551
  31. Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening.
    J Med Chem. 2000 Jul 13;43(14):2664-74 PMID: 10893304
  32. Discovering novel ligands for macromolecules using X-ray crystallographic screening.
    Nat Biotechnol. 2000 Oct;18(10):1105-8 PMID: 11017052
  33. Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin.
    Nature. 2000 Oct 26;407(6807):1029-34 PMID: 11069186
  34. X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes.
    Nature. 1989 Nov 16;342(6247):299-302 PMID: 2682266
  35. Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution.
    Science. 1989 Dec 1;246(4934):1149-52 PMID: 2686029
  36. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction.
    Proc Biol Sci. 1990 Aug 22;241(1301):132-45 PMID: 1978340
  37. A method to identify protein sequences that fold into a known three-dimensional structure.
    Science. 1991 Jul 12;253(5016):164-70 PMID: 1853201
  38. Analysis of the steric strain in the polypeptide backbone of protein molecules.
    Proteins. 1991;11(3):223-9 PMID: 1749775
  39. A new approach to protein fold recognition.
    Nature. 1992 Jul 2;358(6381):86-9 PMID: 1614539
  40. Domain closure in mitochondrial aspartate aminotransferase.
    J Mol Biol. 1992 Sep 5;227(1):197-213 PMID: 1522585
  41. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.
    Protein Sci. 1992 Feb;1(2):216-26 PMID: 1304904
  42. Protein structural alignments and functional genomics.
    Proteins. 2001 Feb 15;42(3):378-82 PMID: 11151008
  43. CODA: a combined algorithm for predicting the structurally variable regions of protein models.
    Protein Sci. 2001 Mar;10(3):599-612 PMID: 11344328
  44. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
    J Mol Biol. 2001 Jun 29;310(1):243-57 PMID: 11419950
  45. High-throughput docking for lead generation.
    Curr Opin Chem Biol. 2001 Aug;5(4):375-82 PMID: 11470599
  46. Crystal structure of an Xrcc4-DNA ligase IV complex.
    Nat Struct Biol. 2001 Dec;8(12):1015-9 PMID: 11702069
  47. Evolutionary predictions of binding surfaces and interactions.
    Curr Opin Struct Biol. 2002 Feb;12(1):21-7 PMID: 11839485
  48. Combinatorial chemistry and high-throughput screening in drug discovery: different strategies and formats.
    Mol Divers. 2000;5(2):75-89 PMID: 11865648
  49. SAR and X-ray. A new approach combining fragment-based screening and rational drug design: application to the discovery of nanomolar inhibitors of Src SH2.
    J Med Chem. 2002 Jun 6;45(12):2379-87 PMID: 12036348
  50. Lead discovery using molecular docking.
    Curr Opin Chem Biol. 2002 Aug;6(4):439-46 PMID: 12133718
  51. The druggable genome.
    Nat Rev Drug Discov. 2002 Sep;1(9):727-30 PMID: 12209152
  52. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.
    Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11664-9 PMID: 12193646
  53. A review of protein-small molecule docking methods.
    J Comput Aided Mol Des. 2002 Mar;16(3):151-66 PMID: 12363215
  54. A new test set for validating predictions of protein-ligand interaction.
    Proteins. 2002 Dec 1;49(4):457-71 PMID: 12402356
  55. Structural genomics. Tapping DNA for structures produces a trickle.
    Science. 2002 Nov 1;298(5595):948-50 PMID: 12411682
  56. Integration of virtual and high-throughput screening.
    Nat Rev Drug Discov. 2002 Nov;1(11):882-94 PMID: 12415248
  57. Insights into DNA recombination from the structure of a RAD51-BRCA2 complex.
    Nature. 2002 Nov 21;420(6913):287-93 PMID: 12442171
  58. Structure-based screening of low-affinity compounds.
    Drug Discov Today. 2002 May 1;7(9):522-7 PMID: 11983569
  59. Structure-based virtual screening: an overview.
    Drug Discov Today. 2002 Oct 15;7(20):1047-55 PMID: 12546894
  60. Facilities and methods for the high-throughput crystal structural analysis of human proteins.
    Acc Chem Res. 2003 Mar;36(3):157-63 PMID: 12641472
  61. High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility.
    Acc Chem Res. 2003 Mar;36(3):173-81 PMID: 12641474
  62. Crystallography, NMR and virtual screening: integrated tools for drug discovery.
    Curr Opin Drug Discov Devel. 2003 Jul;6(4):544-9 PMID: 12951817
  63. Assessment of progress over the CASP experiments.
    Proteins. 2003;53 Suppl 6:585-95 PMID: 14579350
  64. Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design.
    J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):97-100 PMID: 14646145
  65. Structural analysis of DNA-PKcs: modelling of the repeat units and insights into the detailed molecular architecture.
    J Struct Biol. 2004 Mar;145(3):295-306 PMID: 14960380
  66. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
    J Med Chem. 2004 Mar 25;47(7):1739-49 PMID: 15027865
  67. Ligand efficiency: a useful metric for lead selection.
    Drug Discov Today. 2004 May 15;9(10):430-1 PMID: 15109945
  68. Fragment-based drug discovery.
    J Med Chem. 2004 Jul 1;47(14):3463-82 PMID: 15214773
  69. Ku80: product of the XRCC5 gene and its role in DNA repair and V(D)J recombination.
    Science. 1994 Sep 2;265(5177):1442-5 PMID: 8073286
  70. Protein structure--based drug design.
    Annu Rev Biophys Biomol Struct. 1994;23:349-75 PMID: 7919786
  71. Restoration of X-ray resistance and V(D)J recombination in mutant cells by Ku cDNA.
    Science. 1994 Oct 14;266(5183):288-91 PMID: 7939667
  72. DNA-dependent kinase (p350) as a candidate gene for the murine SCID defect.
    Science. 1995 Feb 24;267(5201):1178-83 PMID: 7855601
  73. Defective DNA-dependent protein kinase activity is linked to V(D)J recombination and DNA repair defects associated with the murine scid mutation.
    Cell. 1995 Mar 10;80(5):813-23 PMID: 7889575
  74. Loss of the catalytic subunit of the DNA-dependent protein kinase in DNA double-strand-break-repair mutant mammalian cells.
    Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3171-4 PMID: 7724535
  75. Purification and characterization of the double-stranded DNA-activated protein kinase, DNA-PK, from human placenta.
    Biochem Cell Biol. 1996;74(1):67-73 PMID: 9035691
  76. Structure-based drug design.
    Nature. 1996 Nov 7;384(6604 Suppl):23-6 PMID: 8895597
  77. Discovering high-affinity ligands for proteins: SAR by NMR.
    Science. 1996 Nov 29;274(5292):1531-4 PMID: 8929414
Article Info
Journal
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Abbr.
Philos Trans R Soc Lond B Biol Sci
ISSN
0962-8436
Published
2006-03-29
Pages
413-23
Language
English
Region
England
NLM ID
7503623
PMCID
PMC1609333
Subset
IM
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com