Drug discovery and computational evolutionary analysis

Drug Discovery Today

Volumn 12, Issue 19-20, 2007, Pages 826-832

  Holbrook, Joanna D ^a   Sanseau, Philippe ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 12; DOPAMINE 4 RECEPTOR; G PROTEIN COUPLED RECEPTOR; LEPTIN; PRODYNORPHIN; SEROTONIN 3 RECEPTOR;

BRAC1 GENE; CELL LINEAGE; CLINICAL STUDY; COMPUTATIONAL EVOLUTIONARY ANALYSIS; DISEASE MODEL; DRUG EFFECT; DRUG SAFETY; DRUG SCREENING; GENE; GENE DUPLICATION; GENE LOSS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; MATHEMATICAL GENETICS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENY; REVIEW; SEQUENCE ANALYSIS; SEROTONINERGIC SYSTEM; VALIDATION PROCESS;

ANIMALS; COMPUTATIONAL BIOLOGY; DRUG DESIGN; EVOLUTION, MOLECULAR; GENOMICS; HUMANS; PHYLOGENY; RESEARCH DESIGN; SPECIES SPECIFICITY;

EID: 35148878237     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.drudis.2007.08.015     Document Type: Review

References (75)

1. Kola I., and Landis J. Can the pharmaceutical industry reduce attrition rates?. Nat. Rev. Drug Discov. 3 (2004) 711-715
2. International HapMap Consortium. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
3. Searls D.B. Pharmacophylogenomics: genes, evolution and drug targets. Nat. Rev. Drug Discov. 2 (2003) 623
4. Koonin E.V. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39 (2005) 309-338
5. Stephen F., et al. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
6. Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85 (1998) 2444-2448
7. McInerney J.O., et al. Gene evolution and drug discovery. Methods Mol. Biol. 316 (2006) 87-109
8. Lake B.G. Coumarin metabolism, toxicity and carcinogenicity: relevance for human risk assessment. Food Chem. Toxicol. 37 (1999) 423-453
9. Yang, Z. (2006). In Harvey P.H. and Robert, M.M. (eds), Computational Molecular Evolution Oxford series in Ecology and Evolution
10. Yang Z. Inference of selection from multiple sequence alignments. Curr. Opin. Genet. Dev. 12 (2002) 688-694
11. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
12. Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-43
13. Choi S.S., and Lahn B.T. Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception. Gen. Res. 13 (2003) 2252-2259
14. Yang Z. Likelihood ratios tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15 (1998) 568-573
15. Nielsen R., and Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
16. Yang Z., et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449
17. Yang Z., and Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19 (2002) 908-917
18. Yang Z., and Swanson W.J. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19 (2002) 49-57
19. Zhang J., et al. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22 (2005) 2472-2479
20. Hinds D.A., et al. Whole-genome patterns of common DNA variation in three human populations. Science 307 (2005) 1072-1079
21. Sabeti P.C., et al. Positive natural selection in the human lineage. Science 312 (2006) 1614-1620
22. Voight B.F., et al. A map of recent positive selection in the human genome. PloS. Biol. 4 (2006) e72
23. Hellman I., et al. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72 (2003) 1527-1535
24. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
25. Fu Y.X., and Li W.H. Statistical tests of neutrality of mutations. Genetics 133 (1993) 693-709
26. Fay J.C., and Wu C.I. Hitchhiking under positive Darwinian selection. Genetics 155 (2000) 1405-1413
27. Akey J.M., et al. Interrogating a high-density snp map for signatures of natural selection. Genome Res. 12 (2002) 1805-1814
28. Lewontin R.C., and Krakauer J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74 (1973) 175-195
29. Kreitman M. Methods to detect selection in populations with applications to the human. Annu. Rev. Genomics Hum. Genet. 1 (2000) 539-559
30. Tishkoff S.A., and Verelli B.C. Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu. Rev. Genomics Hum. Genet. 4 (2003) 240-293
31. Di Rienzo A., and Hudson R.R. An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet. 21 (2005) 596-601
32. Tishkoff S.A., et al. Convergent adaptation of human lactase persistence in Africa and Europe. Nat. Genet. 39 (2007) 31-40
33. Carlson C.S., et al. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15 (2005) 1553-1565
34. Nielsen R., et al. Genomic scans for selective sweep using SNP data. Genome Res. 15 (2005) 1666-1675
35. Kelley J.L., et al. Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res. 16 (2006) 980-989
36. Wang E.T., et al. Global landscape of recent inferred Darwinian selection in Homo sapiens. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 135-140
37. Tang K., et al. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 7 (2007) e171
38. 3 serotonin receptor-like genes HTR3C, HTR3D and HTR3E. Gene 310 (2003) 101-111
39. Nielser B., et al. Characterization of the novel human serotonin receptor subunits 5-HT3C, 5-HT3D, and 5-HT3E. Mol. Pharmacol. 72 (2007) 8-17
40. Karnovsky A.M., et al. A cluster of novel serotonin receptor 3-like genes on human chromosome 3. Gene 319 (2003) 137-148
41. 3 receptor antagonists in the treatment of irritable bowel syndrome. Aliment. Pharmacol. Ther. 13 (1999) 31-38
42. Kinloch R.A., and Cox P.J. New targets for neuropathic pain therapeutics. Expert Opin. Ther. Targets 9 (2005) 685-698
43. Dong X., et al. A diverse family of GPCRs expressed in specific subsets of nociceptive sensory neurons. Cell 106 (2001) 619-632
44. Chen H., et al. Evidence that the diabetes gene encodes the leptin receptor: identification of a mutation in the leptin receptor gene in db/db mice. Cell 84 (1996) 491-495
45. Benner S.A., et al. Functional inferences from reconstructed evolutionary biology involving rectified databases: an evolutionary grounded approach to functional genomics. Res. Microbiol. 151 (2000) 97-106
46. Miki Y., et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRAC1. Science 266 (1994) 66-71
47. Huttley G.A., et al. Adaptive evolution of the tumour suppressor BRAC1 in humans and chimpanzees. Nat. Genet. 25 (2000) 410-413
48. Rockman M., et al. Ancient and recent positive selection transformed opioid cis-regulation in humans. PloS Biol. 3 (2005) e387
49. Cheng H.Y., et al. DREAM is a critical transcriptional repressor for pain modulation. Cell 108 (2002) 31-43
50. Moles A., et al. Deficit in attachment behaviour in mice lacking the mu-opioid receptor gene. Science 304 (2004) 1983-1986
51. Saleh M., et al. Differential modulation of endotoxin responsiveness by human capsase-12 polymorphisms. Nature 429 (2004) 75-79
52. Xue Y., et al. Spread of an inactive form of Capsase-12 in humans is due to recent positive selection. Am. J. Hum. Genet. 78 (2006) 659-670
53. Faranone S.V., et al. Meta-analysis of the association between the 7-repeat allele of the dopamine D4 receptor gene and attention deficit hyperactivity disorder. Am. J. Psychiatry 158 (2001) 1052-1057
54. Jovanovic V., et al. Comparative pharmacological and functional analysis of the human dopamine D4.2 and D4.10 receptor variants. Pharmacogenetics 9 (1999) 561-568
55. Ding Y.-C., et al. Evidence of positive selection acting at the human dopamine receptor D4 locus. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 309-314
56. Wang E., et al. The genetic architecture of selection at the human dopamine receptor D4 (DRD4) gene locus. Am. J. Hum. Genet. 74 (2004) 931-944
57. Smith N.G.C., and Eyre-Walker A. Human disease genes: patterns and predictions. Gene 318 (2003) 169-175
58. Huang H., et al. Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biol. 5 (2004) R47
59. Clark A.G., et al. Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios. Science 302 (2003) 1960-1963
60. Bustamante C.D., et al. Natural selection on protein-coding genes in the human genome. Nature 437 (2005) 1153-1157
61. Bakewell M., et al. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 7489-7494
62. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
63. Young J.H., et al. Differential susceptibility to hypertension is due to selection during the out-of-Africa expansion. PLoS Genet. 1 (2005) e82
64. Camon E., et al. The gene ontology annotation (GOA) database: sharing knowledge in uniprot with gene ontology. Nucleic Acids Res. 1, 32 Database issue (2004) D262-D266
65. Mi H., et al. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 1, 33 Database issue (2005) D284-D288
66. Nielsen R., et al. A scan for positively selected genes in the genomes of human and chimpanzees. PloS Biol. 3 (2005) e170
67. Rhesus Macaque Genome Sequencing and Anlaysis Consortium. Evolutionary and biomedical insights from the Rhesus Macaque Genome. Science 316 (2007) 222-234
68. Arbiza L., et al. Positive selection, relaxation and acceleration in the evolution of the human and chimp genome. PLoS Comput. Biol. 2 (2006) 288-300
69. Crespi B.J., and Summers K. Positive selection in the evolution of cancer. Biol. Rev. 81 (2006) 407-424
70. Dorus S., et al. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119 (2004) 1027-1040
71. Crespi B.J. The natural selection of psychosis. Behav. Brain Sci. 29 (2006) 410-411
72. Nesse R.M., et al. Medicine needs evolution. Science 311 (2006) 1071
73. MacCallum C.J. Does medicine without evolution make sense?. PLoS Biol. 5 (2007) e112
74. Tate S.K., and Goldstein D.B. Will tomorrow's medicines work for everyone?. Nat. Genet. 36 Suppl. 11 (2004) S34-S42
75. Varmus H., and Satcher D. Ethical complexities of conducting research in developing countries. N. Engl. J. Med. 337 (1997) 1003-1005