The evolving role of infectomics in drug discovery

Expert Opinion on Drug Discovery

Volumn 2, Issue 7, 2007, Pages 961-975

  Huang, Sheng He ^a   Wang, Xiaoning ^b   Jong, Ambrose ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Chemical infectomics; Drug discovery; Ecological infectomics; Functional genomics; Host defense; Immunoinfectomics; Infectome; Microbial pathogen; Nanobody; Proteomics

Indexed keywords

ALPHA DEFENSIN; ANTIBIOTIC AGENT; ANTIBODY CONJUGATE; ANTIVIRUS AGENT; BCG VACCINE; FRUCTOSE OLIGOSACCHARIDE; GALACTOOLIGOSACCHARIDE DERIVATIVE; GENTIOOLIGOSACCHARIDE DERIVATIVE; GLUCOOLIGOSACCHARIDE DERIVATIVE; HELICOBACTER PYLORI VACCINE; IMMUNOSUPPRESSIVE AGENT; INULIN; ISOMALTOOLIGOSACCHARIDE DERIVATIVE; LACTIC ACID; LACTITOL; LACTULOSE; MAJOR HISTOCOMPATIBILITY ANTIGEN; MALARIA VACCINE; METICILLIN; MYCOBACTERIUM VACCINE; NATURAL PRODUCT; OLIGOSACCHARIDE; PECTICOLIGOSACCHARIDE DERIVATIVE; PHAGICIN; PLASMODIUM FALCIPARUM VACCINE; PREBIOTIC AGENT; PROBIOTIC AGENT; SOYOLIGOSACCHARIDE DERIVATIVE; UNCLASSIFIED DRUG; UNINDEXED DRUG; XYLOOLIGOSACCHARIDE DERIVATIVE;

AFRICAN TRYPANOSOMIASIS; ANTIBIOTIC RESISTANCE; BACTERIAL COLONIZATION; BACTERIAL INFECTION; BACTERIAL STRAIN; CELLULAR IMMUNITY; CLINICAL TRIAL; DATA BASE; DNA MICROARRAY; DRUG DELIVERY SYSTEM; DRUG EFFICACY; DRUG MECHANISM; DRUG RESEARCH; DRUG TARGETING; FUNGAL STRAIN; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; HUMORAL IMMUNITY; ILEITIS; IMMUNE DEFICIENCY; INFECTION; INNATE IMMUNITY; MALARIA FALCIPARUM; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MICROBIAL ACTIVITY; MYCOSIS; NONHUMAN; PARASITOSIS; PATHOGENESIS; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SYMBIOSIS; TUBERCULOSIS; VACCINE PRODUCTION; VIRUS INFECTION; VIRUS STRAIN;

EID: 34547450024     PISSN: 17460441     EISSN: None     Source Type: Journal    
DOI: 10.1517/17460441.2.7.961     Document Type: Review

References (97)

1. FAUCI AS: Infectious diseases: considerations for the 21st century. Clin. Infect. Dis. (2001) 32(5):675-685.
2. HUANG SH: Infectomics: Study of Response to Infection Using Microarrays. In: Encyclopedia of the Human Genome (Voume 3). Cooper DN (Ed.) Nature Publishing Group, (2003):453-458.
3. HUANG SH, TRICHE T, JONG AY: Infectomics: genomics and proteomics of microbial infections. Funct. Integr. Genom. (2002) 1(6):331-344.
4. LEDERBERG J: Infectious history. Science (2000) 288(5464):287-293.
5. LEDERBERG J: The future of infectious diseases. J. Urban Health (1998) 75(3):463-470.
6. WOOLHOUSE ME, WEBSTER JP, DOMINGO E, CHARLESWORTH B, LEVIN BR: Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. (2002) 32(4):569-577.
7. MCCRACKEN VJ, LORENZ RG: The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota. Cell. Microbiol. (2001) 3(1):1-11.
8. LEY RE, PETERSON DA, GORDON JI: Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 124(4):837-848.
9. LEY RE, TURNBAUGH PJ, KLEIN S, GORDON JI: Microbial ecology: human gut microbes associated with obesity. Nature (2006) 444(7122):1022-1023.
10. TURNBAUGH PJ, LEY RE, MAHOWALD MA, MAGRINI V, MARDIS ER, GORDON JI: An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 444(7122):1027-1031.
11. FALKOW S: Is persistent bacterial infection good for your health? Cell (2006) 124(4):699-702.
12. KUKLINSKA D, KILIAN M: Relative proportions of Haemophilus species in the throat of healthy children and adults. Eur. J. Clin. Microbiol. (1984) 3(3):249-252.
13. VAN DEN DRIESSCHE M, VEEREMAN-WAUTERS G: Functional foods in pediatrics. Acta Gastroenterol. Belg. (2002) 65(1):45-51.
14. HUANG SH, JONG A, WARBURTON D: Infectomics in the discovery and development of new antimicrobial agents. Curr. Med. Chem-Anti-Infective Agents (2004) 3(1):57-67.
15. BRUSSOW H: Phage therapy: the Escherichia coli experience. Microbiology (2005) 151(Pt7):2133-2140.
16. LEVIN BR, BULL JJ: Population and evolutionary dynamics of phage therapy. Nat. Rev. Microbiol. (2004) 2(2):166-173.
17. VERGIN F: Antibiotics and probiotics. Hippokrates (1954) 25(4):116-119.
18. DE MORALS MB, JACOB CM: The role of probiotics and prebiotics in pediatric practice. J. Pediatr. (Rio. J). (2006) 82(Suppl. 5):S189-S197.
19. ALVAREZ-OLMOS MI, OBERHELMAN RA: Probiotic agents and infectious diseases: a modern perspective on a traditional therapy. Clin. Infect. Dis. (2001) 32(11):1567-1576.
20. ISOLAURI E: Probiotics in human disease. Am. J. Clin. Nutr. (2001) 73(6):S1142-S1146.
21. LEE DJ, DRONGOWSKI RA, CORAN AG, HARMON CM: Evaluation of probiotic treatment in a neonatal animal model. Pediatr. Surg. Int. (2000) 16(4):237-242.
22. MATTAR AF, DRONGOWSKI RA, CORAN AG, HARMON CM: Effect of probiotics on enterocyte bacterial translocation in vitro. Pediatr. Surg. Int. (2001) 17(4):265-268.
23. HOOPER LV, GORDON JI: Commensal host-bacterial relationships in the gut. Science (2001) 292(5519):1115-1118.
24. TUOHY KM, PROBERT HM, SMEJKAL CW, GIBSON GR: Using probiotics and prebiotics to improve gut health. Drug Discov. Today (2003) 8(15):692-700.
25. BRUSSOW H, CANCHAYA C, HARDT WD: Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. (2004) 68(3):560-602.
26. HAUSLER T: Viruses vs Superbugs: A Solution to the Antibiotics Crisis?. Macmillan, New York, USA (2006):1-7.
27. MIEDZYBRODZKI R, FORTUNA W, WEBER-DABROWSKA B, GORSKI A: Bacterial viruses against viruses pathogenic for man? Virus Res. (2005) 110(1-2):1-8.
28. CENTIFANTO YM: Antiviral agent from lambda-infected Escherichia coli K-12. I. isolation. Appl. Microbiol. (1968) 16(6):827-834.
29. CLARK JR, MARCH JB: Bacteriophage-mediated nucleic acid immunization. FEMS Immunol. Med. Microbiol. (2004) 40(1):21-26.
30. HUANG J, GUTTERIDGE A, HONDA W, KANEHISA M MIMOX: A web tool for phage display based epitope mapping. BMC Bioinformatics (2006) 7:451.
31. TARNOVITSKI N, MATTHEWS LJ, SUI J, GERSHONI JM, MARASCO WA: Mapping a neutralizing epitope on the SAILS coronavirus spike protein: computational prediction based on affinity-selected peptides. J. Mol. Biol. (2006) 359(1):190-201.
32. BJORKHOLM B, LUNDIN A, SILLEN A et al.: Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori. Inject. Immun. (2001) 69(12):7832-7838.
33. RELMAN DA. New technologies, human-microbe interactions, and the search for previously unrecognized pathogens. J. Infect Dis. (2002) 186(Suppl. 2):S254-S258.
34. LONG CJ, QI H, HUANG SH: A Dynamic model for hepatitis B virus infection. J. Syst. Cybernect. Inform. (2007) 5(1):1-5.
35. BIANCHI ME: DAMPs, PAMPs and alarmins: all we need to know about danger. J. Leukocyte Biol. (2007) 81(1):1-5.
36. RUBIN GM, YANDELL MD, WORTMAN JR et al.: Comparative genomics of the eukaryotes. Science (2000) 287(5461):2204-2211.
37. HOFFMANN JA, KAFATOS FC, JANEWAY CA, EZEKOWITZ RA: Phylogenetic perspectives in innate immunity. Science (1999) 284(5418):1313-1318.
38. SABROE I, PRINCE LR, JONES EC et al.: Selective roles for Toll-like receptor (TLR)2 and TLR4 in the regulation of neutrophil activation and life span. J. Immunol. (2003) 170(10):5268-5275.
39. QURESHI ST, SKAMENE E, MALO D: Comparative genomics and host resistance against infectious diseases. Emerg. Infect. Dis. (1999) 5(1):36-47.
40. VENTER JC, ADAMS MD, MYERS EW et al.: The sequence of the human genome. Science (2001) 291(5507):1304-1351.
41. CORTEZ-RETAMOZO V, BACKMANN N, SENTER PD et al.: Efficient cancer therapy with a nanobody-based conjugate. Cancer Res. (2004) 64(8):2853-2857.
42. BARAL TN, MAGEZ S, STIJLEMANS B et al.: Experimental therapy of African trypanosomiasis with a nanobody-conjugated human trypanolytic factor. Nat. Med. (2006) 12(5):580-584.
43. BRADDOCK M: Overcoming resistance with designer immunotoxins. Expert Opin. Pharmacother. (2006) 7(10):1409-1412.
44. KELLER MA, STIEHM ER: Passive immunity in prevention and treatment of infectious diseases. Clin. Microbiol. Rev. (2000) 13(4):602-614.
45. DE GROOT AS: Immunomics: discovering new targets for vaccines and therapeutics. Drug Discov. Today (2006) 11(5-6):203-209.
46. FLOWER DJ, DAVIES MN, GUAN P, BLYTHE MJ et al.: Using databases and data mining in vaccinology. Expert Opin. Drug Discov. (2007) 2(1):19-35.
47. HUANG J, HONDA W: CED: a conformational epitope database. BMC Immunol. (2006) 7:7.
48. BRAGA-NETO UM, MARQUES ET Jr. From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput. Biol. (2006) 2(7):651-662.
49. SETTE A, FLERI W, PETERS B, SATHIAMURTHY M, BUI HH, WILSON S: A roadmap for the immunomics of category A-C pathogens. Immunity. (2005) 22(2):155-161.
50. GRIFANTINI R, BARTOLINI E, MUZZI A et al.: Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat. Biotechnol. (2002) 20(9):914-921.
51. RIGDEN DJ, GALPERIN MY, JEDRZEJAS MJ: Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: a bioinformatics-based approach to vaccine and drug design. Crit. Rev. Biochem. Mol. Biol. (2003) 38(2):143-168.
52. BOSHOFF HI, DOWD CS: Chemical genetics: an evolving toolbox for target identification and lead optimization. Prog. Drug Res. (2007) 64(49):51-77.
53. JACOBY E: Chemogenomics: drug discovery's panacea? Mol. Biosyst. (2006) 2(5):218-220.
54. SZYMKOWSKI DE: Chemical genomics versus orthodox drug development. Drug Discov. Today (2003) 8(4):157-159.
55. FALB D, JINDAL S: Chemical genomics: bridging the gap between the proteome and therapeutics. Curr. Opin. Drug Discov. Devel. (2002) 5(4):532-539.
56. ZANDERS ED, BAILEY DS, DEAN PM: Probes for chemical genomics by design. Drug Discov. Today (2002) 7(13):711-718.
57. CROSTON GE: Functional cell-based uHTS in chemical genomic drug discovery. Trends Biotechnol. (2002) 20(3):110-115.
58. SHOKAT K, VELLECA M: Novel chemical genetic approaches to the discovery of signal transduction inhibitors. Drug Discov. Today (2002) 7(16):872-879.
59. ALAOUI-ISMAILI MH, LOMEDICO PT, JINDAL S: Chemical genomics: discovery of disease genes and drugs. Drug Discov. Today (2002) 7(5):292-294.
60. WINTNER EA, MOALLEMI CC: Quantized surface complementarity diversity (QSCD): a model based on small molecule-target complementarity. J. Med. Chem. (2000) 43(10):1993-2006.
61. STRAUSBERG RL, SCHREIBER SL: From knowing to controlling: a path from genomics to drugs using small molecule probes. Science (2003) 300(5617):294-295.
62. CHAN PF, MACARRON R, PAYNE DJ, ZALACAIN M, HOLMES DJ: Novel antibacterials: a genomics approach to drug discovery. Curr. Drug Targets Infect. Disord. (2002) 2(4):291-308.
63. CHENG Q, WANG S, SALYERS AA: New approaches for anti-infective drug discovery: antibiotics, vaccines and beyond. Curr. Drug Targets Infect. Disord. (2003) 3(1):66-75.
64. SCHMID MB: Microbial genomics - new targets, new drugs. Expert Opin. Ther. Targets. (2001) 5(4):465-475.
65. MCDEVITT D, PAYNE DJ, HOLMES DJ, ROSENBERG M: Novel targets for the future development of antibacterial agents. Symp. Ser. Soc. Appl. Microbiol. (2002) 31(Suppl.):28S-34S.
66. FRITZ B, RACZNIAK GA: Bacterial genomics: potential for antimicrobial drug discovery. BioDrugs (2002) 16(5):331-337.
67. PARKINSON T: The impact of genomics on anti-infectives drug discovery and development. Trends Microbiol. (2002) 10(10 Suppl.):S22-S26.
68. DIEDEREN BM, KLUYTMANS JA: The emergence of infections with community-associated methicillin resistant Staphylococcus aureus. J. Infect. (2006) 52(3):157-168.
69. FITZGERALD JR, STURDEVANT DE, MACKIE SM, GILL SR, MUSSER JM: Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA (2001) 98(15):8821-8826.
70. ROSAMOND J, ALLSOP A: Harnessing the power of the genome in the search for new antibiotics. Science (2000) 287(5460):1973-1976.
71. HUANG SH, JONG AY, SUMMERSGILL JT: Infectomic analysis of microbial infections using proteomics. In: Handbook of Proteomics. Conn PM (Ed.). Humana Press Inc., Totowa, New Jersey, USA (2003):347-356.
72. KINGSMORE SF: Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat. Rev. Drug Discov. (2006) 5(4):310-320.
73. SCHMID MB: Structural proteomics: the potential of high-throughput structure determination. Trends Microbiol. (2002) 10(10 Suppl.):S27-S31.
74. HE QY, CHIU JF: Proteomics in biomarker discovery and drug development. J. Cell Biochem. (2003) 89(5):868-886.
75. WITZMANN FA, GRANT RA: Pharmacoproteomics in drug development. Pharmacogenomics J. (2003) 3(2):69-76.
76. STEINER S, WITZMANN FA: Proteomics: applications and opportunities in preclinical drug development. Electrophoresis (2000) 21(11):2099-2104.
77. HANASH S: Disease proteomics. Nature (2003) 422(6928):226-232.
78. SPEERS AE, ADAM GC, CRAVATT BF: Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3 + 2] cydoaddition. J. Am. Chem Soc. (2003) 125(16):4686-4687.
79. ZHANG D, SARAF A, KOLASA T et al.: Fatty acid amide hydrolase inhibitors display broad selectivity and inhibit multiple carboxylesterases as off-targets. Neuropharmacology (2007) 52(4):1095-1105.
80. JUNGBLUT PR, MULLER EC, MATTOW J, KAUFMANN SH: Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect. Immun. (2001) 69(9):5905-5907.
81. GRAVES PR, HAYSTEAD TA: Molecular biologist's guide to proteomics. Microbiol. Mol. Biol. Rev. (2002) 66(1):39-63.
82. DELEHANTY JB, LIGLER FS: A microarray immunoassay for simultaneous detection of proteins and bacteria. Anal. Chem. (2002) 74(21):5681-5687.
83. WALTER G, BUSSOW K, LUEKING A, GLOKLER J: High-throughput protein arrays: prospects for molecular diagnostics. Trends Mol. Med. (2002) 8(6):250-253.
84. KUDVA IT, KRASTINS B, SHENG H et al.: Proteomics-based expression library screening (PELS): a novel method for rapidly defining microbial immunoproteomes. Mol. Cell Proteomics (2006) 5(8):1514-1519.
85. RAMACHANDRAN N, HAINSWORTH E, DEMIRKAN G, LABAER J: On-chip protein synthesis for making microarvays. Methods Mol. Biol. (2006) 328:1-14.
86. ZHANG L, YU W, HE T et al.: Contribution of human alpha-defensin 1, 2, and 3 to the anti-HIV-1 activity of CD8 antiviral factor. Science (2002) 298(5595):995-1000.
87. BACARESE-HMILTON T, BISTONI F, CRISANTI A: Protein microarrays: from serodiagnosis to whole proteome scale analysis of the immune response against pathogenic microorganisms. Biotechniques (2002) (Suppl.):24-29.
88. LIU Y, PATRICELLI MP, CRAVATT BF: Activity-based protein profiling: the serine hydrolases. Proc. Natl. Acad. Sci. USA (1999) 96(26):14694-12499.
89. KIM E, PARK JM: Identification of novel target proteins of cyclic gmp signaling pathways using chemical proteomics. J. Biochem. Mol. Biol. (2003) 36(3):299-304.
90. ODA Y, OWA T, SATO T et al.: Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. (2003) 75(9):2159-2165.
91. JEFFERY DA, BOGYO M. Chemical proteomics and its application to drug discovery. Curr. Opin. Biotechnol. (2003) 14(1):87-95.
92. LEUNG D, HARDOUIN C, BOGER DL, CRAVATT BF: Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat. Biotechnol. (2003) 21(6):687-691.
93. ADAM GC, SORENSEN EJ, CRAVATT BF: Trifunctional chemical probes for the consolidated detection and identification of enzyme activities from complex proteomes. Mol. Cell Proteomics (2002) 1(10):828-835.
94. GREENBAUM DC, BARUCH A, GRAINGER M et al.: A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science (2002) 298(5600):2002-2006.
95. LEVIN SA, GRENFELL B, HASTINGS A, PERELSON AS: Mathematical and computational challenges in population biology and ecosystems science. Science (1997) 275(5298):334-343.
96. BUTCHER EC, BERG EL, KUNKEL EJ: Systems biology in drug discovery. Nat. Biotechnol. (2004) 22(10):1253-1259.
97. WOLKENHAUER O, MESAROVIC M: Feedback dynamics and cell function: Why systems biology is called Systems Biology. Mol. Biosyst. (2005) 1(1):14-16.