Microbial Genomics and Drug Discovery

255 Pages·2003·3.79 MB·English

by  Thomas J. Dougherty (Editor)

Preface
To date no antibacterial compounds identified by target based screening have
advanced into clinical testing much less been used clinically to treat bacterial
infections. This well-noted futility has led some to suggest that this approach
willneverproveproductive,thatthemajorityof“novel”targetsarenot“drugg-
able,”andthatindustryresearchdollarsarebetterspentelsewhere.Afterall,even
the most stubborn of bacterial infections rarely, if ever, require more than six
months of treatment, and the average course of therapy is under seven days. It
hasbeenreasonedthatitmakesmorecommercialsensetotreatchronicconditions
requiringyearsoftherapyratherthancuringdiseaseswithshortcoursesoftreat-
ment.Theuseofthispharmaceuticalindustrycalculushaslongbeentherationale
used for the chronic underresourcing of antibacterial research programs (not to
mentionanemicpublicfundingforthestudyofpathogenicbacteriaandantibacte-
rial drug resistance) but this actually flies in the face of commercial and public
health realities. Not only are infectious disease therapeutics the second largest
source of revenue for pharmaceutical companies (behind cardiovascular drugs),
with antibacterial drugstaking the lion’s share,but there are also nofewer than
six branded products garnering over $1 billion annually, despite fierce generic
competition.Nootherareaoftherapeuticfocuscanboastthislevelofcommercial,
not to mention therapeutic success.
Thereislessargumentontheneedfornewantibacterialagentsandthera-
peutic strategiesto avoidthe emergenceand disseminationof resistantbacteria.
Partandparceloftheresistanceproblemaredramaticallychangingdemographics
iii
iv Preface
consistingofanagingpopulationwithadeclineintherobustresponsetoinfec-
tions.Thishasproducedapopulationthatisbecomingincreasinglyimmunosup-
pressed.Indevelopingcountriesperiodicmalnutrition,poorsanitation,thespread
ofHIVinfection,and,almostparadoxically,increasingpopulationdensity,cou-
pled with the ready availability of cheap, generic antibacterials (often of poor
quality), are leading to a mushrooming of resistant bacterial strains. In sum,
bacterial diseasesin general, andantibiotic-resistant bacterialinfections specifi-
cally,areincreasinginbothdevelopinganddevelopedcountries.Ironically,even
improvedtherapiesforotherdiseasesarecontributingtoanincreaseininfectious
diseases, e.g. immune suppressive therapies in transplant patients, aggressive
chemotherapeutic practices in oncology, and most recently the use of TNF-(cid:1)
antagonistsintreatingrheumatoidarthritis.Alongwiththisincreasedsusceptibil-
itytoinfection,ithasbeenwelldocumentedthatanumberofpathogens,including
Streptococcuspneumoniae,Staphylococcusaureus,andMycobacteriumtubercu-
losis,havedevelopedresistancetoarangeofantimicrobialsatanalarmingrate.
Yet despite the well-documented commercial opportunity and the clear unmet
medical need many large pharmaceutical companies are withdrawing from this
field.Contributingtothediminishinginterestistheperceivedinabilityoftarget-
based screening to produce commercially successful antibacterials. Some in the
industry are now convinced that this approach was doomed from the start.
This is reminiscentof prevailing public and scientific opinionprior to the
firstsuccessfuldemonstrationofpoweredflightbytheWrightbrothers.Priorto
theirsuccessatKittyHawkthereweremanywell-documentedattemptsatpow-
eredflightthatliterallycrashedandburned.WhydidOrvilleandWilburWright
succeed where so many others had so visibly, repeatedly—and at times tragi-
cally—failed?Threereasonsareprominent:(1)expertise:especially(asbicycle
builders)intheuseofdurable,lightweightmaterials,andtheabilitytolearnfrom
thefailuresoftheircompetitors,(2)resources:theWrightshadadequate,although
not copious, financial backing, and (3) a sensitive assay: the Wrights used the
winds of Kitty Hawk to produce additional lift and built what was essentially a
glider with an engine. A fourth reason is persistence: they were undeterred by
thefailureofothers,patientlyworkinginasystematicfashiontosolveproblems.
Anotherimportantpointtoconsiderintarget-basedscreeningforantibacte-
rialagentsisthat,inthepursuitofbroad-spectrumagents,thegoalisnotanew
molecular entity that is a potent inhibitor of a single molecular target. Rather,
we aresearching for inhibitors ofa family ofrelated but not identicaltargets in
a wide range of pathogenic bacteria. Several groups have been successful at
identifying narrow-spectrum inhibitors with excellent in vitro potency and even
efficacyinanimalmodelsofinfection.Butsuchnarrow-spectrumagentsarenot
considered commercially or therapeutically viable because the vast majority of
therapeutic applications involve empiric therapy (where an antibacterial drug is
administereduponpresentationofsymptomsbutpriortotheidentificationofthe
Preface v
The Wright Brothers Memorial in Kitty Hawk, N.C. The reconstructed
hangerandcampbuildingisattheleftcenter.Inthedistance,thegraniteMemorial
Pylon,completedin1932,sitsatopKillDevilHill.Thewalkwaytotherighthas
four stone markers, representing the distances of the four flights made on Dec.
17,1903.Thefourthmarker,representingthelongestflightof852feet,isatthe
far right of the photograph. The inscription on the Memorial Pylon reads:
IN COMMEMORATION OF THE CONQUEST OF THE AIR
BY THE BROTHERS WILBUR AND ORVILLE WRIGHT
CONCEIVED BY GENIUS, ACHIEVED BY DAUNTLESS
RESOLUTION AND UNCONQUERABLE FAITH
infectiousagent).Thiswillbethefocusofmostantibacterialdiscoveryprograms
unlessanduntilrapid(read“bedside”)diagnosticsbecomewidelyavailable.Even
then, the enormous expense to bring a drug to market (currently estimated at
$700–800million)makesanarrow-spectrumagentadifficultcommercialpropo-
sition. Therefore the assumption made here is that goal of antibacterial drug
discovery is a novel class of broad-spectrum agent so the themes of the target
classes below are, for the most part, those that are generally well conserved
(genetically and structurally) among pathogenic bacteria.
vi Preface
Thenotionthatthemereidentificationofnewtargetswouldquicklyresult
in a flood of novel antibiotics was naive. The rapid delivery of the genomic
sequencesofpathogenicbacteriaoverthepasteightyearsraisedtheexpectation
that a large number of new targets for therapy would be identified. Indeed, a
number of groups have done precisely that using a variety of clever strategies.
Genomictargetidentificationcertainlyhasresultedinamorerationalandacceler-
atedprocessinantibiotictargetscreening.Italsosuggestedseveralnewwaysto
return to cell-based antimicrobial screens in a targeted approach with increased
sensitivitytoinhibitors.However,thebottleneckhasshiftedfromtargetidentifi-
cation to the process of identifying inhibitors that have the potential to become
leads, that is, to be modified to drug-like characteristics. This is a difficult and
empiricprocess,involvingthebalanceofcontinuedorimprovedtargetinhibition
withinstillingtheproperpharmacologicalpropertiesandlackofhumantoxicity
inthecandidatemolecule.Thegenomics-approachgoalistodeliveranincreasing
numberofantibacterialinhibitorsagainstabroaderrangeoftargetsintheexpecta-
tionthatasmallsubsetofthesemoleculeswillindeedbeamenabletotheneces-
sary pharmacological modifications for safe and effective use as antibiotics.
Inthisbook,abroadrangeofgenomics-basedapproachestotheproblemof
identifyingnovelantibioticclassesarepresented.Thechaptersfocusondifferent
aspectsoftheproblemspresentedinidentifying,selecting,andprosecutingnovel
antibacterial targets. Much like the approach to powered flight a hundred years
ago,itisstilltooearlytosaywhichtechniqueswillultimatelyyieldsuccess.But
given the stakes, we must maintain the same faith in our goals as those early
pioneers of the air.
Finally, we would like to express our gratitude to the expert authors who
agreed to contribute to this endeavor. Their creativity and diligence in the field
areclearfromthecaliberoftheworkpresented.WealsothankAnitaLekhwani
andDanaBigelowofMarcelDekker,Inc.,fortheireffortsinbringingthisproject
forward.
Thomas J. Dougherty
Steven J. Projan
Contents
Preface iii
Contributors ix
1. Global Aspects of Antibiotic Resistance 1
Julian Davies
2. Genomics of Bacterial Pathogens 9
Steven R. Gill, Karen E. Nelson, and Claire M. Fraser
3. Bioinformatics, Genomics, and Antimicrobial Drug Discovery 27
Brian A. Dougherty and Daniel B. Davison
4. The Pathway Tools Software and Its Role in Antimicrobial Drug
Discovery 43
Peter D. Karp
5. Genomic Strategies in Antibacterial Drug Discovery 55
Christopher P. Gray and Wolfgang Keck
6. Genomics-Based Approaches to Novel Antimicrobial Target
Discovery 71
Thomas J. Dougherty, John F. Barrett, and Michael J. Pucci
7. Pathogenesis Genes as Novel Targets 97
Andrea Marra
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viii Contents
8. Application of Genomics to the Discovery of New Drugs Against
Tuberculosis 111
Richard A. Slayden, Dean C. Crick, Michael R. McNeil, and
Patrick J. Brennan
9. Phenotype MicroArrays: Their Use in Antibiotic Discovery 135
Barry R. Bochner
10. Microbial Proteomics: New Approaches for Therapeutic
Vaccines and Drug Discovery 147
C. Patrick McAtee
11. Surrogate Ligand-Based Assay Systems for Discovery of
Antibacterial Agents for Genomic Targets 173
Dale J. Christensen and Paul T. Hamilton
12. Expression Profiling Uses in Antibacterial Chemotherapy
Development 187
Paul M. Dunman and Steven J. Projan
13. Using Fungal Genomes for the Discovery, Development, and
Clinical Application of Novel and Current Antifungal
Therapeutics 201
Todd A. Black, Joan K. Brieland, Jonathan Greene, Catherine
Hardalo, Scott S. Walker, and Guillaume Cottarel
14. Genomics in Novel Natural Products Generation 221
Zhiqiang An and William R. Strohl
Index 239
Contributors
ZhiqiangAn MerckResearchLaboratories,Merck&Co.,Rahway,NewJer-
sey, U.S.A.
John F. Barrett Merck Research Laboratories, Merck & Co., Rahway, New
Jersey, U.S.A.
Todd A. Black Chemotherapy and Molecular Genetics, Schering-Plough Re-
search Institute, Kenilworth, New Jersey, U.S.A.
BarryR.Bochner Research&Development,Biolog,Inc.,Hayward,Califor-
nia, U.S.A.
Patrick J. Brennan Department of Microbiology, Colorado State University,
Fort Collins, Colorado, U.S.A.
Joan K. Brieland Chemotherapy and Molecular Genetics, Schering-Plough
Research Institute, Kenilworth, New Jersey, U.S.A.
Dale J. Christensen Karo Bio USA, Inc., Durham, North Carolina, U.S.A.
ix
x Contributors
Guillaume Cottarel Genome Therapeutics Corp., Waltham, Massachusetts,
U.S.A.
Dean C. Crick Department of Microbiology, Colorado State University, Fort
Collins, Colorado, U.S.A.
Julian Davies Department of Microbiology and Immunology, University of
BritishColumbia, andCubistPharmaceuticals, Inc.,Vancouver, BritishColum-
bia, Canada
DanielB.Davison DepartmentofBioinformatics,Bristol-MyersSquibbPhar-
maceutical Research Institute Pennington, New Jersey, U.S.A.
BrianA.Dougherty DepartmentofAppliedGenomics,Bristol-MyersSquibb
Pharmaceutical Research Institute, Wallingford, Connecticut, U.S.A.
ThomasJ.Dougherty MolecularScience,PfizerGlobalResearchandDevel-
opment, Groton, Connecticut, U.S.A.
PaulM.Dunman InfectiousDisease-AntibacterialResearch,WyethResearch,
Pearl River, New York, U.S.A.
ClaireM.Fraser TheInstituteforGenomeResearch(TIGR),Rockville,Mary-
land, U.S.A.
Steven R. Gill The Institute forGenomic Research (TIGR), Rockville, Mary-
land, U.S.A.
Christopher P. Gray Morphochem AG, Basel, Switzerland
Jonathan Greene Bioinformatics, Schering-Plough Research Institute, Ken-
ilworth, New Jersey, U.S.A.
Paul T. Hamilton Karo Bio USA, Inc., Durham, North Carolina, U.S.A.
Catherine Hardalo Clinical Research, Infectious Diseases, Schering-Plough
Research Institute, Kenilworth, New Jersey, U.S.A.
PeterD.Karp BioinformaticsResearchGroup,SRIInternational,MenloPark,
California, U.S.A.
Wolfgang Keck Morphochem AG, Basel, Switzerland
Contributors xi
AndreaMarra AntibacterialsDiscovery,PfizerGlobalResearchandDevelop-
ment, Groton, Connecticut, U.S.A.
C. Patrick McAtee Lexicon Genetics, Inc., The Woodlands, Texas, U.S.A.
Michael R. McNeil Department of Microbiology, Colorado State University,
Fort Collins, Colorado, U.S.A.
KarenE.Nelson TheInstituteforGenomicResearch(TIGR),Rockville,Mary-
land, U.S.A.
Steven J. Projan Wyeth Research, Pearl River, New York, U.S.A.
MichaelJ.Pucci AchillionPharmaceuticals,NewHaven,Connecticut,U.S.A.
RichardA.Slayden DepartmentofMicrobiology,ColoradoStateUniversity,
Fort Collins, Colorado, U.S.A.
WilliamR.Strohl MerckResearchLaboratories,Merck&Co.,Rahway,New
Jersey, U.S.A.
ScottS.Walker ChemotherapyandMolecularGenetics,Schering-PloughRe-
search Institute, Kenilworth, New Jersey, U.S.A.