microbial functional genomics
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Chapter 13. The Impact of Genomics on Antimicrobial Drug Discovery and Toxicology. Microbial Functional Genomics. CBBL - Young- sik Sohn -. Introduction. Genome-scale DNA sequence information offers potential molecular targets - PowerPoint PPT PresentationTRANSCRIPT
Microbial Functional Ge-nomicsChapter 13. The Impact of Genomics on Antimicrobial Drug
Discovery and Toxicology
CBBL- Young-sik Sohn-
Introduction
Genome-scale DNA sequence information offers potential molecular targets
Newly developed genomic technologies promise to impact all facets of the drug discovery
Target-based drug discovery
Challenges of New Drug Discovery Need for new antibiotic discovery
A mechanism that contributes to antibiotic resistance is drug exclusion by efflux systems
Challenges of New Drug Discovery
Desirable properties of antimicrobial targetsAntimicrobial targets should meet the criteria of spectrum,
selectivity, functionality, and essentiality ① provide adequate spectrum and selectivity ② essential for growth or viability of the pathogen ③ knowledge on the function is necessary in order to
design assays and high-throughput screens
Mining genomes for antimicrobial drug targets
Microbial Genomics and Drug Target Se-lection
Comparative genomics: target spectrum and selectivityUseful approach to estimate target spectrum and selectivityOffer the opportunity to develop broad-spectrum antibioticsSignificant proportion of genomes encode proteins with no
known function
Microbial Genomics and Drug Target Se-lection
Genetic strategies: verifying the essentiality or expression of gene targets
Combine molecular biology and common drug screening ↓
expediting the identification of antimicrobials with unique modes of action
① signature-tagged mutagenesis (STM) ② in vivo expression technology (IVET) ③ differential fluorescence induction (DFI)
Microbial Genomics and Drug Target Se-lection
Microarray analysis: establishing function for new targetsIdentification of new regulatory pathways or networks
↓design novel drugs
Screen populations of clinical isolates or related strains (Used as a comparative genomics tool)
↓conserved genes/genetic variation
Microbial Genomics and Drug Target Se-lection
Determining Therapeutic Utility: Drug Target Screening and Validation
Target-based drug screeningStrain array for antibacterial discovery
○ any target○ the molecular target can be confirmed with a functional assay○ identify several compounds with good inhibitory activity○ Strains be screened at any time and at low cost
Determining Therapeutic Utility: Drug Target Screening and Validation
Target-based drug screeningIn silico screening and structure-based drug design
Determining Therapeutic Utility: Drug Target Screening and Validation
Target-based drug screeningSurrogate-ligand-based screening
○ Surrogate ligand: short peptides bind to functional sites of target proteinsinhibiting target’s function
○ Important aspect: data of protein activity isn’t required identify active site of unknown function
Determining Therapeutic Utility: Drug Target Screening and Validation
Microarrays and drug target validationMicroarray analysis of inhibition of gene function
○ establish whether a putative target is required to generate the drug signature
○ Microarray analysis of inhibition may be useful for validation(a compound often may affect unintended components)
Using microarray-based gene expression profiling to identify an unknown toxicant’s mechanism of
action
Genomics and Toxicology: The Emer-gence of Toxicogenomics
Microarrays in mechanistic toxicologyToxBlot arrays: investigating toxicity processes
≒ 600 marker genes for array constructiongenes for toxicology
Goal of toxicogenomics Identify groups of genes that are tightly correlated with
known classes of toxicants
Genomics and Toxicology: The Emer-gence of Toxicogenomics
Microarrays in predictive toxicologyGoal :
predict adverse drugreduce the time reduce expense
Summary Therapeutic inhibition will be done by target-based strate-
gies which combine computational and experimental ap-proaches
Microarray-based gene expression profiling is becoming a standard in mechanistic toxicology and is providing impor-tant insights into the mechanisms of action
Toxicogenomics is expected to impact the safety assess-ment of new drugs and to reduce the number of drug fail-ures
Thank you for your attention