Microbial Functional Genomics

1. Chapter 13. The Impact of Genomics on Antimicrobial Drug Discovery and Toxicology Microbial Functional Genomics CBBL - Young-sikSohn-

2. Introduction • Genome-scale DNA sequence information offers potential molecular targets • Newly developed genomic technologies promise to impact all facets of the drug discovery

3. Target-based drug discovery

4. Challenges of New Drug Discovery • Need for new antibiotic discovery • A mechanism that contributes to antibiotic resistance is drug exclusion by efflux systems

5. Challenges of New Drug Discovery • Desirable properties of antimicrobial targets • Antimicrobial 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

6. Microbial Genomics and Drug Target Selection • Mining genomes for antimicrobial drug targets

7. Microbial Genomics and Drug Target Selection • Comparative genomics: target spectrum and selectivity • Useful approach to estimatetarget spectrum and selectivity • Offer the opportunity to develop broad-spectrum antibiotics • Significant proportion of genomes encode proteins with no known function

8. Microbial Genomics and Drug Target Selection • 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)

9. Microbial Genomics and Drug Target Selection • Microarray analysis: establishing function for new targets • Identification 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

10. Determining Therapeutic Utility: Drug Target Screening and Validation • Target-based drug screening • Strain 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

11. Determining Therapeutic Utility: Drug Target Screening and Validation • Target-based drug screening • In silico screening and structure-based drug design

12. Determining Therapeutic Utility: Drug Target Screening and Validation • Target-based drug screening • Surrogate-ligand-based screening • Surrogate ligand: short peptides bind to functional sites of target proteins inhibiting target’s function • Important aspect: data of protein activity isn’t required identify active site of unknown function

13. Determining Therapeutic Utility: Drug Target Screening and Validation • Microarrays and drug target validation • Microarray 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)

14. Using microarray-based gene expression profiling to identify an unknown toxicant’s mechanism of action

15. Genomics and Toxicology: The Emergence of Toxicogenomics • Microarrays in mechanistic toxicology • ToxBlot arrays: investigating toxicity processes ≒ 600 marker genes for array construction genes for toxicology • Goal of toxicogenomics • Identify groups of genes that are tightly correlated with known classes of toxicants

16. Genomics and Toxicology: The Emergence of Toxicogenomics • Microarrays in predictive toxicology • Goal : predict adverse drug reduce the time reduce expense

17. Summary • Therapeutic inhibition will be done by target-based strategies which combine computational and experimental approaches • Microarray-based gene expression profiling is becoming a standard in mechanistic toxicology and is providing important insights into the mechanisms of action • Toxicogenomics is expected to impact the safety assessment of new drugs and to reduce the number of drug failures

18. Thank you for your attention