Chapter 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 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

 Mining genomes for antimicrobial drug targets Microbial Genomics and Drug Target Selection

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

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

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

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

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)

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

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

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

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

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