microbial functional genomics

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