Discovering antibiotic efficacy biomarkers: toward mechanism-specific high content compound screening.
As current antibiotic therapy is increasingly challenged by emerging drug-resistant bacteria, new technologies are required to identify and develop novel classes of antibiotics. A major bottleneck in today's discovery efforts, however, is a lack of an efficient and standardized method for assaying the efficacy of a drug candidate. We propose a new high content screening approach for identifying efficacious molecules suitable for development of antibiotics. Key to our approach is a new microarray-based efficacy biomarker discovery strategy. We first produced a large dataset of transcriptional responses of Bacillus subtilis to numerous structurally diverse antibacterial drugs. Second we evaluated different protocols to optimize drug concentration and exposure time selection for profiling compounds of unknown mechanism. Finally we identified a surprisingly low number of gene transcripts (approximately 130) that were sufficient for identifying the mechanism of novel substances with reasonable accuracy (approximately 90%). We show that the statistics-based approach reveals a physiologically meaningful set of biomarkers that can be related to major bacterial defense mechanisms against antibiotics. We provide statistical evidence that a parallel measurement of the expression of the biomarkers guarantees optimal performance when using expression systems for screening libraries of novel substances. The general approach is also applicable to drug discovery for medical indications other than infectious diseases.
Freiberg
Christoph
C
Pharma Global Drug Discovery, European Research Center, Bayer HealthCare AG, D-42096 Wuppertal, Germany.
Brunner
Nina
N
Macko
Ludwig
L
Fischer
Hans Peter
HP
D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001412:Bacillus subtilis / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D015415:Biomarkers / Q000032:analysis*; D015195:Drug Design; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000187:drug effects; D005798:Genes, Bacterial; D008826:Microbial Sensitivity Tests / Q000379:methods*; D009675:Novobiocin / Q000494:pharmacology; D014295:Trimethoprim / Q000494:pharmacology
D000900:Anti-Bacterial Agents; D015415:Biomarkers; D009675:Novobiocin; D014295:Trimethoprim