Systematic functional annotation of compound libraries through large-scale analysis of chemical-genetic interactions
Creators: name: Simpkins, Scott
Publisher: name: F1000Research
Year: 2016

description: Current technologies allow rapid isolation or synthesis of many thousands of compounds with potentially interesting and useful biological properties. Chemical genomics is an unbiased method to discover the modes-of-action of these compounds that is complementary to current “target-centric” approaches. Target-centric approaches are inherently limited in the scope of targets they can discover, which makes genome-wide, compound-centric methods appealing for jump-starting progress in such areas as therapeutic development, toxicology screening, and biological probe discovery. To characterize large compound libraries that remain largely functionally unannotated, we developed an optimized yeast chemical genomics pipeline for high-throughput generation of chemical-genetic interaction profiles as well as data processing and interpretation. To date, we have screened more than 18,000 compounds to generate more than 15 million chemical-genetic interaction scores.<br><br>Our high-throughput yeast chemical-genomics assay leverages the yeast genetic interaction network, the power of which has remained largely untapped in the field of chemical genomics. For example, we used the genetic interaction network to effect an order of magnitude improvement in throughput by selecting a diagnostic set of 300 strains that recovers the functional information contained in the whole genome deletion collection (~5000 strains). In addition, our method for predicting a compound’s modes-of-action utilizes genetic interaction profiles to interpret the chemical-genetic interaction profile1 and aggregates the genetic interaction-based predictions into biological process predictions. Other improvements in throughput were made possible by hypersensitizing the mutant strains to compounds (less compound required) and using massively parallel sequencing instead of microarrays to measure barcode abundance.<br> <br>We performed chemical-genomic screens for more than 18,000 compounds from a diversity of sources, including natural products and derivatives, compounds from combinatorial syntheses, and several hundred approved drugs.2,3 Our large-scale chemical-genomic screen revealed insights into the biological function of compounds, at both the individual compound and compound collection levels. Interestingly, the larger and least biased collections were depleted for compounds affecting nuclear processes (e.g. DNA repair, transcription) – suggesting these targets tend to be relatively less accessible – and enriched for compounds affecting processes related to the periphery of the cell (e.g. glycosylation) (Figure 1). Additionally, we discovered molecular substructures that are enriched in sets of compounds with similar biological effects, which shows chemical genomics’ ability to relate chemical structure to function. After identifying compounds that were likely to possess multiple modes-of-action, with predictions driven by distinct subsets of their chemical-genetic interaction profiles, we discovered a compound that perturbs DNA and disrupts the yeast cell wall. We confirmed the accuracy of our predictions by comparing them against known modes-of-action and performing large-scale validation experiments using orthogonal assays. Overall, we estimate that high confidence target predictions across all biological processes can be made for over 10% of the screened compounds.<br>