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Pek Yee Lum, Christopher D. Armour, Daniel D. Shoemaker, et al.

Discovering Modes of Action for Therapeutic Compounds Using a Genome-Wide Screen of Yeast Heterozygotes. Pek Yee Lum, Christopher D. Armour, Daniel D. Shoemaker, et al. Cell, Vol. 116, 121-137, January 9, 2004. Purpose of this paper:.

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Pek Yee Lum, Christopher D. Armour, Daniel D. Shoemaker, et al.

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  1. Discovering Modes of Action for Therapeutic Compounds Using a Genome-Wide Screen of Yeast Heterozygotes Pek Yee Lum, Christopher D. Armour, Daniel D. Shoemaker, et al. Cell, Vol. 116, 121-137, January 9, 2004

  2. Purpose of this paper: • Knowledge of the underlying molecular mechanisms of drugs + their targets • Use of “Fitness Profiling” for understanding drug activities

  3. INTRODUCTION • Need for new tools that can rapidly identify protein targets of small molecules. • i.e. Protein arrays, reverse transfection, and DNA microarrays • Saccharomyces cerevisiae

  4. APPROACH • A study by Giaever et al. (1999) demonstrated that parallel analysis of yeast strains with heterozygous deletions of drug target genes can be used to monitor compound activities in vivo. • reducing the gene copy number of drug targets in a diploid cell can result in sensitization to the drug of interest. • NOW……in this paper: • They extended this approach to analyze the activities of 78 chemical entities, most of which are medically relevant. • Increased the number of mutant strains…why?? • Used high-density oligonucleotide arrays with a two-color labelling strategy…..to do what ?? • Finally, a strain-specific error model was used….to do what ?? • In this study, they correctly identified the reported targets for many well-characterized compounds in addition to discovering many potentially novel drug targets.

  5. Result #1:Study Design RationaleFigure 1. Schematic Representation of the Fitness Profiling Experimental Strategy

  6. RESULT #2:Identifying Drug-Specific Growth Defects

  7. Result #3:Large-Scale Analysis of 78 CompoundsFigure 3. Comprehensive View of Fitness Profiles for 78 Compounds

  8. Result #4: Inhibition of Lanosterol Synthase (Erg7p) by Molsidomine

  9. Result #5: Disruption of Exosome-Specific rRNA Processing by 5-Fluorouracil

  10. Result #5….continued

  11. Discussion • Use of Fitness Profiling for Understanding Drug Activities • Advantages: • Requires no prior knowledge of compound mode of action, which allows truly novel drug activities to be uncovered in a systematic and unbiased fashion • Biological processes that are affected by a given compound are identified in addition to the precise protein target(s) • Limitations and Technical Considerations: • The compound of interest must be able to affect the growth rate of the cell. • However, the ability of a compound to affect the growth rate of yeast does not guarantee that a target will be identified by this approach. • The activity level of the targeted protein must be influenced by the dosage level of the corresponding gene under the conditions profiled. • Finally, compounds that exert their effects through direct interaction with nonprotein elements in the cell, such as DNA or ergosterol, do not appear suitable for this approach.

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