Download Lum, 2004

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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Knowledge of the underlying molecular
mechanisms of drugs + their targets
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Use of “Fitness Profiling” for understanding drug
activities
INTRODUCTION
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Need for new tools that can rapidly
identify protein targets of small molecules.
 i.e.
Protein arrays, reverse transfection, and DNA
microarrays
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Saccharomyces cerevisiae
APPROACH
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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.
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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:
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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.
Result #1:
Study Design
Rationale
Figure 1. Schematic
Representation of
the Fitness Profiling
Experimental
Strategy
RESULT #2:
Identifying Drug-Specific Growth Defects
Result #3:
Large-Scale
Analysis of 78
Compounds
Figure 3.
Comprehensive
View of Fitness
Profiles for 78
Compounds
Result #4: Inhibition of Lanosterol Synthase (Erg7p) by
Molsidomine
Result #5: Disruption of Exosome-Specific rRNA Processing
by 5-Fluorouracil
Result #5….continued
Discussion

Use of Fitness Profiling for Understanding Drug Activities
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Advantages:
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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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