Chloroquine is one of the most effective antimalarials, but resistance to it is becoming widespread. However, we do not fully understand either the drug's mode of action or the mechanism of resistance. In an effort to expand our understanding of the mechanism of action and resistance associated with chloroquine, we used Saccharomyces cerevisiae as a model eukaryotic system. To aid in the discovery of potential drug targets we applied the transcriptional profiling method to identify genes transcriptionally responsive to chloroquine treatment in S. cerevisiae. Among the genes that were differentially expressed with chloroquine treatment were a number of metal transporters involved in iron acquisition (SIT1, ARN2, ARN4, and SMF2). These genes exhibit similar expression patterns, and several are known to be regulated by AFT1, a DNA binding protein, which responds to iron levels in the cell. We investigated the role of chloroquine in iron metabolism by using a variety of approaches, including pharmacological, genetic, and biochemical techniques. For these experiments, we utilized yeast lacking the major iron uptake pathways (FET3 and FET4) and yeast deficient in SIT1, encoding the major up-regulated iron siderophore transporter. Our experiments show that yeast genetically or environmentally limited in iron availability has increased sensitivity to chloroquine in pharmacological assays and that the addition of iron rescues these cells from chloroquine killing.55 FeCl 3 accumulation was inhibited in the presence of chloroquine, and kinetic analysis demonstrated that inhibition was competitive. These results are consistent with deprivation of iron as a mechanism of chloroquine killing in yeast.Chloroquine (CQ) is commonly used for treatment of malaria; however, its mode of action and the mechanism of resistance are still not fully understood. Better knowledge of CQ's mode of action may make it possible to identify new drugs that target similar pathways or to reverse existing resistant phenotypes.CQ has been shown to interact in both mammalian cells and Plasmodium spp. with a number of different pathways, including changes in vacuolar (or lysosomal) pH (9,22,39,56), binding to DNA and RNA (3,11,41,53), binding to heme and -hematin in Plasmodium falciparum (1, 55; reviewed in reference 20). In the case of P. falciparum, CQ was an effective drug whose efficacy has been severely compromised by the emergence of drug-resistant parasites (8,20).To analyze the mechanism of CQ action, we used transcriptional profiling in a model eukaryotic system, Saccharomyces cerevisiae. Differential transcriptional profiling using microarray analysis is based on detecting differences in expression of mRNAs in cells treated under different conditions. No information other than the genomic sequence and the open reading frame (ORF) predictions is necessary to assay mRNA expression. Such whole-genome analysis allows the determination of expression profiles without preselection of genes. For the experiments described here, we used the Affymetrix...