Several models describing how amino acid substitutions in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) confer resistance to chloroquine (CQ) and other antimalarial drugs have been proposed. Further progress requires molecular analysis of interactions between purified reconstituted PfCRT protein and these drugs. We have thus designed and synthesized several perfluorophenyl azido (pfpa) CQ analogues for PfCRT photolabeling studies. One particularly useful probe (AzBCQ) places the pfpa group at the terminal aliphatic N of CQ via a flexible four-carbon ester linker and includes a convenient biotin tag. This probe photolabels PfCRT in situ with high specificity. Using reconstituted proteoliposomes harboring partially purified recombinant PfCRT, we analyze AzBCQ photolabeling versus competition with CQ and other drugs to probe the nature of the CQ binding site. We also inspect how pH, the chemoreversal agent verapamil (VPL), and various amino acid mutations in PfCRT that cause CQ resistance (CQR) affect the efficiency of AzBCQ photolabeling. Upon gel isolation of AzBCQ-labeled PfCRT followed by trypsin digestion and mass spectrometry analysis, we are able to define a single AzBCQ covalent attachment site lying within the digestive vacuolar-disposed loop between putative helices 9 and 10 of PfCRT. Taken together, the data provide important new insight into PfCRT function and, along with previous results, allow us to propose a model for a single CQ binding site in the PfCRT protein.

Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.

Nuclear magnetic resonance (NMR) measurements of magnetic susceptibility have been utilized to study the equilibrium between two forms (high-spin monomer vs the antiferromagnetically coupled μ-oxo dimer) of ferriprotoporphyrin(IX) as a function of pH. The pH dependence of this equilibrium is significantly altered by the addition of either chloroquine or quinine. Chloroquine promotes the μ-oxo dimer whereas quinine promotes the monomer.

Systematic variation of the branching and basicity of the side chain of chloroquine yielded a series of new 7-chloro-4-aminoquinoline derivatives exhibiting high in vitro activity against four different strains of P. falciparum. Many of the compounds tested showed excellent potency against chloroquine sensitive and resistant strains. In particular 4b, 5a, 5b, 5d, 17a, and 17b were found to be significantly more potent than chloroquine against the resistant strains Dd2 and FCB.

Several models for how amino acid substitutions in the Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) confer resistance to chloroquine (CQ) and other antimalarial drugs have been proposed. Distinguishing between these models requires detailed analysis of high resolution CQ transport data that is unfortunately impossible to obtain with traditional radio–tracer methods. Thus, we have designed and synthesized fluorescent CQ analogues for drug transport studies. One probe places a NBD (6–(N–(7–nitrobenz–2–oxa–1,3–diazol–4–yl)amino)hexanoate acid) group at the tertiary aliphatic N of CQ, via a flexible 6 C amide linker. This probe localizes to the malarial parasite digestive vacuole (DV) during initial perfusion under physiologic conditions and exhibits similar pharmacology relative to CQ, vs. both CQ sensitive (CQS) and resistant (CQR) parasites. Using live, synchronized intraerythrocytic parasites under continuous perfusion we define NBD-CQ influx and efflux kinetics for CQS vs. CQR parasites. Since this fluorescence approach provides data at much higher kinetic resolution relative to fast–filtration methods using 3H–CQ, rate constants vs. linear initial rates for CQ probe flux can be analyzed in detail. Importantly, we find CQR parasites have a decreased rate constant for CQ influx into the DV, and that this is due to mutation of PfCRT. Analysis of zero trans efflux for CQS and CQR parasites suggests distinguishing between bound vs. free pools of intra-DV drug probe is essential for proper kinetic analysis of efflux. The accompanying paper [Paguio et al., (2009), XXXX-XXXX] further probes efflux kinetics for proteoliposomes containing purified, reconstituted PfCRT.