Identification and Validation of Tetracyclic Benzothiazepines as Plasmodium falciparum Cytochrome bc1 Inhibitors

Dong, Carolyn K.; Urgaonkar, Sameer; Cortese, Joseph F.; Gamo, Francisco‐Javier; Garcia-Bustos, José; Lafuente, María José; Patel, Vipul; Ross, Leila; Coleman, Bradley I.; Derbyshire, Emily R.; Clish, Clary B.; Serrano, Adelfa E.; Cromwell, Mandy; Barker, Robert H.; Dvorin, Jeffrey D.; Duraisingh, Manoj T.; Wirth, Dyann F.; Clardy, Jon; Mazitschek, Ralph

doi:10.1016/j.chembiol.2011.09.016

Cited by 51 publications

(58 citation statements)

References 49 publications

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“…After correcting for multiple testing (Bonferroni correction for 25,757 SNPs, P < 2 × 10 −6 ), EMMA is able to detect a number of previously known markers of drug resistance, such as four nonsynonymous SNPs in pfcrt (conferring amino acid changes: N75E/K, K76T, Q271E, R371I) (16,17) associated with chloroquine response, one pfmdr1 SNP (conferring amino acid change: N86Y) (18,19) associated with halofantrine, lumefantrine, and mefloquine response, and three dhfr SNPs (conferring amino acid changes: N51I, C59R, S108N) (20) associated with pyrimethamine response. We note here that, although mitochondrial and apicoplast genomes were also sequenced, no significant associations were found and the known mitochondrial mutations associated with atovaquone resistance in cytochrome b (codons 268, 133, and 280) (21,22) were fixed in all 45 individuals for the drugsensitive alleles. In all, EMMA detects 34 significant SNPs associated with parasite response to five drugs ( five are previously unknown associations with pyrimethamine response (Dataset S1).…”

Section: Resultsmentioning

confidence: 99%

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

Park

Lukens

Neafsey

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

108

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Through rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite-the deadliest of those that cause malaria-is able to develop resistance to antimalarial drugs, thwarting present efforts to control it. Genome-wide association studies (GWAS) provide a critical hypothesis-generating tool for understanding how this occurs. However, in P. falciparum, the limited amount of linkage disequilibrium hinders the power of traditional array-based GWAS. Here, we demonstrate the feasibility and power improvements gained by using whole-genome sequencing for association studies. We analyzed data from 45 Senegalese parasites and identified genetic changes associated with the parasites' in vitro response to 12 different antimalarials. To further increase statistical power, we adapted a common test for natural selection, XP-EHH (cross-population extended haplotype homozygosity), and used it to identify genomic regions associated with resistance to drugs. Using this sequence-based approach and the combination of association and selection-based tests, we detected several loci associated with drug resistance. These loci included the previously known signals at pfcrt, dhfr, and pfmdr1, as well as many genes not previously implicated in drug-resistance roles, including genes in the ubiquitination pathway. Based on the success of the analysis presented in this study, and on the demonstrated shortcomings of array-based approaches, we argue for a complete transition to sequence-based GWAS for small, low linkage-disequilibrium genomes like that of P. falciparum.

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Section: Resultsmentioning

confidence: 99%

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

Park

Lukens

Neafsey

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

108

View full text Add to dashboard Cite

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“…It may provide a valuable addition to the current modeling methodologies that focus on nuclear mutations. Specifically, it could be helpful for studying the evolution of mitochondrial genes whose products are targeted by antimalarials under drug development (65)(66)(67)(68). It is currently not clear how many mutant cytb copies per parasite are necessary to confer high-grade atovaquone resistance.…”

Section: Discussionmentioning

confidence: 99%

Emergence of Resistance to Atovaquone-Proguanil in Malaria Parasites: Insights from Computational Modeling and Clinical Case Reports

Cottrell

Musset

Hubert

et al. 2014

Antimicrob Agents Chemother

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eThe usefulness of atovaquone-proguanil (AP) as an antimalarial treatment is compromised by the emergence of atovaquone resistance during therapy. However, the origin of the parasite mitochondrial DNA (mtDNA) mutation conferring atovaquone resistance remains elusive. Here, we report a patient-based stochastic model that tracks the intrahost emergence of mutations in the multicopy mtDNA during the first erythrocytic parasite cycles leading to the malaria febrile episode. The effect of mtDNA copy number, mutation rate, mutation cost, and total parasite load on the mutant parasite load per patient was evaluated. Computer simulations showed that almost any infected patient carried, after four to seven erythrocytic cycles, de novo mutant parasites at low frequency, with varied frequencies of parasites carrying varied numbers of mutant mtDNA copies. A large interpatient variability in the size of this mutant reservoir was found; this variability was due to the different parameters tested but also to the relaxed replication and partitioning of mtDNA copies during mitosis. We also report seven clinical cases in which AP-resistant infections were treated by AP. These provided evidence that parasiticidal drug concentrations against AP-resistant parasites were transiently obtained within days after treatment initiation. Altogether, these results suggest that each patient carries new mtDNA mutant parasites that emerge before treatment but are killed by high starting drug concentrations. However, because the size of this mutant reservoir is highly variable from patient to patient, we propose that some patients fail to eliminate all of the mutant parasites, repeatedly producing de novo AP treatment failures.

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“…Forward genetic drug resistance screening and genomic analysis have previously been used to identify new targets for drug development and understand new drug resistance mechanisms [4–9]. The targets of more than 12 families of small molecules (reviewed in [10]) have been identified in Plasmodia through in vitro selection and genomic characterization of the end-points of these selections.…”

Section: Introductionmentioning

confidence: 99%

A genomic and evolutionary approach reveals non-genetic drug resistance in malaria

et al. 2014

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Background: Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. Results: We previously described two mutations in the cytoplasmic prolyl-tRNA synthetase (cPRS) gene that confer resistance to halofuginone. We describe here the evolutionary trajectory of halofuginone resistance of two independent drug resistance selections in Plasmodium falciparum. Using this novel methodology, we discover an unexpected non-genetic drug resistance mechanism that P. falciparum utilizes before genetic modification of the cPRS. P. falciparum first upregulates its proline amino acid homeostasis in response to halofuginone pressure. We show that this non-genetic adaptation to halofuginone is not likely mediated by differential RNA expression and precedes mutation or amplification of the cPRS gene. By tracking the evolution of the two drug resistance selections with whole genome sequencing, we further demonstrate that the cPRS locus accounts for the majority of genetic adaptation to halofuginone in P. falciparum. We further validate that copy-number variations at the cPRS locus also contribute to halofuginone resistance. Conclusions: We provide a three-step model for multi-locus evolution of halofuginone drug resistance in P. falciparum. Informed by genomic approaches, our results provide the first comprehensive view of the evolutionary trajectory malaria parasites take to achieve drug resistance. Our understanding of the multiple genetic and non-genetic mechanisms of drug resistance informs how we will design and pair future anti-malarials for clinical use.

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Identification and Validation of Tetracyclic Benzothiazepines as Plasmodium falciparum Cytochrome bc1 Inhibitors

Cited by 51 publications

References 49 publications

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

Emergence of Resistance to Atovaquone-Proguanil in Malaria Parasites: Insights from Computational Modeling and Clinical Case Reports

A genomic and evolutionary approach reveals non-genetic drug resistance in malaria

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