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Wirth, Dyann

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Wirth

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Dyann

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Wirth, Dyann
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    Diversity-Oriented Synthesis Probe Targets Plasmodium falciparum Cytochrome b Ubiquinone Reduction Site and Synergizes With Oxidation Site Inhibitors
    (Oxford University Press, 2014) Lukens, Amanda; Heidebrecht, Richard W.; Mulrooney, Carol; Beaudoin, Jennifer A.; Comer, Eamon; Duvall, Jeremy R.; Fitzgerald, Mark E.; Masi, Daniela; Galinsky, Kevin; Scherer, Christina A.; Palmer, Michelle; Munoz, Benito; Foley, Michael; Schreiber, Stuart L.; Wiegand, Roger C.; Wirth, Dyann
    Background. The emergence and spread of drug resistance to current antimalarial therapies remains a pressing concern, escalating the need for compounds that demonstrate novel modes of action. Diversity-Oriented Synthesis (DOS) libraries bridge the gap between conventional small molecule and natural product libraries, allowing the interrogation of more diverse chemical space in efforts to identify probes of novel parasite pathways. Methods. We screened and optimized a probe from a DOS library using whole-cell phenotypic assays. Resistance selection and whole-genome sequencing approaches were employed to identify the cellular target of the compounds. Results. We identified a novel macrocyclic inhibitor of Plasmodium falciparum with nanomolar potency and identified the reduction site of cytochrome b as its cellular target. Combination experiments with reduction and oxidation site inhibitors showed synergistic inhibition of the parasite. Conclusions. The cytochrome b oxidation center is a validated antimalarial target. We show that the reduction site of cytochrome b is also a druggable target. Our results demonstrating a synergistic relationship between oxidation and reduction site inhibitors suggests a future strategy for new combination therapies in the treatment of malaria.
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    Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections
    (Public Library of Science, 2015) Baniecki, Mary Lynn; Faust, Aubrey; Schaffner, Stephen F.; Park, Daniel J.; Galinsky, Kevin; Daniels, Rachel; Hamilton, Elizabeth; Ferreira, Marcelo U.; Karunaweera, Nadira D.; Serre, David; Zimmerman, Peter A.; Sá, Juliana M.; Wellems, Thomas E.; Musset, Lise; Legrand, Eric; Melnikov, Alexandre; Neafsey, Daniel E.; Volkman, Sarah K.; Wirth, Dyann; Sabeti, Pardis
    Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.
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    Triaminopyrimidine is a fast-killing and long-acting antimalarial clinical candidate
    (Nature Pub. Group, 2015) Hameed P., Shahul; Solapure, Suresh; Patil, Vikas; Henrich, Philipp P.; Magistrado, Pamela; Bharath, Sowmya; Murugan, Kannan; Viswanath, Pavithra; Puttur, Jayashree; Srivastava, Abhishek; Bellale, Eknath; Panduga, Vijender; Shanbag, Gajanan; Awasthy, Disha; Landge, Sudhir; Morayya, Sapna; Koushik, Krishna; Saralaya, Ramanatha; Raichurkar, Anandkumar; Rautela, Nikhil; Roy Choudhury, Nilanjana; Ambady, Anisha; Nandishaiah, Radha; Reddy, Jitendar; Prabhakar, K. R.; Menasinakai, Sreenivasaiah; Rudrapatna, Suresh; Chatterji, Monalisa; Jiménez-Díaz, María Belén; Martínez, María Santos; Sanz, Laura María; Coburn-Flynn, Olivia; Fidock, David A.; Lukens, Amanda; Wirth, Dyann; Bandodkar, Balachandra; Mukherjee, Kakoli; McLaughlin, Robert E.; Waterson, David; Rosenbrier-Ribeiro, Lyn; Hickling, Kevin; Balasubramanian, V.; Warner, Peter; Hosagrahara, Vinayak; Dudley, Adam; Iyer, Pravin S.; Narayanan, Shridhar; Kavanagh, Stefan; Sambandamurthy, Vasan K.
    The widespread emergence of Plasmodium falciparum (Pf) strains resistant to frontline agents has fuelled the search for fast-acting agents with novel mechanism of action. Here, we report the discovery and optimization of novel antimalarial compounds, the triaminopyrimidines (TAPs), which emerged from a phenotypic screen against the blood stages of Pf. The clinical candidate (compound 12) is efficacious in a mouse model of Pf malaria with an ED99 <30 mg kg−1 and displays good in vivo safety margins in guinea pigs and rats. With a predicted half-life of 36 h in humans, a single dose of 260 mg might be sufficient to maintain therapeutic blood concentration for 4–5 days. Whole-genome sequencing of resistant mutants implicates the vacuolar ATP synthase as a genetic determinant of resistance to TAPs. Our studies highlight the potential of TAPs for single-dose treatment of Pf malaria in combination with other agents in clinical development.
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    Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission
    (Public Library of Science, 2018) Wong, Wesley; Wenger, Edward A.; Hartl, Daniel; Wirth, Dyann
    Unlike in most pathogens, multiple-strain (polygenomic) infections of P. falciparum are frequently composed of genetic siblings. These genetic siblings are the result of sexual reproduction and can coinfect the same host when cotransmitted by the same mosquito. The degree with which coinfecting strains are related varies among infections and populations. Because sexual recombination occurs within the mosquito, the relatedness of cotransmitted strains could depend on transmission dynamics, but little is actually known of the factors that influence the relatedness of cotransmitted strains. Part of the uncertainty stems from an incomplete understanding of how within-host and within-vector dynamics affect cotransmission. Cotransmission is difficult to examine experimentally but can be explored using a computational model. We developed a malaria transmission model that simulates sexual reproduction in order to understand what determines the relatedness of cotransmitted strains. This study highlights how the relatedness of cotransmitted strains depends on both within-host and within-vector dynamics including the complexity of infection. We also used our transmission model to analyze the genetic relatedness of polygenomic infections following a series of multiple transmission events and examined the effects of superinfection. Understanding the factors that influence the relatedness of cotransmitted strains could lead to a better understanding of the population-genetic correlates of transmission and therefore be important for public health.
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    malERA: An updated research agenda for malaria elimination and eradication
    (Public Library of Science, 2017) Rabinovich, Regina N.; Drakeley, Chris; Djimde, Abdoulaye A.; Hall, B. Fenton; Hay, Simon I.; Hemingway, Janet; Kaslow, David C.; Noor, Abdisalan; Okumu, Fredros; Steketee, Richard; Tanner, Marcel; Wells, Timothy N. C.; Whittaker, Maxine A.; Winzeler, Elizabeth A.; Wirth, Dyann; Whitfield, Kate; Alonso, Pedro L.
    Achieving a malaria-free world presents exciting scientific challenges as well as overwhelming health, equity, and economic benefits. WHO and countries are setting ambitious goals for reducing the burden and eliminating malaria through the “Global Technical Strategy” and 21 countries are aiming to eliminate malaria by 2020. The commitment to achieve these targets should be celebrated. However, the need for innovation to achieve these goals, sustain elimination, and free the world of malaria is greater than ever. Over 180 experts across multiple disciplines are engaged in the Malaria Eradication Research Agenda (malERA) Refresh process to address problems that need to be solved. The result is a research and development agenda to accelerate malaria elimination and, in the longer term, transform the malaria community’s ability to eradicate it globally.
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    De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria
    (Oxford University Press, 2018) Redmond, Seth N; MacInnis, Bronwyn M; Bopp, Selina; Bei, Amy; Ndiaye, Daouda; Hartl, Daniel; Wirth, Dyann; Volkman, Sarah; Neafsey, Daniel
    Abstract Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However, these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here, we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a combination of sequencing, library preparation, and genotyping methods that have been optimized for accuracy in low-complexity genomic regions, we have detected de novo mutations that distinguish nominally identical parasites from clonal lineages. Despite its slower evolutionary rate compared with bacterial or viral species, de novo mutation can be detected in P. falciparum across timescales of just 1–2 years and evolutionary rates in low-complexity regions of the genome can be up to twice that detected in the rest of the genome. The increased mutation rate allows the identification of separate clade expansions that cannot be found using previous genomic epidemiology approaches and could be a crucial tool for mapping residual transmission patterns in disease elimination campaigns and reintroduction scenarios.
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    Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections
    (Nature Publishing Group UK, 2018) Early, Angela; Lievens, Marc; MacInnis, Bronwyn L.; Ockenhouse, Christian F.; Volkman, Sarah K.; Adjei, Samuel; Agbenyega, Tsiri; Ansong, Daniel; Gondi, Stacey; Greenwood, Brian; Hamel, Mary; Odero, Chris; Otieno, Kephas; Otieno, Walter; Owusu-Agyei, Seth; Asante, Kwaku Poku; Sorgho, Hermann; Tina, Lucas; Tinto, Halidou; Valea, Innocent; Wirth, Dyann; Neafsey, Daniel
    Host immunity exerts strong selective pressure on pathogens. Population-level genetic analysis can identify signatures of this selection, but these signatures reflect the net selective effect of all hosts and vectors in a population. In contrast, analysis of pathogen diversity within hosts provides information on individual, host-specific selection pressures. Here, we combine these complementary approaches in an analysis of the malaria parasite Plasmodium falciparum using haplotype sequences from thousands of natural infections in sub-Saharan Africa. We find that parasite genotypes show preferential clustering within multi-strain infections in young children, and identify individual amino acid positions that may contribute to strain-specific immunity. Our results demonstrate that natural host defenses to P. falciparum act in an allele-specific manner to block specific parasite haplotypes from establishing blood-stage infections. This selection partially explains the extreme amino acid diversity of many parasite antigens and suggests that vaccines targeting such proteins should account for allele-specific immunity.
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    Identification of Collateral Sensitivity to Dihydroorotate Dehydrogenase Inhibitors in Plasmodium falciparum
    (American Chemical Society, 2018) Ross, Leila Saxby; Lafuente-Monasterio, Maria José; Sakata-Kato, Tomoyo; Mandt, Rebecca E. K.; Gamo, Francisco Javier; Wirth, Dyann; Lukens, Amanda
    Drug resistance has been reported for every antimalarial in use highlighting the need for new strategies to protect the efficacy of therapeutics in development. We have previously shown that resistance can be suppressed with a population biology trap: by identifying situations where resistance to one compound confers hypersensitivity to another (collateral sensitivity), we can design combination therapies that not only kill the parasite but also guide its evolution away from resistance. We applied this concept to the Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) enzyme, a well validated antimalarial target with inhibitors in the development pipeline. Here, we report a high-throughput screen to identify compounds specifically active against PfDHODH resistant mutants. We additionally perform extensive cross-resistance profiling allowing us to identify compound pairs demonstrating the potential for mutually incompatible resistance. These combinations represent promising starting points for exploiting collateral sensitivity to extend the useful lifespan of new antimalarial therapeutics.
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    Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics
    (2018) Cowell, Annie N.; Istvan, Eva S.; Lukens, Amanda; Gomez-Lorenzo, Maria G.; Vanaerschot, Manu; Sakata-Kato, Tomoyo; Flannery, Erika L.; Magistrado, Pamela; Owen, Edward; Abraham, Matthew; LaMonte, Gregory; Painter, Heather J.; Williams, Roy M.; Franco, Virginia; Linares, Maria; Arriaga, Ignacio; Bopp, Selina; Corey, Victoria C.; Gnädig, Nina F.; Coburn-Flynn, Olivia; Reimer, Christin; Gupta, Purva; Murithi, James M.; Moura, Pedro A.; Fuchs, Olivia; Sasaki, Erika; Kim, Sang W.; Teng, Christine H.; Wang, Lawrence T.; Akidil, Aslı; Adjalley, Sophie; Willis, Paul A.; Siegel, Dionicio; Tanaseichuk, Olga; Zhong, Yang; Zhou, Yingyao; Llinás, Manuel; Ottilie, Sabine; Gamo, Francisco-Javier; Lee, Marcus C. S.; Goldberg, Daniel E.; Fidock, David A.; Wirth, Dyann; Winzeler, Elizabeth A.
    Chemogenetic characterization through in vitro evolution combined with whole-genome analysis can identify antimalarial drug targets and drug-resistance genes. We performed a genome analysis of 262 Plasmodium falciparum parasites resistant to 37 diverse compounds. We found 159 gene amplifications and 148 nonsynonymous changes in 83 genes associated with drug-resistance acquisition, where gene amplifications contributed to one-third of resistance acquisition events. Beyond confirming previously identified multidrug-resistance mechanisms, we discovered hitherto unrecognized drug target–inhibitor pairs, including thymidylate synthase and a benzoquinazolinone, farnesyltransferase and a pyrimidinedione, and a dipeptidylpeptidase and an arylurea. This exploration of the P. falciparum resistome and druggable genome will likely guide drug discovery and structural biology efforts, while also advancing our understanding of resistance mechanisms available to the malaria parasite.
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    Global action for training in malaria elimination
    (BioMed Central, 2018) Wirth, Dyann; Casamitjana, Núria; Tanner, Marcel; Reich, Michael
    The Rethinking Malaria Leadership Forum, held at Harvard Business School in February 2017 with collaboration of the Barcelona Institute for Global Health and the Swiss Tropical and Public Health Institute, identified this training gap as a high priority for both analysis and action. The gap in human resource training for malaria elimination needs to be addressed in order to assure continued progress. This paper identifies major gaps in skills and human resources, suggests institutions that can assist in filling the training gaps, and proposes global actions to implement expanded training for malaria elimination in endemic countries.