1
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Early AM, Pelleau S, Musset L, Neafsey DE. Temporal Patterns of Haplotypic and Allelic Diversity Reflect the Changing Selection Landscape of the Malaria Parasite Plasmodium falciparum. Mol Biol Evol 2025; 42:msaf075. [PMID: 40164958 PMCID: PMC12004115 DOI: 10.1093/molbev/msaf075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 03/14/2025] [Accepted: 03/21/2025] [Indexed: 04/02/2025] Open
Abstract
The malaria parasite Plasmodium falciparum regularly confronts orchestrated changes in frontline drug treatment that drastically alter its selection landscape. When this has occurred, the parasite has successfully adapted to new drugs through novel resistance mutations. These novel mutations, however, emerge in a genetic background already shaped by prior drug selection. In some instances, selection imposed by different drugs targets the same loci in either synergistic or antagonistic ways, which may leave genomic signatures that are hard to attribute to a specific agent. Here, we use two approaches for detecting sequential bouts of drug adaptation: haplotype-based selection testing and temporal changes in allele frequencies. Using a set of longitudinal samples from French Guiana, we determine that since the official introduction of artemisinin combination therapy in 2007 there have been rapid hard selective sweeps at both known and novel loci. At four high-profile genes with demonstrated involvement in drug resistance (pfcrt, pfmdr1, pfaat1, and pfgch1), we see selection signals both before and after drug regime change; however, selection favored different haplotypes in the two time periods. Similarly, allele frequency analysis identified coding variants whose frequency trajectory changed signs under the new drug pressure. These selected alleles were enriched for genes implicated in artemisinin or partner-drug resistance in other global populations. Overall, these results suggest that drug resistance in P. falciparum is governed by known alleles of large effect along with a polygenic architecture of potentially more subtle variants, any of which can experience fitness reversals under distinct drug regimes.
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Affiliation(s)
- Angela M Early
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stéphane Pelleau
- Infectious Diseases Epidemiology and Analytics Unit, Department of Global Health, lnstitut Pasteur, Université Paris Cité, Paris 75015, France
- Centre National de Référence du Paludisme, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, lnstitut Pasteur de la Guyane, Cayenne 97300, French Guiana
| | - Lise Musset
- Centre National de Référence du Paludisme, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, lnstitut Pasteur de la Guyane, Cayenne 97300, French Guiana
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
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2
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Tanner JD, Richards SN, Corry B. Molecular basis of the functional conflict between chloroquine and peptide transport in the Malaria parasite chloroquine resistance transporter PfCRT. Nat Commun 2025; 16:2987. [PMID: 40140375 PMCID: PMC11947230 DOI: 10.1038/s41467-025-58244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 03/16/2025] [Indexed: 03/28/2025] Open
Abstract
The Plasmodium falciparum chloroquine resistance transporter (PfCRT) is a key protein contributing to resistance against the antimalarial chloroquine (CQ). Mutations such as K76T enable PfCRT to transport CQ away from its target in the parasite's digestive vacuole, but this comes at a cost to its natural peptide transport function. This creates fitness costs which can drive changes to drug susceptibility in parasite populations, but the molecular basis of this is not well understood. To investigate, here we run 130 μs of molecular dynamics simulations of CQ-sensitive and CQ-resistant PfCRT isoforms with CQ and peptide substrates. We identify the CQ binding site and characterized diverse peptide binding modes. The K76T mutation allows CQ to access the binding site but disrupts peptide binding, highlighting the importance of cavity charge in determining substrate specificity. This study provides insight into PfCRT polyspecific peptide transport and will aid in rational, structure-based inhibitor design.
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Affiliation(s)
- John D Tanner
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Sashika N Richards
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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3
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Mok S, Yeo T, Hong D, Shears MJ, Ross LS, Ward KE, Dhingra SK, Kanai M, Bridgford JL, Tripathi AK, Mlambo G, Burkhard AY, Ansbro MR, Fairhurst KJ, Gil-Iturbe E, Park H, Rozenberg FD, Kim J, Mancia F, Fairhurst RM, Quick M, Uhlemann AC, Sinnis P, Fidock DA. Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness. SCIENCE ADVANCES 2023; 9:eadi2364. [PMID: 37939186 PMCID: PMC10631731 DOI: 10.1126/sciadv.adi2364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Drug-resistant Plasmodium falciparum parasites have swept across Southeast Asia and now threaten Africa. By implementing a P. falciparum genetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mapped k13 as the central mediator of ART resistance in vitro and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping using 34 recombinant haplotypes, and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.
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Affiliation(s)
- Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Davin Hong
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Melanie J. Shears
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Leila S. Ross
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kurt E. Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Satish K. Dhingra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mariko Kanai
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica L. Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Abhai K. Tripathi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Godfree Mlambo
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Y. Burkhard
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan R. Ansbro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Kate J. Fairhurst
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Felix D. Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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4
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Berger F, Gomez GM, Sanchez CP, Posch B, Planelles G, Sohraby F, Nunes-Alves A, Lanzer M. pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle. Nat Commun 2023; 14:4234. [PMID: 37454114 PMCID: PMC10349806 DOI: 10.1038/s41467-023-39969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The chloroquine resistance transporter, PfCRT, of the human malaria parasite Plasmodium falciparum is sensitive to acidic pH. Consequently, PfCRT operates at 60% of its maximal drug transport activity at the pH of 5.2 of the digestive vacuole, a proteolytic organelle from which PfCRT expels drugs interfering with heme detoxification. Here we show by alanine-scanning mutagenesis that E207 is critical for pH sensing. The E207A mutation abrogates pH-sensitivity, while preserving drug substrate specificity. Substituting E207 with Asp or His, but not other amino acids, restores pH-sensitivity. Molecular dynamics simulations and kinetics analyses suggest an allosteric binding model in which PfCRT can accept both protons and chloroquine in a partial noncompetitive manner, with increased proton concentrations decreasing drug transport. Further simulations reveal that E207 relocates from a peripheral to an engaged location during the transport cycle, forming a salt bridge with residue K80. We propose that the ionized carboxyl group of E207 acts as a hydrogen acceptor, facilitating transport cycle progression, with pH sensing as a by-product.
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Affiliation(s)
- Fiona Berger
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Guillermo M Gomez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Cecilia P Sanchez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Britta Posch
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Gabrielle Planelles
- INSERM, Centre de Recherche des Cordeliers, Unité 1138, CNRS ERL8228, Université Pierre et Marie Curie and Université Paris-Descartes, Paris, 75006, France
| | - Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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5
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Gomez GM, D’Arrigo G, Sanchez CP, Berger F, Wade RC, Lanzer M. PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport. PLoS Pathog 2023; 19:e1011436. [PMID: 37285379 PMCID: PMC10281575 DOI: 10.1371/journal.ppat.1011436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/20/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023] Open
Abstract
The chloroquine resistance transporter (PfCRT) confers resistance to a wide range of quinoline and quinoline-like antimalarial drugs in Plasmodium falciparum, with local drug histories driving its evolution and, hence, the drug transport specificities. For example, the change in prescription practice from chloroquine (CQ) to piperaquine (PPQ) in Southeast Asia has resulted in PfCRT variants that carry an additional mutation, leading to PPQ resistance and, concomitantly, to CQ re-sensitization. How this additional amino acid substitution guides such opposing changes in drug susceptibility is largely unclear. Here, we show by detailed kinetic analyses that both the CQ- and the PPQ-resistance conferring PfCRT variants can bind and transport both drugs. Surprisingly, the kinetic profiles revealed subtle yet significant differences, defining a threshold for in vivo CQ and PPQ resistance. Competition kinetics, together with docking and molecular dynamics simulations, show that the PfCRT variant from the Southeast Asian P. falciparum strain Dd2 can accept simultaneously both CQ and PPQ at distinct but allosterically interacting sites. Furthermore, combining existing mutations associated with PPQ resistance created a PfCRT isoform with unprecedented non-Michaelis-Menten kinetics and superior transport efficiency for both CQ and PPQ. Our study provides additional insights into the organization of the substrate binding cavity of PfCRT and, in addition, reveals perspectives for PfCRT variants with equal transport efficiencies for both PPQ and CQ.
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Affiliation(s)
- Guillermo M. Gomez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Giulia D’Arrigo
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg, Heidelberg, Germany
| | - Cecilia P. Sanchez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Fiona Berger
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg, Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld, Heidelberg, Germany
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
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6
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Okombo J, Kumar M, Redhi D, Wicht KJ, Wiesner L, Egan TJ, Chibale K. Pyrido-Dibemequine Metabolites Exhibit Improved Druglike Features, Inhibit Hemozoin Formation in Plasmodium falciparum, and Synergize with Clinical Antimalarials. ACS Infect Dis 2023; 9:653-667. [PMID: 36802523 DOI: 10.1021/acsinfecdis.2c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Structural modification of existing chemical scaffolds to afford new molecules able to circumvent drug resistance constitutes one of the rational approaches to antimalarial drug discovery. Previously synthesized compounds based on the 4-aminoquinoline core hybridized with a chemosensitizing dibenzylmethylamine side group showed in vivo efficacy in Plasmodium berghei-infected mice despite low microsomal metabolic stability, suggesting a contribution from their pharmacologically active metabolites. Here, we report on a series of these dibemequine (DBQ) metabolites with low resistance indices against chloroquine-resistant parasites and improved metabolic stability in liver microsomes. The metabolites also exhibit improved pharmacological properties including lower lipophilicity, cytotoxicity, and hERG channel inhibition. Using cellular heme fractionation experiments, we also demonstrate that these derivatives inhibit hemozoin formation by causing a buildup of toxic "free" heme in a similar manner to chloroquine. Finally, assessment of drug interactions also revealed synergy between these derivatives and several clinically relevant antimalarials, thus highlighting their potential interest for further development.
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Affiliation(s)
- John Okombo
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Malkeet Kumar
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Devasha Redhi
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Kathryn J Wicht
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, Holistic Drug Discovery and Development (H3D) Centre, Rondebosch, 7701 Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, Holistic Drug Discovery and Development (H3D) Centre, Rondebosch, 7701 Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
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7
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Okombo J, Mok S, Qahash T, Yeo T, Bath J, Orchard LM, Owens E, Koo I, Albert I, Llinás M, Fidock DA. Piperaquine-resistant PfCRT mutations differentially impact drug transport, hemoglobin catabolism and parasite physiology in Plasmodium falciparum asexual blood stages. PLoS Pathog 2022; 18:e1010926. [PMID: 36306287 PMCID: PMC9645663 DOI: 10.1371/journal.ppat.1010926] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/09/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The emergence of Plasmodium falciparum parasite resistance to dihydroartemisinin + piperaquine (PPQ) in Southeast Asia threatens plans to increase the global use of this first-line antimalarial combination. High-level PPQ resistance appears to be mediated primarily by novel mutations in the P. falciparum chloroquine resistance transporter (PfCRT), which enhance parasite survival at high PPQ concentrations in vitro and increase the risk of dihydroartemisinin + PPQ treatment failure in patients. Using isogenic Dd2 parasites expressing contemporary pfcrt alleles with differential in vitro PPQ susceptibilities, we herein characterize the molecular and physiological adaptations that define PPQ resistance in vitro. Using drug uptake and cellular heme fractionation assays we report that the F145I, M343L, and G353V PfCRT mutations differentially impact PPQ and chloroquine efflux. These mutations also modulate proteolytic degradation of host hemoglobin and the chemical inactivation of reactive heme species. Peptidomic analyses reveal significantly higher accumulation of putative hemoglobin-derived peptides in the PPQ-resistant mutant PfCRT isoforms compared to parental PPQ-sensitive Dd2. Joint transcriptomic and metabolomic profiling of late trophozoites from PPQ-resistant or -sensitive isogenic lines reveals differential expression of genes involved in protein translation and cellular metabolism. PPQ-resistant parasites also show increased susceptibility to an inhibitor of the P. falciparum M17 aminopeptidase that operates on short globin-derived peptides. These results reveal unique physiological changes caused by the gain of PPQ resistance and highlight the potential therapeutic value of targeting peptide metabolism in P. falciparum.
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Affiliation(s)
- John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tarrick Qahash
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Center for Malaria Research, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Jade Bath
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Lindsey M. Orchard
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Center for Malaria Research, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Edward Owens
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Center for Malaria Research, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Istvan Albert
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Center for Malaria Research, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
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8
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Sanchez CP, Manson EDT, Moliner Cubel S, Mandel L, Weidt SK, Barrett MP, Lanzer M. The Knock-Down of the Chloroquine Resistance Transporter PfCRT Is Linked to Oligopeptide Handling in Plasmodium falciparum. Microbiol Spectr 2022; 10:e0110122. [PMID: 35867395 PMCID: PMC9431119 DOI: 10.1128/spectrum.01101-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
The chloroquine resistance transporter, PfCRT, is an essential factor during intraerythrocytic development of the human malaria parasite Plasmodium falciparum. PfCRT resides at the digestive vacuole of the parasite, where hemoglobin taken up by the parasite from its host cell is degraded. PfCRT can acquire several mutations that render PfCRT a drug transporting system expelling compounds targeting hemoglobin degradation from the digestive vacuole. The non-drug related function of PfCRT is less clear, although a recent study has suggested a role in oligopeptide transport based on studies conducted in a heterologous expression system. The uncertainty about the natural function of PfCRT is partly due to a lack of a null mutant and a dearth of functional assays in the parasite. Here, we report on the generation of a conditional PfCRT knock-down mutant in P. falciparum. The mutant accumulated oligopeptides 2 to at least 8 residues in length under knock-down conditions, as shown by comparative global metabolomics. The accumulated oligopeptides were structurally diverse, had an isoelectric point between 4.0 and 5.4 and were electrically neutral or carried a single charge at the digestive vacuolar pH of 5.2. Fluorescently labeled dipeptides and live cell imaging identified the digestive vacuole as the compartment where oligopeptides accumulated. Our findings suggest a function of PfCRT in oligopeptide transport across the digestive vacuolar membrane in P. falciparum and associated with it a role in nutrient acquisition and the maintenance of the colloid osmotic balance. IMPORTANCE The chloroquine resistance transporter, PfCRT, is important for the survival of the human malaria parasite Plasmodium falciparum. It increases the tolerance to many antimalarial drugs, and it is essential for the development of the parasite within red blood cells. While we understand the role of PfCRT in drug resistance in ever increasing detail, the non-drug resistance functions are still debated. Identifying the natural substrate of PfCRT has been hampered by a paucity of functional assays to test putative substrates in the parasite system and the absence of a parasite mutant deficient for the PfCRT encoding gene. By generating a conditional PfCRT knock-down mutant, together with comparative metabolomics and uptake studies using fluorescently labeled oligopeptides, we could show that PfCRT is an oligopeptide transporter. The oligopeptides were structurally diverse and were electrically neutral or carried a single charge. Our data support a function of PfCRT in oligopeptide transport.
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Affiliation(s)
- Cecilia P. Sanchez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Sonia Moliner Cubel
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Stefan K. Weidt
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Glasgow, United Kingdom
| | - Michael P. Barrett
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Glasgow, United Kingdom
- The Wellcome Centre for Integrative Parasitology, Institute for Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
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9
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Mechanistic basis for multidrug resistance and collateral drug sensitivity conferred to the malaria parasite by polymorphisms in PfMDR1 and PfCRT. PLoS Biol 2022; 20:e3001616. [PMID: 35507548 PMCID: PMC9067703 DOI: 10.1371/journal.pbio.3001616] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/31/2022] [Indexed: 01/16/2023] Open
Abstract
Polymorphisms in the Plasmodium falciparum multidrug resistance protein 1 (pfmdr1) gene and the Plasmodium falciparum chloroquine resistance transporter (pfcrt) gene alter the malaria parasite’s susceptibility to most of the current antimalarial drugs. However, the precise mechanisms by which PfMDR1 contributes to multidrug resistance have not yet been fully elucidated, nor is it understood why polymorphisms in pfmdr1 and pfcrt that cause chloroquine resistance simultaneously increase the parasite’s susceptibility to lumefantrine and mefloquine—a phenomenon known as collateral drug sensitivity. Here, we present a robust expression system for PfMDR1 in Xenopus oocytes that enables direct and high-resolution biochemical characterizations of the protein. We show that wild-type PfMDR1 transports diverse pharmacons, including lumefantrine, mefloquine, dihydroartemisinin, piperaquine, amodiaquine, methylene blue, and chloroquine (but not the antiviral drug amantadine). Field-derived mutant isoforms of PfMDR1 differ from the wild-type protein, and each other, in their capacities to transport these drugs, indicating that PfMDR1-induced changes in the distribution of drugs between the parasite’s digestive vacuole (DV) and the cytosol are a key driver of both antimalarial resistance and the variability between multidrug resistance phenotypes. Of note, the PfMDR1 isoforms prevalent in chloroquine-resistant isolates exhibit reduced capacities for chloroquine, lumefantrine, and mefloquine transport. We observe the opposite relationship between chloroquine resistance-conferring mutations in PfCRT and drug transport activity. Using our established assays for characterizing PfCRT in the Xenopus oocyte system and in live parasite assays, we demonstrate that these PfCRT isoforms transport all 3 drugs, whereas wild-type PfCRT does not. We present a mechanistic model for collateral drug sensitivity in which mutant isoforms of PfMDR1 and PfCRT cause chloroquine, lumefantrine, and mefloquine to remain in the cytosol instead of sequestering within the DV. This change in drug distribution increases the access of lumefantrine and mefloquine to their primary targets (thought to be located outside of the DV), while simultaneously decreasing chloroquine’s access to its target within the DV. The mechanistic insights presented here provide a basis for developing approaches that extend the useful life span of antimalarials by exploiting the opposing selection forces they exert upon PfCRT and PfMDR1.
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10
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Wicht KJ, Mok S, Fidock DA. Molecular Mechanisms of Drug Resistance in Plasmodium falciparum Malaria. Annu Rev Microbiol 2021; 74:431-454. [PMID: 32905757 DOI: 10.1146/annurev-micro-020518-115546] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding and controlling the spread of antimalarial resistance, particularly to artemisinin and its partner drugs, is a top priority. Plasmodium falciparum parasites resistant to chloroquine, amodiaquine, or piperaquine harbor mutations in the P. falciparum chloroquine resistance transporter (PfCRT), a transporter resident on the digestive vacuole membrane that in its variant forms can transport these weak-base 4-aminoquinoline drugs out of this acidic organelle, thus preventing these drugs from binding heme and inhibiting its detoxification. The structure of PfCRT, solved by cryogenic electron microscopy, shows mutations surrounding an electronegative central drug-binding cavity where they presumably interact with drugs and natural substrates to control transport. P. falciparum susceptibility to heme-binding antimalarials is also modulated by overexpression or mutations in the digestive vacuole membrane-bound ABC transporter PfMDR1 (P. falciparum multidrug resistance 1 transporter). Artemisinin resistance is primarily mediated by mutations in P. falciparum Kelch13 protein (K13), a protein involved in multiple intracellular processes including endocytosis of hemoglobin, which is required for parasite growth and artemisinin activation. Combating drug-resistant malaria urgently requires the development of new antimalarial drugs with novel modes of action.
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Affiliation(s)
- Kathryn J Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA; , ,
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA; , ,
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA; , , .,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
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11
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Relitti N, Federico S, Pozzetti L, Butini S, Lamponi S, Taramelli D, D'Alessandro S, Martin RE, Shafik SH, Summers RL, Babij SK, Habluetzel A, Tapanelli S, Caldelari R, Gemma S, Campiani G. Synthesis and biological evaluation of benzhydryl-based antiplasmodial agents possessing Plasmodium falciparum chloroquine resistance transporter (PfCRT) inhibitory activity. Eur J Med Chem 2021; 215:113227. [PMID: 33601312 DOI: 10.1016/j.ejmech.2021.113227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 11/18/2022]
Abstract
Due to the surge in resistance to common therapies, malaria remains a significant concern to human health worldwide. In chloroquine (CQ)-resistant (CQ-R) strains of Plasmodium falciparum, CQ and related drugs are effluxed from the parasite's digestive vacuole (DV). This process is mediated by mutant isoforms of a protein called CQ resistance transporter (PfCRT). CQ-R strains can be partially re-sensitized to CQ by verapamil (VP), primaquine (PQ) and other compounds, and this has been shown to be due to the ability of these molecules to inhibit drug transport via PfCRT. We have previously developed a series of clotrimazole (CLT)-based antimalarial agents that possess inhibitory activity against PfCRT (4a,b). In our endeavor to develop novel PfCRT inhibitors, and to perform a structure-activity relationship analysis, we synthesized a new library of analogues. When the benzhydryl system was linked to a 4-aminoquinoline group (5a-f) the resulting compounds exhibited good cytotoxicity against both CQ-R and CQ-S strains of P. falciparum. The most potent inhibitory activity against the PfCRT-mediated transport of CQ was obtained with compound 5k. When compared to the reference compound, benzhydryl analogues of PQ (5i,j) showed a similar activity against blood-stage parasites, and a stronger in vitro potency against liver-stage parasites. Unfortunately, in the in vivo transmission blocking assays, 5i,j were inactive against gametocytes.
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Affiliation(s)
- Nicola Relitti
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Stefano Federico
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Luca Pozzetti
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Donatella Taramelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Sarah D'Alessandro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Rowena E Martin
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Robert L Summers
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Simone K Babij
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Annette Habluetzel
- School of Pharmacy, University of Camerino, Piazza Cavour 19F, 62032, Camerino, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Sofia Tapanelli
- School of Pharmacy, University of Camerino, Piazza Cavour 19F, 62032, Camerino, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
| | - Reto Caldelari
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012, Bern, Switzerland
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy.
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; Centro Interuniversitario di Ricerche Sulla Malaria (CIRM), University of Milan, Milano, Italy
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12
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Shalini, Kumar S, Gendrot M, Fonta I, Mosnier J, Cele N, Awolade P, Singh P, Pradines B, Kumar V. Amide Tethered 4-Aminoquinoline-naphthalimide Hybrids: A New Class of Possible Dual Function Antiplasmodials. ACS Med Chem Lett 2020; 11:2544-2552. [PMID: 33335678 DOI: 10.1021/acsmedchemlett.0c00536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
A series of amide tethered 4-aminoquinoline-naphthalimide hybrids has been synthesized to assess their in vitro antiplasmodial potential against chloroquine-susceptible (3D7) and chloroquine-resistant (W2) strains of Plasmodium falciparum. The most active and noncytotoxic compound had an IC50 value of 0.07 μM against W2 strain and was more active than standard antimalarial drugs, including chloroquine, desethylamodiaquine, and quinine, particularly for drug resistant malaria. The promising scaffold, when subjected to heme binding and molecular modeling studies, was identified as a possible potent inhibitor of hemozoin formation and P. falciparum chloroquine resistance transporter (PfCRT), respectively, and, therefore, could act as a dual function antiplasmodial.
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Affiliation(s)
- Shalini
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Pin 143005, India
| | - Sumit Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Pin 143005, India
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille 13234, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille 13234, France
- IHU Méditerranée Infection, Marseille 13234, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille 13234, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille 13234, France
- IHU Méditerranée Infection, Marseille 13234, France
- Centre National de Référence du Paludisme, Marseille 13234, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille 13234, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille 13234, France
- IHU Méditerranée Infection, Marseille 13234, France
- Centre National de Référence du Paludisme, Marseille 13234, France
| | - Nosipho Cele
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban 4000, South Africa
| | - Paul Awolade
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban 4000, South Africa
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban 4000, South Africa
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille 13234, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille 13234, France
- IHU Méditerranée Infection, Marseille 13234, France
- Centre National de Référence du Paludisme, Marseille 13234, France
| | - Vipan Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Pin 143005, India
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13
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Shafik SH, Cobbold SA, Barkat K, Richards SN, Lancaster NS, Llinás M, Hogg SJ, Summers RL, McConville MJ, Martin RE. The natural function of the malaria parasite's chloroquine resistance transporter. Nat Commun 2020; 11:3922. [PMID: 32764664 PMCID: PMC7413254 DOI: 10.1038/s41467-020-17781-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 07/15/2020] [Indexed: 01/27/2023] Open
Abstract
The Plasmodium falciparum chloroquine resistance transporter (PfCRT) is a key contributor to multidrug resistance and is also essential for the survival of the malaria parasite, yet its natural function remains unresolved. We identify host-derived peptides of 4-11 residues, varying in both charge and composition, as the substrates of PfCRT in vitro and in situ, and show that PfCRT does not mediate the non-specific transport of other metabolites and/or ions. We find that drug-resistance-conferring mutations reduce both the peptide transport capacity and substrate range of PfCRT, explaining the impaired fitness of drug-resistant parasites. Our results indicate that PfCRT transports peptides from the lumen of the parasite's digestive vacuole to the cytosol, thereby providing a source of amino acids for parasite metabolism and preventing osmotic stress of this organelle. The resolution of PfCRT's native substrates will aid the development of drugs that target PfCRT and/or restore the efficacy of existing antimalarials.
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Affiliation(s)
- Sarah H Shafik
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon A Cobbold
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Kawthar Barkat
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sashika N Richards
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nicole S Lancaster
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Simon J Hogg
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Robert L Summers
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Malcolm J McConville
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Rowena E Martin
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
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14
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Dziekan JM, Wirjanata G, Dai L, Go KD, Yu H, Lim YT, Chen L, Wang LC, Puspita B, Prabhu N, Sobota RM, Nordlund P, Bozdech Z. Cellular thermal shift assay for the identification of drug-target interactions in the Plasmodium falciparum proteome. Nat Protoc 2020; 15:1881-1921. [PMID: 32341577 DOI: 10.1038/s41596-020-0310-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Despite decades of research, little is known about the cellular targets and the mode of action of the vast majority of antimalarial drugs. We recently demonstrated that the cellular thermal shift assay (CETSA) protocol in its two variants: the melt curve and the isothermal dose-response, represents a comprehensive strategy for the identification of antimalarial drug targets. CETSA enables proteome-wide target screening for unmodified antimalarial compounds with undetermined mechanisms of action, providing quantitative evidence about direct drug-protein interactions. The experimental workflow involves treatment of P. falciparum-infected erythrocytes with a compound of interest, heat exposure to denature proteins, soluble protein isolation, enzymatic digestion, peptide labeling with tandem mass tags, offline fractionation, and liquid chromatography-tandem mass spectrometry analysis. Methodological optimizations necessary for the analysis of this intracellular parasite are discussed, including enrichment of parasitized cells and hemoglobin depletion strategies to overcome high hemoglobin abundance in the host red blood cells. We outline an effective data processing workflow using the mineCETSA R package, which enables prioritization of drug-target candidates for follow-up studies. The entire protocol can be completed within 2 weeks.
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Affiliation(s)
- Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yan Ting Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Liyan Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Brenda Puspita
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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15
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Structural and evolutionary analyses of the Plasmodium falciparum chloroquine resistance transporter. Sci Rep 2020; 10:4842. [PMID: 32179795 PMCID: PMC7076037 DOI: 10.1038/s41598-020-61181-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) confer resistance to several antimalarial drugs such as chloroquine (CQ) or piperaquine (PPQ), a partner molecule in current artemisinin-based combination therapies. As a member of the Drug/Metabolite Transporter (DMT) superfamily, the vacuolar transporter PfCRT may translocate substrate molecule(s) across the membrane of the digestive vacuole (DV), a lysosome-like organelle. However, the physiological substrate(s), the transport mechanism and the functional regions of PfCRT remain to be fully characterized. Here, we hypothesized that identification of evolutionary conserved sites in a tertiary structural context could help locate putative functional regions of PfCRT. Hence, site-specific substitution rates were estimated over Plasmodium evolution at each amino acid sites, and the PfCRT tertiary structure was predicted in both inward-facing (open-to-vacuole) and occluded states through homology modeling using DMT template structures sharing <15% sequence identity with PfCRT. We found that the vacuolar-half and membrane-spanning domain (and especially the transmembrane helix 9) of PfCRT were more conserved, supporting that its physiological substrate is expelled out of the parasite DV. In the PfCRT occluded state, some evolutionary conserved sites, including positions related to drug resistance mutations, participate in a putative binding pocket located at the core of the PfCRT membrane-spanning domain. Through structural comparison with experimentally-characterized DMT transporters, we identified several conserved PfCRT amino acid sites located in this pocket as robust candidates for mediating substrate transport. Finally, in silico mutagenesis revealed that drug resistance mutations caused drastic changes in the electrostatic potential of the transporter vacuolar entry and pocket, facilitating the escape of protonated CQ and PPQ from the parasite DV.
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16
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Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Nature 2019; 576:315-320. [PMID: 31776516 PMCID: PMC6911266 DOI: 10.1038/s41586-019-1795-x] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/06/2019] [Indexed: 01/21/2023]
Abstract
The emergence and spread of drug-resistant Plasmodium falciparum impedes global efforts to control and eliminate malaria. For decades, treatment of malaria has relied on chloroquine (CQ), a safe and affordable 4-aminoquinoline that was highly effective against intra-erythrocytic asexual blood-stage parasites, until resistance arose in Southeast Asia and South America and spread worldwide1. Clinical resistance to the chemically related current first-line combination drug piperaquine (PPQ) has now emerged regionally, reducing its efficacy2. Resistance to CQ and PPQ has been associated with distinct sets of point mutations in the P. falciparum CQ-resistance transporter PfCRT, a 49-kDa member of the drug/metabolite transporter superfamily that traverses the membrane of the acidic digestive vacuole of the parasite3-9. Here we present the structure, at 3.2 Å resolution, of the PfCRT isoform of CQ-resistant, PPQ-sensitive South American 7G8 parasites, using single-particle cryo-electron microscopy and antigen-binding fragment technology. Mutations that contribute to CQ and PPQ resistance localize primarily to moderately conserved sites on distinct helices that line a central negatively charged cavity, indicating that this cavity is the principal site of interaction with the positively charged CQ and PPQ. Binding and transport studies reveal that the 7G8 isoform binds both drugs with comparable affinities, and that these drugs are mutually competitive. The 7G8 isoform transports CQ in a membrane potential- and pH-dependent manner, consistent with an active efflux mechanism that drives CQ resistance5, but does not transport PPQ. Functional studies on the newly emerging PfCRT F145I and C350R mutations, associated with decreased PPQ susceptibility in Asia and South America, respectively6,9, reveal their ability to mediate PPQ transport in 7G8 variant proteins and to confer resistance in gene-edited parasites. Structural, functional and in silico analyses suggest that distinct mechanistic features mediate the resistance to CQ and PPQ in PfCRT variants. These data provide atomic-level insights into the molecular mechanism of this key mediator of antimalarial treatment failures.
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17
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Martin RE. The transportome of the malaria parasite. Biol Rev Camb Philos Soc 2019; 95:305-332. [PMID: 31701663 DOI: 10.1111/brv.12565] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022]
Abstract
Membrane transport proteins, also known as transporters, control the movement of ions, nutrients, metabolites, and waste products across the membranes of a cell and are central to its biology. Proteins of this type also serve as drug targets and are key players in the phenomenon of drug resistance. The malaria parasite has a relatively reduced transportome, with only approximately 2.5% of its genes encoding transporters. Even so, assigning functions and physiological roles to these proteins, and ascertaining their contributions to drug action and drug resistance, has been very challenging. This review presents a detailed critique and synthesis of the disruption phenotypes, protein subcellular localisations, protein functions (observed or predicted), and links to antimalarial drug resistance for each of the parasite's transporter genes. The breadth and depth of the gene disruption data are particularly impressive, with at least one phenotype determined in the parasite's asexual blood stage for each transporter gene, and multiple phenotypes available for 76% of the genes. Analysis of the curated data set revealed there to be relatively little redundancy in the Plasmodium transportome; almost two-thirds of the parasite's transporter genes are essential or required for normal growth in the asexual blood stage of the parasite, and this proportion increased to 78% when the disruption phenotypes available for the other parasite life stages were included in the analysis. These observations, together with the finding that 22% of the transportome is implicated in the parasite's resistance to existing antimalarials and/or drugs within the development pipeline, indicate that transporters are likely to serve, or are already serving, as drug targets. Integration of the different biological and bioinformatic data sets also enabled the selection of candidates for transport processes known to be essential for parasite survival, but for which the underlying proteins have thus far remained undiscovered. These include potential transporters of pantothenate, isoleucine, or isopentenyl diphosphate, as well as putative anion-selective channels that may serve as the pore component of the parasite's 'new permeation pathways'. Other novel insights into the parasite's biology included the identification of transporters for the potential development of antimalarial treatments, transmission-blocking drugs, prophylactics, and genetically attenuated vaccines. The syntheses presented herein set a foundation for elucidating the functions and physiological roles of key members of the Plasmodium transportome and, ultimately, to explore and realise their potential as therapeutic targets.
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Affiliation(s)
- Rowena E Martin
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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18
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Sanchez CP, Moliner Cubel S, Nyboer B, Jankowska-Döllken M, Schaeffer-Reiss C, Ayoub D, Planelles G, Lanzer M. Phosphomimetic substitution at Ser-33 of the chloroquine resistance transporter PfCRT reconstitutes drug responses in Plasmodium falciparum. J Biol Chem 2019; 294:12766-12778. [PMID: 31285265 DOI: 10.1074/jbc.ra119.009464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/24/2019] [Indexed: 01/01/2023] Open
Abstract
The chloroquine resistance transporter PfCRT of the human malaria parasite Plasmodium falciparum confers resistance to the former first-line antimalarial drug chloroquine, and it modulates the responsiveness to a wide range of quinoline and quinoline-like compounds. PfCRT is post-translationally modified by phosphorylation, palmitoylation, and, possibly, ubiquitination. However, the impact of these post-translational modifications on P. falciparum biology and, in particular, the drug resistance-conferring activity of PfCRT has remained elusive. Here, we confirm phosphorylation at Ser-33 and Ser-411 of PfCRT of the chloroquine-resistant P. falciparum strain Dd2 and show that kinase inhibitors can sensitize drug responsiveness. Using CRISPR/Cas9 genome editing to generate genetically engineered PfCRT variants in the parasite, we further show that substituting Ser-33 with alanine reduced chloroquine and quinine resistance by ∼50% compared with the parental P. falciparum strain Dd2, whereas the phosphomimetic amino acid aspartic acid could fully and glutamic acid could partially reconstitute the level of chloroquine/quinine resistance. Transport studies conducted in the parasite and in PfCRT-expressing Xenopus laevis oocytes linked phosphomimetic substitution at Ser-33 to increased transport velocity. Our data are consistent with phosphorylation of Ser-33 relieving an autoinhibitory intramolecular interaction within PfCRT, leading to a stimulated drug transport activity. Our findings shed additional light on the function of PfCRT and suggest that chloroquine could be reevaluated as an antimalarial drug by targeting the kinase in P. falciparum that phosphorylates Ser-33 of PfCRT.
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Affiliation(s)
- Cecilia P Sanchez
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Sonia Moliner Cubel
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Britta Nyboer
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Monika Jankowska-Döllken
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien (IPHC) UMR 7178, 67037 Strasbourg, France
| | - Daniel Ayoub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien (IPHC) UMR 7178, 67037 Strasbourg, France
| | - Gabrielle Planelles
- INSERM, Centre de Recherche des Cordeliers, Unité 1138, CNRS, ERL8228, Université Pierre et Marie Curie and Université Paris-Descartes, 75006 Paris, France
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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19
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201802416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stefano Agnello
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Michael Brand
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Mathieu F. Chellat
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Silvia Gazzola
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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20
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. A Structural View on Medicinal Chemistry Strategies against Drug Resistance. Angew Chem Int Ed Engl 2019; 58:3300-3345. [PMID: 29846032 DOI: 10.1002/anie.201802416] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/24/2018] [Indexed: 12/31/2022]
Abstract
The natural phenomenon of drug resistance is a widespread issue that hampers the performance of drugs in many major clinical indications. Antibacterial and antifungal drugs are affected, as well as compounds for the treatment of cancer, viral infections, or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, the underlying molecular mechanisms have been identified to understand the emergence of resistance and to overcome this detrimental process. Detailed structural information on the root causes for drug resistance is nowadays frequently available, so next-generation drugs can be designed that are anticipated to suffer less from resistance. This knowledge-based approach is essential for fighting the inevitable occurrence of drug resistance.
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Affiliation(s)
- Stefano Agnello
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Silvia Gazzola
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
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21
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Evidence for Regulation of Hemoglobin Metabolism and Intracellular Ionic Flux by the Plasmodium falciparum Chloroquine Resistance Transporter. Sci Rep 2018; 8:13578. [PMID: 30206341 PMCID: PMC6134138 DOI: 10.1038/s41598-018-31715-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/22/2018] [Indexed: 11/30/2022] Open
Abstract
Plasmodium falciparum multidrug resistance constitutes a major obstacle to the global malaria elimination campaign. Specific mutations in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) mediate resistance to the 4-aminoquinoline drug chloroquine and impact parasite susceptibility to several partner agents used in current artemisinin-based combination therapies, including amodiaquine. By examining gene-edited parasites, we report that the ability of the wide-spread Dd2 PfCRT isoform to mediate chloroquine and amodiaquine resistance is substantially reduced by the addition of the PfCRT L272F mutation, which arose under blasticidin selection. We also provide evidence that L272F confers a significant fitness cost to asexual blood stage parasites. Studies with amino acid-restricted media identify this mutant as a methionine auxotroph. Metabolomic analysis also reveals an accumulation of short, hemoglobin-derived peptides in the Dd2 + L272F and Dd2 isoforms, compared with parasites expressing wild-type PfCRT. Physiologic studies with the ionophores monensin and nigericin support an impact of PfCRT isoforms on Ca2+ release, with substantially reduced Ca2+ levels observed in Dd2 + L272F parasites. Our data reveal a central role for PfCRT in regulating hemoglobin catabolism, amino acid availability, and ionic balance in P. falciparum, in addition to its role in determining parasite susceptibility to heme-binding 4-aminoquinoline drugs.
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22
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Emerging Southeast Asian PfCRT mutations confer Plasmodium falciparum resistance to the first-line antimalarial piperaquine. Nat Commun 2018; 9:3314. [PMID: 30115924 PMCID: PMC6095916 DOI: 10.1038/s41467-018-05652-0] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/11/2018] [Indexed: 11/16/2022] Open
Abstract
The widely used antimalarial combination therapy dihydroartemisinin + piperaquine (DHA + PPQ) has failed in Cambodia. Here, we perform a genomic analysis that reveals a rapid increase in the prevalence of novel mutations in the Plasmodium falciparum chloroquine resistance transporter PfCRT following DHA + PPQ implementation. These mutations occur in parasites harboring the K13 C580Y artemisinin resistance marker. By introducing PfCRT mutations into sensitive Dd2 parasites or removing them from resistant Cambodian isolates, we show that the H97Y, F145I, M343L, or G353V mutations each confer resistance to PPQ, albeit with fitness costs for all but M343L. These mutations sensitize Dd2 parasites to chloroquine, amodiaquine, and quinine. In Dd2 parasites, multicopy plasmepsin 2, a candidate molecular marker, is not necessary for PPQ resistance. Distended digestive vacuoles were observed in pfcrt-edited Dd2 parasites but not in Cambodian isolates. Our findings provide compelling evidence that emerging mutations in PfCRT can serve as a molecular marker and mediator of PPQ resistance. Increasing resistance of Plasmodium falciparum strains to piperaquine (PPQ) in Southeast Asia is of concern and resistance mechanisms are incompletely understood. Here, Ross et al. show that mutations in the P. falciparum chloroquine resistance transporter are rapidly increasing in prevalence in Cambodia and confer resistance to PPQ.
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23
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Bakouh N, Bellanca S, Nyboer B, Moliner Cubel S, Karim Z, Sanchez CP, Stein WD, Planelles G, Lanzer M. Iron is a substrate of the Plasmodium falciparum chloroquine resistance transporter PfCRT in Xenopus oocytes. J Biol Chem 2017; 292:16109-16121. [PMID: 28768767 DOI: 10.1074/jbc.m117.805200] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/01/2017] [Indexed: 01/01/2023] Open
Abstract
The chloroquine resistance transporter of the human malaria parasite Plasmodium falciparum, PfCRT, is an important determinant of resistance to several quinoline and quinoline-like antimalarial drugs. PfCRT also plays an essential role in the physiology of the parasite during development inside erythrocytes. However, the function of this transporter besides its role in drug resistance is still unclear. Using electrophysiological and flux experiments conducted on PfCRT-expressing Xenopus laevis oocytes, we show here that both wild-type PfCRT and a PfCRT variant associated with chloroquine resistance transport both ferrous and ferric iron, albeit with different kinetics. In particular, we found that the ability to transport ferrous iron is reduced by the specific polymorphisms acquired by the PfCRT variant as a result of chloroquine selection. We further show that iron and chloroquine transport via PfCRT is electrogenic. If these findings in the Xenopus model extend to P. falciparum in vivo, our data suggest that PfCRT might play a role in iron homeostasis, which is essential for the parasite's development in erythrocytes.
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Affiliation(s)
- Naziha Bakouh
- From INSERM, Centre de Recherche des Cordeliers, Unité 1138, CNRS ERL8228, Université Pierre et Marie Curie and Université Paris-Descartes, Paris 75006, France
| | - Sebastiano Bellanca
- the Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Britta Nyboer
- the Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Sonia Moliner Cubel
- the Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Zoubida Karim
- INSERM, UMR1149, CNRS ERL 8252, Université Paris Diderot Paris 75890, France, and
| | - Cecilia P Sanchez
- the Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Wilfred D Stein
- Biological Chemistry, Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gabrielle Planelles
- From INSERM, Centre de Recherche des Cordeliers, Unité 1138, CNRS ERL8228, Université Pierre et Marie Curie and Université Paris-Descartes, Paris 75006, France,
| | - Michael Lanzer
- the Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany,
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24
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Plasmodium falciparum and Plasmodium vivax Demonstrate Contrasting Chloroquine Resistance Reversal Phenotypes. Antimicrob Agents Chemother 2017; 61:AAC.00355-17. [PMID: 28533239 PMCID: PMC5527611 DOI: 10.1128/aac.00355-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/08/2017] [Indexed: 01/12/2023] Open
Abstract
High-grade chloroquine (CQ) resistance has emerged in both Plasmodium falciparum and P. vivax The aim of the present study was to investigate the phenotypic differences of CQ resistance in both of these species and the ability of known CQ resistance reversal agents (CQRRAs) to alter CQ susceptibility. Between April 2015 and April 2016, the potential of verapamil (VP), mibefradil (MF), L703,606 (L7), and primaquine (PQ) to reverse CQ resistance was assessed in 46 P. falciparum and 34 P. vivax clinical isolates in Papua, Indonesia, where CQ resistance is present in both species, using a modified schizont maturation assay. In P. falciparum, CQ 50% inhibitory concentrations (IC50s) were reduced when CQ was combined with VP (1.4-fold), MF (1.2-fold), L7 (4.2-fold), or PQ (1.8-fold). The degree of CQ resistance reversal in P. falciparum was highly correlated with CQ susceptibility for all CQRRAs (R2 = 0.951, 0.852, 0.962, and 0.901 for VP, MF, L7, and PQ, respectively), in line with observations in P. falciparum laboratory strains. In contrast, no reduction in the CQ IC50s was observed with any of the CQRRAs in P. vivax, even in those isolates with high chloroquine IC50s. The differential effect of CQRRAs in P. falciparum and P. vivax suggests significant differences in CQ kinetics and, potentially, the likely mechanism of CQ resistance between these two species.
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25
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The "pushmi-pullyu" of resistance to chloroquine in malaria. Essays Biochem 2017; 61:167-175. [PMID: 28258239 DOI: 10.1042/ebc20160060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/27/2016] [Accepted: 01/03/2017] [Indexed: 11/17/2022]
Abstract
Malarial infection continues to impart devastating health problems in the developing world. Treatment of malaria has involved chemotherapy since 168 BC, with the most prevalent and successful forms using plant alkaloids. Perhaps the greatest treatment success against malaria was by chloroquine, a synthetic derivative of the quinines found in the Cinchona tree bark. Chloroquine is able to kill parasites by interfering with haem metabolism in the parasite's digestive vacuole. The widespread use of chloroquine predictably resulted in the development of drug-resistant malaria and the most highly implicated resistance mediators are the transporter proteins P-glycoprotein (P-gp) homologue 1 (P-gh1) and Plasmodium falciparum chloroquine-resistance transporter (PfCRT), which reside on the parasite's digestive vacuole. The presence of PfCRT and P-gh1 on the vacuole membrane is analogous to the two-headed fictional creature known as the "Pushmi-Pullyu". P-gh1 (Pushmi) increases influx of chloroquine into the vacuole, while PfCRT (Pullmi) causes efflux of chloroquine from the vacuole. This review describes how drug-resistant malarial parasites co-ordinate chloroquine distribution through adaptive mutations to promote their survival in the presence of this cytotoxic drug.
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26
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Jida M, Sanchez CP, Urgin K, Ehrhardt K, Mounien S, Geyer A, Elhabiri M, Lanzer M, Davioud-Charvet E. A Redox-Active Fluorescent pH Indicator for Detecting Plasmodium falciparum Strains with Reduced Responsiveness to Quinoline Antimalarial Drugs. ACS Infect Dis 2017; 3:119-131. [PMID: 28183182 DOI: 10.1021/acsinfecdis.5b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mutational changes in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) have been associated with differential responses to a wide spectrum of biologically active compounds including current and former quinoline and quinoline-like antimalarial drugs. PfCRT confers altered drug responsiveness by acting as a transport system, expelling drugs from the parasite's digestive vacuole where these drugs exert, at least part of, their antiplasmodial activity. To preserve the efficacy of these invaluable drugs, novel functional tools are required for epidemiological surveys of parasite strains carrying mutant PfCRT variants and for drug development programs aimed at inhibiting or circumventing the action of PfCRT. Here we report the synthesis and characterization of a pH-sensitive fluorescent chloroquine analogue consisting of 7-chloro-N-{2-[(propan-2-yl)amino]ethyl}quinolin-4-amine functionalized with the fluorochrome 7-nitrobenzofurazan (NBD) (henceforth termed Fluo-CQ). In the parasite, Fluo-CQ accumulates in the digestive vacuole, giving rise to a strong fluorescence signal but only in parasites carrying the wild type PfCRT. In parasites carrying the mutant PfCRT, Fluo-CQ does not accumulate. The differential handling of the fluorescent probe, combined with live cell imaging, provides a diagnostic tool for quick detection of those P. falciparum strains that carry a PfCRT variant associated with altered responsiveness to quinoline and quinoline-like antimalarial drugs. In contrast to the accumulation studies, chloroquine (CQ)-resistant parasites were observed cross-resistant to Fluo-CQ when the chemical probe was tested in various CQ-sensitive and -resistant parasite strains. NBD derivatives were found to act as redox cyclers of two essential targets, using a coupled assay based on methemoglobin and the NADPH-dependent glutathione reductase (GRs) from P. falciparum. This redox activity is proposed to contribute to the dual action of Fluo-CQ on redox equilibrium and methemoglobin reduction via PfCRT-mediated drug efflux in the cytosol and then continuous redox-dependent shuttling between food vacuole and cytosol. Taking into account these physicochemical characteristics, a model was proposed to explain Fluo-CQ antimalarial effects involving the contribution of PfCRT-mediated transport, methemoglobin reduction, hematin binding, and NBD reduction activity catalyzed by PfGR in CQ-resistant versus CQ-sensitive parasites. Therefore, introduction of NBD fluorophore in drugs is not inert and should be taken into account in drug transport and imaging studies.
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Affiliation(s)
- Mouhamad Jida
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
| | - Cecilia P. Sanchez
- Zentrum
für Infektiologie, Parasitologie, Universität Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Karène Urgin
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
| | - Katharina Ehrhardt
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
- Zentrum
für Infektiologie, Parasitologie, Universität Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Saravanan Mounien
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
| | - Aurelia Geyer
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
| | - Mourad Elhabiri
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
| | - Michael Lanzer
- Zentrum
für Infektiologie, Parasitologie, Universität Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Elisabeth Davioud-Charvet
- UMR 7509 Centre National de la Recherche Scientifique and University of Strasbourg, European School of Chemistry, Polymers and Materials (ECPM), 25 rue Becquerel, F-67087 Strasbourg, France
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27
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Magistrado PA, Corey VC, Lukens AK, LaMonte G, Sasaki E, Meister S, Wree M, Winzeler E, Wirth DF. Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL), a Resistance Mechanism for Two Distinct Compound Classes. ACS Infect Dis 2016; 2:816-826. [PMID: 27933786 PMCID: PMC5109296 DOI: 10.1021/acsinfecdis.6b00025] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
MMV007564
is a novel antimalarial benzimidazolyl piperidine chemotype
identified in cellular screens. To identify the genetic determinant
of MMV007564 resistance, parasites were cultured in the presence of
the compound to generate resistant lines. Whole genome sequencing
revealed distinct mutations in the gene named Plasmodium
falciparum cyclic amine resistance locus (pfcarl), encoding a conserved protein of unknown function.
Mutations in pfcarl are strongly associated with
resistance to a structurally unrelated class of compounds, the imidazolopiperazines,
including KAF156, currently in clinical trials. Our data demonstrate
that pfcarl mutations confer resistance to two distinct
compound classes, benzimidazolyl piperidines and imidazolopiperazines.
However, MMV007564 and the imidazolopiperazines, KAF156 and GNF179,
have different timings of action in the asexual blood stage and different
potencies against the liver and sexual blood stages. These data suggest
that pfcarl is a multidrug-resistance gene rather
than a common target for benzimidazolyl piperidines and imidazolopiperazines.
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Affiliation(s)
- Pamela A. Magistrado
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Victoria C. Corey
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Amanda K. Lukens
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Infectious
Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Greg LaMonte
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Erika Sasaki
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Stephan Meister
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Melanie Wree
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Elizabeth Winzeler
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Dyann F. Wirth
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Infectious
Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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28
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Njokah MJ, Kang'ethe JN, Kinyua J, Kariuki D, Kimani FT. In vitro selection of Plasmodium falciparum Pfcrt and Pfmdr1 variants by artemisinin. Malar J 2016; 15:381. [PMID: 27449110 PMCID: PMC4957835 DOI: 10.1186/s12936-016-1443-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/18/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Anti-malarial drugs are the major focus in the prevention and treatment of malaria. Artemisinin-based combination therapy (ACT) is the WHO recommended first-line treatment for Plasmodium falciparum malaria across the endemic world. Also ACT is increasingly relied upon in treating Plasmodium vivax malaria where chloroquine is failing. The emergence of artemisinin drug-resistant parasites is a serious threat faced by global malaria control programmes. Therefore, the success of treatment and intervention strategies is highly pegged on understanding the genetic basis of resistance. METHODS Here, resistance in P. falciparum was generated in vitro for artemisinin to produce levels above clinically relevant concentrations in vivo, and the molecular haplotypes investigated. Genomic DNA was extracted using the QIAamp mini DNA kit. DNA sequences of Pfk13, Pfcrt and Pfmdr1 genes were amplified by PCR and the amplicons were successfully sequenced. Single nucleotide polymorphisms were traced by standard bidirectional sequencing and reading the transcripts against wild-type sequences in Codon code Aligner Version 5.1 and NCBI blast. RESULTS Exposure of parasite strains D6 and W2 to artemisinin resulted in a decrease in parasite susceptibility to artemisinin (W2 and D6) and lumefantrine (D6 only). The parasites exhibited elevated IC50s to multiple artemisinins, with >twofold resistance to artemisinin; however, the resistance index obtained with standard methods was noticeably less than expected for parasite lines recovered from 50 µg/ml 48 h drug pressure. The change in parasite susceptibility was associated with Pfmdr-185K mutation, a mutation never reported before. The Pfcrt-CVMNK genotype (Pfcrt codons 72-76) was retained and notably, the study did not detect any polymorphisms reported to reduce P. falciparum susceptibility in vivo in the coding sequences of the Pfk13 gene. DISCUSSION This data demonstrate that P. falciparum has the capacity to develop resistance to artemisinin derivatives in vitro and that this phenotype is achieved by mutations in Pfmdr1, the genetic changes that are also underpinning lumefantrine resistance. This finding is of practical importance, because artemisinin drugs in Kenya are used in combination with lumefantrine for the treatment of malaria. CONCLUSION Artemisinin resistance phenotype as has been shown in this work, is a decrease in parasites susceptibility to artemisinin derivatives together with the parasite's ability to recover from drug-induced dormancy after exposure to drug dosage above the in vivo clinical concentrations. The study surmises that Pfmdr1 may play a role in the anti-malarial activity of artemisinin.
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Affiliation(s)
- Muturi J Njokah
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
| | - Joseph N Kang'ethe
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
| | - Johnson Kinyua
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
| | - Daniel Kariuki
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
| | - Francis T Kimani
- Kenya Medical Research Institute (KEMRI), Centre for Biotechnology Research and Development (CBRD), P.O. Box 54840-00200, Nairobi, Kenya.
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Richards SN, Nash MN, Baker ES, Webster MW, Lehane AM, Shafik SH, Martin RE. Molecular Mechanisms for Drug Hypersensitivity Induced by the Malaria Parasite's Chloroquine Resistance Transporter. PLoS Pathog 2016; 12:e1005725. [PMID: 27441371 PMCID: PMC4956231 DOI: 10.1371/journal.ppat.1005725] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/03/2016] [Indexed: 01/23/2023] Open
Abstract
Mutations in the Plasmodium falciparum ‘chloroquine resistance transporter’ (PfCRT) confer resistance to chloroquine (CQ) and related antimalarials by enabling the protein to transport these drugs away from their targets within the parasite’s digestive vacuole (DV). However, CQ resistance-conferring isoforms of PfCRT (PfCRTCQR) also render the parasite hypersensitive to a subset of structurally-diverse pharmacons. Moreover, mutations in PfCRTCQR that suppress the parasite’s hypersensitivity to these molecules simultaneously reinstate its sensitivity to CQ and related drugs. We sought to understand these phenomena by characterizing the functions of PfCRTCQR isoforms that cause the parasite to become hypersensitive to the antimalarial quinine or the antiviral amantadine. We achieved this by measuring the abilities of these proteins to transport CQ, quinine, and amantadine when expressed in Xenopus oocytes and complemented this work with assays that detect the drug transport activity of PfCRT in its native environment within the parasite. Here we describe two mechanistic explanations for PfCRT-induced drug hypersensitivity. First, we show that quinine, which normally accumulates inside the DV and therewithin exerts its antimalarial effect, binds extremely tightly to the substrate-binding site of certain isoforms of PfCRTCQR. By doing so it likely blocks the normal physiological function of the protein, which is essential for the parasite’s survival, and the drug thereby gains an additional killing effect. In the second scenario, we show that although amantadine also sequesters within the DV, the parasite’s hypersensitivity to this drug arises from the PfCRTCQR-mediated transport of amantadine from the DV into the cytosol, where it can better access its antimalarial target. In both cases, the mutations that suppress hypersensitivity also abrogate the ability of PfCRTCQR to transport CQ, thus explaining why rescue from hypersensitivity restores the parasite’s sensitivity to this antimalarial. These insights provide a foundation for understanding clinically-relevant observations of inverse drug susceptibilities in the malaria parasite. In acquiring resistance to one drug, many pathogens and cancer cells become hypersensitive to other drugs. This phenomenon could be exploited to combat existing drug resistance and to delay the emergence of resistance to new drugs. However, much remains to be understood about the mechanisms that underlie drug hypersensitivity in otherwise drug-resistant microbes. Here, we describe two mechanisms by which the Plasmodium falciparum ‘chloroquine resistance transporter’ (PfCRT) causes the malaria parasite to become hypersensitive to structurally-diverse drugs. First, we show that an antimalarial drug that normally exerts its killing effect within the parasite’s digestive vacuole is also able to bind extremely tightly to certain forms of PfCRT. This activity will block the natural, essential function of the protein and thereby provide the drug with an additional killing effect. The second mechanism arises when a cytosolic-acting drug that normally sequesters within the digestive vacuole is leaked back into the cytosol via PfCRT. In both cases, mutations that suppress hypersensitivity also abrogate the ability of PfCRT to transport chloroquine, thus explaining why rescue from hypersensitivity restores the parasite’s sensitivity to this antimalarial. These insights provide a foundation for understanding and exploiting the hypersensitivity of chloroquine-resistant parasites to several of the current antimalarials.
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Affiliation(s)
- Sashika N. Richards
- Research School of Biology, Australian National University, Canberra, Australia
| | - Megan N. Nash
- Research School of Biology, Australian National University, Canberra, Australia
| | - Eileen S. Baker
- Research School of Biology, Australian National University, Canberra, Australia
| | - Michael W. Webster
- Research School of Biology, Australian National University, Canberra, Australia
| | - Adele M. Lehane
- Research School of Biology, Australian National University, Canberra, Australia
| | - Sarah H. Shafik
- Research School of Biology, Australian National University, Canberra, Australia
| | - Rowena E. Martin
- Research School of Biology, Australian National University, Canberra, Australia
- * E-mail:
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30
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Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies. Nat Commun 2016; 7:11553. [PMID: 27189525 PMCID: PMC4873939 DOI: 10.1038/ncomms11553] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/07/2016] [Indexed: 02/07/2023] Open
Abstract
Antimalarial chemotherapy, globally reliant on artemisinin-based combination therapies (ACTs), is threatened by the spread of drug resistance in Plasmodium falciparum parasites. Here we use zinc-finger nucleases to genetically modify the multidrug resistance-1 transporter PfMDR1 at amino acids 86 and 184, and demonstrate that the widely prevalent N86Y mutation augments resistance to the ACT partner drug amodiaquine and the former first-line agent chloroquine. In contrast, N86Y increases parasite susceptibility to the partner drugs lumefantrine and mefloquine, and the active artemisinin metabolite dihydroartemisinin. The PfMDR1 N86 plus Y184F isoform moderately reduces piperaquine potency in strains expressing an Asian/African variant of the chloroquine resistance transporter PfCRT. Mutations in both digestive vacuole-resident transporters are thought to differentially regulate ACT drug interactions with host haem, a product of parasite-mediated haemoglobin degradation. Global mapping of these mutations illustrates where the different ACTs could be selectively deployed to optimize treatment based on regional differences in PfMDR1 haplotypes. Antimalarial chemotherapy relies on combination therapies (ACTs) consisting of an artemisinin derivative and a partner drug. Here, the authors study the effects of globally prevalent mutations in a multidrug resistance transporter (PfMDR1) on the parasite's susceptibility to ACT drugs.
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31
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van Schalkwyk DA, Nash MN, Shafik SH, Summers RL, Lehane AM, Smith PJ, Martin RE. Verapamil-Sensitive Transport of Quinacrine and Methylene Blue via the Plasmodium falciparum Chloroquine Resistance Transporter Reduces the Parasite's Susceptibility to these Tricyclic Drugs. J Infect Dis 2015; 213:800-10. [PMID: 26503982 DOI: 10.1093/infdis/jiv509] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND It is becoming increasingly apparent that certain mutations in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) alter the parasite's susceptibility to diverse compounds. Here we investigated the interaction of PfCRT with 3 tricyclic compounds that have been used to treat malaria (quinacrine [QC] and methylene blue [MB]) or to study P. falciparum (acridine orange [AO]). METHODS We measured the antiplasmodial activities of QC, MB, and AO against chloroquine-resistant and chloroquine-sensitive P. falciparum and determined whether QC and AO affect the accumulation and activity of chloroquine in these parasites. We also assessed the ability of mutant (PfCRT(Dd2)) and wild-type (PfCRT(D10)) variants of the protein to transport QC, MB, and AO when expressed at the surface of Xenopus laevis oocytes. RESULTS Chloroquine resistance-conferring isoforms of PfCRT reduced the susceptibility of the parasite to QC, MB, and AO. In chloroquine-resistant (but not chloroquine-sensitive) parasites, AO and QC increased the parasite's accumulation of, and susceptibility to, chloroquine. All 3 compounds were shown to bind to PfCRT(Dd2), and the transport of QC and MB via this protein was saturable and inhibited by the chloroquine resistance-reverser verapamil. CONCLUSIONS Our findings reveal that the PfCRT(Dd2)-mediated transport of tricyclic antimalarials reduces the parasite's susceptibility to these drugs.
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Affiliation(s)
| | - Megan N Nash
- Research School of Biology, Australian National University, Canberra, Australia
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, Australia
| | - Robert L Summers
- Research School of Biology, Australian National University, Canberra, Australia
| | - Adele M Lehane
- Research School of Biology, Australian National University, Canberra, Australia
| | - Peter J Smith
- Division of Pharmacology, Department of Medicine, University of Cape Town, Rondebosch, South Africa
| | - Rowena E Martin
- Research School of Biology, Australian National University, Canberra, Australia
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Pulcini S, Staines HM, Lee AH, Shafik SH, Bouyer G, Moore CM, Daley DA, Hoke MJ, Altenhofen LM, Painter HJ, Mu J, Ferguson DJP, Llinás M, Martin RE, Fidock DA, Cooper RA, Krishna S. Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, enlarge the parasite's food vacuole and alter drug sensitivities. Sci Rep 2015; 5:14552. [PMID: 26420308 PMCID: PMC4588581 DOI: 10.1038/srep14552] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/14/2015] [Indexed: 12/30/2022] Open
Abstract
Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, are the major determinant of chloroquine resistance in this lethal human malaria parasite. Here, we describe P. falciparum lines subjected to selection by amantadine or blasticidin that carry PfCRT mutations (C101F or L272F), causing the development of enlarged food vacuoles. These parasites also have increased sensitivity to chloroquine and some other quinoline antimalarials, but exhibit no or minimal change in sensitivity to artemisinins, when compared with parental strains. A transgenic parasite line expressing the L272F variant of PfCRT confirmed this increased chloroquine sensitivity and enlarged food vacuole phenotype. Furthermore, the introduction of the C101F or L272F mutation into a chloroquine-resistant variant of PfCRT reduced the ability of this protein to transport chloroquine by approximately 93 and 82%, respectively, when expressed in Xenopus oocytes. These data provide, at least in part, a mechanistic explanation for the increased sensitivity of the mutant parasite lines to chloroquine. Taken together, these findings provide new insights into PfCRT function and PfCRT-mediated drug resistance, as well as the food vacuole, which is an important target of many antimalarial drugs.
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Affiliation(s)
- Serena Pulcini
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Henry M Staines
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Andrew H Lee
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Guillaume Bouyer
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK.,Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Comparative Physiology of Erythrocytes, Station Biologique de Roscoff, Roscoff, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Comparative Physiology of Erythrocytes, Station Biologique de Roscoff, Roscoff, France
| | - Catherine M Moore
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Daniel A Daley
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Matthew J Hoke
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Lindsey M Altenhofen
- Department of Biochemistry and Molecular Biology and Center for Malaria Research, Pennsylvania State University, State College, Pennsylvania 16802, USA
| | - Heather J Painter
- Department of Biochemistry and Molecular Biology and Center for Malaria Research, Pennsylvania State University, State College, Pennsylvania 16802, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD 20852, USA
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Center for Malaria Research, Pennsylvania State University, State College, Pennsylvania 16802, USA
| | - Rowena E Martin
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Roland A Cooper
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, USA
| | - Sanjeev Krishna
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK
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Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt. Proc Natl Acad Sci U S A 2015; 112:11672-7. [PMID: 26261345 DOI: 10.1073/pnas.1507142112] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In regions with high malaria endemicity, the withdrawal of chloroquine (CQ) as first-line treatment of Plasmodium falciparum infections has typically led to the restoration of CQ susceptibility through the reexpansion of the wild-type (WT) allele K76 of the chloroquine resistance transporter gene (pfcrt) at the expense of less fit mutant alleles carrying the CQ resistance (CQR) marker K76T. In low-transmission settings, such as South America, drug resistance mutations can attain 100% prevalence, thereby precluding the return of WT parasites after the complete removal of drug pressure. In French Guiana, despite the fixation of the K76T allele, the prevalence of CQR isolates progressively dropped from >90% to <30% during 17 y after CQ withdrawal in 1995. Using a genome-wide association study with CQ-sensitive (CQS) and CQR isolates, we have identified a single mutation in pfcrt encoding a C350R substitution that is associated with the restoration of CQ susceptibility. Genome editing of the CQR reference strain 7G8 to incorporate PfCRT C350R caused a complete loss of CQR. A retrospective molecular survey on 580 isolates collected from 1997 to 2012 identified all C350R mutant parasites as being CQS. This mutation emerged in 2002 and rapidly spread throughout the P. falciparum population. The C350R allele is also associated with a significant decrease in piperaquine susceptibility in vitro, suggesting that piperaquine pressure in addition to potential fitness costs associated with the 7G8-type CQR pfcrt allele may have selected for this mutation. These findings have important implications for understanding the evolutionary dynamics of antimalarial drug resistance.
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Petersen I, Gabryszewski SJ, Johnston GL, Dhingra SK, Ecker A, Lewis RE, de Almeida MJ, Straimer J, Henrich PP, Palatulan E, Johnson DJ, Coburn-Flynn O, Sanchez C, Lehane AM, Lanzer M, Fidock DA. Balancing drug resistance and growth rates via compensatory mutations in the Plasmodium falciparum chloroquine resistance transporter. Mol Microbiol 2015; 97:381-95. [PMID: 25898991 DOI: 10.1111/mmi.13035] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 11/28/2022]
Abstract
The widespread use of chloroquine to treat Plasmodium falciparum infections has resulted in the selection and dissemination of variant haplotypes of the primary resistance determinant PfCRT. These haplotypes have encountered drug pressure and within-host competition with wild-type drug-sensitive parasites. To examine these selective forces in vitro, we genetically engineered P. falciparum to express geographically diverse PfCRT haplotypes. Variant alleles from the Philippines (PH1 and PH2, which differ solely by the C72S mutation) both conferred a moderate gain of chloroquine resistance and a reduction in growth rates in vitro. Of the two, PH2 showed higher IC50 values, contrasting with reduced growth. Furthermore, a highly mutated pfcrt allele from Cambodia (Cam734) conferred moderate chloroquine resistance and enhanced growth rates, when tested against wild-type pfcrt in co-culture competition assays. These three alleles mediated cross-resistance to amodiaquine, an antimalarial drug widely used in Africa. Each allele, along with the globally prevalent Dd2 and 7G8 alleles, rendered parasites more susceptible to lumefantrine, the partner drug used in the leading first-line artemisinin-based combination therapy. These data reveal ongoing region-specific evolution of PfCRT that impacts drug susceptibility and relative fitness in settings of mixed infections, and raise important considerations about optimal agents to treat chloroquine-resistant malaria.
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Affiliation(s)
- Ines Petersen
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - Stanislaw J Gabryszewski
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Geoffrey L Johnston
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,School of International and Public Affairs, Columbia University, New York, NY, 10027, USA
| | - Satish K Dhingra
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Department of Biological Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Andrea Ecker
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rebecca E Lewis
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | | | - Judith Straimer
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Philipp P Henrich
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Eugene Palatulan
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - David J Johnson
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Cecilia Sanchez
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - Adele M Lehane
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael Lanzer
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
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