1
|
Hoo R, Ruiz-Morales ER, Kelava I, Rawat M, Mazzeo CI, Tuck E, Sancho-Serra C, Chelaghma S, Predeus AV, Murray S, Fernandez-Antoran D, Waller RF, Álvarez-Errico D, Lee MCS, Vento-Tormo R. Acute response to pathogens in the early human placenta at single-cell resolution. Cell Syst 2024:S2405-4712(24)00117-0. [PMID: 38703772 DOI: 10.1016/j.cels.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
Abstract
The placenta is a selective maternal-fetal barrier that provides nourishment and protection from infections. However, certain pathogens can attach to and even cross the placenta, causing pregnancy complications with potential lifelong impacts on the child's health. Here, we profiled at the single-cell level the placental responses to three pathogens associated with intrauterine complications-Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We found that upon exposure to the pathogens, all placental lineages trigger inflammatory responses that may compromise placental function. Additionally, we characterized the responses of fetal macrophages known as Hofbauer cells (HBCs) to each pathogen and propose that they are the probable niche for T. gondii. Finally, we revealed how P. falciparum adapts to the placental microenvironment by modulating protein export into the host erythrocyte and nutrient uptake pathways. Altogether, we have defined the cellular networks and signaling pathways mediating acute placental inflammatory responses that could contribute to pregnancy complications.
Collapse
Affiliation(s)
- Regina Hoo
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Iva Kelava
- Wellcome Sanger Institute, Cambridge, UK
| | - Mukul Rawat
- Wellcome Sanger Institute, Cambridge, UK; Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | | | | | | | - Sara Chelaghma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - David Fernandez-Antoran
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Marcus C S Lee
- Wellcome Sanger Institute, Cambridge, UK; Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK.
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| |
Collapse
|
2
|
Rawat M, Padalino G, Yeo T, Brancale A, Fidock DA, Hoffmann KF, Lee MCS. Quinoxaline-Based Anti-Schistosomal Compounds Have Potent Anti-Malarial Activity. bioRxiv 2024:2024.04.23.590861. [PMID: 38712185 PMCID: PMC11071471 DOI: 10.1101/2024.04.23.590861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The human pathogens Plasmodium and Schistosoma are each responsible for over 200 million infections annually, being particularly problematic in low- and middle-income countries. There is a pressing need for new drug targets for these diseases, driven by emergence of drug-resistance in Plasmodium and the overall dearth of new drug targets for Schistosoma . Here, we explored the opportunity for pathogen-hopping by evaluating a series of quinoxaline-based anti-schistosomal compounds for activity against P. falciparum . We identified compounds with low nanomolar potency against 3D7 and multidrug-resistant strains. Evolution of resistance using a mutator P. falciparum line revealed a low propensity for resistance. Only one of the series, compound 22, yielded resistance mutations, including point mutations in a non-essential putative hydrolase pfqrp1, as well as copy-number amplification of a phospholipid-translocating ATPase, pfatp2 , a potential target. Notably, independently generated CRISPR-edited mutants in pfqrp1 also showed resistance to compound 22 and a related analogue. Moreover, previous lines with pfatp2 copy-number variations were similarly less susceptible to challenge with the new compounds. Finally, we examined whether the predicted hydrolase activity of PfQRP1 underlies its mechanism of resistance, showing that both mutation of the putative catalytic triad and a more severe loss of function mutation elicited resistance. Collectively, we describe a compound series with potent activity against two important pathogens and their potential target in P. falciparum .
Collapse
|
3
|
Mambwe D, Coertzen D, Leshabane M, Mulubwa M, Njoroge M, Gibhard L, Girling G, Wicht KJ, Lee MCS, Wittlin S, Moreira DRM, Birkholtz LM, Chibale K. hERG, Plasmodium Life Cycle, and Cross Resistance Profiling of New Azabenzimidazole Analogues of Astemizole. ACS Med Chem Lett 2024; 15:463-469. [PMID: 38628794 PMCID: PMC11017395 DOI: 10.1021/acsmedchemlett.3c00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 04/19/2024] Open
Abstract
Toward addressing the cardiotoxicity liability associated with the antimalarial drug astemizole (AST, hERG IC50 = 0.0042 μM) and its derivatives, we designed and synthesized analogues based on compound 1 (Pf NF54 IC50 = 0.012 μM; hERG IC50 = 0.63 μM), our previously identified 3-trifluoromethyl-1,2,4-oxadiazole AST analogue. Compound 11 retained in vitro multistage antiplasmodium activity (ABS PfNF54 IC50 = 0.017 μM; gametocytes PfiGc/PfLGc IC50 = 1.24/1.39 μM, and liver-stage PbHepG2 IC50 = 2.30 μM), good microsomal metabolic stability (MLM CLint < 11 μL·min-1·mg-1, EH < 0.33), and solubility (150 μM). It shows a ∼6-fold and >6000-fold higher selectivity against human ether-á-go-go-related gene higher selectively potential over hERG relative to 1 and AST, respectively. Despite the excellent in vitro antiplasmodium activity profile, in vivo efficacy in the Plasmodium berghei mouse infection model was diminished, attributable to suboptimal oral bioavailability (F = 14.9%) at 10 mg·kg-1 resulting from poor permeability (log D7.4 = -0.82). No cross-resistance was observed against 44 common Pf mutant lines, suggesting activity via a novel mechanism of action.
Collapse
Affiliation(s)
- Dickson Mambwe
- Department
of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Dina Coertzen
- Department
of Biochemistry, Genetics & Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Meta Leshabane
- Department
of Biochemistry, Genetics & Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Mwila Mulubwa
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Mathew Njoroge
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Liezl Gibhard
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Gareth Girling
- Wellcome
Sanger Institute, Wellcome
Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Kathryn J. Wicht
- Department
of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Marcus C. S. Lee
- Wellcome
Sanger Institute, Wellcome
Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
- Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, United Kingdom
| | - Sergio Wittlin
- Swiss
Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University
of Basel, 4003 Basel, Switzerland
| | | | - Lyn-Marie Birkholtz
- Department
of Biochemistry, Genetics & Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Kelly Chibale
- Department
of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, 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
| |
Collapse
|
4
|
Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MCS, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun 2024; 15:937. [PMID: 38297033 PMCID: PMC10831071 DOI: 10.1038/s41467-024-45224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.
Collapse
Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, VIC, Australia
| | - Riley D Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kate J Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Peter J Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- 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
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 4HN, UK
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK.
- Structural Genomics Consortium, University College London, London, WC1N 1AX, UK.
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| |
Collapse
|
5
|
Stadler E, Maiga M, Friedrich L, Thathy V, Demarta-Gatsi C, Dara A, Sogore F, Striepen J, Oeuvray C, Djimdé AA, Lee MCS, Dembélé L, Fidock DA, Khoury DS, Spangenberg T. Author Correction: Propensity of selecting mutant parasites for the antimalarial drug cabamiquine. Nat Commun 2023; 14:5447. [PMID: 37673924 PMCID: PMC10482846 DOI: 10.1038/s41467-023-41287-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Affiliation(s)
- Eva Stadler
- The Kirby Institute, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Mohamed Maiga
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Lukas Friedrich
- Medicinal Chemistry & Drug Design Global Research & Development, Discovery Technologies, Merck Healthcare, 64293, Darmstadt, Germany
| | - Vandana Thathy
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Claudia Demarta-Gatsi
- Global Health Institute of Merck, Ares Trading S.A., (an affiliate of Merck KGaA, Darmstadt, Germany), 1262, Eysins, Switzerland
| | - Antoine Dara
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Fanta Sogore
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Weill Cornell Medical College, New York, NY, 10021, USA
| | - Claude Oeuvray
- Global Health Institute of Merck, Ares Trading S.A., (an affiliate of Merck KGaA, Darmstadt, Germany), 1262, Eysins, Switzerland
| | - Abdoulaye A Djimdé
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA, Hinxton, UK
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, DD1 4HN, Scotland, UK
| | - Laurent Dembélé
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali.
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - David S Khoury
- The Kirby Institute, UNSW Sydney, Kensington, NSW, 2052, Australia.
| | - Thomas Spangenberg
- Global Health Institute of Merck, Ares Trading S.A., (an affiliate of Merck KGaA, Darmstadt, Germany), 1262, Eysins, Switzerland.
| |
Collapse
|
6
|
Stadler E, Maiga M, Friedrich L, Thathy V, Demarta-Gatsi C, Dara A, Sogore F, Striepen J, Oeuvray C, Djimdé AA, Lee MCS, Dembélé L, Fidock DA, Khoury DS, Spangenberg T. Propensity of selecting mutant parasites for the antimalarial drug cabamiquine. Nat Commun 2023; 14:5205. [PMID: 37626093 PMCID: PMC10457284 DOI: 10.1038/s41467-023-40974-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
We report an analysis of the propensity of the antimalarial agent cabamiquine, a Plasmodium-specific eukaryotic elongation factor 2 inhibitor, to select for resistant Plasmodium falciparum parasites. Through in vitro studies of laboratory strains and clinical isolates, a humanized mouse model, and volunteer infection studies, we identified resistance-associated mutations at 11 amino acid positions. Of these, six (55%) were present in more than one infection model, indicating translatability across models. Mathematical modelling suggested that resistant mutants were likely pre-existent at the time of drug exposure across studies. Here, we estimated a wide range of frequencies of resistant mutants across the different infection models, much of which can be attributed to stochastic differences resulting from experimental design choices. Structural modelling implicates binding of cabamiquine to a shallow mRNA binding site adjacent to two of the most frequently identified resistance mutations.
Collapse
Affiliation(s)
- Eva Stadler
- The Kirby Institute, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Mohamed Maiga
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Lukas Friedrich
- Medicinal Chemistry & Drug Design Global Research & Development, Discovery Technologies, Merck Healthcare, 64293, Darmstadt, Germany
| | - Vandana Thathy
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Claudia Demarta-Gatsi
- Global Health Institute of Merck, Ares Trading S.A., (an affiliate of Merck KGaA, Darmstadt, Germany), 1262, Eysins, Switzerland
| | - Antoine Dara
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Fanta Sogore
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Weill Cornell Medical College, New York, NY, 10021, USA
| | - Claude Oeuvray
- Global Health Institute of Merck, Ares Trading S.A., (an affiliate of Merck KGaA, Darmstadt, Germany), 1262, Eysins, Switzerland
| | - Abdoulaye A Djimdé
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA, Hinxton, UK
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, DD1 4HN, Scotland, UK
| | - Laurent Dembélé
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Faculté de Pharmacie, Malaria Research and Training Center (MRTC), Point G, PB1805, Bamako, Mali.
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - David S Khoury
- The Kirby Institute, UNSW Sydney, Kensington, NSW, 2052, Australia.
| | - Thomas Spangenberg
- Global Health Institute of Merck, Ares Trading S.A., (an affiliate of Merck KGaA, Darmstadt, Germany), 1262, Eysins, Switzerland.
| |
Collapse
|
7
|
Yipsirimetee A, Tipthara P, Hanboonkunupakarn B, Tripura R, Lek D, Kümpornsin K, Lee MCS, Sattabongkot J, Dondorp AM, White NJ, Kobylinski KC, Tarning J, Chotivanich K. Activity of Ivermectin and Its Metabolites against Asexual Blood Stage Plasmodium falciparum and Its Interactions with Antimalarial Drugs. Antimicrob Agents Chemother 2023; 67:e0173022. [PMID: 37338381 PMCID: PMC10368210 DOI: 10.1128/aac.01730-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/12/2023] [Indexed: 06/21/2023] Open
Abstract
Ivermectin is an endectocide used widely to treat a variety of internal and external parasites. Field trials of ivermectin mass drug administration for malaria transmission control have demonstrated a reduction of Anopheles mosquito survival and human malaria incidence. Ivermectin will mostly be deployed together with artemisinin-based combination therapies (ACT), the first-line treatment of falciparum malaria. It has not been well established if ivermectin has activity against asexual stage Plasmodium falciparum or if it interacts with the parasiticidal activity of other antimalarial drugs. This study evaluated antimalarial activity of ivermectin and its metabolites in artemisinin-sensitive and artemisinin-resistant P. falciparum isolates and assessed in vitro drug-drug interaction with artemisinins and its partner drugs. The concentration of ivermectin causing half of the maximum inhibitory activity (IC50) on parasite survival was 0.81 μM with no significant difference between artemisinin-sensitive and artemisinin-resistant isolates (P = 0.574). The ivermectin metabolites were 2-fold to 4-fold less active than the ivermectin parent compound (P < 0.001). Potential pharmacodynamic drug-drug interactions of ivermectin with artemisinins, ACT-partner drugs, and atovaquone were studied in vitro using mixture assays providing isobolograms and derived fractional inhibitory concentrations. There were no synergistic or antagonistic pharmacodynamic interactions when combining ivermectin and antimalarial drugs. In conclusion, ivermectin does not have clinically relevant activity against the asexual blood stages of P. falciparum. It also does not affect the in vitro antimalarial activity of artemisinins or ACT-partner drugs against asexual blood stages of P. falciparum.
Collapse
Affiliation(s)
- Achaporn Yipsirimetee
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phornpimon Tipthara
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Borimas Hanboonkunupakarn
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rupam Tripura
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Krittikorn Kümpornsin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Calibr, Division of the Scripps Research Institute, La Jolla, California, USA
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Arjen M. Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas J. White
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kevin C. Kobylinski
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Joel Tarning
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kesinee Chotivanich
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
8
|
Kümpornsin K, Kochakarn T, Yeo T, Okombo J, Luth MR, Hoshizaki J, Rawat M, Pearson RD, Schindler KA, Mok S, Park H, Uhlemann AC, Jana GP, Maity BC, Laleu B, Chenu E, Duffy J, Moliner Cubel S, Franco V, Gomez-Lorenzo MG, Gamo FJ, Winzeler EA, Fidock DA, Chookajorn T, Lee MCS. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum. Nat Commun 2023; 14:3059. [PMID: 37244916 DOI: 10.1038/s41467-023-38774-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/12/2023] [Indexed: 05/29/2023] Open
Abstract
In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an "irresistible" compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this "mutator" parasite can be leveraged to drive P. falciparum resistome discovery.
Collapse
Affiliation(s)
- Krittikorn Kümpornsin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, USA
| | - Theerarat Kochakarn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, 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
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, 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
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Benoît Laleu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - Elodie Chenu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | | | - Virginia Franco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | | | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 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, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Thanat Chookajorn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
- Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK.
| |
Collapse
|
9
|
Armstrong JF, Campo B, Alexander SPH, Arendse LB, Cheng X, Davenport AP, Faccenda E, Fidock DA, Godinez-Macias KP, Harding SD, Kato N, Lee MCS, Luth MR, Mazitschek R, Mittal N, Niles JC, Okombo J, Ottilie S, Pasaje CFA, Probst AS, Rawat M, Rocamora F, Sakata-Kato T, Southan C, Spedding M, Tye MA, Yang T, Zhao N, Davies JA. Advances in Malaria Pharmacology and the online Guide to MALARIA PHARMACOLOGY: IUPHAR Review X. Br J Pharmacol 2023. [PMID: 37197802 DOI: 10.1111/bph.16144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 05/10/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023] Open
Abstract
Antimalarial drug discovery has until recently been driven by high-throughput phenotypic cellular screening, allowing millions of compounds to be assayed and delivering clinical drug candidates. In this review, we will focus on target-based approaches, describing recent advances in our understanding of druggable targets in the malaria parasite. Targeting multiple stages of the Plasmodium lifecycle, rather than just the clinically symptomatic asexual blood stage, has become a requirement for new antimalarial medicines, and we link pharmacological data clearly to the parasite stages to which it applies. Finally, we highlight the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY, a web resource developed for the malaria research community that provides open and optimized access to published data on malaria pharmacology.
Collapse
Affiliation(s)
- Jane F Armstrong
- Deanery of Biomedical Sciences, The University of Edinburgh, Edinburgh, UK
| | - Brice Campo
- Medicines for Malaria Venture, 20 Route de Pré-Bois, 1215, Geneva, Switzerland
| | | | - Lauren B Arendse
- Drug Discovery and Development Centre (H3D), South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, Western Cape, 7701, South Africa
| | - Xiu Cheng
- Global Health Drug Discovery Institute, Bldg 2, Zhongguancun Dongsheng International Science Park, 1 Yongtaizhuang N Rd, Beijing, 100192, China
| | - Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Cambridge, UK
| | - Elena Faccenda
- Deanery of Biomedical Sciences, The University of Edinburgh, Edinburgh, UK
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, 10032, USA
| | - Karla P Godinez-Macias
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego (UCSD), La Jolla, CA, 92093, USA
| | - Simon D Harding
- Deanery of Biomedical Sciences, The University of Edinburgh, Edinburgh, UK
| | - Nobutaka Kato
- Global Health Drug Discovery Institute, Bldg 2, Zhongguancun Dongsheng International Science Park, 1 Yongtaizhuang N Rd, Beijing, 100192, China
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Madeline R Luth
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Okombo
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, USA
| | - Sabine Ottilie
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- The Scripps Research Institute, Calibr, 11119 North Torrey Pines Road, Suite 100, La Jolla, CA, 92037, USA
| | | | - Alexandra S Probst
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, USA
| | - Mukul Rawat
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Frances Rocamora
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Tomoyo Sakata-Kato
- Global Health Drug Discovery Institute, Bldg 2, Zhongguancun Dongsheng International Science Park, 1 Yongtaizhuang N Rd, Beijing, 100192, China
| | | | | | - Mark A Tye
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Tuo Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, 92093, USA
| | - Na Zhao
- Global Health Drug Discovery Institute, Bldg 2, Zhongguancun Dongsheng International Science Park, 1 Yongtaizhuang N Rd, Beijing, 100192, China
| | - Jamie A Davies
- Deanery of Biomedical Sciences, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
10
|
Ward KE, Christensen P, Racklyeft A, Dhingra SK, Chua ACY, Remmert C, Suwanarusk R, Matheson J, Blackman MJ, Kaneko O, Kyle DE, Lee MCS, Moon RW, Snounou G, Rénia L, Fidock DA, Russell B, Bifani P. Integrative Genetic Manipulation of Plasmodium cynomolgi Reveals Multidrug Resistance-1 Y976F Associated With Increased In Vitro Susceptibility to Mefloquine. J Infect Dis 2023; 227:1121-1126. [PMID: 36478252 PMCID: PMC10175063 DOI: 10.1093/infdis/jiac469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/24/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
The lack of a long-term in vitro culture method has severely restricted the study of Plasmodium vivax, in part because it limits genetic manipulation and reverse genetics. We used the recently optimized Plasmodium cynomolgi Berok in vitro culture model to investigate the putative P. vivax drug resistance marker MDR1 Y976F. Introduction of this mutation using clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) increased sensitivity to mefloquine, but had no significant effect on sensitivity to chloroquine, amodiaquine, piperaquine, and artesunate. To our knowledge, this is the first reported use of CRISPR-Cas9 in P. cynomolgi, and the first reported integrative genetic manipulation of this species.
Collapse
Affiliation(s)
- Kurt E Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Peter Christensen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Annie Racklyeft
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Satish K Dhingra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Adeline C Y Chua
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- A*STAR Infectious Diseases Laboratory, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Caroline Remmert
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rossarin Suwanarusk
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Jessica Matheson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert W Moon
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Georges Snounou
- 11-INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, Infectious Disease Models and Innovative Therapies Department, Institut de biologie François Jacob, Direction de Recherche Fondamentale, Commissariat à l'énergie atomique et aux énergies alternatives-Université Paris Sud, Fontenay-aux-Roses, France
| | - Laurent Rénia
- A*STAR Infectious Diseases Laboratory, Agency for Science, Technology, and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Pablo Bifani
- A*STAR Infectious Diseases Laboratory, Agency for Science, Technology, and Research, Singapore, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
11
|
Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ, Lee MCS. Correction: A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics 2023; 24:189. [PMID: 37024784 PMCID: PMC10080737 DOI: 10.1186/s12864-023-09164-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Affiliation(s)
- Johanna Hoshizaki
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sophie H Adjalley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Micrographia Bio, London, W12 0BZ, UK
| | - Vandana Thathy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Present address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY10032, USA
| | - Kim Judge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA, UK
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Present address: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| |
Collapse
|
12
|
Istvan ES, Guerra F, Abraham M, Huang KS, Rocamora F, Zhao H, Xu L, Pasaje C, Kumpornsin K, Luth MR, Cui H, Yang T, Diaz SP, Gomez-Lorenzo MG, Qahash T, Mittal N, Ottilie S, Niles J, Lee MCS, Llinas M, Kato N, Okombo J, Fidock DA, Schimmel P, Gamo FJ, Goldberg DE, Winzeler EA. Cytoplasmic isoleucyl tRNA synthetase as an attractive multistage antimalarial drug target. Sci Transl Med 2023; 15:eadc9249. [PMID: 36888694 PMCID: PMC10286833 DOI: 10.1126/scitranslmed.adc9249] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
Development of antimalarial compounds into clinical candidates remains costly and arduous without detailed knowledge of the target. As resistance increases and treatment options at various stages of disease are limited, it is critical to identify multistage drug targets that are readily interrogated in biochemical assays. Whole-genome sequencing of 18 parasite clones evolved using thienopyrimidine compounds with submicromolar, rapid-killing, pan-life cycle antiparasitic activity showed that all had acquired mutations in the P. falciparum cytoplasmic isoleucyl tRNA synthetase (cIRS). Engineering two of the mutations into drug-naïve parasites recapitulated the resistance phenotype, and parasites with conditional knockdowns of cIRS became hypersensitive to two thienopyrimidines. Purified recombinant P. vivax cIRS inhibition, cross-resistance, and biochemical assays indicated a noncompetitive, allosteric binding site that is distinct from that of known cIRS inhibitors mupirocin and reveromycin A. Our data show that Plasmodium cIRS is an important chemically and genetically validated target for next-generation medicines for malaria.
Collapse
Affiliation(s)
- Eva S. Istvan
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Francisco Guerra
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Matthew Abraham
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | | | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | | | - Lan Xu
- The Global Health Drug Discovery Institute, Tsinghua University 30 Shuangqing Rd, Haidian District, Beijing, China
| | - Charisse Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tuo Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Sara Palomo Diaz
- Global Health Medicines, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | | | - Tarrick Qahash
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Jacquin Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Manuel Llinas
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Nobutaka Kato
- The Global Health Drug Discovery Institute, Tsinghua University 30 Shuangqing Rd, Haidian District, Beijing, China
| | - John Okombo
- 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
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Daniel E. Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| |
Collapse
|
13
|
Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ, Lee MCS. A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics 2022; 23:780. [PMID: 36451097 PMCID: PMC9710153 DOI: 10.1186/s12864-022-09017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. RESULTS We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. CONCLUSIONS The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.
Collapse
Affiliation(s)
- Johanna Hoshizaki
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie H. Adjalley
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,Micrographia Bio, London, W12 0BZ UK
| | - Vandana Thathy
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS UK ,grid.239585.00000 0001 2285 2675Present address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY10032 USA
| | - Kim Judge
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew Berriman
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.8756.c0000 0001 2193 314XWellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA UK
| | - Adam J. Reid
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.5335.00000000121885934Present address: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN UK
| | - Marcus C. S. Lee
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| |
Collapse
|
14
|
Carrasquilla M, Drammeh NF, Rawat M, Sanderson T, Zenonos Z, Rayner JC, Lee MCS. Barcoding Genetically Distinct Plasmodium falciparum Strains for Comparative Assessment of Fitness and Antimalarial Drug Resistance. mBio 2022; 13:e0093722. [PMID: 35972144 PMCID: PMC9600763 DOI: 10.1128/mbio.00937-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022] Open
Abstract
The repeated emergence of antimalarial drug resistance in Plasmodium falciparum, including to the current frontline antimalarial artemisinin, is a perennial problem for malaria control. Next-generation sequencing has greatly accelerated the identification of polymorphisms in resistance-associated genes but has also highlighted the need for more sensitive and accurate laboratory tools to profile current and future antimalarials and to quantify the impact of drug resistance acquisition on parasite fitness. The interplay of fitness and drug response is of fundamental importance in understanding why particular genetic backgrounds are better at driving the evolution of drug resistance in natural populations, but the impact of parasite fitness landscapes on the epidemiology of drug resistance has typically been laborious to accurately quantify in the lab, with assays being limited in accuracy and throughput. Here we present a scalable method to profile fitness and drug response of genetically distinct P. falciparum strains with well-described sensitivities to several antimalarials. We leverage CRISPR/Cas9 genome-editing and barcode sequencing to track unique barcodes integrated into a nonessential gene (pfrh3). We validate this approach in multiplex competitive growth assays of three strains with distinct geographical origins. Furthermore, we demonstrate that this method can be a powerful approach for tracking artemisinin response as it can identify an artemisinin resistant strain within a mix of multiple parasite lines, suggesting an approach for scaling the laborious ring-stage survival assay across libraries of barcoded parasite lines. Overall, we present a novel high-throughput method for multiplexed competitive growth assays to evaluate parasite fitness and drug response. IMPORTANCE The complex interplay between antimalarial resistance and parasite fitness has important implications for understanding the development and spread of drug resistance alleles and the impact of genetic background on transmission. One limitation with current methodologies to measure parasite fitness is the ability to scale this beyond simple head-to-head competition experiments between a wildtype control line and test line, with a need for a scalable approach that allows tracking of parasite growth in complex mixtures. In our study, we have used CRISPR editing to insert unique DNA barcodes into a safe-harbor genomic locus to tag multiple parasite strains and use next-generation sequencing to read out strain dynamics. We observe inherent fitness differences between the strains, as well as sensitive modulation of responses to challenge with clinically relevant antimalarials, including artemisinin.
Collapse
Affiliation(s)
- Manuela Carrasquilla
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Ndey F. Drammeh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Zenon Zenonos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Biologics Engineering, Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Julian C. Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| |
Collapse
|
15
|
Qiu D, Pei JV, Rosling JEO, Thathy V, Li D, Xue Y, Tanner JD, Penington JS, Aw YTV, Aw JYH, Xu G, Tripathi AK, Gnadig NF, Yeo T, Fairhurst KJ, Stokes BH, Murithi JM, Kümpornsin K, Hasemer H, Dennis ASM, Ridgway MC, Schmitt EK, Straimer J, Papenfuss AT, Lee MCS, Corry B, Sinnis P, Fidock DA, van Dooren GG, Kirk K, Lehane AM. A G358S mutation in the Plasmodium falciparum Na + pump PfATP4 confers clinically-relevant resistance to cipargamin. Nat Commun 2022; 13:5746. [PMID: 36180431 PMCID: PMC9525273 DOI: 10.1038/s41467-022-33403-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Diverse compounds target the Plasmodium falciparum Na+ pump PfATP4, with cipargamin and (+)-SJ733 the most clinically-advanced. In a recent clinical trial for cipargamin, recrudescent parasites emerged, with most having a G358S mutation in PfATP4. Here, we show that PfATP4G358S parasites can withstand micromolar concentrations of cipargamin and (+)-SJ733, while remaining susceptible to antimalarials that do not target PfATP4. The G358S mutation in PfATP4, and the equivalent mutation in Toxoplasma gondii ATP4, decrease the sensitivity of ATP4 to inhibition by cipargamin and (+)-SJ733, thereby protecting parasites from disruption of Na+ regulation. The G358S mutation reduces the affinity of PfATP4 for Na+ and is associated with an increase in the parasite’s resting cytosolic [Na+]. However, no defect in parasite growth or transmissibility is observed. Our findings suggest that PfATP4 inhibitors in clinical development should be tested against PfATP4G358S parasites, and that their combination with unrelated antimalarials may mitigate against resistance development. In a recent clinical trial for oral administration of cipargamin in individuals with malaria, there was an emergence of recrudescent parasites with a G358S mutation in PfATP4. In this work, the authors investigate the effect of this mutation on the function of the ATPase, on parasite growth and susceptibility to antimalarial drugs.
Collapse
Affiliation(s)
- Deyun Qiu
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Jinxin V Pei
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - James E O Rosling
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Vandana Thathy
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dongdi Li
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Yi Xue
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - John D Tanner
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Jocelyn Sietsma Penington
- Bioinformatic Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Yi Tong Vincent Aw
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Jessica Yi Han Aw
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Guoyue Xu
- Department of Molecular Microbiology & Immunology and Johns Hopkins Malaria Institute, Johns Hopkins School of Public Health, Baltimore, MD, 21205, USA
| | - Abhai K Tripathi
- Department of Molecular Microbiology & Immunology and Johns Hopkins Malaria Institute, Johns Hopkins School of Public Health, Baltimore, MD, 21205, USA
| | - Nina F Gnadig
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Barbara H Stokes
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - James M Murithi
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Heath Hasemer
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Adelaide S M Dennis
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Melanie C Ridgway
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | | | - Judith Straimer
- Novartis Institute for Tropical Diseases, Emeryville, CA, 94608, USA
| | - Anthony T Papenfuss
- Bioinformatic Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Photini Sinnis
- Department of Molecular Microbiology & Immunology and Johns Hopkins Malaria Institute, Johns Hopkins School of Public Health, Baltimore, MD, 21205, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Adele M Lehane
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia.
| |
Collapse
|
16
|
Hoshizaki J, Jagoe H, Lee MCS. Efficient generation of mNeonGreen Plasmodium falciparum reporter lines enables quantitative fitness analysis. Front Cell Infect Microbiol 2022; 12:981432. [PMID: 36189342 PMCID: PMC9523114 DOI: 10.3389/fcimb.2022.981432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR editing has enabled the rapid creation of fluorescent Plasmodium transgenic lines, facilitating a deeper understanding of parasite biology. The impact of genetic perturbations such as gene disruption or the introduction of drug resistance alleles on parasite fitness is typically quantified in competitive growth assays between the query line and a wild type reference. Although fluorescent reporter lines offer a facile and frequently used method to measure relative growth, this approach is limited by the strain background of the existing reporter, which may not match the growth characteristics of the query strains, particularly if these are slower-growing field isolates. Here, we demonstrate an efficient CRISPR-based approach to generate fluorescently labelled parasite lines using mNeonGreen derived from the LanYFP protein in Branchiostoma lanceolatum, which is one of the brightest monomeric green fluorescent proteins identified. Using a positive-selection approach by insertion of an in-frame blasticidin S deaminase marker, we generated a Dd2 reporter line expressing mNeonGreen under the control of the pfpare (P. falciparum Prodrug Activation and Resistance Esterase) locus. We selected the pfpare locus as an integration site because it is highly conserved across P. falciparum strains, expressed throughout the intraerythrocytic cycle, not essential, and offers the potential for negative selection to further enrich for integrants. The mNeonGreen@pare line demonstrates strong fluorescence with a negligible fitness defect. In addition, the construct developed can serve as a tool to fluorescently tag other P. falciparum strains for in vitro experimentation.
Collapse
|
17
|
Kümpornsin K, Loesbanluechai D, de Cozar C, Kotanan N, Chotivanich K, White NJ, Wilairat P, Gomez-Lorenzo MG, Gamo FJ, Sanz LM, Lee MCS, Chookajorn T. Lumefantrine attenuates Plasmodium falciparum artemisinin resistance during the early ring stage. Int J Parasitol Drugs Drug Resist 2021; 17:186-190. [PMID: 34673330 PMCID: PMC8528645 DOI: 10.1016/j.ijpddr.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
Emerging artemisinin resistance in Plasmodium falciparum malaria has the potential to become a global public health crisis. In Southeast Asia, this phenomenon clinically manifests in the form of delayed parasite clearance following artemisinin treatment. Reduced artemisinin susceptibility is limited to the early ring stage window, which is sufficient to allow parasites to survive the short half-life of artemisinin exposure. A screen of known clinically-implemented antimalarial drugs was performed to identify a drug capable of enhancing the killing activity of artemisinins during this critical resistance window. As a result, lumefantrine was found to increase the killing activity of artemisinin against an artemisinin-resistant clinical isolate harboring the C580Y kelch13 mutation. Isobologram analysis revealed synergism during the early ring stage resistance window, when lumefantrine was combined with artemether, an artemisinin derivative clinically partnered with lumefantrine. These findings suggest that lumefantrine should be clinically explored as a partner drug in artemisinin-based combination therapies to control emerging artemisinin resistance. Artemisinin booster compound screening targeting the early ring resistance window in Plasmodium falciparum was performed. Lumefantrine improves the activity of artesunate against the parasite during the resistance window. Artemether and lumefantrine are synergistic during the early ring stage resistance window.
Collapse
Affiliation(s)
| | - Duangkamon Loesbanluechai
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Namfon Kotanan
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kesinee Chotivanich
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Churchill Hospital, Oxford, United Kingdom
| | - Prapon Wilairat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | | | | | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
18
|
Yang T, Ottilie S, Istvan ES, Godinez-Macias KP, Lukens AK, Baragaña B, Campo B, Walpole C, Niles JC, Chibale K, Dechering KJ, Llinás M, Lee MCS, Kato N, Wyllie S, McNamara CW, Gamo FJ, Burrows J, Fidock DA, Goldberg DE, Gilbert IH, Wirth DF, Winzeler EA. MalDA, Accelerating Malaria Drug Discovery. Trends Parasitol 2021; 37:493-507. [PMID: 33648890 PMCID: PMC8261838 DOI: 10.1016/j.pt.2021.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/24/2022]
Abstract
The Malaria Drug Accelerator (MalDA) is a consortium of 15 leading scientific laboratories. The aim of MalDA is to improve and accelerate the early antimalarial drug discovery process by identifying new, essential, druggable targets. In addition, it seeks to produce early lead inhibitors that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans. By sharing resources, including expertise, knowledge, materials, and reagents, the consortium strives to eliminate the structural barriers often encountered in the drug discovery process. Here we discuss the mission of the consortium and its scientific achievements, including the identification of new chemically and biologically validated targets, as well as future scientific directions.
Collapse
Affiliation(s)
- Tuo Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Eva S Istvan
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Karla P Godinez-Macias
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Beatriz Baragaña
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Brice Campo
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - Chris Walpole
- Structural Genomics Consortium, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Building 56-341, 77 Massachusetts Avenue, Cambridge MA 02139-4307, USA
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | | | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA 16082, USA
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nobutaka Kato
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Susan Wyllie
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Case W McNamara
- Calibr, a division of The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Jeremy Burrows
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - David A Fidock
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniel E Goldberg
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Ian H Gilbert
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
| |
Collapse
|
19
|
Rocamora F, Gupta P, Istvan ES, Luth MR, Carpenter EF, Kümpornsin K, Sasaki E, Calla J, Mittal N, Carolino K, Owen E, Llinás M, Ottilie S, Goldberg DE, Lee MCS, Winzeler EA. PfMFR3: A Multidrug-Resistant Modulator in Plasmodium falciparum. ACS Infect Dis 2021; 7:811-825. [PMID: 33715347 PMCID: PMC8042660 DOI: 10.1021/acsinfecdis.0c00676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
In
malaria, chemical genetics is a powerful method for assigning
function to uncharacterized genes. MMV085203 and GNF-Pf-3600 are two
structurally related napthoquinone phenotypic screening hits that
kill both blood- and sexual-stage P. falciparum parasites in the low nanomolar to low micromolar range. In order
to understand their mechanism of action, parasites from two different
genetic backgrounds were exposed to sublethal concentrations of MMV085203
and GNF-Pf-3600 until resistance emerged. Whole genome sequencing
revealed all 17 resistant clones acquired nonsynonymous mutations
in the gene encoding the orphan apicomplexan transporter PF3D7_0312500
(pfmfr3) predicted to encode a member of the major
facilitator superfamily (MFS). Disruption of pfmfr3 and testing against a panel of antimalarial compounds showed decreased
sensitivity to MMV085203 and GNF-Pf-3600 as well as other compounds
that have a mitochondrial mechanism of action. In contrast, mutations
in pfmfr3 provided no protection against compounds
that act in the food vacuole or the cytosol. A dihydroorotate dehydrogenase
rescue assay using transgenic parasite lines, however, indicated a
different mechanism of action for both MMV085203 and GNF-Pf-3600 than
the direct inhibition of cytochrome bc1. Green fluorescent protein
(GFP) tagging of PfMFR3 revealed that it localizes to the parasite
mitochondrion. Our data are consistent with PfMFR3 playing roles in
mitochondrial transport as well as drug resistance for clinically
relevant antimalarials that target the mitochondria. Furthermore,
given that pfmfr3 is naturally polymorphic, naturally
occurring mutations may lead to differential sensitivity to clinically
relevant compounds such as atovaquone.
Collapse
Affiliation(s)
- Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Purva Gupta
- VA San Diego Healthcare System, Medical and Research Sections, La Jolla, California 92161, United States
- Department of Medicine, Division of Pulmonary and Critical Care, University of California, San Diego, La Jolla, California 92037, United States
| | - Eva S. Istvan
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
| | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | | | | | - Erika Sasaki
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jaeson Calla
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Krypton Carolino
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Edward Owen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Daniel E. Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
| | | | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
20
|
Vanaerschot M, Murithi JM, Pasaje CFA, Ghidelli-Disse S, Dwomoh L, Bird M, Spottiswoode N, Mittal N, Arendse LB, Owen ES, Wicht KJ, Siciliano G, Bösche M, Yeo T, Kumar TRS, Mok S, Carpenter EF, Giddins MJ, Sanz O, Ottilie S, Alano P, Chibale K, Llinás M, Uhlemann AC, Delves M, Tobin AB, Doerig C, Winzeler EA, Lee MCS, Niles JC, Fidock DA. Inhibition of Resistance-Refractory P. falciparum Kinase PKG Delivers Prophylactic, Blood Stage, and Transmission-Blocking Antiplasmodial Activity. Cell Chem Biol 2020; 27:806-816.e8. [PMID: 32359426 PMCID: PMC7369637 DOI: 10.1016/j.chembiol.2020.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/20/2020] [Accepted: 03/31/2020] [Indexed: 12/28/2022]
Abstract
The search for antimalarial chemotypes with modes of action unrelated to existing drugs has intensified with the recent failure of first-line therapies across Southeast Asia. Here, we show that the trisubstituted imidazole MMV030084 potently inhibits hepatocyte invasion by Plasmodium sporozoites, merozoite egress from asexual blood stage schizonts, and male gamete exflagellation. Metabolomic, phosphoproteomic, and chemoproteomic studies, validated with conditional knockdown parasites, molecular docking, and recombinant kinase assays, identified cGMP-dependent protein kinase (PKG) as the primary target of MMV030084. PKG is known to play essential roles in Plasmodium invasion of and egress from host cells, matching MMV030084's activity profile. Resistance selections and gene editing identified tyrosine kinase-like protein 3 as a low-level resistance mediator for PKG inhibitors, while PKG itself never mutated under pressure. These studies highlight PKG as a resistance-refractory antimalarial target throughout the Plasmodium life cycle and promote MMV030084 as a promising Plasmodium PKG-targeting chemotype.
Collapse
Affiliation(s)
- Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - James M Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Louis Dwomoh
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, Scotland
| | - Megan Bird
- Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Natasha Spottiswoode
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nimisha Mittal
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Lauren B Arendse
- Drug Discovery and Development Centre (H3D), South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Edward S Owen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16801, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Kathryn J Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giulia Siciliano
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy
| | - Markus Bösche
- Cellzome GmbH, GlaxoSmithKline, 69117 Heidelberg, Germany
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - T R Santha Kumar
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Emma F Carpenter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Marla J Giddins
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Olalla Sanz
- Diseases of the Developing World Global Health Pharma Unit, GlaxoSmithKline, 28760 Tres Cantos, Spain
| | - Sabine Ottilie
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Pietro Alano
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16801, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael Delves
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Andrew B Tobin
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, Scotland
| | - Christian Doerig
- Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora VIC 3083, Australia
| | | | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
21
|
LaMonte GM, Rocamora F, Marapana DS, Gnädig NF, Ottilie S, Luth MR, Worgall TS, Goldgof GM, Mohunlal R, Santha Kumar TR, Thompson JK, Vigil E, Yang J, Hutson D, Johnson T, Huang J, Williams RM, Zou BY, Cheung AL, Kumar P, Egan TJ, Lee MCS, Siegel D, Cowman AF, Fidock DA, Winzeler EA. Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway. Nat Commun 2020; 11:1780. [PMID: 32286267 PMCID: PMC7156427 DOI: 10.1038/s41467-020-15440-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
A promising new compound class for treating human malaria is the imidazolopiperazines (IZP) class. IZP compounds KAF156 (Ganaplacide) and GNF179 are effective against Plasmodium symptomatic asexual blood-stage infections, and are able to prevent transmission and block infection in animal models. But despite the identification of resistance mechanisms in P. falciparum, the mode of action of IZPs remains unknown. To investigate, we here combine in vitro evolution and genome analysis in Saccharomyces cerevisiae with molecular, metabolomic, and chemogenomic methods in P. falciparum. Our findings reveal that IZP-resistant S. cerevisiae clones carry mutations in genes involved in Endoplasmic Reticulum (ER)-based lipid homeostasis and autophagy. In Plasmodium, IZPs inhibit protein trafficking, block the establishment of new permeation pathways, and cause ER expansion. Our data highlight a mechanism for blocking parasite development that is distinct from those of standard compounds used to treat malaria, and demonstrate the potential of IZPs for studying ER-dependent protein processing.
Collapse
Affiliation(s)
- Gregory M LaMonte
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Danushka S Marapana
- Division of Infection and Immunity, Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nina F Gnädig
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Gregory M Goldgof
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94143, USA
| | - Roxanne Mohunlal
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Chemistry, University of Cape Town, Rondebosch, 7700, South Africa
| | - T R Santha Kumar
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jennifer K Thompson
- Division of Infection and Immunity, Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Edgar Vigil
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jennifer Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Dylan Hutson
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Trevor Johnson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jianbo Huang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Roy M Williams
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Yu Zou
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Andrea L Cheung
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Prianka Kumar
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch, 7700, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7700, South Africa
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alan F Cowman
- Division of Infection and Immunity, Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
22
|
Gnädig NF, Stokes BH, Edwards RL, Kalantarov GF, Heimsch KC, Kuderjavy M, Crane A, Lee MCS, Straimer J, Becker K, Trakht IN, Odom John AR, Mok S, Fidock DA. Insights into the intracellular localization, protein associations and artemisinin resistance properties of Plasmodium falciparum K13. PLoS Pathog 2020; 16:e1008482. [PMID: 32310999 PMCID: PMC7192513 DOI: 10.1371/journal.ppat.1008482] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/30/2020] [Accepted: 03/17/2020] [Indexed: 12/23/2022] Open
Abstract
The emergence of artemisinin (ART) resistance in Plasmodium falciparum intra-erythrocytic parasites has led to increasing treatment failure rates with first-line ART-based combination therapies in Southeast Asia. Decreased parasite susceptibility is caused by K13 mutations, which are associated clinically with delayed parasite clearance in patients and in vitro with an enhanced ability of ring-stage parasites to survive brief exposure to the active ART metabolite dihydroartemisinin. Herein, we describe a panel of K13-specific monoclonal antibodies and gene-edited parasite lines co-expressing epitope-tagged versions of K13 in trans. By applying an analytical quantitative imaging pipeline, we localize K13 to the parasite endoplasmic reticulum, Rab-positive vesicles, and sites adjacent to cytostomes. These latter structures form at the parasite plasma membrane and traffic hemoglobin to the digestive vacuole wherein artemisinin-activating heme moieties are released. We also provide evidence of K13 partially localizing near the parasite mitochondria upon treatment with dihydroartemisinin. Immunoprecipitation data generated with K13-specific monoclonal antibodies identify multiple putative K13-associated proteins, including endoplasmic reticulum-resident molecules, mitochondrial proteins, and Rab GTPases, in both K13 mutant and wild-type isogenic lines. We also find that mutant K13-mediated resistance is reversed upon co-expression of wild-type or mutant K13. These data help define the biological properties of K13 and its role in mediating P. falciparum resistance to ART treatment.
Collapse
Affiliation(s)
- Nina F. Gnädig
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Barbara H. Stokes
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Rachel L. Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Gavreel F. Kalantarov
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Kim C. Heimsch
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | | | - Audrey Crane
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Judith Straimer
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Ilya N. Trakht
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Audrey R. Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States of America
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Sachel Mok
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - David A. Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, United States of America
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| |
Collapse
|
23
|
Murithi JM, Owen ES, Istvan ES, Lee MCS, Ottilie S, Chibale K, Goldberg DE, Winzeler EA, Llinás M, Fidock DA, Vanaerschot M. Combining Stage Specificity and Metabolomic Profiling to Advance Antimalarial Drug Discovery. Cell Chem Biol 2019; 27:158-171.e3. [PMID: 31813848 PMCID: PMC7031696 DOI: 10.1016/j.chembiol.2019.11.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/18/2019] [Accepted: 11/14/2019] [Indexed: 01/08/2023]
Abstract
We report detailed susceptibility profiling of asexual blood stages of the malaria parasite Plasmodium falciparum to clinical and experimental antimalarials, combined with metabolomic fingerprinting. Results revealed a variety of stage-specific and metabolic profiles that differentiated the modes of action of clinical antimalarials including chloroquine, piperaquine, lumefantrine, and mefloquine, and identified late trophozoite-specific peak activity and stage-specific biphasic dose-responses for the mitochondrial inhibitors DSM265 and atovaquone. We also identified experimental antimalarials hitting previously unexplored druggable pathways as reflected by their unique stage specificity and/or metabolic profiles. These included several ring-active compounds, ones affecting hemoglobin catabolism through distinct pathways, and mitochondrial inhibitors with lower propensities for resistance than either DSM265 or atovaquone. This approach, also applicable to other microbes that undergo multiple differentiation steps, provides an effective tool to prioritize compounds for further development within the context of combination therapies.
Collapse
Affiliation(s)
- James M Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward S Owen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Eva S Istvan
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis MO 63130, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sabine Ottilie
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Daniel E Goldberg
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis MO 63130, USA
| | - Elizabeth A Winzeler
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
24
|
Karpiyevich M, Adjalley S, Mol M, Ascher DB, Mason B, van der Heden van Noort GJ, Laman H, Ovaa H, Lee MCS, Artavanis-Tsakonas K. Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathog 2019; 15:e1008086. [PMID: 31658303 PMCID: PMC6837540 DOI: 10.1371/journal.ppat.1008086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/07/2019] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Plasmodium parasites are the causative agents of malaria, a disease with wide public health repercussions. Increasing drug resistance and the absence of a vaccine make finding new chemotherapeutic strategies imperative. Components of the ubiquitin and ubiquitin-like pathways have garnered increased attention as novel targets given their necessity to parasite survival. Understanding how these pathways are regulated in Plasmodium and identifying differences to the host is paramount to selectively interfering with parasites. Here, we focus on Nedd8 modification in Plasmodium falciparum, given its central role to cell division and DNA repair, processes critical to Plasmodium parasites given their unusual cell cycle and requirement for refined repair mechanisms. By applying a functional chemical approach, we show that deNeddylation is controlled by a different set of enzymes in the parasite versus the human host. We elucidate the molecular determinants of the unusual dual ubiquitin/Nedd8 recognition by the essential PfUCH37 enzyme and, through parasite transgenics and drug assays, determine that only its ubiquitin activity is critical to parasite survival. Our experiments reveal interesting evolutionary differences in how neddylation is controlled in higher versus lower eukaryotes, and highlight the Nedd8 pathway as worthy of further exploration for therapeutic targeting in antimalarial drug design. Ubiquitin and ubiquitin-like post-translational modifications are evolutionarily conserved and involved in fundamental cellular processes essential to all eukaryotes. As such, enzymatic components of these pathways present attractive targets for therapeutic intervention for both chronic and communicable diseases. Nedd8 modification of cullin ubiquitin E3 ligases is critical to the viability of eukaryotic organisms and mediates cell cycle progression and DNA damage repair. Given the complex lifecycle and unusual replication mechanisms of the malaria parasite, one would expect neddylation to be of central importance to its survival, yet little is known about this pathway in Plasmodium. Here we present our findings on how Nedd8 removal is controlled in Plasmodium falciparum and how this pathway differs to that of its human host.
Collapse
Affiliation(s)
- Maryia Karpiyevich
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sophie Adjalley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Marco Mol
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Melbourne, Melbourne, Australia
| | - Bethany Mason
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Heike Laman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcus C. S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | |
Collapse
|
25
|
Lee MCS, Lindner SE, Lopez-Rubio JJ, Llinás M. Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium. Brief Funct Genomics 2019; 18:281-289. [PMID: 31365053 PMCID: PMC6859820 DOI: 10.1093/bfgp/elz012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/15/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas9 approaches are revolutionizing our ability to perform functional genomics across a wide range of organisms, including the Plasmodium parasites that cause malaria. The ability to deliver single point mutations, epitope tags and gene deletions at increased speed and scale is enabling our understanding of the biology of these complex parasites, and pointing to potential new therapeutic targets. In this review, we describe some of the biological and technical considerations for designing CRISPR-based experiments, and discuss potential future developments that broaden the applications for CRISPR/Cas9 interrogation of the malaria parasite genome.
Collapse
Affiliation(s)
- Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA
| | - Jose-Juan Lopez-Rubio
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, INSERM, Université Montpellier, Montpellier, France
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA
- Department of Chemistry, The Pennsylvania State University, Pennsylvania, USA
| |
Collapse
|
26
|
White J, Dhingra SK, Deng X, El Mazouni F, Lee MCS, Afanador GA, Lawong A, Tomchick DR, Ng CL, Bath J, Rathod PK, Fidock DA, Phillips MA. Identification and Mechanistic Understanding of Dihydroorotate Dehydrogenase Point Mutations in Plasmodium falciparum that Confer in Vitro Resistance to the Clinical Candidate DSM265. ACS Infect Dis 2019; 5:90-101. [PMID: 30375858 DOI: 10.1021/acsinfecdis.8b00211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is one of the most challenging human infectious diseases, and both prevention and control have been hindered by the development of Plasmodium falciparum resistance to existing therapies. Several new compounds with novel mechanisms are in clinical development for the treatment of malaria, including DSM265, an inhibitor of Plasmodium dihydroorotate dehydrogenase. To explore the mechanisms by which resistance might develop to DSM265 in the field, we selected for DSM265-resistant P. falciparum parasites in vitro. Any of five different amino acid changes led to reduced efficacy on the parasite and to decreased DSM265 binding to P. falciparum DHODH. The DSM265-resistant parasites retained full sensitivity to atovaquone. All but one of the observed mutations were in the DSM265 binding site, and the remaining C276F was in the adjacent flavin cofactor site. The C276F mutation was previously identified in a recrudescent parasite during a Phase IIa clinical study. We confirmed that this mutation (and the related C276Y) accounted for the full level of observed DSM265 resistance by regenerating the mutation using CRISPR/Cas9 genome editing. X-ray structure analysis of the C276F mutant enzyme showed that conformational changes of nearby residues were required to accommodate the larger F276 residue, which in turn led to a restriction in the size of the DSM265 binding pocket. These findings underscore the importance of developing DSM265 as part of a combination therapy with other agents for successful use against malaria.
Collapse
Affiliation(s)
- John White
- Departments of Chemistry and Global Health, University of Washington, 36 Bagley Hall, 400 15th Avenue NE, Seattle, Washington 98195, United States
| | - Satish K. Dhingra
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Marcus C. S. Lee
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, U.K
| | - Gustavo A. Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Caroline L. Ng
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Jade Bath
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Pradipsinh K. Rathod
- Departments of Chemistry and Global Health, University of Washington, 36 Bagley Hall, 400 15th Avenue NE, Seattle, Washington 98195, United States
| | - David A. Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, PH8-W, 630 West 168th Street, PH 8-West, New York, New York 10032, United States
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| |
Collapse
|
27
|
Loesbanluechai D, Kotanan N, de Cozar C, Kochakarn T, Ansbro MR, Chotivanich K, White NJ, Wilairat P, Lee MCS, Gamo FJ, Sanz LM, Chookajorn T, Kümpornsin K. Overexpression of plasmepsin II and plasmepsin III does not directly cause reduction in Plasmodium falciparum sensitivity to artesunate, chloroquine and piperaquine. Int J Parasitol Drugs Drug Resist 2018; 9:16-22. [PMID: 30580023 PMCID: PMC6304341 DOI: 10.1016/j.ijpddr.2018.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 11/22/2018] [Accepted: 11/24/2018] [Indexed: 01/31/2023]
Abstract
Artemisinin derivatives and their partner drugs in artemisinin combination therapies (ACTs) have played a pivotal role in global malaria mortality reduction during the last two decades. The loss of artemisinin efficacy due to evolving drug-resistant parasites could become a serious global health threat. Dihydroartemisinin-piperaquine is a well tolerated and generally highly effective ACT. The implementation of a partner drug in ACTs is critical in the control of emerging artemisinin resistance. Even though artemisinin is highly effective in parasite clearance, it is labile in the human body. A partner drug is necessary for killing the remaining parasites when the pulses of artemisinin have ceased. A population of Plasmodium falciparum parasites in Cambodia and adjacent countries has become resistant to piperaquine. Increased copy number of the genes encoding the haemoglobinases Plasmepsin II and Plasmepsin III has been linked with piperaquine resistance by genome-wide association studies and in clinical trials, leading to the use of increased plasmepsin II/plasmepsin III copy number as a molecular marker for piperaquine resistance. Here we demonstrate that overexpression of plasmepsin II and plasmepsin III in the 3D7 genetic background failed to change the susceptibility of P. falciparum to artemisinin, chloroquine and piperaquine by both a standard dose-response analysis and a piperaquine survival assay. Whilst plasmepsin copy number polymorphism is currently implemented as a molecular surveillance resistance marker, further studies to discover the molecular basis of piperaquine resistance and potential epistatic interactions are needed.
Collapse
Affiliation(s)
- Duangkamon Loesbanluechai
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Namfon Kotanan
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Cristina de Cozar
- Tres Cantos Medicine Development Campus, GlaxoSmithKline, Parque Tecnológico de Madrid, Tres Cantos, 28760, Spain
| | - Theerarat Kochakarn
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Megan R Ansbro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA; Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Kesinee Chotivanich
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Churchill Hospital, Oxford, OX3 7LJ, United Kingdom
| | - Prapon Wilairat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Francisco Javier Gamo
- Tres Cantos Medicine Development Campus, GlaxoSmithKline, Parque Tecnológico de Madrid, Tres Cantos, 28760, Spain
| | - Laura Maria Sanz
- Tres Cantos Medicine Development Campus, GlaxoSmithKline, Parque Tecnológico de Madrid, Tres Cantos, 28760, Spain
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
| | - Krittikorn Kümpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom.
| |
Collapse
|
28
|
Paquet T, Le Manach C, Cabrera DG, Younis Y, Henrich PP, Abraham TS, Lee MCS, Basak R, Ghidelli-Disse S, Lafuente-Monasterio MJ, Bantscheff M, Ruecker A, Blagborough AM, Zakutansky SE, Zeeman AM, White KL, Shackleford DM, Mannila J, Morizzi J, Scheurer C, Angulo-Barturen I, Martínez MS, Ferrer S, Sanz LM, Gamo FJ, Reader J, Botha M, Dechering KJ, Sauerwein RW, Tungtaeng A, Vanachayangkul P, Lim CS, Burrows J, Witty MJ, Marsh KC, Bodenreider C, Rochford R, Solapure SM, Jiménez-Díaz MB, Wittlin S, Charman SA, Donini C, Campo B, Birkholtz LM, Hanson KK, Drewes G, Kocken CHM, Delves MJ, Leroy D, Fidock DA, Waterson D, Street LJ, Chibale K. Antimalarial efficacy of MMV390048, an inhibitor of Plasmodium phosphatidylinositol 4-kinase. Sci Transl Med 2018; 9:9/387/eaad9735. [PMID: 28446690 DOI: 10.1126/scitranslmed.aad9735] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 11/21/2016] [Indexed: 12/13/2022]
Abstract
As part of the global effort toward malaria eradication, phenotypic whole-cell screening revealed the 2-aminopyridine class of small molecules as a good starting point to develop new antimalarial drugs. Stemming from this series, we found that the derivative, MMV390048, lacked cross-resistance with current drugs used to treat malaria. This compound was efficacious against all Plasmodium life cycle stages, apart from late hypnozoites in the liver. Efficacy was shown in the humanized Plasmodium falciparum mouse model, and modest reductions in mouse-to-mouse transmission were achieved in the Plasmodium berghei mouse model. Experiments in monkeys revealed the ability of MMV390048 to be used for full chemoprotection. Although MMV390048 was not able to eliminate liver hypnozoites, it delayed relapse in a Plasmodium cynomolgi monkey model. Both genomic and chemoproteomic studies identified a kinase of the Plasmodium parasite, phosphatidylinositol 4-kinase, as the molecular target of MMV390048. The ability of MMV390048 to block all life cycle stages of the malaria parasite suggests that this compound should be further developed and may contribute to malaria control and eradication as part of a single-dose combination treatment.
Collapse
Affiliation(s)
- Tanya Paquet
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Claire Le Manach
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | | | - Yassir Younis
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Philipp P Henrich
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Tara S Abraham
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, 1020 Locust Street, Suite 368, Philadelphia, PA 19107, USA
| | - Marcus C S Lee
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Rajshekhar Basak
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - María José Lafuente-Monasterio
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Marcus Bantscheff
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andrea Ruecker
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | | | | | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, 2280 GH Rijswijk, Netherlands
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Janne Mannila
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia.,Admescope Ltd., Typpitie 1, 90620 Oulu, Finland
| | - Julia Morizzi
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Christian Scheurer
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Iñigo Angulo-Barturen
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - María Santos Martínez
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Santiago Ferrer
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Laura María Sanz
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Francisco Javier Gamo
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Janette Reader
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Mariette Botha
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Koen J Dechering
- TropIQ Health Sciences, Transistorweg 5, 6534 AT Nijmegen, Netherlands
| | - Robert W Sauerwein
- TropIQ Health Sciences, Transistorweg 5, 6534 AT Nijmegen, Netherlands.,Radboud University Medical Center, Department of Medical Microbiology, 6500 HB Nijmegen, Netherlands
| | - Anchalee Tungtaeng
- Department of Veterinary Medicine, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Pattaraporn Vanachayangkul
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Chek Shik Lim
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
| | - Jeremy Burrows
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Michael J Witty
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Kennan C Marsh
- AbbVie, 1 North Waukegan Road, North Chicago, IL 60064-6104, USA
| | - Christophe Bodenreider
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
| | - Rosemary Rochford
- Departments of Immunology and Microbiology and Environmental and Occupational Health, University of Colorado Denver, Aurora, CO 80045, USA
| | - Suresh M Solapure
- Nagarjuna Gardens, 60 Feet Road, Sahakaranagar, Bangalore 560092, India
| | - María Belén Jiménez-Díaz
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, 1020 Locust Street, Suite 368, Philadelphia, PA 19107, USA
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Cristina Donini
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Kirsten K Hanson
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Clemens H M Kocken
- Department of Parasitology, Biomedical Primate Research Centre, 2280 GH Rijswijk, Netherlands
| | - Michael J Delves
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Didier Leroy
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - 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
| | - David Waterson
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Leslie J Street
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa. .,South African Medical Research Council Drug Discovery and Development Research Unit, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
29
|
Cowell AN, Istvan ES, Lukens AK, Gomez-Lorenzo MG, Vanaerschot M, Sakata-Kato T, Flannery EL, Magistrado P, Owen E, Abraham M, LaMonte G, Painter HJ, Williams RM, Franco V, Linares M, Arriaga I, Bopp S, Corey VC, Gnädig NF, Coburn-Flynn O, Reimer C, Gupta P, Murithi JM, Moura PA, Fuchs O, Sasaki E, Kim SW, Teng CH, Wang LT, Akidil A, Adjalley S, Willis PA, Siegel D, Tanaseichuk O, Zhong Y, Zhou Y, Llinás M, Ottilie S, Gamo FJ, Lee MCS, Goldberg DE, Fidock DA, Wirth DF, Winzeler EA. Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics. Science 2018; 359:191-199. [PMID: 29326268 PMCID: PMC5925756 DOI: 10.1126/science.aan4472] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 11/02/2017] [Indexed: 12/21/2022]
Abstract
Chemogenetic characterization through in vitro evolution combined with whole-genome analysis can identify antimalarial drug targets and drug-resistance genes.We performed a genome analysis of 262 Plasmodium falciparum parasites resistant to 37 diverse compounds.We found 159 gene amplifications and 148 nonsynonymous changes in 83 genes associated with drug-resistance acquisition, where gene amplifications contributed to one-third of resistance acquisition events. Beyond confirming previously identified multidrug-resistance mechanisms, we discovered hitherto unrecognized drug target–inhibitor pairs, including thymidylate synthase and a benzoquinazolinone, farnesyltransferase and a pyrimidinedione, and a dipeptidylpeptidase and an arylurea.This exploration of the P. falciparum resistome and druggable genome will likely guide drug discovery and structural biology efforts, while also advancing our understanding of resistance mechanisms available to the malaria parasite.
Collapse
Affiliation(s)
- Annie N Cowell
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Eva S Istvan
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.,Infectious Disease Program, The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Maria G Gomez-Lorenzo
- Tres Cantos Medicines Development Campus, Malaria Discovery Performance Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Erika L Flannery
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pamela Magistrado
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Edward Owen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Abraham
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gregory LaMonte
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Heather J Painter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Roy M Williams
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Virginia Franco
- Tres Cantos Medicines Development Campus, Malaria Discovery Performance Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Maria Linares
- Tres Cantos Medicines Development Campus, Malaria Discovery Performance Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Ignacio Arriaga
- Tres Cantos Medicines Development Campus, Malaria Discovery Performance Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Selina Bopp
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Victoria C Corey
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nina F Gnädig
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Christin Reimer
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Purva Gupta
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - James M Murithi
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pedro A Moura
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Olivia Fuchs
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Erika Sasaki
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sang W Kim
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Christine H Teng
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lawrence T Wang
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Aslı Akidil
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sophie Adjalley
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Paul A Willis
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Olga Tanaseichuk
- Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Yang Zhong
- Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sabine Ottilie
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Francisco-Javier Gamo
- Tres Cantos Medicines Development Campus, Malaria Discovery Performance Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Marcus C S Lee
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.,Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.,Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.,Infectious Disease Program, The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Elizabeth A Winzeler
- School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
30
|
Corey VC, Lukens AK, Istvan ES, Lee MCS, Franco V, Magistrado P, Coburn-Flynn O, Sakata-Kato T, Fuchs O, Gnädig NF, Goldgof G, Linares M, Gomez-Lorenzo MG, De Cózar C, Lafuente-Monasterio MJ, Prats S, Meister S, Tanaseichuk O, Wree M, Zhou Y, Willis PA, Gamo FJ, Goldberg DE, Fidock DA, Wirth DF, Winzeler EA. A broad analysis of resistance development in the malaria parasite. Nat Commun 2016; 7:11901. [PMID: 27301419 PMCID: PMC4912613 DOI: 10.1038/ncomms11901] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 05/10/2016] [Indexed: 01/25/2023] Open
Abstract
Microbial resistance to chemotherapy has caused countless deaths where malaria is endemic. Chemotherapy may fail either due to pre-existing resistance or evolution of drug-resistant parasites. Here we use a diverse set of antimalarial compounds to investigate the acquisition of drug resistance and the degree of cross-resistance against common resistance alleles. We assess cross-resistance using a set of 15 parasite lines carrying resistance-conferring alleles in pfatp4, cytochrome bc1, pfcarl, pfdhod, pfcrt, pfmdr, pfdhfr, cytoplasmic prolyl t-RNA synthetase or hsp90. Subsequently, we assess whether resistant parasites can be obtained after several rounds of drug selection. Twenty-three of the 48 in vitro selections result in resistant parasites, with time to resistance onset ranging from 15 to 300 days. Our data indicate that pre-existing resistance may not be a major hurdle for novel-target antimalarial candidates, and focusing our attention on fast-killing compounds may result in a slower onset of clinical resistance. It is unclear whether new antimalarial compounds may rapidly lose effectiveness in the field because of parasite resistance. Here, Corey et al. investigate the acquisition of drug resistance and the extent to which common resistance mechanisms decrease susceptibility to a diverse set of 50 antimalarial compounds.
Collapse
Affiliation(s)
- Victoria C Corey
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA.,Infectious Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Eva S Istvan
- Department of Medicine and Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Marcus C S Lee
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Virginia Franco
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Pamela Magistrado
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Olivia Fuchs
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Nina F Gnädig
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Greg Goldgof
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Maria Linares
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Maria G Gomez-Lorenzo
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Cristina De Cózar
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Maria Jose Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Sara Prats
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Stephan Meister
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Olga Tanaseichuk
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, California 92121, USA
| | - Melanie Wree
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Yingyao Zhou
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, California 92121, USA
| | - Paul A Willis
- Medicines for Malaria Venture, PO Box 1826, 20 route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Francisco-Javier Gamo
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Daniel E Goldberg
- Department of Medicine and Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA.,Infectious Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| |
Collapse
|
31
|
Ng CL, Siciliano G, Lee MCS, de Almeida MJ, Corey VC, Bopp SE, Bertuccini L, Wittlin S, Kasdin RG, Le Bihan A, Clozel M, Winzeler EA, Alano P, Fidock DA. CRISPR-Cas9-modified pfmdr1 protects Plasmodium falciparum asexual blood stages and gametocytes against a class of piperazine-containing compounds but potentiates artemisinin-based combination therapy partner drugs. Mol Microbiol 2016; 101:381-93. [PMID: 27073104 DOI: 10.1111/mmi.13397] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2016] [Indexed: 01/08/2023]
Abstract
Emerging resistance to first-line antimalarial combination therapies threatens malaria treatment and the global elimination campaign. Improved therapeutic strategies are required to protect existing drugs and enhance treatment efficacy. We report that the piperazine-containing compound ACT-451840 exhibits single-digit nanomolar inhibition of the Plasmodium falciparum asexual blood stages and transmissible gametocyte forms. Genome sequence analyses of in vitro-derived ACT-451840-resistant parasites revealed single nucleotide polymorphisms in pfmdr1, which encodes a digestive vacuole membrane-bound ATP-binding cassette transporter known to alter P. falciparum susceptibility to multiple first-line antimalarials. CRISPR-Cas9 based gene editing confirmed that PfMDR1 point mutations mediated ACT-451840 resistance. Resistant parasites demonstrated increased susceptibility to the clinical drugs lumefantrine, mefloquine, quinine and amodiaquine. Stage V gametocytes harboring Cas9-introduced pfmdr1 mutations also acquired ACT-451840 resistance. These findings reveal that PfMDR1 mutations can impart resistance to compounds active against asexual blood stages and mature gametocytes. Exploiting PfMDR1 resistance mechanisms provides new opportunities for developing disease-relieving and transmission-blocking antimalarials.
Collapse
Affiliation(s)
- Caroline L Ng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Giulia Siciliano
- Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marcus C S Lee
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Mariana J de Almeida
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Victoria C Corey
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Selina E Bopp
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lucia Bertuccini
- Dipartimento Tecnologie e Salute, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Sergio Wittlin
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland
| | - Rachel G Kasdin
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Amélie Le Bihan
- Department of Drug Discovery, Actelion Pharmaceuticals Ltd., CH-4123 Allschwil, Switzerland
| | - Martine Clozel
- Department of Drug Discovery, Actelion Pharmaceuticals Ltd., CH-4123 Allschwil, Switzerland
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pietro Alano
- Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - 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
| |
Collapse
|
32
|
Ramachandran S, Hameed P. S, Srivastava A, Shanbhag G, Morayya S, Rautela N, Awasthy D, Kavanagh S, Bharath S, Reddy J, Panduga V, Prabhakar KR, Saralaya R, Nanduri R, Raichurkar A, Menasinakai S, Achar V, Jiménez-Díaz MB, Martínez MS, Angulo-Barturen I, Ferrer S, Sanz LM, Gamo FJ, Duffy S, Avery VM, Waterson D, Lee MCS, Coburn-Flynn O, Fidock DA, Iyer PS, Narayanan S, Hosagrahara V, Sambandamurthy VK. N-Aryl-2-aminobenzimidazoles: Novel, Efficacious, Antimalarial Lead Compounds. J Med Chem 2014; 57:6642-52. [DOI: 10.1021/jm500715u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Stefan Kavanagh
- Safety
Assessment, AstraZeneca, Alderley Park, Macclesfield, U.K
| | | | | | | | | | | | | | | | | | | | - María Belén Jiménez-Díaz
- Tres
Cantos Medicines Development Campus, Diseases of the Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - María Santos Martínez
- Tres
Cantos Medicines Development Campus, Diseases of the Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Iñigo Angulo-Barturen
- Tres
Cantos Medicines Development Campus, Diseases of the Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Santiago Ferrer
- Tres
Cantos Medicines Development Campus, Diseases of the Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Laura María Sanz
- Tres
Cantos Medicines Development Campus, Diseases of the Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Francisco Javier Gamo
- Tres
Cantos Medicines Development Campus, Diseases of the Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Sandra Duffy
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia
| | - Vicky M. Avery
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia
| | - David Waterson
- Medicines
for Malaria Venture, International Center Cointrin, Route de Pré-Bois
20, Post Office Box 1826, 1215 Geneva, Switzerland
| | - Marcus C. S. Lee
- Department
of Microbiology and Immunology and Division of Infectious Diseases,
Department of Medicine, Columbia University Medical Center, Columbia University, 116th Street and Broadway, New York, New York 10027, United States
| | - Olivia Coburn-Flynn
- Department
of Microbiology and Immunology and Division of Infectious Diseases,
Department of Medicine, Columbia University Medical Center, Columbia University, 116th Street and Broadway, New York, New York 10027, United States
| | - David A. Fidock
- Department
of Microbiology and Immunology and Division of Infectious Diseases,
Department of Medicine, Columbia University Medical Center, Columbia University, 116th Street and Broadway, New York, New York 10027, United States
| | | | | | | | | |
Collapse
|
33
|
Straimer J, Lee MCS, Lee AH, Zeitler B, Williams AE, Pearl JR, Zhang L, Rebar EJ, Gregory PD, Llinás M, Urnov FD, Fidock DA. Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases. Nat Methods 2012; 9:993-8. [PMID: 22922501 DOI: 10.1038/nmeth.2143] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/27/2012] [Indexed: 01/21/2023]
Abstract
Malaria afflicts over 200 million people worldwide, and its most lethal etiologic agent, Plasmodium falciparum, is evolving to resist even the latest-generation therapeutics. Efficient tools for genome-directed investigations of P. falciparum-induced pathogenesis, including drug-resistance mechanisms, are clearly required. Here we report rapid and targeted genetic engineering of this parasite using zinc-finger nucleases (ZFNs) that produce a double-strand break in a user-defined locus and trigger homology-directed repair. Targeting an integrated egfp locus, we obtained gene-deletion parasites with unprecedented speed (2 weeks), both with and without direct selection. ZFNs engineered against the parasite gene pfcrt, responsible for escape under chloroquine treatment, rapidly produced parasites that carried either an allelic replacement or a panel of specified point mutations. This method will enable a diverse array of genome-editing approaches to interrogate this human pathogen.
Collapse
Affiliation(s)
- Judith Straimer
- Department of Microbiology & Immunology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Meister S, Plouffe DM, Kuhen KL, Bonamy GMC, Wu T, Barnes SW, Bopp SE, Borboa R, Bright AT, Che J, Cohen S, Dharia NV, Gagaring K, Gettayacamin M, Gordon P, Groessl T, Kato N, Lee MCS, McNamara CW, Fidock DA, Nagle A, Nam TG, Richmond W, Roland J, Rottmann M, Zhou B, Froissard P, Glynne RJ, Mazier D, Sattabongkot J, Schultz PG, Tuntland T, Walker JR, Zhou Y, Chatterjee A, Diagana TT, Winzeler EA. Imaging of Plasmodium liver stages to drive next-generation antimalarial drug discovery. Science 2011; 334:1372-7. [PMID: 22096101 DOI: 10.1126/science.1211936] [Citation(s) in RCA: 252] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Most malaria drug development focuses on parasite stages detected in red blood cells, even though, to achieve eradication, next-generation drugs active against both erythrocytic and exo-erythrocytic forms would be preferable. We applied a multifactorial approach to a set of >4000 commercially available compounds with previously demonstrated blood-stage activity (median inhibitory concentration < 1 micromolar) and identified chemical scaffolds with potent activity against both forms. From this screen, we identified an imidazolopiperazine scaffold series that was highly enriched among compounds active against Plasmodium liver stages. The orally bioavailable lead imidazolopiperazine confers complete causal prophylactic protection (15 milligrams/kilogram) in rodent models of malaria and shows potent in vivo blood-stage therapeutic activity. The open-source chemical tools resulting from our effort provide starting points for future drug discovery programs, as well as opportunities for researchers to investigate the biology of exo-erythrocytic forms.
Collapse
Affiliation(s)
- Stephan Meister
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Rottmann M, McNamara C, Yeung BKS, Lee MCS, Zou B, Russell B, Seitz P, Plouffe DM, Dharia NV, Tan J, Cohen SB, Spencer KR, González-Páez GE, Lakshminarayana SB, Goh A, Suwanarusk R, Jegla T, Schmitt EK, Beck HP, Brun R, Nosten F, Renia L, Dartois V, Keller TH, Fidock DA, Winzeler EA, Diagana TT. Spiroindolones, a potent compound class for the treatment of malaria. Science 2010; 329:1175-80. [PMID: 20813948 DOI: 10.1126/science.1193225] [Citation(s) in RCA: 902] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Recent reports of increased tolerance to artemisinin derivatives--the most recently adopted class of antimalarials--have prompted a need for new treatments. The spirotetrahydro-beta-carbolines, or spiroindolones, are potent drugs that kill the blood stages of Plasmodium falciparum and Plasmodium vivax clinical isolates at low nanomolar concentration. Spiroindolones rapidly inhibit protein synthesis in P. falciparum, an effect that is ablated in parasites bearing nonsynonymous mutations in the gene encoding the P-type cation-transporter ATPase4 (PfATP4). The optimized spiroindolone NITD609 shows pharmacokinetic properties compatible with once-daily oral dosing and has single-dose efficacy in a rodent malaria model.
Collapse
Affiliation(s)
- Matthias Rottmann
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, CH-4002 Basel, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Exit from the endoplasmic reticulum (ER) often occurs at distinct sites of vesicle formation known as transitional ER (tER) that are enriched for COPII vesicle coat proteins. We have characterized the organization of ER export in the malaria parasite, Plasmodium falciparum, by examining the localization of two components of the COPII machinery, PfSec12 and PfSec24a. PfSec12 was found throughout the ER, whereas the COPII cargo adaptor, PfSec24a, was concentrated at distinct foci that likely correspond to tER sites. These foci were closely apposed to cis-Golgi sites marked by PfGRASP-GFP, and upon treatment with brefeldin A they accumulated a model cargo protein via a process dependent on the presence of an intact diacidic export motif. Our data suggest that the cargo-binding function of PfSec24a is conserved and that accumulation of cargo in discrete tER sites depends upon positive sorting signals. Furthermore, the number and position of tER sites with respect to the cis-Golgi suggests a co-ordinated biogenesis of these domains.
Collapse
Affiliation(s)
- Marcus C S Lee
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | | | | | | |
Collapse
|
37
|
Abstract
The first step in protein secretion from eukaryotic cells is mediated by COPII vesicles, known for the cytoplasmic coat proteins that are the minimal machinery required to generate these small transport carriers. The five COPII coat components coordinate to create a vesicle by locally generating membrane curvature and populating the incipient bud with the appropriate cargo. This review describes the molecular details of how the COPII coat sculpts vesicles from the endoplasmic reticulum and highlights some unresolved questions regarding the regulation of this process in the complex environment of the eukaryotic cell.
Collapse
Affiliation(s)
- Marcus C S Lee
- Department of Microbiology, Columbia University, New York, NY, United States
| | | |
Collapse
|
38
|
Lee MCS, Orci L, Hamamoto S, Futai E, Ravazzola M, Schekman R. Sar1p N-terminal helix initiates membrane curvature and completes the fission of a COPII vesicle. Cell 2005; 122:605-17. [PMID: 16122427 DOI: 10.1016/j.cell.2005.07.025] [Citation(s) in RCA: 360] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 07/17/2005] [Accepted: 07/29/2005] [Indexed: 10/25/2022]
Abstract
Secretory proteins traffic from the ER to the Golgi via COPII-coated transport vesicles. The five core COPII proteins (Sar1p, Sec23/24p, and Sec13/31p) act in concert to capture cargo proteins and sculpt the ER membrane into vesicles of defined geometry. The molecular details of how the coat proteins deform the lipid bilayer into vesicles are not known. Here we show that the small GTPase Sar1p directly initiates membrane curvature during vesicle biogenesis. Upon GTP binding by Sar1p, membrane insertion of the N-terminal amphipathic alpha helix deforms synthetic liposomes into narrow tubules. Replacement of bulky hydrophobic residues in the alpha helix with alanine yields Sar1p mutants that are unable to generate highly curved membranes and are defective in vesicle formation from native ER membranes despite normal recruitment of coat and cargo proteins. Thus, the initiation of vesicle budding by Sar1p couples the generation of membrane curvature with coat-protein assembly and cargo capture.
Collapse
Affiliation(s)
- Marcus C S Lee
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94702, USA
| | | | | | | | | | | |
Collapse
|
39
|
Abstract
The endoplasmic reticulum (ER) and the Golgi comprise the first two steps in protein secretion. Vesicular carriers mediate a continuous flux of proteins and lipids between these compartments, reflecting the transport of newly synthesized proteins out of the ER and the retrieval of escaped ER residents and vesicle machinery. Anterograde and retrograde transport is mediated by distinct sets of cytosolic coat proteins, the COPII and COPI coats, respectively, which act on the membrane to capture cargo proteins into nascent vesicles. We review the mechanisms that govern coat recruitment to the membrane, cargo capture into a transport vesicle, and accurate delivery to the target organelle.
Collapse
Affiliation(s)
- Marcus C S Lee
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
| | | | | | | | | |
Collapse
|
40
|
Affiliation(s)
- Marcus C S Lee
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | | |
Collapse
|
41
|
Miller EA, Beilharz TH, Malkus PN, Lee MCS, Hamamoto S, Orci L, Schekman R. Multiple cargo binding sites on the COPII subunit Sec24p ensure capture of diverse membrane proteins into transport vesicles. Cell 2003; 114:497-509. [PMID: 12941277 DOI: 10.1016/s0092-8674(03)00609-3] [Citation(s) in RCA: 398] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have characterized the mechanisms of cargo selection into ER-derived vesicles by the COPII subunit Sec24p. We identified a site on Sec24p that recognizes the v-SNARE Bet1p and show that packaging of a number of cargo molecules is disrupted when mutations are introduced at this site. Surprisingly, cargo proteins affected by these mutations did not share a single common sorting signal, nor were proteins sharing a putative class of signal affected to the same degree. We show that the same site is conserved as a cargo-interaction domain on the Sec24p homolog Lst1p, which only packages a subset of the cargoes recognized by Sec24p. Finally, we identified an additional mutation that defines another cargo binding domain on Sec24p, which specifically interacts with the SNARE Sec22p. Together, our data support a model whereby Sec24p proteins contain multiple independent cargo binding domains that allow for recognition of a diverse set of sorting signals.
Collapse
Affiliation(s)
- Elizabeth A Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | | | | | | | | |
Collapse
|
42
|
Lee MCS, Hamamoto S, Schekman R. Ceramide biosynthesis is required for the formation of the oligomeric H+-ATPase Pma1p in the yeast endoplasmic reticulum. J Biol Chem 2002; 277:22395-401. [PMID: 11950838 DOI: 10.1074/jbc.m200450200] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast plasma membrane H(+)-ATPase Pma1p is one of the most abundant proteins to traverse the secretory pathway. Newly synthesized Pma1p exits the endoplasmic reticulum (ER) via COPII-coated vesicles bound for the Golgi. Unlike most secreted proteins, efficient incorporation of Pma1p into COPII vesicles requires the Sec24p homolog Lst1p, suggesting a unique role for Lst1p in ER export. Vesicles formed with mixed Sec24p-Lst1p coats are larger than those with Sec24p alone. Here, we examined the relationship between Pma1p biosynthesis and the requirement for this novel coat subunit. We show that Pma1p forms a large oligomeric complex of >1 MDa in the ER, which is packaged into COPII vesicles. Furthermore, oligomerization of Pma1p is linked to membrane lipid composition; Pma1p is rendered monomeric in cells depleted of ceramide, suggesting that association with lipid rafts may influence oligomerization. Surprisingly, monomeric Pma1p present in ceramide-deficient membranes can be exported from the ER in COPII vesicles in a reaction that is stimulated by Lst1p. We suggest that Lst1p directly conveys Pma1p into a COPII vesicle and that the larger size of mixed Sec24pLst1p COPII vesicles is not essential to the packaging of large oligomeric complexes.
Collapse
Affiliation(s)
- Marcus C S Lee
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | | | | |
Collapse
|