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Knapp K, Verchio V, Coburn-Flynn O, Li Y, Xiong Z, Morrison JC, Shersher DD, Spitz F, Chen X. Exploring cell competition for the prevention and therapy of esophageal squamous cell carcinoma. Biochem Pharmacol 2023; 214:115639. [PMID: 37290594 PMCID: PMC10528900 DOI: 10.1016/j.bcp.2023.115639] [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: 04/03/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is characterized by the development of cancer in the esophageal squamous epithelium through a step-by-step accumulation of genetic, epigenetic, and histopathological alterations. Recent studies have demonstrated that cancer-associated gene mutations exist in histologically normal or precancerous clones of the human esophageal epithelium. However, only a small proportion of such mutant clones will develop ESCC, and most ESCC patients develop only one cancer. This suggests that most of these mutant clones are kept in a histologically normal state by neighboring cells with higher competitive fitness. When some of the mutant cells evade cell competition, they become "super-competitors" and develop into clinical cancer. It is known that human ESCC is composed of a heterogeneous population of cancer cells that interact with and influence their environment and neighbors. During cancer therapy, these cancer cells not only respond to therapeutic agents but also compete with each other. Therefore, competition between ESCC cells within the same ESCC tumor is a constantly dynamic process. However, it remains challenging to fine-tune the competitive fitness of various clones for therapeutic benefits. In this review, we will explore the role of cell competition in carcinogenesis, cancer prevention, and therapy, using NRF2, NOTCH pathway, and TP53 as examples. We believe that cell competition is a research area with promising targets for clinical translation. Manipulating cell competition may help improve the prevention and therapy of ESCC.
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Affiliation(s)
- Kristen Knapp
- Department of Surgery, Cooper University Hospital, Camden, NJ 08103, USA
| | - Vincent Verchio
- Department of Surgery, Cooper University Hospital, Camden, NJ 08103, USA
| | | | - Yahui Li
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Zhaohui Xiong
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Jamin C Morrison
- MD Anderson Cancer Center at Cooper, Camden, NJ 08103, USA; Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - David D Shersher
- Department of Surgery, Cooper University Hospital, Camden, NJ 08103, USA; MD Anderson Cancer Center at Cooper, Camden, NJ 08103, USA; Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Francis Spitz
- Department of Surgery, Cooper University Hospital, Camden, NJ 08103, USA; MD Anderson Cancer Center at Cooper, Camden, NJ 08103, USA; Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Xiaoxin Chen
- Department of Surgery, Cooper University Hospital, Camden, NJ 08103, USA; Coriell Institute for Medical Research, Camden, NJ 08103, USA; MD Anderson Cancer Center at Cooper, Camden, NJ 08103, USA; Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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2
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Murithi JM, Deni I, Pasaje CFA, Okombo J, Bridgford JL, Gnädig NF, Edwards RL, Yeo T, Mok S, Burkhard AY, Coburn-Flynn O, Istvan ES, Sakata-Kato T, Gomez-Lorenzo MG, Cowell AN, Wicht KJ, Le Manach C, Kalantarov GF, Dey S, Duffey M, Laleu B, Lukens AK, Ottilie S, Vanaerschot M, Trakht IN, Gamo FJ, Wirth DF, Goldberg DE, Odom John AR, Chibale K, Winzeler EA, Niles JC, Fidock DA. The Plasmodium falciparum ABC transporter ABCI3 confers parasite strain-dependent pleiotropic antimalarial drug resistance. Cell Chem Biol 2022; 29:824-839.e6. [PMID: 34233174 PMCID: PMC8727639 DOI: 10.1016/j.chembiol.2021.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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] [Received: 04/06/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 01/21/2023]
Abstract
Widespread Plasmodium falciparum resistance to first-line antimalarials underscores the vital need to develop compounds with novel modes of action and identify new druggable targets. Here, we profile five compounds that potently inhibit P. falciparum asexual blood stages. Resistance selection studies with three carboxamide-containing compounds, confirmed by gene editing and conditional knockdowns, identify point mutations in the parasite transporter ABCI3 as the primary mediator of resistance. Selection studies with imidazopyridine or quinoline-carboxamide compounds also yield changes in ABCI3, this time through gene amplification. Imidazopyridine mode of action is attributed to inhibition of heme detoxification, as evidenced by cellular accumulation and heme fractionation assays. For the copy-number variation-selecting imidazopyridine and quinoline-carboxamide compounds, we find that resistance, manifesting as a biphasic concentration-response curve, can independently be mediated by mutations in the chloroquine resistance transporter PfCRT. These studies reveal the interconnectedness of P. falciparum transporters in overcoming drug pressure in different parasite strains.
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Affiliation(s)
- James M. Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jessica L. Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nina F. Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel L. Edwards
- Division of Infectious Diseases, Allergy and Immunology, Center for Vaccine Development, St. Louis University, St. Louis, MO 63104, USA
| | - Tomas Yeo
- 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
| | - Anna Y. Burkhard
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Eva S. Istvan
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoyo Sakata-Kato
- 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
| | | | - Annie N. Cowell
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Kathryn J. Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA,Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Claire Le Manach
- Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Gavreel F. Kalantarov
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maëlle Duffey
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - 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
| | - Sabine Ottilie
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ilya N. Trakht
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francisco-Javier Gamo
- Global Health Pharma Research Unit, GlaxoSmithKline, 28760 Tres Cantos, Madrid, Spain
| | - 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
| | - Daniel E. Goldberg
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kelly Chibale
- Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Elizabeth A. Winzeler
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - 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, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA,Corresponding author
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3
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Schlott AC, Mayclin S, Reers AR, Coburn-Flynn O, Bell AS, Green J, Knuepfer E, Charter D, Bonnert R, Campo B, Burrows J, Lyons-Abbott S, Staker BL, Chung CW, Myler PJ, Fidock DA, Tate EW, Holder AA. Structure-Guided Identification of Resistance Breaking Antimalarial N‑Myristoyltransferase Inhibitors. Cell Chem Biol 2019; 26:991-1000.e7. [PMID: 31080074 PMCID: PMC6658617 DOI: 10.1016/j.chembiol.2019.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 01/02/2019] [Revised: 02/25/2019] [Accepted: 03/25/2019] [Indexed: 01/26/2023]
Abstract
The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic target in numerous infectious diseases including malaria. In Plasmodium falciparum, NMT substrates are important in essential processes including parasite gliding motility and host cell invasion. Here, we generated parasites resistant to a particular NMT inhibitor series and show that resistance in an in vitro parasite growth assay is mediated by a single amino acid substitution in the NMT substrate-binding pocket. The basis of resistance was validated and analyzed with a structure-guided approach using crystallography, in combination with enzyme activity, stability, and surface plasmon resonance assays, allowing identification of another inhibitor series unaffected by this substitution. We suggest that resistance studies incorporated early in the drug development process help selection of drug combinations to impede rapid evolution of parasite resistance.
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Affiliation(s)
- Anja C Schlott
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
| | - Stephen Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Alexandra R Reers
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrew S Bell
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK
| | - Judith Green
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ellen Knuepfer
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Charter
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Roger Bonnert
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Jeremy Burrows
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK; Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA; Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, USA; Department of Global Health, University of Washington, Seattle, USA
| | - David A Fidock
- Department of Microbiology & 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
| | - Edward W Tate
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
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4
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Mayclin S, Schlott A, Reers A, Coburn-Flynn O, Holder A, Bell A, Fidock D, Tate E. Structural insights on three series of anti-malarial N-myristoyltransferase inhibitors. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318095727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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5
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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.
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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
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6
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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.
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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
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7
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Petersen I, Gabryszewski SJ, Johnston GL, Dhingra SK, Ecker A, Lewis RE, de Almeida MJ, Straimer J, Henrich PP, Palatulan E, Johnson DJ, Coburn-Flynn O, Sanchez C, Lehane AM, Lanzer M, Fidock DA. Balancing drug resistance and growth rates via compensatory mutations in the Plasmodium falciparum chloroquine resistance transporter. Mol Microbiol 2015; 97:381-95. [PMID: 25898991 DOI: 10.1111/mmi.13035] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 11/28/2022]
Abstract
The widespread use of chloroquine to treat Plasmodium falciparum infections has resulted in the selection and dissemination of variant haplotypes of the primary resistance determinant PfCRT. These haplotypes have encountered drug pressure and within-host competition with wild-type drug-sensitive parasites. To examine these selective forces in vitro, we genetically engineered P. falciparum to express geographically diverse PfCRT haplotypes. Variant alleles from the Philippines (PH1 and PH2, which differ solely by the C72S mutation) both conferred a moderate gain of chloroquine resistance and a reduction in growth rates in vitro. Of the two, PH2 showed higher IC50 values, contrasting with reduced growth. Furthermore, a highly mutated pfcrt allele from Cambodia (Cam734) conferred moderate chloroquine resistance and enhanced growth rates, when tested against wild-type pfcrt in co-culture competition assays. These three alleles mediated cross-resistance to amodiaquine, an antimalarial drug widely used in Africa. Each allele, along with the globally prevalent Dd2 and 7G8 alleles, rendered parasites more susceptible to lumefantrine, the partner drug used in the leading first-line artemisinin-based combination therapy. These data reveal ongoing region-specific evolution of PfCRT that impacts drug susceptibility and relative fitness in settings of mixed infections, and raise important considerations about optimal agents to treat chloroquine-resistant malaria.
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Affiliation(s)
- Ines Petersen
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - Stanislaw J Gabryszewski
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Geoffrey L Johnston
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,School of International and Public Affairs, Columbia University, New York, NY, 10027, USA
| | - Satish K Dhingra
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Department of Biological Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Andrea Ecker
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rebecca E Lewis
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | | | - Judith Straimer
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Philipp P Henrich
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Eugene Palatulan
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - David J Johnson
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Cecilia Sanchez
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - Adele M Lehane
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael Lanzer
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
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8
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Frame IJ, Deniskin R, Rinderspacher A, Katz F, Deng SX, Moir RD, Adjalley SH, Coburn-Flynn O, Fidock DA, Willis IM, Landry DW, Akabas MH. Yeast-based high-throughput screen identifies Plasmodium falciparum equilibrative nucleoside transporter 1 inhibitors that kill malaria parasites. ACS Chem Biol 2015; 10:775-83. [PMID: 25602169 DOI: 10.1021/cb500981y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Equilibrative transporters are potential drug targets; however, most functional assays involve radioactive substrate uptake that is unsuitable for high-throughput screens (HTS). We developed a robust yeast-based growth assay that is potentially applicable to many equilibrative transporters. As proof of principle, we applied our approach to Equilibrative Nucleoside Transporter 1 of the malarial parasite Plasmodium falciparum (PfENT1). PfENT1 inhibitors might serve as novel antimalarial drugs since PfENT1-mediated purine import is essential for parasite proliferation. To identify PfENT1 inhibitors, we screened 64 560 compounds and identified 171 by their ability to rescue the growth of PfENT1-expressing fui1Δ yeast in the presence of a cytotoxic PfENT1 substrate, 5-fluorouridine (5-FUrd). In secondary assays, nine of the highest activity compounds inhibited PfENT1-dependent growth of a purine auxotrophic yeast strain with adenosine as the sole purine source (IC50 0.2-2 μM). These nine compounds completely blocked [(3)H]adenosine uptake into PfENT1-expressing yeast and erythrocyte-free trophozoite-stage parasites (IC50 5-50 nM), and inhibited chloroquine-sensitive and -resistant parasite proliferation (IC50 5-50 μM). Wild-type (WT) parasite IC50 values were up to 4-fold lower compared to PfENT1-knockout (pfent1Δ) parasites. pfent1Δ parasite killing showed a delayed-death phenotype not observed with WT. We infer that, in parasites, the compounds inhibit both PfENT1 and a secondary target with similar efficacy. The secondary target identity is unknown, but its existence may reduce the likelihood of parasites developing resistance to PfENT1 inhibitors. Our data support the hypothesis that blocking purine transport through PfENT1 may be a novel and compelling approach for antimalarial drug development.
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Affiliation(s)
- I. J. Frame
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Roman Deniskin
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Alison Rinderspacher
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Francine Katz
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Shi-Xian Deng
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Robyn D. Moir
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Sophie H. Adjalley
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Olivia Coburn-Flynn
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - David A. Fidock
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Ian M. Willis
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Donald W. Landry
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
| | - Myles H. Akabas
- Department of Physiology & Biophysics, ‡Department of Biochemistry, §Department of Neuroscience, and ∥Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Medicine and #Department of Microbiology & Immunology, Columbia University Medical Center, 630 and 701 West 168th Street, New York, New York 10032, United States
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9
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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
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