1
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Awalt JK, Su W, Nguyen W, Loi K, Jarman KE, Penington JS, Ramesh S, Fairhurst KJ, Yeo T, Park H, Uhlemann AC, Chandra Maity B, De N, Mukherjee P, Chakraborty A, Churchyard A, Famodimu MT, Delves MJ, Baum J, Mittal N, Winzeler EA, Papenfuss AT, Chowdury M, de Koning-Ward TF, Maier AG, van Dooren GG, Baud D, Brand S, Fidock DA, Jackson PF, Cowman AF, Dans MG, Sleebs BE. Exploration and characterization of the antimalarial activity of cyclopropyl carboxamides that target the mitochondrial protein, cytochrome b. Eur J Med Chem 2024; 280:116921. [PMID: 39388903 DOI: 10.1016/j.ejmech.2024.116921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 09/25/2024] [Accepted: 09/26/2024] [Indexed: 10/12/2024]
Abstract
Drug resistance against antimalarials is rendering them increasingly ineffective and so there is a need for the development of new antimalarials. To discover new antimalarial chemotypes a phenotypic screen of the Janssen Jumpstarter library against the P. falciparum asexual stage was undertaken, uncovering the cyclopropyl carboxamide structural hit class. Structure-activity analysis revealed that each structural moiety was largely resistant to change, although small changes led to the frontrunner compound, WJM280, which has potent asexual stage activity (EC50 40 nM) and no human cell cytotoxicity. Forward genetics uncovered that cyclopropyl carboxamide resistant parasites have mutations and an amplification in the cytochrome b gene. Cytochrome b was then verified as the target with profiling against cytochrome b drug-resistant parasites and a mitochondrial oxygen consumption assay. Accordingly, the cyclopropyl carboxamide class was shown to have slow-acting asexual stage activity and activity against male gametes and exoerythrocytic forms. Enhancing metabolic stability to attain efficacy in malaria mouse models remains a challenge in the future development of this antimalarial chemotype.
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Affiliation(s)
- Jon Kyle Awalt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Wenyin Su
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Katie Loi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia
| | - Kate E Jarman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Jocelyn S Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Saishyam Ramesh
- Research School of Biology, The Australian National University, Canberra, 2600, Australia
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Nirupam De
- TCG Lifesciences, Kolkata, West Bengal, 700091, India
| | | | | | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, South Kensington, SW7 2AZ, UK
| | - Mufuliat T Famodimu
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Michael J Delves
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South Kensington, SW7 2AZ, UK; School of Biomedical Sciences, University of New South Wales, Sydney, 2031, Australia
| | - Nimisha Mittal
- School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth A Winzeler
- School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anthony T Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Mrittika Chowdury
- School of Medicine, Deakin University, Waurn Ponds, Victoria, 3216, Australia; Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, 3216, Australia
| | - Tania F de Koning-Ward
- School of Medicine, Deakin University, Waurn Ponds, Victoria, 3216, Australia; Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, 3216, Australia
| | - Alexander G Maier
- Research School of Biology, The Australian National University, Canberra, 2600, Australia
| | - Giel G van Dooren
- Research School of Biology, The Australian National University, Canberra, 2600, Australia
| | - Delphine Baud
- Medicines for Malaria Venture, Geneva, 1215, Switzerland
| | - Stephen Brand
- Medicines for Malaria Venture, Geneva, 1215, Switzerland
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul F Jackson
- Global Public Health, Janssen R&D LLC, La Jolla, 92121, USA
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Madeline G Dans
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia.
| | - Brad E Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia.
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2
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Braillard S, Keenan M, Breese KJ, Heppell J, Abbott M, Islam R, Shackleford DM, Katneni K, Crighton E, Chen G, Patil R, Lee G, White KL, Carvalho S, Wall RJ, Chemi G, Zuccotto F, González S, Marco M, Deakyne J, Standing D, Brunori G, Lyon JJ, Castañeda Casado P, Camino I, Martinez MSM, Zulfiqar B, Avery VM, Feijens PB, Van Pelt N, Matheeussen A, Hendrickx S, Maes L, Caljon G, Yardley V, Wyllie S, Charman SA, Chatelain E. DNDI-6174 is a preclinical candidate for visceral leishmaniasis that targets the cytochrome bc 1. Sci Transl Med 2023; 15:eadh9902. [PMID: 38091406 PMCID: PMC7615677 DOI: 10.1126/scitranslmed.adh9902] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/12/2023] [Indexed: 12/18/2023]
Abstract
New drugs for visceral leishmaniasis that are safe, low cost, and adapted to the field are urgently required. Despite concerted efforts over the last several years, the number of new chemical entities that are suitable for clinical development for the treatment of Leishmania remains low. Here, we describe the discovery and preclinical development of DNDI-6174, an inhibitor of Leishmania cytochrome bc1 complex activity that originated from a phenotypically identified pyrrolopyrimidine series. This compound fulfills all target candidate profile criteria required for progression into preclinical development. In addition to good metabolic stability and pharmacokinetic properties, DNDI-6174 demonstrates potent in vitro activity against a variety of Leishmania species and can reduce parasite burden in animal models of infection, with the potential to approach sterile cure. No major flags were identified in preliminary safety studies, including an exploratory 14-day toxicology study in the rat. DNDI-6174 is a cytochrome bc1 complex inhibitor with acceptable development properties to enter preclinical development for visceral leishmaniasis.
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Affiliation(s)
- Stéphanie Braillard
- Drugs for Neglected Diseases initiative (DNDi), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | | | | | - Jacob Heppell
- Epichem Pty Ltd, Perth, Western Australia, Australia
| | | | - Rafiqul Islam
- Epichem Pty Ltd, Perth, Western Australia, Australia
| | - David M. Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Rahul Patil
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Given Lee
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Karen L. White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Sandra Carvalho
- Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Richard J. Wall
- Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Giulia Chemi
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Fabio Zuccotto
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Silvia González
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | - Maria Marco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | | | | | - Gino Brunori
- Global Investigative Safety, GSK, Ware, United Kingdom
| | | | | | | | | | - Bilal Zulfiqar
- Discovery Biology, Griffith University, Nathan, Queensland, Australia 4111
| | - Vicky M. Avery
- Discovery Biology, Griffith University, Nathan, Queensland, Australia 4111
| | - Pim-Bart Feijens
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Natascha Van Pelt
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - An Matheeussen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Vanessa Yardley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Eric Chatelain
- Drugs for Neglected Diseases initiative (DNDi), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
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3
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Mandt REK, Luth MR, Tye MA, Mazitschek R, Ottilie S, Winzeler EA, Lafuente-Monasterio MJ, Gamo FJ, Wirth DF, Lukens AK. Diverse evolutionary pathways challenge the use of collateral sensitivity as a strategy to suppress resistance. eLife 2023; 12:e85023. [PMID: 37737220 PMCID: PMC10695565 DOI: 10.7554/elife.85023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/21/2023] [Indexed: 09/23/2023] Open
Abstract
Drug resistance remains a major obstacle to malaria control and eradication efforts, necessitating the development of novel therapeutic strategies to treat this disease. Drug combinations based on collateral sensitivity, wherein resistance to one drug causes increased sensitivity to the partner drug, have been proposed as an evolutionary strategy to suppress the emergence of resistance in pathogen populations. In this study, we explore collateral sensitivity between compounds targeting the Plasmodium dihydroorotate dehydrogenase (DHODH). We profiled the cross-resistance and collateral sensitivity phenotypes of several DHODH mutant lines to a diverse panel of DHODH inhibitors. We focus on one compound, TCMDC-125334, which was active against all mutant lines tested, including the DHODH C276Y line, which arose in selections with the clinical candidate DSM265. In six selections with TCMDC-125334, the most common mechanism of resistance to this compound was copy number variation of the dhodh locus, although we did identify one mutation, DHODH I263S, which conferred resistance to TCMDC-125334 but not DSM265. We found that selection of the DHODH C276Y mutant with TCMDC-125334 yielded additional genetic changes in the dhodh locus. These double mutant parasites exhibited decreased sensitivity to TCMDC-125334 and were highly resistant to DSM265. Finally, we tested whether collateral sensitivity could be exploited to suppress the emergence of resistance in the context of combination treatment by exposing wildtype parasites to both DSM265 and TCMDC-125334 simultaneously. This selected for parasites with a DHODH V532A mutation which were cross-resistant to both compounds and were as fit as the wildtype parent in vitro. The emergence of these cross-resistant, evolutionarily fit parasites highlights the mutational flexibility of the DHODH enzyme.
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Affiliation(s)
- Rebecca EK Mandt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Madeline R Luth
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Mark A Tye
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
- Harvard Graduate School of Arts and SciencesCambridgeUnited States
| | - Ralph Mazitschek
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
| | - Sabine Ottilie
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Elizabeth A Winzeler
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Skaggs School of Pharmaceutical Sciences, University of California, San DiegoLa JollaUnited States
| | | | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKlineMadridSpain
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
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4
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Hayward JA, Makota FV, Cihalova D, Leonard RA, Rajendran E, Zwahlen SM, Shuttleworth L, Wiedemann U, Spry C, Saliba KJ, Maier AG, van Dooren GG. A screen of drug-like molecules identifies chemically diverse electron transport chain inhibitors in apicomplexan parasites. PLoS Pathog 2023; 19:e1011517. [PMID: 37471441 PMCID: PMC10403144 DOI: 10.1371/journal.ppat.1011517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/04/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Apicomplexans are widespread parasites of humans and other animals, and include the causative agents of malaria (Plasmodium species) and toxoplasmosis (Toxoplasma gondii). Existing anti-apicomplexan therapies are beset with issues around drug resistance and toxicity, and new treatment options are needed. The mitochondrial electron transport chain (ETC) is one of the few processes that has been validated as a drug target in apicomplexans. To identify new inhibitors of the apicomplexan ETC, we developed a Seahorse XFe96 flux analyzer approach to screen the 400 compounds contained within the Medicines for Malaria Venture 'Pathogen Box' for ETC inhibition. We identified six chemically diverse, on-target inhibitors of the ETC in T. gondii, at least four of which also target the ETC of Plasmodium falciparum. Two of the identified compounds (MMV024937 and MMV688853) represent novel ETC inhibitor chemotypes. MMV688853 belongs to a compound class, the aminopyrazole carboxamides, that were shown previously to target a kinase with a key role in parasite invasion of host cells. Our data therefore reveal that MMV688853 has dual targets in apicomplexans. We further developed our approach to pinpoint the molecular targets of these inhibitors, demonstrating that all target Complex III of the ETC, with MMV688853 targeting the ubiquinone reduction (Qi) site of the complex. Most of the compounds we identified remain effective inhibitors of parasites that are resistant to Complex III inhibitors that are in clinical use or development, indicating that they could be used in treating drug resistant parasites. In sum, we have developed a versatile, scalable approach to screen for compounds that target the ETC in apicomplexan parasites, and used this to identify and characterize novel inhibitors.
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Affiliation(s)
- Jenni A. Hayward
- Research School of Biology, Australian National University, Canberra, Australia
| | - F. Victor Makota
- Research School of Biology, Australian National University, Canberra, Australia
| | - Daniela Cihalova
- Research School of Biology, Australian National University, Canberra, Australia
| | - Rachel A. Leonard
- Research School of Biology, Australian National University, Canberra, Australia
| | - Esther Rajendran
- Research School of Biology, Australian National University, Canberra, Australia
| | - Soraya M. Zwahlen
- Research School of Biology, Australian National University, Canberra, Australia
| | - Laura Shuttleworth
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ursula Wiedemann
- Research School of Biology, Australian National University, Canberra, Australia
| | - Christina Spry
- Research School of Biology, Australian National University, Canberra, Australia
| | - Kevin J. Saliba
- Research School of Biology, Australian National University, Canberra, Australia
| | - Alexander G. Maier
- Research School of Biology, Australian National University, Canberra, Australia
| | - Giel G. van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
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5
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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] [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.
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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.
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6
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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: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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.
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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
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7
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Chemoprotective antimalarials identified through quantitative high-throughput screening of Plasmodium blood and liver stage parasites. Sci Rep 2021; 11:2121. [PMID: 33483532 PMCID: PMC7822874 DOI: 10.1038/s41598-021-81486-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
The spread of Plasmodium falciparum parasites resistant to most first-line antimalarials creates an imperative to enrich the drug discovery pipeline, preferably with curative compounds that can also act prophylactically. We report a phenotypic quantitative high-throughput screen (qHTS), based on concentration–response curves, which was designed to identify compounds active against Plasmodium liver and asexual blood stage parasites. Our qHTS screened over 450,000 compounds, tested across a range of 5 to 11 concentrations, for activity against Plasmodium falciparum asexual blood stages. Active compounds were then filtered for unique structures and drug-like properties and subsequently screened in a P. berghei liver stage assay to identify novel dual-active antiplasmodial chemotypes. Hits from thiadiazine and pyrimidine azepine chemotypes were subsequently prioritized for resistance selection studies, yielding distinct mutations in P. falciparum cytochrome b, a validated antimalarial drug target. The thiadiazine chemotype was subjected to an initial medicinal chemistry campaign, yielding a metabolically stable analog with sub-micromolar potency. Our qHTS methodology and resulting dataset provides a large-scale resource to investigate Plasmodium liver and asexual blood stage parasite biology and inform further research to develop novel chemotypes as causal prophylactic antimalarials.
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8
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Bahuguna A, Rawat S, Rawat DS. QcrB in Mycobacterium tuberculosis: The new drug target of antitubercular agents. Med Res Rev 2021; 41:2565-2581. [PMID: 33400275 DOI: 10.1002/med.21779] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/23/2020] [Accepted: 12/12/2020] [Indexed: 11/08/2022]
Abstract
Drug-resistance in mycobacterial infections is a major global health problem that leads to high mortality and socioeconomic pressure in developing countries around the world. From finding new targets to discovering novel chemical scaffolds, there is an urgent need for the development of better approaches for the cure of tuberculosis. Recently, energy metabolism in mycobacteria, particularly the oxidative phosphorylation pathway of cellular respiration, has emerged as a novel target pathway in drug discovery. New classes of antibacterials which target oxidative phosphorylation pathway either by interacting with a protein or any step in the pathway of oxidative phosphorylation can combat dormant mycobacterial infections leading to shortening of tuberculosis chemotherapy. Adenosine triphosphate synthase is one such recently discovered target of the newly approved antitubercular drug bedaquiline. Cytochrome bcc is another new target of the antitubercular drug candidate Q203, currently in phase II clinical trial. Research suggests that b subunit of cytochrome bcc, QcrB, is the target of Q203. The review article describes the structure, function, and importance of targeting QcrB throwing light on all chemical classes of QcrB inhibitors discovered to date. An understanding of the structure and function of validated targets and their inhibitors would enable the development of new chemical entities.
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Affiliation(s)
| | - Srishti Rawat
- Department of Chemistry, University of Delhi, Delhi, India
| | - Diwan S Rawat
- Department of Chemistry, University of Delhi, Delhi, India
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9
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Wall RJ, Carvalho S, Milne R, Bueren-Calabuig JA, Moniz S, Cantizani-Perez J, MacLean L, Kessler A, Cotillo I, Sastry L, Manthri S, Patterson S, Zuccotto F, Thompson S, Martin J, Marco M, Miles TJ, De Rycker M, Thomas MG, Fairlamb AH, Gilbert IH, Wyllie S. The Q i Site of Cytochrome b is a Promiscuous Drug Target in Trypanosoma cruzi and Leishmania donovani. ACS Infect Dis 2020; 6:515-528. [PMID: 31967783 PMCID: PMC7076694 DOI: 10.1021/acsinfecdis.9b00426] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Indexed: 01/29/2023]
Abstract
Available treatments for Chagas' disease and visceral leishmaniasis are inadequate, and there is a pressing need for new therapeutics. Drug discovery efforts for both diseases principally rely upon phenotypic screening. However, the optimization of phenotypically active compounds is hindered by a lack of information regarding their molecular target(s). To combat this issue we initiate target deconvolution studies at an early stage. Here, we describe comprehensive genetic and biochemical studies to determine the targets of three unrelated phenotypically active compounds. All three structurally diverse compounds target the Qi active-site of cytochrome b, part of the cytochrome bc1 complex of the electron transport chain. Our studies go on to identify the Qi site as a promiscuous drug target in Leishmania donovani and Trypanosoma cruzi with a propensity to rapidly mutate. Strategies to rapidly identify compounds acting via this mechanism are discussed to ensure that drug discovery portfolios are not overwhelmed with inhibitors of a single target.
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Affiliation(s)
- Richard J. Wall
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Sandra Carvalho
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Rachel Milne
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Juan A. Bueren-Calabuig
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Sonia Moniz
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | | | - Lorna MacLean
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Albane Kessler
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Ignacio Cotillo
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Lalitha Sastry
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Sujatha Manthri
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Stephen Patterson
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Fabio Zuccotto
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Stephen Thompson
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Julio Martin
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Maria Marco
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | | | - Manu De Rycker
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Michael G. Thomas
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Alan H. Fairlamb
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Ian H. Gilbert
- Drug Discovery Unit,
Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Susan Wyllie
- Division of Biological
Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
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10
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Antonova-Koch Y, Meister S, Abraham M, Luth MR, Ottilie S, Lukens AK, Sakata-Kato T, Vanaerschot M, Owen E, Jado JC, Maher SP, Calla J, Plouffe D, Zhong Y, Chen K, Chaumeau V, Conway AJ, McNamara CW, Ibanez M, Gagaring K, Serrano FN, Eribez K, Taggard CM, Cheung AL, Lincoln C, Ambachew B, Rouillier M, Siegel D, Nosten F, Kyle DE, Gamo FJ, Zhou Y, Llinás M, Fidock DA, Wirth DF, Burrows J, Campo B, Winzeler EA. Open-source discovery of chemical leads for next-generation chemoprotective antimalarials. Science 2019; 362:362/6419/eaat9446. [PMID: 30523084 PMCID: PMC6516198 DOI: 10.1126/science.aat9446] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/18/2018] [Indexed: 11/19/2022]
Abstract
To discover leads for next-generation chemoprotective antimalarial drugs,we tested more than 500,000 compounds for their ability to inhibit liver-stage development of luciferase-expressing Plasmodium spp. parasites (681 compounds showed a half-maximal inhibitory concentration of less than 1micromolar).Cluster analysis identified potent and previously unreported scaffold families as well as other series previously associated with chemoprophylaxis. Further testing through multiple phenotypic assays that predict stage-specific and multispecies antimalarial activity distinguished compound classes that are likely to provide symptomatic relief by reducing asexual blood-stage parasitemia from those which are likely to only prevent malaria. Target identification by using functional assays, in vitro evolution, or metabolic profiling revealed 58 mitochondrial inhibitors but also many chemotypes possibly with previously unidentified mechanisms of action.
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Affiliation(s)
- Yevgeniya Antonova-Koch
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Stephan Meister
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Matthew Abraham
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Madeline R Luth
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Sabine Ottilie
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Amanda K Lukens
- Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.,The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Manu Vanaerschot
- Division of Infectious Diseases, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Edward Owen
- Department of Biochemistry and Molecular Biology and Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Juan Carlos Jado
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Steven P Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.,Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Jaeson Calla
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - David Plouffe
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Yang Zhong
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Kaisheng Chen
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Victor Chaumeau
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amy J Conway
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.,Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Case W McNamara
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Maureen Ibanez
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Kerstin Gagaring
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Fernando Neria Serrano
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Korina Eribez
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Cullin McLean Taggard
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Andrea L Cheung
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Christie Lincoln
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Biniam Ambachew
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Melanie Rouillier
- 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, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, CA 92093, USA
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.,Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Francisco-Javier Gamo
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Yingyao Zhou
- The 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 and Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA.,Department of Chemistry and Center for Infectious Diseases Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - David A Fidock
- Division of Infectious Diseases, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Dyann F Wirth
- Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.,The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Elizabeth A Winzeler
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, CA 92093, USA
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11
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Ross LS, Lafuente-Monasterio MJ, Sakata-Kato T, Mandt REK, Gamo FJ, Wirth DF, Lukens AK. Identification of Collateral Sensitivity to Dihydroorotate Dehydrogenase Inhibitors in Plasmodium falciparum. ACS Infect Dis 2018; 4:508-515. [PMID: 29336544 PMCID: PMC5899019 DOI: 10.1021/acsinfecdis.7b00217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Drug
resistance has been reported for every antimalarial in use highlighting
the need for new strategies to protect the efficacy of therapeutics
in development. We have previously shown that resistance can be suppressed
with a population biology trap: by identifying situations where resistance
to one compound confers hypersensitivity to another (collateral sensitivity),
we can design combination therapies that not only kill the parasite
but also guide its evolution away from resistance. We applied this
concept to the Plasmodium falciparum dihydroorotate
dehydrogenase (PfDHODH) enzyme, a well validated
antimalarial target with inhibitors in the development pipeline. Here,
we report a high-throughput screen to identify compounds specifically
active against PfDHODH resistant mutants. We additionally
perform extensive cross-resistance profiling allowing us to identify
compound pairs demonstrating the potential for mutually incompatible
resistance. These combinations represent promising starting points
for exploiting collateral sensitivity to extend the useful lifespan
of new antimalarial therapeutics.
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Affiliation(s)
- Leila Saxby Ross
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Maria José Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Rebecca E. K. Mandt
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
- Infectious Disease and Microbiome Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
- Infectious Disease and Microbiome Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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12
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Luth MR, Gupta P, Ottilie S, Winzeler EA. Using in Vitro Evolution and Whole Genome Analysis To Discover Next Generation Targets for Antimalarial Drug Discovery. ACS Infect Dis 2018; 4:301-314. [PMID: 29451780 PMCID: PMC5848146 DOI: 10.1021/acsinfecdis.7b00276] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Although
many new anti-infectives have been discovered and developed solely
using phenotypic cellular screening and assay optimization, most researchers
recognize that structure-guided drug design is more practical and
less costly. In addition, a greater chemical space can be interrogated
with structure-guided drug design. The practicality of structure-guided
drug design has launched a search for the targets of compounds discovered
in phenotypic screens. One method that has been used extensively in
malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA).
Here, small molecules from phenotypic screens with demonstrated antiparasitic
activity are used in genome-based target discovery methods. In this
Review, we discuss the newest, most promising druggable targets discovered
or further validated by evolution-based methods, as well as some exceptions.
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Affiliation(s)
- Madeline R. Luth
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Purva Gupta
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Sabine Ottilie
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Elizabeth A. Winzeler
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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13
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Bown L, Srivastava SK, Piercey BM, McIsaac CK, Tahlan K. Mycobacterial Membrane Proteins QcrB and AtpE: Roles in Energetics, Antibiotic Targets, and Associated Mechanisms of Resistance. J Membr Biol 2017; 251:105-117. [DOI: 10.1007/s00232-017-9997-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/20/2017] [Indexed: 02/08/2023]
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14
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Gomes AR, Ravenhall M, Benavente ED, Talman A, Sutherland C, Roper C, Clark TG, Campino S. Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017; 7:174-180. [PMID: 28376349 PMCID: PMC5379905 DOI: 10.1016/j.ijpddr.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 11/19/2022]
Abstract
Drug resistance is a recurrent problem in the fight against malaria. Genetic and epidemiological surveillance of antimalarial resistant parasite alleles is crucial to guide drug therapies and clinical management. New antimalarial compounds are currently at various stages of clinical trials and regulatory evaluation. Using ∼2000 Plasmodium falciparum genome sequences, we investigated the genetic diversity of eleven gene-targets of promising antimalarial compounds and assessed their potential efficiency across malaria endemic regions. We determined if the loci are under selection prior to the introduction of new drugs and established a baseline of genetic variance, including potential resistant alleles, for future surveillance programmes. Genetic diversity of 11gene-targets of new antimalarial compounds was investigated. Genetic data was analysed for 18 malaria endemic countries. No signals of selective pressure was observed. A mutation linked to resistance to a new antimalarial was found in African parasites. Amino-acid changes close to reported antimalarial resistant mutations were detected.
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Affiliation(s)
- Ana Rita Gomes
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Matt Ravenhall
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Arthur Talman
- Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Colin Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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15
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Sakata-Kato T, Wirth DF. A Novel Methodology for Bioenergetic Analysis of Plasmodium falciparum Reveals a Glucose-Regulated Metabolic Shift and Enables Mode of Action Analyses of Mitochondrial Inhibitors. ACS Infect Dis 2016; 2:903-916. [PMID: 27718558 DOI: 10.1021/acsinfecdis.6b00101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Given that resistance to all drugs in clinical use has arisen, discovery of new antimalarial drug targets is eagerly anticipated. The Plasmodium mitochondrion has been considered a promising drug target largely based on its significant divergence from the host organelle as well as its involvement in ATP production and pyrimidine biosynthesis. However, the functions of Plasmodium mitochondrial protein complexes and associated metabolic pathways are not fully characterized. Here, we report the development of novel and robust bioenergetic assay protocols for Plasmodium falciparum asexual parasites utilizing a Seahorse Bioscience XFe24 Extracellular Flux Analyzer. These protocols allowed us to simultaneously assess the direct effects of metabolites and inhibitors on mitochondrial respiration and glycolytic activity in real-time with the readout of oxygen consumption rate and extracellular acidification rate. Using saponin-freed parasites at the schizont stage, we found that succinate, malate, glycerol-3-phosphate, and glutamate, but not pyruvate, were able to increase the oxygen consumption rate and that glycerol-3-phosphate dehydrogenase had the largest potential as an electron donor among tested mitochondrial dehydrogenases. Furthermore, we revealed the presence of a glucose-regulated metabolic shift between oxidative phosphorylation and glycolysis. We measured proton leak and reserve capacity and found bioenergetic evidence for oxidative phosphorylation in erythrocytic stage parasites but at a level much lower than that observed in mammalian cells. Lastly, we developed an assay platform for target identification and mode of action studies of mitochondria-targeting antimalarials. This study provides new insights into the bioenergetics and metabolomics of the Plasmodium mitochondria.
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Affiliation(s)
- Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
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16
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Magistrado PA, Corey VC, Lukens AK, LaMonte G, Sasaki E, Meister S, Wree M, Winzeler E, Wirth DF. Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL), a Resistance Mechanism for Two Distinct Compound Classes. ACS Infect Dis 2016; 2:816-826. [PMID: 27933786 PMCID: PMC5109296 DOI: 10.1021/acsinfecdis.6b00025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
MMV007564
is a novel antimalarial benzimidazolyl piperidine chemotype
identified in cellular screens. To identify the genetic determinant
of MMV007564 resistance, parasites were cultured in the presence of
the compound to generate resistant lines. Whole genome sequencing
revealed distinct mutations in the gene named Plasmodium
falciparum cyclic amine resistance locus (pfcarl), encoding a conserved protein of unknown function.
Mutations in pfcarl are strongly associated with
resistance to a structurally unrelated class of compounds, the imidazolopiperazines,
including KAF156, currently in clinical trials. Our data demonstrate
that pfcarl mutations confer resistance to two distinct
compound classes, benzimidazolyl piperidines and imidazolopiperazines.
However, MMV007564 and the imidazolopiperazines, KAF156 and GNF179,
have different timings of action in the asexual blood stage and different
potencies against the liver and sexual blood stages. These data suggest
that pfcarl is a multidrug-resistance gene rather
than a common target for benzimidazolyl piperidines and imidazolopiperazines.
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Affiliation(s)
- Pamela A. Magistrado
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Victoria C. Corey
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Amanda K. Lukens
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Infectious
Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Greg LaMonte
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Erika Sasaki
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Stephan Meister
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Melanie Wree
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Elizabeth Winzeler
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Dyann F. Wirth
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Infectious
Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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17
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Edwards RL, Odom John AR. Muddled mechanisms: recent progress towards antimalarial target identification. F1000Res 2016; 5:2514. [PMID: 27803804 PMCID: PMC5070598 DOI: 10.12688/f1000research.9477.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/06/2016] [Indexed: 01/06/2023] Open
Abstract
In the past decade, malaria rates have plummeted as a result of aggressive infection control measures and the adoption of artemisinin-based combination therapies (ACTs). However, a potential crisis looms ahead. Treatment failures to standard antimalarial regimens have been reported in Southeast Asia, and devastating consequences are expected if resistance spreads to the African continent. To prevent a potential public health emergency, the antimalarial arsenal must contain therapeutics with novel mechanisms of action (MOA). An impressive number of high-throughput screening (HTS) campaigns have since been launched, identifying thousands of compounds with activity against one of the causative agents of malaria,
Plasmodium falciparum. Now begins the difficult task of target identification, for which studies are often tedious, labor intensive, and difficult to interpret. In this review, we highlight approaches that have been instrumental in tackling the challenges of target assignment and elucidation of the MOA for hit compounds. Studies that apply these innovative techniques to antimalarial target identification are described, as well as the impact of the data in the field.
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Affiliation(s)
- Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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18
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Carrasco MP, Machado M, Gonçalves L, Sharma M, Gut J, Lukens AK, Wirth DF, André V, Duarte MT, Guedes RC, Dos Santos DJVA, Rosenthal PJ, Mazitschek R, Prudêncio M, Moreira R. Probing the Azaaurone Scaffold against the Hepatic and Erythrocytic Stages of Malaria Parasites. ChemMedChem 2016; 11:2194-2204. [PMID: 27538856 DOI: 10.1002/cmdc.201600327] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 11/09/2022]
Abstract
The potential of azaaurones as dual-stage antimalarial agents was investigated by assessing the effect of a small library of azaaurones on the inhibition of liver and intraerythrocytic lifecycle stages of the malaria parasite. The whole series was screened against the blood stage of a chloroquine-resistant Plasmodium falciparum strain and the liver stage of P. berghei, yielding compounds with dual-stage activity and sub-micromolar potency against erythrocytic parasites. Studies with genetically modified parasites, using a phenotypic assay based on the P. falciparum Dd2-ScDHODH line, which expresses yeast dihydroorotate dehydrogenase (DHODH), showed that one of the azaaurone derivatives has the potential to inhibit the parasite mitochondrial electron-transport chain. The global urgency in finding new therapies for malaria, especially against the underexplored liver stage, associated with chemical tractability of azaaurones, warrants further development of this chemotype. Overall, these results emphasize the azaaurone chemotype as a promising scaffold for dual-stage antimalarials.
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Affiliation(s)
- Marta P Carrasco
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal. .,Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Göteborg, Sweden.
| | - Marta Machado
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Lídia Gonçalves
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Moni Sharma
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California San Francisco, 1001 Potrero Avenue, San Francisco, CA, 94110, USA
| | - Amanda K Lukens
- The Broad Institute, Infectious Diseases Program, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Dyann F Wirth
- The Broad Institute, Infectious Diseases Program, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Vânia André
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Maria Teresa Duarte
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Rita C Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Daniel J V A Dos Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.,LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal
| | - Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California San Francisco, 1001 Potrero Avenue, San Francisco, CA, 94110, USA
| | - Ralph Mazitschek
- The Broad Institute, Infectious Diseases Program, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Miguel Prudêncio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
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19
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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: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [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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20
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Skinner-Adams TS, Sumanadasa SD, Fisher GM, Davis RA, Doolan DL, Andrews KT. Defining the targets of antiparasitic compounds. Drug Discov Today 2016; 21:725-39. [DOI: 10.1016/j.drudis.2016.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/04/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
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21
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Goodman CD, Siregar JE, Mollard V, Vega-Rodríguez J, Syafruddin D, Matsuoka H, Matsuzaki M, Toyama T, Sturm A, Cozijnsen A, Jacobs-Lorena M, Kita K, Marzuki S, McFadden GI. Parasites resistant to the antimalarial atovaquone fail to transmit by mosquitoes. Science 2016; 352:349-53. [PMID: 27081071 DOI: 10.1126/science.aad9279] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022]
Abstract
Drug resistance compromises control of malaria. Here, we show that resistance to a commonly used antimalarial medication, atovaquone, is apparently unable to spread. Atovaquone pressure selects parasites with mutations in cytochrome b, a respiratory protein with low but essential activity in the mammalian blood phase of the parasite life cycle. Resistance mutations rescue parasites from the drug but later prove lethal in the mosquito phase, where parasites require full respiration. Unable to respire efficiently, resistant parasites fail to complete mosquito development, arresting their life cycle. Because cytochrome b is encoded by the maternally inherited parasite mitochondrion, even outcrossing with wild-type strains cannot facilitate spread of resistance. Lack of transmission suggests that resistance will be unable to spread in the field, greatly enhancing the utility of atovaquone in malaria control.
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Affiliation(s)
| | - Josephine E Siregar
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia. Eijkman Institute for Molecular Biology, JI Diponegoro no. 69, Jakarta, 10430, Indonesia. Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Vanessa Mollard
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Joel Vega-Rodríguez
- Johns Hopkins University Bloomberg School of Public Health, Department of Molecular Microbiology and Immunology, Malaria Research Institute, Baltimore, MD 21205, USA
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, JI Diponegoro no. 69, Jakarta, 10430, Indonesia. Department of Parasitology, Faculty of Medicine, Hasanuddin University, Jalan Perintis Kemerdekaan Km10, Makassar 90245, Indonesia
| | - Hiroyuki Matsuoka
- Division of Medical Zoology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoko Toyama
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Angelika Sturm
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anton Cozijnsen
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marcelo Jacobs-Lorena
- Johns Hopkins University Bloomberg School of Public Health, Department of Molecular Microbiology and Immunology, Malaria Research Institute, Baltimore, MD 21205, USA
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
| | - Sangkot Marzuki
- Eijkman Institute for Molecular Biology, JI Diponegoro no. 69, Jakarta, 10430, Indonesia
| | - Geoffrey I McFadden
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
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22
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Swann J, Corey V, Scherer CA, Kato N, Comer E, Maetani M, Antonova-Koch Y, Reimer C, Gagaring K, Ibanez M, Plouffe D, Zeeman AM, Kocken CHM, McNamara CW, Schreiber SL, Campo B, Winzeler EA, Meister S. High-Throughput Luciferase-Based Assay for the Discovery of Therapeutics That Prevent Malaria. ACS Infect Dis 2016; 2:281-293. [PMID: 27275010 PMCID: PMC4890880 DOI: 10.1021/acsinfecdis.5b00143] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Indexed: 11/29/2022]
Abstract
In order to identify the most attractive starting points for drugs that can be used to prevent malaria, a diverse chemical space comprising tens of thousands to millions of small molecules may need to be examined. Achieving this throughput necessitates the development of efficient ultra-high-throughput screening methods. Here, we report the development and evaluation of a luciferase-based phenotypic screen of malaria exoerythrocytic-stage parasites optimized for a 1536-well format. This assay uses the exoerythrocytic stage of the rodent malaria parasite, Plasmodium berghei, and a human hepatoma cell line. We use this assay to evaluate several biased and unbiased compound libraries, including two small sets of molecules (400 and 89 compounds, respectively) with known activity against malaria erythrocytic-stage parasites and a set of 9886 diversity-oriented synthesis (DOS)-derived compounds. Of the compounds screened, we obtain hit rates of 12-13 and 0.6% in preselected and naïve libraries, respectively, and identify 52 compounds with exoerythrocytic-stage activity less than 1 μM and having minimal host cell toxicity. Our data demonstrate the ability of this method to identify compounds known to have causal prophylactic activity in both human and animal models of malaria, as well as novel compounds, including some exclusively active against parasite exoerythrocytic stages.
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Affiliation(s)
- Justine Swann
- School of Medicine, Department of Pediatrics, Pharmacology & Drug Discovery, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Victoria Corey
- School of Medicine, Department of Pediatrics, Pharmacology & Drug Discovery, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Christina A. Scherer
- The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Nobutaka Kato
- The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Eamon Comer
- The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Micah Maetani
- The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Yevgeniya Antonova-Koch
- School of Medicine, Department of Pediatrics, Pharmacology & Drug Discovery, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Christin Reimer
- School of Medicine, Department of Pediatrics, Pharmacology & Drug Discovery, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Kerstin Gagaring
- Genomics Institute of the Novartis Research Foundation (GNF), 10675
John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Maureen Ibanez
- Genomics Institute of the Novartis Research Foundation (GNF), 10675
John Jay Hopkins Drive, San Diego, California 92121, United States
| | - David Plouffe
- Genomics Institute of the Novartis Research Foundation (GNF), 10675
John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Clemens H. M. Kocken
- Department of Parasitology, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Case W. McNamara
- The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Stuart L. Schreiber
- The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Brice Campo
- Medicines for Malaria Venture (MMV), Meyrin 2015, Switzerland
| | - Elizabeth A. Winzeler
- School of Medicine, Department of Pediatrics, Pharmacology & Drug Discovery, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Stephan Meister
- School of Medicine, Department of Pediatrics, Pharmacology & Drug Discovery, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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23
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Herman JD, Pepper LR, Cortese JF, Estiu G, Galinsky K, Zuzarte-Luis V, Derbyshire ER, Ribacke U, Lukens AK, Santos SA, Patel V, Clish CB, Sullivan WJ, Zhou H, Bopp SE, Schimmel P, Lindquist S, Clardy J, Mota MM, Keller TL, Whitman M, Wiest O, Wirth DF, Mazitschek R. The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs. Sci Transl Med 2016; 7:288ra77. [PMID: 25995223 DOI: 10.1126/scitranslmed.aaa3575] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug resistance selection, whole-genome sequencing, and an orthogonal yeast model, we demonstrate that the cytoplasmic prolyl-tRNA (transfer RNA) synthetase (PfcPRS) of the malaria parasite Plasmodium falciparum is a biochemical and functional target of febrifugine and its synthetic derivative halofuginone. Febrifugine is the active principle of a traditional Chinese herbal remedy for malaria. We show that treatment with febrifugine derivatives activated the amino acid starvation response in both P. falciparum and a transgenic yeast strain expressing PfcPRS. We further demonstrate in the Plasmodium berghei mouse model of malaria that halofuginol, a new halofuginone analog that we developed, is active against both liver and asexual blood stages of the malaria parasite. Halofuginol, unlike halofuginone and febrifugine, is well tolerated at efficacious doses and represents a promising lead for the development of dual-stage next-generation antimalarials.
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Affiliation(s)
- Jonathan D Herman
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Biological and Biomedical Sciences, Boston, MA 02115, USA. Harvard/Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Boston, MA 02115, USA. Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren R Pepper
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Joseph F Cortese
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA
| | - Guillermina Estiu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kevin Galinsky
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA
| | - Vanessa Zuzarte-Luis
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa,1649-028 Lisbon, Portugal
| | - Emily R Derbyshire
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ulf Ribacke
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amanda K Lukens
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sofia A Santos
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA. Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Professor Gama Pinto, Lisbon 1640-003, Portugal
| | - Vishal Patel
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Clary B Clish
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA
| | - William J Sullivan
- Departments of Pharmacology and Toxicology and Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Huihao Zhou
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Selina E Bopp
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Paul Schimmel
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. The Scripps Research Institute, Florida, Jupiter, FL 33458, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Jon Clardy
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa,1649-028 Lisbon, Portugal
| | - Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA. School of Chemical Biology and Biotechnology, Laboratory for Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Dyann F Wirth
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Ralph Mazitschek
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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Aneja B, Kumar B, Jairajpuri MA, Abid M. A structure guided drug-discovery approach towards identification of Plasmodium inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra19673f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article provides a comprehensive review of inhibitors from natural, semisynthetic or synthetic sources against key targets ofPlasmodium falciparum.
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Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Bhumika Kumar
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohammad Abid
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
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25
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Discovery of Dual-Stage Malaria Inhibitors with New Targets. Antimicrob Agents Chemother 2015; 60:1430-7. [PMID: 26666931 DOI: 10.1128/aac.02110-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/08/2015] [Indexed: 11/20/2022] Open
Abstract
Malaria remains a major global health problem, with more than half of the world population at risk of contracting the disease and nearly a million deaths each year. Here, we report the discovery of inhibitors that target multiple stages of malaria parasite growth. To identify these inhibitors, we took advantage of the Tres Cantos Antimalarial Compound Set (TCAMS) small-molecule library, which is comprised of diverse and potent chemical scaffolds with activities against the blood stage of the malaria parasite, and investigated their effects against the elusive liver stage of the malaria parasite using a forward chemical screen. From a screen of nearly 14,000 compounds, we identified and confirmed 103 compounds as dual-stage malaria inhibitors. Interestingly, these compounds show preferential inhibition of parasite growth in liver- versus blood-stage malaria parasite assays, highlighting the drug susceptibility of this parasite form. Mode-of-action studies were completed using genetically modified and drug-resistant Plasmodium parasite strains. While we identified some compound targets as classical antimalarial pathways, such as the mitochondrial electron transport chain through cytochrome bc1 complex inhibition or the folate biosynthesis pathway, most compounds induced parasite death through as yet unknown mechanisms of action. Importantly, the identification of new chemotypes with different modes of action in killing Plasmodium parasites represents a promising opportunity for probing essential and novel molecular processes that remain to be discovered. The chemical scaffolds identified with activity against drug-resistant Plasmodium parasites represent starting points for dual-stage antimalarial development to surmount the threat of malaria parasite drug resistance.
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Herman JD, Rice DP, Ribacke U, Silterra J, Deik AA, Moss EL, Broadbent KM, Neafsey DE, Desai MM, Clish CB, Mazitschek R, Wirth DF. A genomic and evolutionary approach reveals non-genetic drug resistance in malaria. Genome Biol 2015; 15:511. [PMID: 25395010 DOI: 10.1186/preaccept-1067113631444973] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS We previously described two mutations in the cytoplasmic prolyl-tRNA synthetase (cPRS) gene that confer resistance to halofuginone. We describe here the evolutionary trajectory of halofuginone resistance of two independent drug resistance selections in Plasmodium falciparum. Using this novel methodology, we discover an unexpected non-genetic drug resistance mechanism that P. falciparum utilizes before genetic modification of the cPRS. P. falciparum first upregulates its proline amino acid homeostasis in response to halofuginone pressure. We show that this non-genetic adaptation to halofuginone is not likely mediated by differential RNA expression and precedes mutation or amplification of the cPRS gene. By tracking the evolution of the two drug resistance selections with whole genome sequencing, we further demonstrate that the cPRS locus accounts for the majority of genetic adaptation to halofuginone in P. falciparum. We further validate that copy-number variations at the cPRS locus also contribute to halofuginone resistance. CONCLUSIONS We provide a three-step model for multi-locus evolution of halofuginone drug resistance in P. falciparum. Informed by genomic approaches, our results provide the first comprehensive view of the evolutionary trajectory malaria parasites take to achieve drug resistance. Our understanding of the multiple genetic and non-genetic mechanisms of drug resistance informs how we will design and pair future anti-malarials for clinical use.
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Herman JD, Rice DP, Ribacke U, Silterra J, Deik AA, Moss EL, Broadbent KM, Neafsey DE, Desai MM, Clish CB, Mazitschek R, Wirth DF. A genomic and evolutionary approach reveals non-genetic drug resistance in malaria. Genome Biol 2015. [PMID: 25395010 PMCID: PMC4272547 DOI: 10.1186/s13059-014-0511-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. Results We previously described two mutations in the cytoplasmic prolyl-tRNA synthetase (cPRS) gene that confer resistance to halofuginone. We describe here the evolutionary trajectory of halofuginone resistance of two independent drug resistance selections in Plasmodium falciparum. Using this novel methodology, we discover an unexpected non-genetic drug resistance mechanism that P. falciparum utilizes before genetic modification of the cPRS. P. falciparum first upregulates its proline amino acid homeostasis in response to halofuginone pressure. We show that this non-genetic adaptation to halofuginone is not likely mediated by differential RNA expression and precedes mutation or amplification of the cPRS gene. By tracking the evolution of the two drug resistance selections with whole genome sequencing, we further demonstrate that the cPRS locus accounts for the majority of genetic adaptation to halofuginone in P. falciparum. We further validate that copy-number variations at the cPRS locus also contribute to halofuginone resistance. Conclusions We provide a three-step model for multi-locus evolution of halofuginone drug resistance in P. falciparum. Informed by genomic approaches, our results provide the first comprehensive view of the evolutionary trajectory malaria parasites take to achieve drug resistance. Our understanding of the multiple genetic and non-genetic mechanisms of drug resistance informs how we will design and pair future anti-malarials for clinical use. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0511-2) contains supplementary material, which is available to authorized users.
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28
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Saccharomyces cerevisiae-based mutational analysis of the bc1 complex Qo site residue 279 to study the trade-off between atovaquone resistance and function. Antimicrob Agents Chemother 2015; 59:4053-8. [PMID: 25918152 DOI: 10.1128/aac.00710-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/19/2015] [Indexed: 11/20/2022] Open
Abstract
The bc1 complex is central to mitochondrial bioenergetics and the target of the antimalarial drug atovaquone that binds in the quinol oxidation (Qo) site of the complex. Structural analysis has shown that the Qo site residue Y279 (Y268 in Plasmodium falciparum) is key for atovaquone binding. Consequently, atovaquone resistance can be acquired by mutation of that residue. In addition to the probability of amino acid substitution, the level of atovaquone resistance and the loss of bc1 complex activity that are associated with the novel amino acid would restrict the nature of resistance-driven mutations occurring on atovaquone exposure in native parasite populations. Using the yeast model, we characterized the effect of all the amino acid replacements resulting from a single nucleotide substitution at codon 279: Y279C, Y279D, Y279F, Y279H, Y279N, and Y279S (Y279C, D, F, H, N, and S). Two residue changes that required a double nucleotide substitution, Y279A and W, were added to the series. We found that mutations Y279A, C, and S conferred high atovaquone resistance but decreased the catalytic activity. Y279F had wild-type enzymatic activity and sensitivity to atovaquone, while the other substitutions caused a dramatic respiratory defect. The results obtained with the yeast model were examined in regard to atomic structure and compared to the reported data on the evolution of acquired atovaquone resistance in P. falciparum.
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Schulze CJ, Navarro G, Ebert D, DeRisi J, Linington RG. Salinipostins A–K, Long-Chain Bicyclic Phosphotriesters as a Potent and Selective Antimalarial Chemotype. J Org Chem 2015; 80:1312-20. [DOI: 10.1021/jo5024409] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Christopher J. Schulze
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Gabriel Navarro
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Daniel Ebert
- Department
of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Joseph DeRisi
- Department
of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Roger G. Linington
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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30
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Lukens AK, Heidebrecht RW, Mulrooney C, Beaudoin JA, Comer E, Duvall JR, Fitzgerald ME, Masi D, Galinsky K, Scherer CA, Palmer M, Munoz B, Foley M, Schreiber SL, Wiegand RC, Wirth DF. Diversity-oriented synthesis probe targets Plasmodium falciparum cytochrome b ubiquinone reduction site and synergizes with oxidation site inhibitors. J Infect Dis 2014; 211:1097-103. [PMID: 25336726 PMCID: PMC4354981 DOI: 10.1093/infdis/jiu565] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background. The emergence and spread of drug resistance to current antimalarial therapies remains a pressing concern, escalating the need for compounds that demonstrate novel modes of action. Diversity-Oriented Synthesis (DOS) libraries bridge the gap between conventional small molecule and natural product libraries, allowing the interrogation of more diverse chemical space in efforts to identify probes of novel parasite pathways. Methods. We screened and optimized a probe from a DOS library using whole-cell phenotypic assays. Resistance selection and whole-genome sequencing approaches were employed to identify the cellular target of the compounds. Results. We identified a novel macrocyclic inhibitor of Plasmodium falciparum with nanomolar potency and identified the reduction site of cytochrome b as its cellular target. Combination experiments with reduction and oxidation site inhibitors showed synergistic inhibition of the parasite. Conclusions. The cytochrome b oxidation center is a validated antimalarial target. We show that the reduction site of cytochrome b is also a druggable target. Our results demonstrating a synergistic relationship between oxidation and reduction site inhibitors suggests a future strategy for new combination therapies in the treatment of malaria.
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Affiliation(s)
- Amanda K Lukens
- Infectious Disease Initiative, The Broad Institute, Cambridge Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stuart L Schreiber
- Center for the Science of Therapeutics, The Broad Institute, Cambridge, Massachusetts
| | - Roger C Wiegand
- Infectious Disease Initiative, The Broad Institute, Cambridge
| | - Dyann F Wirth
- Infectious Disease Initiative, The Broad Institute, Cambridge Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston
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31
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Abstract
Due to an increased need for new antimalarial chemotherapies that show potency against Plasmodium falciparum, researchers are targeting new processes within the parasite in an effort to circumvent or delay the onset of drug resistance. One such promising area for antimalarial drug development has been the parasite mitochondrial electron transport chain (ETC). Efforts have been focused on targeting key processes along the parasite ETC specifically the dihydroorotate dehydrogenase (DHOD) enzyme, the cytochrome bc 1 enzyme and the NADH type II oxidoreductase (PfNDH2) pathway. This review summarizes the most recent efforts in antimalarial drug development reported in the literature and describes the evolution of these compounds.
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Emergence of resistance to atovaquone-proguanil in malaria parasites: insights from computational modeling and clinical case reports. Antimicrob Agents Chemother 2014; 58:4504-14. [PMID: 24867967 DOI: 10.1128/aac.02550-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The usefulness of atovaquone-proguanil (AP) as an antimalarial treatment is compromised by the emergence of atovaquone resistance during therapy. However, the origin of the parasite mitochondrial DNA (mtDNA) mutation conferring atovaquone resistance remains elusive. Here, we report a patient-based stochastic model that tracks the intrahost emergence of mutations in the multicopy mtDNA during the first erythrocytic parasite cycles leading to the malaria febrile episode. The effect of mtDNA copy number, mutation rate, mutation cost, and total parasite load on the mutant parasite load per patient was evaluated. Computer simulations showed that almost any infected patient carried, after four to seven erythrocytic cycles, de novo mutant parasites at low frequency, with varied frequencies of parasites carrying varied numbers of mutant mtDNA copies. A large interpatient variability in the size of this mutant reservoir was found; this variability was due to the different parameters tested but also to the relaxed replication and partitioning of mtDNA copies during mitosis. We also report seven clinical cases in which AP-resistant infections were treated by AP. These provided evidence that parasiticidal drug concentrations against AP-resistant parasites were transiently obtained within days after treatment initiation. Altogether, these results suggest that each patient carries new mtDNA mutant parasites that emerge before treatment but are killed by high starting drug concentrations. However, because the size of this mutant reservoir is highly variable from patient to patient, we propose that some patients fail to eliminate all of the mutant parasites, repeatedly producing de novo AP treatment failures.
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Abstract
Malaria elimination has recently been reinstated as a global health priority but current therapies seem to be insufficient for the task. Elimination efforts require new drug classes that alleviate symptoms, prevent transmission and provide a radical cure. To develop these next-generation medicines, public-private partnerships are funding innovative approaches to identify compounds that target multiple parasite species at multiple stages of the parasite life cycle. In this Review, we discuss the cell-, chemistry- and target-based approaches used to discover new drug candidates that are currently in clinical trials or undergoing preclinical testing.
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Flannery EL, Fidock DA, Winzeler EA. Using genetic methods to define the targets of compounds with antimalarial activity. J Med Chem 2013; 56:7761-71. [PMID: 23927658 DOI: 10.1021/jm400325j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although phenotypic cellular screening has been used to drive antimalarial drug discovery in recent years, in some cases target-based drug discovery remains more attractive. This is especially true when appropriate high-throughput cellular assays are lacking, as is the case for drug discovery efforts that aim to provide a replacement for primaquine (4-N-(6-methoxyquinolin-8-yl)pentane-1,4-diamine), the only drug that can block Plasmodium transmission to Anopheles mosquitoes and eliminate liver-stage hypnozoites. At present, however, there are no known chemically validated parasite protein targets that are important in all Plasmodium parasite developmental stages and that can be used in traditional biochemical compound screens. We propose that a plethora of novel, chemically validated, cross-stage antimalarial targets still remain to be discovered from the ~5,500 proteins encoded by the Plasmodium genomes. Here we discuss how in vitro evolution of drug-resistant strains of Plasmodium falciparum and subsequent whole-genome analysis can be used to find the targets of some of the many compounds discovered in whole-cell phenotypic screens.
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Affiliation(s)
- Erika L Flannery
- Department of Pediatrics, University of California, San Diego, School of Medicine , 9500 Gilman Drive 0741, La Jolla, California 92093, United States
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Carrasco MP, Gut J, Rodrigues T, Ribeiro MHL, Lopes F, Rosenthal PJ, Moreira R, Dos Santos DJVA. Exploring the Molecular Basis of Qo bc1 Complex Inhibitors Activity to Find Novel Antimalarials Hits. Mol Inform 2013; 32:659-70. [PMID: 27481771 DOI: 10.1002/minf.201300024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/11/2013] [Indexed: 02/01/2023]
Abstract
Cytochrome bc1 complex is a crucial element in the mitochondrial respiratory chain, being indispensable for the survival of several species of Plasmodia that cause malaria and, therefore, it is a promising target for antimalarial drug development. We report a molecular docking study building on the most recently obtained X-ray structure of the Saccharomyces cerevisiae bc1 complex (PDB code: 3CX5) using several reported inhibitors with experimentally determined IC50 values against the Plasmodium falciparum bc1 complex. We produced a molecular docking model that correlated the calculated binding free energy with the experimental inhibitory activity of each compound. This Qo model was used to search the drug-like database included in the MOE package for novel potential bc1 complex inhibitors. Twenty three compounds were chosen to be tested for their antimalarial activity and four of these compounds demonstrated activity against the chloroquine-resistant W2 strain of P. falciparum. The most active compounds were also active against the atovaquone-resistant P. falciparum FCR3 strain and S. cerevisiae. Our study suggests the validity of the yeast bc1 complex structure as a model for the discovery of new antimalarial hits.
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Affiliation(s)
- Marta P Carrasco
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA 94143-0811, USA
| | - Tiago Rodrigues
- Departement Chemie und Angewandte Biowissenschaften, Eidgenössische Technische Hochschule (ETH), Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Maria H L Ribeiro
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Francisca Lopes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA 94143-0811, USA
| | - Rui Moreira
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Daniel J V A Dos Santos
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470. .,REQUIMTE, Department of Chemistry & Biochemistry, Faculty of Sciences, University of Porto, R. do Campo Alegre, 4169-007 Porto, Portugal.
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36
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Exploration of 4(1H)-pyridones as a novel family of potent antimalarial inhibitors of the plasmodial cytochrome bc1. Future Med Chem 2013; 4:2311-23. [PMID: 23234553 DOI: 10.4155/fmc.12.177] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A novel family of antimalarials based on the 4(1H)-pyridone scaffold is described. The compounds display potent antimalarial activity against Plasmodium falciparum in vitro and in vivo. Like atovaquone, 4(1H)-pyridones exert their antimalarial action by inhibiting selectively the electron-transport chain in P. falciparum at the cytochrome bc1 level (complex III). However, despite the similar mechanism of action, no cross-resistance with atovaquone has been found, suggesting that the binding mode of 4(1H)-pyridones might be different from that of atovaquone. The medicinal chemistry program, focused on improving potency and physicochemical properties, ultimately led to the discovery of GSK932121, which was progressed efficiently into first time in human studies. However, progression of GSK932121 was terminated when new toxicology results were obtained in the rat with a soluble phosphate prodrug of the candidate, indicating a potentially narrow therapeutic index.
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Calderón F, Wilson DM, Gamo FJ. Antimalarial drug discovery: recent progress and future directions. PROGRESS IN MEDICINAL CHEMISTRY 2013; 52:97-151. [PMID: 23384667 DOI: 10.1016/b978-0-444-62652-3.00003-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Félix Calderón
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Spain
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38
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Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite. Proc Natl Acad Sci U S A 2012; 109:13052-7. [PMID: 22826220 DOI: 10.1073/pnas.1210585109] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Through rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite--the deadliest of those that cause malaria--is able to develop resistance to antimalarial drugs, thwarting present efforts to control it. Genome-wide association studies (GWAS) provide a critical hypothesis-generating tool for understanding how this occurs. However, in P. falciparum, the limited amount of linkage disequilibrium hinders the power of traditional array-based GWAS. Here, we demonstrate the feasibility and power improvements gained by using whole-genome sequencing for association studies. We analyzed data from 45 Senegalese parasites and identified genetic changes associated with the parasites' in vitro response to 12 different antimalarials. To further increase statistical power, we adapted a common test for natural selection, XP-EHH (cross-population extended haplotype homozygosity), and used it to identify genomic regions associated with resistance to drugs. Using this sequence-based approach and the combination of association and selection-based tests, we detected several loci associated with drug resistance. These loci included the previously known signals at pfcrt, dhfr, and pfmdr1, as well as many genes not previously implicated in drug-resistance roles, including genes in the ubiquitination pathway. Based on the success of the analysis presented in this study, and on the demonstrated shortcomings of array-based approaches, we argue for a complete transition to sequence-based GWAS for small, low linkage-disequilibrium genomes like that of P. falciparum.
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