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Gilleran JA, Ashraf K, Delvillar M, Eck T, Fondekar R, Miller EB, Hutchinson A, Dong A, Seitova A, De Souza ML, Augeri D, Halabelian L, Siekierka J, Rotella DP, Gordon J, Childers WE, Grier MC, Staker BL, Roberge JY, Bhanot P. Structure-Activity Relationship of a Pyrrole Based Series of PfPKG Inhibitors as Anti-Malarials. J Med Chem 2024; 67:3467-3503. [PMID: 38372781 DOI: 10.1021/acs.jmedchem.3c01795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Controlling malaria requires new drugs against Plasmodium falciparum. The P. falciparum cGMP-dependent protein kinase (PfPKG) is a validated target whose inhibitors could block multiple steps of the parasite's life cycle. We defined the structure-activity relationship (SAR) of a pyrrole series for PfPKG inhibition. Key pharmacophores were modified to enable full exploration of chemical diversity and to gain knowledge about an ideal core scaffold. In vitro potency against recombinant PfPKG and human PKG were used to determine compound selectivity for the parasite enzyme. P. berghei sporozoites and P. falciparum asexual blood stages were used to assay multistage antiparasitic activity. Cellular specificity of compounds was evaluated using transgenic parasites expressing PfPKG carrying a substituted "gatekeeper" residue. The structure of PfPKG bound to an inhibitor was solved, and modeling using this structure together with computational tools was utilized to understand SAR and establish a rational strategy for subsequent lead optimization.
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Affiliation(s)
- John A Gilleran
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Kutub Ashraf
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Melvin Delvillar
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Tyler Eck
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life Sciences, Montclair State University, Montclair, New Jersey 07043, United States
| | - Raheel Fondekar
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Rutgers School of Pharmacy, 160 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Edward B Miller
- Schrödinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Mariana Laureano De Souza
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
| | - David Augeri
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Schrödinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - John Siekierka
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life Sciences, Montclair State University, Montclair, New Jersey 07043, United States
| | - David P Rotella
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life Sciences, Montclair State University, Montclair, New Jersey 07043, United States
| | - John Gordon
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States
| | - Wayne E Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States
| | - Mark C Grier
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109, United States
| | - Jacques Y Roberge
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Purnima Bhanot
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
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2
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Vyas VK, Shukla T, Sharma M. Medicinal chemistry approaches for the discovery of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. Future Med Chem 2023; 15:1295-1321. [PMID: 37551689 DOI: 10.4155/fmc-2023-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Malaria is a severe human disease and a global health problem because of drug-resistant strains. Drugs reported to prevent the growth of Plasmodium parasites target various phases of the parasites' life cycle. Antimalarial drugs can inhibit key enzymes that are responsible for the cellular growth and development of parasites. Plasmodium falciparum dihydroorotate dehydrogenase is one such enzyme that is necessary for de novo pyrimidine biosynthesis. This review focuses on various medicinal chemistry approaches used for the discovery and identification of selective P. falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. This comprehensive review discusses recent advances in the selective therapeutic activity of distinct chemical classes of compounds as P. falciparum dihydroorotate dehydrogenase inhibitors and antimalarial drugs.
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Affiliation(s)
- Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Tanvi Shukla
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
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3
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Kümpornsin K, Kochakarn T, Yeo T, Okombo J, Luth MR, Hoshizaki J, Rawat M, Pearson RD, Schindler KA, Mok S, Park H, Uhlemann AC, Jana GP, Maity BC, Laleu B, Chenu E, Duffy J, Moliner Cubel S, Franco V, Gomez-Lorenzo MG, Gamo FJ, Winzeler EA, Fidock DA, Chookajorn T, Lee MCS. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum. Nat Commun 2023; 14:3059. [PMID: 37244916 DOI: 10.1038/s41467-023-38774-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/12/2023] [Indexed: 05/29/2023] Open
Abstract
In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an "irresistible" compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this "mutator" parasite can be leveraged to drive P. falciparum resistome discovery.
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Affiliation(s)
- Krittikorn Kümpornsin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, USA
| | - Theerarat Kochakarn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Benoît Laleu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - Elodie Chenu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | | | - Virginia Franco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | | | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Thanat Chookajorn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
- Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK.
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4
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Ward KE, Christensen P, Racklyeft A, Dhingra SK, Chua ACY, Remmert C, Suwanarusk R, Matheson J, Blackman MJ, Kaneko O, Kyle DE, Lee MCS, Moon RW, Snounou G, Rénia L, Fidock DA, Russell B, Bifani P. Integrative Genetic Manipulation of Plasmodium cynomolgi Reveals Multidrug Resistance-1 Y976F Associated With Increased In Vitro Susceptibility to Mefloquine. J Infect Dis 2023; 227:1121-1126. [PMID: 36478252 PMCID: PMC10175063 DOI: 10.1093/infdis/jiac469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/24/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
The lack of a long-term in vitro culture method has severely restricted the study of Plasmodium vivax, in part because it limits genetic manipulation and reverse genetics. We used the recently optimized Plasmodium cynomolgi Berok in vitro culture model to investigate the putative P. vivax drug resistance marker MDR1 Y976F. Introduction of this mutation using clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) increased sensitivity to mefloquine, but had no significant effect on sensitivity to chloroquine, amodiaquine, piperaquine, and artesunate. To our knowledge, this is the first reported use of CRISPR-Cas9 in P. cynomolgi, and the first reported integrative genetic manipulation of this species.
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Affiliation(s)
- Kurt E Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Peter Christensen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Annie Racklyeft
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Satish K Dhingra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Adeline C Y Chua
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- A*STAR Infectious Diseases Laboratory, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Caroline Remmert
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rossarin Suwanarusk
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Jessica Matheson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert W Moon
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Georges Snounou
- 11-INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, Infectious Disease Models and Innovative Therapies Department, Institut de biologie François Jacob, Direction de Recherche Fondamentale, Commissariat à l'énergie atomique et aux énergies alternatives-Université Paris Sud, Fontenay-aux-Roses, France
| | - Laurent Rénia
- A*STAR Infectious Diseases Laboratory, Agency for Science, Technology, and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Pablo Bifani
- A*STAR Infectious Diseases Laboratory, Agency for Science, Technology, and Research, Singapore, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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5
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Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu XM, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez LM, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb OS, Le Roch KG, Mamoun CB. Babesia duncani multi-omics identifies virulence factors and drug targets. Nat Microbiol 2023; 8:845-859. [PMID: 37055610 PMCID: PMC10159843 DOI: 10.1038/s41564-023-01360-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/14/2023] [Indexed: 04/15/2023]
Abstract
Babesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis. Unlike other apicomplexan parasites that infect red blood cells, B. duncani can be continuously cultured in vitro in human erythrocytes and can infect mice resulting in fulminant babesiosis and death. We report comprehensive, detailed molecular, genomic, transcriptomic and epigenetic analyses to gain insights into the biology of B. duncani. We completed the assembly, 3D structure and annotation of its nuclear genome, and analysed its transcriptomic and epigenetics profiles during its asexual life cycle stages in human erythrocytes. We used RNA-seq data to produce an atlas of parasite metabolism during its intraerythrocytic life cycle. Characterization of the B. duncani genome, epigenome and transcriptome identified classes of candidate virulence factors, antigens for diagnosis of active infection and several attractive drug targets. Furthermore, metabolic reconstitutions from genome annotation and in vitro efficacy studies identified antifolates, pyrimethamine and WR-99210 as potent inhibitors of B. duncani to establish a pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.
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Affiliation(s)
- Pallavi Singh
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Pratap Vydyam
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | - Tiffany Fang
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Shalev Gihaz
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Jose Thekkiniath
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Muhammad Munshi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Loic Ciampossin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Xueqing Maggie Lu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Sakshar Chakravarty
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle (IBC), and Institut de Recherche en Cancérologie de Montpellier (IRCM - INSERM U1194), Institut régional du Cancer Montpellier (ICM) and Université de Montpellier, Montpellier, France
| | - Yangyang Hu
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, USA
| | - Luis Miguel Gonzalez
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sergio Sánchez
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Karel Estrada
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sánchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Estrella Montero
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.
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6
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Wicht KJ, Small-Saunders JL, Hagenah LM, Mok S, Fidock DA. Mutant PfCRT Can Mediate Piperaquine Resistance in African Plasmodium falciparum With Reduced Fitness and Increased Susceptibility to Other Antimalarials. J Infect Dis 2022; 226:2021-2029. [PMID: 36082431 PMCID: PMC9704436 DOI: 10.1093/infdis/jiac365] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/06/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Additional therapeutic strategies could benefit efforts to reverse the recent increase in malaria cases in sub-Saharan Africa, which mostly affects young children. A primary candidate is dihydroartemisinin + piperaquine (DHA + PPQ), which is effective for uncomplicated malaria treatment, seasonal malaria chemoprevention, and intermittent preventive treatment. In Southeast Asia, Plasmodium falciparum parasites acquired PPQ resistance, mediated primarily by mutations in the P falciparum chloroquine resistance transporter PfCRT. The recent emergence in Africa of DHA-resistant parasites creates an imperative to assess whether PPQ resistance could emerge in African parasites with distinct PfCRT isoforms. METHODS We edited 2 PfCRT mutations known to mediate high-grade PPQ resistance in Southeast Asia into GB4 parasites from Gabon. Gene-edited clones were profiled in antimalarial concentration-response and fitness assays. RESULTS The PfCRT F145I mutation mediated moderate PPQ resistance in GB4 parasites but with a substantial fitness cost. No resistance was observed with the PfCRT G353V mutant. Both edited clones became significantly more susceptible to amodiaquine, chloroquine, and quinine. CONCLUSIONS A single PfCRT mutation can mediate PPQ resistance in GB4 parasites, but with a growth defect that may preclude its spread without further genetic adaptations. Our findings support regional use of drug combinations that exert opposing selective pressures on PfCRT.
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Affiliation(s)
- Kathryn J Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer L Small-Saunders
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Center for Malaria Therapeutics and Antimalarial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York , New York, USA
| | - Laura M Hagenah
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Center for Malaria Therapeutics and Antimalarial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York , New York, USA
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7
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Murithi JM, Deni I, Pasaje CFA, Okombo J, Bridgford JL, Gnädig NF, Edwards RL, Yeo T, Mok S, Burkhard AY, Coburn-Flynn O, Istvan ES, Sakata-Kato T, Gomez-Lorenzo MG, Cowell AN, Wicht KJ, Le Manach C, Kalantarov GF, Dey S, Duffey M, Laleu B, Lukens AK, Ottilie S, Vanaerschot M, Trakht IN, Gamo FJ, Wirth DF, Goldberg DE, Odom John AR, Chibale K, Winzeler EA, Niles JC, Fidock DA. The Plasmodium falciparum ABC transporter ABCI3 confers parasite strain-dependent pleiotropic antimalarial drug resistance. Cell Chem Biol 2022; 29:824-839.e6. [PMID: 34233174 PMCID: PMC8727639 DOI: 10.1016/j.chembiol.2021.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 01/21/2023]
Abstract
Widespread Plasmodium falciparum resistance to first-line antimalarials underscores the vital need to develop compounds with novel modes of action and identify new druggable targets. Here, we profile five compounds that potently inhibit P. falciparum asexual blood stages. Resistance selection studies with three carboxamide-containing compounds, confirmed by gene editing and conditional knockdowns, identify point mutations in the parasite transporter ABCI3 as the primary mediator of resistance. Selection studies with imidazopyridine or quinoline-carboxamide compounds also yield changes in ABCI3, this time through gene amplification. Imidazopyridine mode of action is attributed to inhibition of heme detoxification, as evidenced by cellular accumulation and heme fractionation assays. For the copy-number variation-selecting imidazopyridine and quinoline-carboxamide compounds, we find that resistance, manifesting as a biphasic concentration-response curve, can independently be mediated by mutations in the chloroquine resistance transporter PfCRT. These studies reveal the interconnectedness of P. falciparum transporters in overcoming drug pressure in different parasite strains.
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Affiliation(s)
- James M. Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jessica L. Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nina F. Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel L. Edwards
- Division of Infectious Diseases, Allergy and Immunology, Center for Vaccine Development, St. Louis University, St. Louis, MO 63104, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Anna Y. Burkhard
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Eva S. Istvan
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | | | - Annie N. Cowell
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Kathryn J. Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA,Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Claire Le Manach
- Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Gavreel F. Kalantarov
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maëlle Duffey
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Sabine Ottilie
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ilya N. Trakht
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francisco-Javier Gamo
- Global Health Pharma Research Unit, GlaxoSmithKline, 28760 Tres Cantos, Madrid, Spain
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Daniel E. Goldberg
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kelly Chibale
- Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Elizabeth A. Winzeler
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA,Corresponding author
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8
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Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response. Commun Biol 2022; 5:274. [PMID: 35347215 PMCID: PMC8960834 DOI: 10.1038/s42003-022-03215-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/16/2022] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of artemisinin-resistant Plasmodium falciparum, first in the Greater Mekong Subregion (GMS), and now in East Africa, is a major threat to global malaria elimination ambitions. To investigate the artemisinin resistance mechanism, transcriptome analysis was conducted of 577 P. falciparum isolates collected in the GMS between 2016–2018. A specific artemisinin resistance-associated transcriptional profile was identified that involves a broad but discrete set of biological functions related to proteotoxic stress, host cytoplasm remodelling, and REDOX metabolism. The artemisinin resistance-associated transcriptional profile evolved from initial transcriptional responses of susceptible parasites to artemisinin. The genetic basis for this adapted response is likely to be complex. Transcriptomic analysis of isolates from the malaria parasite (Plasmodium falciparum) in the Greater Mekong Subregion of Southeast Asia identifies gene expression patterns that are correlated with resistance to a common anti-malaria drug, artemisinin.
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9
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Eck T, Laureano de Souza M, Delvillar M, Ashraf K, Yadav Bheemanaboina RR, Chakrasali R, Kreiss T, Siekierka JJ, Rotella DP, Bhanot P, Goodey NM. Characterization of competitive inhibitors of P. falciparum cGMP‐dependent protein kinase. Chembiochem 2022; 23:e202100704. [PMID: 35044710 PMCID: PMC9132199 DOI: 10.1002/cbic.202100704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/18/2022] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) is an enticing antimalarial drug target. Novel chemotypes are needed because existing inhibitors have safety issues that may prevent further development. This work demonstrates isoxazole-based compounds are potent ATP competitive inhibitors of PfPKG and discloses a new analogue in this series. Isoxazoles 3 and 5 had Ki values that are comparable to a known standard, 4-[2-(4-fluorophenyl)-5-(1-methylpiperidine-4-yl)-1H pyrrol-3-yl] pyridine. They also exhibited excellent selectivity for PfPKG over the human orthologue and the gatekeeper mutant T618Q PfPKG, which mimics the less accessible binding site of the human orthologue. The human orthologue's larger binding site volume is predicted to explain the selectivity of the inhibitors for the P. falciparum enzyme.
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Affiliation(s)
- Tyler Eck
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - Mariana Laureano de Souza
- Rutgers New Jersey Medical School Department of Microbiology, Biochemistry, and Molecular Genetics UNITED STATES
| | - Melvin Delvillar
- Rutgers New Jersey Medical School Microbiology, Biochemistry and Molecular Genetics UNITED STATES
| | - Kutub Ashraf
- Rutgers New Jersey Medical School Microbiology, Biochemistry and Molecular Genetics UNITED STATES
| | | | | | - Tamara Kreiss
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - John J Siekierka
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - David P Rotella
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - Purnima Bhanot
- Rutgers New Jersey Medical School Department of Microbiology, Biochemistry and Molecular Genetics UNITED STATES
| | - Nina M Goodey
- Montclair State University Chemistry and Biochemistry 1 Normal Avenue 07043 Montclair UNITED STATES
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10
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Nishi T, Shinzawa N, Yuda M, Iwanaga S. Highly efficient CRISPR/Cas9 system in Plasmodium falciparum using Cas9-expressing parasites and a linear donor template. Sci Rep 2021; 11:18501. [PMID: 34531479 PMCID: PMC8445982 DOI: 10.1038/s41598-021-97984-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/30/2021] [Indexed: 02/06/2023] Open
Abstract
The CRISPR/Cas9 system is a powerful genetic engineering technology for Plasmodium falciparum. We here report further improvement of the CRISPR/Cas9 system by combining the Cas9-expressing parasite with a liner donor template DNA. The Cas9-expressing parasite was generated by inserting the cas9 gene in the genome by double crossover recombination. The site-directed mutagenesis and the fusion of fluorescence protein was achieved within two weeks with high efficiency (> 85%), by transfecting the schizonts of the Cas9-expressing parasite with the liner donor template and the plasmid carrying the sgRNAs. Notably, there were neither off-target mutations in the resultant transgenic parasites nor unexpected recombination, that are the technical problems of the current CRISPR/Cas9 system. Furthermore, with our system, two genes on different chromosomes were successfully modified in single transfection. Because of its high efficiency and robustness, our improved CRISPR/Cas9 system will become a standard technique for genetic engineering of P. falciparum, which dramatically advances future studies of this parasite.
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Affiliation(s)
- Tsubasa Nishi
- Laboratory of Medical Zoology, Department of Medicine, Mie University, Mie, Japan
| | - Naoaki Shinzawa
- Department of Environmental Parasitology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masao Yuda
- Laboratory of Medical Zoology, Department of Medicine, Mie University, Mie, Japan
| | - Shiroh Iwanaga
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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11
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Duffey M, Blasco B, Burrows JN, Wells TNC, Fidock DA, Leroy D. Assessing risks of Plasmodium falciparum resistance to select next-generation antimalarials. Trends Parasitol 2021; 37:709-721. [PMID: 34001441 DOI: 10.1016/j.pt.2021.04.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023]
Abstract
Strategies to counteract or prevent emerging drug resistance are crucial for the design of next-generation antimalarials. In the past, resistant parasites were generally identified following treatment failures in patients, and compounds would have to be abandoned late in development. An early understanding of how candidate therapeutics lose efficacy as parasites evolve resistance is important to facilitate drug design and improve resistance detection and monitoring up to the postregistration phase. We describe a new strategy to assess resistance to antimalarial compounds as early as possible in preclinical development by leveraging tools to define the Plasmodium falciparum resistome, predict potential resistance risks of clinical failure for candidate therapeutics, and inform decisions to guide antimalarial drug development.
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Affiliation(s)
| | - Benjamin Blasco
- Medicines for Malaria Venture, Geneva, Switzerland; Global Antibiotic Research and Development Partnership, Geneva, Switzerland
| | | | | | - David A Fidock
- Department of Microbiology and Immunology, 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
| | - Didier Leroy
- Medicines for Malaria Venture, Geneva, Switzerland.
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12
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Palmer MJ, Deng X, Watts S, Krilov G, Gerasyuto A, Kokkonda S, El Mazouni F, White J, White KL, Striepen J, Bath J, Schindler KA, Yeo T, Shackleford DM, Mok S, Deni I, Lawong A, Huang A, Chen G, Wang W, Jayaseelan J, Katneni K, Patil R, Saunders J, Shahi SP, Chittimalla R, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Tumwebaze PK, Rosenthal PJ, Cooper RA, Aguiar ACC, Guido RVC, Pereira DB, Mittal N, Winzeler EA, Tomchick DR, Laleu B, Burrows JN, Rathod PK, Fidock DA, Charman SA, Phillips MA. Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series. J Med Chem 2021; 64:6085-6136. [PMID: 33876936 DOI: 10.1021/acs.jmedchem.1c00173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydroorotate dehydrogenase (DHODH) has been clinically validated as a target for the development of new antimalarials. Experience with clinical candidate triazolopyrimidine DSM265 (1) suggested that DHODH inhibitors have great potential for use in prophylaxis, which represents an unmet need in the malaria drug discovery portfolio for endemic countries, particularly in areas of high transmission in Africa. We describe a structure-based computationally driven lead optimization program of a pyrrole-based series of DHODH inhibitors, leading to the discovery of two candidates for potential advancement to preclinical development. These compounds have improved physicochemical properties over prior series frontrunners and they show no time-dependent CYP inhibition, characteristic of earlier compounds. Frontrunners have potent antimalarial activity in vitro against blood and liver schizont stages and show good efficacy in Plasmodium falciparum SCID mouse models. They are equally active against P. falciparum and Plasmodium vivax field isolates and are selective for Plasmodium DHODHs versus mammalian enzymes.
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Affiliation(s)
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Shawn Watts
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Aleksey Gerasyuto
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jade Bath
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Ann Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Wen Wang
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jaya Jayaseelan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Rahul Patil
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jessica Saunders
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | | | | | - Iñigo Angulo-Barturen
- TAD, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- TAD, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Rafael V C Guido
- University of Sao Paulo, Sao Carlos Institute of Physics, Sáo Carlos, SP 13560-970, Brazil
| | - Dhelio B Pereira
- Tropical Medicine Research Center of Rondonia, Av. Guaporé, 215, Porto Velho, RO 76812-329, Brazil
| | - Nimisha Mittal
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Diana R Tomchick
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
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13
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Ippolito MM, Moser KA, Kabuya JBB, Cunningham C, Juliano JJ. Antimalarial Drug Resistance and Implications for the WHO Global Technical Strategy. CURR EPIDEMIOL REP 2021; 8:46-62. [PMID: 33747712 PMCID: PMC7955901 DOI: 10.1007/s40471-021-00266-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Five years have passed since the World Health Organization released its Global Technical Strategy for Malaria (GTS). In that time, progress against malaria has plateaued. This review focuses on the implications of antimalarial drug resistance for the GTS and how interim progress in parasite genomics and antimalarial pharmacology offer a bulwark against it. RECENT FINDINGS For the first time, drug resistance-conferring genes have been identified and validated before their global expansion in malaria parasite populations. More efficient methods for their detection and elaboration have been developed, although low-density infections and polyclonality remain a nuisance to be solved. Clinical trials of alternative regimens for multidrug-resistant malaria have delivered promising results. New agents continue down the development pipeline, while a nascent infrastructure in sub-Saharan Africa for conducting phase I trials and trials of transmission-blocking agents has come to fruition after years of preparation. SUMMARY These and other developments can help inform the GTS as the world looks ahead to the next two decades of its implementation. To remain ahead of the threat that drug resistance poses, wider application of genomic-based surveillance and optimization of existing and forthcoming antimalarial drugs are essential.
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Affiliation(s)
- Matthew M. Ippolito
- Divisions of Clinical Pharmacology and Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- The Johns Hopkins Malaria Research Institute, Johns Hopkins University School of Public Health, Baltimore, MD USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Kara A. Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC USA
| | | | - Clark Cunningham
- School of Medicine, University of North Carolina, Chapel Hill, NC USA
| | - Jonathan J. Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina, CB#7030, 130 Mason Farm Rd, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
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14
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Lawong A, Gahalawat S, Okombo J, Striepen J, Yeo T, Mok S, Deni I, Bridgford JL, Niederstrasser H, Zhou A, Posner B, Wittlin S, Gamo FJ, Crespo B, Churchyard A, Baum J, Mittal N, Winzeler E, Laleu B, Palmer MJ, Charman SA, Fidock DA, Ready JM, Phillips MA. Novel Antimalarial Tetrazoles and Amides Active against the Hemoglobin Degradation Pathway in Plasmodium falciparum. J Med Chem 2021; 64:2739-2761. [PMID: 33620219 DOI: 10.1021/acs.jmedchem.0c02022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Malaria control programs continue to be threatened by drug resistance. To identify new antimalarials, we conducted a phenotypic screen and identified a novel tetrazole-based series that shows fast-kill kinetics and a relatively low propensity to develop high-level resistance. Preliminary structure-activity relationships were established including identification of a subseries of related amides with antiplasmodial activity. Assaying parasites with resistance to antimalarials led us to test whether the series had a similar mechanism of action to chloroquine (CQ). Treatment of synchronized Plasmodium falciparum parasites with active analogues revealed a pattern of intracellular inhibition of hemozoin (Hz) formation reminiscent of CQ's action. Drug selections yielded only modest resistance that was associated with amplification of the multidrug resistance gene 1 (pfmdr1). Thus, we have identified a novel chemical series that targets the historically druggable heme polymerization pathway and that can form the basis of future optimization efforts to develop a new malaria treatment.
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Affiliation(s)
- Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Suraksha Gahalawat
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jessica L Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Hanspeter Niederstrasser
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Anwu Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | - Benigno Crespo
- Medicines Development Campus, GlaxoSmithKline, Tres Cantos, 28760 Madrid, Spain
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, SW7 2AZ South Kensington, U.K
| | - Jake Baum
- Department of Life Sciences, Imperial College London, SW7 2AZ South Kensington, U.K
| | - Nimisha Mittal
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, United States
| | - Elizabeth Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, United States
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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15
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Kwarteng A, Sylverken A, Asiedu E, Ahuno ST. Genome editing as control tool for filarial infections. Biomed Pharmacother 2021; 137:111292. [PMID: 33581654 DOI: 10.1016/j.biopha.2021.111292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/26/2022] Open
Abstract
Human filarial infections are vector-borne nematode infections, which include lymphatic filariasis, onchocerciasis, loiasis, and mansonella filariasis. With a high prevalence in developing countries, filarial infections are responsible for some of the most debilitating morbidities and a vicious cycle of poverty and disease. Global initiatives set to eradicate these infections include community mass treatments, vector control, provision of care for morbidity, and search for vaccines. However, there are growing challenges associated with mass treatments, vector control, and antifilarial vaccine development. With the emergence of genome editing tools and successful applications in other infectious diseases, the integration of genetic editing techniques in future control strategies for filarial infections would offer the best option for eliminating filarial infections. In this review, we briefly discuss the mechanisms of the three main genetic editing techniques and explore the potential applications of these powerful tools to control filarial infections.
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Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana; Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana.
| | - Augustina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana; Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Ebenezer Asiedu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana; Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
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16
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Venugopal K, Hentzschel F, Valkiūnas G, Marti M. Plasmodium asexual growth and sexual development in the haematopoietic niche of the host. Nat Rev Microbiol 2020; 18:177-189. [PMID: 31919479 PMCID: PMC7223625 DOI: 10.1038/s41579-019-0306-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2019] [Indexed: 12/28/2022]
Abstract
Plasmodium spp. parasites are the causative agents of malaria in humans and animals, and they are exceptionally diverse in their morphology and life cycles. They grow and develop in a wide range of host environments, both within blood-feeding mosquitoes, their definitive hosts, and in vertebrates, which are intermediate hosts. This diversity is testament to their exceptional adaptability and poses a major challenge for developing effective strategies to reduce the disease burden and transmission. Following one asexual amplification cycle in the liver, parasites reach high burdens by rounds of asexual replication within red blood cells. A few of these blood-stage parasites make a developmental switch into the sexual stage (or gametocyte), which is essential for transmission. The bone marrow, in particular the haematopoietic niche (in rodents, also the spleen), is a major site of parasite growth and sexual development. This Review focuses on our current understanding of blood-stage parasite development and vascular and tissue sequestration, which is responsible for disease symptoms and complications, and when involving the bone marrow, provides a niche for asexual replication and gametocyte development. Understanding these processes provides an opportunity for novel therapies and interventions.
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Affiliation(s)
- Kannan Venugopal
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Franziska Hentzschel
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | | | - Matthias Marti
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
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