1
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Huang Q, Jiang H, Wei J, Dou Y, Pan G, Chen J, Reinke AW. Small-molecule screen in C. elegans identifies benzenesulfonamides as inhibitors of microsporidia spores. NPJ ANTIMICROBIALS AND RESISTANCE 2025; 3:41. [PMID: 40399462 PMCID: PMC12095817 DOI: 10.1038/s44259-025-00116-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Accepted: 05/08/2025] [Indexed: 05/23/2025]
Abstract
Microsporidia, a large group of fungal-related intracellular parasites, infect several economically significant animals, leading to substantial economic losses. As currently available anti-microsporidia therapies are either ineffective or come with numerous adverse effects, there is a need for alternative microsporidia inhibitors. Here we screen a subset of the ChemBridge DIVERset library, comprising 2500 diverse compounds, using Caenorhabditis elegans infected with its natural microsporidian parasite, Nematocida parisii. By testing these compounds at 60 μM in 96-well assay plates, we identified 26 hits that restored the ability of C. elegans to produce progeny in the presence of N. parisii. We confirmed that out of 20 tested compounds, 18 ChemBridge compounds effectively inhibit N. parisii infection in C. elegans. Of these 18, 10 were benzenesulfonamide derivatives which inhibit microsporidia infection by inactivating spores. We screened an additional 475-compound benzenesulfonamide library, successfully identifying three compounds that are effective at a lower concentration than the initial hits. We further show that one benzenesulfonamide compound displays inhibitory activity against several species of microsporidia, inhibiting infection of species belonging to the Nematocida, Enterocytozoon, and Encephalitozoon genera. Together our results suggest that benzenesulfonamides are a potential scaffold for the development of microsporidia antiseptics.
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Affiliation(s)
- Qingyuan Huang
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Haiyi Jiang
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Junhong Wei
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Yabin Dou
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jie Chen
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China.
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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2
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Smith C, Hajisadeghian M, van Noort GJVDH, Deery MJ, Pinto-Fernández A, Kessler BM, Artavanis-Tsakonas K. Activity-based protein profiling reveals both canonical and novel ubiquitin pathway enzymes in Plasmodium. PLoS Pathog 2025; 21:e1013032. [PMID: 40249735 PMCID: PMC12007708 DOI: 10.1371/journal.ppat.1013032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Accepted: 03/11/2025] [Indexed: 04/20/2025] Open
Abstract
The ubiquitin-proteasome system (UPS) is essential for Plasmodium falciparum survival and represents a potential target for antimalarial therapies. We utilised a ubiquitin- activity based probe (Ub-Dha) to capture active components of the ubiquitin conjugating machinery during asexual blood-stage development. Several E2 ubiquitin-conjugating enzymes, the E1 activating enzyme, and the HECT E3 ligase PfHEUL were identified and validated through in vitro ubiquitination assays. We also demonstrate selective functional interactions between PfHEUL and a subset of both human and P. falciparum E2s. Additionally, the Ub-Dha probe captured an uncharacterized protein, PF3D7_0811400 (C0H4U0) with no known homology to ubiquitin-pathway enzymes in other organisms. Through structural and biochemical analysis, we validate it as a novel E2 enzyme, capable of binding ubiquitin in a cysteine-specific manner. These findings contribute to our understanding of the P. falciparum UPS, identifying promising novel drug targets and highlighting the evolutionary uniqueness of the Ub-proteasome system in this parasite.
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Affiliation(s)
- Cameron Smith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Michael J. Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adán Pinto-Fernández
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
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3
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Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Godoy Magalhaes L, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean KJ, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining. NPJ DRUG DISCOVERY 2025; 2:3. [PMID: 40066064 PMCID: PMC11892419 DOI: 10.1038/s44386-025-00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 01/22/2025] [Indexed: 03/19/2025]
Abstract
Identification of novel drug targets is a key component of modern drug discovery. While antimalarial targets are often identified through the mechanism of action studies on phenotypically derived inhibitors, this method tends to be time- and resource-consuming. The discoverable target space is also constrained by existing compound libraries and phenotypic assay conditions. Leveraging recent advances in protein structure prediction, we systematically assessed the Plasmodium falciparum genome and identified 867 candidate protein targets with evidence of small-molecule binding and blood-stage essentiality. Of these, 540 proteins showed strong essentiality evidence and lack inhibitors that have progressed to clinical trials. Expert review and rubric-based scoring of this subset based on additional criteria such as selectivity, structural information, and assay developability yielded 27 high-priority antimalarial target candidates. This study also provides a genome-wide data resource for P. falciparum and implements a generalizable framework for systematically evaluating and prioritizing novel pathogenic disease targets.
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Affiliation(s)
| | - Daisy Chen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | | | | | - Anna Adam
- MMV Medicines for Malaria Venture, 1215, Geneva, Switzerland
| | - Selina Bopp
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Krypton Carolino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | - Lauren B. Coulson
- Holistic Drug Discovery and Development (H3D) Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Greg Durst
- Lgenia, Inc., 412 S Maple St, Fortville, IN USA
| | - Vandana Thathy
- 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
| | - Lisl Esherick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Madeline A. Farringer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA USA
| | | | - Barbara Forte
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - Tiqing Liu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
| | - Luma Godoy Magalhaes
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - Anil K. Gupta
- Calibr-Skaggs Institute for Innovative Medicines, a division of The Scripps Research Institute, La Jolla, CA USA
| | - Eva S. Istvan
- Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO USA
| | - Tiantian Jiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | - Krittikorn Kumpornsin
- Calibr-Skaggs Institute for Innovative Medicines, a division of The Scripps Research Institute, La Jolla, CA USA
| | - Karen Lobb
- Lgenia, Inc., 412 S Maple St, Fortville, IN USA
| | - Kyle J. McLean
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Igor M. R. Moura
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY USA
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - John Okombo
- 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
| | - N. Connor Payne
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA USA
| | - Andrew Plater
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | | | - Jair L. Siqueira-Neto
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
| | | | - Robert L. Summers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA USA
| | - Rumin Zhang
- Global Health Drug Discovery Institute, Beijing, China
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
| | | | - Brice Campo
- MMV Medicines for Malaria Venture, 1215, Geneva, Switzerland
| | - Beatriz Baragaña
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - James Duffy
- MMV Medicines for Malaria Venture, 1215, Geneva, Switzerland
| | - Ian H. Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA USA
| | | | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Case W. McNamara
- Calibr-Skaggs Institute for Innovative Medicines, a division of The Scripps Research Institute, La Jolla, CA USA
| | - Xiu Cheng
- Global Health Drug Discovery Institute, Beijing, China
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics & Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa
| | | | - 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
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA USA
| | - Daniel E. Goldberg
- Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO USA
| | - Marcus C. S. Lee
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Elizabeth A. Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
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4
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Cui L. Predicting Plasmodium drug resistance through in vitro evolution. Trends Parasitol 2025; 41:170-171. [PMID: 39933988 PMCID: PMC11884984 DOI: 10.1016/j.pt.2025.01.008] [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: 01/21/2025] [Accepted: 01/22/2025] [Indexed: 02/13/2025]
Abstract
Knowledge about the resistibility and targets of compounds critically informs antimalarial drug development. Luth et al. systematically analyzed the resistome of Plasmodium falciparum through in vitro evolution and whole-genome analysis of 724 clones resistant to 118 compounds, revealing novel drug targets, multidrug resistance loci, and key determinants of resistance.
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Affiliation(s)
- Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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5
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Evbuomwan IO, Adeyemi OS, Oluba OM. Aqueous extract of Enantia chlorantha Oliv. demonstrates antimalarial activity and improves redox imbalance and biochemical alterations in mice. BMC Complement Med Ther 2025; 25:73. [PMID: 39994639 PMCID: PMC11849376 DOI: 10.1186/s12906-025-04745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 01/03/2025] [Indexed: 02/26/2025] Open
Abstract
BACKGROUND Malaria is an infectious disease, which has continued to cause inconceivable loss of lives every year, almost unabatedly. Currently, it has become more difficult to treat the disease due to the emergence and spread of resistance to recommended antimalarial drugs. This situation necessitates an urgent search for antimalarial compounds with unique modes of action. Here, we investigate the antimalarial activity, antioxidant and anti-inflammatory capacity of Enantia chlorantha aqueous stem bark extract (EcASBE) in vivo. METHODS The extract was screened for selected phytoconstituents including alkaloids and flavonoids. We evaluated the antimalarial activity of EcASBE against Plasmodium berghei NK65 infection in mice, using curative, prophylactic, and suppressive antimalarial test models, respectively. In addition, the antioxidant and anti-inflammatory activities of the extract were assessed. RESULTS The EcASBE significantly (p < 0.05) inhibited parasitaemia dose-dependently, with the highest inhibition (80.4%) and prolonged survival (MST = 20) observed in the curative test. Our findings reveal significant (p < 0.05) improvement of serum ALT, AST, ALP, GGT, and levels of TNF-α, creatinine and urea following extract administration. Furthermore, the extract led to a significant (p < 0.05) rise in the levels of CAT, SOD, GPx, and GSH, with a concomitant reduction in NO and MDA levels. CONCLUSION The antimalarial, antioxidative, antiperoxidative, and inflammatory-inhibiting properties of the plant in infected mice demonstrate its great value for therapeutic intervention, and substantiate its use in traditional medicine for malaria treatment. Hence, further investigation to identify the repertoire of the active antimalarial components is warranted.
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Affiliation(s)
- Ikponmwosa Owen Evbuomwan
- SDG #03 Group - Good Health and Well-being Research Cluster, Landmark University, Ipetu Road, PMB 1001, Omu-Aran- 251101, Nigeria.
- Department of Biochemistry, Landmark University, Ipetu Road, PMB 1001, Omu-Aran-251101, Nigeria.
- Department of Food Science and Microbiology, Landmark University, Ipetu Road, PMB 1001, Omu-Aran-251101, Nigeria.
- Host-Pathogen Interactions and Disease Modeling Laboratory, Special Center for Molecular Medicine, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, Delhi-110067, India.
| | - Oluyomi Stephen Adeyemi
- Department of Biochemistry, Medicinal Biochemistry, Nanomedicine & Toxicology Laboratory, Bowen University, Iwo, 232101, Nigeria.
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan.
| | - Olarewaju Michael Oluba
- International Centre for Infectious Diseases, Biosafety and Biosecurity Research, Department of Medical Biochemistry, David Umahi Federal University of Health Sciences, Uburu, Nigeria.
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6
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Bremers E, Butler JH, Do Amaral LS, Merino EF, Almolhim H, Zhou B, Baptista RP, Totrov M, Carlier PR, Cassera MB. Stereospecific Resistance to N2-Acyl Tetrahydro-β-carboline Antimalarials Is Mediated by a PfMDR1 Mutation That Confers Collateral Drug Sensitivity. ACS Infect Dis 2025; 11:529-542. [PMID: 39808111 PMCID: PMC11828674 DOI: 10.1021/acsinfecdis.4c01001] [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: 12/12/2024] [Revised: 12/18/2024] [Accepted: 12/27/2024] [Indexed: 01/16/2025]
Abstract
Half the world's population is at risk of developing a malaria infection, which is caused by parasites of the genus Plasmodium. Currently, resistance has been identified to all clinically available antimalarials, highlighting an urgent need to develop novel compounds and better understand common mechanisms of resistance. We previously identified a novel tetrahydro-β-carboline compound, PRC1590, which potently kills the malaria parasite. To better understand its mechanism of action, we selected for and characterized resistance to PRC1590 in Plasmodium falciparum. Through in vitro selection of resistance to PRC1590, we have identified that a single-nucleotide polymorphism on the parasite's multidrug resistance protein 1 (PfMDR1 G293V) mediates resistance to PRC1590. This mutation results in stereospecific resistance and sensitizes parasites to other antimalarials, such as mefloquine, quinine, and MMV019017. Intraerythrocytic asexual stage specificity assays have revealed that PRC1590 is most potent during the trophozoite stage when the parasite forms a single digestive vacuole (DV) and actively digests hemoglobin. Moreover, fluorescence microscopy revealed that PRC1590 disrupts the function of the DV, indicating a potential molecular target associated with this organelle. Our findings mark a significant step in understanding the mechanism of resistance and the mode of action of this emerging class of antimalarials. In addition, our results suggest a potential link between resistance mediated by PfMDR1 and PRC1590's molecular target. This research underscores the pressing need for future research aimed at investigating the intricate relationship between a compound's chemical scaffold, molecular target, and resistance mutations associated with PfMDR1.
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Affiliation(s)
- Emily
K. Bremers
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Joshua H. Butler
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Leticia S. Do Amaral
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Emilio F. Merino
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Hanan Almolhim
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Bo Zhou
- Department
of Pharmaceutical Sciences, University of
Illinois Chicago, Chicago, Illinois 60612, United States
| | - Rodrigo P. Baptista
- Department
of Medicine, Houston Methodist Research
Institute, Houston, Texas 77030, United States
| | - Maxim Totrov
- MolSoft
LLC, San Diego, California 92121, United States
| | - Paul R. Carlier
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Pharmaceutical Sciences, University of
Illinois Chicago, Chicago, Illinois 60612, United States
| | - Maria Belen Cassera
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
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7
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Rawat M, Padalino G, Adika E, Okombo J, Yeo T, Brancale A, Fidock DA, Hoffmann KF, Lee MCS. Quinoxaline-based anti-schistosomal compounds have potent anti-plasmodial activity. PLoS Pathog 2025; 21:e1012216. [PMID: 39899599 PMCID: PMC11809919 DOI: 10.1371/journal.ppat.1012216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 02/10/2025] [Accepted: 01/14/2025] [Indexed: 02/05/2025] Open
Abstract
The human pathogens Plasmodium and Schistosoma are each responsible for over 200 million infections annually, especially in low- and middle-income countries. There is a pressing need for new drug targets for these diseases, driven by emergence of drug-resistance in Plasmodium and an overall dearth of drug targets against Schistosoma. Here, we explored the opportunity for pathogen-hopping by evaluating a series of quinoxaline-based anti-schistosomal compounds for their activity against P. falciparum. We identified compounds with low nanomolar potency against 3D7 and multidrug-resistant strains. In vitro resistance selections using wildtype and mutator P. falciparum lines revealed a low propensity for resistance. Only one of the series, compound 22, yielded resistance mutations, including point mutations in a non-essential putative hydrolase pfqrp1, as well as copy number amplification of a phospholipid-translocating ATPase, pfatp2, a potential target. Notably, independently generated CRISPR-edited mutants in pfqrp1 also showed resistance to compound 22 and a related analogue. Moreover, previous lines with pfatp2 copy number variations were similarly less susceptible to challenge with the new compounds. Finally, we examined whether the predicted hydrolase activity of PfQRP1 underlies its mechanism of resistance, showing that both mutation of the putative catalytic triad and a more severe loss of function mutation elicited resistance. Collectively, we describe a compound series with potent activity against two important pathogens and their potential target in P. falciparum.
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Affiliation(s)
- Mukul Rawat
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gilda Padalino
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, United Kingdom
- Swansea University Medical School, Swansea, United Kingdom
| | - Edem Adika
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Andrea Brancale
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Karl F. Hoffmann
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Marcus C. S. Lee
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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8
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Bouzón-Arnáiz I, Rawat M, Coyle R, Feufack-Donfack LB, Ea M, Orban A, Popovici J, Román-Álamo L, Fallica AN, Domínguez-Asenjo B, Moreno J, Arce EM, Mallo-Abreu A, Muñoz-Torrero D, Lee MCS, Fernàndez-Busquets X. YAT2150 is irresistible in Plasmodium falciparum and active against Plasmodium vivax and Leishmania clinical isolates. Sci Rep 2025; 15:2941. [PMID: 39848983 PMCID: PMC11758391 DOI: 10.1038/s41598-025-85346-y] [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: 09/10/2024] [Accepted: 01/02/2025] [Indexed: 01/25/2025] Open
Abstract
We recently characterized the potent antiplasmodial activity of the aggregated protein dye YAT2150, whose presumed mode of action is the inhibition of protein aggregation in the malaria parasite. Using single-dose and ramping methods, assays were done to select Plasmodium falciparum parasites resistant to YAT2150 concentrations ranging from 3× to 0.25× the in vitro IC50 of the compound (in the two-digit nM range) and performed a cross-resistance assessment in P. falciparum lines harboring mutations that make them resistant to a variety of antimalarial drugs. Resistant parasites did not emerge in vitro after 60 days of incubation, which postulates YAT2150 as an 'irresistible' antimalarial. The lyophilized compound is stable for at least one year stored at 25 °C. Tests performed in clinical isolates indicated that YAT2150 had also strong activity against Plasmodium vivax (IC50 between 4 and 36 nM) and Leishmania infantum (1.27 and 1.11 µM), placing it as a unique compound with perspectives of becoming the first drug to be used against both malaria and leishmaniasis.
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Affiliation(s)
- Inés Bouzón-Arnáiz
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, Barcelona, 08036, Spain
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Rachael Coyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Malen Ea
- Malaria Research Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, 120210, Phnom Penh, Cambodia
| | - Agnes Orban
- Malaria Research Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, 120210, Phnom Penh, Cambodia
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, 120210, Phnom Penh, Cambodia
- Infectious Disease Epidemiology and Analytics, Institut Pasteur, Paris, 75015, France
| | - Lucía Román-Álamo
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, Barcelona, 08036, Spain
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Antonino Nicolò Fallica
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, Barcelona, 08036, Spain
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Bárbara Domínguez-Asenjo
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology Instituto de Salud Carlos III, Majadahonda, 28220, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Moreno
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology Instituto de Salud Carlos III, Majadahonda, 28220, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, Madrid, Spain
| | - Elsa M Arce
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Ana Mallo-Abreu
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Xavier Fernàndez-Busquets
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-University of Barcelona), Rosselló 149-153, Barcelona, 08036, Spain.
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain.
- Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, Barcelona, 08028, Spain.
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9
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Shi Q, Wang C, Yang W, Ma X, Tang J, Zhang J, Zhu G, Wang Y, Liu Y, He X. Plasmodium falciparum transcription factor AP2-06B is mutated at high frequency in Southeast Asia but does not associate with drug resistance. Front Cell Infect Microbiol 2025; 14:1521152. [PMID: 39835275 PMCID: PMC11744005 DOI: 10.3389/fcimb.2024.1521152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 12/02/2024] [Indexed: 01/22/2025] Open
Abstract
Introduction A continuing challenge for malaria control is the ability of Plasmodium falciparum to develop resistance to antimalarial drugs. Members within the Plasmodium transcription factor family AP2 regulate the growth and development of the parasite, and are also thought to be involved in unclear aspects of drug resistance. Here we screened for single nucleotide polymorphisms (SNPs) within the AP2 family and identified 6 non-synonymous mutations within AP2-06B (PF3D7_0613800), with allele frequencies greater than 0.05. One mutation, K3124R, was located in a PfAP2-06B AP2 domain. Methods To investigate transcriptional regulation by PfAP2-06B, ChIP-seq assays were performed on 3D7/PfAP2-06B-GFP schizonts using antibodies against GFP. The DNA sequences of the artemisinin-resistant CWX and the quinoline-resistant strains PfDd2 and Pf7G8 were analyzed for the genetic diversity of AP2-06B, compared with the Pf3D7 strain as a reference sequence. To determine whether AP2-06B can alter the expression of pfk13 and pfcrt, as well as cause artemisinin and quinoline resistance in Plasmodium, we generated both a K3124R mutation and conditional knockdown of AP2-06B in Pf3D7 using CRISPR/Cas9-mediated genome editing. Results ChIP-Seq analysis showed that AP2-06B can bind to the loci of the Plasmodium genes pfk13 and pfcrt. The AP2-06B K3124R mutation was also found in the artemisinin-resistant parasite strain CWX and the chloroquine-resistant strains Dd2 and 7G8. Contrary to expectation, Pf3D7 Plasmodium lines modified by either K3124R mutation of AP2-06B or conditional knockdown of AP2-06B did not have altered sensitivity to artemisinin or quinolines by modulating pfk13 or pfcrt expression. Discussion AP2-06B was predicted to be associated with artemisinin and quinoline resistance, but no change in resistance was observed after mutation or conditional knockdown. Given the multigenic nature of resistance, it might be difficult to recreate a resistance phenotype. In conclusion, whether AP2-06B regulates the development of artemisinin or quinoline resistance remains to be studied.
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Affiliation(s)
- Qiyang Shi
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai, China
| | - Wenluan Yang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Xiaoqin Ma
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Jiayao Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yinlong Wang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
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10
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Bravo P, Bizzarri L, Steinbrunn D, Lohse J, Hirsch AKH, Mäser P, Rottmann M, Hahne H. Integral Solvent-Induced Protein Precipitation for Target-Engagement Studies in Plasmodium falciparum. ACS Infect Dis 2024; 10:4073-4086. [PMID: 39631773 DOI: 10.1021/acsinfecdis.4c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
The limited understanding of the mechanism of action (MoA) of several antimalarials and the rise of drug resistance toward existing malaria therapies emphasizes the need for new strategies to uncover the molecular target of compounds in Plasmodium falciparum. Integral solvent-induced protein precipitation (iSPP) is a quantitative mass spectrometry-based (LC-MS/MS) proteomics technique. The iSPP leverages the change in solvent-induced denaturation of the drug-bound protein relative to its unbound state, allowing identification of the direct drug-protein target without the need to modify the drug. Here, we demonstrate proof-of-concept of iSPP in P. falciparum (Pf) lysate. At first, we profiled the solvent-induced denaturation behavior of the Pf proteome, generating denaturation curves and determining the melting concentration (CM) of 2712 proteins. We then assessed the extent of stabilization of three antimalarial target proteins in multiple organic solvent gradients, allowing for a rational selection of an optimal solvent gradient. Subsequently, we validated iSPP by successfully showing target-engagement of several standard antimalarials. The iSPP assay allows the testing of multiple conditions within reasonable LC-MS/MS measurement time. Furthermore, it requires a minimal amount of protein input, reducing culturing time and simplifying protein extraction. We envision that iSPP will be useful as a complementary tool for MoA studies for next-generation antimalarials.
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Affiliation(s)
- Patricia Bravo
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Lorenzo Bizzarri
- OmicScouts GmbH, Lise-Meitner-Straße 30, D-85354 Freising, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, D-66123 Saarbrücken, Germany
| | - Dominik Steinbrunn
- OmicScouts GmbH, Lise-Meitner-Straße 30, D-85354 Freising, Germany
- TUM School of Natural Sciences, Department of Bioscience, Technical University of Munich, Center for Functional Protein Assemblies (CPA), D-85748 Garching bei München, Germany
| | - Jonas Lohse
- OmicScouts GmbH, Lise-Meitner-Straße 30, D-85354 Freising, Germany
| | - Anna K H Hirsch
- Department of Pharmacy, Saarland University, Campus E8.1, D-66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8.1, D-66123 Saarbrücken, Germany
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Hannes Hahne
- OmicScouts GmbH, Lise-Meitner-Straße 30, D-85354 Freising, Germany
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11
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Sakura T, Ishii R, Yoshida E, Kita K, Kato T, Inaoka DK. Accelerating Antimalarial Drug Discovery with a New High-Throughput Screen for Fast-Killing Compounds. ACS Infect Dis 2024; 10:4115-4126. [PMID: 39561299 DOI: 10.1021/acsinfecdis.4c00328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
The urgent need for rapidly acting compounds in the development of antimalarial drugs underscores the significance of such compounds in overcoming resistance issues and improving patient adherence to antimalarial treatments. The present study introduces a high-throughput screening (HTS) approach using 1536-well plates, employing Plasmodium falciparum lactate dehydrogenase (PfLDH) combined with nitroreductase (NTR) and fluorescent probes to evaluate inhibition of the growth of the asexual blood stage of malaria parasites. This method was adapted to efficiently assess the speed of action profiling (SAP) in a 384-well plate format, streamlining the traditionally time-consuming screening process. By successfully screening numerous compounds, this approach identified fast-killing hits early in the screening process, addressing challenges associated with artemisinin-based combination therapies. The high-throughput SAP method is expected to be of value in continuously monitoring fast-killing properties during structure-activity relationship studies, expediting the identification and development of novel, rapidly acting antimalarial drugs within phenotypic drug discovery campaigns.
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Affiliation(s)
- Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
| | - Ryuta Ishii
- Department of Cellular Architecture Studies, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Eri Yoshida
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Teruhisa Kato
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
- Exploratory Research for Drug Discovery, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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12
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Xie SC, Tai CW, Morton CJ, Ma L, Huang SC, Wittlin S, Du Y, Hu Y, Dogovski C, Salimimarand M, Griffin R, England D, de la Cruz E, Deni I, Yeo T, Burkhard AY, Striepen J, Schindler KA, Crespo B, Gamo FJ, Khandokar Y, Hutton CA, Rabie T, Birkholtz LM, Famodimu MT, Delves MJ, Bolsher J, Koolen KMJ, van der Laak R, Aguiar ACC, Pereira DB, Guido RVC, Creek DJ, Fidock DA, Dick LR, Brand SL, Gould AE, Langston S, Griffin MDW, Tilley L. A potent and selective reaction hijacking inhibitor of Plasmodium falciparum tyrosine tRNA synthetase exhibits single dose oral efficacy in vivo. PLoS Pathog 2024; 20:e1012429. [PMID: 39652589 DOI: 10.1371/journal.ppat.1012429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 12/26/2024] [Accepted: 10/31/2024] [Indexed: 12/28/2024] Open
Abstract
The Plasmodium falciparum cytoplasmic tyrosine tRNA synthetase (PfTyrRS) is an attractive drug target that is susceptible to reaction-hijacking by AMP-mimicking nucleoside sulfamates. We previously identified an exemplar pyrazolopyrimidine ribose sulfamate, ML901, as a potent reaction hijacking inhibitor of PfTyrRS. Here we examined the stage specificity of action of ML901, showing very good activity against the schizont stage, but lower trophozoite stage activity. We explored a series of ML901 analogues and identified ML471, which exhibits improved potency against trophozoites and enhanced selectivity against a human cell line. Additionally, it has no inhibitory activity against human ubiquitin-activating enzyme (UAE) in vitro. ML471 exhibits low nanomolar activity against asexual blood stage P. falciparum and potent activity against liver stage parasites, gametocytes and transmissible gametes. It is fast-acting and exhibits a long in vivo half-life. ML471 is well-tolerated and shows single dose oral efficacy in the SCID mouse model of P. falciparum malaria. We confirm that ML471 is a reaction hijacking inhibitor that is converted into a tight binding Tyr-ML471 conjugate by the PfTyrRS enzyme. A crystal structure of the PfTyrRS/ Tyr-ML471 complex offers insights into improved potency, while molecular docking into UAE provides a rationale for improved selectivity.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Chia-Wei Tai
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, Victoria, Australia
| | - Liting Ma
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Shih-Chung Huang
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yongbo Hu
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mina Salimimarand
- School of Chemistry, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robert Griffin
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Dylan England
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Elisa de la Cruz
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Ioanna Deni
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Anna Y Burkhard
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Josefine Striepen
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Kyra A Schindler
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Benigno Crespo
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | | | | | - Craig A Hutton
- School of Chemistry, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tayla Rabie
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
| | - Mufuliat T Famodimu
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael J Delves
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | | | - Anna C C Aguiar
- Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | - Dhelio B Pereira
- Research Center for Tropical Medicine of Rondonia, Porto Velho, Brazil
| | - Rafael V C Guido
- Sao Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Darren J Creek
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, New York, United States of America
| | - Lawrence R Dick
- Seofon Consulting, Natick, Massachusetts, United States of America
| | | | - Alexandra E Gould
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Steven Langston
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
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13
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Luth MR, Godinez-Macias KP, Chen D, Okombo J, Thathy V, Cheng X, Daggupati S, Davies H, Dhingra SK, Economy JM, Edgar RCS, Gomez-Lorenzo MG, Istvan ES, Jado JC, LaMonte GM, Melillo B, Mok S, Narwal SK, Ndiaye T, Ottilie S, Diaz SP, Park H, Peña S, Rocamora F, Sakata-Kato T, Small-Saunders JL, Summers RL, Tumwebaze PK, Vanaerschot M, Xia G, Yeo T, You A, Gamo FJ, Goldberg DE, Lee MC, McNamara CW, Ndiaye D, Rosenthal PJ, Schreiber SL, Serra G, De Siqueira-Neto JL, Skinner-Adams TS, Uhlemann AC, Kato N, Lukens AK, Wirth DF, Fidock DA, Winzeler EA. Systematic in vitro evolution in Plasmodium falciparum reveals key determinants of drug resistance. Science 2024; 386:eadk9893. [PMID: 39607932 PMCID: PMC11809290 DOI: 10.1126/science.adk9893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 05/21/2024] [Accepted: 10/07/2024] [Indexed: 11/30/2024]
Abstract
Surveillance of drug resistance and the discovery of novel targets-key objectives in the fight against malaria-rely on identifying resistance-conferring mutations in Plasmodium parasites. Current approaches, while successful, require laborious experimentation or large sample sizes. To elucidate shared determinants of antimalarial resistance that can empower in silico inference, we examined the genomes of 724 Plasmodium falciparum clones, each selected in vitro for resistance to one of 118 compounds. We identified 1448 variants in 128 recurrently mutated genes, including drivers of antimalarial multidrug resistance. In contrast to naturally occurring variants, those selected in vitro are more likely to be missense or frameshift, involve bulky substitutions, and occur in conserved, ordered protein domains. Collectively, our dataset reveals mutation features that predict drug resistance in eukaryotic pathogens.
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Affiliation(s)
- Madeline R. Luth
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | | | - Daisy Chen
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Vandana Thathy
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Xiu Cheng
- Global Health Drug Discovery Institute; Beijing, 100192, China
| | - Sindhu Daggupati
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - Heledd Davies
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Satish K. Dhingra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Jan M. Economy
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - Rebecca C. S. Edgar
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | | | - 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
| | - Juan Carlos Jado
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - Gregory M. LaMonte
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - Bruno Melillo
- Chemical Biology and Therapeutics Science Program, Broad Institute; Cambridge, MA 02142, USA
| | - Sachel Mok
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Sunil K. Narwal
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Tolla Ndiaye
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Sabine Ottilie
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - Sara Palomo Diaz
- Global Health Medicines R&D, GSK; Tres Cantos, Madrid 28760, Spain
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Stella Peña
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República; Montevideo, Montevideo CC1157, Uruguay
| | - Frances Rocamora
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
| | - Tomoyo Sakata-Kato
- Global Health Drug Discovery Institute; Beijing, 100192, China
- Department of Protozoology, Nekken Institute for Tropical Medicine, Nagasaki University; Nagasaki, 852-8523, Japan
| | - Jennifer L. Small-Saunders
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Robert L. Summers
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, The Broad Institute; Cambridge, MA 02142, USA
| | | | - Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Ashley You
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, 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
| | - Marcus C.S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Case W. McNamara
- Calibr, a division of The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Daouda Ndiaye
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Philip J. Rosenthal
- Department of Medicine, University of California San Francisco; San Francisco, CA 94115, USA
| | | | - Gloria Serra
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República; Montevideo, Montevideo CC1157, Uruguay
| | - Jair Lage De Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego; La Jolla, CA 92037, USA
| | - Tina S. Skinner-Adams
- Griffith Institute for Drug Discovery, Griffith University; Nathan, Queensland 4111, Australia
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Nobutaka Kato
- Global Health Drug Discovery Institute; Beijing, 100192, China
- Department of Protozoology, Nekken Institute for Tropical Medicine, Nagasaki University; Nagasaki, 852-8523, Japan
| | - Amanda K. Lukens
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, The Broad Institute; Cambridge, MA 02142, USA
| | - Dyann F. Wirth
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, The Broad Institute; Cambridge, MA 02142, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center; New York, New York 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego; La Jolla, CA 92037, USA
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14
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Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Magalhaes LG, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean K, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining. RESEARCH SQUARE 2024:rs.3.rs-5412515. [PMID: 39649165 PMCID: PMC11623766 DOI: 10.21203/rs.3.rs-5412515/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2024]
Abstract
The identification of novel drug targets for the purpose of designing small molecule inhibitors is key component to modern drug discovery. In malaria parasites, discoveries of antimalarial targets have primarily occurred retroactively by investigating the mode of action of compounds found through phenotypic screens. Although this method has yielded many promising candidates, it is time- and resource-consuming and misses targets not captured by existing antimalarial compound libraries and phenotypic assay conditions. Leveraging recent advances in protein structure prediction and data mining, we systematically assessed the Plasmodium falciparum genome for proteins amenable to target-based drug discovery, identifying 867 candidate targets with evidence of small molecule binding and blood stage essentiality. Of these, 540 proteins showed strong essentiality evidence and lack inhibitors that have progressed to clinical trials. Expert review and rubric-based scoring of this subset based on additional criteria such as selectivity, structural information, and assay developability yielded 67 high priority candidates. This study also provides a genome-wide data resource and implements a generalizable framework for systematically evaluating and prioritizing novel pathogenic disease targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anil K Gupta
- Calibr-Skaggs Institute for Innovative Medicines
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xiu Cheng
- Global Health Drug Discovery Institute
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15
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Mathew J, Zhou B, Haney RS, Kunz KA, Do Amaral LS, Roy Chowdhury R, Butler JH, Li H, Chakraborty AJ, Tabassum A, Bremers EK, Merino EF, Coyle R, Lee MCS, Baud D, Brand S, Totrov M, Cassera MB, Carlier PR. β-Carboline-3-carboxamide Antimalarials: Structure-Activity Relationship, ADME-Tox Studies, and Resistance Profiling. ACS Infect Dis 2024; 10:3951-3962. [PMID: 39466084 PMCID: PMC11973535 DOI: 10.1021/acsinfecdis.4c00653] [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] [Indexed: 10/29/2024]
Abstract
The development of parasite resistance to both artemisinin derivatives and their partner drugs jeopardizes the effectiveness of the artemisinin combination therapy. Thus, the discovery of new antimalarial drugs, with new mechanisms of action, is urgently needed. We recently disclosed that β-carboline 1a was orally efficacious in Plasmodium berghei-infected mice and that it showed low cross-resistance between susceptible Plasmodium falciparum and four different drug-resistant strains. In this report, we describe the synthesis and in vitro antimalarial evaluation of 91 new derivatives of 1a. The asexual blood stage growth inhibition data show a clear preference for a 3,4-dihalogenated, 3,5-dihalogenated, 3,4,5-trichloro-, or 4-trifluoromethyphenyl ring at the C1-position. The most potent compound, 3,4,5-trichlorophenyl-substituted 42a, is twice as potent as 1a. Six potent analogues were assessed for their drug-like properties, and four of these were subjected to in vitro barcoded cross-resistance profiling. Compounds 1a, 1m, 42a, and 42m showed no cross-resistance to 32 resistance mutations on the Dd2 genetic background and 10 resistance mutations on the 3D7 genetic background. These data suggest that compounds in this scaffold possess a novel mechanism of antimalarial action.
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Affiliation(s)
- Jopaul Mathew
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
| | - Bo Zhou
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Reagan S Haney
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, 120 E. Green Street, Athens, Georgia 30602, United States
| | - Kevin A Kunz
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Leticia S Do Amaral
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, 120 E. Green Street, Athens, Georgia 30602, United States
| | - Rudraneel Roy Chowdhury
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Joshua H Butler
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, 120 E. Green Street, Athens, Georgia 30602, United States
| | - Haibo Li
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
| | - Amarraj J Chakraborty
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
| | - Anika Tabassum
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
| | - Emily K Bremers
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, 120 E. Green Street, Athens, Georgia 30602, United States
| | - Emilio F Merino
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, 120 E. Green Street, Athens, Georgia 30602, United States
| | - Rachael Coyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, U.K
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 4HN, U.K
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, U.K
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 4HN, U.K
| | - Delphine Baud
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Stephen Brand
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Maxim Totrov
- Molsoft LLC, 11999 Sorrento Valley Road, San Diego, California 92121, United States
| | - Maria Belen Cassera
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, 120 E. Green Street, Athens, Georgia 30602, United States
| | - Paul R Carlier
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 1040 Drillfield Drive, Blacksburg, Virginia 24061, United States
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Chemistry, University of Illinois Chicago, 845 W Taylor Street, Chicago, Illinois 60607, United States
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16
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Wunderlich J, Kotov V, Votborg-Novél L, Ntalla C, Geffken M, Peine S, Portugal S, Strauss J. Iron transport pathways in the human malaria parasite Plasmodium falciparum revealed by RNA-sequencing. Front Cell Infect Microbiol 2024; 14:1480076. [PMID: 39575308 PMCID: PMC11578967 DOI: 10.3389/fcimb.2024.1480076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 10/14/2024] [Indexed: 11/24/2024] Open
Abstract
Host iron deficiency is protective against severe malaria as the human malaria parasite Plasmodium falciparum depends on bioavailable iron from its host to proliferate. The essential pathways of iron acquisition, storage, export, and detoxification in the parasite differ from those in humans, as orthologs of the mammalian transferrin receptor, ferritin, or ferroportin, and a functional heme oxygenase are absent in P. falciparum. Thus, the proteins involved in these processes may be excellent targets for therapeutic development, yet remain largely unknown. Here, we show that parasites cultured in erythrocytes from an iron-deficient donor displayed significantly reduced growth rates compared to those grown in red blood cells from healthy controls. Sequencing of parasite RNA revealed diminished expression of genes involved in overall metabolism, hemoglobin digestion, and metabolite transport under low-iron versus control conditions. Supplementation with hepcidin, a specific ferroportin inhibitor, resulted in increased labile iron levels in erythrocytes, enhanced parasite replication, and transcriptional upregulation of genes responsible for merozoite motility and host cell invasion. Through endogenous GFP tagging of differentially expressed putative transporter genes followed by confocal live-cell imaging, proliferation assays with knockout and knockdown lines, and protein structure predictions, we identified six proteins that are likely required for ferrous iron transport in P. falciparum. Of these, we localized PfVIT and PfZIPCO to cytoplasmic vesicles, PfMRS3 to the mitochondrion, and the novel putative iron transporter PfE140 to the plasma membrane for the first time in P. falciparum. PfNRAMP/PfDMT1 and PfCRT were previously reported to efflux Fe2+ from the digestive vacuole. Our data support a new model for parasite iron homeostasis, in which PfE140 is involved in iron uptake across the plasma membrane, PfMRS3 ensures non-redundant Fe2+ supply to the mitochondrion as the main site of iron utilization, PfVIT transports excess iron into cytoplasmic vesicles, and PfZIPCO exports Fe2+ from these organelles in case of iron scarcity. These results provide new insights into the parasite's response to differential iron availability in its environment and into the mechanisms of iron transport in P. falciparum as promising candidate targets for future antimalarial drugs.
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Affiliation(s)
- Juliane Wunderlich
- Malaria Parasite Biology Group, Max Planck Institute for Infection Biology (MPIIB), Berlin, Germany
- Membrane Protein Structural Biology Group, Center for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Vadim Kotov
- Membrane Protein Structural Biology Group, Center for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Lasse Votborg-Novél
- Malaria Parasite Biology Group, Max Planck Institute for Infection Biology (MPIIB), Berlin, Germany
| | - Christina Ntalla
- Malaria Parasite Biology Group, Max Planck Institute for Infection Biology (MPIIB), Berlin, Germany
| | - Maria Geffken
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Silvia Portugal
- Malaria Parasite Biology Group, Max Planck Institute for Infection Biology (MPIIB), Berlin, Germany
| | - Jan Strauss
- Membrane Protein Structural Biology Group, Center for Structural Systems Biology (CSSB), Hamburg, Germany
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17
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Singhal R, Prata IO, Bonnell VA, Llinás M. Unraveling the complexities of ApiAP2 regulation in Plasmodium falciparum. Trends Parasitol 2024; 40:987-999. [PMID: 39419713 DOI: 10.1016/j.pt.2024.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 09/13/2024] [Accepted: 09/13/2024] [Indexed: 10/19/2024]
Abstract
The regulation of gene expression in Plasmodium spp., the causative agents of malaria, relies on precise transcriptional control. Malaria parasites encode a limited repertoire of sequence-specific transcriptional regulators dominated by the apicomplexan APETALA 2 (ApiAP2) protein family. ApiAP2 DNA-binding proteins play critical roles at all stages of the parasite life cycle. Recent studies have provided mechanistic insight into the functional roles of many ApiAP2 proteins. Two major areas that have advanced significantly are the identification of ApiAP2-containing protein complexes and the role of ApiAP2 proteins in malaria parasite sexual development. In this review, we present recent advances on the functional biology of ApiAP2 proteins and their role in regulating gene expression across the blood stages of the parasite life cycle.
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Affiliation(s)
- Ritwik Singhal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Isadora O Prata
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Victoria A Bonnell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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18
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Shaw PJ, Prommana P, Thongpanchang C, Kamchonwongpaisan S, Kongkasuriyachai D, Wang Y, Zhou Z, Zhou Y. Antimalarial mechanism of action of the natural product 9-methoxystrobilurin G. Mol Omics 2024; 20:584-594. [PMID: 39262389 DOI: 10.1039/d4mo00088a] [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: 09/13/2024]
Abstract
The natural product 9-methoxystrobilurin G (9MG) from Favolaschia spp basidiomycetes is a potent and selective antimalarial. The mechanism of action of 9MG is unknown. We induced 9MG resistance in Plasmodium falciparum 3D7 and Dd2 strains and identified mutations associated with resistance by genome sequencing. All 9MG-resistant clones possessed missense mutations in the cytochrome b (CYTB) gene, a key component of mitochondrial complex III. The mutations map to the quinol oxidation site of CYTB, which is also the target of antimalarials such as atovaquone. In a complementary approach to identify protein targets of 9MG, a photoactivatable derivative of 9MG was synthesized and applied in chemoproteomic-based target profiling. Three components of mitochondrial complex III (QCR7, QCR9, and COX15) were specifically enriched consistent with 9MG targeting CYTB and complex III function in P. falciparum. Inhibition of complex III activity by 9MG was confirmed by ubiquinone cytochrome c reductase assay using P. falciparum extract. The findings from this study may be useful for developing novel antimalarials targeting CYTB.
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Affiliation(s)
- Philip J Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Parichat Prommana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Chawanee Thongpanchang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Darin Kongkasuriyachai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yiqing Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, China.
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19
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Wall RJ, MacGowan SA, Hallyburton I, Syed AJ, Ajay Castro S, Dey G, Milne R, Patterson S, Phelan J, Wiedemar N, Wyllie S. ResMAP-a saturation mutagenesis platform enabling parallel profiling of target-specific resistance-conferring mutations in Plasmodium. mBio 2024; 15:e0170824. [PMID: 39191404 PMCID: PMC11481570 DOI: 10.1128/mbio.01708-24] [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: 06/04/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
New and improved drugs are required for the treatment and ultimate eradication of malaria. The efficacy of front-line therapies is now threatened by emerging drug resistance; thus, new tools to support the development of drugs with a lower propensity for resistance are needed. Here, we describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in Plasmodium drug targets. Proof-of-concept studies focused on interrogating the antimalarial drug target, Plasmodium falciparum lysyl tRNA synthetase (PfKRS). Saturation mutagenesis was used to construct a plasmid library encoding all conceivable mutations within a 20-residue span at the base of the PfKRS ATP-binding pocket. The superior transfection efficiency of Plasmodium knowlesi was exploited to generate a high coverage parasite library expressing PfKRS bearing all possible amino acid changes within this region of the enzyme. The selection of the library with PfKRS inhibitors, cladosporin and DDD01510706, successfully identified multiple resistance-conferring substitutions. Genetic validation of a subset of these mutations confirmed their direct role in resistance, with computational modeling used to dissect the structural basis of resistance. The application of ResMAP to inform the development of resistance-resilient antimalarials of the future is discussed. IMPORTANCE An increase in treatment failures for malaria highlights an urgent need for new tools to understand and minimize the spread of drug resistance. We describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in Plasmodium spp, the causative agent of malaria. Saturation mutagenesis was used to generate a mutation library containing all conceivable mutations for a region of the antimalarial-binding site of a promising drug target, Plasmodium falciparum lysyl tRNA synthetase (PfKRS). Screening of this high-coverage library with characterized PfKRS inhibitors revealed multiple resistance-conferring substitutions including several clinically relevant mutations. Genetic validation of these mutations confirmed resistance of up to 100-fold and computational modeling dissected their role in drug resistance. We discuss potential applications of this data including the potential to design compounds that can bypass the most serious resistance mutations and future resistance surveillance.
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Affiliation(s)
- Richard J. Wall
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Stuart A. MacGowan
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Irene Hallyburton
- Drug Discovery Unit, Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Aisha J. Syed
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Gourav Dey
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Rachel Milne
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Stephen Patterson
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Natalie Wiedemar
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
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20
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Ferreira LT, Cassiano GC, Alvarez LCS, Okombo J, Calit J, Fontinha D, Gil-Iturbe E, Coyle R, Andrade CH, Sunnerhagen P, Bargieri DY, Prudêncio M, Quick M, Cravo PV, Lee MCS, Fidock DA, Costa FTM. A novel 4-aminoquinoline chemotype with multistage antimalarial activity and lack of cross-resistance with PfCRT and PfMDR1 mutants. PLoS Pathog 2024; 20:e1012627. [PMID: 39471233 PMCID: PMC11521309 DOI: 10.1371/journal.ppat.1012627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/30/2024] [Indexed: 11/01/2024] Open
Abstract
Artemisinin-based combination therapy (ACT) is the mainstay of effective treatment of Plasmodium falciparum malaria. However, the long-term utility of ACTs is imperiled by widespread partial artemisinin resistance in Southeast Asia and its recent emergence in parts of East Africa. This underscores the need to identify chemotypes with new modes of action (MoAs) to circumvent resistance to ACTs. In this study, we characterized the asexual blood stage antiplasmodial activity and resistance mechanisms of LDT-623, a 4-aminoquinoline (4-AQ). We also detected LDT-623 activity against multiple stages (liver schizonts, stage IV-V gametocytes, and ookinetes) of Plasmodium's life cycle, a feature unlike other 4-AQs such as chloroquine (CQ) and piperaquine (PPQ). Using heme fractionation profiling and drug uptake studies in PfCRT-containing proteoliposomes, we observed inhibition of hemozoin formation and PfCRT-mediated transport, which constitute characteristic features of 4-AQs' MoA. We also found minimal cross-resistance to LDT-623 in a panel of mutant pfcrt or pfmdr1 lines, but not the PfCRT F145I mutant that is highly resistant to PPQ resistance yet is very unfit. No P. falciparum parasites were recovered in an in vitro resistance selection study, suggesting a high barrier for resistance to emerge. Finally, a competitive growth assay comprising >50 barcoded parasite lines with mutated resistance mediators or major drug targets found no evidence of cross-resistance. Our findings support further exploration of this promising 4-AQ.
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Affiliation(s)
- Letícia Tiburcio Ferreira
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Gustavo Capatti Cassiano
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Luis Carlos Salazar Alvarez
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Juliana Calit
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Diana Fontinha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Rachael Coyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- Center for the Research and Advancement in Fragments and molecular Targets, School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Center for Excellence in Artificial Intelligence, Institute of Informatics, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Youssef Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Miguel Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Physiology & Cellular Biophysics, Columbia University Irving Medical Center, New York, New York, United States of America
- New York State Psychiatric Institute, Area Neuroscience – Molecular Therapeutics, New York, New York, United States of America
| | - Pedro V. Cravo
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, New York, United States of America
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
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21
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Kanai M, Mok S, Yeo T, Shears MJ, Ross LS, Jeon JH, Narwal S, Haile MT, Tripathi AK, Mlambo G, Kim J, Gil-Iturbe E, Okombo J, Fairhurst KJ, Bloxham T, Bridgford JL, Sheth T, Ward KE, Park H, Rozenberg FD, Quick M, Mancia F, Lee MC, Small-Saunders JL, Uhlemann AC, Sinnis P, Fidock DA. Identification of the drug/metabolite transporter 1 as a marker of quinine resistance in a NF54×Cam3.II P. falciparum genetic cross. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.27.615529. [PMID: 39386571 PMCID: PMC11463348 DOI: 10.1101/2024.09.27.615529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The genetic basis of Plasmodium falciparum resistance to quinine (QN), a drug used to treat severe malaria, has long been enigmatic. To gain further insight, we used FRG-NOD human liver-chimeric mice to conduct a P. falciparum genetic cross between QN-sensitive and QN-resistant parasites, which also differ in their susceptibility to chloroquine (CQ). By applying different selective conditions to progeny pools prior to cloning, we recovered 120 unique recombinant progeny. These progeny were subjected to drug profiling and QTL analyses with QN, CQ, and monodesethyl-CQ (md-CQ, the active metabolite of CQ), which revealed predominant peaks on chromosomes 7 and 12, consistent with a multifactorial mechanism of resistance. A shared chromosome 12 region mapped to resistance to all three antimalarials and was preferentially co-inherited with pfcrt. We identified an ATP-dependent zinc metalloprotease (FtsH1) as one of the top candidates and observed using CRISPR/Cas9 SNP-edited lines that ftsh1 is a potential mediator of QN resistance and a modulator of md-CQ resistance. As expected, CQ and md-CQ resistance mapped to a chromosome 7 region harboring pfcrt. However, for QN, high-grade resistance mapped to a chromosome 7 peak centered 295kb downstream of pfcrt. We identified the drug/metabolite transporter 1 (DMT1) as the top candidate due to its structural similarity to PfCRT and proximity to the peak. Deleting DMT1 in QN-resistant Cam3.II parasites significantly sensitized the parasite to QN but not to the other drugs tested, suggesting that DMT1 mediates QN response specifically. We localized DMT1 to structures associated with vesicular trafficking, as well as the parasitophorous vacuolar membrane, lipid bodies, and the digestive vacuole. We also observed that mutant DMT1 transports more QN than the wild-type isoform in vitro. Our study demonstrates that DMT1 is a novel marker of QN resistance and a new chromosome 12 locus associates with CQ and QN response, with ftsh1 is a potential candidate, suggesting these genes should be genotyped in surveillance and clinical settings.
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Affiliation(s)
- Mariko Kanai
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Sachel Mok
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, NY, USA
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Melanie J. Shears
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, MD, USA
| | - Leila S. Ross
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
| | - Jin H. Jeon
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Sunil Narwal
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Meseret T. Haile
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
| | - Abhai K. Tripathi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, MD, USA
| | - Godfree Mlambo
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, MD, USA
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, NY, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, NY, USA
| | - John Okombo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Kate J. Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Talia Bloxham
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Jessica L. Bridgford
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Tanaya Sheth
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Kurt E. Ward
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, NY, USA
| | - Felix D. Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, NY, USA
| | - Matthias Quick
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, NY, USA
- Department of Psychiatry, Columbia University Irving Medical Center, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, NY, USA
| | - 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
| | - Jennifer L. Small-Saunders
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, NY, USA
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, MD, USA
| | - David A. Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, NY, USA
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22
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Li X, Li S, Zhang W, Wang Q, Zou W. Impacts of P4-ATPase Deletion on Membrane Asymmetry and Disease Development. Cell Biochem Funct 2024; 42:e70004. [PMID: 39425455 DOI: 10.1002/cbf.70004] [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: 06/11/2024] [Revised: 10/01/2024] [Accepted: 10/04/2024] [Indexed: 10/21/2024]
Abstract
Phospholipids exhibit an asymmetrical distribution on the cell membrane. P4-ATPases, type IV lipid flippases, are responsible for establishing and maintaining this phospholipid compositional asymmetry. The essential β subunit CDC50 (also known as TMEM30) assists in the transport and proper functioning of P4-ATPases. Deletion of P4-ATPases and its β subunit disrupts the membrane asymmetry, impacting the growth and development and leading to various diseases affecting the nervous, skeletal muscle, digestive, and hematopoietic systems. This review discusses the crucial roles of P4-ATPases and their β subunit in Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, and mammals, offering valuable insights for future research.
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Affiliation(s)
- Xinyu Li
- School of Public Health, Kunming Medical University, Kunming, China
| | - Shuzhen Li
- School of Public Health, Kunming Medical University, Kunming, China
| | - Weipu Zhang
- School of Public Health, Kunming Medical University, Kunming, China
| | - Qi Wang
- School of Public Health, Kunming Medical University, Kunming, China
| | - Wei Zou
- School of Public Health, Kunming Medical University, Kunming, China
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23
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Acosta-Zaldívar M, Qi W, Mishra A, Roy U, King WR, Li Y, Patton-Vogt J, Anderson MZ, Köhler JR. Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity. PLoS Genet 2024; 20:e1011156. [PMID: 39137212 PMCID: PMC11343460 DOI: 10.1371/journal.pgen.1011156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 08/23/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling, oxidative stress resistance and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. Initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity eventually resolved, as populations gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while severity of others like membrane stress responses diverged from Pi scarcity fitness. Among preliminary candidate genes for contributors to fitness recovery, those with links to TORC1 were overrepresented. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth, stress resistance and virulence.
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Affiliation(s)
- Maikel Acosta-Zaldívar
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Abhishek Mishra
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Udita Roy
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - William R. King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Yuping Li
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Matthew Z. Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Julia R. Köhler
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
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24
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Giannangelo C, Challis MP, Siddiqui G, Edgar R, Malcolm TR, Webb CT, Drinkwater N, Vinh N, Macraild C, Counihan N, Duffy S, Wittlin S, Devine SM, Avery VM, De Koning-Ward T, Scammells P, McGowan S, Creek DJ. Chemoproteomics validates selective targeting of Plasmodium M1 alanyl aminopeptidase as an antimalarial strategy. eLife 2024; 13:RP92990. [PMID: 38976500 PMCID: PMC11230628 DOI: 10.7554/elife.92990] [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] [Indexed: 07/10/2024] Open
Abstract
New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum (PfA-M1) and Plasmodium vivax (PvA-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets PfA-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on PfA-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of PfA-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.
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Affiliation(s)
- Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Matthew P Challis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Rebecca Edgar
- School of Medicine, Deakin UniversityGeelongAustralia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin UniversityGeelongAustralia
| | - Tess R Malcolm
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityClaytonAustralia
- Centre to Impact AMR, Monash UniversityClaytonAustralia
| | - Chaille T Webb
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityClaytonAustralia
- Centre to Impact AMR, Monash UniversityClaytonAustralia
| | - Nyssa Drinkwater
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityClaytonAustralia
- Centre to Impact AMR, Monash UniversityClaytonAustralia
| | - Natalie Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Christopher Macraild
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Natalie Counihan
- School of Medicine, Deakin UniversityGeelongAustralia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin UniversityGeelongAustralia
| | - Sandra Duffy
- Discovery Biology, Centre for Cellular Phenomics, Griffith UniversityNathanAustralia
| | - Sergio Wittlin
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Shane M Devine
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, The University of MelbourneParkvilleAustralia
| | - Vicky M Avery
- Discovery Biology, Centre for Cellular Phenomics, Griffith UniversityNathanAustralia
- School of Environment and Science, Griffith UniversityNathanAustralia
| | - Tania De Koning-Ward
- School of Medicine, Deakin UniversityGeelongAustralia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin UniversityGeelongAustralia
| | - Peter Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Sheena McGowan
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityClaytonAustralia
- Centre to Impact AMR, Monash UniversityClaytonAustralia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
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25
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Jado JC, Dow M, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep 2024; 14:13989. [PMID: 38886371 PMCID: PMC11183241 DOI: 10.1038/s41598-024-63943-7] [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: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
In vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cells could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.
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Affiliation(s)
- Juan Carlos Jado
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michelle Dow
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
- Health Science, Department of Biomedical Informatics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Krypton Carolino
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Adam Klie
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gregory J Fonseca
- Department of Medicine, Meakins-Christie Laboratories, McGill University Health Centre, 1001 Decaire Blvd, Montreal, QC, H4A 3J1, Canada
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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26
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Achan J, Barry A, Leroy D, Kamara G, Duparc S, Kaszubska W, Gandhi P, Buffet B, Tshilab P, Ogutu B, Taylor T, Krishna S, Richardson N, Ramachandruni H, Rietveld H. Defining the next generation of severe malaria treatment: a target product profile. Malar J 2024; 23:174. [PMID: 38835069 DOI: 10.1186/s12936-024-04986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Severe malaria is a life-threatening infection, particularly affecting children under the age of 5 years in Africa. Current treatment with parenteral artemisinin derivatives is highly efficacious. However, artemisinin partial resistance is widespread in Southeast Asia, resulting in delayed parasite clearance after therapy, and has emerged independently in South America, Oceania, and Africa. Hence, new treatments for severe malaria are needed, and it is prudent to define their characteristics now. This manuscript focuses on the target product profile (TPP) for new treatments for severe malaria. It also highlights preparedness when considering ways of protecting the utility of artemisinin-based therapies. TARGET PRODUCT PROFILE Severe malaria treatments must be highly potent, with rapid onset of antiparasitic activity to clear the infection as quickly as possible to prevent complications. They should also have a low potential for drug resistance selection, given the high parasite burden in patients with severe malaria. Combination therapies are needed to deter resistance selection and dissemination. Partner drugs which are approved for uncomplicated malaria treatment would provide the most rapid development pathway for combinations, though new candidate molecules should be considered. Artemisinin combination approaches to severe malaria would extend the lifespan of current therapy, but ideally, completely novel, non-artemisinin-based combination therapies for severe malaria should be developed. These should be advanced to at least phase 2 clinical trials, enabling rapid progression to patient use should current treatment fail clinically. New drug combinations for severe malaria should be available as injectable formulations for rapid and effective treatment, or as rectal formulations for pre-referral intervention in resource-limited settings. CONCLUSION Defining the TPP is a key step to align responses across the community to proactively address the potential for clinical failure of artesunate in severe malaria. In the shorter term, artemisinin-based combination therapies should be developed using approved or novel drugs. In the longer term, novel combination treatments should be pursued. Thus, this TPP aims to direct efforts to preserve the efficacy of existing treatments while improving care and outcomes for individuals affected by this life-threatening disease.
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Affiliation(s)
| | - Aïssata Barry
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Didier Leroy
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, CH-1215, Geneva 15, Switzerland
| | - George Kamara
- Médecins Sans Frontières, Magburaka District Hospital, Freetown, Sierra Leone
| | - Stephan Duparc
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, CH-1215, Geneva 15, Switzerland
| | - Wiweka Kaszubska
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, CH-1215, Geneva 15, Switzerland
| | | | - Bénédicte Buffet
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, CH-1215, Geneva 15, Switzerland
| | | | - Bernhards Ogutu
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Terrie Taylor
- Queen Elizabeth Central Hospital and Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Sanjeev Krishna
- Institut Für Tropenmedizin, Eberhard Karls Universität Tübingen, and German Center for Infection Research (Dzif), Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Clinical Academic Group, Institute for Infection and Immunity, St. George's University of London, London, UK
- St George's University Hospitals NHS Foundation Trust, London, UK
| | | | - Hanu Ramachandruni
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, CH-1215, Geneva 15, Switzerland.
| | - Hans Rietveld
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, CH-1215, Geneva 15, Switzerland.
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27
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Duffey M, Shafer RW, Timm J, Burrows JN, Fotouhi N, Cockett M, Leroy D. Combating antimicrobial resistance in malaria, HIV and tuberculosis. Nat Rev Drug Discov 2024; 23:461-479. [PMID: 38750260 DOI: 10.1038/s41573-024-00933-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 06/07/2024]
Abstract
Antimicrobial resistance poses a significant threat to the sustainability of effective treatments against the three most prevalent infectious diseases: malaria, human immunodeficiency virus (HIV) infection and tuberculosis. Therefore, there is an urgent need to develop novel drugs and treatment protocols capable of reducing the emergence of resistance and combating it when it does occur. In this Review, we present an overview of the status and underlying molecular mechanisms of drug resistance in these three diseases. We also discuss current strategies to address resistance during the research and development of next-generation therapies. These strategies vary depending on the infectious agent and the array of resistance mechanisms involved. Furthermore, we explore the potential for cross-fertilization of knowledge and technology among these diseases to create innovative approaches for minimizing drug resistance and advancing the discovery and development of new anti-infective treatments. In conclusion, we advocate for the implementation of well-defined strategies to effectively mitigate and manage resistance in all interventions against infectious diseases.
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Affiliation(s)
- Maëlle Duffey
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland
- The Global Antibiotic Research & Development Partnership, Geneva, Switzerland
| | - Robert W Shafer
- Department of Medicine/Infectious Diseases, Stanford University, Palo Alto, CA, USA
| | | | - Jeremy N Burrows
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland
| | | | | | - Didier Leroy
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland.
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28
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Mogire RM, Miruka SA, Juma DW, McNamara CW, Andagalu B, Burrows JN, Chenu E, Duffy J, Ogutu BR, Akala HM. Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum. J Cheminform 2024; 16:63. [PMID: 38831351 PMCID: PMC11145868 DOI: 10.1186/s13321-024-00856-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Drug discovery is an intricate and costly process. Repurposing existing drugs and active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomedical information, it is possible to predict compounds' activity and identify their potential targets across diverse organisms. In this study, we aimed to assess the antiplasmodial activity of compounds from the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library using in vitro and bioinformatics approaches. We assessed the in vitro antiplasmodial activity of the compounds using blood-stage and liver-stage drug susceptibility assays. We used protein sequences of known targets of the ReFRAME compounds with high antiplasmodial activity (EC50 < 10 uM) to conduct a protein-pairwise search to identify similar Plasmodium falciparum 3D7 proteins (from PlasmoDB) using NCBI protein BLAST. We further assessed the association between the compounds' in vitro antiplasmodial activity and level of similarity between their known and predicted P. falciparum target proteins using simple linear regression analyses. BLAST analyses revealed 735 P. falciparum proteins that were similar to the 226 known protein targets associated with the ReFRAME compounds. Antiplasmodial activity of the compounds was positively associated with the degree of similarity between the compounds' known targets and predicted P. falciparum protein targets (percentage identity, E value, and bit score), the number of the predicted P. falciparum targets, and their respective mutagenesis index and fitness scores (R2 between 0.066 and 0.92, P < 0.05). Compounds predicted to target essential P. falciparum proteins or those with a druggability index of 1 showed the highest antiplasmodial activity.
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Affiliation(s)
- Reagan M Mogire
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
| | - Silviane A Miruka
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Dennis W Juma
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya
| | - Case W McNamara
- Calibr-Skaggs Institute for Innovative Medicine, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Ben Andagalu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
| | | | - Elodie Chenu
- Medicines for Malaria Venture, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Bernhards R Ogutu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Hoseah M Akala
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya.
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29
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Liu M, Wu X, Dyson PJ. Tandem catalysis enables chlorine-containing waste as chlorination reagents. Nat Chem 2024; 16:700-708. [PMID: 38396160 PMCID: PMC11087255 DOI: 10.1038/s41557-024-01462-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
Chlorinated compounds are ubiquitous. However, accumulation of chlorine-containing waste has a negative impact on human health and the environment due to the inapplicability of common disposal methods, such as landfill and incineration. Here we report a sustainable approach to valorize chlorine-containing hydrocarbon waste, including solids (chlorinated polymers) and liquids (chlorinated solvents), based on copper and palladium catalysts with a NaNO3 promoter. In the process, waste is oxidized to release the chlorine in the presence of N-directing arenes to afford valuable aryl chlorides, such as the FDA-approved drug vismodegib. The remaining hydrocarbon component is mineralized to afford CO, CO2 and H2O. Moreover, the CO and CO2 generated could be further utilized directly. Thus, chlorine-containing hydrocarbon waste, including mixed waste, can serve as chlorination reagents that neither generate hazardous by-products nor involve specialty chlorination reagents. This tandem catalytic approach represents a promising method for the viable management of a wide and diverse range of chlorine-containing hydrocarbon wastes.
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Affiliation(s)
- Mingyang Liu
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Xinbang Wu
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paul J Dyson
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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30
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Creek D, Giannangelo C, Challis M, Siddiqui G, Edgar R, Malcolm T, Webb C, Drinkwater N, Vinh N, MacRaild C, Counihan N, Duffy S, Wittlin S, Devine S, Avery V, de Koning-Ward T, Scammells P, McGowan S. Chemoproteomics validates selective targeting of Plasmodium M1 alanyl aminopeptidase as an antimalarial strategy. RESEARCH SQUARE 2024:rs.3.rs-3251230. [PMID: 38746424 PMCID: PMC11092810 DOI: 10.21203/rs.3.rs-3251230/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum ( Pf A-M1) and Plasmodium vivax ( Pv A-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets Pf A-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on Pf A-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of Pf A-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.
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31
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Rawat M, Padalino G, Yeo T, Brancale A, Fidock DA, Hoffmann KF, Lee MCS. Quinoxaline-Based Anti-Schistosomal Compounds Have Potent Anti-Malarial Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590861. [PMID: 38712185 PMCID: PMC11071471 DOI: 10.1101/2024.04.23.590861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The human pathogens Plasmodium and Schistosoma are each responsible for over 200 million infections annually, being particularly problematic in low- and middle-income countries. There is a pressing need for new drug targets for these diseases, driven by emergence of drug-resistance in Plasmodium and the overall dearth of new drug targets for Schistosoma. Here, we explored the opportunity for pathogen-hopping by evaluating a series of quinoxaline-based anti-schistosomal compounds for activity against P. falciparum. We identified compounds with low nanomolar potency against 3D7 and multidrug-resistant strains. Evolution of resistance using a mutator P. falciparum line revealed a low propensity for resistance. Only one of the series, compound 22, yielded resistance mutations, including point mutations in a non-essential putative hydrolase pfqrp1, as well as copy-number amplification of a phospholipid-translocating ATPase, pfatp2, a potential target. Notably, independently generated CRISPR-edited mutants in pfqrp1 also showed resistance to compound 22 and a related analogue. Moreover, previous lines with pfatp2 copy-number variations were similarly less susceptible to challenge with the new compounds. Finally, we examined whether the predicted hydrolase activity of PfQRP1 underlies its mechanism of resistance, showing that both mutation of the putative catalytic triad and a more severe loss of function mutation elicited resistance. Collectively, we describe a compound series with potent activity against two important pathogens and their potential target in P. falciparum.
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Affiliation(s)
- Mukul Rawat
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gilda Padalino
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, United Kingdom
- Swansea University Medical School, Swansea, United Kingdom
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States
| | - Andrea Brancale
- Department of Organic Chemistry, UCT Prague, Prague, Czech Republic
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States
| | - Karl F Hoffmann
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Marcus C S Lee
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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32
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Wirjanata G, Lin J, Dziekan JM, El Sahili A, Chung Z, Tjia S, Binte Zulkifli NE, Boentoro J, Tham R, Jia LS, Go KD, Yu H, Partridge A, Olsen D, Prabhu N, Sobota RM, Nordlund P, Lescar J, Bozdech Z. Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Cell Chem Biol 2024; 31:743-759.e8. [PMID: 38593807 DOI: 10.1016/j.chembiol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/02/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.
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Affiliation(s)
- Grennady Wirjanata
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Infectious Diseases Labs & Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore, Singapore
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore
| | - Zara Chung
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Roy Tham
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Lai Si Jia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - David Olsen
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 637551, Singapore.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.
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33
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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34
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Ahmad T, Alhammadi BA, Almaazmi SY, Arafa S, Blatch GL, Dutta T, Gestwicki JE, Keyzers RA, Shonhai A, Singh H. Plasmodium falciparum heat shock proteins as antimalarial drug targets: An update. Cell Stress Chaperones 2024; 29:326-337. [PMID: 38518861 PMCID: PMC10990865 DOI: 10.1016/j.cstres.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024] Open
Abstract
Global efforts to eradicate malaria are threatened by multiple factors, particularly the emergence of antimalarial drug resistant strains of Plasmodium falciparum. Heat shock proteins (HSPs), particularly P. falciparum HSPs (PfHSPs), represent promising drug targets due to their essential roles in parasite survival and virulence across the various life cycle stages. Despite structural similarities between human and malarial HSPs posing challenges, there is substantial evidence for subtle differences that could be exploited for selective drug targeting. This review provides an update on the potential of targeting various PfHSP families (particularly PfHSP40, PfHSP70, and PfHSP90) and their interactions within PfHSP complexes as a strategy to develop new antimalarial drugs. In addition, the need for a deeper understanding of the role of HSP complexes at the host-parasite interface is highlighted, especially heterologous partnerships between human and malarial HSPs, as this opens novel opportunities for targeting protein-protein interactions crucial for malaria parasite survival and pathogenesis.
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Affiliation(s)
- Tanveer Ahmad
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Bushra A Alhammadi
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Shaikha Y Almaazmi
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Sahar Arafa
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Gregory L Blatch
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates; Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
| | - Tanima Dutta
- Department of Diagnostic Genomics, Pathwest, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Robert A Keyzers
- Centre for Biodiscovery & School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Addmore Shonhai
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab, India
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35
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CK, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase PhoD as a determinant of antiparasitic resistance. Proc Natl Acad Sci U S A 2024; 121:e2312987121. [PMID: 38377214 PMCID: PMC10907312 DOI: 10.1073/pnas.2312987121] [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: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites and the lack of specific drugs necessitate the discovery of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of Babesia spp. (B. bovis and B. divergens). We identified a potent antibabesial, MMV019266, from the Malaria Box, and selected for resistance in two species of Babesia. After sequencing of multiple independently derived lines in the two species, we identified mutations in a membrane-bound metallodependent phosphatase (phoD). In both species, the mutations were found in the phoD-like phosphatase domain. Using reverse genetics, we validated that mutations in bdphoD confer resistance to MMV019266 in B. divergens. We have also demonstrated that BdPhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of BdPhoD alter the sensitivity to MMV019266 in the parasite. Overexpression of BdPhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting BdPhoD is a pro-susceptibility factor. Together, we have generated a robust pipeline for identification of resistance loci and identified BdPhoD as a resistance mechanism in Babesia species.
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Affiliation(s)
- Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Jacob A. Tennessen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Aditya S. Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Renee Hua
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Luz Ramirez-Ramirez
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Sida Ye
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Cristina K. Moreira
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Marvin J. Meyers
- Department of Chemistry, Saint Louis University, St. Louis, MO63103
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
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36
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Wiser MF. The Digestive Vacuole of the Malaria Parasite: A Specialized Lysosome. Pathogens 2024; 13:182. [PMID: 38535526 PMCID: PMC10974218 DOI: 10.3390/pathogens13030182] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 02/11/2025] Open
Abstract
The malaria parasite resides within erythrocytes during one stage of its life cycle. During this intraerythrocytic period, the parasite ingests the erythrocyte cytoplasm and digests approximately two-thirds of the host cell hemoglobin. This digestion occurs within a lysosome-like organelle called the digestive vacuole. Several proteases are localized to the digestive vacuole and these proteases sequentially breakdown hemoglobin into small peptides, dipeptides, and amino acids. The peptides are exported into the host cytoplasm via the chloroquine-resistance transporter and an amino acid transporter has also been identified on the digestive vacuole membrane. The environment of the digestive vacuole also provides appropriate conditions for the biocrystallization of toxic heme into non-toxic hemozoin by a poorly understood process. Hemozoin formation is an attribute of Plasmodium and Haemoproteus and is not exhibited by other intraerythrocytic protozoan parasites. The efficient degradation of hemoglobin and detoxification of heme likely plays a major role in the high level of replication exhibited by malaria parasites within erythrocytes. Unique features of the digestive vacuole and the critical importance of nutrient acquisition provide therapeutic targets for the treatment of malaria.
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Affiliation(s)
- Mark F Wiser
- Department of Tropical Medicine and Infectious Disease, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112-2824, USA
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37
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Collins JE, Lee JW, Rocamora F, Saggu GS, Wendt KL, Pasaje CFA, Smick S, Santos NM, Paes R, Jiang T, Mittal N, Luth MR, Chin T, Chang H, McLellan JL, Morales-Hernandez B, Hanson KK, Niles JC, Desai SA, Winzeler EA, Cichewicz RH, Chakrabarti D. Antiplasmodial peptaibols act through membrane directed mechanisms. Cell Chem Biol 2024; 31:312-325.e9. [PMID: 37995692 PMCID: PMC10923054 DOI: 10.1016/j.chembiol.2023.10.025] [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: 10/28/2022] [Revised: 08/29/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Our previous study identified 52 antiplasmodial peptaibols isolated from fungi. To understand their antiplasmodial mechanism of action, we conducted phenotypic assays, assessed the in vitro evolution of resistance, and performed a transcriptome analysis of the most potent peptaibol, HZ NPDG-I. HZ NPDG-I and 2 additional peptaibols were compared for their killing action and stage dependency, each showing a loss of digestive vacuole (DV) content via ultrastructural analysis. HZ NPDG-I demonstrated a stepwise increase in DV pH, impaired DV membrane permeability, and the ability to form ion channels upon reconstitution in planar membranes. This compound showed no signs of cross resistance to targets of current clinical candidates, and 3 independent lines evolved to resist HZ NPDG-I acquired nonsynonymous changes in the P. falciparum multidrug resistance transporter, pfmdr1. Conditional knockdown of PfMDR1 showed varying effects to other peptaibol analogs, suggesting differing sensitivity.
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Affiliation(s)
- Jennifer E Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA
| | - Jin Woo Lee
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, Norman OK 73019, USA
| | - Frances Rocamora
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Gagandeep S Saggu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20852, USA
| | - Karen L Wendt
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, Norman OK 73019, USA
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Smick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Natalia Mojica Santos
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA
| | - Raphaella Paes
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA
| | - Tiantian Jiang
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Nimisha Mittal
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeline R Luth
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Taylor Chin
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Howard Chang
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - James L McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Beatriz Morales-Hernandez
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Kirsten K Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sanjay A Desai
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20852, USA
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, Norman OK 73019, USA.
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA.
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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Schäfer TM, Pessanha de Carvalho L, Inoue J, Kreidenweiss A, Held J. The problem of antimalarial resistance and its implications for drug discovery. Expert Opin Drug Discov 2024; 19:209-224. [PMID: 38108082 DOI: 10.1080/17460441.2023.2284820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
INTRODUCTION Malaria remains a devastating infectious disease with hundreds of thousands of casualties each year. Antimalarial drug resistance has been a threat to malaria control and elimination for many decades and is still of concern today. Despite the continued effectiveness of current first-line treatments, namely artemisinin-based combination therapies, the emergence of drug-resistant parasites in Southeast Asia and even more alarmingly the occurrence of resistance mutations in Africa is of great concern and requires immediate attention. AREAS COVERED A comprehensive overview of the mechanisms underlying the acquisition of drug resistance in Plasmodium falciparum is given. Understanding these processes provides valuable insights that can be harnessed for the development and selection of novel antimalarials with reduced resistance potential. Additionally, strategies to mitigate resistance to antimalarial compounds on the short term by using approved drugs are discussed. EXPERT OPINION While employing strategies that utilize already approved drugs may offer a prompt and cost-effective approach to counter antimalarial drug resistance, it is crucial to recognize that only continuous efforts into the development of novel antimalarial drugs can ensure the successful treatment of malaria in the future. Incorporating resistance propensity assessment during this developmental process will increase the likelihood of effective and enduring malaria treatments.
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Affiliation(s)
| | | | - Juliana Inoue
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research (DZIF), Tübingen, Germany
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40
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Acosta-Zaldívar M, Qi W, Mishra A, Roy U, King WR, Patton-Vogt J, Anderson MZ, Köhler JR. Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577887. [PMID: 38352318 PMCID: PMC10862840 DOI: 10.1101/2024.01.29.577887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. In this process, initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity were eventually lost as populations presumably gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while that of others like membrane stress responses diverged from these fitness phenotypes. C. albicans therefore has diverse options to reconfigure Pi management during prolonged scarcity. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth and virulence.
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Affiliation(s)
- Maikel Acosta-Zaldívar
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
- Current affiliation: Planasa, Valladolid, Spain
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Abhishek Mishra
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
| | - Udita Roy
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - William R. King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Matthew Z. Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| | - Julia R. Köhler
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
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41
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MCS, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun 2024; 15:937. [PMID: 38297033 PMCID: PMC10831071 DOI: 10.1038/s41467-024-45224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, VIC, Australia
| | - Riley D Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kate J Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Peter J Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 4HN, UK
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK.
- Structural Genomics Consortium, University College London, London, WC1N 1AX, UK.
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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Piro F, Masci S, Kannan G, Focaia R, Schultz TL, Thaprawat P, Carruthers VB, Di Cristina M. A Toxoplasma gondii putative amino acid transporter localizes to the plant-like vacuolar compartment and controls parasite extracellular survival and stage differentiation. mSphere 2024; 9:e0059723. [PMID: 38051073 PMCID: PMC10871165 DOI: 10.1128/msphere.00597-23] [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: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023] Open
Abstract
Toxoplasma gondii is a protozoan parasite that infects a broad spectrum of hosts and can colonize many organs and cell types. The ability to reside within a wide range of different niches requires substantial adaptability to diverse microenvironments. Very little is known about how this parasite senses various milieus and adapts its metabolism to survive, replicate during the acute stage, and then differentiate to the chronic stage. T. gondii possesses a lysosome-like organelle known as the plant-like vacuolar compartment (PLVAC), which serves various functions, including digestion, ion storage and homeostasis, endocytosis, and autophagy. Lysosomes are critical for maintaining cellular health and function by degrading waste materials and recycling components. To supply the cell with the essential building blocks and energy sources required for the maintenance of its functions and structures, the digested solutes generated within the lysosome are transported into the cytosol by proteins embedded in the lysosomal membrane. Currently, a limited number of PLVAC transporters have been characterized, with TgCRT being the sole potential transporter of amino acids and small peptides identified thus far. To bridge this knowledge gap, we used lysosomal amino acid transporters from other organisms as queries to search the T. gondii proteome. This led to the identification of four potential amino acid transporters, which we have designated as TgAAT1-4. Assessing their expression and sub-cellular localization, we found that one of them, TgAAT1, localized to the PLVAC and is necessary for normal parasite extracellular survival and bradyzoite differentiation. Moreover, we present preliminary data showing the possible involvement of TgAAT1 in the PLVAC transport of arginine.IMPORTANCEToxoplasma gondii is a highly successful parasite infecting a broad range of warm-blooded organisms, including about one-third of all humans. Although Toxoplasma infections rarely result in symptomatic disease in individuals with a healthy immune system, the incredibly high number of persons infected, along with the risk of severe infection in immunocompromised patients and the potential link of chronic infection to mental disorders, makes this infection a significant public health concern. As a result, there is a pressing need for new treatment approaches that are both effective and well tolerated. The limitations in understanding how Toxoplasma gondii manages its metabolism to adapt to changing environments and triggers its transformation into bradyzoites have hindered the discovery of vulnerabilities in its metabolic pathways or nutrient acquisition mechanisms to identify new therapeutic targets. In this work, we have shown that the lysosome-like organelle plant-like vacuolar compartment (PLVAC), acting through the putative arginine transporter TgAAT1, plays a pivotal role in regulating the parasite's extracellular survival and differentiation into bradyzoites.
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Affiliation(s)
- Federica Piro
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Silvia Masci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Geetha Kannan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Riccardo Focaia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Tracey L. Schultz
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Pariyamon Thaprawat
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vern B. Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Manlio Di Cristina
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
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43
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Wang L, Bohmer MJ, Wang J, Nardella F, Calla J, Laureano De Souza M, Schindler KA, Montejo L, Mittal N, Rocamora F, Treat M, Charlton JT, Tumwebaze PK, Rosenthal PJ, Cooper RA, Chakrabarti R, Winzeler EA, Chakrabarti D, Gray NS. Discovery of Potent Antimalarial Type II Kinase Inhibitors with Selectivity over Human Kinases. J Med Chem 2024; 67:1460-1480. [PMID: 38214254 PMCID: PMC10950204 DOI: 10.1021/acs.jmedchem.3c02046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
While progress has been made in the effort to eradicate malaria, the disease remains a significant threat to global health. Acquired resistance to frontline treatments is emerging in Africa, urging a need for the development of novel antimalarial agents. Repurposing human kinase inhibitors provides a potential expedited route given the availability of a diverse array of kinase-targeting drugs that are approved or in clinical trials. Phenotypic screening of a library of type II human kinase inhibitors identified compound 1 as a lead antimalarial, which was initially developed to target human ephrin type A receptor 2 (EphA2). Here, we report a structure-activity relationship study and lead optimization of compound 1, which led to compound 33, with improved antimalarial activity and selectivity.
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Affiliation(s)
- Lushun Wang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Monica J Bohmer
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Flore Nardella
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jaeson Calla
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Lukas Montejo
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mayland Treat
- School of Public Health, University of California, Berkeley California 94704, United States
| | - Jordan T Charlton
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94110, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | - Ratna Chakrabarti
- Division of Cancer Research, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
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Casanova D, Baptista V, Costa M, Freitas B, Pereira MDNI, Calçada C, Mota P, Kythrich O, Pereira MHJS, Osório NS, Veiga MI. Artemisinin resistance-associated gene mutations in Plasmodium falciparum: A case study of severe malaria from Mozambique. Travel Med Infect Dis 2024; 57:102684. [PMID: 38159875 DOI: 10.1016/j.tmaid.2023.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The effectiveness of artemisinin-based combination therapies (ACT) in treating Plasmodium falciparum, is vital for global malaria control efforts, particularly in sub-Saharan Africa. The examination of imported cases from endemic areas holds implications for malaria chemotherapy on a global scale. METHOD A 45-year-old male presented with high fever, dry cough, diarrhoea and generalized muscle pain, following a two-week trip to Mozambique. P. falciparum infection with hiperparasitemia was confirmed and the patient was treated initially with quinine and doxycycline, then intravenous artesunate. To assess drug susceptibility, ex vivo half-maximal inhibitory concentration assays were conducted, and the isolated P. falciparum genome was deep sequenced. RESULTS The clinical isolate exhibited elevated ex vivo half-maximal inhibitory concentration values to dihydroartemisinin, lumefantrine, mefloquine and piperaquine. Genomic analysis identified a I416V mutation in the P. falciparum Kelch13 (PF3D7_1343700) gene, and several mutations at the Kelch13 interaction candidate genes, pfkics (PF3D7_0813000, PF3D7_1138700, PF3D7_1246300), including the ubiquitin carboxyl-terminal hydrolase 1, pfubp1 (PF3D7_0104300). Mutations at the drug transporters and genes linked to next-generation antimalarial drug resistance were also present. CONCLUSIONS This case highlights the emergence of P. falciparum strains carrying mutations in artemisinin resistance-associated genes in Mozambique, couple with a reduction in ex vivo susceptibility to ACT drugs. Continuous surveillance of mutations linked to drug resistance and regular monitoring of drug susceptibility are imperative to anticipate the spread of potential resistant strains emerging in Mozambique and to maintain effective malaria control strategies.
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Affiliation(s)
- Daniela Casanova
- Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Vitória Baptista
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal; Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, University of Minho, Campus de Azurém, 4800-058, Guimarães, Portugal
| | - Magda Costa
- Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Bruno Freitas
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Maria das Neves Imaculada Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Carla Calçada
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Paula Mota
- Clinical Pathology Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Olena Kythrich
- Clinical Pathology Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | | | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Maria Isabel Veiga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal; Clinical Academic Center-Braga (2CA-Braga), 4710-243, Braga, Portugal.
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45
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Liu S, Ebel ER, Luniewski A, Zulawinska J, Simpson ML, Kim J, Ene N, Braukmann TWA, Congdon M, Santos W, Yeh E, Guler JL. Direct long read visualization reveals metabolic interplay between two antimalarial drug targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528367. [PMID: 36824743 PMCID: PMC9948948 DOI: 10.1101/2023.02.13.528367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Increases in the copy number of large genomic regions, termed genome amplification, are an important adaptive strategy for malaria parasites. Numerous amplifications across the Plasmodium falciparum genome contribute directly to drug resistance or impact the fitness of this protozoan parasite. During the characterization of parasite lines with amplifications of the dihydroorotate dehydrogenase (DHODH) gene, we detected increased copies of an additional genomic region that encompassed 3 genes (~5 kb) including GTP cyclohydrolase I (GCH1 amplicon). While this gene is reported to increase the fitness of antifolate resistant parasites, GCH1 amplicons had not previously been implicated in any other antimalarial resistance context. Here, we further explored the association between GCH1 and DHODH copy number. Using long read sequencing and single read visualization, we directly observed a higher number of tandem GCH1 amplicons in parasites with increased DHODH copies (up to 9 amplicons) compared to parental parasites (3 amplicons). While all GCH1 amplicons shared a consistent structure, expansions arose in 2-unit steps (from 3 to 5 to 7, etc copies). Adaptive evolution of DHODH and GCH1 loci was further bolstered when we evaluated prior selection experiments; DHODH amplification was only successful in parasite lines with pre-existing GCH1 amplicons. These observations, combined with the direct connection between metabolic pathways that contain these enzymes, lead us to propose that the GCH1 locus is beneficial for the fitness of parasites exposed to DHODH inhibitors. This finding highlights the importance of studying variation within individual parasite genomes as well as biochemical connections of drug targets as novel antimalarials move towards clinical approval.
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Affiliation(s)
- Shiwei Liu
- University of Virginia, Department of Biology, Charlottesville, VA, USA
- Current affiliation: Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emily R. Ebel
- Stanford, Departments of Pediatrics and Microbiology & Immunology, Stanford, CA, USA
| | | | - Julia Zulawinska
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Jane Kim
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | - Nnenna Ene
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Molly Congdon
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Webster Santos
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Ellen Yeh
- Stanford University, Departments of Pathology and Microbiology & Immunology, Stanford, CA, USA
| | - Jennifer L. Guler
- University of Virginia, Department of Biology, Charlottesville, VA, USA
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46
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Simwela NV, Guiguemde WA, Straimer J, Regnault C, Stokes BH, Tavernelli LE, Yokokawa F, Taft B, Diagana TT, Barrett MP, Waters AP. A conserved metabolic signature associated with response to fast-acting anti-malarial agents. Microbiol Spectr 2023; 11:e0397622. [PMID: 37800971 PMCID: PMC10714989 DOI: 10.1128/spectrum.03976-22] [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: 10/02/2022] [Accepted: 01/27/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE In malaria drug discovery, understanding the mode of action of lead compounds is important as it helps in predicting the potential emergence of drug resistance in the field when these drugs are eventually deployed. In this study, we have employed metabolomics technologies to characterize the potential targets of anti-malarial drug candidates in the developmental pipeline at NITD. We show that NITD fast-acting leads belonging to spiroindolone and imidazothiadiazole class induce a common biochemical theme in drug-exposed malaria parasites which is similar to another fast-acting, clinically available drug, DHA. These biochemical features which are absent in a slower acting NITD lead (GNF17) point to hemoglobin digestion and inhibition of the pyrimidine pathway as potential action points for these drugs. These biochemical themes can be used to identify and inform on the mode of action of fast drug candidates of similar profiles in future drug discovery programs.
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Affiliation(s)
- Nelson V. Simwela
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | | | - Judith Straimer
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | - Clement Regnault
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Barbara H. Stokes
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Luis E. Tavernelli
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Fumiaki Yokokawa
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | - Benjamin Taft
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | | | - Michael P. Barrett
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Andrew P. Waters
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
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47
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Craven HM, Nettesheim G, Cicuta P, Blagborough AM, Merrick CJ. Effects of the G-quadruplex-binding drugs quarfloxin and CX-5461 on the malaria parasite Plasmodium falciparum. Int J Parasitol Drugs Drug Resist 2023; 23:106-119. [PMID: 38041930 PMCID: PMC10711401 DOI: 10.1016/j.ijpddr.2023.11.007] [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: 08/15/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
Plasmodium falciparum is the deadliest causative agent of human malaria. This parasite has historically developed resistance to most drugs, including the current frontline treatments, so new therapeutic targets are needed. Our previous work on guanine quadruplexes (G4s) in the parasite's DNA and RNA has highlighted their influence on parasite biology, and revealed G4 stabilising compounds as promising candidates for repositioning. In particular, quarfloxin, a former anticancer agent, kills blood-stage parasites at all developmental stages, with fast rates of kill and nanomolar potency. Here we explored the molecular mechanism of quarfloxin and its related derivative CX-5461. In vitro, both compounds bound to P. falciparum-encoded G4 sequences. In cellulo, quarfloxin was more potent than CX-5461, and could prevent establishment of blood-stage malaria in vivo in a murine model. CX-5461 showed clear DNA damaging activity, as reported in human cells, while quarfloxin caused weaker signatures of DNA damage. Both compounds caused transcriptional dysregulation in the parasite, but the affected genes were largely different, again suggesting different modes of action. Therefore, CX-5461 may act primarily as a DNA damaging agent in both Plasmodium parasites and mammalian cells, whereas the complete antimalarial mode of action of quarfloxin may be parasite-specific and remains somewhat elusive.
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Affiliation(s)
- Holly M Craven
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Guilherme Nettesheim
- Department of Physics, Cavendish Laboratory University of Cambridge, J.J. Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory University of Cambridge, J.J. Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Andrew M Blagborough
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Catherine J Merrick
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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48
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Mok S, Yeo T, Hong D, Shears MJ, Ross LS, Ward KE, Dhingra SK, Kanai M, Bridgford JL, Tripathi AK, Mlambo G, Burkhard AY, Ansbro MR, Fairhurst KJ, Gil-Iturbe E, Park H, Rozenberg FD, Kim J, Mancia F, Fairhurst RM, Quick M, Uhlemann AC, Sinnis P, Fidock DA. Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness. SCIENCE ADVANCES 2023; 9:eadi2364. [PMID: 37939186 PMCID: PMC10631731 DOI: 10.1126/sciadv.adi2364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Drug-resistant Plasmodium falciparum parasites have swept across Southeast Asia and now threaten Africa. By implementing a P. falciparum genetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mapped k13 as the central mediator of ART resistance in vitro and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping using 34 recombinant haplotypes, and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.
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Affiliation(s)
- Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Davin Hong
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Melanie J. Shears
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Leila S. Ross
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kurt E. Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Satish K. Dhingra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mariko Kanai
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica L. Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Abhai K. Tripathi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Godfree Mlambo
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Y. Burkhard
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan R. Ansbro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Kate J. Fairhurst
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Felix D. Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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49
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Henshall IG, Spielmann T. Critical interdependencies between Plasmodium nutrient flux and drugs. Trends Parasitol 2023; 39:936-944. [PMID: 37716852 PMCID: PMC10580322 DOI: 10.1016/j.pt.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/18/2023]
Abstract
Nutrient import and waste efflux are critical dependencies for intracellular Plasmodium falciparum parasites. Nutrient transport proteins are often lineage specific and can provide unique targets for antimalarial drug development. P. falciparum nutrient transport pathways can be a double-edged sword for the parasite, not only mediating the import of nutrients and excretion of waste products but also providing an access route for drugs. Here we briefly summarise the nutrient acquisition pathways of intracellular P. falciparum blood-stage parasites and then highlight how these pathways influence many aspects relevant to antimalarial drugs, resulting in complex and often underappreciated interdependencies.
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Affiliation(s)
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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50
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Coonahan E, Gage H, Chen D, Noormahomed EV, Buene TP, Mendes de Sousa I, Akrami K, Chambal L, Schooley RT, Winzeler EA, Cowell AN. Whole-genome surveillance identifies markers of Plasmodium falciparum drug resistance and novel genomic regions under selection in Mozambique. mBio 2023; 14:e0176823. [PMID: 37750720 PMCID: PMC10653802 DOI: 10.1128/mbio.01768-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Malaria is a devastating disease caused by Plasmodium parasites. The evolution of parasite drug resistance continues to hamper progress toward malaria elimination, and despite extensive efforts to control malaria, it remains a leading cause of death in Mozambique and other countries in the region. The development of successful vaccines and identification of molecular markers to track drug efficacy are essential for managing the disease burden. We present an analysis of the parasite genome in Mozambique, a country with one of the highest malaria burdens globally and limited available genomic data, revealing current selection pressure. We contribute additional evidence to limited prior studies supporting the effectiveness of SWGA in producing reliable genomic data from complex clinical samples. Our results provide the identity of genomic loci that may be associated with current antimalarial drug use, including artemisinin and lumefantrine, and reveal selection pressure predicted to compromise the efficacy of current vaccine candidates.
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Affiliation(s)
- Erin Coonahan
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Hunter Gage
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Daisy Chen
- Department of Pediatrics, University of California San Diego (UCSD), La Jolla, California, USA
| | - Emilia Virginia Noormahomed
- School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Microbiology, Parasitology Laboratory, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
| | - Titos Paulo Buene
- Department of Microbiology, Parasitology Laboratory, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
| | - Irina Mendes de Sousa
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
- Biological Sciences Department, Faculty of Sciences, Eduardo Mondlane University, Maputo, Mozambique
| | - Kevan Akrami
- School of Medicine, University of California San Diego, La Jolla, California, USA
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Lucia Chambal
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
- Department of Internal Medicine, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Maputo Central Hospital, Maputo, Mozambique
| | - Robert T. Schooley
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, University of California San Diego (UCSD), La Jolla, California, USA
| | - Annie N. Cowell
- School of Medicine, University of California San Diego, La Jolla, California, USA
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