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Maher SP, Bakowski MA, Vantaux A, Flannery EL, Andolina C, Gupta M, Antonova-Koch Y, Argomaniz M, Cabrera-Mora M, Campo B, Chao AT, Chatterjee AK, Cheng WT, Chuenchob E, Cooper CA, Cottier K, Galinski MR, Harupa-Chung A, Ji H, Joseph SB, Lenz T, Lonardi S, Matheson J, Mikolajczak SA, Moeller T, Orban A, Padín-Irizarry V, Pan K, Péneau J, Prudhomme J, Roesch C, Ruberto AA, Sabnis SS, Saney CL, Sattabongkot J, Sereshki S, Suriyakan S, Ubalee R, Wang Y, Wasisakun P, Yin J, Popovici J, McNamara CW, Joyner CJ, Nosten F, Witkowski B, Le Roch KG, Kyle DE. A Drug Repurposing Approach Reveals Targetable Epigenetic Pathways in Plasmodium vivax Hypnozoites. bioRxiv 2024:2023.01.31.526483. [PMID: 36778461 PMCID: PMC9915689 DOI: 10.1101/2023.01.31.526483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Radical cure of Plasmodium vivax malaria must include elimination of quiescent 'hypnozoite' forms in the liver; however, the only FDA-approved treatments are contraindicated in many vulnerable populations. To identify new drugs and drug targets for hypnozoites, we screened the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library and a collection of epigenetic inhibitors against P. vivax liver stages. From both libraries, we identified inhibitors targeting epigenetics pathways as selectively active against P. vivax and P. cynomolgi hypnozoites. These include DNA methyltransferase (DNMT) inhibitors as well as several inhibitors targeting histone post-translational modifications. Immunofluorescence staining of Plasmodium liver forms showed strong nuclear 5-methylcystosine signal, indicating liver stage parasite DNA is methylated. Using bisulfite sequencing, we mapped genomic DNA methylation in sporozoites, revealing DNA methylation signals in most coding genes. We also demonstrated that methylation level in proximal promoter regions as well as in the first exon of the genes may affect, at least partially, gene expression in P. vivax. The importance of selective inhibitors targeting epigenetic features on hypnozoites was validated using MMV019721, an acetyl-CoA synthetase inhibitor that affects histone acetylation and was previously reported as active against P. falciparum blood stages. In summary, our data indicate that several epigenetic mechanisms are likely modulating hypnozoite formation or persistence and provide an avenue for the discovery and development of improved radical cure antimalarials.
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Affiliation(s)
- S. P. Maher
- Center for Tropical & Emerging Global Disease, University of Georgia; Athens, GA, 30602, USA
| | - M. A. Bakowski
- Calibr, a division of The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - A. Vantaux
- Malaria Molecular Epidemiology Unit, Institute Pasteur of Cambodia; Phnom Penh, 120 210, Cambodia
| | - E. L. Flannery
- Novartis Institute for Tropical Diseases, Novartis Institutes for Biomedical Research; Emeryville, CA, 94608, USA
| | - C. Andolina
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit; Mae Sot, Tak, 63110, Thailand
| | - M. Gupta
- Department of Molecular, Cell, and Systems Biology, University of California; Riverside, CA, 92521, USA
| | - Y. Antonova-Koch
- Calibr, a division of The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - M. Argomaniz
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA, 30602, USA
| | - M. Cabrera-Mora
- International Center for Malaria Research, Education and Development, Emory Vaccine Center, Emory National Primate Research Center, Emory University; Atlanta, GA, 30329, USA
| | - B. Campo
- Medicines for Malaria Venture (MMV); Geneva, 1215, Switzerland
| | - A. T. Chao
- Novartis Institute for Tropical Diseases, Novartis Institutes for Biomedical Research; Emeryville, CA, 94608, USA
| | - A. K. Chatterjee
- Calibr, a division of The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - W. T. Cheng
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA, 30602, USA
| | - E. Chuenchob
- Novartis Institute for Tropical Diseases, Novartis Institutes for Biomedical Research; Emeryville, CA, 94608, USA
| | - C. A. Cooper
- Center for Tropical & Emerging Global Disease, University of Georgia; Athens, GA, 30602, USA
| | | | - M. R. Galinski
- International Center for Malaria Research, Education and Development, Emory Vaccine Center, Emory National Primate Research Center, Emory University; Atlanta, GA, 30329, USA
- Division of Infectious Diseases, Department of Medicine, Emory University; Atlanta, GA, 30329, USA
| | - A. Harupa-Chung
- Novartis Institute for Tropical Diseases, Novartis Institutes for Biomedical Research; Emeryville, CA, 94608, USA
| | - H. Ji
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA, 30602, USA
| | - S. B. Joseph
- Calibr, a division of The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - T. Lenz
- Department of Molecular, Cell, and Systems Biology, University of California; Riverside, CA, 92521, USA
| | - S. Lonardi
- Department of Computer Science and Engineering, University of California; Riverside, CA, 92521, USA
| | - J. Matheson
- Department of Microbiology and Immunology, University of Otago; Dunedin, 9016, New Zealand
| | - S. A. Mikolajczak
- Novartis Institute for Tropical Diseases, Novartis Institutes for Biomedical Research; Emeryville, CA, 94608, USA
| | | | - A. Orban
- Malaria Molecular Epidemiology Unit, Institute Pasteur of Cambodia; Phnom Penh, 120 210, Cambodia
| | - V. Padín-Irizarry
- Center for Tropical & Emerging Global Disease, University of Georgia; Athens, GA, 30602, USA
- School of Sciences, Clayton State University; Morrow, GA, 30260, USA
| | - K. Pan
- Calibr, a division of The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - J. Péneau
- Malaria Molecular Epidemiology Unit, Institute Pasteur of Cambodia; Phnom Penh, 120 210, Cambodia
| | - J. Prudhomme
- Department of Molecular, Cell, and Systems Biology, University of California; Riverside, CA, 92521, USA
| | - C. Roesch
- Malaria Molecular Epidemiology Unit, Institute Pasteur of Cambodia; Phnom Penh, 120 210, Cambodia
| | - A. A. Ruberto
- Center for Tropical & Emerging Global Disease, University of Georgia; Athens, GA, 30602, USA
| | - S. S. Sabnis
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA, 30602, USA
| | - C. L. Saney
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA, 30602, USA
| | - J. Sattabongkot
- Mahidol Vivax Research Unit, Mahidol University; Bangkok, 10400, Thailand
| | - S. Sereshki
- Department of Computer Science and Engineering, University of California; Riverside, CA, 92521, USA
| | - S. Suriyakan
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit; Mae Sot, Tak, 63110, Thailand
| | - R. Ubalee
- Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS); Bangkok, 10400, Thailand
| | - Y. Wang
- Department of Chemistry, University of California; Riverside, CA, 92521
- Environmental Toxicology Graduate Program, University of California; Riverside, CA, 92521, USA
| | - P. Wasisakun
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit; Mae Sot, Tak, 63110, Thailand
| | - J. Yin
- Environmental Toxicology Graduate Program, University of California; Riverside, CA, 92521, USA
| | - J. Popovici
- Malaria Molecular Epidemiology Unit, Institute Pasteur of Cambodia; Phnom Penh, 120 210, Cambodia
| | - C. W. McNamara
- Calibr, a division of The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - C. J. Joyner
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA, 30602, USA
- International Center for Malaria Research, Education and Development, Emory Vaccine Center, Emory National Primate Research Center, Emory University; Atlanta, GA, 30329, USA
| | - F. Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit; Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford; Oxford, OX3 7LG, UK
| | - B. Witkowski
- Malaria Molecular Epidemiology Unit, Institute Pasteur of Cambodia; Phnom Penh, 120 210, Cambodia
| | - K. G. Le Roch
- Department of Molecular, Cell, and Systems Biology, University of California; Riverside, CA, 92521, USA
| | - D. E. Kyle
- Center for Tropical & Emerging Global Disease, University of Georgia; Athens, GA, 30602, USA
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Iroh Tam P, Arnold SLM, Barrett LK, Chen CR, Conrad TM, Douglas E, Gordon MA, Hebert D, Henrion M, Hermann D, Hollingsworth B, Houpt E, Jere KC, Lindblad R, Love MS, Makhaza L, McNamara CW, Nedi W, Nyirenda J, Operario DJ, Phulusa J, Quinnan GV, Sawyer LA, Thole H, Toto N, Winter A, Van Voorhis WC. Clofazimine for Treatment of Cryptosporidiosis in Human Immunodeficiency Virus Infected Adults: An Experimental Medicine, Randomized, Double-blind, Placebo-controlled Phase 2a Trial. Clin Infect Dis 2021; 73:183-191. [PMID: 32277809 PMCID: PMC8282326 DOI: 10.1093/cid/ciaa421] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/09/2020] [Indexed: 01/01/2023] Open
Abstract
Background We evaluated the efficacy, pharmacokinetics (PK), and safety of clofazimine (CFZ) in patients living with human immunodeficiency virus (HIV) with cryptosporidiosis. Methods We performed a randomized, double-blind, placebo-controlled study. Primary outcomes in part A were reduction in Cryptosporidium shedding, safety, and PK. Primary analysis was according to protocol (ATP). Part B of the study compared CFZ PK in matched individuals living with HIV without cryptosporidiosis. Results Twenty part A and 10 part B participants completed the study ATP. Almost all part A participants had high viral loads and low CD4 counts, consistent with failure of antiretroviral (ARV) therapy. At study entry, the part A CFZ group had higher Cryptosporidium shedding, total stool weight, and more diarrheal episodes compared with the placebo group. Over the inpatient period, compared with those who received placebo, the CFZ group Cryptosporidium shedding increased by 2.17 log2 Cryptosporidium per gram stool (95% upper confidence limit, 3.82), total stool weight decreased by 45.3 g (P = .37), and number of diarrheal episodes increased by 2.32 (P = .87). The most frequent solicited adverse effects were diarrhea, abdominal pain, and malaise. One placebo and 3 CFZ participants died during the study. Plasma levels of CFZ in participants with cryptosporidiosis were 2-fold lower than in part B controls. Conclusions Our findings do not support the efficacy of CFZ for the treatment of cryptosporidiosis in a severely immunocompromised HIV population. However, this trial demonstrates a pathway to assess the therapeutic potential of drugs for cryptosporidiosis treatment. Screening persons living with HIV for diarrhea, and especially Cryptosporidium infection, may identify those failing ARV therapy. Clinical Trials Registration NCT03341767.
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Affiliation(s)
- Py Iroh Tam
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - S L M Arnold
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - L K Barrett
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | | | | | - E Douglas
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - M A Gordon
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - M Henrion
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - D Hermann
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - E Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - K C Jere
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - M S Love
- Calibr, La Jolla, California, USA
| | - L Makhaza
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - W Nedi
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - J Nyirenda
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - D J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - J Phulusa
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | - H Thole
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - N Toto
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - W C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
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Jumani RS, Bessoff K, Love MS, Miller P, Stebbins EE, Teixeira JE, Campbell MA, Meyers MJ, Zambriski JA, Nunez V, Woods AK, McNamara CW, Huston CD. A Novel Piperazine-Based Drug Lead for Cryptosporidiosis from the Medicines for Malaria Venture Open-Access Malaria Box. Antimicrob Agents Chemother 2018; 62:e01505-17. [PMID: 29339392 PMCID: PMC5913971 DOI: 10.1128/aac.01505-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/05/2018] [Indexed: 12/21/2022] Open
Abstract
Cryptosporidiosis causes life-threatening diarrhea in children under the age of 5 years and prolonged diarrhea in immunodeficient people, especially AIDS patients. The standard of care, nitazoxanide, is modestly effective in children and ineffective in immunocompromised individuals. In addition to the need for new drugs, better knowledge of drug properties that drive in vivo efficacy is needed to facilitate drug development. We report the identification of a piperazine-based lead compound for Cryptosporidium drug development, MMV665917, and a new pharmacodynamic method used for its characterization. The identification of MMV665917 from the Medicines for Malaria Venture Malaria Box was followed by dose-response studies, in vitro toxicity studies, and structure-activity relationship studies using commercial analogues. The potency of this compound against Cryptosporidium parvum Iowa and field isolates was comparable to that against Cryptosporidium hominis Furthermore, unlike nitazoxanide, clofazimine, and paromomycin, MMV665917 appeared to be curative in a NOD SCID gamma mouse model of chronic cryptosporidiosis. MMV665917 was also efficacious in a gamma interferon knockout mouse model of acute cryptosporidiosis. To determine if efficacy in this mouse model of chronic infection might relate to whether compounds are parasiticidal or parasitistatic for C. parvum, we developed a novel in vitro parasite persistence assay. This assay suggested that MMV665917 was parasiticidal, unlike nitazoxanide, clofazimine, and paromomycin. The assay also enabled determination of the concentration of the compound required to maximize the rate of parasite elimination. This time-kill assay can be used to prioritize early-stage Cryptosporidium drug leads and may aid in planning in vivo efficacy experiments. Collectively, these results identify MMV665917 as a promising lead and establish a new method for characterizing potential anticryptosporidial agents.
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Affiliation(s)
- R S Jumani
- Department of Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, USA
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, Vermont, USA
| | - K Bessoff
- Department of Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, USA
| | - M S Love
- California Institute for Biomedical Research, La Jolla, California, USA
| | - P Miller
- Department of Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, USA
| | - E E Stebbins
- Department of Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, USA
| | - J E Teixeira
- Department of Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, USA
| | - M A Campbell
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - M J Meyers
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - J A Zambriski
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - V Nunez
- California Institute for Biomedical Research, La Jolla, California, USA
| | - A K Woods
- California Institute for Biomedical Research, La Jolla, California, USA
| | - C W McNamara
- California Institute for Biomedical Research, La Jolla, California, USA
| | - C D Huston
- Department of Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, USA
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, Vermont, USA
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