1
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Mandt REK, Luth MR, Tye MA, Mazitschek R, Ottilie S, Winzeler EA, Lafuente-Monasterio MJ, Gamo FJ, Wirth DF, Lukens AK. Diverse evolutionary pathways challenge the use of collateral sensitivity as a strategy to suppress resistance. eLife 2023; 12:e85023. [PMID: 37737220 PMCID: PMC10695565 DOI: 10.7554/elife.85023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/21/2023] [Indexed: 09/23/2023] Open
Abstract
Drug resistance remains a major obstacle to malaria control and eradication efforts, necessitating the development of novel therapeutic strategies to treat this disease. Drug combinations based on collateral sensitivity, wherein resistance to one drug causes increased sensitivity to the partner drug, have been proposed as an evolutionary strategy to suppress the emergence of resistance in pathogen populations. In this study, we explore collateral sensitivity between compounds targeting the Plasmodium dihydroorotate dehydrogenase (DHODH). We profiled the cross-resistance and collateral sensitivity phenotypes of several DHODH mutant lines to a diverse panel of DHODH inhibitors. We focus on one compound, TCMDC-125334, which was active against all mutant lines tested, including the DHODH C276Y line, which arose in selections with the clinical candidate DSM265. In six selections with TCMDC-125334, the most common mechanism of resistance to this compound was copy number variation of the dhodh locus, although we did identify one mutation, DHODH I263S, which conferred resistance to TCMDC-125334 but not DSM265. We found that selection of the DHODH C276Y mutant with TCMDC-125334 yielded additional genetic changes in the dhodh locus. These double mutant parasites exhibited decreased sensitivity to TCMDC-125334 and were highly resistant to DSM265. Finally, we tested whether collateral sensitivity could be exploited to suppress the emergence of resistance in the context of combination treatment by exposing wildtype parasites to both DSM265 and TCMDC-125334 simultaneously. This selected for parasites with a DHODH V532A mutation which were cross-resistant to both compounds and were as fit as the wildtype parent in vitro. The emergence of these cross-resistant, evolutionarily fit parasites highlights the mutational flexibility of the DHODH enzyme.
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Affiliation(s)
- Rebecca EK Mandt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Madeline R Luth
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Mark A Tye
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
- Harvard Graduate School of Arts and SciencesCambridgeUnited States
| | - Ralph Mazitschek
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
| | - Sabine Ottilie
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Elizabeth A Winzeler
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Skaggs School of Pharmaceutical Sciences, University of California, San DiegoLa JollaUnited States
| | | | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKlineMadridSpain
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
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2
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Vyas VK, Shukla T, Sharma M. Medicinal chemistry approaches for the discovery of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. Future Med Chem 2023; 15:1295-1321. [PMID: 37551689 DOI: 10.4155/fmc-2023-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Malaria is a severe human disease and a global health problem because of drug-resistant strains. Drugs reported to prevent the growth of Plasmodium parasites target various phases of the parasites' life cycle. Antimalarial drugs can inhibit key enzymes that are responsible for the cellular growth and development of parasites. Plasmodium falciparum dihydroorotate dehydrogenase is one such enzyme that is necessary for de novo pyrimidine biosynthesis. This review focuses on various medicinal chemistry approaches used for the discovery and identification of selective P. falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. This comprehensive review discusses recent advances in the selective therapeutic activity of distinct chemical classes of compounds as P. falciparum dihydroorotate dehydrogenase inhibitors and antimalarial drugs.
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Affiliation(s)
- Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Tanvi Shukla
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
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3
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Murithi JM, Deni I, Pasaje CFA, Okombo J, Bridgford JL, Gnädig NF, Edwards RL, Yeo T, Mok S, Burkhard AY, Coburn-Flynn O, Istvan ES, Sakata-Kato T, Gomez-Lorenzo MG, Cowell AN, Wicht KJ, Le Manach C, Kalantarov GF, Dey S, Duffey M, Laleu B, Lukens AK, Ottilie S, Vanaerschot M, Trakht IN, Gamo FJ, Wirth DF, Goldberg DE, Odom John AR, Chibale K, Winzeler EA, Niles JC, Fidock DA. The Plasmodium falciparum ABC transporter ABCI3 confers parasite strain-dependent pleiotropic antimalarial drug resistance. Cell Chem Biol 2022; 29:824-839.e6. [PMID: 34233174 PMCID: PMC8727639 DOI: 10.1016/j.chembiol.2021.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 01/21/2023]
Abstract
Widespread Plasmodium falciparum resistance to first-line antimalarials underscores the vital need to develop compounds with novel modes of action and identify new druggable targets. Here, we profile five compounds that potently inhibit P. falciparum asexual blood stages. Resistance selection studies with three carboxamide-containing compounds, confirmed by gene editing and conditional knockdowns, identify point mutations in the parasite transporter ABCI3 as the primary mediator of resistance. Selection studies with imidazopyridine or quinoline-carboxamide compounds also yield changes in ABCI3, this time through gene amplification. Imidazopyridine mode of action is attributed to inhibition of heme detoxification, as evidenced by cellular accumulation and heme fractionation assays. For the copy-number variation-selecting imidazopyridine and quinoline-carboxamide compounds, we find that resistance, manifesting as a biphasic concentration-response curve, can independently be mediated by mutations in the chloroquine resistance transporter PfCRT. These studies reveal the interconnectedness of P. falciparum transporters in overcoming drug pressure in different parasite strains.
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Affiliation(s)
- James M. Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jessica L. Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nina F. Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel L. Edwards
- Division of Infectious Diseases, Allergy and Immunology, Center for Vaccine Development, St. Louis University, St. Louis, MO 63104, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Anna Y. Burkhard
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Eva S. Istvan
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | | | - Annie N. Cowell
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Kathryn J. Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA,Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Claire Le Manach
- Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Gavreel F. Kalantarov
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maëlle Duffey
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Sabine Ottilie
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ilya N. Trakht
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francisco-Javier Gamo
- Global Health Pharma Research Unit, GlaxoSmithKline, 28760 Tres Cantos, Madrid, Spain
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Daniel E. Goldberg
- Department of Medicine, Division of Infectious Diseases, and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kelly Chibale
- Drug Discovery and Development Center (H3D) and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Elizabeth A. Winzeler
- School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA,Corresponding author
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4
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Horwitz SM, Blue TC, Ambarian JA, Hoshino S, Seyedsayamdost MR, Davis KM. Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines. RSC Chem Biol 2022; 3:420-425. [PMID: 35441142 PMCID: PMC8984913 DOI: 10.1039/d1cb00255d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Hydroxyalkylquinolines (HAQs) are ubiquitious natural products but their interactions with associated protein targets remain elusive. We report X-ray crystal structures of two HAQs in complex with dihydroorotate dehydrogenase (DHODH). Our results reveal the structural basis of DHODH inhibition by HAQs and open the door to downstream structure-activity relationship studies.
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Affiliation(s)
| | - Tamra C Blue
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | | | - Shotaro Hoshino
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
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5
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Atypical Molecular Basis for Drug Resistance to Mitochondrial Function Inhibitors in Plasmodium falciparum. Antimicrob Agents Chemother 2021; 65:AAC.02143-20. [PMID: 33361312 DOI: 10.1128/aac.02143-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
The continued emergence of drug-resistant Plasmodium falciparum parasites hinders global attempts to eradicate malaria, emphasizing the need to identify new antimalarial drugs. Attractive targets for chemotherapeutic intervention are the cytochrome (cyt) bc 1 complex, which is an essential component of the mitochondrial electron transport chain (mtETC) required for ubiquinone recycling and mitochondrially localized dihydroorotate dehydrogenase (DHODH) critical for de novo pyrimidine synthesis. Despite the essentiality of this complex, resistance to a novel acridone class of compounds targeting cyt bc 1 was readily attained, resulting in a parasite strain (SB1-A6) that was panresistant to both mtETC and DHODH inhibitors. Here, we describe the molecular mechanism behind the resistance of the SB1-A6 parasite line, which lacks the common cyt bc 1 point mutations characteristic of resistance to mtETC inhibitors. Using Illumina whole-genome sequencing, we have identified both a copy number variation (∼2×) and a single-nucleotide polymorphism (C276F) associated with pfdhodh in SB1-A6. We have characterized the role of both genetic lesions by mimicking the copy number variation via episomal expression of pfdhodh and introducing the identified single nucleotide polymorphism (SNP) using CRISPR-Cas9 and assessed their contributions to drug resistance. Although both of these genetic polymorphisms have been previously identified as contributing to both DSM-1 and atovaquone resistance, SB1-A6 represents a unique genotype in which both alterations are present in a single line, suggesting that the combination contributes to the panresistant phenotype. This novel mechanism of resistance to mtETC inhibition has critical implications for the development of future drugs targeting the bc 1 complex or de novo pyrimidine synthesis that could help guide future antimalarial combination therapies and reduce the rapid development of drug resistance in the field.
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6
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Driving antimalarial design through understanding of target mechanism. Biochem Soc Trans 2020; 48:2067-2078. [PMID: 32869828 PMCID: PMC7609028 DOI: 10.1042/bst20200224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022]
Abstract
Malaria continues to be a global health threat, affecting approximately 219 million people in 2018 alone. The recurrent development of resistance to existing antimalarials means that the design of new drug candidates must be carefully considered. Understanding of drug target mechanism can dramatically accelerate early-stage target-based development of novel antimalarials and allows for structural modifications even during late-stage preclinical development. Here, we have provided an overview of three promising antimalarial molecular targets, PfDHFR, PfDHODH and PfA-M1, and their associated inhibitors which demonstrate how mechanism can inform drug design and be effectively utilised to generate compounds with potent inhibitory activity.
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7
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Mandt REK, Lafuente-Monasterio MJ, Sakata-Kato T, Luth MR, Segura D, Pablos-Tanarro A, Viera S, Magan N, Ottilie S, Winzeler EA, Lukens AK, Gamo FJ, Wirth DF. In vitro selection predicts malaria parasite resistance to dihydroorotate dehydrogenase inhibitors in a mouse infection model. Sci Transl Med 2020; 11:11/521/eaav1636. [PMID: 31801884 DOI: 10.1126/scitranslmed.aav1636] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/04/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022]
Abstract
Resistance has developed in Plasmodium malaria parasites to every antimalarial drug in clinical use, prompting the need to characterize the pathways mediating resistance. Here, we report a framework for assessing development of resistance of Plasmodium falciparum to new antimalarial therapeutics. We investigated development of resistance by P. falciparum to the dihydroorotate dehydrogenase (DHODH) inhibitors DSM265 and DSM267 in tissue culture and in a mouse model of P. falciparum infection. We found that resistance to these drugs arose rapidly both in vitro and in vivo. We identified 13 point mutations mediating resistance in the parasite DHODH in vitro that overlapped with the DHODH mutations that arose in the mouse infection model. Mutations in DHODH conferred increased resistance (ranging from 2- to ~400-fold) to DHODH inhibitors in P. falciparum in vitro and in vivo. We further demonstrated that the drug-resistant parasites carrying the C276Y mutation had mitochondrial energetics comparable to the wild-type parasite and also retained their fitness in competitive growth experiments. Our data suggest that in vitro selection of drug-resistant P. falciparum can predict development of resistance in a mouse model of malaria infection.
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Affiliation(s)
- Rebecca E K Mandt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Maria Jose Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Madeline R Luth
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Delfina Segura
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Alba Pablos-Tanarro
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Sara Viera
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Noemi Magan
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Sabine Ottilie
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth A Winzeler
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Skaggs School of Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. .,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
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8
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Clark RD, Morris DN, Chinigo G, Lawless MS, Prudhomme J, Le Roch KG, Lafuente MJ, Ferrer S, Gamo FJ, Gadwood R, Woltosz WS. Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones. J Comput Aided Mol Des 2020; 34:1117-1132. [PMID: 32833084 PMCID: PMC7533260 DOI: 10.1007/s10822-020-00333-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/21/2020] [Indexed: 10/31/2022]
Abstract
There is a pressing need to improve the efficiency of drug development, and nowhere is that need more clear than in the case of neglected diseases like malaria. The peculiarities of pyrimidine metabolism in Plasmodium species make inhibition of dihydroorotate dehydrogenase (DHODH) an attractive target for antimalarial drug design. By applying a pair of complementary quantitative structure-activity relationships derived for inhibition of a truncated, soluble form of the enzyme from Plasmodium falciparum (s-PfDHODH) to data from a large-scale phenotypic screen against cultured parasites, we were able to identify a class of antimalarial leads that inhibit the enzyme and abolish parasite growth in blood culture. Novel analogs extending that class were designed and synthesized with a goal of improving potency as well as the general pharmacokinetic and toxicological profiles. Their synthesis also represented an opportunity to prospectively validate our in silico property predictions. The seven analogs synthesized exhibited physicochemical properties in good agreement with prediction, and five of them were more active against P. falciparum growing in blood culture than any of the compounds in the published lead series. The particular analogs prepared did not inhibit s-PfDHODH in vitro, but advanced biological assays indicated that other examples from the class did inhibit intact PfDHODH bound to the mitochondrial membrane. The new analogs, however, killed the parasites by acting through some other, unidentified mechanism 24-48 h before PfDHODH inhibition would be expected to do so.
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Affiliation(s)
- Robert D Clark
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534-7059, USA.
| | - Denise N Morris
- Cognigen Corporation, a Simulations Plus Company, Buffalo, NY, USA
| | - Gary Chinigo
- Kalexsyn, Inc., Kalamazoo, MI, USA.,Pfizer Inc., Groton, CT, USA
| | - Michael S Lawless
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534-7059, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Maria José Lafuente
- Tres Cantos Medicines Development Campus-Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Santiago Ferrer
- Tres Cantos Medicines Development Campus-Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus-Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | - Walter S Woltosz
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534-7059, USA
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9
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Kokkonda S, Deng X, White KL, El Mazouni F, White J, Shackleford DM, Katneni K, Chiu FCK, Barker H, McLaren J, Crighton E, Chen G, Angulo-Barturen I, Jimenez-Diaz MB, Ferrer S, Huertas-Valentin L, Martinez-Martinez MS, Lafuente-Monasterio MJ, Chittimalla R, Shahi SP, Wittlin S, Waterson D, Burrows JN, Matthews D, Tomchick D, Rathod PK, Palmer MJ, Charman SA, Phillips MA. Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria. J Med Chem 2020; 63:4929-4956. [PMID: 32248693 DOI: 10.1021/acs.jmedchem.0c00311] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Malaria puts at risk nearly half the world's population and causes high mortality in sub-Saharan Africa, while drug resistance threatens current therapies. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated target for malaria treatment based on our finding that triazolopyrimidine DSM265 (1) showed efficacy in clinical studies. Herein, we describe optimization of a pyrrole-based series identified using a target-based DHODH screen. Compounds with nanomolar potency versus Plasmodium DHODH and Plasmodium parasites were identified with good pharmacological properties. X-ray studies showed that the pyrroles bind an alternative enzyme conformation from 1 leading to improved species selectivity versus mammalian enzymes and equivalent activity on Plasmodium falciparum and Plasmodium vivax DHODH. The best lead DSM502 (37) showed in vivo efficacy at similar levels of blood exposure to 1, although metabolic stability was reduced. Overall, the pyrrole-based DHODH inhibitors provide an attractive alternative scaffold for the development of new antimalarial compounds.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Xiaoyi Deng
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Farah El Mazouni
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Francis C K Chiu
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Helena Barker
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jenna McLaren
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | | | | | - Santiago Ferrer
- GSK, Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | | | | | | | | | | | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | | | - Dave Matthews
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Diana Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Margaret A Phillips
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
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10
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Ashton TD, Devine SM, Möhrle JJ, Laleu B, Burrows JN, Charman SA, Creek DJ, Sleebs BE. The Development Process for Discovery and Clinical Advancement of Modern Antimalarials. J Med Chem 2019; 62:10526-10562. [DOI: 10.1021/acs.jmedchem.9b00761] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Trent D. Ashton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Shane M. Devine
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Jörg J. Möhrle
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Jeremy N. Burrows
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Susan A. Charman
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Darren J. Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
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11
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Strašek N, Lavrenčič L, Oštrek A, Slapšak D, Grošelj U, Klemenčič M, Brodnik Žugelj H, Wagger J, Novinec M, Svete J. Tetrahydro-1H,5H-pyrazolo[1,2-a]pyrazole-1-carboxylates as inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. Bioorg Chem 2019; 89:102982. [PMID: 31132601 DOI: 10.1016/j.bioorg.2019.102982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/29/2019] [Accepted: 05/08/2019] [Indexed: 11/25/2022]
Abstract
The reactions between 5-substituted pyrazolidine-3-ones, aldehydes, and methyl methacrylate provided tetrahydropyrazolo[1,2-a]pyrazole-1-carboxylates as mixtures of syn- and anti-diastereomers. Testing for inhibition of dihydroorotate dehydrogenase of Plasmodium falciparum (PfDHODH) revealed high activity of some anti-isomers of the methyl esters, while the corresponding carboxylic acids and carboxamides were not active. The most active representative, methyl (1S*,3S*,5R*)-1,5-dimethyl-7-oxo-3-phenyltetrahydro-1H,5H-pyrazolo[1,2-a]pyrazole-1-carboxylate (IC50 = 2.9 ± 0.3 μM), also exhibited very high selectivity of the parasite enzyme vs. the human enzyme, PfDHODH/HsDHODH > 350. According to the molecular docking score, this high activity is explainable by synergic interactions of the methyl, phenyl and the CO2Me substituent with the hydrophobic pockets in the active site of the enzyme. The carboxylic acid and carboxamides derived from this compound did not inhibit PfDHODH.
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Affiliation(s)
- Nika Strašek
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Lara Lavrenčič
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Andraž Oštrek
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Dejan Slapšak
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Uroš Grošelj
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Marina Klemenčič
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Helena Brodnik Žugelj
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Jernej Wagger
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Marko Novinec
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia.
| | - Jurij Svete
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia.
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12
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Nonato MC, de Pádua RA, David JS, Reis RA, Tomaleri GP, D'Muniz Pereira H, Calil FA. Structural basis for the design of selective inhibitors for Schistosoma mansoni dihydroorotate dehydrogenase. Biochimie 2019; 158:180-190. [DOI: 10.1016/j.biochi.2019.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/10/2019] [Indexed: 10/27/2022]
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13
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Antonova-Koch Y, Meister S, Abraham M, Luth MR, Ottilie S, Lukens AK, Sakata-Kato T, Vanaerschot M, Owen E, Jado JC, Maher SP, Calla J, Plouffe D, Zhong Y, Chen K, Chaumeau V, Conway AJ, McNamara CW, Ibanez M, Gagaring K, Serrano FN, Eribez K, Taggard CM, Cheung AL, Lincoln C, Ambachew B, Rouillier M, Siegel D, Nosten F, Kyle DE, Gamo FJ, Zhou Y, Llinás M, Fidock DA, Wirth DF, Burrows J, Campo B, Winzeler EA. Open-source discovery of chemical leads for next-generation chemoprotective antimalarials. Science 2019; 362:362/6419/eaat9446. [PMID: 30523084 PMCID: PMC6516198 DOI: 10.1126/science.aat9446] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/18/2018] [Indexed: 11/19/2022]
Abstract
To discover leads for next-generation chemoprotective antimalarial drugs,we tested more than 500,000 compounds for their ability to inhibit liver-stage development of luciferase-expressing Plasmodium spp. parasites (681 compounds showed a half-maximal inhibitory concentration of less than 1micromolar).Cluster analysis identified potent and previously unreported scaffold families as well as other series previously associated with chemoprophylaxis. Further testing through multiple phenotypic assays that predict stage-specific and multispecies antimalarial activity distinguished compound classes that are likely to provide symptomatic relief by reducing asexual blood-stage parasitemia from those which are likely to only prevent malaria. Target identification by using functional assays, in vitro evolution, or metabolic profiling revealed 58 mitochondrial inhibitors but also many chemotypes possibly with previously unidentified mechanisms of action.
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Affiliation(s)
- Yevgeniya Antonova-Koch
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Stephan Meister
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Matthew Abraham
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Madeline R Luth
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Sabine Ottilie
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Amanda K Lukens
- Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.,The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Manu Vanaerschot
- Division of Infectious Diseases, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Edward Owen
- Department of Biochemistry and Molecular Biology and Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Juan Carlos Jado
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Steven P Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.,Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Jaeson Calla
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - David Plouffe
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Yang Zhong
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Kaisheng Chen
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Victor Chaumeau
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amy J Conway
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.,Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Case W McNamara
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Maureen Ibanez
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Kerstin Gagaring
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Fernando Neria Serrano
- Tres Cantos Medicines Development Campus, Malaria DPU, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain
| | - Korina Eribez
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Cullin McLean Taggard
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Andrea L Cheung
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Christie Lincoln
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Biniam Ambachew
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA
| | - Melanie Rouillier
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, CA 92093, USA
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.,Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Francisco-Javier Gamo
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Yingyao Zhou
- The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA.,Department of Chemistry and Center for Infectious Diseases Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - David A Fidock
- Division of Infectious Diseases, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Dyann F Wirth
- Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.,The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, Post Office Box 1826, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Elizabeth A Winzeler
- School of Medicine, University of California, San Diego, 9500 Gilman Drive 0760, La Jolla, CA 92093, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, CA 92093, USA
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14
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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15
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Le Manach C, Paquet T, Wicht K, Nchinda AT, Brunschwig C, Njoroge M, Gibhard L, Taylor D, Lawrence N, Wittlin S, Eyermann CJ, Basarab GS, Duffy J, Fish PV, Street LJ, Chibale K. Antimalarial Lead-Optimization Studies on a 2,6-Imidazopyridine Series within a Constrained Chemical Space To Circumvent Atypical Dose–Response Curves against Multidrug Resistant Parasite Strains. J Med Chem 2018; 61:9371-9385. [DOI: 10.1021/acs.jmedchem.8b01333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claire Le Manach
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Tanya Paquet
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kathryn Wicht
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Aloysius T. Nchinda
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Christel Brunschwig
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Mathew Njoroge
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Liezl Gibhard
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Dale Taylor
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Nina Lawrence
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
| | - Charles J. Eyermann
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Gregory S. Basarab
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - James Duffy
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, PO Box 1826, 1215 Geneva, Switzerland
| | - Paul V. Fish
- Alzheimer’s Research UK, UCL Drug Discovery Institute, The Cruciform Building, University College London, Gower Street, London WC1E 6BT, U.K
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Leslie J. Street
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Center (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council, Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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16
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Mathews ES, Odom John AR. Tackling resistance: emerging antimalarials and new parasite targets in the era of elimination. F1000Res 2018; 7. [PMID: 30135714 PMCID: PMC6073090 DOI: 10.12688/f1000research.14874.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Malaria remains a significant contributor to global human mortality, and roughly half the world’s population is at risk for infection with
Plasmodium spp. parasites. Aggressive control measures have reduced the global prevalence of malaria significantly over the past decade. However, resistance to available antimalarials continues to spread, including resistance to the widely used artemisinin-based combination therapies. Novel antimalarial compounds and therapeutic targets are greatly needed. This review will briefly discuss several promising current antimalarial development projects, including artefenomel, ferroquine, cipargamin, SJ733, KAF156, MMV048, and tafenoquine. In addition, we describe recent large-scale genetic and resistance screens that have been instrumental in target discovery. Finally, we highlight new antimalarial targets, which include essential transporters and proteases. These emerging antimalarial compounds and therapeutic targets have the potential to overcome multi-drug resistance in ongoing efforts toward malaria elimination.
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Affiliation(s)
- Emily S Mathews
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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17
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Plasmodium falciparum dihydroorotate dehydrogenase: a drug target against malaria. Future Med Chem 2018; 10:1853-1874. [PMID: 30019917 DOI: 10.4155/fmc-2017-0250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Malaria remains one of the most lethal infectious diseases worldwide, and the most severe form is caused by Plasmodium falciparum. In recent decades, the major challenge to treatment of this disease has been the ability of the protozoan parasite to develop resistance to the drugs that are currently in use. Among P. falciparum enzymes, P. falciparum dihydroorotate dehydrogenase has been identified as an important target in drug discovery. Interference with the activity of this enzyme inhibits de novo pyrimidine biosynthesis and consequently prevents malarial infection. Organic synthesis, x-ray crystallography, high-throughput screening and molecular modeling methods such as molecular docking, quantitative structure-activity relationships, structure-based pharmacophore mapping and molecular dynamics simulations have been applied to the discovery of new inhibitors of P. falciparum dihydroorotate dehydrogenase.
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18
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Xu L, Li W, Diao Y, Sun H, Li H, Zhu L, Zhou H, Zhao Z. Synthesis, Design, and Structure⁻Activity Relationship of the Pyrimidone Derivatives as Novel Selective Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase. Molecules 2018; 23:molecules23061254. [PMID: 29794978 PMCID: PMC6099574 DOI: 10.3390/molecules23061254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022] Open
Abstract
The inhibition of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) potentially represents a new treatment option for malaria, as P. falciparum relies entirely on a de novo pyrimidine biosynthetic pathway for survival. Herein, we report a series of pyrimidone derivatives as novel inhibitors of PfDHODH. The most potent compound, 26, showed high inhibition activity against PfDHODH (IC50 = 23 nM), with >400-fold species selectivity over human dihydroorotate dehydrogenase (hDHODH). The brand-new inhibitor scaffold targeting PfDHODH reported in this work may lead to the discovery of new antimalarial agents.
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Affiliation(s)
- Le Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Wenjie Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Hongxia Sun
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Hongchang Zhou
- Department of Microbiology, Medical School of Huzhou Teachers College, Huzhou 313000, China.
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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19
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Ross LS, Lafuente-Monasterio MJ, Sakata-Kato T, Mandt REK, Gamo FJ, Wirth DF, Lukens AK. Identification of Collateral Sensitivity to Dihydroorotate Dehydrogenase Inhibitors in Plasmodium falciparum. ACS Infect Dis 2018; 4:508-515. [PMID: 29336544 PMCID: PMC5899019 DOI: 10.1021/acsinfecdis.7b00217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Drug
resistance has been reported for every antimalarial in use highlighting
the need for new strategies to protect the efficacy of therapeutics
in development. We have previously shown that resistance can be suppressed
with a population biology trap: by identifying situations where resistance
to one compound confers hypersensitivity to another (collateral sensitivity),
we can design combination therapies that not only kill the parasite
but also guide its evolution away from resistance. We applied this
concept to the Plasmodium falciparum dihydroorotate
dehydrogenase (PfDHODH) enzyme, a well validated
antimalarial target with inhibitors in the development pipeline. Here,
we report a high-throughput screen to identify compounds specifically
active against PfDHODH resistant mutants. We additionally
perform extensive cross-resistance profiling allowing us to identify
compound pairs demonstrating the potential for mutually incompatible
resistance. These combinations represent promising starting points
for exploiting collateral sensitivity to extend the useful lifespan
of new antimalarial therapeutics.
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Affiliation(s)
- Leila Saxby Ross
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Maria José Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Rebecca E. K. Mandt
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
- Infectious Disease and Microbiome Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
- Infectious Disease and Microbiome Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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20
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Synthesis, SAR, and Docking Studies Disclose 2-Arylfuran-1,4-naphthoquinones as In Vitro Antiplasmodial Hits. J Trop Med 2017; 2017:7496934. [PMID: 29225629 PMCID: PMC5684547 DOI: 10.1155/2017/7496934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/11/2017] [Accepted: 08/27/2017] [Indexed: 12/13/2022] Open
Abstract
A total of 28 lapachol-related naphthoquinones with four different scaffolds were synthesized and spectroscopically characterized. In vitro antiplasmodial activity was assayed against the chloroquine-resistant Plasmodium falciparum W2 strain by the parasite lactate dehydrogenase (pLDH) method. Cytotoxicity against Hep G2A16 cell was determined by the MTT assay. All compounds disclosed higher in vitro antiplasmodial activity than lapachol. Ortho- and para-naphthoquinones with a furan ring fused to the quinonoid moiety were more potent than 2-hydroxy-3-(1′-alkenyl)-1,4-naphthoquinones, while ortho-furanonaphthoquinones were more cytotoxic. Molecular docking to Plasmodium targets Pfcyt bc1 complex and PfDHOD enzyme showed that five out of the 28 naphthoquinones disclosed favorable binding energies. Furanonaphthoquinones endowed with an aryl moiety linked to the furan ring are highlighted as new in vitro antiplasmodial lead compounds and warrant further investigation.
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21
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+Targeting Mitochondrial Functions as Antimalarial Regime, What Is Next? CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0075-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Interconvertible geometric isomers of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors exhibit multiple binding modes. Bioorg Med Chem Lett 2017; 27:3878-3882. [DOI: 10.1016/j.bmcl.2017.06.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/15/2017] [Accepted: 06/17/2017] [Indexed: 11/21/2022]
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23
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Manhas A, Lone MY, Jha PC. Multicomplex-based pharmacophore modeling coupled with molecular dynamics simulations: An efficient strategy for the identification of novel inhibitors of Pf DHODH. J Mol Graph Model 2017; 75:413-423. [DOI: 10.1016/j.jmgm.2017.04.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 01/08/2023]
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Reis RAG, Calil FA, Feliciano PR, Pinheiro MP, Nonato MC. The dihydroorotate dehydrogenases: Past and present. Arch Biochem Biophys 2017; 632:175-191. [PMID: 28666740 DOI: 10.1016/j.abb.2017.06.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 01/24/2023]
Abstract
The flavoenzyme dihydroorotate dehydrogenase catalyzes the stereoselective oxidation of (S)-dihydroorotate to orotate in the fourth of the six conserved enzymatic reactions involved in the de novo pyrimidine biosynthetic pathway. Inhibition of pyrimidine metabolism by selectively targeting DHODHs has been exploited in the development of new therapies against cancer, immunological disorders, bacterial and viral infections, and parasitic diseases. Through a chronological narrative, this review summarizes the efforts of the scientific community to achieve our current understanding of structural and biochemical properties of DHODHs. It also attempts to describe the latest advances in medicinal chemistry for therapeutic development based on the selective inhibition of DHODH, including an overview of the experimental techniques used for ligand screening during the process of drug discovery.
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Affiliation(s)
- Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Felipe Antunes Calil
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Patricia Rosa Feliciano
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Matheus Pinto Pinheiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, 13083-970, Brazil
| | - M Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil.
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25
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Magistrado PA, Corey VC, Lukens AK, LaMonte G, Sasaki E, Meister S, Wree M, Winzeler E, Wirth DF. Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL), a Resistance Mechanism for Two Distinct Compound Classes. ACS Infect Dis 2016; 2:816-826. [PMID: 27933786 PMCID: PMC5109296 DOI: 10.1021/acsinfecdis.6b00025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
MMV007564
is a novel antimalarial benzimidazolyl piperidine chemotype
identified in cellular screens. To identify the genetic determinant
of MMV007564 resistance, parasites were cultured in the presence of
the compound to generate resistant lines. Whole genome sequencing
revealed distinct mutations in the gene named Plasmodium
falciparum cyclic amine resistance locus (pfcarl), encoding a conserved protein of unknown function.
Mutations in pfcarl are strongly associated with
resistance to a structurally unrelated class of compounds, the imidazolopiperazines,
including KAF156, currently in clinical trials. Our data demonstrate
that pfcarl mutations confer resistance to two distinct
compound classes, benzimidazolyl piperidines and imidazolopiperazines.
However, MMV007564 and the imidazolopiperazines, KAF156 and GNF179,
have different timings of action in the asexual blood stage and different
potencies against the liver and sexual blood stages. These data suggest
that pfcarl is a multidrug-resistance gene rather
than a common target for benzimidazolyl piperidines and imidazolopiperazines.
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Affiliation(s)
- Pamela A. Magistrado
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Victoria C. Corey
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Amanda K. Lukens
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Infectious
Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Greg LaMonte
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Erika Sasaki
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Stephan Meister
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Melanie Wree
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Elizabeth Winzeler
- School
of Medicine, University of California—San Diego, La Jolla, California 92093, United States
| | - Dyann F. Wirth
- Department
of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Infectious
Disease Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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26
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Pavadai E, El Mazouni F, Wittlin S, de Kock C, Phillips MA, Chibale K. Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:548-62. [PMID: 26915022 DOI: 10.1021/acs.jcim.5b00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a key enzyme in the de novo pyrimidine biosynthesis pathway, which the Plasmodium falciparum relies on exclusively for survival, has emerged as a promising target for antimalarial drugs. In an effort to discover new and potent PfDHODH inhibitors, 3D-QSAR pharmacophore models were developed based on the structures of known PfDHODH inhibitors and the validated Hypo1 model was used as a 3D search query for virtual screening of the National Cancer Institute database. The virtual hit compounds were further filtered based on molecular docking and Molecular Mechanics/Generalized Born Surface Area binding energy calculations. The combination of the pharmacophore and structure-based virtual screening resulted in the identification of nine new compounds that showed >25% inhibition of PfDHODH at a concentration of 10 μM, three of which exhibited IC50 values in the range of 0.38-20 μM. The most active compound, NSC336047, displayed species-selectivity for PfDHODH over human DHODH and inhibited parasite growth with an IC50 of 26 μM. In addition to this, 13 compounds inhibited parasite growth with IC50 values of ≤ 50 μM, 4 of which showed IC50 values in the range of 5-12 μM. These compounds could be further explored in the identification and development of more potent PfDHODH and parasite growth inhibitors.
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Affiliation(s)
| | - Farah El Mazouni
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel , 4002 Basel, Switzerland
| | - Carmen de Kock
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town , Observatory 7925, South Africa
| | - Margaret A Phillips
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
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27
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Hou X, Chen X, Zhang M, Yan A. QSAR study on the antimalarial activity of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:101-124. [PMID: 26911561 DOI: 10.1080/1062936x.2015.1134652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Plasmodium falciparum, the most fatal parasite that causes malaria, is responsible for over one million deaths per year. P. falciparum dihydroorotate dehydrogenase (PfDHODH) has been validated as a promising drug development target for antimalarial therapy since it catalyzes the rate-limiting step for DNA and RNA biosynthesis. In this study, we investigated the quantitative structure-activity relationships (QSAR) of the antimalarial activity of PfDHODH inhibitors by generating four computational models using a multilinear regression (MLR) and a support vector machine (SVM) based on a dataset of 255 PfDHODH inhibitors. All the models display good prediction quality with a leave-one-out q(2) >0.66, a correlation coefficient (r) >0.85 on both training sets and test sets, and a mean square error (MSE) <0.32 on training sets and <0.37 on test sets, respectively. The study indicated that the hydrogen bonding ability, atom polarizabilities and ring complexity are predominant factors for inhibitors' antimalarial activity. The models are capable of predicting inhibitors' antimalarial activity and the molecular descriptors for building the models could be helpful in the development of new antimalarial drugs.
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Affiliation(s)
- X Hou
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
| | - X Chen
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
| | - M Zhang
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
| | - A Yan
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
- b Stake Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing , P.R. China
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28
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Flannery EL, McNamara CW, Kim SW, Kato TS, Li F, Teng CH, Gagaring K, Manary MJ, Barboa R, Meister S, Kuhen K, Vinetz JM, Chatterjee AK, Winzeler EA. Mutations in the P-type cation-transporter ATPase 4, PfATP4, mediate resistance to both aminopyrazole and spiroindolone antimalarials. ACS Chem Biol 2015; 10:413-20. [PMID: 25322084 PMCID: PMC4340351 DOI: 10.1021/cb500616x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Aminopyrazoles are a new class of
antimalarial compounds identified
in a cellular antiparasitic screen with potent activity against Plasmodium falciparum asexual and sexual stage parasites.
To investigate their unknown mechanism of action and thus identify
their target, we cultured parasites in the presence of a representative
member of the aminopyrazole series, GNF-Pf4492, to select for resistance.
Whole genome sequencing of three resistant lines showed that each
had acquired independent mutations in a P-type cation-transporter
ATPase, PfATP4 (PF3D7_1211900), a protein implicated as the novel Plasmodium spp. target of another, structurally unrelated,
class of antimalarials called the spiroindolones and characterized
as an important sodium transporter of the cell. Similarly to the spiroindolones,
GNF-Pf4492 blocks parasite transmission to mosquitoes and disrupts
intracellular sodium homeostasis. Our data demonstrate that PfATP4
plays a critical role in cellular processes, can be inhibited by two
distinct antimalarial pharmacophores, and supports the recent observations
that PfATP4 is a critical antimalarial target.
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Affiliation(s)
| | - Case W. McNamara
- The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | | | - Tomoyo Sakata Kato
- The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | | | | | - Kerstin Gagaring
- The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | | | - Rachel Barboa
- The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | | | - Kelli Kuhen
- The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | | | - Arnab K. Chatterjee
- The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
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29
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Abstract
Due to an increased need for new antimalarial chemotherapies that show potency against Plasmodium falciparum, researchers are targeting new processes within the parasite in an effort to circumvent or delay the onset of drug resistance. One such promising area for antimalarial drug development has been the parasite mitochondrial electron transport chain (ETC). Efforts have been focused on targeting key processes along the parasite ETC specifically the dihydroorotate dehydrogenase (DHOD) enzyme, the cytochrome bc 1 enzyme and the NADH type II oxidoreductase (PfNDH2) pathway. This review summarizes the most recent efforts in antimalarial drug development reported in the literature and describes the evolution of these compounds.
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30
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Abstract
Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.
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31
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Deng X, Kokkonda S, El Mazouni F, White J, Burrows JN, Kaminsky W, Charman SA, Matthews D, Rathod PK, Phillips MA. Fluorine modulates species selectivity in the triazolopyrimidine class of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors. J Med Chem 2014; 57:5381-94. [PMID: 24801997 PMCID: PMC4079327 DOI: 10.1021/jm500481t] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Malaria is one of the most serious global infectious diseases. The pyrimidine biosynthetic enzyme Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) is an important target for antimalarial chemotherapy. We describe a detailed analysis of protein-ligand interactions between DHODH and a triazolopyrimidine-based inhibitor series to explore the effects of fluorine on affinity and species selectivity. We show that increasing fluorination dramatically increases binding to mammalian DHODHs, leading to a loss of species selectivity. Triazolopyrimidines bind Plasmodium and mammalian DHODHs in overlapping but distinct binding sites. Key hydrogen-bond and stacking interactions underlying strong binding to PfDHODH are absent in the mammalian enzymes. Increasing fluorine substitution leads to an increase in the entropic contribution to binding, suggesting that strong binding to mammalian DHODH is a consequence of an enhanced hydrophobic effect upon binding to an apolar pocket. We conclude that hydrophobic interactions between fluorine and hydrocarbons provide significant binding energy to protein-ligand interactions. Our studies define the requirements for species-selective binding to PfDHODH and show that the triazolopyrimidine scaffold can alternatively be tuned to inhibit human DHODH, an important target for autoimmune diseases.
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Affiliation(s)
- Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, United States
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32
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Targeting the mitochondrial electron transport chain of Plasmodium falciparum: new strategies towards the development of improved antimalarials for the elimination era. Future Med Chem 2014; 5:1573-91. [PMID: 24024949 DOI: 10.4155/fmc.13.121] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Despite intense efforts, there has not been a truly new antimalarial, possessing a novel mechanism of action, registered for over 10 years. By virtue of a novel mode of action, it is hoped that the global challenge of multidrug-resistant parasites can be overcome, as well as developing drugs that possess prophylaxis and/or transmission-blocking properties, towards an elimination agenda. Many target-based and whole-cell screening drug development programs have been undertaken in recent years and here an overview of specific projects that have focused on targeting the parasite's mitochondrial electron transport chain is presented. Medicinal chemistry activity has largely focused on inhibitors of the parasite cytochrome bc1 Complex (Complex III) including acridinediones, pyridones and quinolone aryl esters, as well as inhibitors of dihydroorotate dehydrogenase that includes triazolopyrimidines and benzimidazoles. Common barriers to progress and opportunities for novel chemistry and potential additional electron transport chain targets are discussed in the context of the target candidate profiles for uncomplicated malaria.
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33
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Crowther GJ, Booker ML, He M, Li T, Raverdy S, Novelli JF, He P, Dale NRG, Fife AM, Barker RH, Kramer ML, Van Voorhis WC, Carlow CKS, Wang MW. Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens. PLoS Negl Trop Dis 2014; 8:e2628. [PMID: 24416464 PMCID: PMC3886921 DOI: 10.1371/journal.pntd.0002628] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022] Open
Abstract
Cofactor-independent phosphoglycerate mutase (iPGAM) is essential for the growth of C. elegans but is absent from humans, suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi, a cause of lymphatic filariasis (LF). iPGAM's active site is small and hydrophilic, implying that it may not be druggable, but another binding site might permit allosteric inhibition. As a comprehensive assessment of iPGAM's druggability, high-throughput screening (HTS) was conducted at two different locations: ∼220,000 compounds were tested against the C. elegans iPGAM by Genzyme Corporation, and ∼160,000 compounds were screened against the B. malayi iPGAM at the National Center for Drug Screening in Shanghai. iPGAM's catalytic activity was coupled to downstream glycolytic enzymes, resulting in NADH consumption, as monitored by a decline in visible-light absorbance at 340 nm. This assay performed well in both screens (Z′-factor >0.50) and identified two novel inhibitors that may be useful as chemical probes. However, these compounds have very modest potency against the B. malayi iPGAM (IC50 >10 µM) and represent isolated singleton hits rather than members of a common scaffold. Thus, despite the other appealing properties of the nematode iPGAMs, their low druggability makes them challenging to pursue as drug targets. This study illustrates a “druggability paradox” of target-based drug discovery: proteins are generally unsuitable for resource-intensive HTS unless they are considered druggable, yet druggability is often difficult to predict in the absence of HTS data. Parasitic worms like Brugia malayi cause widespread lymphatic filariasis (LF) in southeast Asia and sub-Saharan Africa. The adult worms causing most of the symptoms of LF are difficult to treat with existing drugs. As a possible step toward new LF drugs, we searched for inhibitors of the B. malayi cofactor-independent phosphoglycerate mutase (iPGAM), an enzyme thought to be critical to survival and development of this parasite. Despite testing over 100,000 compounds at each of two screening centers, we found only two compounds that consistently inhibited the B. malayi enzyme more strongly than the cofactor-dependent enzyme found in humans. These compounds have limited potency and are not especially great starting points for drug development. The 3-dimensional structure of iPGAM suggests that the active site is difficult to access from the surrounding solvent, which may partly explain our very low yield of inhibitors. We conclude that iPGAM may not be an ideal drug target in B. malayi or related organisms because it is difficult to inhibit with druglike compounds.
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Affiliation(s)
- Gregory J. Crowther
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Michael L. Booker
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Min He
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ting Li
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Sylvine Raverdy
- Division of Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jacopo F. Novelli
- Division of Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Panqing He
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Natalie R. G. Dale
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Amy M. Fife
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Robert H. Barker
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Martin L. Kramer
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Wesley C. Van Voorhis
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Clotilde K. S. Carlow
- Division of Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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34
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Abstract
The potential of flavoproteins as targets of pharmacological treatments is immense. In this review we present an overview of the current research progress on medical interventions based on flavoproteins with a special emphasis on cancer, infectious diseases, and neurological disorders.
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Affiliation(s)
- Esther Jortzik
- Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
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35
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Abstract
Malaria elimination has recently been reinstated as a global health priority but current therapies seem to be insufficient for the task. Elimination efforts require new drug classes that alleviate symptoms, prevent transmission and provide a radical cure. To develop these next-generation medicines, public-private partnerships are funding innovative approaches to identify compounds that target multiple parasite species at multiple stages of the parasite life cycle. In this Review, we discuss the cell-, chemistry- and target-based approaches used to discover new drug candidates that are currently in clinical trials or undergoing preclinical testing.
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36
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Xu M, Zhu J, Diao Y, Zhou H, Ren X, Sun D, Huang J, Han D, Zhao Z, Zhu L, Xu Y, Li H. Novel Selective and Potent Inhibitors of Malaria Parasite Dihydroorotate Dehydrogenase: Discovery and Optimization of Dihydrothiophenone Derivatives. J Med Chem 2013; 56:7911-24. [DOI: 10.1021/jm400938g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | - Hongchang Zhou
- Department
of Microbiology, Medical School of Huzhou Teachers College, Huzhou 313000, China
| | | | | | | | - Dongmei Han
- Instrumental
Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
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37
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Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
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Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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38
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In silico identification of novel inhibitors against Plasmodium falciparum dihydroorate dehydrogenase. J Mol Graph Model 2013; 40:40-7. [DOI: 10.1016/j.jmgm.2012.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/22/2012] [Accepted: 11/25/2012] [Indexed: 11/19/2022]
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39
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Diao Y, Lu W, Jin H, Zhu J, Han L, Xu M, Gao R, Shen X, Zhao Z, Liu X, Xu Y, Huang J, Li H. Discovery of diverse human dihydroorotate dehydrogenase inhibitors as immunosuppressive agents by structure-based virtual screening. J Med Chem 2012; 55:8341-9. [PMID: 22984987 DOI: 10.1021/jm300630p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study applied an efficient virtual screening strategy integrating molecular docking with MM-GBSA rescoring to identify diverse human dihydroorotate dehydrogenase (hDHODH) inhibitors. Eighteen compounds with IC(50) values ranging from 0.11 to 18.8 μM were identified as novel hDHODH inhibitors that exhibited overall species-selectivity over Plasmodium falciparum dihydroorotate dehydrogenase (pfDHODH). Compound 8, the most potent one, showed low micromolar inhibitory activity against hDHODH with an IC(50) value of 0.11 μM. Moreover, lipopolysaccharide-induced B-cell assay and mixed lymphocyte reaction assay revealed that most of the hits showed potent antiproliferative activity against B and T cells, which demonstrates their potential application as immunosuppressive agents. In particular, compound 18 exhibited potent B-cell inhibitory activity (IC(50) = 1.78 μM) and presents a B-cell-specific profile with 17- and 26-fold selectivities toward T and Jurkat cells, respectively.
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Affiliation(s)
- Yanyan Diao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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40
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Vyas VK, Parikh H, Ghate M. 3D QSAR studies on 5-(2-methylbenzimidazol-1-yl)-N-alkylthiophene-2-carboxamide derivatives as P. falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0216-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Shah P, Kumar S, Tiwari S, Siddiqi MI. 3D-QSAR studies of triazolopyrimidine derivatives of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking, and genetic algorithm-based methods. J Chem Biol 2012; 5:91-103. [PMID: 23382788 PMCID: PMC3375378 DOI: 10.1007/s12154-012-0072-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/18/2012] [Indexed: 12/30/2022] Open
Abstract
A series of 35 triazolopyrimidine analogues reported as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors were optimized using quantum mechanics methods, and their binding conformations were studied by docking and 3D quantitative structure-activity relationship studies. Genetic algorithm-based criteria was adopted for selection of training and test sets while maintaining structural diversity of training and test sets, which is also very crucial for model development and validation. Both the comparative molecular field analyses ([Formula: see text], [Formula: see text]) and comparative molecular similarity indices analyses ([Formula: see text], [Formula: see text]) show excellent correlation and high predictive power. Furthermore, molecular dynamics simulations were performed to explore the binding mode of the two of the most active compounds of the series, 10 and 14. Harmonization in the two simulation results validate the analysis and therefore applicability of docking parameters based on crystallographic conformation of compound 14 bound to receptor molecule. This work provides useful information about the inhibition mechanism of this class of molecules and will assist in the design of more potent inhibitors of PfDHODH.
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Affiliation(s)
- Priyanka Shah
- Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow, 226 001 India
| | - Sumit Kumar
- National Institute of Pharmaceutical Education and Research, Raebareli, UP India
| | - Sunita Tiwari
- Department of Physiology, C.S.M.M.U., Lucknow, UP India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow, 226 001 India
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Hortua Triana MA, Huynh MH, Garavito MF, Fox BA, Bzik DJ, Carruthers VB, Löffler M, Zimmermann BH. Biochemical and molecular characterization of the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase from Toxoplasma gondii. Mol Biochem Parasitol 2012; 184:71-81. [PMID: 22580100 DOI: 10.1016/j.molbiopara.2012.04.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/20/2012] [Accepted: 04/23/2012] [Indexed: 01/27/2023]
Abstract
The pyrimidine biosynthesis pathway in the protozoan pathogen Toxoplasma gondii is essential for parasite growth during infection. To investigate the properties of dihydroorotate dehydrogenase (TgDHOD), the fourth enzyme in the T. gondii pyrimidine pathway, we expressed and purified recombinant TgDHOD. TgDHOD exhibited a specific activity of 84U/mg, a k(cat) of 89s(-1), a K(m)=60μM for l-dihydroorotate, and a K(m)=29μM for decylubiquinone (Q(D)). Quinones lacking or having short isoprenoid side chains yielded lower k(cat)s than Q(D). As expected, fumarate was a poor electron acceptor for this family 2 DHOD. The IC(50)s determined for A77-1726, the active derivative of the human DHOD inhibitor leflunomide, and related compounds MD249 and MD209 were, 91μM, 96μM, and 60μM, respectively. The enzyme was not significantly affected by brequinar or TTFA, known inhibitors of human DHOD, or by atovaquone. DSM190, a known inhibitor of Plasmodium falciparum DHOD, was a poor inhibitor of TgDHOD. TgDHOD exhibits a lengthy 157-residue N-terminal extension, consistent with a potential organellar targeting signal. We constructed C-terminally c-myc tagged TgDHODs to examine subcellular localization of TgDHOD in transgenic parasites expressing the tagged protein. Using both exogenous and endogenous expression strategies, anti-myc fluorescence signal colocalized with antibodies against the mitochondrial marker ATPase. These findings demonstrate that TgDHOD is associated with the parasite's mitochondrion, revealing this organelle as the site of orotate production in T. gondii. The TgDHOD gene appears to be essential because while gene tagging was successful at the TgDHOD gene locus, attempts to delete the TgDHOD gene were not successful in the KU80 background. Collectively, our study suggests that TgDHOD is an excellent target for the development of anti-Toxoplasma drugs.
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Selective inhibitors of protozoan protein N-myristoyltransferases as starting points for tropical disease medicinal chemistry programs. PLoS Negl Trop Dis 2012; 6:e1625. [PMID: 22545171 PMCID: PMC3335879 DOI: 10.1371/journal.pntd.0001625] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/07/2012] [Indexed: 01/11/2023] Open
Abstract
Inhibition of N-myristoyltransferase has been validated pre-clinically as a target for the treatment of fungal and trypanosome infections, using species-specific inhibitors. In order to identify inhibitors of protozoan NMTs, we chose to screen a diverse subset of the Pfizer corporate collection against Plasmodium falciparum and Leishmania donovani NMTs. Primary screening hits against either enzyme were tested for selectivity over both human NMT isoforms (Hs1 and Hs2) and for broad-spectrum anti-protozoan activity against the NMT from Trypanosoma brucei. Analysis of the screening results has shown that structure-activity relationships (SAR) for Leishmania NMT are divergent from all other NMTs tested, a finding not predicted by sequence similarity calculations, resulting in the identification of four novel series of Leishmania-selective NMT inhibitors. We found a strong overlap between the SARs for Plasmodium NMT and both human NMTs, suggesting that achieving an appropriate selectivity profile will be more challenging. However, we did discover two novel series with selectivity for Plasmodium NMT over the other NMT orthologues in this study, and an additional two structurally distinct series with selectivity over Leishmania NMT. We believe that release of results from this study into the public domain will accelerate the discovery of NMT inhibitors to treat malaria and leishmaniasis. Our screening initiative is another example of how a tripartite partnership involving pharmaceutical industries, academic institutions and governmental/non-governmental organisations such as Medical Research Council and Wellcome Trust can stimulate research for neglected diseases. Inhibition of N-myristoyltransferase has been validated pre-clinically as a target for the treatment of fungal and trypanosome infections, using species-specific inhibitors. In order to identify inhibitors of protozoan NMTs, we chose to screen a diverse subset of the Pfizer corporate collection against Plasmodium falciparum and Leishmania donovani NMTs. Primary screening hits against either enzyme were tested for selectivity over both human NMT isoforms (HsNMT1 and HsNMT2) and for broad-spectrum anti-protozoan activity against the NMT from Trypanosoma brucei. We have identified eight series of protozoan NMT inhibitors, six having good selectivity for either Plasmodium or Leishmania NMTs over the other orthologues in this study. We believe that all of these series could form the basis of medicinal chemistry programs to deliver drug candidates against either malaria or leishmaniasis. Our screening initiative is another example of how a tripartite partnership involving pharmaceutical industries, academic institutions and governmental/non-governmental organisations such as the UK Medical Research Council and Wellcome Trust can stimulate research for neglected diseases.
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Identification and validation of tetracyclic benzothiazepines as Plasmodium falciparum cytochrome bc1 inhibitors. ACTA ACUST UNITED AC 2012; 18:1602-10. [PMID: 22195562 DOI: 10.1016/j.chembiol.2011.09.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/01/2011] [Accepted: 09/08/2011] [Indexed: 11/22/2022]
Abstract
Here we report the discovery of tetracyclic benzothiazepines (BTZs) as highly potent and selective antimalarials along with the identification of the Plasmodium falciparum cytochrome bc(1) complex as the primary functional target of this novel compound class. Investigation of the structure activity relationship within this previously unexplored chemical scaffold has yielded inhibitors with low nanomolar activity. A combined approach employing genetically modified parasites, biochemical profiling, and resistance selection validated inhibition of cytochrome bc(1) activity, an essential component of the parasite respiratory chain and target of the widely used antimalarial drug atovaquone, as the mode of action of this novel compound class. Resistance to atovaquone is eroding the efficacy of this widely used antimalarial drug. Intriguingly, BTZ-based inhibitors retain activity against atovaquone resistant parasites, suggesting this chemical class may provide an alternative to atovaquone in combination therapy.
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McNamara C, Winzeler EA. Target identification and validation of novel antimalarials. Future Microbiol 2011; 6:693-704. [PMID: 21707315 DOI: 10.2217/fmb.11.45] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It has been recognized that new antimalarials with a novel mode of action are critical to combat the continued emergence and dissemination of drug-resistant parasites that threaten the efficacy of current malaria treatments. Thus, recent high-throughput screening campaigns have been initiated using asexual intraerythrocytic stage cell-based assays of Plasmodium falciparum. These have led to the unprecedented identification of over 10,000 new antimalarial compounds. Inherently, novel compounds identified by cell-based assays will have poorly defined modes of action. While some of these compounds may have recognizable targets, the majority of cell-based hits are comprised of unique chemical scaffolds usually lacking cross-resistance with known drugs. It is likely that these novel antimalarial scaffolds will reveal new targets. A challenge for the community will be to assign these small molecules to their targets. In this article, we review methodologies to assist in the determination of a compound's mode of action.
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Affiliation(s)
- Case McNamara
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
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Skerlj RT, Bastos CM, Booker ML, Kramer ML, Barker RH, Celatka CA, O’Shea TJ, Munoz B, Sidhu AB, Cortese JF, Wittlin S, Papastogiannidis P, Angulo-Barturen I, Jimenez-Diaz MB, Sybertz E. Optimization of Potent Inhibitors of P. falciparum Dihydroorotate Dehydrogenase for the Treatment of Malaria. ACS Med Chem Lett 2011; 2:708-13. [PMID: 24900364 DOI: 10.1021/ml200143c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 07/10/2011] [Indexed: 11/28/2022] Open
Abstract
Inhibition of dihydroorotate dehydrogenase (DHODH) for P. falciparum potentially represents a new treatment option for malaria, since DHODH catalyzes the rate-limiting step in the pyrimidine biosynthetic pathway and P. falciparum is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. We report herein the synthesis and structure-activity relationship of a series of 5-(2-methylbenzimidazol-1-yl)-N-alkylthiophene-2-carboxamides that are potent inhibitors against PfDHODH but do not inhibit the human enzyme. On the basis of efficacy observed in three mouse models of malaria, acceptable safety pharmacology risk assessment and safety toxicology profile in rodents, lack of potential drug-drug interactions, acceptable ADME/pharmacokinetic profile, and projected human dose, 5-(4-cyano-2-methyl-1H-benzo[d]imidazol-1-yl)-N-cyclopropylthiophene-2-carboxamide 2q was identified as a potential drug development candidate.
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Affiliation(s)
- Renato T. Skerlj
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Cecilia M. Bastos
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Michael L. Booker
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Martin L. Kramer
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Robert H. Barker
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Cassandra A. Celatka
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Thomas J. O’Shea
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Benito Munoz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141, United States
| | - Amar Bir Sidhu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141, United States
| | - Joseph F. Cortese
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002, Basel, Switzerland
- University of Basel, Petersplatz 1, CH-4003, Basel, Switzerland
| | - Petros Papastogiannidis
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002, Basel, Switzerland
- University of Basel, Petersplatz 1, CH-4003, Basel, Switzerland
| | - Inigo Angulo-Barturen
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, c/Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Maria Belen Jimenez-Diaz
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, c/Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Edmund Sybertz
- Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, United States
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Boysen KE, Matuschewski K. Arrested oocyst maturation in Plasmodium parasites lacking type II NADH:ubiquinone dehydrogenase. J Biol Chem 2011; 286:32661-71. [PMID: 21771793 DOI: 10.1074/jbc.m111.269399] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Plasmodium mitochondrial electron transport chain has received considerable attention as a potential target for new antimalarial drugs. Atovaquone, a potent inhibitor of Plasmodium cytochrome bc(1), in combination with proguanil is recommended for chemoprophylaxis and treatment of malaria. The type II NADH:ubiquinone oxidoreductase (NDH2) is considered an attractive drug target, as its inhibition is thought to lead to the arrest of the mitochondrial electron transport chain and, as a consequence, pyrimidine biosynthesis, an essential pathway for the parasite. Using the rodent malaria parasite Plasmodium berghei as an in vivo infection model, we studied the role of NDH2 during Plasmodium life cycle progression. NDH2 can be deleted by targeted gene disruption and, thus, is dispensable for the pathogenic asexual blood stages, disproving the candidacy for an anti-malarial drug target. After transmission to the insect vector, NDH2-deficient ookinetes display an intact mitochondrial membrane potential. However, ndh2(-) parasites fail to develop into mature oocysts in the mosquito midgut. We propose that Plasmodium blood stage parasites rely on glycolysis as the main ATP generating process, whereas in the invertebrate vector, a glucose-deprived environment, the malaria parasite is dependent on an intact mitochondrial respiratory chain.
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Affiliation(s)
- Katja E Boysen
- Parasitology Unit, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
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Coteron JM, Marco M, Esquivias J, Deng X, White KL, White J, Koltun M, El Mazouni F, Kokkonda S, Katneni K, Bhamidipati R, Shackleford DM, Angulo-Barturen I, Ferrer SB, Jiménez-Díaz MB, Gamo FJ, Goldsmith EJ, Charman WN, Bathurst I, Floyd D, Matthews D, Burrows JN, Rathod PK, Charman SA, Phillips MA. Structure-guided lead optimization of triazolopyrimidine-ring substituents identifies potent Plasmodium falciparum dihydroorotate dehydrogenase inhibitors with clinical candidate potential. J Med Chem 2011; 54:5540-61. [PMID: 21696174 DOI: 10.1021/jm200592f] [Citation(s) in RCA: 221] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug therapy is the mainstay of antimalarial therapy, yet current drugs are threatened by the development of resistance. In an effort to identify new potential antimalarials, we have undertaken a lead optimization program around our previously identified triazolopyrimidine-based series of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. The X-ray structure of PfDHODH was used to inform the medicinal chemistry program allowing the identification of a potent and selective inhibitor (DSM265) that acts through DHODH inhibition to kill both sensitive and drug resistant strains of the parasite. This compound has similar potency to chloroquine in the humanized SCID mouse P. falciparum model, can be synthesized by a simple route, and rodent pharmacokinetic studies demonstrated it has excellent oral bioavailability, a long half-life and low clearance. These studies have identified the first candidate in the triazolopyrimidine series to meet previously established progression criteria for efficacy and ADME properties, justifying further development of this compound toward clinical candidate status.
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Affiliation(s)
- Jose M Coteron
- GlaxoSmithKline, Diseases of the Developing World (DDW)-Tres Cantos Medicines Development Campus, Madrid, Spain
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50
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Gujjar R, El Mazouni F, White KL, White J, Creason S, Shackleford DM, Deng X, Charman WN, Bathurst I, Burrows J, Floyd DM, Matthews D, Buckner FS, Charman SA, Phillips MA, Rathod PK. Lead optimization of aryl and aralkyl amine-based triazolopyrimidine inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with antimalarial activity in mice. J Med Chem 2011; 54:3935-49. [PMID: 21517059 DOI: 10.1021/jm200265b] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Malaria is one of the leading causes of severe infectious disease worldwide; yet, our ability to maintain effective therapy to combat the illness is continually challenged by the emergence of drug resistance. We previously reported identification of a new class of triazolopyrimidine-based Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors with antimalarial activity, leading to the discovery of a new lead series and novel target for drug development. Active compounds from the series contained a triazolopyrimidine ring attached to an aromatic group through a bridging nitrogen atom. Herein, we describe systematic efforts to optimize the aromatic functionality with the goal of improving potency and in vivo properties of compounds from the series. These studies led to the identification of two new substituted aniline moieties (4-SF(5)-Ph and 3,5-Di-F-4-CF(3)-Ph), which, when coupled to the triazolopyrimidine ring, showed good plasma exposure and better efficacy in the Plasmodium berghei mouse model of the disease than previously reported compounds from the series.
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Affiliation(s)
- Ramesh Gujjar
- Department of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
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