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de Vries LE, Jansen PAM, Barcelo C, Munro J, Verhoef JMJ, Pasaje CFA, Rubiano K, Striepen J, Abla N, Berning L, Bolscher JM, Demarta-Gatsi C, Henderson RWM, Huijs T, Koolen KMJ, Tumwebaze PK, Yeo T, Aguiar ACC, Angulo-Barturen I, Churchyard A, Baum J, Fernández BC, Fuchs A, Gamo FJ, Guido RVC, Jiménez-Diaz MB, Pereira DB, Rochford R, Roesch C, Sanz LM, Trevitt G, Witkowski B, Wittlin S, Cooper RA, Rosenthal PJ, Sauerwein RW, Schalkwijk J, Hermkens PHH, Bonnert RV, Campo B, Fidock DA, Llinás M, Niles JC, Kooij TWA, Dechering KJ. Preclinical characterization and target validation of the antimalarial pantothenamide MMV693183. Nat Commun 2022; 13:2158. [PMID: 35444200 PMCID: PMC9021288 DOI: 10.1038/s41467-022-29688-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/09/2022] [Indexed: 12/14/2022] Open
Abstract
Drug resistance and a dire lack of transmission-blocking antimalarials hamper malaria elimination. Here, we present the pantothenamide MMV693183 as a first-in-class acetyl-CoA synthetase (AcAS) inhibitor to enter preclinical development. Our studies demonstrate attractive drug-like properties and in vivo efficacy in a humanized mouse model of Plasmodium falciparum infection. The compound shows single digit nanomolar in vitro activity against P. falciparum and P. vivax clinical isolates, and potently blocks P. falciparum transmission to Anopheles mosquitoes. Genetic and biochemical studies identify AcAS as the target of the MMV693183-derived antimetabolite, CoA-MMV693183. Pharmacokinetic-pharmacodynamic modelling predict that a single 30 mg oral dose is sufficient to cure a malaria infection in humans. Toxicology studies in rats indicate a > 30-fold safety margin in relation to the predicted human efficacious exposure. In conclusion, MMV693183 represents a promising candidate for further (pre)clinical development with a novel mode of action for treatment of malaria and blocking transmission. Here, de Vries et al. perform a pre-clinical characterization of the antimalarial compound MMV693183: the compound targets acetyl-CoA synthetase, has efficacy in humanized mice against Plasmodium falciparum infection, blocks transmission to mosquito vectors, is safe in rats, and pharmacokinetic-pharmacodynamic modeling informs about a potential oral human dosing regimen.
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Affiliation(s)
- Laura E de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Patrick A M Jansen
- Department of Dermatology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Justin Munro
- Department of Chemistry and Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, USA
| | - Julie M J Verhoef
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Kelly Rubiano
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Josefine Striepen
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nada Abla
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Luuk Berning
- TropIQ Health Sciences, Nijmegen, The Netherlands
| | | | | | | | - Tonnie Huijs
- TropIQ Health Sciences, Nijmegen, The Netherlands
| | | | | | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna C C Aguiar
- Sao Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil, São Carlos, SP, Brazil
| | | | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | | | - Aline Fuchs
- Medicines for Malaria Venture, Geneva, Switzerland
| | | | - Rafael V C Guido
- Sao Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil, São Carlos, SP, Brazil
| | | | - Dhelio B Pereira
- Research Center for Tropical Medicine of Rondonia, Porto Velho, Brazil
| | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado Anschutz School of Medicine, Aurora, CO, USA
| | - Camille Roesch
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,Malaria Translational Research Unit, Institut Pasteur, Paris & Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Laura M Sanz
- Global Health, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,Malaria Translational Research Unit, Institut Pasteur, Paris & Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA
| | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,TropIQ Health Sciences, Nijmegen, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Brice Campo
- Medicines for Malaria Venture, Geneva, Switzerland
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA.,Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Manuel Llinás
- Department of Chemistry and Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, USA.,Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Taco W A Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Abstract
The Apicomplexa phylum comprises thousands of distinct intracellular parasite species, including coccidians, haemosporidians, piroplasms, and cryptosporidia. These parasites are characterized by complex and divergent life cycles occupying a variety of host niches. Consequently, they exhibit distinct adaptations to the differences in nutritional availabilities, either relying on biosynthetic pathways or by salvaging metabolites from their host. Pantothenate (Pan, vitamin B5) is the precursor for the synthesis of an essential cofactor, coenzyme A (CoA), but among the apicomplexans, only the coccidian subgroup has the ability to synthesize Pan. While the pathway to synthesize CoA from Pan is largely conserved across all branches of life, there are differences in the redundancy of enzymes and possible alternative pathways to generate CoA from Pan. Impeding the scavenge of Pan and synthesis of Pan and CoA have been long recognized as potential targets for antimicrobial drug development, but in order to fully exploit these critical pathways, it is important to understand such differences. Recently, a potent class of pantothenamides (PanAms), Pan analogs, which target CoA-utilizing enzymes, has entered antimalarial preclinical development. The potential of PanAms to target multiple downstream pathways make them a promising compound class as broad antiparasitic drugs against other apicomplexans. In this review, we summarize the recent advances in understanding the Pan and CoA biosynthesis pathways, and the suitability of these pathways as drug targets in Apicomplexa, with a particular focus on the cyst-forming coccidian, Toxoplasma gondii, and the haemosporidian, Plasmodium falciparum.
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Affiliation(s)
- Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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3
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van Esveld SL, Meerstein‐Kessel L, Boshoven C, Baaij JF, Barylyuk K, Coolen JPM, van Strien J, Duim RAJ, Dutilh BE, Garza DR, Letterie M, Proellochs NI, de Ridder MN, Venkatasubramanian PB, de Vries LE, Waller RF, Kooij TWA, Huynen MA. A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. mSphere 2021; 6:e0061421. [PMID: 34494883 PMCID: PMC8550323 DOI: 10.1128/msphere.00614-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by antimalarial drugs. Most mitochondrial proteins are imported into this organelle, and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, coevolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight data sets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 445 proteins with a sensitivity of 87% and a specificity of 97%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and colocalization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria. IMPORTANCE The unique biology and medical relevance of the mitochondrion of the malaria parasite Plasmodium falciparum have made it the subject of many studies. However, we actually do not have a comprehensive assessment of which proteins reside in this organelle. Many omics data are available that are predictive of mitochondrial localization, such as proteomics data and expression data. Individual data sets are, however, rarely complete and can provide conflicting evidence. We integrated a wide variety of available omics data in a manner that exploits the relative strengths of the data sets. Our analysis gave a predictive score for the mitochondrial localization to each nuclear encoded P. falciparum protein and identified 445 likely mitochondrial proteins. We experimentally validated the mitochondrial localization of seven of the new mitochondrial proteins, confirming the quality of the complete list. These include proteins that have not been observed mitochondria before, adding unique mitochondrial functions to P. falciparum.
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Affiliation(s)
- Selma L. van Esveld
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Lisette Meerstein‐Kessel
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Cas Boshoven
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Jochem F. Baaij
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Konstantin Barylyuk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ronald A. J. Duim
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Daniel R. Garza
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marijn Letterie
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Nicholas I. Proellochs
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Michelle N. de Ridder
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | | | - Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
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4
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Schalkwijk J, Allman EL, Jansen PAM, de Vries LE, Verhoef JMJ, Jackowski S, Botman PNM, Beuckens-Schortinghuis CA, Koolen KMJ, Bolscher JM, Vos MW, Miller K, Reeves SA, Pett H, Trevitt G, Wittlin S, Scheurer C, Sax S, Fischli C, Angulo-Barturen I, Jiménez-Diaz MB, Josling G, Kooij TWA, Bonnert R, Campo B, Blaauw RH, Rutjes FPJT, Sauerwein RW, Llinás M, Hermkens PHH, Dechering KJ. Antimalarial pantothenamide metabolites target acetyl-coenzyme A biosynthesis in Plasmodium falciparum. Sci Transl Med 2020; 11:11/510/eaas9917. [PMID: 31534021 DOI: 10.1126/scitranslmed.aas9917] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 09/07/2018] [Accepted: 03/28/2019] [Indexed: 01/09/2023]
Abstract
Malaria eradication is critically dependent on new therapeutics that target resistant Plasmodium parasites and block transmission of the disease. Here, we report that pantothenamide bioisosteres were active against blood-stage Plasmodium falciparum parasites and also blocked transmission of sexual stages to the mosquito vector. These compounds were resistant to degradation by serum pantetheinases, showed favorable pharmacokinetic properties, and cleared parasites in a humanized mouse model of P. falciparum infection. Metabolomics revealed that coenzyme A biosynthetic enzymes converted pantothenamides into coenzyme A analogs that interfered with parasite acetyl-coenzyme A anabolism. Resistant parasites generated in vitro showed mutations in acetyl-coenzyme A synthetase and acyl-coenzyme A synthetase 11. Introduction and reversion of these mutations in P. falciparum using CRISPR-Cas9 gene editing confirmed the roles of these enzymes in the sensitivity of the malaria parasites to pantothenamides. These pantothenamide compounds with a new mode of action may have potential as drugs against malaria parasites.
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Affiliation(s)
- Joost Schalkwijk
- Department of Dermatology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.
| | - Erik L Allman
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802 USA
| | - Patrick A M Jansen
- Department of Dermatology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Laura E de Vries
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Julie M J Verhoef
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | | | | | | | | | - Karen Miller
- St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stacy A Reeves
- St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Helmi Pett
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christian Scheurer
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sibylle Sax
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christoph Fischli
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | | | - Gabrielle Josling
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802 USA
| | - Taco W A Kooij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Brice Campo
- Medicines for Malaria Venture, Geneva, Switzerland
| | | | | | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,TropIQ Health Sciences, Nijmegen, Netherlands
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802 USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
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5
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Sanchez MI, de Vries LE, Lehmann C, Lee JT, Ang KK, Wilson C, Chen S, Arkin MR, Bogyo M, Deu E. Identification of Plasmodium dipeptidyl aminopeptidase allosteric inhibitors by high throughput screening. PLoS One 2019; 14:e0226270. [PMID: 31851699 PMCID: PMC6919601 DOI: 10.1371/journal.pone.0226270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/22/2019] [Indexed: 12/04/2022] Open
Abstract
Dipeptidyl aminopeptidases (DPAPs) are cysteine proteases that cleave dipeptides from the N-terminus of protein substrates and have been shown to play important roles in many pathologies including parasitic diseases such as malaria, toxoplasmosis and Chagas’s disease. Inhibitors of the mammalian homologue cathepsin C have been used in clinical trials as potential drugs to treat chronic inflammatory disorders, thus proving that these enzymes are druggable. In Plasmodium species, DPAPs play important functions at different stages of parasite development, thus making them potential antimalarial targets. Most DPAP inhibitors developed to date are peptide-based or peptidomimetic competitive inhibitors. Here, we used a high throughput screening approach to identify novel inhibitor scaffolds that block the activity of Plasmodium falciparum DPAP1. Most of the hits identified in this screen also inhibit Plasmodium falciparum DPAP3, cathepsin C, and to a lesser extent other malarial clan CA proteases, indicating that these might be general DPAP inhibitors. Interestingly, our mechanism of inhibition studies indicate that most hits are allosteric inhibitors, which opens a completely new strategy to inhibit these enzymes, study their biological function, and potentially develop new inhibitors as starting points for drug development.
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Affiliation(s)
- Mateo I. Sanchez
- Departments of Pathology and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, United States of America
| | - Laura E. de Vries
- Chemical Biology Approaches to Malaria Lab, The Francis Crick Institute, London, United Kingdom
| | - Christine Lehmann
- Chemical Biology Approaches to Malaria Lab, The Francis Crick Institute, London, United Kingdom
| | - Jeong T. Lee
- Departments of Pathology and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, United States of America
| | - Kenny K. Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Christopher Wilson
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Steven Chen
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Matthew Bogyo
- Departments of Pathology and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, United States of America
| | - Edgar Deu
- Chemical Biology Approaches to Malaria Lab, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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6
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de Vries LE, Sanchez MI, Groborz K, Kuppens L, Poreba M, Lehmann C, Nevins N, Withers-Martinez C, Hirst DJ, Yuan F, Arastu-Kapur S, Horn M, Mares M, Bogyo M, Drag M, Deu E. Characterization of P. falciparum dipeptidyl aminopeptidase 3 specificity identifies differences in amino acid preferences between peptide-based substrates and covalent inhibitors. FEBS J 2019; 286:3998-4023. [PMID: 31177613 PMCID: PMC6851853 DOI: 10.1111/febs.14953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
Abstract
Malarial dipeptidyl aminopeptidases (DPAPs) are cysteine proteases important for parasite development thus making them attractive drug targets. In order to develop inhibitors specific to the parasite enzymes, it is necessary to map the determinants of substrate specificity of the parasite enzymes and its mammalian homologue cathepsin C (CatC). Here, we screened peptide-based libraries of substrates and covalent inhibitors to characterize the differences in specificity between parasite DPAPs and CatC, and used this information to develop highly selective DPAP1 and DPAP3 inhibitors. Interestingly, while the primary amino acid specificity of a protease is often used to develop potent inhibitors, we show that equally potent and highly specific inhibitors can be developed based on the sequences of nonoptimal peptide substrates. Finally, our homology modelling and docking studies provide potential structural explanations of the differences in specificity between DPAP1, DPAP3, and CatC, and between substrates and inhibitors in the case of DPAP3. Overall, this study illustrates that focusing the development of protease inhibitors solely on substrate specificity might overlook important structural features that can be exploited to develop highly potent and selective compounds.
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Affiliation(s)
- Laura E de Vries
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mateo I Sanchez
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Katarzyna Groborz
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Laurie Kuppens
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
| | - Marcin Poreba
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Christine Lehmann
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
| | - Neysa Nevins
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | | | - David J Hirst
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Stevenage, UK
| | - Fang Yuan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirin Arastu-Kapur
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Michael Mares
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcin Drag
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Edgar Deu
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
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7
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Lehmann C, Tan MSY, de Vries LE, Russo I, Sanchez MI, Goldberg DE, Deu E. Plasmodium falciparum dipeptidyl aminopeptidase 3 activity is important for efficient erythrocyte invasion by the malaria parasite. PLoS Pathog 2018; 14:e1007031. [PMID: 29768491 PMCID: PMC5973627 DOI: 10.1371/journal.ppat.1007031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/29/2018] [Accepted: 04/15/2018] [Indexed: 11/19/2022] Open
Abstract
Parasite egress from infected erythrocytes and invasion of new red blood cells are essential processes for the exponential asexual replication of the malaria parasite. These two tightly coordinated events take place in less than a minute and are in part regulated and mediated by proteases. Dipeptidyl aminopeptidases (DPAPs) are papain-fold cysteine proteases that cleave dipeptides from the N-terminus of protein substrates. DPAP3 was previously suggested to play an essential role in parasite egress. However, little is known about its enzymatic activity, intracellular localization, or biological function. In this study, we recombinantly expressed DPAP3 and demonstrate that it has indeed dipeptidyl aminopeptidase activity, but contrary to previously studied DPAPs, removal of its internal prodomain is not required for activation. By combining super resolution microscopy, time-lapse fluorescence microscopy, and immunoelectron microscopy, we show that Plasmodium falciparum DPAP3 localizes to apical organelles that are closely associated with the neck of the rhoptries, and from which DPAP3 is secreted immediately before parasite egress. Using a conditional knockout approach coupled to complementation studies with wild type or mutant DPAP3, we show that DPAP3 activity is important for parasite proliferation and critical for efficient red blood cell invasion. We also demonstrate that DPAP3 does not play a role in parasite egress, and that the block in egress phenotype previously reported for DPAP3 inhibitors is due to off target or toxicity effects. Finally, using a flow cytometry assay to differentiate intracellular parasites from extracellular parasites attached to the erythrocyte surface, we show that DPAP3 is involved in the initial attachment of parasites to the red blood cell surface. Overall, this study establishes the presence of a DPAP3-dependent invasion pathway in malaria parasites.
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Affiliation(s)
- Christine Lehmann
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michele Ser Ying Tan
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Laura E. de Vries
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ilaria Russo
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Mateo I. Sanchez
- Department of Genetics, Stanford School of Medicine, Stanford, California, United States of America
| | - Daniel E. Goldberg
- Departments of Molecular Microbiology and Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Edgar Deu
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, United Kingdom
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Di Blasio S, Wortel IMN, van Bladel DAG, de Vries LE, Duiveman-de Boer T, Worah K, de Haas N, Buschow SI, de Vries IJM, Figdor CG, Hato SV. Human CD1c(+) DCs are critical cellular mediators of immune responses induced by immunogenic cell death. Oncoimmunology 2016; 5:e1192739. [PMID: 27622063 PMCID: PMC5007971 DOI: 10.1080/2162402x.2016.1192739] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/29/2016] [Accepted: 05/18/2016] [Indexed: 12/22/2022] Open
Abstract
Chemotherapeutics, including the platinum compounds oxaliplatin (OXP) and cisplatin (CDDP), are standard care of treatment for cancer. Although chemotherapy has long been considered immunosuppressive, evidence now suggests that certain cytotoxic agents can efficiently stimulate antitumor responses, through the induction of a form of apoptosis, called immunogenic cell death (ICD). ICD is characterized by exposure of calreticulin and heat shock proteins (HSPs), secretion of ATP and release of high-mobility group box 1 (HMGB1). Proper activation of the immune system relies on the integration of these signals by dendritic cells (DCs). Studies on the crucial role of DCs, in the context of ICD, have been performed using mouse models or human in vitro-generated monocyte-derived DCs (moDCs), which do not fully recapitulate the in vivo situation. Here, we explore the effect of platinum-induced ICD on phenotype and function of human blood circulating DCs. Tumor cells were treated with OXP or CDDP and induction of ICD was investigated. We show that both platinum drugs triggered translocation of calreticulin and HSP70, as well as the release of ATP and HMGB1. Platinum treatment increased phagocytosis of tumor fragments by human blood DCs and enhanced phenotypic maturation of blood myeloid and plasmacytoid DCs. Moreover, upon interaction with platinum-treated tumor cells, CD1c+ DCs efficiently stimulated allogeneic proliferation of T lymphocytes. Together, our observations indicate that platinum-treated tumor cells may exert an active stimulatory effect on human blood DCs. In particular, these data suggest that CD1c+ DCs are critical mediators of immune responses induced by ICD.
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Affiliation(s)
- Stefania Di Blasio
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Inge M N Wortel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Diede A G van Bladel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Laura E de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Tjitske Duiveman-de Boer
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Kuntal Worah
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Nienke de Haas
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Sonja I Buschow
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - I Jolanda M de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Stanleyson V Hato
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
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