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Dawidowski M, Kalel VC, Napolitano V, Fino R, Schorpp K, Emmanouilidis L, Lenhart D, Ostertag M, Kaiser M, Kolonko M, Tippler B, Schliebs W, Dubin G, Mäser P, Tetko IV, Hadian K, Plettenburg O, Erdmann R, Sattler M, Popowicz GM. Structure-Activity Relationship in Pyrazolo[4,3- c]pyridines, First Inhibitors of PEX14-PEX5 Protein-Protein Interaction with Trypanocidal Activity. J Med Chem 2020; 63:847-879. [PMID: 31860309 DOI: 10.1021/acs.jmedchem.9b01876] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trypanosoma protists are pathogens leading to a spectrum of devastating infectious diseases. The range of available chemotherapeutics against Trypanosoma is limited, and the existing therapies are partially ineffective and cause serious adverse effects. Formation of the PEX14-PEX5 complex is essential for protein import into the parasites' glycosomes. This transport is critical for parasite metabolism and failure leads to mislocalization of glycosomal enzymes, with fatal consequences for the parasite. Hence, inhibiting the PEX14-PEX5 protein-protein interaction (PPI) is an attractive way to affect multiple metabolic pathways. Herein, we have used structure-guided computational screening and optimization to develop the first line of compounds that inhibit PEX14-PEX5 PPI. The optimization was driven by several X-ray structures, NMR binding data, and molecular dynamics simulations. Importantly, the developed compounds show significant cellular activity against Trypanosoma, including the human pathogen Trypanosoma brucei gambiense and Trypanosoma cruzi parasites.
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Affiliation(s)
- Maciej Dawidowski
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany.,Department of Drug Technology and Pharmaceutical Biotechnology , Medical University of Warsaw , Banacha 1 , 02-097 Warszawa , Poland
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Valeria Napolitano
- Faculty of Biochemistry, Biophysics and Biotechnology , Jagiellonian University , Gronostajowa 7 , Krakow 30-387 , Poland.,Małopolska Center of Biotechnology , Jagiellonian University in Kraków , Gronostajowa 7 , Kraków 30-387 , Poland
| | - Roberto Fino
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | | | - Leonidas Emmanouilidis
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Dominik Lenhart
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Michael Ostertag
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , 4001 Basel , Switzerland
| | - Marta Kolonko
- Department of Biochemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Bettina Tippler
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Grzegorz Dubin
- Małopolska Center of Biotechnology , Jagiellonian University in Kraków , Gronostajowa 7 , Kraków 30-387 , Poland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , 4001 Basel , Switzerland
| | | | | | - Oliver Plettenburg
- Institute of Organic Chemistry , Leibniz Universität Hannover , Schneiderberg 1b , Hannover 30167 , Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Grzegorz M Popowicz
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
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Sanchez LM, Knudsen GM, Hartmann C, De Muylder G, Mascuch SM, Mackey ZB, Gerwick L, Clayton C, McKerrow JH, Linington RG. Examination of the mode of action of the almiramide family of natural products against the kinetoplastid parasite Trypanosoma brucei. JOURNAL OF NATURAL PRODUCTS 2013; 76:630-41. [PMID: 23445522 PMCID: PMC3971013 DOI: 10.1021/np300834q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Almiramide C is a marine natural product with low micromolar activity against Leishmania donovani, the causative agent of leishmaniasis. We have now shown that almiramide C is also active against the related parasite Trypanosoma brucei, the causative agent of human African trypanosomiasis. A series of activity-based probes have been synthesized to explore both the molecular target of this compound series in T. brucei lysates and site localization through epifluorescence microscopy. These target identification studies indicate that the almiramides likely perturb glycosomal function through disruption of membrane assembly machinery. Glycosomes, which are organelles specific to kinetoplastid parasites, house the first seven steps of glycolysis and have been shown to be essential for parasite survival in the bloodstream stage. There are currently no reported small-molecule disruptors of glycosome function, making the almiramides unique molecular probes for this understudied parasite-specific organelle. Additionally, examination of toxicity in an in vivo zebrafish model has shown that these compounds have little effect on organism development, even at high concentrations, and has uncovered a potential side effect through localization of fluorescent derivatives to zebrafish neuromast cells. Combined, these results further our understanding of the potential value of this lead series as development candidates against T. brucei.
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Affiliation(s)
- Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Giselle M. Knudsen
- Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, CA 94143
| | - Claudia Hartmann
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Heidelberg, Germany D-69120
| | - Geraldine De Muylder
- Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, CA 94143
| | - Samantha M. Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, University of California San Diego, San Diego, CA 92093
| | - Zachary B. Mackey
- Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, CA 94143
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, University of California San Diego, San Diego, CA 92093
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Heidelberg, Germany D-69120
| | - James H. McKerrow
- Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, CA 94143
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
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Identification, characterization and essentiality of the unusual peroxin 13 from Trypanosoma brucei. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:516-27. [PMID: 19185591 DOI: 10.1016/j.bbamcr.2008.12.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 12/08/2008] [Accepted: 12/18/2008] [Indexed: 11/20/2022]
Abstract
Peroxin 13 (PEX13) is one of the components of a peroxisomal membrane complex involved in import of proteins into the matrix of the organelles and has previously been characterized in a variety of organisms. Trypanosomatids (Trypanosoma, Leishmania), protozoan parasites having peroxisome-like organelles designated glycosomes, possess an unusual PEX13 which shares very low sequence identity with others and lacks some typical PEX13 characteristics. It was identified in the databases through its multiple YGx motifs present in a glycine-rich N-terminal region of low sequence complexity. Like other PEX13s, it contains predicted transmembrane segments and a SH3 domain in its C-terminal half. The localization of T. brucei PEX13 in the glycosomal membrane was confirmed by expression of a fusion construct with Green Fluorescent Protein, and western blot analysis of purified organelles and membranes. The C-terminal half of the protein was shown to interact with the third of three pentapeptide repeats of the previously characterized PEX5, the receptor of glycosomal proteins with a type 1 peroxisome-targeting signal, and with PEX14, another component of the same peroxisomal protein import complex in the membrane. PEX13 is essential for the parasite; depletion by RNA interference results in mislocalization of glycosomal proteins and death of the parasites.
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Structural insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5. J Mol Biol 2008; 381:867-80. [PMID: 18598704 DOI: 10.1016/j.jmb.2008.05.089] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2008] [Revised: 05/29/2008] [Accepted: 05/31/2008] [Indexed: 11/24/2022]
Abstract
Glycosomes are peroxisome-like organelles essential for trypanosomatid parasites. Glycosome biogenesis is mediated by proteins called "peroxins," which are considered to be promising drug targets in pathogenic Trypanosomatidae. The first step during protein translocation across the glycosomal membrane of peroxisomal targeting signal 1 (PTS1)-harboring proteins is signal recognition by the cytosolic receptor peroxin 5 (PEX5). The C-terminal PTS1 motifs interact with the PTS1 binding domain (P1BD) of PEX5, which is made up of seven tetratricopeptide repeats. Obtaining diffraction-quality crystals of the P1BD of Trypanosoma brucei PEX5 (TbPEX5) required surface entropy reduction mutagenesis. Each of the seven tetratricopeptide repeats appears to have a residue in the alpha(L) conformation in the loop connecting helices A and B. Five crystal structures of the P1BD of TbPEX5 were determined, each in complex with a hepta- or decapeptide corresponding to a natural or nonnatural PTS1 sequence. The PTS1 peptides are bound between the two subdomains of the P1BD. These structures indicate precise recognition of the C-terminal Leu of the PTS1 motif and important interactions between the PTS1 peptide main chain and up to five invariant Asn side chains of PEX5. The TbPEX5 structures reported here reveal a unique hydrophobic pocket in the subdomain interface that might be explored to obtain compounds that prevent relative motions of the subdomains and interfere selectively with PTS1 motif binding or release in trypanosomatids, and would therefore disrupt glycosome biogenesis and prevent parasite growth.
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Galland N, Demeure F, Hannaert V, Verplaetse E, Vertommen D, Van der Smissen P, Courtoy PJ, Michels PAM. Characterization of the role of the receptors PEX5 and PEX7 in the import of proteins into glycosomes of Trypanosoma brucei. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:521-35. [PMID: 17320990 DOI: 10.1016/j.bbamcr.2007.01.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 12/20/2006] [Accepted: 01/11/2007] [Indexed: 10/23/2022]
Abstract
Peroxins 5 and 7 are receptors for protein import into the peroxisomal matrix. We studied the involvement of these peroxins in the biogenesis of glycosomes in the protozoan parasite Trypanosoma brucei. Glycosomes are peroxisome-like organelles in which a major part of the glycolytic pathway is sequestered. We here report the characterization of the T. brucei homologue of PEX7 and provide several data strongly suggesting that it can bind to PEX5. Depletion of PEX5 or PEX7 by RNA interference had a severe effect on the growth of both the bloodstream-form of the parasite, that relies entirely on glycolysis for its ATP supply, and the procyclic form representative of the parasite living in the tsetse-fly midgut and in which also other metabolic pathways play a prominent role. The role of the two receptors in import of glycosomal matrix proteins with different types of peroxisome/glycosome-targeting signals (PTS) was analyzed by immunofluorescence and subcellular fractionation studies. Knocking down the expression of either receptor gene resulted, in procyclic cells, in the mislocalization of proteins with both a type 1 or 2 targeting motif (PTS1, PTS2) located at the C- and N-termini, respectively, and proteins with a sequence-internal signal (I-PTS) to the cytosol. Electron microscopy confirmed the apparent integrity of glycosomes in these procyclic cells. In bloodstream-form trypanosomes, PEX7 depletion seemed to affect only the subcellular distribution of PTS2-proteins. Western blot analysis suggested that, in both life-cycle stages of the trypanosome, the levels of both receptors are controlled in a coordinated fashion, by a mechanism that remains to be determined. The observation that both PEX5 and PEX7 are essential for the viability of the parasite indicates that the respective branches of the glycosome-import pathway in which each receptor acts might be interesting drug targets.
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Affiliation(s)
- Nathalie Galland
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université catholique de Louvain, Brussels, Belgium
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