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Gopalswamy M, Zheng C, Gaussmann S, Kooshapur H, Hambruch E, Schliebs W, Erdmann R, Antes I, Sattler M. Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14. Biol Chem 2023; 404:179-194. [PMID: 36437542 DOI: 10.1515/hsz-2022-0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022]
Abstract
The cycling import receptor PEX5 and its membrane-located binding partner PEX14 are key constituents of the peroxisomal import machinery. Upon recognition of newly synthesized cargo proteins carrying a peroxisomal targeting signal type 1 (PTS1) in the cytosol, the PEX5/cargo complex docks at the peroxisomal membrane by binding to PEX14. The PEX14 N-terminal domain (NTD) recognizes (di)aromatic peptides, mostly corresponding to Wxxx(F/Y)-motifs, with nano-to micromolar affinity. Human PEX5 possesses eight of these conserved motifs distributed within its 320-residue disordered N-terminal region. Here, we combine biophysical (ITC, NMR, CD), biochemical and computational methods to characterize the recognition of these (di)aromatic peptides motifs and identify key features that are recognized by PEX14. Notably, the eight motifs present in human PEX5 exhibit distinct affinities and energetic contributions for the interaction with the PEX14 NTD. Computational docking and analysis of the interactions of the (di)aromatic motifs identify the specific amino acids features that stabilize a helical conformation of the peptide ligands and mediate interactions with PEX14 NTD. We propose a refined consensus motif ExWΦxE(F/Y)Φ for high affinity binding to the PEX14 NTD and discuss conservation of the (di)aromatic peptide recognition by PEX14 in other species.
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Affiliation(s)
- Mohanraj Gopalswamy
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Chen Zheng
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Stefan Gaussmann
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Hamed Kooshapur
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Eva Hambruch
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Iris Antes
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Michael Sattler
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
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2
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Structure-based design, synthesis and evaluation of a novel family of PEX5-PEX14 interaction inhibitors against Trypanosoma. Eur J Med Chem 2022; 243:114778. [DOI: 10.1016/j.ejmech.2022.114778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
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3
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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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4
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Buchko GW, Abendroth J, Robinson JI, Phan IQ, Myler PJ, Edwards TE. Structural diversity in the Mycobacteria DUF3349 superfamily. Protein Sci 2019; 29:670-685. [PMID: 31658388 DOI: 10.1002/pro.3758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/11/2022]
Abstract
A protein superfamily with a "Domain of Unknown Function,", DUF3349 (PF11829), is present predominately in Mycobacterium and Rhodococcus bacterial species suggesting that these proteins may have a biological function unique to these bacteria. We previously reported the inaugural structure of a DUF3349 superfamily member, Mycobacterium tuberculosis Rv0543c. Here, we report the structures determined for three additional DUF3349 proteins: Mycobacterium smegmatis MSMEG_1063 and MSMEG_1066 and Mycobacterium abscessus MAB_3403c. Like Rv0543c, the NMR solution structure of MSMEG_1063 revealed a monomeric five α-helix bundle with a similar overall topology. Conversely, the crystal structure of MSMEG_1066 revealed a five α-helix protein with a strikingly different topology and a tetrameric quaternary structure that was confirmed by size exclusion chromatography. The NMR solution structure of a fourth member of the DUF3349 superfamily, MAB_3403c, with 18 residues missing at the N-terminus, revealed a monomeric α-helical protein with a folding topology similar to the three C-terminal helices in the protomer of the MSMEG_1066 tetramer. These structures, together with a GREMLIN-based bioinformatics analysis of the DUF3349 primary amino acid sequences, suggest two subfamilies within the DUF3349 family. The division of the DUF3349 into two distinct subfamilies would have been lost if structure solution had stopped with the first structure in the DUF3349 family, highlighting the insights generated by solving multiple structures within a protein superfamily. Future studies will determine if the structural diversity at the tertiary and quaternary levels in the DUF3349 protein superfamily have functional roles in Mycobacteria and Rhodococcus species with potential implications for structure-based drug discovery.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.,School of Molecular Biosciences, Washington State University, Pullman, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
| | - John I Robinson
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington.,Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
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5
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Kalel VC, Mäser P, Sattler M, Erdmann R, Popowicz GM. Come, sweet death: targeting glycosomal protein import for antitrypanosomal drug development. Curr Opin Microbiol 2018; 46:116-122. [PMID: 30481613 DOI: 10.1016/j.mib.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/09/2018] [Indexed: 01/18/2023]
Abstract
Glycosomes evolved as specialized system for glycolysis in trypanosomatids. These organelle rely on protein import to maintain function. A machinery of peroxin (PEX) proteins is responsible for recognition and transport of glycosomal proteins to the organelle. Disruption of PEX-based import system was expected to be a strategy against trypanosomatids. Recently, a proof of this hypothesis has been presented. Here, we review current information about trypanosomatids' glycosomal transport components as targets for new trypanocidal therapies.
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Affiliation(s)
- Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.
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6
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Watanabe Y, Kawaguchi K, Saito S, Okabe T, Yonesu K, Egashira S, Kameya M, Morita M, Kashiwayama Y, Imanaka T. An HTRF based high-throughput screening for discovering chemical compounds that inhibit the interaction between Trypanosoma brucei Pex5p and Pex14p. Biochem Biophys Rep 2016; 6:260-265. [PMID: 28955883 PMCID: PMC5600434 DOI: 10.1016/j.bbrep.2016.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
The glycosome, a peroxisome-related organelle, is essential for the growth and survival of trypanosomatid protozoa. In glycosome biogenesis, Pex5p recognizes newly synthesized glycosomal matrix proteins via peroxisome-targeting signal type-1 (PTS-1) and transports them into glycosomes through an interaction with Pex14p, a component of the matrix protein import machinery on the glycosomal membrane. Knockdown of the PEX5 or PEX14 with RNAi has been shown to inhibit the growth of Trypanosoma brucei. Thus, compounds that inhibit the interaction of TbPex5p–TbPex14p are expected to become lead compounds in the development of anti-trypanosomal drugs. Here, we report a homogenous time-resolved fluorescence (HTRF) assay for the screening of compounds that inhibit the TbPex5p–TbPex14p interaction. The binding of GST-TbPex14p and TbPex5p-His with or without additional compounds was evaluated by measuring the energy transfer of the HTRF pair, using a terbium-labeled anti GST antibody as the donor and an FITC-labeled anti His antibody as the acceptor. The assay was performed in a 384-well plate platform and exhibits a Z’-factor of 0.85–0.91, while the coefficiency of variation is 1.1–7.7%, suggesting it can be readily adapted to a high-throughput format for the automated screening of chemical libraries. We screened 20,800 compounds and found 11 compounds that inhibited energy transfer. Among them, in a pull-down assay one compound exhibited selective inhibition of TbPex5p–TbPex14p without any HsPex5p–HsPex14p interaction. An HTRF-based TbPex5p–TbPex14p interaction assay system was established. A compound was found that selectively inhibits the TbPex5p–TbPex14p interaction. This system is applicable for drug discovery against other glycosomal proteins.
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Affiliation(s)
- Yuichi Watanabe
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kosuke Kawaguchi
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Syuken Saito
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kiyoaki Yonesu
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinichiro Egashira
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masafumi Kameya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Masashi Morita
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshinori Kashiwayama
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Tsuneo Imanaka
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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