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Phan TN, Park KHP, Shum D, No JH. Identification of Leishmania donovani PEX5-PTS1 Interaction Inhibitors through Fluorescence Polarization-Based High-Throughput Screening. Molecules 2024; 29:1835. [PMID: 38675653 PMCID: PMC11054337 DOI: 10.3390/molecules29081835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Leishmaniasis, an infectious disease caused by pathogenic Leishmania parasites, affects millions of people in developing countries, and its re-emergence in developed countries, particularly in Europe, poses a growing public health concern. The limitations of current treatments and the absence of effective vaccines necessitate the development of novel therapeutics. In this study, we focused on identifying small molecule inhibitors which prevents the interaction between peroxin 5 (PEX5) and peroxisomal targeting signal 1 (PTS1), pivotal for kinetoplastid parasite survival. The Leishmania donovani PEX5, containing a C-terminal tetratricopeptide repeat (TPR) domain, was expressed and purified, followed by the quantification of kinetic parameters of PEX5-PTS1 interactions. A fluorescence polarization-based high-throughput screening assay was developed and small molecules inhibiting the LdPEX5-PTS1 interaction were discovered through the screening of a library of 51,406 compounds. Based on the confirmatory assay, nine compounds showed half maximal inhibitory concentration (IC50) values ranging from 3.89 to 24.50 µM. In silico docking using a homology model of LdPEX5 elucidated that the molecular interactions between LdPEX5 and the inhibitors share amino acids critical for PTS1 binding. Notably, compound P20 showed potent activity against the growth of L. donovani promastigotes, L. major promastigotes, and Trypanosoma brucei blood stream form, with IC50 values of 12.16, 19.21, and 3.06 μM, respectively. The findings underscore the potential of targeting LdPEX5-PTS1 interactions with small molecule inhibitors as a promising strategy for the discovery of new anti-parasitic compounds.
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Affiliation(s)
- Trong-Nhat Phan
- Institute of Applied Science and Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Vietnam;
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Vietnam
- Host-Parasite Research Laboratory, Discovery Biology, Institut Pasteur Korea, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Kyu-Ho Paul Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (K.-H.P.P.); (D.S.)
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (K.-H.P.P.); (D.S.)
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Discovery Biology, Institut Pasteur Korea, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
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Francisco T, Pedrosa AG, Rodrigues TA, Abalkhail T, Li H, Ferreira MJ, van der Heden van Noort GJ, Fransen M, Hettema EH, Azevedo JE. Noncanonical and reversible cysteine ubiquitination prevents the overubiquitination of PEX5 at the peroxisomal membrane. PLoS Biol 2024; 22:e3002567. [PMID: 38470934 PMCID: PMC10959387 DOI: 10.1371/journal.pbio.3002567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
PEX5, the peroxisomal protein shuttling receptor, binds newly synthesized proteins in the cytosol and transports them to the organelle. During its stay at the peroxisomal protein translocon, PEX5 is monoubiquitinated at its cysteine 11 residue, a mandatory modification for its subsequent ATP-dependent extraction back into the cytosol. The reason why a cysteine and not a lysine residue is the ubiquitin acceptor is unknown. Using an established rat liver-based cell-free in vitro system, we found that, in contrast to wild-type PEX5, a PEX5 protein possessing a lysine at position 11 is polyubiquitinated at the peroxisomal membrane, a modification that negatively interferes with the extraction process. Wild-type PEX5 cannot retain a polyubiquitin chain because ubiquitination at cysteine 11 is a reversible reaction, with the E2-mediated deubiquitination step presenting faster kinetics than PEX5 polyubiquitination. We propose that the reversible nonconventional ubiquitination of PEX5 ensures that neither the peroxisomal protein translocon becomes obstructed with polyubiquitinated PEX5 nor is PEX5 targeted for proteasomal degradation.
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Affiliation(s)
- Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Ana G. Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tony A. Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tarad Abalkhail
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Hongli Li
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Maria J. Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | | | - Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ewald H. Hettema
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Jorge E. Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
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Ravindran R, Bacellar IOL, Castellanos-Girouard X, Wahba HM, Zhang Z, Omichinski JG, Kisley L, Michnick SW. Peroxisome biogenesis initiated by protein phase separation. Nature 2023; 617:608-615. [PMID: 37165185 PMCID: PMC10302873 DOI: 10.1038/s41586-023-06044-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
Peroxisomes are organelles that carry out β-oxidation of fatty acids and amino acids. Both rare and prevalent diseases are caused by their dysfunction1. Among disease-causing variant genes are those required for protein transport into peroxisomes. The peroxisomal protein import machinery, which also shares similarities with chloroplasts2, is unique in transporting folded and large, up to 10 nm in diameter, protein complexes into peroxisomes3. Current models postulate a large pore formed by transmembrane proteins4; however, so far, no pore structure has been observed. In the budding yeast Saccharomyces cerevisiae, the minimum transport machinery includes the membrane proteins Pex13 and Pex14 and the cargo-protein-binding transport receptor, Pex5. Here we show that Pex13 undergoes liquid-liquid phase separation (LLPS) with Pex5-cargo. Intrinsically disordered regions in Pex13 and Pex5 resemble those found in nuclear pore complex proteins. Peroxisomal protein import depends on both the number and pattern of aromatic residues in these intrinsically disordered regions, consistent with their roles as 'stickers' in associative polymer models of LLPS5,6. Finally, imaging fluorescence cross-correlation spectroscopy shows that cargo import correlates with transient focusing of GFP-Pex13 and GFP-Pex14 on the peroxisome membrane. Pex13 and Pex14 form foci in distinct time frames, suggesting that they may form channels at different saturating concentrations of Pex5-cargo. Our findings lead us to suggest a model in which LLPS of Pex5-cargo with Pex13 and Pex14 results in transient protein transport channels7.
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Affiliation(s)
- Rini Ravindran
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
| | - Isabel O L Bacellar
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
- Douglas Research Centre, Montreal, Quebec, Canada
| | | | - Haytham M Wahba
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Zhenghao Zhang
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Mitchell Physics Building (MPHY), College Station, TX, USA
| | - James G Omichinski
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada.
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Hochreiter B, Chong CS, Hartig A, Maurer-Stroh S, Berger J, Schmid JA, Kunze M. A Novel FRET Approach Quantifies the Interaction Strength of Peroxisomal Targeting Signals and Their Receptor in Living Cells. Cells 2020; 9:cells9112381. [PMID: 33143123 PMCID: PMC7693011 DOI: 10.3390/cells9112381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 02/02/2023] Open
Abstract
Measuring Förster–resonance–energy–transfer (FRET) efficiency allows the investigation of protein–protein interactions (PPI), but extracting quantitative measures of affinity necessitates highly advanced technical equipment or isolated proteins. We demonstrate the validity of a recently suggested novel approach to quantitatively analyze FRET-based experiments in living mammalian cells using standard equipment using the interaction between different type-1 peroxisomal targeting signals (PTS1) and their soluble receptor peroxin 5 (PEX5) as a model system. Large data sets were obtained by flow cytometry coupled FRET measurements of cells expressing PTS1-tagged EGFP together with mCherry fused to the PTS1-binding domain of PEX5, and were subjected to a fitting algorithm extracting a quantitative measure of the interaction strength. This measure correlates with results obtained by in vitro techniques and a two-hybrid assay, but is unaffected by the distance between the fluorophores. Moreover, we introduce a live cell competition assay based on this approach, capable of depicting dose- and affinity-dependent modulation of the PPI. Using this system, we demonstrate the relevance of a sequence element next to the core tripeptide in PTS1 motifs for the interaction strength between PTS1 and PEX5, which is supported by a structure-based computational prediction of the binding energy indicating a direct involvement of this sequence in the interaction.
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Affiliation(s)
- Bernhard Hochreiter
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, 1090 Vienna, Austria;
| | - Cheng-Shoong Chong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (C.-S.C.); (S.M.-S.)
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Andreas Hartig
- Department of Biochemistry and Cell Biology, Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria;
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (C.-S.C.); (S.M.-S.)
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Johannes Berger
- Center for Brain Research, Department of Pathobiology of the Nervous System, Medical University of Vienna, 1090 Vienna, Austria;
| | - Johannes A. Schmid
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: (J.A.S.); (M.K.)
| | - Markus Kunze
- Center for Brain Research, Department of Pathobiology of the Nervous System, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: (J.A.S.); (M.K.)
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Lee J, Yamamoto S, Takano M, Jung D. Mimicking of a Transient Protein Binding in Mammalian Cells Using a Functionalized Magnetic Nanoparticle. J Nanosci Nanotechnol 2018; 18:6719-6725. [PMID: 29954486 DOI: 10.1166/jnn.2018.15459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Identification of binding proteins is essential for uncovering biological mechanisms of functional small molecules and proteins, but if the binding is transient it may be quite difficult to find the binding proteins using cell extracts that is commonly used for target identification methods. Usually sticky proteins bind to bait molecule first as long as cell extracts are used. In such cases, it would be very difficult to find transient binding proteins. The best way to circumvent the non-specific bindings might be putting bait molecules into living cells and collects the baits after a certain period of incubation time. In here, we evaluated a new target identification method in living cells with magnetic nanoparticles. For the proof-of-concept, we reproduced a transient interaction between peroxisomal proteins and Pex5p, the peroxisome guiding protein. To that end, carboxyl group-functionalized magnetic nanoparticles were labeled with peroxisomal targeting signal 1 (PTS1) peptide to mimic peroxisomal proteins. The PTS1-labeled magnetic nanoparticles translocated into peroxisomes in the mammalian cells, during which they transiently interacted with Pex5p. These results were confirmed using a fluorescence microscope and "in cell pull-down" experiments. Conclusively, the transient interaction between peroxisomal proteins and Pex5p in cells was reproduced with the PTS1-labeled magnetic nanoparticles in living cells by showing its sequential translocation into peroxisomes and transient interaction with Pex5p in parallel. This result indicates that a magnetic nanoparticle can be a useful tool for analyzing dynamic change of interacting proteins to a functional molecule in living cells depending on circumstances the cells encounter.
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