1
|
Karamifard F, Mazaheri M, Dadbinpour A. Abatement of the binding of human hexokinase II enzyme monomers by in-silico method with the design of inhibitory peptides. In Silico Pharmacol 2024; 12:30. [PMID: 38617709 PMCID: PMC11009198 DOI: 10.1007/s40203-024-00201-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/05/2024] [Indexed: 04/16/2024] Open
Abstract
The hexokinase II enzyme is bound to the (VDAC1) channel in the form of a dimer and prevents the release of cell death factors from mitochondria to the cytoplasm. Studies have shown that blocking the binding of hexokinase II enzyme to (VDAC1) led to the initiation of apoptosis in cancer cells. No peptide has been designed so far to inhibit hexokinase II. The aim of this study was to inhibit the dimerization of enzyme subunits in order to inhibition the formation of (VDAC1) and the hexokinase II complex. In this study, the molecular dynamics simulation of the enzyme in monomer and dimer states was investigated in terms of RMSF, RMSD and radius of gyration. The following process involves extracting and designing variable-length peptides from the interacting segments of enzyme monomers. Using molecular dynamics simulation, the stability of the peptide was determined in terms of RMSD. Molecular docking was used to investigate the interaction between the designed peptides. Finally, the inhibitory effect of peptides on subunit association was measured using dynamic light scattering (DLS) technique. Our results showed that the designed peptides, which mimic common amino acids in dimerization, interrupt the bona fide form of the enzyme subunits. The result of this study provides a new way to disrupt the assembly process and thereby decreased the function of the hexokinase II. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00201-8.
Collapse
Affiliation(s)
- Faranak Karamifard
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences of Yazd, Yazd, Iran
| | - Mahta Mazaheri
- Department of Medical Genetics, Faculty of Medicine, Mother and Newborn, Health Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Dadbinpour
- Genetic and Environmental Adventures, Department of Genetics, Medical School, School of Abarkouh Paramedicin, Faculty of Medicine, Shahid Sadoughi University of Medical Science, Yazd, Iran
| |
Collapse
|
2
|
Cannino G, Urbani A, Gaspari M, Varano M, Negro A, Filippi A, Ciscato F, Masgras I, Gerle C, Tibaldi E, Brunati AM, Colombo G, Lippe G, Bernardi P, Rasola A. The mitochondrial chaperone TRAP1 regulates F-ATP synthase channel formation. Cell Death Differ 2022; 29:2335-2346. [PMID: 35614131 PMCID: PMC9751095 DOI: 10.1038/s41418-022-01020-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 01/31/2023] Open
Abstract
Binding of the mitochondrial chaperone TRAP1 to client proteins shapes bioenergetic and proteostatic adaptations of cells, but the panel of TRAP1 clients is only partially defined. Here we show that TRAP1 interacts with F-ATP synthase, the protein complex that provides most cellular ATP. TRAP1 competes with the peptidyl-prolyl cis-trans isomerase cyclophilin D (CyPD) for binding to the oligomycin sensitivity-conferring protein (OSCP) subunit of F-ATP synthase, increasing its catalytic activity and counteracting the inhibitory effect of CyPD. Electrophysiological measurements indicate that TRAP1 directly inhibits a channel activity of purified F-ATP synthase endowed with the features of the permeability transition pore (PTP) and that it reverses PTP induction by CyPD, antagonizing PTP-dependent mitochondrial depolarization and cell death. Conversely, CyPD outcompetes the TRAP1 inhibitory effect on the channel. Our data identify TRAP1 as an F-ATP synthase regulator that can influence cell bioenergetics and survival and can be targeted in pathological conditions where these processes are dysregulated, such as cancer.
Collapse
Affiliation(s)
- Giuseppe Cannino
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Andrea Urbani
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, viale Europa, 88100, Catanzaro, Italy
| | - Mariaconcetta Varano
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, viale Europa, 88100, Catanzaro, Italy
| | - Alessandro Negro
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Antonio Filippi
- Department of Medicine, University of Udine, via Colugna 50, 33100, Udine, Italy
| | - Francesco Ciscato
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Ionica Masgras
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
- Institute of Neuroscience, National Research Council, Viale G. Colombo 3, 35131, Padova, Italy
| | - Christoph Gerle
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Elena Tibaldi
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121, Padova, Italy
| | - Anna Maria Brunati
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121, Padova, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100, Pavia, Italy
- Institute of Chemical and Technological Sciences "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131, Milano, Italy
| | - Giovanna Lippe
- Department of Medicine, University of Udine, via Colugna 50, 33100, Udine, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
- Institute of Neuroscience, National Research Council, Viale G. Colombo 3, 35131, Padova, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy.
| |
Collapse
|
3
|
Rajendran M, Queralt-Martín M, Gurnev PA, Rosencrans WM, Rovini A, Jacobs D, Abrantes K, Hoogerheide DP, Bezrukov SM, Rostovtseva TK. Restricting α-synuclein transport into mitochondria by inhibition of α-synuclein-VDAC complexation as a potential therapeutic target for Parkinson's disease treatment. Cell Mol Life Sci 2022; 79:368. [PMID: 35718804 PMCID: PMC11072225 DOI: 10.1007/s00018-022-04389-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022]
Abstract
Involvement of alpha-synuclein (αSyn) in Parkinson's disease (PD) is complicated and difficult to trace on cellular and molecular levels. Recently, we established that αSyn can regulate mitochondrial function by voltage-activated complexation with the voltage-dependent anion channel (VDAC) on the mitochondrial outer membrane. When complexed with αSyn, the VDAC pore is partially blocked, reducing the transport of ATP/ADP and other metabolites. Further, αSyn can translocate into the mitochondria through VDAC, where it interferes with mitochondrial respiration. Recruitment of αSyn to the VDAC-containing lipid membrane appears to be a crucial prerequisite for both the blockage and translocation processes. Here we report an inhibitory effect of HK2p, a small membrane-binding peptide from the mitochondria-targeting N-terminus of hexokinase 2, on αSyn membrane binding, and hence on αSyn complex formation with VDAC and translocation through it. In electrophysiology experiments, the addition of HK2p at micromolar concentrations to the same side of the membrane as αSyn results in a dramatic reduction of the frequency of blockage events in a concentration-dependent manner, reporting on complexation inhibition. Using two complementary methods of measuring protein-membrane binding, bilayer overtone analysis and fluorescence correlation spectroscopy, we found that HK2p induces detachment of αSyn from lipid membranes. Experiments with HeLa cells using proximity ligation assay confirmed that HK2p impedes αSyn entry into mitochondria. Our results demonstrate that it is possible to regulate αSyn-VDAC complexation by a rationally designed peptide, thus suggesting new avenues in the search for peptide therapeutics to alleviate αSyn mitochondrial toxicity in PD and other synucleinopathies.
Collapse
Affiliation(s)
- Megha Rajendran
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - María Queralt-Martín
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, Castellón, 12071, Spain
| | - Philip A Gurnev
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - William M Rosencrans
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Amandine Rovini
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Daniel Jacobs
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Kaitlin Abrantes
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Sergey M Bezrukov
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Tatiana K Rostovtseva
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA.
| |
Collapse
|