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Chandrasekhar G, Srinivasan E, Nandhini S, Pravallika G, Sanjay G, Rajasekaran R. Computer aided therapeutic tripeptide design, in alleviating the pathogenic proclivities of nocuous α-synuclein fibrils. J Biomol Struct Dyn 2024; 42:483-494. [PMID: 36961221 DOI: 10.1080/07391102.2023.2194003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
Parkinson's disorder (PD) exacerbates neuronal degeneration of motor nerves, thereby effectuating uncoordinated movements and tremors. Aberrant alpha-synuclein (α-syn) is culpable of triggering PD, wherein cytotoxic amyloid aggregates of α-syn get deposited in motor neurons to instigate neuro-degeneration. Amyloid aggregates, typically rich in beta sheets are cardinal targets to mitigate their neurotoxic effects. In this analysis, owing to their interaction specificity, we formulated an efficacious tripeptide out of the aggregation-prone region of α-syn protein. With the help of a proficient computational pipeline, systematic peptide shortening and an adept molecular simulation platform, we formulated a tripeptide, VAV from α-syn structure based hexapeptide KISVRV. Indeed, the VAV tripeptide was able to effectively mitigate the α-syn amyloid fibrils' dynamic rate of beta-sheet formation. Additional trajectory analyses of the VAV- α-syn complex indicated that, upon its dynamic interaction, VAV efficiently altered the distinct pathogenic structural dynamics of α-syn, further advocating its potential in alleviating aberrant α-syn's amyloidogenic proclivities. Consistent findings from various computational analyses have led us to surmise that VAV could potentially re-alter the pathogenic conformational orientation of α-syn, essential to mitigate its cytotoxicity. Hence, VAV tripeptide could be an efficacious therapeutic candidate to efficiently ameliorate aberrant α-syn amyloid mediated neurotoxicity, eventually attenuating the nocuous effects of PD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Chandrasekhar
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - E Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - S Nandhini
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - G Pravallika
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - G Sanjay
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - R Rajasekaran
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
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2
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Pirhaghi M, Frank SA, Alam P, Nielsen J, Sereikaite V, Gupta A, Strømgaard K, Andreasen M, Sharma D, Saboury AA, Otzen DE. A penetratin-derived peptide reduces the membrane permeabilization and cell toxicity of α-synuclein oligomers. J Biol Chem 2022; 298:102688. [PMID: 36370848 PMCID: PMC9791135 DOI: 10.1016/j.jbc.2022.102688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Parkinson's disease is a neurodegenerative movement disorder associated with the intracellular aggregation of α-synuclein (α-syn). Cytotoxicity is mainly associated with the oligomeric species (αSOs) formed at early stages in α-syn aggregation. Consequently, there is an intense focus on the discovery of novel inhibitors such as peptides to inhibit oligomer formation and toxicity. Here, using peptide arrays, we identified nine peptides with high specificity and affinity for αSOs. Of these, peptides p194, p235, and p249 diverted α-syn aggregation from fibrils to amorphous aggregates with reduced β-structures and increased random coil content. However, they did not reduce αSO cytotoxicity and permeabilization of large anionic unilamellar vesicles. In parallel, we identified a non-self-aggregating peptide (p216), derived from the cell-penetrating peptide penetratin, which showed 12-fold higher binding affinity to αSOs than to α-syn monomers (Kdapp 2.7 and 31.2 μM, respectively). p216 reduced αSOs-induced large anionic unilamellar vesicle membrane permeability at 10-1 to 10-3 mg/ml by almost 100%, was not toxic to SH-SY5Y cells, and reduced αSOs cytotoxicity by about 20%. We conclude that p216 is a promising starting point from which to develop peptides targeting toxic αSOs in Parkinson's disease.
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Affiliation(s)
- Mitra Pirhaghi
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus C, Denmark; Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Signe Andrea Frank
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus C, Denmark
| | - Parvez Alam
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus C, Denmark; Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus C, Denmark
| | - Vita Sereikaite
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Arpit Gupta
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India; G.N. Ramachandran Protein Centre, Academy of Scientific & Innovative Research, Chennai, India
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus C, Denmark.
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The current state of amyloidosis therapeutics and the potential role of fluorine in their treatment. Biochimie 2022; 202:123-135. [PMID: 35963462 DOI: 10.1016/j.biochi.2022.08.003] [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: 02/16/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022]
Abstract
Amyloidosis, commonly known as amyloid-associated diseases, is characterized by improperly folded proteins accumulating in tissues and eventually causing organ damage, which is linked to several disorders ranging from neurodegenerative to peripheral diseases. It has an enormous societal and financial impact on the global health sector. Due to the complexity of protein misfolding and intertwined aggregation, there are no effective disease-modifying medications at present, and the condition is likely mis/non-diagnosed half of the time. Nonetheless, over the last two decades, substantial research into aggregation processes has revealed the possibilities of new intervention approaches. On the other hand, fluorine has been a rising star in therapeutic development for numerous neurodegenerative illnesses and other peripheral diseases. In this study, we revised and emphasized the possible significance of fluorine-modified therapeutic molecules and fluorine-modified nanoparticles (NPs) in the modulation of amyloidogenic proteins, including insulin, amyloid beta peptide (Aβ), prion protein (PrP), transthyretin (TTR) and Huntingtin (htt).
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4
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Engel H, Guischard F, Krause F, Nandy J, Kaas P, Höfflin N, Köhn M, Kilb N, Voigt K, Wolf S, Aslan T, Baezner F, Hahne S, Ruckes C, Weygant J, Zinina A, Akmeriç EB, Antwi EB, Dombrovskij D, Franke P, Lesch KL, Vesper N, Weis D, Gensch N, Di Ventura B, Öztürk MA. finDr: A web server for in silico D-peptide ligand identification. Synth Syst Biotechnol 2021; 6:402-413. [PMID: 34901479 PMCID: PMC8632724 DOI: 10.1016/j.synbio.2021.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/20/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
In the rapidly expanding field of peptide therapeutics, the short in vivo half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display. This technique is extremely powerful, but it requires the synthesis of the target in D-form, which is challenging for large proteins. Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. In a separate, heuristic approach to search the chemical space of 12-mer peptides, finDr executes a customizable evolutionary algorithm (EA) for the de novo identification or optimization of D-peptide ligands. As a proof of principle, we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3 (PSMα3), a toxin of methicillin-resistant Staphylococcus aureus (MRSA). We validate the predictions using in vitro binding assays, supporting the success of this approach. Compared to conventional methods, finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation. We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.
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Key Words
- D-AA, dextrorotatory amino acid
- D-peptide
- EA, evolutionary algorithm
- Evolutionary algorithm
- L-AA, levorotatory amino acid
- MD, molecular dynamics
- MIEA, mirror-image evolutionary algorithm
- MIPD, mirror-image phage display
- MIVS, mirror-image virtual screening
- MRSA, methicillin-resistant Staphylococcus aureus
- Mirror-image phage display
- Molecular docking
- NCL, native chemical ligation
- PD-1, receptor programmed death 1
- PPI, protein-protein interaction
- PSMα3, phenol soluble modulin alpha 3
- Peptide design
- SPPS, solid phase peptide synthesis
- Web server
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Affiliation(s)
- Helena Engel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Felix Guischard
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Krause
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Janina Nandy
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Paulina Kaas
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nico Höfflin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Normann Kilb
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- AG Roth-Lab for MicroarrayCopying, ZBSA–Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Karsten Voigt
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3a, 79104, Freiburg, Germany
| | - Tahira Aslan
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Baezner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Salomé Hahne
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Carolin Ruckes
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Joshua Weygant
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Alisa Zinina
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Emir Bora Akmeriç
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Enoch B. Antwi
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Dennis Dombrovskij
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Philipp Franke
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Klara L. Lesch
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
- Internal Medicine IV, Department of Medicine, Medical Center, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - Niklas Vesper
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Daniel Weis
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nicole Gensch
- Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Corresponding author. Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Barbara Di Ventura
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Mehmet Ali Öztürk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
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5
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Fritz ZR, Schloss RS, Yarmush ML, Williams LJ. HSymM-guided engineering of the immunodominant p53 transactivation domain putative peptide antigen for improved binding to its anti-p53 monoclonal antibody. Bioorg Med Chem Lett 2021; 51:128341. [PMID: 34454062 PMCID: PMC8526406 DOI: 10.1016/j.bmcl.2021.128341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 02/07/2023]
Abstract
A novel engineering strategy to improve autoantibody detection with peptide fragments derived from the parent antigen is presented. The model system studied was the binding of the putative p53 TAD peptide antigen (residues 46-55) to its cognate anti-p53 antibody, ab28. Each engineered peptide contained the full decapeptide epitope and differed only in the flanking regions. Since minimal structural information was available to guide the design, a simple epitope:paratope binding model was applied. The Hidden Symmetry Model, which we recently reported, was used to guide peptide design and estimate per-residue contributions to interaction free energy as a function of added C- and N-terminal flanking peptides. Twenty-four peptide constructs were designed, synthesized, and assessed for binding affinity to ab28 by surface plasmon resonance, and a subset of these peptides were evaluated in a simulated immunoassay for limit of detection. Many peptides exhibited over 200-fold enhancements in binding affinity and improved limits of detection. The epitope was reevaluated and is proposed to be the undecapeptide corresponding to residues 45-55. HSymM calculated binding free energy and experimental data were found to be in good agreement (R2 > 0.75).
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Affiliation(s)
- Zachary R Fritz
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, United States
| | - Rene S Schloss
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, United States
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, United States
| | - Lawrence J Williams
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States.
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6
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Popova B, Wang D, Rajavel A, Dhamotharan K, Lázaro DF, Gerke J, Uhrig JF, Hoppert M, Outeiro TF, Braus GH. Identification of Two Novel Peptides That Inhibit α-Synuclein Toxicity and Aggregation. Front Mol Neurosci 2021; 14:659926. [PMID: 33912013 PMCID: PMC8072481 DOI: 10.3389/fnmol.2021.659926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/16/2021] [Indexed: 12/02/2022] Open
Abstract
Aggregation of α-synuclein (αSyn) into proteinaceous deposits is a pathological hallmark of a range of neurodegenerative diseases including Parkinson’s disease (PD). Numerous lines of evidence indicate that the accumulation of toxic oligomeric and prefibrillar αSyn species may underpin the cellular toxicity and spread of pathology between cells. Therefore, aggregation of αSyn is considered a priority target for drug development, as aggregation inhibitors are expected to reduce αSyn toxicity and serve as therapeutic agents. Here, we used the budding yeast S. cerevisiae as a platform for the identification of short peptides that inhibit αSyn aggregation and toxicity. A library consisting of approximately one million peptide variants was utilized in two high-throughput screening approaches for isolation of library representatives that reduce αSyn-associated toxicity and aggregation. Seven peptides were isolated that were able to suppress specifically αSyn toxicity and aggregation in living cells. Expression of the peptides in yeast reduced the accumulation of αSyn-induced reactive oxygen species and increased cell viability. Next, the peptides were chemically synthesized and probed for their ability to modulate αSyn aggregation in vitro. Two synthetic peptides, K84s and K102s, of 25 and 19 amino acids, respectively, significantly inhibited αSyn oligomerization and aggregation at sub-stoichiometric molar ratios. Importantly, K84s reduced αSyn aggregation in human cells. These peptides represent promising αSyn aggregation antagonists for the development of future therapeutic interventions.
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Affiliation(s)
- Blagovesta Popova
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Dan Wang
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Abirami Rajavel
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Karthikeyan Dhamotharan
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Diana F Lázaro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Göttingen, Germany
| | - Jennifer Gerke
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Joachim F Uhrig
- Department of Plant Molecular Biology and Physiology, University of Goettingen, Göttingen, Germany
| | - Michael Hoppert
- Department of General Microbiology, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Göttingen, Germany.,Max Planck Institute for Experimental Medicine, Göttingen, Germany.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen, Germany
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
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7
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Dong C, Garen CR, Mercier P, Petersen NO, Woodside MT. Characterizing the inhibition of α-synuclein oligomerization by a pharmacological chaperone that prevents prion formation by the protein PrP. Protein Sci 2019; 28:1690-1702. [PMID: 31306510 DOI: 10.1002/pro.3684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
Aggregation of the disordered protein α-synuclein into amyloid fibrils is a central feature of synucleinopathies, neurodegenerative disorders that include Parkinson's disease. Small, pre-fibrillar oligomers of misfolded α-synuclein are thought to be the key toxic entities, and α-synuclein misfolding can propagate in a prion-like way. We explored whether a compound with anti-prion activity that can bind to unfolded parts of the protein PrP, the cyclic tetrapyrrole Fe-TMPyP, was also active against α-synuclein aggregation. Observing the initial stages of aggregation via fluorescence cross-correlation spectroscopy, we found that Fe-TMPyP inhibited small oligomer formation in a dose-dependent manner. Fe-TMPyP also inhibited the formation of mature amyloid fibrils in vitro, as detected by thioflavin T fluorescence. Isothermal titration calorimetry indicated Fe-TMPyP bound to monomeric α-synuclein with a stoichiometry of 2, and two-dimensional heteronuclear single quantum coherence NMR spectra revealed significant interactions between Fe-TMPyP and the C-terminus of the protein. These results suggest commonalities among aggregation mechanisms for α-synuclein and the prion protein may exist that can be exploited as therapeutic targets.
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Affiliation(s)
- Chunhua Dong
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Craig R Garen
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Pascal Mercier
- National High Field Nuclear Magnetic Resonance Centre (NANUC), Edmonton, Alberta, Canada
| | - Nils O Petersen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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8
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Oliveri V. Toward the discovery and development of effective modulators of α-synuclein amyloid aggregation. Eur J Med Chem 2019; 167:10-36. [PMID: 30743095 DOI: 10.1016/j.ejmech.2019.01.045] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/17/2022]
Abstract
A host of human diseases, including Parkinson's disease and Dementia with Lewy bodies, are suspected to be directly linked to protein aggregation. Amyloid protein aggregates and oligomeric intermediates of α-synuclein are observed in synucleinopathies and considered to be mediators of cellular toxicity. Hence, α-synuclein has seen as one of the leading and most compelling targets and is receiving a great deal of attention from researchers. Nevertheless, there is no neuroprotective approach directed toward Parkinson's disease or other synucleinopathies so far. In this review, we summarize the available data concerning inhibitors of α-synuclein aggregation and their advancing towards clinical use. The compounds are grouped according to their chemical structures, providing respective insights into their mechanism of action, pharmacology, and pharmacokinetics. Overall, shared structure-activity elements are emerging, as well as specific binding modes related to the ability of the modulators to establish hydrophobic and hydrogen bonds interactions with the protein. Some molecules with encouraging in vivo data support the possibility of translation to the clinic.
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Affiliation(s)
- Valentina Oliveri
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, viale A. Doria 6, 95125, Catania, Italy.
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9
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Rezaeian N, Shirvanizadeh N, Mohammadi S, Nikkhah M, Arab SS. The inhibitory effects of biomimetically designed peptides on α-synuclein aggregation. Arch Biochem Biophys 2017; 634:96-106. [PMID: 28965745 DOI: 10.1016/j.abb.2017.09.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/05/2017] [Accepted: 09/20/2017] [Indexed: 01/10/2023]
Abstract
Parkinson's disease is characterized by accumulation of inclusion bodies in dopaminergic neurons, where insoluble and fibrillar α-synuclein makes up the major component of these inclusion bodies. So far, several strategies have been applied in order to suppress α-synuclein aggregation and toxicity in Parkinson's disease. In the present study, a new database has been established by segmentation of all the proteins deposited in protein Data Bank. The database data base was searched for the sequences which adopt β structure and are identical or very similar to the regions of α-synuclein which are involved in aggregation. The adjacent β strands of the found sequences were chosen as the peptide inhibitors of α-synuclein aggregation. Two of the predicted peptides, namely KISVRV and GQTYVLPG, were experimentally proved to be efficient in suppressing aggregation of α-synuclein in vitro. Moreover, KISVRV exhibited the ability to disrupt oligomers of α-syn which are assumed to be the pathogenic species in Parkinson's disease.
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Affiliation(s)
- Niloofar Rezaeian
- Department of Biology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Niloofar Shirvanizadeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Soheila Mohammadi
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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10
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Wu X, Shaikh AB, Yu Y, Li Y, Ni S, Lu A, Zhang G. Potential Diagnostic and Therapeutic Applications of Oligonucleotide Aptamers in Breast Cancer. Int J Mol Sci 2017; 18:ijms18091851. [PMID: 28841163 PMCID: PMC5618500 DOI: 10.3390/ijms18091851] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is one of the most common causes of cancer related deaths in women. Currently, with the development of early detection, increased social awareness and kinds of treatment options, survival rate has improved in nearly every type of breast cancer patients. However, about one third patients still have increased chances of recurrence within five years and the five-year relative survival rate in patients with metastasis is less than 30%. Breast cancer contains multiple subtypes. Each subtype could cause distinct clinical outcomes and systemic interventions. Thereby, new targeted therapies are of particular importance to solve this major clinical problem. Aptamers, often termed “chemical antibodies”, are functionally similar to antibodies and have demonstrated their superiority of recognizing target with high selectivity, affinity and stability. With these intrinsic properties, aptamers have been widely studied in cancer biology and some are in clinical trials. In this review, we will firstly discuss about the global impacts and mechanisms of breast cancer, then briefly highlight applications of aptamers that have been developed for breast cancer and finally summarize various challenges in clinical translation of aptamers.
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Affiliation(s)
| | - Atik Badshah Shaikh
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yuanyuan Yu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yongshu Li
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Shuaijian Ni
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
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11
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Russo A, Scognamiglio PL, Hong Enriquez RP, Santambrogio C, Grandori R, Marasco D, Giordano A, Scoles G, Fortuna S. In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands. PLoS One 2015; 10:e0133571. [PMID: 26252476 PMCID: PMC4529233 DOI: 10.1371/journal.pone.0133571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Abstract
Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
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Affiliation(s)
- Anna Russo
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Medical Biotechnology, University of Siena, Policlinico Le Scotte, Viale Bracci, Siena, Italy
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
| | | | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
- * E-mail: (SF); (DM)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine & Center for Biotechnology Temple University Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Surgery & Neuroscience University of Siena, Strada delle Scotte n. 6, Siena, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sara Fortuna
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- * E-mail: (SF); (DM)
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12
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Li H, Lu L, Chen R, Quan L, Xia X, Lü Q. PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta. PLoS One 2014; 9:e94769. [PMID: 24801496 PMCID: PMC4011740 DOI: 10.1371/journal.pone.0094769] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 03/19/2014] [Indexed: 01/12/2023] Open
Abstract
Structural information related to protein–peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein–peptide interactions explored by experimental ways. Protein–peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein–peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein–peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.
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Affiliation(s)
- Haiou Li
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Liyao Lu
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rong Chen
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Lijun Quan
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoyan Xia
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Provincial Key Lab for Information Processing Technologies, Suzhou, Jiangsu, China
| | - Qiang Lü
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Provincial Key Lab for Information Processing Technologies, Suzhou, Jiangsu, China
- * E-mail:
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13
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Screening of peptide ligands for pyrroloquinoline quinone glucose dehydrogenase using antagonistic template-based biopanning. Int J Mol Sci 2013; 14:23244-56. [PMID: 24287902 PMCID: PMC3876041 DOI: 10.3390/ijms141223244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/31/2013] [Accepted: 11/11/2013] [Indexed: 01/05/2023] Open
Abstract
We have developed a novel method, antagonistic template-based biopanning, for screening peptide ligands specifically recognizing local tertiary protein structures. We chose water-soluble pyrroloquinoline quinone (PQQ) glucose dehydrogenase (GDH-B) as a model enzyme for this screening. Two GDH-B mutants were constructed as antagonistic templates; these have some point mutations to induce disruption of local tertiary structures within the loop regions that are located at near glucose-binding pocket. Using phage display, we selected 12-mer peptides that specifically bound to wild-type GDH-B but not to the antagonistic templates. Consequently, a peptide ligand showing inhibitory activity against GDH-B was obtained. These results demonstrate that the antagonistic template-based biopanning is useful for screening peptide ligands recognizing the specific local tertiary structure of proteins.
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14
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Feng L, Zhang D, Fan C, Ma C, Yang W, Meng Y, Wu W, Guan S, Jiang B, Yang M, Liu X, Guo D. ER stress-mediated apoptosis induced by celastrol in cancer cells and important role of glycogen synthase kinase-3β in the signal network. Cell Death Dis 2013; 4:e715. [PMID: 23846217 PMCID: PMC3730400 DOI: 10.1038/cddis.2013.222] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 01/13/2023]
Abstract
HeLa cells treated with celastrol, a natural compound with inhibitive effect on proteasome, exhibited increase in apoptotic rate and characteristics of apoptosis. To clarify the signal network activated by celastrol to induce apoptosis, both the direct target proteins and undirect target proteins of celastrol were searched in the present study. Proteasome catalytic subunit β1 was predicted by computational analysis to be a possible direct target of celastrol and confirmed by checking direct effect of celastrol on the activity of recombinant human proteasome subunit β1 in vitro. Undirect target-related proteins of celastrol were searched using proteomic studies including two-dimensional electrophoresis (2-DE) analysis and iTRAQ-based LC-MS analysis. Possible target-related proteins of celastrol such as endoplasmic reticulum protein 29 (ERP29) and mitochondrial import receptor Tom22 (TOM22) were found by 2-DE analysis of total cellular protein expression profiles. Further study showed that celastrol induced ER stress and ER stress inhibitor could ameliorate cell death induced by celastrol. Celastrol induced translocation of Bax into the mitochondria, which might be related to the upregulation of BH-3-only proteins such as BIM and the increase in the expression level of TOM22. To further search possible target-related proteins of celastrol in ER and ER-related fractions, iTRAQ-based LC-MS method was use to analyze protein expression profiles of ER/microsomal vesicles-riched fraction of cells with or without celastrol treatment. Based on possible target-related proteins found in both 2-DE analysis and iTRAQ-based LC-MS analysis, protein–protein interaction (PPI) network was established using bioinformatic analysis. The important role of glycogen synthase kinase-3β (GSK3β) in the signal cascades of celastrol was suggested. Pretreatment of LiCL, an inhibitor of GSK3β, could significantly ameliorate apoptosis induced by celastrol. On the basis of the results of the present study, possible signal network of celastrol activated by celastrol leading to apoptosis was predicted.
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Affiliation(s)
- L Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
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15
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Use of Proteomics and Peptidomics Methods in Food Bioactive Peptide Science and Engineering. FOOD ENGINEERING REVIEWS 2012. [DOI: 10.1007/s12393-012-9058-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Gulati V, Wallace R. Rafts, Nanoparticles and Neural Disease. NANOMATERIALS (BASEL, SWITZERLAND) 2012; 2:217-250. [PMID: 28348305 PMCID: PMC5304588 DOI: 10.3390/nano2030217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/17/2022]
Abstract
This review examines the role of membrane rafts in neural disease as a rationale for drug targeting utilizing lipid-based nanoparticles. The article begins with an overview of methodological issues involving the existence, sizes, and lifetimes of rafts, and then examines raft function in the etiologies of three major neural diseases-epilepsy, Parkinson's disease, and Alzheimer's disease-selected as promising candidates for raft-based therapeutics. Raft-targeting drug delivery systems involving liposomes and solid lipid nanoparticles are then examined in detail.
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Affiliation(s)
- Vishal Gulati
- Ross University School of Medicine, Miami Beach Community Health Center, 11645 Biscayne Boulevard, North Miami, FL 33181, USA.
| | - Ron Wallace
- Department of Anthropology, University of Central Florida, Orlando, FL 32816, USA.
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17
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Recent work in the development and application of protein–peptide docking. Future Med Chem 2012; 4:1619-44. [DOI: 10.4155/fmc.12.99] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Interest in the development of novel peptide-based drugs is growing. There is, thus, a pressing need for the development of effective methods to enable novel peptide-based drug discovery. A cogent case can be made for the development and application of computational or in silico methods to assist with peptide discovery. In particular, there is a need for the development of effective protein–peptide docking methods. Here, recent work in the area of protein–peptide docking method development is reviewed and several drug-discovery projects that benefited from protein–peptide docking are discussed. In the present review, special attention is given to the search and scoring problems, the use of peptide docking to enable hit identification, and the use of peptide docking to help rationalize experimental results, and generate and test structure-based hypotheses. Finally, some recommendations are made for improving the future development and application of protein–peptide docking.
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18
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Tavassoly O, Lee JS. Methamphetamine binds to α-synuclein and causes a conformational change which can be detected by nanopore analysis. FEBS Lett 2012; 586:3222-8. [DOI: 10.1016/j.febslet.2012.06.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/06/2012] [Accepted: 06/25/2012] [Indexed: 01/14/2023]
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19
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Hong Enriquez RP, Pavan S, Benedetti F, Tossi A, Savoini A, Berti F, Laio A. Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach. J Chem Theory Comput 2012; 8:1121-8. [PMID: 26593371 DOI: 10.1021/ct200873y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a method for designing artificial receptors capable of binding with high affinity to a chosen target organic molecule. The primary sequence of the peptide is optimized to maximize its binding affinity. Our algorithm builds on a combination of molecular dynamics, semiflexible docking, and replica exchange Monte Carlo and performs simultaneous sampling in sequence and conformational spaces carefully selecting the degree of flexibility in the mutated peptides. The approach is used to design a decapeptide able to bind efavirenz. The calculated binding energy of the designed peptide (approximately -12 kcal/mol) was confirmed experimentally by fluorescence measurements. NMR spectroscopy confirmed the interactions between the peptide and the efavirenz molecule predicted by the algorithm.
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Affiliation(s)
| | | | | | | | - Adriano Savoini
- T&B associati srl, Area Science Park, Padriciano 91, Trieste, Italy
| | | | - Alessandro Laio
- SISSA/ISAS - International School for Advanced Studies, Trieste 34100, Italy
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20
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Raveh B, London N, Zimmerman L, Schueler-Furman O. Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One 2011; 6:e18934. [PMID: 21572516 PMCID: PMC3084719 DOI: 10.1371/journal.pone.0018934] [Citation(s) in RCA: 211] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 03/12/2011] [Indexed: 11/18/2022] Open
Abstract
Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions.
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Affiliation(s)
- Barak Raveh
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
- The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Nir London
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
| | - Lior Zimmerman
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
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21
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Hinault MP, Farina-Henriquez-Cuendet A, Goloubinoff P. Molecular chaperones and associated cellular clearance mechanisms against toxic protein conformers in Parkinson's disease. NEURODEGENER DIS 2011; 8:397-412. [PMID: 21411979 DOI: 10.1159/000324514] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 01/21/2011] [Indexed: 11/19/2022] Open
Abstract
Parkinson's disease (PD) is a slowly progressive neurodegenerative disorder marked by the loss of dopaminergic neurons (in particular in the substantia nigra) causing severe impairment of movement coordination and locomotion, associated with the accumulation of aggregated α-synuclein (α-Syn) into proteinaceous inclusions named Lewy bodies. Various early forms of misfolded α-Syn oligomers are cytotoxic. Their formation is favored by mutations and external factors, such as heavy metals, pesticides, trauma-related oxidative stress and heat shock. Here, we discuss the role of several complementing cellular defense mechanisms that may counteract PD pathogenesis, especially in youth, and whose effectiveness decreases with age. Particular emphasis is given to the 'holdase' and 'unfoldase' molecular chaperones that provide cells with potent means to neutralize and scavenge toxic protein conformers. Because chaperones can specifically recognize misfolded proteins, they are key specificity factors for other cellular defenses, such as proteolysis by the proteasome and autophagy. The efficiency of the cellular defenses decreases in stressed or aging neurons, leading to neuroinflammation, apoptosis and tissue loss. Thus, drugs that can upregulate the molecular chaperones, the ubiquitin-proteasome system and autophagy in brain tissues are promising avenues for therapies against PD and other mutation-, stress- or age-dependent protein-misfolding diseases.
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Affiliation(s)
- Marie-Pierre Hinault
- DBMV, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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22
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Vanhee P, van der Sloot AM, Verschueren E, Serrano L, Rousseau F, Schymkowitz J. Computational design of peptide ligands. Trends Biotechnol 2011; 29:231-9. [PMID: 21316780 DOI: 10.1016/j.tibtech.2011.01.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 12/19/2022]
Abstract
Peptides possess several attractive features when compared to small molecule and protein therapeutics, such as high structural compatibility with target proteins, the ability to disrupt protein-protein interfaces, and small size. Efficient design of high-affinity peptide ligands via rational methods has been a major obstacle to the development of this potential drug class. However, structural insights into the architecture of protein-peptide interfaces have recently culminated in several computational approaches for the rational design of peptides that target proteins. These methods provide a valuable alternative to experimental high-resolution structures of target protein-peptide complexes, bringing closer the dream of in silico designed peptides for therapeutic applications.
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Affiliation(s)
- Peter Vanhee
- VIB SWITCH Laboratory, Flanders Institute of Biotechnology (VIB), Pleinlaan 2, 1050 Brussels, Belgium
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23
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Auluck PK, Caraveo G, Lindquist S. α-Synuclein: membrane interactions and toxicity in Parkinson's disease. Annu Rev Cell Dev Biol 2010; 26:211-33. [PMID: 20500090 DOI: 10.1146/annurev.cellbio.042308.113313] [Citation(s) in RCA: 407] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the late 1990s, mutations in the synaptic protein α-synuclein (α-syn) were identified in families with hereditary Parkinson's disease (PD). Rapidly, α-syn became the target of numerous investigations that have transformed our understanding of the pathogenesis underlying this disorder. α-Syn is the major component of Lewy bodies (LBs), cytoplasmic protein aggregates that form in the neurons of PD patients. α-Syn interacts with lipid membranes and adopts amyloid conformations that deposit within LBs. Work in yeast and other model systems has revealed that α-syn-associated toxicity might be the consequence of abnormal membrane interactions and alterations in vesicle trafficking. Here we review evidence regarding α-syn's normal interactions with membranes and regulation of synaptic vesicles as well as how overexpression of α-syn yields global cellular dysfunction. Finally, we present a model linking vesicle dynamics to toxicity with the sincere hope that understanding these disease mechanisms will lead to the development of novel, potent therapeutics.
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Affiliation(s)
- Pavan K Auluck
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
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24
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Savory N, Abe K, Sode K, Ikebukuro K. Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing. Biosens Bioelectron 2010; 26:1386-91. [PMID: 20692149 DOI: 10.1016/j.bios.2010.07.057] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 01/10/2023]
Abstract
In order to construct an aptasensor, aptamers that show high affinity for target molecules are required. While the systematic evolution of ligands by exponential enrichment (SELEX) is an efficient method for selecting aptamers, it sometimes fails to obtain aptamers with high affinity and so additional improvements are required. We applied a genetic algorithm (GA) to post-SELEX screening as an in silico maturation of aptamers. First, we pre-selected DNA aptamers against prostate specific antigen (PSA) through three rounds of SELEX. To improve the PSA-binding ability of the aptamers, we carried out post-SELEX screening using GA with the pre-selected oligonucleotide sequences. For screening using GA, we replicated the oligonucleotide sequences obtained through SELEX, crossed over and mutated in silico resulting in 20 sequences. Those oligonucleotide sequences were synthesized and assayed in vitro. Then, the oligonucleotides were ranked according to PSA-binding ability and the top sequences were selected for the next cycle of GA operation. After GA operations, we identified the aptamer showing a 48-fold higher PSA-binding ability than candidates obtained by SELEX. The dissociation constant (K(D)) of the obtained aptamer was estimated to be several tens of nM. We demonstrated sensing of PSA using the obtained aptamer and succeeded in sensing PSA concentrations between 40 and 100 nM. This is the first report of a DNA aptamer against PSA and its application to PSA sensing.
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Affiliation(s)
- Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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25
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Unal EB, Gursoy A, Erman B. VitAL: Viterbi algorithm for de novo peptide design. PLoS One 2010; 5:e10926. [PMID: 20532195 PMCID: PMC2880006 DOI: 10.1371/journal.pone.0010926] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 05/07/2010] [Indexed: 01/18/2023] Open
Abstract
Background Drug design against proteins to cure various diseases has been studied for several years. Numerous design techniques were discovered for small organic molecules for specific protein targets. The specificity, toxicity and selectivity of small molecules are hard problems to solve. The use of peptide drugs enables a partial solution to the toxicity problem. There has been a wide interest in peptide design, but the design techniques of a specific and selective peptide inhibitor against a protein target have not yet been established. Methodology/Principal Findings A novel de novo peptide design approach is developed to block activities of disease related protein targets. No prior training, based on known peptides, is necessary. The method sequentially generates the peptide by docking its residues pair by pair along a chosen path on a protein. The binding site on the protein is determined via the coarse grained Gaussian Network Model. A binding path is determined. The best fitting peptide is constructed by generating all possible peptide pairs at each point along the path and determining the binding energies between these pairs and the specific location on the protein using AutoDock. The Markov based partition function for all possible choices of the peptides along the path is generated by a matrix multiplication scheme. The best fitting peptide for the given surface is obtained by a Hidden Markov model using Viterbi decoding. The suitability of the conformations of the peptides that result upon binding on the surface are included in the algorithm by considering the intrinsic Ramachandran potentials. Conclusions/Significance The model is tested on known protein-peptide inhibitor complexes. The present algorithm predicts peptides that have better binding energies than those of the existing ones. Finally, a heptapeptide is designed for a protein that has excellent binding affinity according to AutoDock results.
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Affiliation(s)
- E. Besray Unal
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Burak Erman
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
- * E-mail:
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26
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Bartolini M, Andrisano V. Strategies for the Inhibition of Protein Aggregation in Human Diseases. Chembiochem 2010; 11:1018-35. [DOI: 10.1002/cbic.200900666] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Maguire-Zeiss KA. alpha-Synuclein: a therapeutic target for Parkinson's disease? Pharmacol Res 2008; 58:271-80. [PMID: 18840530 PMCID: PMC2630208 DOI: 10.1016/j.phrs.2008.09.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/10/2008] [Accepted: 09/11/2008] [Indexed: 12/21/2022]
Abstract
Parkinson's disease is a progressive age-related neurodegenerative disease with invariant loss of substantia nigra dopamine neurons and striatal projections. This disorder is well known for the associated motoric symptoms including resting tremor and the inability to initiate movement. However, it is now apparent that Parkinson's disease is a multisystem disorder with patients exhibiting symptoms derived from peripheral nervous system and extra-nigral dysfunctions in addition to the prototypical nigrostriatal damage. Although the etiology for sporadic Parkinson's disease is unknown, information gleaned from both familial forms of the disease and animal models places misfolded alpha-synuclein at the forefront. The disease is currently without a cure and most therapies target the motoric symptoms relying on increasing dopamine tone. In this review, the role of alpha-synuclein in disease pathogenesis and as a potential therapeutic target focusing on toxic conformers of this protein is considered. The addition of protofibrillar/oligomer-directed neurotherapeutics to the existing armamentarium may extend the symptom-free stage of Parkinson's disease as well as alleviate pathogenesis.
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Affiliation(s)
- Kathleen A Maguire-Zeiss
- Department of Neuroscience, Georgetown University Medical Center, 3970 Reservoir Road, Washington, DC 20057, United States.
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Chapter 6 Molecular and Cellular Biology of Synucleins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 270:225-317. [DOI: 10.1016/s1937-6448(08)01406-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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