1
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Ghosh N, Kundu LM. Cyclic di-peptide in situ inhibited protein-aggregation. Bioorg Med Chem Lett 2023; 91:129379. [PMID: 37331639 DOI: 10.1016/j.bmcl.2023.129379] [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: 04/16/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
An increasing number of neurodegenerative diseases seem to be associated with protein misfolding that often leads to misfolded protein aggregates with a β-sheet conformation and accumulation in the brain which directly contributes to or modulates the associated pathology. Protein aggregation diseases like Huntington's disease results from the deposition of aggregated huntingtin proteins within the nucleus, transmissible prion encephalopathies occur due to extracellular deposition of pathogenic prion proteins whereas Alzheimer's disease from the accumulation of both extracellular β-amyloid and intracellular hyperphosphorylated tau protein aggregates. In the generalized purpose, we have taken the core sequence of amyloid-β (responsible for its aggregation) as the aggregating peptide (AP). Among the various emerging therapeutic approaches against aggregation-related degenerative diseases such as diminishing the monomeric precursor protein, inhibiting aggregation, or blocking aggregation-induced cellular toxicity pathways, we focussed on the strategy based on the inhibition of protein aggregation using rationally designed peptide inhibitors comprising both the recognition and β-breaking component in the sequence. The "O → N acyl migration" concept was used to form cyclic peptide in situ for the generation of a bent unit which may act as disruption moiety for the inhibition process. The kinetics of aggregation was characterized by various biophysical tools (ThT-assay, TEM, CD, and FTIR). Results implied that the designed inhibitor peptides (IP) might be valuable to inhibit all the related aggregated peptides.
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Affiliation(s)
- Nibedita Ghosh
- Centre for the Environment, IIT Guwahati, Assam 781039, India; Symbol Discovery Ltd, Hyderabad 500046, India.
| | - Lal Mohan Kundu
- Centre for the Environment, IIT Guwahati, Assam 781039, India; Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India
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2
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Carrera-Aubesart A, Defaus S, Pérez-Peinado C, Sandín D, Torrent M, Jiménez MÁ, Andreu D. Examining Topoisomers of a Snake-Venom-Derived Peptide for Improved Antimicrobial and Antitumoral Properties. Biomedicines 2022; 10:biomedicines10092110. [PMID: 36140211 PMCID: PMC9495681 DOI: 10.3390/biomedicines10092110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
Ctn[15-34], the C-terminal section of crotalicidin (Ctn), a cathelicidin from a South American pit viper, is an antimicrobial and antitumoral peptide with remarkably longer stability in human serum than the parent Ctn. In this work, a set of topoisomers of both Ctn and Ctn[15-34], including the retro, enantio, and retroenantio versions, were synthesized and tested to investigate the structural requirements for activity. All topoisomers were as active as the cognate sequences against Gram-negative bacteria and tumor cells while slightly more toxic towards normal cells. More importantly, the enhanced serum stability of the D-amino-acid-containing versions suggests that such topoisomers must be preferentially considered as future antimicrobial and anticancer peptide leads.
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Affiliation(s)
- Adam Carrera-Aubesart
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Sira Defaus
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
- Correspondence: (S.D.); (D.A.)
| | - Clara Pérez-Peinado
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Daniel Sandín
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marc Torrent
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Maria Ángeles Jiménez
- Institute of Physical Chemistry “Rocasolano” (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - David Andreu
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
- Correspondence: (S.D.); (D.A.)
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3
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Destabilization of the Alzheimer's amyloid-β peptide by a proline-rich β-sheet breaker peptide: a molecular dynamics simulation study. J Mol Model 2021; 27:356. [PMID: 34796404 DOI: 10.1007/s00894-021-04968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/25/2021] [Indexed: 11/27/2022]
Abstract
The amyloid-β peptide exists in the form of fibrils in the plaques found in the brains of patients with Alzheimer's disease. One of the therapeutic strategies is the design of molecules which can destabilize these fibrils. We present a designed peptide KLVFFP5 with two segments: the self-recognition sequence KLVFF and a β-sheet breaker proline pentamer. Molecular dynamics simulations and docking results showed that this peptide could bind to the protofibrils and destabilize them by establishing hydrophobic contacts and hydrogen bonds with a higher affinity than the KLVFF peptide. In the presence of the KLVFFP5 peptide, the β-sheet content of the protofibrils was reduced significantly; the hydrogen bonding network and the salt bridges were disrupted to a greater extent than the KLVFF peptide. Our results indicate that the KLVFFP5 peptide is an effective β-sheet disruptor which can be considered in the therapy of Alzheimer's disease.
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4
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Breaker peptides against amyloid-β aggregation: a potential therapeutic strategy for Alzheimer's disease. Future Med Chem 2021; 13:1767-1794. [PMID: 34498978 DOI: 10.4155/fmc-2021-0184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder, for which blocking the early steps of extracellular misfolded amyloid-β (Aβ) aggregation is a promising therapeutic approach. However, the pathological features of AD progression include the accumulation of intracellular tau protein, membrane-catalyzed cell death and the abnormal deposition of Aβ. Here, we focus on anti-amyloid breaker peptides derived from the Aβ sequence and non-Aβ-based peptides containing both natural and modified amino acids. Critical aspects of the breaker peptides include N-methylation, conformational restriction through cyclization, incorporation of unnatural amino acid, fluorinated molecules, polymeric nanoparticles and PEGylation. This review confers a general idea of such breaker peptides with in vitro and in vivo studies, which may advance our understanding of AD pathology and develop an effective treatment strategy against AD.
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5
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Hayward S, Milner-White EJ. Determination of amino acids that favour the α L region using Ramachandran propensity plots. Implications for α-sheet as the possible amyloid intermediate. J Struct Biol 2021; 213:107738. [PMID: 33838226 DOI: 10.1016/j.jsb.2021.107738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/28/2022]
Abstract
In amyloid diseases an insoluble amyloid fibril forms via a soluble oligomeric intermediate. It is this intermediate that mediates toxicity and it has been suggested, somewhat controversially, that it has the α-sheet structure. Nests and α-strands are similar peptide motifs in that alternate residues lie in the αR and γL regions of the Ramachandran plot for nests, or αR and αL regions for α-strands. In nests a concavity is formed by the main chain NH atoms whereas in α-strands the main chain is almost straight. Using "Ramachandran propensity plots" to focus on the αL/γL region, it is shown that glycine favours γL (82% of amino acids are glycine), but disfavours αL (3% are glycine). Most charged and polar amino acids favour αL with asparagine having by far the highest propensity. Thus, glycine favours nests but, contrary to common expectation, should not favour α-sheet. By contrast most charged or polar amino acids should favour α-sheet by their propensity for the αL conformation, which is more discriminating amongst amino acids than the αR conformation. Thus, these results suggest the composition of sequences that favour α-sheet formation and point towards effective prediction of α-sheet from sequence.
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Affiliation(s)
- Steven Hayward
- Computational Biology Laboratory, School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - E James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
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6
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Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies. Int J Mol Sci 2021; 22:ijms22031051. [PMID: 33494369 PMCID: PMC7865305 DOI: 10.3390/ijms22031051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Neurodegeneration in Alzheimer's disease (AD) is defined by pathology featuring amyloid-β (Aβ) deposition in the brain. Aβ monomers themselves are generally considered to be nontoxic, but misfold into β-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aβ and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aβ(1-42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aβ in anti-parallel orientation, demonstrated neuroprotection against Aβ(1-42). A third inhibitor, predicted to bind parallel to Aβ, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aβ toxicity.
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7
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Mitra A, Sarkar N. Sequence and structure-based peptides as potent amyloid inhibitors: A review. Arch Biochem Biophys 2020; 695:108614. [PMID: 33010227 DOI: 10.1016/j.abb.2020.108614] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Misfolded and natively disordered globular proteins tend to aggregate together in an interwoven fashion to form fibrous, proteinaceous deposits referred to as amyloid fibrils. Formation and deposition of such insoluble fibrils are the characteristic features of a broad group of diseases, known as amyloidosis. Some of these proteins are known to cause several degenerative disorders in humans, such as Amyloid-Beta (Aβ) in Alzheimer's disease (AD), human Islet Amyloid Polypeptide (hIAPP, amylin) in type 2 diabetes, α-synuclein (α-syn) in Parkinson's disease (PD) and so on. The fact that these proteins do not share any significant sequence or structural homology in their native states make therapy quite challenging. However, it is observed that aggregation-prone proteins and peptides tend to adopt a similar type of secondary structure during the formation of fibrils. Rationally designed peptides can be a potent inhibitor that has been shown to disrupt the fibril structure by binding specifically to the amyloidogenic region(s) within a protein. The following review will analyze the inhibitory potency of both sequence-based and structure-based small peptides that have been shown to inhibit amyloidogenesis of proteins such as Aβ, human amylin, and α-synuclein.
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Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India.
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8
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Jokar S, Erfani M, Bavi O, Khazaei S, Sharifzadeh M, Hajiramezanali M, Beiki D, Shamloo A. Design of peptide-based inhibitor agent against amyloid-β aggregation: Molecular docking, synthesis and in vitro evaluation. Bioorg Chem 2020; 102:104050. [PMID: 32663672 DOI: 10.1016/j.bioorg.2020.104050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 12/30/2022]
Abstract
Formation of the amyloid beta (Aβ) peptide aggregations represents an indispensable role in appearing and progression of Alzheimer disease. β-sheet breaker peptides can be designed and modified with different amino acids in order to improve biological properties and binding affinity to the amyloid beta peptide. In the present study, three peptide sequences were designed based on the hopeful results of LIAIMA peptide and molecular docking studies were carried out onto the monomer and fibril structure of amyloid beta peptide using AutoDock Vina software. According to the obtained interactions and binding energy from docking, the best-designed peptide (d-GABA-FPLIAIMA) was chosen and synthesized in great yield (%96) via the Fmoc solid-phase peptide synthesis. The synthesis and purity of the resulting peptide were estimated and evaluated by Mass spectroscopy and Reversed-phase high-performance liquid chromatography (RP-HPLC) methods, respectively. Stability studies in plasma and Thioflavin T (ThT) assay were performed in order to measure the binding affinity and in vitro aggregation inhibition of Aβ peptide. The d-GABA-FPLIAIMA peptide showed good binding energy and affinity to Aβ fibrils, high stability (more than 90%) in human serum, and a reduction of 20% in inhibition of the Aβ aggregation growth. Finally, the favorable characteristics of our newly designed peptide make it a promising candidate β-sheet breaker agent for further in vivo studies.
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Affiliation(s)
- Safura Jokar
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Erfani
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, Tehran, Iran.
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, Iran.
| | - Saeedeh Khazaei
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sharifzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy; Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - Malihe Hajiramezanali
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Beiki
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
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9
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Jokar S, Behnammanesh H, Erfani M, Sharifzadeh M, Gholami M, Sabzevari O, Amini M, Geramifar P, Hajiramezanali M, Beiki D. Synthesis, biological evaluation and preclinical study of a novel 99mTc-peptide: A targeting probe of amyloid-β plaques as a possible diagnostic agent for Alzheimer's disease. Bioorg Chem 2020; 99:103857. [PMID: 32330736 DOI: 10.1016/j.bioorg.2020.103857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023]
Abstract
With respect to the main role of amyloid-β (Aβ) plaques as one of the pathological hallmarks in the brain of Alzheimer's patients, the development of new imaging probes for targeted detection of Aβ plaques has attracted considerable interests. In this study, a novel cyclopentadienyl tricarbonyl Technetium-99 m (99mTc) agent with peptide scaffold, 99mTc-Cp-GABA-D-(FPLIAIMA)-NH2, for binding to the Aβ plaques was designed and successfully synthesized using the Fmoc solid-phase peptide synthesis method. This radiopeptide revealed a good affinity for Aβ42 aggregations (Kd = 20 µM) in binding affinity study and this result was confirmed by binding to Aβ plaques in brain sections of human Alzheimer's disease (AD) and rat models using in vitro autoradiography, fluorescent staining, and planar scintigraphy. Biodistribution studies of radiopeptide in AD and normal rats demonstrated a moderate initial brain uptake about 0.38 and 0.35% (ID/g) 2 min post-injection, respectively. Whereas, AD rats showed a notable retention time in the brain (0.23% ID/g at 30 min) in comparison with fast clearance in normal rat brains. Normal rats following treatment with cyclosporine A as a p-glycoprotein inhibitor showed a significant increase in the radiopeptide brain accumulation compared to non-treated ones. There was a good correlation between data gathered from single-photon emission computed tomography/computed tomography (SPECT/CT) imaging and biodistribution studies. Therefore, these findings showed that this novel radiopeptide could be a potential SPECT imaging agent for early detection of Aβ plaques in the brain of patients with AD.
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Affiliation(s)
- Safura Jokar
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Behnammanesh
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Erfani
- Radiation Application Research School, Nuclear Science and Technology Research Institute (NSTRI), Tehran, Iran.
| | - Mohammad Sharifzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran; Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Gholami
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran; Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - Omid Sabzevari
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran; Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Parham Geramifar
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maliheh Hajiramezanali
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Beiki
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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10
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Armiento V, Spanopoulou A, Kapurniotu A. Peptide-Based Molecular Strategies To Interfere with Protein Misfolding, Aggregation, and Cell Degeneration. Angew Chem Int Ed Engl 2020; 59:3372-3384. [PMID: 31529602 PMCID: PMC7064928 DOI: 10.1002/anie.201906908] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Indexed: 12/31/2022]
Abstract
Protein misfolding into amyloid fibrils is linked to more than 40 as yet incurable cell- and neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes. So far, however, only one of the numerous anti-amyloid molecules has reached patients. This Minireview gives an overview of molecular strategies and peptide chemistry "tools" to design, develop, and discover peptide-based molecules as anti-amyloid drug candidates. We focus on two major inhibitor rational design strategies: 1) the oldest and most common strategy, based on molecular recognition elements of amyloid self-assembly, and 2) a more recent approach, based on cross-amyloid interactions. We discuss why peptide-based amyloid inhibitors, in particular their advanced generations, can be promising leads or candidates for anti-amyloid drugs as well as valuable tools for deciphering amyloid-mediated cell damage and its link to disease pathogenesis.
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Affiliation(s)
- Valentina Armiento
- Division of Peptide BiochemistryTUM School of Life SciencesTechnische Universität MünchenEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Anna Spanopoulou
- Division of Peptide BiochemistryTUM School of Life SciencesTechnische Universität MünchenEmil-Erlenmeyer-Forum 585354FreisingGermany
- Current address: Coriolis Pharma Research GmbHFraunhoferstrasse 18B82152PlaneggGermany
| | - Aphrodite Kapurniotu
- Division of Peptide BiochemistryTUM School of Life SciencesTechnische Universität MünchenEmil-Erlenmeyer-Forum 585354FreisingGermany
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11
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Aggregation Mechanism of Alzheimer's Amyloid β-Peptide Mediated by α-Strand/α-Sheet Structure. Int J Mol Sci 2020; 21:ijms21031094. [PMID: 32046006 PMCID: PMC7038184 DOI: 10.3390/ijms21031094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases and a widespread form of dementia. Aggregated forms of the amyloid β-peptide (Aβ) are identified as a toxic species responsible for neuronal damage in AD. Extensive research has been conducted to reveal the aggregation mechanism of Aβ. However, the structure of pathological aggregates and the mechanism of aggregation are not well understood. Recently, experimental studies have confirmed that the α-sheet structure in Aβ drives aggregation and toxicity in AD. However, how the α-sheet structure is formed in Aβ and how it contributes to Aβ aggregation remains elusive. In the present study, molecular dynamics simulations suggest that Aβ adopts the α-strand conformation by peptide-plane flipping. Multiple α-strands interact through hydrogen bonding to form α-sheets. This structure acts as a nucleus that initiates and promotes aggregation and fibrillation of Aβ. Our findings are supported by previous experimental as well as theoretical studies. This study provides valuable structural insights for the design of anti-AD drugs exploiting the α-strand/α-sheet structure.
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12
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Armiento V, Spanopoulou A, Kapurniotu A. Peptid‐basierte molekulare Strategien zum Einsatz bei Proteinfehlfaltung, Proteinaggregation und Zelldegeneration. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Valentina Armiento
- Fachgebiet PeptidbiochemieTUM School of Life SciencesTechnische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
| | - Anna Spanopoulou
- Fachgebiet PeptidbiochemieTUM School of Life SciencesTechnische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
- Aktuelle Adresse: Coriolis Pharma Research GmbH Fraunhoferstraße 18B 82152 Planegg Deutschland
| | - Aphrodite Kapurniotu
- Fachgebiet PeptidbiochemieTUM School of Life SciencesTechnische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
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13
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Milner-White EJ. Protein three-dimensional structures at the origin of life. Interface Focus 2019; 9:20190057. [PMID: 31641431 DOI: 10.1098/rsfs.2019.0057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 12/22/2022] Open
Abstract
Proteins are relatively easy to synthesize, compared to nucleic acids and it is likely that there existed a stage prior to the RNA world which can be called the protein world. Some of the three-dimensional (3D) peptide structures in these proteins have, we argue, been conserved since then and may constitute the oldest biological relics in existence. We focus on 3D peptide motifs consisting of up to eight or so amino acid residues. The best known of these is the 'nest', a three- to seven-residue protein motif, which has the function of binding anionic atoms or groups of atoms. Ten per cent of amino acids in typical proteins belong to a nest, so it is a common motif. A five-residue nest is found as part of the well-known P-loop that is a recurring feature of many ATP or GTP-binding proteins and it has the function of binding the phosphate part of these ligands. A synthetic hexapeptide, ser-gly-ala-gly-lys-thr, designed to resemble the P-loop, has been shown to bind inorganic phosphate. Another type of nest binds iron-sulfur centres. A range of other simple motifs occur with various intriguing 3D structures; others bind cations or form channels that transport potassium ions; other peptides form catalytically active haem-like or sheet structures with certain transition metals. Amyloid peptides are also discussed. It now seems that the earliest polypeptides were far from being functionless stretches, and had many of the properties, both binding and catalytic, that might be expected to encourage and stabilize simple life forms in the hydrothermal vents of ocean depths.
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Affiliation(s)
- E James Milner-White
- Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G128QQ, UK
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14
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Opare SKA, Rauk A. Pseudopeptide Designed to Inhibit Oligomerization and Redox Chemistry in Alzheimer’s Disease. J Phys Chem B 2019; 123:5206-5215. [DOI: 10.1021/acs.jpcb.9b01665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stanley K. A. Opare
- Department of Chemistry, The University of Calgary, Calgary, Alberta Canada, T2N 1N4
| | - Arvi Rauk
- Department of Chemistry, The University of Calgary, Calgary, Alberta Canada, T2N 1N4
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15
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Computational insights into the role of α-strand/sheet in aggregation of α-synuclein. Sci Rep 2019; 9:59. [PMID: 30635607 PMCID: PMC6329781 DOI: 10.1038/s41598-018-37276-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023] Open
Abstract
The α-synuclein is a major component of amyloid fibrils found in Lewy bodies, the characteristic intracellular proteinaceous deposits which are pathological hallmarks of neurodegenerative diseases such as Parkinson’s disease (PD) and dementia. It is an intrinsically disordered protein that may undergo dramatic structural changes to form amyloid fibrils. Aggregation process from α-synuclein monomers to amyloid fibrils through oligomeric intermediates is considered as the disease-causative toxic mechanism. However, mechanism underlying aggregation is not well-known despite several attempts. To characterize the mechanism, we have explored the effects of pH and temperature on the structural properties of wild-type and mutant α-synuclein using molecular dynamics (MD) simulation technique. MD studies suggested that amyloid fibrils can grow by monomer. Conformational transformation of the natively unfolded protein into partially folded intermediate could be accountable for aggregation and fibrillation. An intermediate α-strand was observed in the hydrophobic non-amyloid-β component (NAC) region of α-synuclein that could proceed to α-sheet and initiate early assembly events. Water network around the intermediate was analyzed to determine its influence on the α-strand structure. Findings of this study provide novel insights into possible mechanism of α-synuclein aggregation and promising neuroprotective strategy that could aid alleviate PD and its symptoms.
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16
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Mehrazma B, Opare S, Petoyan A, Rauk A. d-Amino Acid Pseudopeptides as Potential Amyloid-Beta Aggregation Inhibitors. Molecules 2018; 23:E2387. [PMID: 30231520 PMCID: PMC6225248 DOI: 10.3390/molecules23092387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/06/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022] Open
Abstract
A causative factor for neurotoxicity associated with Alzheimer's disease is the aggregation of the amyloid-β (Aβ) peptide into soluble oligomers. Two all d-amino acid pseudo-peptides, SGB1 and SGD1, were designed to stop the aggregation. Molecular dynamics (MD) simulations have been carried out to study the interaction of the pseudo-peptides with both Aβ13⁻23 (the core recognition site of Aβ) and full-length Aβ1⁻42. Umbrella sampling MD calculations have been used to estimate the free energy of binding, ∆G, of these peptides to Aβ13⁻23. The highest ∆Gbinding is found for SGB1. Each of the pseudo-peptides was also docked to Aβ1⁻42 and subjected up to seven microseconds of all atom molecular dynamics simulations. The resulting structures lend insight into how the dynamics of Aβ1⁻42 are altered by complexation with the pseudo-peptides and confirmed that SGB1 may be a better candidate for developing into a drug to prevent Alzheimer's disease.
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Affiliation(s)
- Banafsheh Mehrazma
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
| | - Stanley Opare
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
| | - Anahit Petoyan
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
| | - Arvi Rauk
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
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17
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Ribarič S. Peptides as Potential Therapeutics for Alzheimer's Disease. Molecules 2018; 23:E283. [PMID: 29385735 PMCID: PMC6017258 DOI: 10.3390/molecules23020283] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/22/2022] Open
Abstract
Intracellular synthesis, folding, trafficking and degradation of proteins are controlled and integrated by proteostasis. The frequency of protein misfolding disorders in the human population, e.g., in Alzheimer's disease (AD), is increasing due to the aging population. AD treatment options are limited to symptomatic interventions that at best slow-down disease progression. The key biochemical change in AD is the excessive accumulation of per-se non-toxic and soluble amyloid peptides (Aβ(1-37/44), in the intracellular and extracellular space, that alters proteostasis and triggers Aβ modification (e.g., by reactive oxygen species (ROS)) into toxic intermediate, misfolded soluble Aβ peptides, Aβ dimers and Aβ oligomers. The toxic intermediate Aβ products aggregate into progressively less toxic and less soluble protofibrils, fibrils and senile plaques. This review focuses on peptides that inhibit toxic Aβ oligomerization, Aβ aggregation into fibrils, or stabilize Aβ peptides in non-toxic oligomers, and discusses their potential for AD treatment.
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Affiliation(s)
- Samo Ribarič
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, SI-1000 Ljubljana, Slovenia.
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18
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Pseudo-peptide amyloid-β blocking inhibitors: molecular dynamics and single molecule force spectroscopy study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1707-1718. [PMID: 28844735 DOI: 10.1016/j.bbapap.2017.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
Abstract
By combining MD simulations and AFS experimental technique, we demonstrated a powerful approach for rational design and single molecule testing of novel inhibitor molecules which can block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. We designed and tested novel pseudo-peptide amyloid-β (Aβ) inhibitors that bind to the Aβ peptide and effectively prevent amyloid-amyloid binding. First, molecular dynamics (MD) simulations have provided information on the structures and binding characteristics of the designed pseudo-peptides targeting amyloid fragment Aβ (13-23). The binding affinities between the inhibitor and Aβ as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations. Atomic Force Spectroscopy (AFS) was used to experimentally test several proposed inhibitors in their ability to block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. The experimental AFS data are in a good agreement with theoretical MD calculations and demonstrate that three proposed pseudo-peptides bind to amyloid fragment with different affinities and all effectively prevent Aβ-Aβ binding in similar way. We propose that the designed pseudo-peptides can be used as potential drug candidates to prevent Aβ toxicity in Alzheimer's disease.
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19
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Goyal D, Shuaib S, Mann S, Goyal B. Rationally Designed Peptides and Peptidomimetics as Inhibitors of Amyloid-β (Aβ) Aggregation: Potential Therapeutics of Alzheimer's Disease. ACS COMBINATORIAL SCIENCE 2017; 19:55-80. [PMID: 28045249 DOI: 10.1021/acscombsci.6b00116] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease with no clinically accepted treatment to cure or halt its progression. The worldwide effort to develop peptide-based inhibitors of amyloid-β (Aβ) aggregation can be considered an unplanned combinatorial experiment. An understanding of what has been done and achieved may advance our understanding of AD pathology and the discovery of effective therapeutic agents. We review here the history of such peptide-based inhibitors, including those based on the Aβ sequence and those not derived from that sequence, containing both natural and unnatural amino acid building blocks. Peptide-based aggregation inhibitors hold significant promise for future AD therapy owing to their high selectivity, effectiveness, low toxicity, good tolerance, low accumulation in tissues, high chemical and biological diversity, possibility of rational design, and highly developed methods for analyzing their mode of action, proteolytic stability (modified peptides), and blood-brain barrier (BBB) permeability.
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Affiliation(s)
- Deepti Goyal
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Suniba Shuaib
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Sukhmani Mann
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Bhupesh Goyal
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
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20
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Bansal S, Maurya IK, Yadav N, Thota CK, Kumar V, Tikoo K, Chauhan VS, Jain R. C-Terminal Fragment, Aβ32-37, Analogues Protect Against Aβ Aggregation-Induced Toxicity. ACS Chem Neurosci 2016; 7:615-23. [PMID: 26835536 DOI: 10.1021/acschemneuro.6b00006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Amyloid-β aggregation is a major etiological phenomenon in Alzheimer's disease. Herein, we report peptide-based inhibitors that diminish the amyloid load by obviating Aβ aggregation. Taking the hexapeptide fragment, Aβ32-37, as lead, more than 40 new peptides were synthesized. Upon evaluation of the newly synthesized hexapeptides as inhibitors of Aβ toxicity by the MTT-based cell viability assay, a number of peptides exhibited significant Aβ aggregation inhibitory activity at sub-micromolar concentration range. A hexapeptide (1) showed complete mitigation of Aβ toxicity in the cell culture assay at 2 μM. In the ThT fluorescence assay, upon incubation of Aβ with this peptide, we observed no increase in the ThT fluorescence relative to control. The secondary structure estimation by circular dichroism spectroscopy and morphological examination by transmission electron microscopy further confirmed the results.
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Affiliation(s)
- Sunil Bansal
- Department
of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar 160 062, Punjab India
| | - Indresh Kumar Maurya
- Department
of Microbial Biotechnology, Panjab University, Sector 14, Chandigarh 160 014, India
| | - Nitin Yadav
- International Center for Genetic Engineering and Biotechnology, Aruna Asif Ali Marg, New
Delhi 110 067, India
| | - Chaitanya Kumar Thota
- International Center for Genetic Engineering and Biotechnology, Aruna Asif Ali Marg, New
Delhi 110 067, India
| | - Vinod Kumar
- Department
of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar 160 062, Punjab India
| | - Kulbhushan Tikoo
- Department
of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar 160 062, Punjab India
| | - Virander Singh Chauhan
- International Center for Genetic Engineering and Biotechnology, Aruna Asif Ali Marg, New
Delhi 110 067, India
| | - Rahul Jain
- Department
of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar 160 062, Punjab India
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21
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Giralt E. Josef Rudinger Memorial Lecture: Use of peptides to modulate protein-protein interactions. J Pept Sci 2015; 21:447-53. [PMID: 25847600 DOI: 10.1002/psc.2768] [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: 12/23/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 11/06/2022]
Abstract
Peptides are destined to play a major role as therapeutic agents. My laboratory is contributing to speeding up this process. On the one hand, we devote efforts to studying the molecular details and dynamics of the events that occur during molecular recognition at protein surfaces. We succeeded to design and synthesize peptides able to modulate these recognition events either permanently or in response to light. On the other hand, we are discovering and designing peptides able to cross biological barriers. Our aim is to use these peptides as shuttles for targeting therapeutic agents to organs, tissues, or cells, with a special emphasis on drug delivery to the brain.
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Affiliation(s)
- Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028, Barcelona, Spain.,Department of Organic Chemistry, University of Barcelona, Marti Franqués 1, 08028, Barcelona, Spain
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22
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Prades R, Oller-Salvia B, Schwarzmaier SM, Selva J, Moros M, Balbi M, Grazú V, de La Fuente JM, Egea G, Plesnila N, Teixidó M, Giralt E. Applying the Retro-Enantio Approach To Obtain a Peptide Capable of Overcoming the Blood-Brain Barrier. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411408] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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23
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Prades R, Oller-Salvia B, Schwarzmaier SM, Selva J, Moros M, Balbi M, Grazú V, de La Fuente JM, Egea G, Plesnila N, Teixidó M, Giralt E. Applying the Retro-Enantio Approach To Obtain a Peptide Capable of Overcoming the Blood-Brain Barrier. Angew Chem Int Ed Engl 2015; 54:3967-72. [DOI: 10.1002/anie.201411408] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 02/05/2023]
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24
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Antimisiaris S, Mourtas S, Markoutsa E, Skouras A, Papadia K. Nanoparticles for Diagnosis and/or Treatment of Alzheimer's Disease. Adv Healthc Mater 2014. [DOI: 10.1002/9781118774205.ch4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Hayward S, Leader DP, Al-Shubailly F, Milner-White EJ. Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides. Proteins 2013; 82:230-9. [DOI: 10.1002/prot.24357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Steven Hayward
- School of Computing Sciences; University of East Anglia; Norwich NR4 7TJ United Kingdom
| | - David P. Leader
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - Fawzia Al-Shubailly
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - E. James Milner-White
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
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26
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Taraban MB, Feng Y, Hammouda B, Hyland LL, Yu YB. Chirality-Mediated Mechanical and Structural Properties of Oligopeptide Hydrogels. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2012; 24:2299-2310. [PMID: 23641124 PMCID: PMC3639503 DOI: 10.1021/cm300422q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The origin and the effects of homochirality in the biological world continuously stimulate numerous hypotheses and much debate. This work attempts to look at the biohomochirality issue from a different angle-the mechanical properties of the bulk biomaterial and their relation to nanoscale structures. Using a pair of oppositely charged peptides that co-assemble into hydrogels, we systematically investigated the effect of chirality on the mechanical properties of these hydrogels through different combinations of syndiotactic and isotactic peptides. It was found that homochirality confers mechanical advantage, resulting in higher elastic modulus and strain yield value. Yet, heterochirality confer kinetic advantage, resulting in faster gelation. Structurally, both homochiral and heterochiral hydrogels are made of fibers interconnected by lappet-like webs, but the homochiral peptide fibers are thicker and denser. The result highlights the possible role of biohomochirality in the evolution and/or natural selection of biomaterials.
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Affiliation(s)
- Marc B Taraban
- Fischell Department of Bioengineering, University of Maryland, College Park, USA
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27
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Funke SA, Willbold D. Peptides for therapy and diagnosis of Alzheimer's disease. Curr Pharm Des 2012; 18:755-67. [PMID: 22236121 PMCID: PMC3426787 DOI: 10.2174/138161212799277752] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 12/09/2011] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with devastating effects. The greatest risk factor to develop AD is age. Today, only symptomatic therapies are available. Additionally, AD can be diagnosed with certainty only post mortem, whereas the diagnosis "probable AD" can be established earliest when severe clinical symptoms appear. Specific neuropathological changes like neurofibrillary tangles and amyloid plaques define AD. Amyloid plaques are mainly composed of the amyloid-βpeptide (Aβ). Several lines of evidence suggest that the progressive concentration and subsequent aggregation and accumulation of Aβ play a fundamental role in the disease progress. Therefore, substances which bind to Aβ and influence aggregation thereof are of great interest. An enormous number of organic substances for therapeutic purposes are described. This review focuses on peptides developed for diagnosis and therapy of AD and discusses the pre- and disadvantages of peptide drugs.
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Affiliation(s)
| | - Dieter Willbold
- Forschungszentrum Jülich, ICS-6, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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28
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Milner-White EJ, Russell MJ. Functional capabilities of the earliest peptides and the emergence of life. Genes (Basel) 2011; 2:671-88. [PMID: 24710286 PMCID: PMC3927598 DOI: 10.3390/genes2040671] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/14/2011] [Accepted: 09/14/2011] [Indexed: 02/01/2023] Open
Abstract
Considering how biological macromolecules first evolved, probably within a marine environment, it seems likely the very earliest peptides were not encoded by nucleic acids, or at least not via the genetic code as we know it. An objective of the present work is to demonstrate that sequence-independent peptides, or peptides with variable and unreliable lengths and sequences, have the potential to perform a variety of chemically useful functions such as anion and cation binding and membrane and channel formation as well as simple types of catalysis. These functions tend to be performed with the assistance of the main chain CONH atoms rather than the more variable or limited side chain atoms of the peptides presumed to exist then.
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Affiliation(s)
- E James Milner-White
- College of Medical, Veterinary and Life Sciences, Glasgow University, Glasgow G128QQ, UK.
| | - Michael J Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA.
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29
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Abstract
The development of peptides with therapeutic activities can be based on naturally occurring peptides or alternatively on de novo design. The discovery of natural peptides is often a matter of serendipity. In part, this is because natural peptides are typically proteolytically cleaved out from precursor proteins, a feature that averts the direct benefits of the genomic revolution. The first part of this review describes attempts to create a more systematic identification of natural peptides relying on a two step process. In the initial step, an in silico peptidome is predicted through the use of machine learning. Then, various computational biology tools are tailored to focus on peptides predicted to have the desired biological activity; for example, activating a GPCR or modulating the cellular arm of the immune system. The second part of the review is devoted to de novo peptide design and focuses on arguably the simplest scenario in which the designed peptide corresponds to a contiguous protein subsequence. Amongst these peptides, those corresponding to helical segments are prominent, mainly due to their relative ability to fold independently. Inspired by the clinical success of viral entry inhibitors, which are peptides corresponding to helical segments in viral envelope proteins, a computational tool for the identification of intramolecular helix-helix interactions was developed. Using this approach, peptides having anti-cancer, anti-angiogenic, and anti-inflammatory activities have been recently rationally designed and biologically characterized.
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Affiliation(s)
- Yossef Kliger
- Compugen LTD, 72 Pinchas Rosen, Tel Aviv 69512, Israel.
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30
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Dyachenko A, Goldflam M, Vilaseca M, Giralt E. Molecular recognition at protein surface in solution and gas phase: Five VEGF peptidic ligands show inverse affinity when studied by NMR and CID-MS. Biopolymers 2011; 94:689-700. [PMID: 20564038 DOI: 10.1002/bip.21462] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions comprise of collection of molecular recognition events that take place at protein surfaces. A better understanding of the mechanism behind these interactions would provide deeper insight into the nature of many diseases, caused by the malfunction of protein networks, and contribute to design of molecules for efficient modulating of these interactions. One major factor in molecular recognition mechanism is interaction of reacting species with aqueous media. Thus, comparative study of noncovalent complex behavior in solution and gas phase can provide valuable information about the role of the solvent. Here examined interactions of vascular endothelial growth factor (VEGF) protein with five peptidic ligands of the same molecular weight but with different affinities. Interactions of VEGF with ligands in solution were studied by ITC and NMR, and K(D)s were determined. Gas phase stability was addressed using CID-MS approach. The energy transfer model was taken and adapted for the calculation of binding energy. Peptides were ranked on the basis of both solution and gas phase affinity to VEGF. The results indicate that the ranking of peptides in terms of affinity in solution is reversed compared with the gas phase ranking. This observation opens up a vast field for the future study of the system, and the determination and characterization of factors, responsible for the change of stability of noncovalent protein-ligand complexes upon complete or partial removal of the solvent.
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Affiliation(s)
- Andrey Dyachenko
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
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31
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Designed Short Peptides that Form Amyloid-Like Fibrils in Coassembly with Amyloid β-Peptide (Aβ) Decrease the Toxicity of Aβ to Neuronal PC12 Cells. Chembiochem 2010; 11:1525-30. [DOI: 10.1002/cbic.201000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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