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Sharma H, Yang H, Sharma N, An SSA. Trachyspermum ammi Bioactives Promote Neuroprotection by Inhibiting Acetylcholinesterase, Aβ-Oligomerization/Fibrilization, and Mitigating Oxidative Stress In Vitro. Antioxidants (Basel) 2023; 13:9. [PMID: 38275629 PMCID: PMC10812417 DOI: 10.3390/antiox13010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Neurodegenerative diseases (NDs) are a large category of progressive neurological disorders with diverse clinical and pathological characteristics. Among the NDs, Alzheimer's disease (AD) is the most widespread disease, which affects more than 400 million people globally. Oxidative stress is evident in the pathophysiology of nearly all NDs by affecting several pathways in neurodegeneration. No single drug can manage multi-faceted diseases like NDs. Therefore, an alternative therapeutic strategy is required, which can affect several pathophysiological pathways at a time. To achieve this aim, hexane and ethyl acetate extract from Trachyspermum ammi (Carom) were prepared, and GC/MS identified the bioactive compounds. For the cell-based assays, oxidative stress was induced in SH-SY5Y neuroblastoma cells using hydrogen peroxide to evaluate the neuroprotective potential of the Carom extracts/bioactives. The extracts/bioactives provided neuroprotection in the cells by modulating multiple pathways involved in neurodegeneration, such as alleviating oxidative stress and mitochondrial membrane potential. They were potent inhibitors of acetylcholine esterase enzymes and displayed competitive/mixed-type inhibition. Additionally, anti-Aβ1-42 fibrilization/oligomerization and anti-glycation activities were also analyzed. The multi-faceted neuroprotection shown via Carom/Carvacrol makes it a prospective contender in drug development for NDs.
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Affiliation(s)
| | | | - Niti Sharma
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
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Kuila S, Dey S, Singh P, Shrivastava A, Nanda J. Phenylalanine-based fibrillar systems. Chem Commun (Camb) 2023; 59:14509-14523. [PMID: 37987167 DOI: 10.1039/d3cc04138g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.
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Affiliation(s)
- Soumen Kuila
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Sukantha Dey
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Pijush Singh
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Akash Shrivastava
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
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Emamyari S, Mirzaei M, Mohammadinejad S, Fazli D, Fazli H. Impact of flexibility on the aggregation of polymeric macromolecules. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:66. [PMID: 37522950 DOI: 10.1140/epje/s10189-023-00324-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
Dependence of the dimerization probability and the aggregation behavior of polymeric macromolecules on their flexibility is studied using Langevin dynamics simulations. It is found that the dimerization probability is a non-monotonic function of the polymers persistence length. For a given value of inter-polymer attraction strength, semiflexible polymers have lower dimerization probability relative to flexible and rigid polymers of the same length. The threshold temperature of the formation of aggregates in a many-polymer system and its dependence on the polymers persistence length is also investigated. The simulation results of two- and many-polymer systems are in good agreement and show how the amount of flexibility affects the dimerization and the aggregation behaviors of polymeric macromolecules.
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Affiliation(s)
- Soheila Emamyari
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Masoud Mirzaei
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Sarah Mohammadinejad
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Davood Fazli
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Hossein Fazli
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran.
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran.
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4
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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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5
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Mohammed AA, Barale SS, Kamble SA, Paymal SB, Sonawane KD. Molecular insights into the inhibition of early stage of Aβ peptide aggregation and destabilization of Alzheimer's Aβ protofibril by dipeptide D-Trp-Aib: A molecular modelling approach. Int J Biol Macromol 2023; 242:124880. [PMID: 37217059 DOI: 10.1016/j.ijbiomac.2023.124880] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023]
Abstract
Amyloid beta (Aβ) peptide aggregates rapidly into the soluble oligomers, protofibrils and fibrils to form senile plaques, a neurotoxic component and pathological hallmark of Alzheimer's disease (AD). Experimentally, it has been demonstrated the inhibition of an early stages of Aβ aggregation by a dipeptide D-Trp-Aib inhibitor, but its molecular mechanism is still unclear. Hence, in the present study, we used molecular docking and molecular dynamics (MD) simulations to explore the molecular mechanism of inhibition of an early oligomerization and destabilization of preformed Aβ protofibril by D-Trp-Aib. Molecular docking study showed that the D-Trp-Aib binds at the aromatic (Phe19, Phe20) region of Aβ monomer, Aβ fibril and hydrophobic core of Aβ protofibril. MD simulations revealed the binding of D-Trp-Aib at the aggregation prone region (Lys16-Glu22) resulted in the stabilization of Aβ monomer by π-π stacking interactions between Tyr10 and indol ring of D-Trp-Aib, which decreases the β-sheet content and increases the α-helices. The interaction between Lys28 of Aβ monomer to D-Trp-Aib could be responsible to block the initial nucleation and may impede the fibril growth and elongation. The loss of hydrophobic contacts between two β-sheets of Aβ protofibril upon binding of D-Trp-Aib at the hydrophobic cavity resulted in the partial opening of β-sheets. This also disrupts a salt bridge (Asp23-Lys28) leading to the destabilization of Aβ protofibril. Binding energy calculations revealed that van der Waals and electrostatic interactions maximally favours the binding of D-Trp-Aib to Aβ monomer and Aβ protofibril respectively. The residues Tyr10, Phe19, Phe20, Ala21, Glu22, Lys28 of Aβ monomer, whereas Leu17, Val18, Phe19, Val40, Ala42 of protofibril contributing for the interactions with D-Trp-Aib. Thus, the present study provides structural insights into the inhibition of an early oligomerization of Aβ peptides and destabilization of Aβ protofibril, which could be useful to design novel inhibitors for the treatment of AD.
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Affiliation(s)
- Ali Abdulmawjood Mohammed
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra, (M.S.), India
| | - Sagar S Barale
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (MS), India
| | - Subodh Ashok Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra, (M.S.), India
| | - Sneha B Paymal
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (MS), India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra, (M.S.), India; Department of Chemistry, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India.
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Sharma H, Sharma N, An SSA. Black Pepper ( Piper nigrum) Alleviates Oxidative Stress, Exerts Potential Anti-Glycation and Anti-AChE Activity: A Multitargeting Neuroprotective Agent against Neurodegenerative Diseases. Antioxidants (Basel) 2023; 12:antiox12051089. [PMID: 37237954 DOI: 10.3390/antiox12051089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Neurodegenerative diseases (NDs) are a family of disorders that cause progressive structural and functional degeneration of neurons. Among all the organs in the body, the brain is the one that is the most affected by the production and accumulation of ROS. Various studies have shown that an increase in oxidative stress is a common pathophysiology for almost all NDs, which further affects various other pathways. The available drugs lack the wide spectrum necessary to confront these complexities altogether. Hence, a safe therapeutic approach to target multiple pathways is highly desirable. In the present study, the hexane and ethyl acetate extracts of Piper nigrum (black pepper), an important spice, were evaluated for their neuroprotective potential in hydrogen peroxide-induced oxidative stress in human neuroblastoma cells (SH-SY5Y). The extracts were also subjected to GC/MS to identify the important bioactives present. The extracts exhibited neuroprotection by significantly decreasing the oxidative stress and restoring the mitochondrial membrane potential in the cells. Additionally, the extracts displayed potent anti-glycation and significant anti-Aβ fibrilization activities. The extracts were competitive inhibitors of AChE. The multitarget neuroprotective mechanism displayed by Piper nigrum indicates it as a potential candidate in the treatment of NDs.
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Affiliation(s)
- Himadri Sharma
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
| | - Niti Sharma
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
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7
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Sharma H, Kim DY, Shim KH, Sharma N, An SSA. Multi-Targeting Neuroprotective Effects of Syzygium aromaticum Bud Extracts and Their Key Phytocompounds against Neurodegenerative Diseases. Int J Mol Sci 2023; 24:8148. [PMID: 37175851 PMCID: PMC10178913 DOI: 10.3390/ijms24098148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that causes a gradual loss of normal motor and cognitive function. The complex AD pathophysiology involves various factors such as oxidative stress, neuroinflammation, amyloid-beta (Aβ) aggregation, disturbed neurotransmission, and apoptosis. The available drugs suffer from a range of side effects and are not able to cover different aspects of the disease. Therefore, finding a safer therapeutic approach that can affect multiple targets at a time is highly desirable. In the present study, the underlying neuroprotective mechanism of an important culinary spice, Syzygium aromaticum (Clove) extract, and major bioactive compounds were studied in hydrogen peroxide-induced oxidative stress in human neuroblastoma SH-SY5Y cell lines as a model. The extracts were subjected to GC-MS to identify important bioactive components. The extracts and key bio-actives reduced reactive oxygen species (ROS), restored mitochondrial membrane potential (MMP), and provided neuroprotection from H2O2-induced oxidative stress in cell-based assays due to the antioxidant action. They also reduced lipid peroxidation significantly and restored GSH content. Clove extracts have also displayed anti-acetylcholinesterase (AChE) activity, anti-glycation potential, and Aβ aggregation/fibrilization inhibition. The multitarget neuroprotective approach displayed by Clove makes it a potential candidate for AD drug development.
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Affiliation(s)
| | | | | | - Niti Sharma
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 461-701, Gyeonggi-do, Republic of Korea
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8
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Mitra A, Sarkar N. Elucidating the inhibitory effects of rationally designed novel hexapeptide against hen egg white lysozyme fibrillation at acidic and physiological pH. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140899. [PMID: 36693516 DOI: 10.1016/j.bbapap.2023.140899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/23/2023]
Abstract
Inhibition of highly ordered cross-β-sheet-rich aggregates of misfolded amyloid proteins using rationally designed sequence-based short peptides is a promising therapeutic strategy for the treatment of neurodegenerative diseases. Here, we have explored the anti-amyloidogenic potency of a rationally designed hexapeptide (Tyr-Pro-Gln-Ile-Pro-Asn) on in vitro hen egg white lysozyme (HEWL) amyloid fibril formation at acidic pH and physiological pH using computational docking as well as various biophysical techniques such as fluorescence spectroscopy, UV-vis spectroscopy, FTIR spectroscopy, confocal microscopy and TEM. The peptide was designed based on the aggregation-prone region (APR) of HEWL and thus referred to as SqP1 (Sequence-based Peptide 1). SqP1 showed over 70% inhibition of HEWL amyloid formation at pH 2.2 and approximately 50% inhibition at pH 7.5. We propose that SqP1 binds to the APR of HEWL and interacts strongly with the Trp62/Trp63, ultimately stabilizing monomeric HEWL at both the pH conditions and preventing conformation changes in the structure of HEWL, leading to the formation of amyloidogenic fibrillar structures. A sequence-based peptide inhibitor of HEWL amyloid formation was not reported previously, making this a critical study that will further emphasize the importance of short synthetic peptides as amyloid inhibitors.
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Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela 769008, Odisha, India.
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9
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Zimbone S, Giuffrida ML, Sabatino G, Di Natale G, Tosto R, Consoli GML, Milardi D, Pappalardo G, Sciacca MFM. Aβ 8-20 Fragment as an Anti-Fibrillogenic and Neuroprotective Agent: Advancing toward Efficient Alzheimer's Disease Treatment. ACS Chem Neurosci 2023; 14:1126-1136. [PMID: 36857606 PMCID: PMC10020970 DOI: 10.1021/acschemneuro.2c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia, characterized by a spectrum of symptoms associated with memory loss and cognitive decline with deleterious consequences in everyday life. The lack of specific drugs for the treatment and/or prevention of this pathology makes AD an ever-increasing economic and social emergency. Oligomeric species of amyloid-beta (Aβ) are recognized as the primary cause responsible for synaptic dysfunction and neuronal degeneration, playing a crucial role in the onset of the pathology. Several studies have been focusing on the use of small molecules and peptides targeting oligomeric species to prevent Aβ aggregation and toxicity. Among them, peptide fragments derived from the primary sequence of Aβ have also been used to exploit any eventual recognition abilities toward the full-length Aβ parent peptide. Here, we test the Aβ8-20 fragment which contains the self-recognizing Lys-Leu-Val-Phe-Phe sequence and lacks Arg 5 and Asp 7 and the main part of the C-terminus, key points involved in the aggregation pathway and stabilization of the fibrillary structure of Aβ. In particular, by combining chemical and biological techniques, we show that Aβ8-20 does not undergo random coil to β sheet conformational transition, does not form amyloid fibrils by itself, and is not toxic for neuronal cells. Moreover, we demonstrate that Aβ8-20 mainly interacts with the 4-11 region of Aβ1-42 and inhibits the formation of toxic oligomeric species and Aβ fibrils. Finally, our data show that Aβ8-20 protects neuron-like cells from Aβ1-42 oligomer toxicity. We propose Aβ8-20 as a promising drug candidate for the treatment of AD.
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Affiliation(s)
- Stefania Zimbone
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Maria Laura Giuffrida
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Giuseppina Sabatino
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Giuseppe Di Natale
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Rita Tosto
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Grazia M L Consoli
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Danilo Milardi
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Giuseppe Pappalardo
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
| | - Michele F M Sciacca
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Via Paolo Gaifami, 18, Catania 95126, Italy
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Hakeem MJ, Khan JM, Malik A, Husain FM, Alresaini SM, Ahmad A, Alam P. Molecular insight into the modulation of ovalbumin fibrillation by allura red dye at acidic pH. Int J Biol Macromol 2023; 230:123254. [PMID: 36641020 DOI: 10.1016/j.ijbiomac.2023.123254] [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: 11/05/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
The synthetic food additive dye induces amyloid fibrillation has many implications in the laboratory and industries. The effect of Allura red (AR), on the fibrillation of ovalbumin (Ova) at pH 2.0 was investigated. The influence of salt and pH was also seen on AR-induced Ova aggregation. We have used several spectroscopic and microscopy techniques to characterize the changes. The turbidity data suggest that concentrations above 0.05 mM of AR induce aggregation, and the size of aggregates increased in response to AR concentration. The kinetics data showed that the AR induces Ova aggregation quickly without lag time. The aggregates induced by AR have amyloid-like aggregates confirmed by far-UV CD and TEM. NaCl has very marginal effects in AR-induced aggregation. The turbidity results clearly state that Ova is not forming aggregates with pH above 4.0 due to electrostatic repulsion. However, Ova forms bigger aggregates in the presence of 0.5 mM AR at a pH below 4.0. These spectroscopic data suggest that the amyloid fibrillation that occurs in Ova is due to electrostatic and hydrophobic interaction. The amyloid fibrillation induced by AR dye in protein should be taken seriously for food safety purposes.
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Affiliation(s)
- Mohammed J Hakeem
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, 2460, Riyadh, 11451, Saudi Arabia
| | - Javed Masood Khan
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, 2460, Riyadh, 11451, Saudi Arabia.
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, 2460, Riyadh, 11451, Saudi Arabia
| | | | - Aqeel Ahmad
- Department of Medical Biochemistry, College of Medicine, Shaqra University, Shaqra 11961, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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11
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Rasmussen HØ, Kumar A, Shin B, Stylianou F, Sewell L, Xu Y, Otzen DE, Pedersen JS, Matthews SJ. FapA is an Intrinsically Disordered Chaperone for Pseudomonas Functional Amyloid FapC. J Mol Biol 2023; 435:167878. [PMID: 36368411 DOI: 10.1016/j.jmb.2022.167878] [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: 09/01/2022] [Revised: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Bacterial functional amyloids contribute to biofilm development by bacteria and provide protection from the immune system and prevent antibiotic treatment. Strategies to target amyloid formation and interrupt biofilm formation have attracted recent interest due to their antimicrobial potential. Functional amyloid in Pseudomonas (Fap) includes FapC as the major component of the fibril while FapB is a minor component suggested to function as a nucleator of FapC. The system also includes the small periplasmic protein FapA, which has been shown to regulate fibril composition and morphology. The interplay between these three components is central in Fap fibril biogenesis. Here we present a comprehensive biophysical and spectroscopy analysis of FapA, FapB and FapC and provide insight into their molecular interactions. We show that all three proteins are primarily disordered with some regions with structural propensities for α-helix and β-sheet. FapA inhibits FapC fibrillation by targeting the nucleation step, whereas for FapB the elongation step is modulated. Furthermore, FapA alters the morphology of FapC (more than FapB) fibrils. Complex formation is observed between FapA and FapC, but not between FapA and FapB, and likely involves the N-terminus of FapA. We conclude that FapA is an intrinsically disordered chaperone for FapC that guards against fibrillation within the periplasm. This new understanding of a natural protective mechanism of Pseudomonas against amyloid formations can serve as inspiration for strategies blocking biofilm formation in infections.
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Affiliation(s)
- Helena Ø Rasmussen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Amit Kumar
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Ben Shin
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Lee Sewell
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Steve J Matthews
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom.
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12
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Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study. Comput Struct Biotechnol J 2023; 21:1746-1758. [PMID: 36890879 PMCID: PMC9986244 DOI: 10.1016/j.csbj.2023.02.031] [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: 12/16/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The aggregation of epitopes that are also able to bind major histocompatibility complex (MHC) alleles raises questions around the potential connection between the formation of epitope aggregates and their affinities to MHC receptors. We first performed a general bioinformatic assessment over a public dataset of MHC class II epitopes, finding that higher experimental binding correlates with higher aggregation-propensity predictors. We then focused on the case of P10, an epitope used as a vaccine candidate against Paracoccidioides brasiliensis that aggregates into amyloid fibrils. We used a computational protocol to design variants of the P10 epitope to study the connection between the binding stabilities towards human MHC class II alleles and their aggregation propensities. The binding of the designed variants was tested experimentally, as well as their aggregation capacity. High-affinity MHC class II binders in vitro were more disposed to aggregate forming amyloid fibrils capable of binding Thioflavin T and congo red, while low affinity MHC class II binders remained soluble or formed rare amorphous aggregates. This study shows a possible connection between the aggregation propensity of an epitope and its affinity for the MHC class II cleft.
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13
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Design of short peptides and peptide amphiphiles as collagen mimics and an investigation of their interactions with collagen using molecular dynamics simulations and docking studies. J Mol Model 2022; 29:19. [PMID: 36565373 DOI: 10.1007/s00894-022-05419-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X-Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)3 and (Ala-His-Hyp)3 formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200 ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)3 and (Ala-His-Hyp)3. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery.
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14
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Narsineni L, Rao PPN, Pham AT, Foldvari M. Peptide-Modified Gemini Surfactants as Delivery System Building Blocks with Dual Functionalities for Glaucoma Treatment: Gene Carriers and Amyloid-Beta (Aβ) Self-Aggregation Inhibitors. Mol Pharm 2022; 19:2737-2753. [PMID: 35802484 DOI: 10.1021/acs.molpharmaceut.2c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinal ganglion cell (RGC) neurodegeneration in glaucoma has potential links with amyloid-β (Aβ) deposition. Targeting the Aβ pathway was shown to reduce RGC apoptosis and protect RGCs from degeneration. We report exploratory studies on the amyloid Aβ40 aggregation inhibition properties of four cell adhesion peptide (CAP)-gemini surfactants that are intended as building blocks for gene carrier nanoparticles for glaucoma treatment. The CAP-gemini surfactants (18-7N(p1-4)-18) were evaluated as potential Aβ40 peptide aggregation inhibitors by a fluorescence kinetic assay and for their binding interactions with Aβ40 dimers by molecular docking studies. In vitro Aβ40 peptide aggregation inhibition studies showed that the 18-7N(p3)-18 and 18-7N(p1)-18 ligands inhibit Aβ40 peptide aggregation and prevent the formation of higher order structures. CDOCKER energies and CDOCKER interaction energies demonstrated that the CAP-gemini surfactants formed more stable complexes in the Aβ40 dimer assembly and underwent both polar and nonpolar interactions compared to CAP peptides alone. Also, 18-7N(p3)-18 showed a significantly lower CDOCKER energy compared to that of the unmodified gemini surfactant 18-7NH-18 (p < 0.0001) and 18-7N(p4)-18 (p < 0.001), 18-7N(p1)-18, and 18-7N(p2)-18. Similarly, 18-7N(p3)-18 showed a significantly lower CDOCKER interaction energy compared to that of 18-7NH-18, 18-7N(p4)-18 (p < 0.0001), and 18-7N(p2)-18 (p < 0.001), while 18-7N(p3)-18 and 18-7N(p1)-18 showed similar CDOCKER interaction energies. These studies suggest that a combination of both hydrophobic and electrostatic interactions contributes to the anti-Aβ40 aggregation activity of CAP-gemini surfactants. CAP-gemini surfactants showed 10-fold better Aβ40 peptide aggregation inhibition compared to previously reported values and could provide a new opportunity for glaucoma treatment as dual-functional gene carriers.
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15
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Jarmuła A, Zubalska M, Stępkowski D. Consecutive Aromatic Residues Are Required for Improved Efficacy of β-Sheet Breakers. Int J Mol Sci 2022; 23:ijms23095247. [PMID: 35563639 PMCID: PMC9102079 DOI: 10.3390/ijms23095247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 01/25/2023] Open
Abstract
Alzheimer’s disease is a fatal neurodegenerative malady which up to very recently did not have approved therapy modifying its course. After controversial approval of aducanumab (monoclonal antibody clearing β-amyloid plaques) by FDA for use in very early stages of disease, possibly new avenue opened for the treatment of patients. In line with this approach is search for compounds blocking aggregation into amyloid oligomers subsequently forming fibrils or compounds helping in getting rid of plaques formed by β-amyloid fibrils. Here we present in silico work on 627 sixtapeptide β-sheet breakers (BSBs) containing consecutive three aromatic residues. Three of these BSBs caused dissociation of one or two β-amyloid chains from U-shaped β-amyloid protofibril model 2BEG after docking and subsequent molecular dynamics simulations. Thorough analysis of our results let us postulate that the first steps of binding these successful BSBs involve π–π interactions with stacked chains of F19 and later also with F20 (F3 and F4 in 2BEG model of protofibril). The consecutive location of aromatic residues in BSBs makes them more attractive for chains of stacked F3 and F4 within the 2BEG model. Spotted by us, BSBs may be prospective lead compounds for an anti-Alzheimer’s therapy.
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Affiliation(s)
- Adam Jarmuła
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteur 3 St., 02-093 Warsaw, Poland
- Correspondence: ; Tel.: +48-66-955-7696
| | - Monika Zubalska
- Faculty of Physics, University of Warsaw, Pasteur 5 St., 02-093 Warsaw, Poland;
| | - Dariusz Stępkowski
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Pasteur 3 St., 02-093 Warsaw, Poland;
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16
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Ciccone L, Nencetti S, Camodeca C, Ortore G, Cuffaro D, Socci S, Orlandini E. Synthesis and Evaluation of Monoaryl Derivatives as Transthyretin Fibril Formation Inhibitors. Pharm Chem J 2022. [DOI: 10.1007/s11094-022-02600-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Marchetti A, Pizzi A, Bergamaschi G, Demitri N, Stollberg U, Diederichsen U, Pigliacelli C, Metrangolo P. Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self‐Assembly. Chemistry 2022; 28:e202104089. [PMID: 35084787 PMCID: PMC9306938 DOI: 10.1002/chem.202104089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Alessandro Marchetti
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche National Research Council of Italy Via M. Bianco 9 20131 Milano Italy
| | - Nicola Demitri
- Elettra – Sincrotrone Trieste S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza Trieste Italy
| | - Ulrike Stollberg
- Institute for Organic and Biomolecular Chemistry Georg-August-University Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry Georg-August-University Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Claudia Pigliacelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
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18
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Abstract
This review discusses peptide epitopes used as antigens in the development of vaccines in clinical trials as well as future vaccine candidates. It covers peptides used in potential immunotherapies for infectious diseases including SARS-CoV-2, influenza, hepatitis B and C, HIV, malaria, and others. In addition, peptides for cancer vaccines that target examples of overexpressed proteins are summarized, including human epidermal growth factor receptor 2 (HER-2), mucin 1 (MUC1), folate receptor, and others. The uses of peptides to target cancers caused by infective agents, for example, cervical cancer caused by human papilloma virus (HPV), are also discussed. This review also provides an overview of model peptide epitopes used to stimulate non-specific immune responses, and of self-adjuvanting peptides, as well as the influence of other adjuvants on peptide formulations. As highlighted in this review, several peptide immunotherapies are in advanced clinical trials as vaccines, and there is great potential for future therapies due the specificity of the response that can be achieved using peptide epitopes.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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19
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Castelletto V, Hamley IW. Amyloid
and Hydrogel Formation of a Peptide Sequence
from a Coronavirus Spike Protein. ACS NANO 2022; 16:1857-1867. [PMCID: PMC8867915 DOI: 10.1021/acsnano.1c10658] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 05/28/2023]
Abstract
![]()
We demonstrate that
a conserved coronavirus spike protein peptide
forms amyloid structures, differing from the native helical conformation
and not predicted by amyloid aggregation algorithms. We investigate
the conformation and aggregation of peptide RSAIEDLLFDKV,
which is a sequence common to many animal and human coronavirus spike
proteins. This sequence is part of a native α-helical S2 glycoprotein
domain, close to and partly spanning the fusion sequence. This peptide
aggregates into β-sheet amyloid nanotape structures close to
the calculated pI = 4.2, but forms disordered monomers at high and
low pH. The β-sheet conformation revealed by FTIR and circular
dichroism (CD) spectroscopy leads to peptide nanotape structures,
imaged using transmission electron microscopy (TEM) and probed by
small-angle X-ray scattering (SAXS). The nanotapes comprise arginine-coated
bilayers. A Congo red dye UV–vis assay is used to probe the
aggregation of the peptide into amyloid structures, which enabled
the determination of a critical aggregation concentration (CAC). This
peptide also forms hydrogels under precisely defined conditions of
pH and concentration, the rheological properties of which were probed.
The observation of amyloid formation by a coronavirus spike has relevance
to the stability of the spike protein conformation (or its destabilization via pH change), and the peptide may have potential utility
as a functional material. Hydrogels formed by coronavirus peptides
may also be of future interest in the development of slow-release
systems, among other applications.
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Affiliation(s)
- Valeria Castelletto
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Ian W. Hamley
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
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20
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Disaggregation of Islet Amyloid Polypeptide Fibrils as a Potential Anti-Fibrillation Mechanism of Tetrapeptide TNGQ. Int J Mol Sci 2022; 23:ijms23041972. [PMID: 35216095 PMCID: PMC8876742 DOI: 10.3390/ijms23041972] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Islet amyloid polypeptide (IAPP) fibrillation has been commonly associated with the exacerbation of type 2 diabetes prognosis. Consequently, inhibition of IAPP fibrillation to minimize β-cell cytotoxicity is an important approach towards β-cell preservation and type 2 diabetes management. In this study, we identified three tetrapeptides, TNGQ, MANT, and YMSV, that inhibited IAPP fibrillation. Using thioflavin T (ThT) fluorescence assay, circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and molecular docking, we evaluated the potential anti-fibrillation mechanism of the tetrapeptides. ThT fluorescence kinetics and microscopy as well as transmission electron microscopy showed that TNGQ was the most effective inhibitor based on the absence of normal IAPP fibrillar morphology. CD spectroscopy showed that TNGQ maintained the α-helical conformation of monomeric IAPP, while DLS confirmed the presence of varying fibrillation species. Molecular docking showed that TNGQ and MANT interact with monomeric IAPP mainly by hydrogen bonding and electrostatic interaction, with TNGQ binding at IAPP surface compared to YMSV, which had the highest docking score, but interact mainly through hydrophobic interaction in IAPP core. The highly polar TNGQ was the most active and appeared to inhibit IAPP fibrillation by disaggregation of preformed IAPP fibrils. These findings indicate the potential of TNGQ in the development of peptide-based anti-fibrillation and antidiabetic nutraceuticals.
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21
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Basu A, Mahammad A, Das A. Inhibition of the formation of lysozyme fibrillar assemblies by the isoquinoline alkaloid coralyne. NEW J CHEM 2022. [DOI: 10.1039/d1nj06007d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The isoquinoline alkaloid coralyne can efficiently attenuate fibrillogenesis in lysozyme.
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Affiliation(s)
- Anirban Basu
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| | - Adil Mahammad
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| | - Arindam Das
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
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22
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Cukkemane A, Becker N, Zielinski M, Frieg B, Lakomek NA, Heise H, Schröder GF, Willbold D, Weiergräber OH. Conformational heterogeneity coupled with β-fibril formation of a scaffold protein involved in chronic mental illnesses. Transl Psychiatry 2021; 11:639. [PMID: 34921141 PMCID: PMC8683410 DOI: 10.1038/s41398-021-01765-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 12/17/2022] Open
Abstract
Chronic mental illnesses (CMIs) pose a significant challenge to global health due to their complex and poorly understood etiologies and hence, absence of causal therapies. Research of the past two decades has revealed dysfunction of the disrupted in schizophrenia 1 (DISC1) protein as a predisposing factor involved in several psychiatric disorders. DISC1 is a multifaceted protein that serves myriads of functions in mammalian cells, for instance, influencing neuronal development and synapse maintenance. It serves as a scaffold hub forming complexes with a variety (~300) of partners that constitute its interactome. Herein, using combinations of structural and biophysical tools, we demonstrate that the C-region of the DISC1 protein is highly polymorphic, with important consequences for its physiological role. Results from solid-state NMR spectroscopy and electron microscopy indicate that the protein not only forms symmetric oligomers but also gives rise to fibrils closely resembling those found in certain established amyloid proteinopathies. Furthermore, its aggregation as studied by isothermal titration calorimetry (ITC) is an exergonic process, involving a negative enthalpy change that drives the formation of oligomeric (presumably tetrameric) species as well as β-fibrils. We have been able to narrow down the β-core region participating in fibrillization to residues 716-761 of full-length human DISC1. This region is absent in the DISC1Δ22aa splice variant, resulting in reduced association with proteins from the dynein motor complex, viz., NDE-like 1 (NDEL1) and lissencephaly 1 (LIS1), which are crucial during mitosis. By employing surface plasmon resonance, we show that the oligomeric DISC1 C-region has an increased affinity and shows cooperativity in binding to LIS1 and NDEL1, in contrast to the noncooperative binding mode exhibited by the monomeric version. Based on the derived structural models, we propose that the association between the binding partners involves two neighboring subunits of DISC1 C-region oligomers. Altogether, our findings highlight the significance of the DISC1 C-region as a crucial factor governing the balance between its physiological role as a multifunctional scaffold protein and aggregation-related aberrations with potential significance for disease.
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Affiliation(s)
- Abhishek Cukkemane
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Nina Becker
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Mara Zielinski
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Benedikt Frieg
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nils-Alexander Lakomek
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Henrike Heise
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Gunnar F. Schröder
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. .,Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
| | - Oliver H. Weiergräber
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
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23
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Shaham-Niv S, Rencus-Lazar S, Gazit E. Metabolite medicine offers a path beyond lists of metabolites. Commun Chem 2021; 4:115. [PMID: 36697841 PMCID: PMC9814037 DOI: 10.1038/s42004-021-00551-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/08/2021] [Indexed: 01/28/2023] Open
Affiliation(s)
- Shira Shaham-Niv
- BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Rencus-Lazar
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, Israel.
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24
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Koshti B, Kshtriya V, Nardin C, Gour N. Chemical Perspective of the Mechanism of Action of Antiamyloidogenic Compounds Using a Minimalistic Peptide as a Reductionist Model. ACS Chem Neurosci 2021; 12:2851-2864. [PMID: 34264635 DOI: 10.1021/acschemneuro.1c00221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The diphenylalanine (FF) residue which is present at the 19 and 20 positions of the amyloid beta (1-42) (Aβ42) peptide sequence is considered as a reductionist model for studying Aβ42 aggregation. FF self-assembles into well-ordered tubular structures via aromatic π-π stacking. Herein the manuscript, we have presented a chemical perspective on the mechanism of action of antiamyloid compounds by assessing their interaction with FF. Therefore, we first coincubated FF fibers with single amino acids, since they are constituted of different R side chains yet have a common structural unit. This study revealed a crucial role of aromatic rings and functional groups like thiol (-SH) in causing destabilization of FF assembly via their interaction with π-electrons participating in π-π stacking present in FF. We further studied the interaction of different nonsteroidal anti-inflammatory drugs (NSAIDs), other known antiamyloidogenic compounds, and host-guest inclusion compounds like cyclodextrin (CD) to assess their mechanism of action and to decipher the functional moiety present in these compounds which could cause destabilization of π-π stacking. From the coincubation experiments, we could surmise a crucial role of aromatic rings present in these compounds for causing interference in aromatic stacking. We further consolidated our observations through microscopy analysis by various spectroscopic methods such as aggregation-induced emission enhancement (AIEE), fluorescence spectroscopy, solution-state 1H NMR, FTIR, and circular dichroism. The studies presented in the manuscript thus provide significant insights into the role of functional groups in imparting antiamyloid action and open new avenues for an efficient design of antiamyloid drugs in the future.
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Affiliation(s)
- Bharti Koshti
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
| | - Vivekshinh Kshtriya
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
| | - Corinne Nardin
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Nidhi Gour
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
- Department of Medicinal Chemistry, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
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25
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Michno W, Blennow K, Zetterberg H, Brinkmalm G. Refining the amyloid β peptide and oligomer fingerprint ambiguities in Alzheimer's disease: Mass spectrometric molecular characterization in brain, cerebrospinal fluid, blood, and plasma. J Neurochem 2021; 159:234-257. [PMID: 34245565 DOI: 10.1111/jnc.15466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 01/05/2023]
Abstract
Since its discovery, amyloid-β (Aβ) has been the principal target of investigation of in Alzheimer's disease (AD). Over the years however, no clear correlation was found between the Aβ plaque burden and location, and AD-associated neurodegeneration and cognitive decline. Instead, diagnostic potential of specific Aβ peptides and/or their ratio, was established. For instance, a selective reduction in the concentration of the aggregation-prone 42 amino acid-long Aβ peptide (Aβ42) in cerebrospinal fluid (CSF) was put forward as reflective of Aβ peptide aggregation in the brain. With time, Aβ oligomers-the proposed toxic Aβ intermediates-have emerged as potential drivers of synaptic dysfunction and neurodegeneration in the disease process. Oligomers are commonly agreed upon to come in different shapes and sizes, and are very poorly characterized when it comes to their composition and their "toxic" properties. The concept of structural polymorphism-a diversity in conformational organization of amyloid aggregates-that depends on the Aβ peptide backbone, makes the characterization of Aβ aggregates and their role in AD progression challenging. In this review, we revisit the history of Aβ discovery and initial characterization and highlight the crucial role mass spectrometry (MS) has played in this process. We critically review the common knowledge gaps in the molecular identity of the Aβ peptide, and how MS is aiding the characterization of higher order Aβ assemblies. Finally, we go on to present recent advances in MS approaches for characterization of Aβ as single peptides and oligomers, and convey our optimism, as to how MS holds a promise for paving the way for progress toward a more comprehensive understanding of Aβ in AD research.
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Affiliation(s)
- Wojciech Michno
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.,Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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Zhang TD, Chen LL, Lin WJ, Shi WP, Wang JQ, Zhang CY, Guo WH, Deng X, Yin DC. Searching for conditions of protein self-assembly by protein crystallization screening method. Appl Microbiol Biotechnol 2021; 105:2759-2773. [PMID: 33683398 DOI: 10.1007/s00253-021-11188-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/29/2021] [Accepted: 02/17/2021] [Indexed: 11/28/2022]
Abstract
The self-assembly of biomacromolecules is an extremely important process. It is potentially useful in the fields of life science and materials science. To carry out the study on the self-assembly of proteins, it is necessary to find out the suitable self-assembly conditions, which have always been a challenging task in practice. Inspired by the screening technique in the field of protein crystallization, we proposed using the same screening technique for seeking suitable protein self-assembly conditions. Based on this consideration, we selected 5 proteins (β-lactoglobulin, hemoglobin, pepsin, lysozyme, α-chymotrypsinogen (II) A) together with 5 screening kits (IndexTM, BML, Morpheus, JCSG, PEG/Ion ScreenTM) to investigate the performance of these crystallization screening techniques in order to discover new optimized conditions of protein self-assembly. The screens were all kept at 293 K for certain days, and were analyzed using optical microscope, scanning electron microscope, transmission electron microscope, atomic force microscope, fluorescence microscope, and atomic absorption spectroscope. The results demonstrated that the method of protein crystallization screening can be successfully applied in the screening of self-assembly conditions. This method is fast, high throughput, and easily implemented in an automated system, with a low protein consumption feature. These results suggested that such strategy can be applied to finding new conditions or forms in routine research of protein self-assembly. KEY POINTS: • Protein crystallization screening method is successfully applied in the screening of self-assembly conditions. • This screening method can be applied on various kinds of proteins and possess a feature of low protein consumption. • This screening method is fast, high throughput, and easily implemented in an automated system.
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Affiliation(s)
- Tuo-Di Zhang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liang-Liang Chen
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wen-Juan Lin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wen-Pu Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jia-Qi Wang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chen-Yan Zhang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | | | - Xudong Deng
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.
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Holubová M, Lobaz V, Loukotová L, Rabyk M, Hromádková J, Trhlíková O, Pechrová Z, Groborz O, Štěpánek P, Hrubý M. Chemically modified glycogens: how they influence formation of amyloid fibrils? SOFT MATTER 2021; 17:1614-1627. [PMID: 33355593 DOI: 10.1039/d0sm01829e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The formation of amyloid fibrils from certain proteins stays behind a number of pathologies, so-called amyloidoses. Glycosaminoglycans are polysaccharides and are known natural constituents of amyloids in vivo. However, little is known about the effect of other naturally abundant polysaccharides, and even less is known about the effect of chemically modified polysaccharides on the formation of amyloid fibrils. In the case of low-molecular weight compounds, aromatic substances are known to often influence amyloid formation significantly. We investigated the influence of glycogen (GG) and several modifications of GG with cinnamoyl groups, benzoyl groups and phenylacetyl groups. As model systems, hen egg-white lysozyme (HEWL) and amyloid beta peptide (1-42) (Aβ1-42), which is an Alzheimer disease-relevant system, were used. The fluorescence of thioflavin-T (ThT) was used for the rapid detection of fibrils, and the fluorescence results were confirmed by transmission electron microscopy (TEM). Other techniques, such as isothermal titration calorimetry (ITC) and dynamic light scattering (DLS), were employed to determine the interactions between HEWL and the modifications. We achieved similar results with both model systems (HEWL and Aβ1-42). We showed that π-π interactions played an important role in the process of amyloid fibril formation because fundamental changes were observed in this process even with a very small number of groups containing an aromatic ring. It was found that almost all GG modifications accelerated the formation of amyloid fibrils in both model systems, HEWL and Aβ1-42, except for GG-Ph1 (1.6 mol% phenylacetyl groups), which had a retarding effect compared to all other modifications.
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Affiliation(s)
- Monika Holubová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic. and Charles University in Prague, Faculty of Science, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Volodymyr Lobaz
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Lenka Loukotová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Mariia Rabyk
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Jiřina Hromádková
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Olga Trhlíková
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Zdislava Pechrová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Ondřej Groborz
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic. and Charles University in Prague, Faculty of Science, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Petr Štěpánek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Martin Hrubý
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
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Holubová M, Lobaz V, Loukotová L, Rabyk M, Hromádková J, Trhlíková O, Pechrová Z, Groborz O, Štěpánek P, Hrubý M. Does polysaccharide glycogen behave as a promoter of amyloid fibril formation at physiologically relevant concentrations? SOFT MATTER 2021; 17:1628-1641. [PMID: 33355589 DOI: 10.1039/d0sm01884h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We investigated the influence of glycogen (GG), phytoglycogen (PG), mannan (MAN) and cinnamoyl-modified GG (GG-CIN) on amyloid fibril formation. We used hen egg-white lysozyme (HEWL) as a model system and amyloid beta peptide (1-42) (Aβ1-42) as an Alzheimer's disease-relevant system. For brief detection of fibrils was used thioflavin T (ThT) fluorescence assay and the results were confirmed by transmission electron microscopy (TEM). We also deal with the interaction of polysaccharides and HEWL with isothermal titration calorimetry (ITC) and dynamic light scattering (DLS). We found that all polysaccharides accelerated the formation of amyloid fibrils from both HEWL and Aβ1-42. At high but physiologically relevant concentrations of GG, amyloid fibril formation was extremely accelerated for HEWL. Therefore, on the basis of the herein presented in vitro data, we hypothesize, that dietary d-glucose intake may influence amyloid fibril formation not only by influencing regulatory pathways, but also by direct glycogen-amyloid precursor protein molecular interaction, as glycogen levels in tissues are highly dependent on d-glucose intake.
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Affiliation(s)
- Monika Holubová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic. and Charles University in Prague, Faculty of Science, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Volodymyr Lobaz
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Lenka Loukotová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Mariia Rabyk
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Jiřina Hromádková
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Olga Trhlíková
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Zdislava Pechrová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Ondřej Groborz
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic. and Charles University in Prague, Faculty of Science, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Petr Štěpánek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
| | - Martin Hrubý
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
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Oakes A, Menefee K, Lamba A, Palato LM, Rinauro DJ, Tun A, Jauregui B, Chang K, Nogaj LA, Moffet DA. Nonhuman IAPP Variants Inhibit Human IAPP Aggregation. Protein Pept Lett 2021; 28:963-971. [PMID: 34365921 PMCID: PMC10712300 DOI: 10.2174/0929866528666210806152706] [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: 02/28/2021] [Revised: 04/13/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022]
Abstract
AIM To identify naturally occurring variants of IAPP capable of inhibiting the aggregation of human IAPP and protecting living cells from the toxic effects of human IAPP. BACKGROUND The loss of insulin-producing β-cells and the overall progression of type 2 diabetes appears to be linked to the formation of toxic human IAPP (hIAPP, Islet Amyloid Polypeptide, amylin) amyloid in the pancreas. Inhibiting the initial aggregation of hIAPP has the potential to slow, if not stop entirely, the loss of β-cells and halt the progression of the disease. OBJECTIVE To identify and characterize naturally occurring variants of IAPP capable of inhibiting human IAPP aggregation. METHODS Synthetic human IAPP was incubated with synthetic IAPP variants identified from natural sources under conditions known to promote amyloid-based aggregation. To identify IAPP variants capable of inhibiting human IAPP aggregation, Thioflavin T-binding fluorescence, atomic force microscopy, and cell-rescue assays were performed. RESULTS While most IAPP variants showed little to no ability to inhibit human IAPP aggregation, several variants showed some ability to inhibit aggregation, with two variants showing substantial inhibitory potential. CONCLUSION Several naturally occurring IAPP variants capable of inhibiting human IAPP aggregation were identified and characterized.
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Affiliation(s)
- Alissa Oakes
- Department of Biology, Mount Saint Mary’s University, Los Angeles, CA 90049, USA
| | - Kate Menefee
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Arleen Lamba
- Department of Biology, Mount Saint Mary’s University, Los Angeles, CA 90049, USA
| | - Larry M. Palato
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Dillon J. Rinauro
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Angela Tun
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Betssy Jauregui
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Kevin Chang
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Luiza A. Nogaj
- Department of Biology, Mount Saint Mary’s University, Los Angeles, CA 90049, USA
| | - David A. Moffet
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA 90045, USA
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Mayans E, Alemán C. Revisiting the Self-Assembly of Highly Aromatic Phenylalanine Homopeptides. Molecules 2020; 25:E6037. [PMID: 33419355 PMCID: PMC7766750 DOI: 10.3390/molecules25246037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023] Open
Abstract
Diphenylalanine peptide (FF), which self-assembles into rigid tubular nanostructures, is a very short core recognition motif in Alzheimer's disease β-amyloid (Aβ) polypeptide. Moreover, the ability of the phenylalanine (F or Phe)-homopeptides to self-assemble into ordered nanostructures has been proved. Within this context it was shown that the assembly preferences of this family of compounds is altered by capping both the N- and C-termini using highly aromatic fluorenyl groups (i.e., fluorenyl-9-methoxycarbonyl and 9-fluorenylmethyl ester, named Fmoc and OFm, respectively). In this article the work performed in the field of the effect of the structure and incubation conditions on the morphology and polymorphism of short (from two to four amino acid residues) Phe-homopeptides is reviewed and accompanied by introducing some new results for completing the comparison. Special attention has been paid to the influence of solvent: co-solvent mixture used to solubilize the peptide, the peptide concentration and, in some cases, the temperature. More specifically, uncapped (FF, FFF, and FFFF), N-capped with Fmoc (Fmoc-FF, Fmoc-FFF, and Fmoc-FFFF), C-capped with OFm (FF-OFm), and doubly capped (Fmoc-FF-OFm, Fmoc-FFF-OFm, and Fmoc-FFFF-OFm) Phe-homopeptides have been re-measured. Although many of the experienced assembly conditions have been only revisited as they were previously reported, other experimental conditions have been examined by the first time in this work. In any case, pooling the effect of highly aromatic blocking groups in a single study, using a wide variety of experimental conditions, allows a perspective of how the disappearance of head-to-tail electrostatic interactions and the gradual increase in the amount of π-π stacking interactions, affects the morphology of the assemblies. Future technological applications of Phe-homopeptides can be envisaged by choosing the most appropriate self-assemble structure, defining not only the length of the peptide but also the amount and the position of fluorenyl capping groups.
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Affiliation(s)
| | - Carlos Alemán
- Departament d’Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain;
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31
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Ciccone L, Tonali N, Nencetti S, Orlandini E. Natural compounds as inhibitors of transthyretin amyloidosis and neuroprotective agents: analysis of structural data for future drug design. J Enzyme Inhib Med Chem 2020; 35:1145-1162. [PMID: 32419519 PMCID: PMC7301710 DOI: 10.1080/14756366.2020.1760262] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Natural compounds, such as plant and fruit extracts have shown neuroprotective effect against neurodegenerative diseases. It has been reported that several natural compounds binding to transthyretin (TTR) can be useful in amyloidosis prevention. TTR is a transporter protein that under physiological condition carries thyroxine (T4) and retinol in plasma and in cerebrospinal fluid (CSF); it also has a neuroprotective role against Alzheimer's disease (AD). However, TTR also is an amyloidogenic protein responsible for familial amyloid polyneuropathy (FAP) and familial amyloid cardiomyopathy (FAC). The TTR amyloidogenic potential is speeded up by several point mutations. One therapeutic strategy against TTR amyloidosis is the stabilisation of the native tetramer by natural compounds and small molecules. In this review, we examine the natural products that, starting from 2012 to present, have been studied as a stabiliser of TTR tetramer. In particular, we discussed the chemical and structural features which will be helpful for future drug design of new TTR stabilisers.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Nicoló Tonali
- CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Pisa, Italy
- Interdepartmental Research Centre “Nutraceuticals and Food for Health (NUTRAFOOD), University of Pisa, Pisa, Italy
| | - Elisabetta Orlandini
- Department of Earth Sciences, University of Pisa, Pisa, Italy
- Research Center “E. Piaggio”, University of Pisa, Pisa, Italy
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32
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Sharma M, Tiwari V, Shukla S, Panda JJ. Fluorescent Dopamine-Tryptophan Nanocomposites as Dual-Imaging and Antiaggregation Agents: New Generation of Amyloid Theranostics with Trimeric Effects. ACS APPLIED MATERIALS & INTERFACES 2020; 12:44180-44194. [PMID: 32870652 DOI: 10.1021/acsami.0c13223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The aggregation of neurotoxic amyloid-β (Aβ) polypeptides into aberrant extracellular senile plaques is the major neuropathological hallmark of Alzheimer's disease (AD). Inhibiting aggregation of these peptides to control the progression of this deadly disease can serve as a viable therapeutic option. In the current work, inherently fluorescent theranostic dopamine-tryptophan nanocomposites (DTNPs) were developed and investigated for their amyloid inhibition propensity along with their ability to act as a cellular bioimaging agent in neuronal cells. The antiaggregation potency of the nanocomposites was further investigated against an in vitro established reductionist amyloid aggregation model consisting of a mere dipeptide, phenylalanine-phenylalanine (FF). As opposed to large peptide/protein-derived robust and high-molecular-weight amyloid aggregation models of Alzheimer's disease, our dipeptide-based amyloid model provides an edge over others in terms of the ease of handling, synthesis, and cost-effectiveness. Results demonstrated positive antiaggregation behavior of the DTNPs toward both FF-derived amyloid fibrils and preformed Aβ-peptide fibers by means of electron microscopic and circular dichroism-based studies. Our results further pointed toward the neuroprotective effects of the DTNPs in neuroblastoma cells against FF amyloid fibril-induced toxicity and also that they significantly suppressed the accumulation of Aβ42 oligomers in both cortex and hippocampus regions and improved cognitive impairment in an intracerebroventricular streptozotocin (ICV-STZ)-induced animal model of dementia. Besides, DTNPs also exhibited excellent fluorescent properties and light up the cytoplasm of neuroblastoma cells when being coincubated with cells, confirming their ability to serve as an intracellular bioimaging agent. Overall, these results signify the potency of the DTNPs as promising multifunctional theranostic agents for treating AD.
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Affiliation(s)
- Manju Sharma
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Virendra Tiwari
- CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Shubha Shukla
- CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Jiban Jyoti Panda
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
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Paul A, Frenkel-Pinter M, Escobar Alvarez D, Milordini G, Gazit E, Zacco E, Segal D. Tryptophan-galactosylamine conjugates inhibit and disaggregate amyloid fibrils of Aβ42 and hIAPP peptides while reducing their toxicity. Commun Biol 2020; 3:484. [PMID: 32879439 PMCID: PMC7468108 DOI: 10.1038/s42003-020-01216-5] [Citation(s) in RCA: 26] [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: 02/25/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Self-assembly of proteins into amyloid fibrils is a hallmark of various diseases, including Alzheimer's disease (AD) and Type-2 diabetes Mellitus (T2DM). Aggregation of specific peptides, like Aβ42 in AD and hIAPP in T2DM, causes cellular dysfunction resulting in the respective pathology. While these amyloidogenic proteins lack sequence homology, they all contain aromatic amino acids in their hydrophobic core that play a major role in their self-assembly. Targeting these aromatic residues by small molecules may be an attractive approach for inhibiting amyloid aggregation. Here, various biochemical and biophysical techniques revealed that a panel of tryptophan-galactosylamine conjugates significantly inhibit fibril formation of Aβ42 and hIAPP, and disassemble their pre-formed fibrils in a dose-dependent manner. They are also not toxic to mammalian cells and can reduce the cytotoxicity induced by Aβ42 and hIAPP aggregates. These tryptophan-galactosylamine conjugates can therefore serve as a scaffold for the development of therapeutics towards AD and T2DM.
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Affiliation(s)
- Ashim Paul
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Moran Frenkel-Pinter
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Daniela Escobar Alvarez
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Giulia Milordini
- The Maurice Wohl Clinical Neuroscience Institute, King's College London, Brixton, London, SE5 9RT, UK
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Elsa Zacco
- The Maurice Wohl Clinical Neuroscience Institute, King's College London, Brixton, London, SE5 9RT, UK.
- RNA Central Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, 16152, Genova, Italy.
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel.
- Sagol Interdisciplinary School of Neuroscience, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel.
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Holubová M, Štěpánek P, Hrubý M. Polymer materials as promoters/inhibitors of amyloid fibril formation. Colloid Polym Sci 2020. [DOI: 10.1007/s00396-020-04710-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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36
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Ovotransferrin nanofibril formation in the presence of glycerol or sorbitol. Food Chem 2020; 305:125453. [DOI: 10.1016/j.foodchem.2019.125453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/29/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
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37
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Kurpiewska K, Miłaczewska A, Lewiński K. Insulin conformational changes under high pressure in structural studies and molecular dynamics simulations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Yadav N, Chauhan MK, Chauhan VS. Short to ultrashort peptide-based hydrogels as a platform for biomedical applications. Biomater Sci 2019; 8:84-100. [PMID: 31696870 DOI: 10.1039/c9bm01304k] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Short peptides have attracted significant attention from researchers in the past few years due to their easy design, synthesis and characterization, diverse functionalisation possibilities, low cost, possibility to make a large range of hierarchical nanostructures and most importantly their high biocompatibility and biodegradability. Generally, short peptides are also relatively more stable than their longer variants, non-immunogenic in nature and many of them self-assemble to provide an exciting range of nanostructures, including hydrogels. Thus, the development of short peptide-based hydrogels has become an area of intense investigation. Although these hydrogels have a water content of greater than 90%, they are surprisingly highly stable structures, and thus have been used for various biomedical applications, including cell therapeutics, drug delivery, tissue engineering and regeneration, contact lenses, biosensors, and wound healing, by different researchers. Herein, we review the progress of research in the rapidly expanding field of short to ultrashort peptide-based hydrogels and their possible applications. Special attention is paid to address and review this field with regard to the stability of peptide-based hydrogels, particularly to enzymatic degradation.
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Affiliation(s)
- Nitin Yadav
- Molecular Medicine Group, International Centre for Genetic Engineering & Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India. and Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli-Badarpur Road, Sector-3, Pushpvihar, New Delhi-110017, India
| | - Meenakshi K Chauhan
- Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli-Badarpur Road, Sector-3, Pushpvihar, New Delhi-110017, India
| | - Virander S Chauhan
- Molecular Medicine Group, International Centre for Genetic Engineering & Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
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39
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Sahoo JK, VandenBerg MA, Ruiz Bello EE, Nazareth CD, Webber MJ. Electrostatic-driven self-sorting and nanostructure speciation in self-assembling tetrapeptides. NANOSCALE 2019; 11:16534-16543. [PMID: 31455952 DOI: 10.1039/c9nr03440d] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Significant efforts in the field of supramolecular materials have strived to co-assemble small molecules in order to realize individual nanostructures with multiple, tunable activities. The design of self-assembling motifs bearing opposite charges is one commonly used method, with favorable electrostatic interactions used to promote mixing in a resulting co-assembly. This approach, at the same time, contrasts with a typical thermodynamic preference for self-sorting. Moreover, rigorous experimental techniques which can clearly elucidate co-assembly from self-sorting are limited. Here we describe the self-assembly of two oppositely charged tetrapeptides yielding highly disparate nanostructures of fibrillar and spherical assemblies. Upon mixing at different ratios, the disparate nanostructure of the parent peptides remain. Interestingly, while the assemblies appear self-sorted, surface-mediated interactions between spherical and fibrous assemblies translate to increased mechanical properties through enhanced fiber bundling. Moreover, the observed self-sorting is a thermodynamic product and not a result of kinetically trapped pre-existing structures. Taken together, and with the benefit of disparate nanostructures in the parent peptides, we have shown in our system experimental evidence for electrostatic-driven self-sorting in oligopeptide self-assembly.
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Affiliation(s)
- Jugal Kishore Sahoo
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Michael A VandenBerg
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Edgar E Ruiz Bello
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Calvin D Nazareth
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Matthew J Webber
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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40
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Stoichiometry-controlled secondary structure transition of amyloid-derived supramolecular dipeptide co-assemblies. Commun Chem 2019. [DOI: 10.1038/s42004-019-0170-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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41
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Roy D, Bhattacharyya D, Bhunia A. Do Catechins (ECG and EGCG) Bind to the Same Site as Thioflavin T (ThT) in Amyloid Fibril? Answer From Saturation Transfer Difference NMR. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Dipanwita Roy
- Department of Biophysics, Bose Institute, Kolkata, WB, India
| | | | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, WB, India
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42
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Martial B, Lefèvre T, Buffeteau T, Auger M. Vibrational Circular Dichroism Reveals Supramolecular Chirality Inversion of α-Synuclein Peptide Assemblies upon Interactions with Anionic Membranes. ACS NANO 2019; 13:3232-3242. [PMID: 30811930 DOI: 10.1021/acsnano.8b08932] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Parkinson's disease is an incurable neurodegenerative disorder caused by the aggregation of α-synuclein (AS). This amyloid protein contains a 12-residue-long segment, AS71-82, that triggers AS pathological aggregation. This peptide is then essential to better understand the polymorphism and the dynamics of formation of AS fibrillar structures. In this work, vibrational circular dichroism showed that AS71-82 is random coil in solution and forms parallel β-sheet fibrillar aggregates in the presence of anionic vesicles. Vibrational circular dichroism, with transmission electronic microscopy, revealed that the fibrillar structures exhibit a nanoscale tape-like morphology with a preferential supramolecular helicity. Whereas the structure handedness of some other amyloid peptides has been shown to be driven by pH, that of AS71-82 is controlled by peptide concentration and peptide-to-lipid (P:L) molar ratio. At low concentrations and low P:L molar ratios, AS71-82 assemblies have a left-twisted handedness, whereas at high concentrations and high P:L ratios, a right-twisted handedness is adopted. Left-twisted assemblies interconvert into right-twisted ones with time, suggesting a maturation of the amyloid structures. As fibril species with two chiralities have also been reported previously in Parkinson's disease Lewy bodies and fibrils, the present results seem relevant to better understand AS amyloid assembly and fibrillization in vivo. From a diagnosis or therapeutic point of view, it becomes essential that future fibril probes, inhibitors, or breakers target pathological assemblies with specific chirality and morphology, in particular, because they may change with the stage of the disease.
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Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF) , Université Laval , Québec , QC G1 V 0A6 , Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF) , Université Laval , Québec , QC G1 V 0A6 , Canada
| | - Thierry Buffeteau
- Université Bordeaux , Institut des Sciences Moléculaires, CNRS UMR 5255, 33405 Talence , France
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF) , Université Laval , Québec , QC G1 V 0A6 , Canada
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43
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Arnon ZA, Gilead S, Gazit E. Microfluidics for real-time direct monitoring of self- and co-assembly biomolecular processes. NANOTECHNOLOGY 2019; 30:102001. [PMID: 30537683 DOI: 10.1088/1361-6528/aaf7b1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Molecular self-assembly is a major approach for the fabrication of functional supramolecular nanomaterials. This dynamic, straightforward, bottom-up procedure may result in the formation of various architectures at the nano-scale, with remarkable physical and chemical characteristics. Biological and bio-inspired building blocks are especially attractive due to their intrinsic tendency to assemble into well-organized structures, as well as their inherent biocompatibility. To further expand the morphological diversity, co-assembly methods have been developed, allowing to produce alternative unique architectures, enhanced properties, and improved structural control. However, in many cases, mechanistic understanding of the self- and co-assembly processes is still lacking. Microfluidic techniques offer a set of exclusive tools for real-time monitoring of biomolecular self-organization, which is crucial for the study of such dynamic processes. Assembled nuclei, confined by micron-scale pillars, could be subjected to controlled environments aiming to assess the effect of different conditions on the assembly process. Other microfluidics setups can produce droplets at a rate of over 100 s-1, with volumes as small as several picoliters. Under these conditions, each droplet can serve as an individual pico/nano-reactor allowing nucleation and assembly. These processes can be monitored, analyzed and imaged, by various techniques including simple bright-field microscopy. Elucidating the mechanism of such molecular events may serve as a conceptual stepping-stone for the rational control of the resulting physicochemical properties.
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Affiliation(s)
- Zohar A Arnon
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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Kilic B, Erdogan M, Gulcan HO, Aksakal F, Oruklu N, Bagriacik EU, Dogruer DS. Design, Synthesis and Investigation of New Diphenyl Substituted Pyridazinone Derivatives as Both Cholinesterase and Aβ-Aggregation Inhibitors. Med Chem 2019; 15:59-76. [DOI: 10.2174/1573406414666180524073241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/30/2018] [Accepted: 04/17/2018] [Indexed: 11/22/2022]
Abstract
Background:
With respect to the increase in the average life expectancy, Alzheimer
Disease (AD), the most common form of age-related dementia, has become a major threat to the
population over the age of 65 during the past several decades. The majority of AD treatments are
focused on cholinergic and amyloid hypotheses.
Objective:
In this study, three series of diphenyl-2-(2-(4-substitutedpiperazin-1-yl)ethyl)pyridazin-
3(2H)-one derivatives were designed, synthesized and investigated for their ability to inhibit both
cholinesterase enzymes and amyloid-β aggregation.
Method:
The inhibitory activities of the synthesized compounds on AChE (from electric eel) and
BChE (from equine serum) were determined by the modified Ellman’s method. The reported
thioflavin T-based fluorometric assay was performed to investigate the effect of the selected compounds
on the aggregation of Aβ1-42. The cytotoxic effect of the compounds (4g, 11g and 18g) was
monitored in 3T3 cell lines to gain insight into therapeutic potential of the compounds by using
MTT assay. The crystal structures of the AChE (1EVE) and BChE (1P0I) enzymes were retrieved
from the RCSB Protein Data Bank and Molecular Operating Environment (MOE) software was
used for molecular docking of the ligands.
Results:
Among the tested compounds, 5,6-diphenyl derivative 18g was identified as the most potent
and selective AChE inhibitor (IC50 = 1.75 µM, Selectivity Index for AChE > 22.857). 4,6-
Diphenyl derivative 11g showed the highest and the most selectivity for BChE (IC50= 4.97 µM, SI
for AChE < 0.124). Interestingly, 4,5-diphenyl derivative 4g presented dual cholinesterase inhibition
(AChE IC50= 5.11 µM; BChE IC50= 14.16 µM, SI for AChE = 2.771).
Conclusion:
Based on biological activity results and low toxicity of the compounds, it can be said
that diphenyl substituted pyridazinone core is a valuable scaffold. Especially, dual inhibitory potencies
of 4,5-diphenylpyridazin-3(2H)-one core for the cholinesterase enzymes and Aβ-
aggregation makes this core a promising disease-modifying agent.
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Affiliation(s)
- Burcu Kilic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Turkey
| | - Merve Erdogan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Turkey
| | - Hayrettin O. Gulcan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Eastern Mediterranean University, Gazimagosa, North Cyprus, Cyprus
| | - Fatma Aksakal
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Nihan Oruklu
- Department of Immunology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Emin U. Bagriacik
- Department of Immunology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Deniz S. Dogruer
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Turkey
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45
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Mason TO, Buell AK. The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:61-112. [PMID: 31713197 DOI: 10.1007/978-981-13-9791-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid β sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DTU, Lyngby, Denmark.
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Bera S, Arad E, Schnaider L, Shaham-Niv S, Castelletto V, Peretz Y, Zaguri D, Jelinek R, Gazit E, Hamley IW. Unravelling the role of amino acid sequence order in the assembly and function of the amyloid-β core. Chem Commun (Camb) 2019; 55:8595-8598. [DOI: 10.1039/c9cc03654g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Here we report the influence of amino acid sequence order on the self-assembly and biological functions of the core recognition motif of Amyloid β.
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Affiliation(s)
- Santu Bera
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 69978
- Israel
| | - Elad Arad
- Department of Chemistry & Ilse Katz Institute (IKI) for Nanoscale Science and Technology
- Ben Gurion University of the Negev
- Beer Sheva 8410501
- Israel
| | - Lee Schnaider
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 69978
- Israel
| | - Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 69978
- Israel
| | | | - Yossef Peretz
- Department of Chemistry & Ilse Katz Institute (IKI) for Nanoscale Science and Technology
- Ben Gurion University of the Negev
- Beer Sheva 8410501
- Israel
| | - Dor Zaguri
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 69978
- Israel
| | - Raz Jelinek
- Department of Chemistry & Ilse Katz Institute (IKI) for Nanoscale Science and Technology
- Ben Gurion University of the Negev
- Beer Sheva 8410501
- Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 69978
- Israel
| | - Ian W. Hamley
- Department of Chemistry
- University of Reading
- Reading RG6 6AD
- UK
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47
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Exploring the aggregation-prone regions from structural domains of human TDP-43. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:286-296. [PMID: 30315897 DOI: 10.1016/j.bbapap.2018.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/15/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
Abstract
TDP-43 (transactive- response DNA binding protein) amazes structural biologist as its aberrant ubiquitinated cytosolic inclusions is largely involved in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). An important question in TDP-43 research is to identify the structural region mediating the formation of cytoplasmic pathological aggregates. In this study, we attempted to delineate the aggregation-prone sequences of the structural domain of TDP-43. Here, we investigated the self-assembly of peptides of TDP-43 using aggregation prediction algorithms, Zipper DB and AMYLPRED2. The three aggregation-prone peptides identified were from N-terminal domain (24GTVLLSTV31), and RNA recognition motifs, RRM1 (128GEVLMVQV135) and RRM2 (247DLIIKGIS254). Furthermore, the amyloid fibril forming propensities of these peptides were analyzed through different biophysical techniques and molecular dynamics simulation. Our study shows the different aggregation ability of conserved stretches in structural domain of TDP-43 that will possibly induce full-length aggregation of TDP-43 in vivo. The peptide form RRM2 demonstrates the higher intrinsic amyloid forming propensity and suggests that RRM2 might form the structural core of TDP-43 aggregation seen in vivo. The results of this study would help in designing peptide based inhibitors of TDP-43 aggregation.
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48
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Tomar K, Kaur G, Verma S, Ramanathan G. A self-assembled tetrapeptide that acts as a “turn-on” fluorescent sensor for Hg2+ ion. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.08.043] [Citation(s) in RCA: 5] [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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49
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Bansal S, Maurya IK, Yadav N, Thota CK, Kumar V, Tikoo K, Chauhan VS, Jain R. C-Terminal Fragment, Aβ 39-42-Based Tetrapeptides Mitigates Amyloid-β Aggregation-Induced Toxicity. ACS OMEGA 2018; 3:10019-10032. [PMID: 31459130 PMCID: PMC6645473 DOI: 10.1021/acsomega.8b01522] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/20/2018] [Indexed: 06/07/2023]
Abstract
Since the introduction of acetyl cholinesterase inhibitors as the first approved drugs by the US Food and Drug Administration for Alzheimer's disease (AD) in clinics, less than satisfactory success in the design of anti-AD agents has impelled the scientists to also focus toward inhibition of Aβ aggregation. Considering the specific binding of fragments for their parent peptide, herein, we synthesized more than 40 new peptides based on a C-terminus tetrapeptide fragment of Aβ1-42. Initial screening by MTT cell viability assay and supportive results by ThT fluorescence assay led us to identify a tetrapeptide showing complete inhibition for Aβ1-42 aggregation. Peptide 20 displayed 100% cell viability at 20 μM concentration, while at lower concentrations of 10 and 2 μM 76.6 and 70% of cells were viable. Peptide 20 was found to restrict the conformational transition of Aβ1-42 peptide toward β-sheet structure. Inhibitory activity of tetrapeptide 20 was further evidenced by the absence of Aβ1-42 aggregates in electron microscopy. Peptide 20 and other significantly active tetrapeptide analogues could prove imperative in the future design of anti-AD agents.
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Affiliation(s)
- Sunil Bansal
- Department
of Medicinal Chemistry and Department of Pharmacology and
Toxicology, National Institute of Pharmaceutical
Education and Research, Sector 67, S.A.S Nagar, 160 062 Punjab, India
| | - Indresh Kumar Maurya
- Department
of Microbial Biotechnology, Punjab University, Sector 14, Chandigarh 160 014, India
| | - Nitin Yadav
- International
Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Chaitanya Kumar Thota
- International
Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Vinod Kumar
- Department
of Medicinal Chemistry and 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 Medicinal Chemistry and 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 Asaf Ali Marg, New Delhi 110 067, India
| | - Rahul Jain
- Department
of Medicinal Chemistry and Department of Pharmacology and
Toxicology, National Institute of Pharmaceutical
Education and Research, Sector 67, S.A.S Nagar, 160 062 Punjab, India
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50
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Mohanrao R, Sureshan KM. Synthesis and Reversible Hydration of a Pseudoprotein, a Fully Organic Polymeric Desiccant by Multiple Single-Crystal-to-Single-Crystal Transformations. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806451] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Raja Mohanrao
- School of Chemistry; Indian Institute of Science Education and Research Thiruvananthapuram; Kerala- 695551 India
| | - Kana M. Sureshan
- School of Chemistry; Indian Institute of Science Education and Research Thiruvananthapuram; Kerala- 695551 India
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