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Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site. Heliyon 2022; 8:e11568. [PMID: 36406731 PMCID: PMC9663143 DOI: 10.1016/j.heliyon.2022.e11568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus identified as the cause of the coronavirus outbreak in December 2019 (COVID-19). Like all the RNA viruses, SARS-CoV-2 constantly evolves through mutations in its genome, accumulating 1–2 nucleotide changes every month, giving the virus a selective advantage through enhanced transmissibility, greater pathogenicity, and the possibility of circumventing immunity previously acquired by an individual either by natural infection or by vaccination. Several SARS-CoV-2 variants of concern (VoC) have been identified, among which we find Alpha (Lineage B.1.1.7), Beta (Lineage B.1.351), and Gamma (Lineage P.1) variants. Most of the mutations occur in the spike (S) protein, a surface glycoprotein that plays a crucial role in viral infection; the S protein binds the host cell receptor, the angiotensin-converting enzyme of type 2 (ACE2) via the receptor binding domain (RBD) and catalyzes the fusion of the viral membrane with the host cell. In this work, we present the development of a simplified system that would afford to study the change in the SARS-CoV-2 S RBD/ACE2 binding related to the frequent mutations. In particular, we synthesized and studied the structure of short amino acid sequences, mimicking the two proteins’ critical portions. Variations in the residues were easily managed through the one-point alteration of the sequences. Nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies provide insights into ACE2 and SARS-CoV-2 S RBD structure with its related three variants (Alpha, Beta, and Gamma). Spectroscopy data supported by molecular dynamics lead to the description of an ACE2/RBD binding model in which the effect of a single amino acid mutation in changing the binding of S protein to the ACE2 receptor is predictable.
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Santoro A, Grimaldi M, Buonocore M, Stillitano I, Gloria A, Santin M, Bobba F, Sublimi Saponetti M, Ciaglia E, D'Ursi AM. New Aβ(1-42) ligands from anti-amyloid antibodies: Design, synthesis, and structural interaction. Eur J Med Chem 2022; 237:114400. [PMID: 35489223 DOI: 10.1016/j.ejmech.2022.114400] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/17/2022] [Accepted: 04/15/2022] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease (AD), is the most common neurodegenerative disorder of the aging population resulting in progressive cognitive and functional decline. Accumulation of amyloid plaques around neuronal cells is considered a critical pathogenetic event and, in most cases, a hallmark of the pathology. In the attempt to identify anti-AD drug candidates, hundreds of molecules targeting Aβ peptides have been screened. Peptide molecules have been widely explored, appreciating chemical stability, biocompatibility, and low production cost. More recently, many anti-Aβ(1-42) monoclonal antibodies have been developed, given the excellent potential of immunotherapy for treating or preventing AD. Antibodies are versatile ligands that bind a large variety of molecules with high affinity and specificity; however, their extensive therapeutic application is complex and requires huge economic investments. Novel approaches to identify alternative antibody formats are considered with great interest. In this context, taking advantage of the favorable peptide properties and the availability of Aβ-antibodies structural data, we followed an innovative research approach to identify short peptide sequences on the model of the binding sites of Aβ(1-42)/antibodies. WAibH and SYSTPGK were designed as mimics of solanezumab and aducanumab, respectively. Circular dichroism and nuclear magnetic resonance analysis reveal that the antibody-derived peptides interact with Aβ(1-42) in the soluble monomeric form. Moreover, AFM microscopy imaging shows that WAibH and SYSTPGK are capable of controlling the Aβ(1-42) aggregation. The strategy to identify WAibH and SYSTPGK is innovative and can be widely applied for new anti-Aβ antibody mimicking peptides.
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Affiliation(s)
- Angelo Santoro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy
| | - Manuela Grimaldi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy
| | - Michela Buonocore
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy
| | - Ilaria Stillitano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy
| | - Antonio Gloria
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, V.le J.F. Kennedy 54 - Pad. 20, Mostra d'Oltremare, 80125, Naples, Italy
| | - Matteo Santin
- Centre for Regenerative Medicine and Devices, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - Fabrizio Bobba
- Department of Physics, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy
| | - Matilde Sublimi Saponetti
- Department of Physics, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Via Salvatore Allende, 84081, Baronissi, Salerno, Italy
| | - Anna Maria D'Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132 - 84084, Fisciano, Salerno, Italy.
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Ashrafian H, Zadeh EH, Khan RH. Review on Alzheimer's disease: Inhibition of amyloid beta and tau tangle formation. Int J Biol Macromol 2020; 167:382-394. [PMID: 33278431 DOI: 10.1016/j.ijbiomac.2020.11.192] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/18/2020] [Accepted: 11/28/2020] [Indexed: 12/19/2022]
Abstract
It is reported that approximately 40 million people are suffering from dementia, globally. Dementia is a group of symptoms that affect neurons and cause some mental disorders, such as losing memory. Alzheimer's disease (AD) which is known as the most common cause of dementia, is one of the top medical care concerns across the world. Although the exact sources of the disease are not understood, is it believed that aggregation of amyloid-beta (Aβ) outside of neuron cells and tau aggregation or neurofibrillary tangles (NFTs) formation inside the cell may play crucial roles. In this paper, we are going to review studies that targeted inhibition of amyloid plaque and tau protein tangle formation, to suppress or postpone AD.
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Affiliation(s)
- Hossein Ashrafian
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA; Department of Chemistry, Sharif University of Technology, Tehran, Iran.
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Xu J, Wang K, Yuan Y, Li H, Zhang R, Guan S, Wang L. A Novel Peroxidase Mimics and Ameliorates Alzheimer's Disease-Related Pathology and Cognitive Decline in Mice. Int J Mol Sci 2018; 19:ijms19113304. [PMID: 30352982 PMCID: PMC6274722 DOI: 10.3390/ijms19113304] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/14/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder in the elderly, which is characterized by the accumulation of amyloid β (Aβ) plaques, oxidative stress, and neuronal loss. Therefore, clearing Aβ aggregates and reducing oxidative stress could be an effective therapeutic strategy for AD. Deuterohemin-AlaHisThrValGluLys (DhHP-6), a novel deuterohemin-containing peptide mimetic of the natural microperoxidase-11 (MP-11), shows higher antioxidant activity and stability compared to the natural microperoxidases. DhHP-6 possesses the ability of extending lifespan and alleviating paralysis in the Aβ1-42 transgenic Caenorhabditis elegans CL4176 model of AD, as shown in our previous study. Therefore, this study was aimed at exploring the neuroprotective effect of DhHP-6 in the APPswe/PSEN1dE9 transgenic mouse model of AD. DhHP-6 reduced the diameter and fiber structure of Aβ1-42 aggregation in vitro, as shown by dynamic light scattering and transmission electron microscope. DhHP-6 exerted its neuroprotective effect by inhibiting Aβ aggregation and plaque formation, and by reducing Aβ1-42 oligomers-induced neurotoxicity on HT22 (mouse hippocampal neuronal) and SH-SY5Y (human neuroblastoma) cells. In the AD mouse model, DhHP-6 significantly ameliorated cognitive decline and improved spatial learning ability in behavioral tests including the Morris water maze, Y-maze, novel object recognition, open field, and nest-building test. Moreover, DhHP-6 reduced the deposition of Aβ plaques in the cerebral cortex and hippocampus. More importantly, DhHP-6 restored the morphology of astrocytes and microglia, and significantly reduced the levels of pro-inflammatory cytokines. Our findings provide a basis for considering the non-toxic, peroxidase mimetic DhHP-6 as a new candidate drug against AD.
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Affiliation(s)
- Jia Xu
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Kai Wang
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Ye Yuan
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Hui Li
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Ruining Zhang
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Shuwen Guan
- School of Life Sciences, Jilin University, Changchun 130012, China.
- Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun 130012, China.
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin Universtiy, Changchun 130012, China.
| | - Liping Wang
- School of Life Sciences, Jilin University, Changchun 130012, China.
- Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun 130012, China.
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin Universtiy, Changchun 130012, China.
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β-Amyloid-acetylcholine molecular interaction: new role of cholinergic mediators in anti-Alzheimer therapy? Future Med Chem 2016; 8:1179-89. [PMID: 27402297 DOI: 10.4155/fmc-2016-0006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND For long time Alzheimer's disease has been attributed to a cholinergic deficit. More recently, it has been considered dependent on the accumulation of the amyloid beta peptide (Aβ), which promotes neuronal loss and impairs neuronal function. Results/methodology: In the present study, using biophysical and biochemical experiments we tested the hypothesis that in addition to its role as a neurotransmitter, acetylcholine may exert its action as an anti-Alzheimer agent through a direct interaction with Aβ. CONCLUSION Our data provide evidence that acetylcholine favors the soluble peptide conformation and exerts a neuroprotective effect against the neuroinflammatory and toxic effects of Aβ. The present paper paves the way toward the development of new polyfunctional anti-Alzheimer therapeutics capable of intervening on both the cholinergic transmission and the Aβ aggregation.
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Bag S, Chaudhury S, Pramanik D, DasGupta S, Dasgupta S. Hydrophobic tail length plays a pivotal role in amyloid beta (25-35) fibril-surfactant interactions. Proteins 2016; 84:1213-23. [DOI: 10.1002/prot.25069] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/05/2016] [Accepted: 05/12/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Sudipta Bag
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | | | - Dibyendu Pramanik
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Sunando DasGupta
- Department of Chemical Engineering; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Swagata Dasgupta
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
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Emendato A, Spadaccini R, De Santis A, Guerrini R, D'Errico G, Picone D. Preferential interaction of the Alzheimer peptide Aβ-(1-42) with Omega-3-containing lipid bilayers: structure and interaction studies. FEBS Lett 2016; 590:582-91. [PMID: 26821608 DOI: 10.1002/1873-3468.12082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 01/08/2023]
Abstract
Many age-related neurodegenerative diseases, including Alzheimer Disease (AD), are elicited by an interplay of genetic, environmental, and dietary factors. Food rich in Omega-3 phospholipids seems to reduce the AD incidence. To investigate the molecular basis of this beneficial effect, we have investigated by CD and ESR studies the interaction between the Alzheimer peptide Aβ-(1-42) and biomimetic lipid bilayers. The inclusion of 1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine does not change significantly the bilayers organization, but favors its Aβ-(1-42) interaction. The Omega-3 lipid amount modulates the effect intensity, suggesting a peptide selectivity for membranes containing polyunsatured fatty acids (PUFA) and providing hints for the mechanism and therapy of AD.
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Affiliation(s)
| | - Roberta Spadaccini
- Department of Chemical Sciences, University of Naples Federico II, Italy.,Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Augusta De Santis
- Department of Chemical Sciences, University of Naples Federico II, Italy.,CSGI, Consorzio interuniversitario per lo sviluppo dei Sistemi a Grande Interfase, Unit of Naples, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences and Laboratorio per le tecnologie delle terapie avanzate (LTTA), University of Ferrara, Italy
| | - Gerardino D'Errico
- Department of Chemical Sciences, University of Naples Federico II, Italy.,CSGI, Consorzio interuniversitario per lo sviluppo dei Sistemi a Grande Interfase, Unit of Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Italy
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Aggregation of Aß(25-35) on DOPC and DOPC/DHA bilayers: an atomic force microscopy study. PLoS One 2014; 9:e115780. [PMID: 25551704 PMCID: PMC4281140 DOI: 10.1371/journal.pone.0115780] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023] Open
Abstract
β amyloid peptide plays an important role in both the manifestation and progression of Alzheimer disease. It has a tendency to aggregate, forming low-molecular weight soluble oligomers, higher-molecular weight protofibrillar oligomers and insoluble fibrils. The relative importance of these single oligomeric-polymeric species, in relation to the morbidity of the disease, is currently being debated. Here we present an Atomic Force Microscopy (AFM) study of Aβ(25–35) aggregation on hydrophobic dioleoylphosphatidylcholine (DOPC) and DOPC/docosahexaenoic 22∶6 acid (DHA) lipid bilayers. Aβ(25–35) is the smallest fragment retaining the biological activity of the full-length peptide, whereas DOPC and DOPC/DHA lipid bilayers were selected as models of cell-membrane environments characterized by different fluidity. Our results provide evidence that in hydrophobic DOPC and DOPC/DHA lipid bilayers, Aβ(25-35) forms layered aggregates composed of mainly annular structures. The mutual interaction between annular structures and lipid surfaces end-results into a membrane solubilization. The presence of DHA as a membrane-fluidizing agent is essential to protect the membrane from damage caused by interactions with peptide aggregates; to reduces the bilayer defects where the delipidation process starts.
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Lin LX, Bo XY, Tan YZ, Sun FX, Song M, Zhao J, Ma ZH, Li M, Zheng KJ, Xu SM. Feasibility of β-sheet breaker peptide-H102 treatment for Alzheimer's disease based on β-amyloid hypothesis. PLoS One 2014; 9:e112052. [PMID: 25372040 PMCID: PMC4221228 DOI: 10.1371/journal.pone.0112052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 10/11/2014] [Indexed: 01/29/2023] Open
Abstract
β-amyloid hypothesis is the predominant hypothesis in the study of pathogenesis of Alzheimer's disease. This hypothesis claims that aggregation and neurotoxic effects of amyloid β (Aβ) is the common pathway in a variety of etiological factors for Alzheimer's disease. Aβ peptide derives from amyloid precursor protein (APP). β-sheet breaker peptides can directly prevent and reverse protein misfolding and aggregation in conformational disorders. Based on the stereochemical structure of Aβ1-42 and aggregation character, we had designed a series of β-sheet breaker peptides in our previous work and screened out a 10-residue peptide β-sheet breaker peptide, H102. We evaluated the effects of H102 on expression of P-tau, several associated proteins, inflammatory factors and apoptosis factors, and examined the cognitive ability of APP transgenic mice by behavioral test. This study aims to validate the β-amyloid hypothesis and provide an experimental evidence for the feasibility of H102 treatment for Alzheimer's disease.
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Affiliation(s)
- Lai-xiang Lin
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Hormone and Development (Ministry of Health), Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Xiang-yu Bo
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Yuan-zhen Tan
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Feng-xian Sun
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Ming Song
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Juan Zhao
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Zhi-hong Ma
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Mei Li
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Kai-jun Zheng
- Department of physiology, Tianjin Medical University, Tianjin, China
| | - Shu-mei Xu
- Department of physiology, Tianjin Medical University, Tianjin, China
- * E-mail:
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Vitiello G, Di Marino S, D'Ursi AM, D'Errico G. Omega-3 fatty acids regulate the interaction of the Alzheimer's aβ(25-35) peptide with lipid membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14239-14245. [PMID: 24144219 DOI: 10.1021/la403416b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Polyunsaturated omega-3 fatty acids are increasingly proposed as dietary supplements able to reduce the risk of development or progression of the Alzheimer's disease (AD). To date, the molecular mechanism through which these lipids act has not been yet univocally identified. In this work, we investigate whether omega-3 fatty acids could interfere with the fate of the Alzheimer-related amyloid peptide by tuning the microstructural and dynamical properties of the neuronal membrane. To this aim, the influence of the omega-3 lipid, 1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine [22:6(cis)PC] on the biophysical properties of lipid bilayers, and on their interaction with the amyloid peptide fragment Aβ(25-35) has been investigated by Electron Spin Resonance (ESR), using spin-labeled phospholipids. The results show that the peptide selectively interacts with bilayers enriched in cholesterol (Chol) and sphingomyelin (SM). [22:6(cis)PC] enhances the Aβ(25-35)/membrane interaction, favoring a deeper internalization of the peptide among the lipid acyl chains and, consequently, hindering its pathogenic self-aggregation.
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Affiliation(s)
- Giuseppe Vitiello
- Department of Chemical Science, University of Naples ''Federico II'' , Complesso di Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy
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