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Jayawardena BM, Azzi A, Jones CE. Investigating the role of phenylalanine residues for amyloid formation of the neuropeptide neurokinin B. Biochem Biophys Res Commun 2024; 705:149732. [PMID: 38447390 DOI: 10.1016/j.bbrc.2024.149732] [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: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Neurokinin B (NKB) is a tachykinin peptide that has diverse roles in biology, including in human reproductive development. Cellular processing of this peptide is thought to involve formation of a dense core vesicle during transit through the regulated secretory pathway. The ability of NKB to rapidly form an amyloid can contribute to formation of the secretory granule but features that support amyloid formation of NKB are not well understood. NKB contains a diphenylalanine sequence well recognised as an important motif for self-assembly of other peptides including amyloid β. Using mutations of the diphenylalanine motif we show that this motif in NKB is necessary for amyloid formation, and it is the unique combination of aromaticity and hydrophobicity of phenylalanine that is crucial for aggregation. Using disulfide cross-linking we propose that phenylalanine at sequence position 6 is important for stabilising inter-sheet interactions in the NKB amyloid fibril. Although having a highly conserved sequence, the NKB peptide from zebrafish only contains a single phenylalanine and does not fibrillise as extensively as mammalian NKB. Analysis of self-assembly of NKB-like peptides from different species may help in elucidating their biological roles. Taken together, this work shows that mammalian NKB has evolved, within only 10 residues, a sequence optimised for rapid self-assembly, whilst also containing residues for metal-binding, receptor binding and receptor discrimination.
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Affiliation(s)
- Bhawantha M Jayawardena
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, New South Wales, Australia
| | - Annabelle Azzi
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, New South Wales, Australia
| | - Christopher E Jones
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, New South Wales, Australia.
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2
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Wang M, Pan D, Zhang Q, Lei Y, Wang C, Jia H, Mou L, Miao X, Ren X, Xu Z. Site-Selective Polyfluoroaryl Modification and Unsymmetric Stapling of Unprotected Peptides. J Am Chem Soc 2024; 146:6675-6685. [PMID: 38427024 DOI: 10.1021/jacs.3c12879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Peptide stapling is recognized as an effective strategy for improving the proteolytic stability and cell permeability of peptides. In this study, we present a novel approach for the site-selective unsymmetric perfluoroaryl stapling of Ser and Cys residues in unprotected peptides. The stapling reaction proceeds smoothly under very mild conditions, exhibiting a remarkably rapid reaction rate. It can furnish stapled products in both liquid and solid phases, and the presence of nucleophilic groups other than Cys thiol within the peptide does not impede the reaction, resulting in uniformly high yields. Importantly, the chemoselective activation of Ser β-C(sp3)-H enables the unreacted -OH to serve as a reactive handle for subsequent divergent modification of the staple moiety with various therapeutic functionalities, including a clickable azido group, a polar moiety, a lipid tag, and a fluorescent dye. In our study, we have also developed a visible-light-induced chemoselective C(sp3)-H polyfluoroarylation of the Ser β-position. This reaction avoids interference with the competitive reaction of Ser -OH, enabling the precise late-stage polyfluoroarylative modification of Ser residues in various unprotected peptides containing other highly reactive amino acid residues. The biological assay suggested that our peptide stapling strategy would potentially enhance the proteolytic stability and cellular permeability of peptides.
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Affiliation(s)
- Mengran Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Da Pan
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Qi Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongjia Lei
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chao Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Haoyuan Jia
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Lingyun Mou
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaokang Miao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoyu Ren
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhaoqing Xu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
- Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou 730000, China
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Wang X, Li B, Yu X, Zhou Y, Wang K, Gao Y. Notoginsenoside R1 ameliorates the inflammation induced by amyloid‑β by suppressing SphK1‑mediated NF‑κB activation in PC12 cells. Mol Med Rep 2024; 29:16. [PMID: 38063180 PMCID: PMC10716814 DOI: 10.3892/mmr.2023.13139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023] Open
Abstract
Alzheimer's disease (AD) is the most common type of age‑related dementia, and causes progressive memory degradation, neuronal loss and brain atrophy. The pathological hallmarks of AD consist of amyloid‑β (Aβ) plaque accumulation and abnormal neurofibrillary tangles. Amyloid fibrils are constructed from Aβ peptides, which are recognized to assemble into toxic oligomers and exert cytotoxicity. The fibrillar Aβ‑protein fragment 25‑35 (Aβ25‑35) induces local inflammation, thereby exacerbating neuronal apoptosis. Notoginsenoside R1 (NGR1), one of the primary bioactive ingredients isolated from Panax notoginseng, exhibits effective anti‑inflammatory and anti‑oxidative activities. However, NGR1 pharmacotherapies targeting Aβ‑induced inflammation and cell injury cascade remain to be elucidated. The present study investigated the effect and mechanism of NGR1 in Aβ25‑35‑treated PC12 cells. NGR1 doses between 250 and 1,000 µg/ml significantly increased cell viability suppressed by 20 µM Aβ25‑35 peptide treatment. Notably, the present study demonstrated that Aβ25‑35 peptide‑induced sphingosine kinase 1 (SphK1) signaling activation was reduced after NGR1 treatment, further inhibiting the downstream NF‑κB inflammatory signaling pathway. In addition, administration of SphK1 inhibitor II (SKI‑II), a SphK1 inhibitor, also significantly reduced Aβ25‑35 peptide‑induced apoptosis and the ratio of NF‑κB p‑p65/p65. Furthermore, SphK1 knockdown in PC12 cells using small interfering RNA alleviated Aβ‑induced cell apoptosis and inflammation, suggesting a pivotal role of SphK1 signaling in the anti‑inflammatory effect of NGR1. In summary, NGR1 alleviated inflammation and apoptosis stimulated by Aβ25‑35 by inhibiting the SphK1/NF‑κB signaling pathway and may be a promising agent for future AD treatment.
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Affiliation(s)
- Xiaonan Wang
- Department of Geriatric Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Bei Li
- Department of Geriatric Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaohong Yu
- Department of Geriatric Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Ye Zhou
- Department of Geriatric Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Kaile Wang
- Department of Geriatric Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Yue Gao
- Department of Geriatric Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
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Liu X, Duan S, Jin Y, Walker E, Tsao M, Jang JH, Chen Z, Singh AK, Cantrell KL, Ingolfsson HI, Buratto SK, Bowers MT. Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43 307-319 Aggregation. ACS Chem Neurosci 2023; 14:4395-4408. [PMID: 38050862 DOI: 10.1021/acschemneuro.3c00582] [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] [Indexed: 12/07/2023] Open
Abstract
Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43307-319, but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43307-319 monomer. The JPS-designed molecules can insert themselves between the β-strands in the hexameric cylindrin structure of TDP-43307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43307-319 oligomers on an atomistic scale are proposed.
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Affiliation(s)
- Xikun Liu
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Shuya Duan
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yingying Jin
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ethan Walker
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Michelle Tsao
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joshua H Jang
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Ziying Chen
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ambuj K Singh
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kristi Lazar Cantrell
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Helgi I Ingolfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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Mukherjee N, Ghosh S. Substance P-Derived Extracellular-Matrix-Mimicking Peptide Hydrogel as a Cytocompatible Biomaterial Platform. Chembiochem 2023; 24:e202300286. [PMID: 37461811 DOI: 10.1002/cbic.202300286] [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: 04/10/2023] [Revised: 07/15/2023] [Indexed: 08/19/2023]
Abstract
Self-assembled short peptide-based hydrogel platforms have become widely applicable biomedical therapeutic maneuvers for their soft, tunable architecture, which can influence cellular behavior and morphology to an inordinate extent. In this work, a short supramolecular hydrogelator peptide, substance P, has been designed and synthesized from the C terminus conserved "FFGLM" section of a biologically abundant neuropeptide by using a fusion approach. In addition, to incorporate a good hydrophobic-hydrophilic balance, the truncated pentapeptide segment was further C-terminally modified by the incorporation of an integrin-binding "RGD" motif. Thanks to its N-terminal Fmoc group, this octapeptide ensemble "FFGLMRGD" undergoes rapid self-assembly to give rise to an injectable, pH-responsive, hydrogel-based self-supporting platform that exhibited good cytocompatibility with the cultured mammalian cells under both 2D and 3D culture conditions without exerting any potent cytotoxic effect in a Live/Dead experiment. A rheological experiment demonstrated its hydrogel-like mechanical properties, including thixotropicity. The atomic force microscopy and field emission scanning electron microscopy images of the fabricated hydrogel show a tangled fibrous surface topography owing to the presence of the N-terminal Fmoc-FF residue. Furthermore, an in-vitro scratch assay performed on fibroblast cell lines confirmed the wound-ameliorating potency of this designed hydrogel; this substantiates its future therapeutic prospects.
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Affiliation(s)
- Nabanita Mukherjee
- Smart Healthcare, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan, 342037, India
| | - Surajit Ghosh
- Smart Healthcare, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan, 342037, India
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan, 342037, India
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Gutierrez-Merino C. Brain Hydrophobic Peptides Antagonists of Neurotoxic Amyloid β Peptide Monomers/Oligomers-Protein Interactions. Int J Mol Sci 2023; 24:13846. [PMID: 37762148 PMCID: PMC10531495 DOI: 10.3390/ijms241813846] [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: 08/04/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Amyloid β (Aβ) oligomers have been linked to Alzheimer's disease (AD) pathogenesis and are the main neurotoxic forms of Aβ. This review focuses on the following: (i) the Aβ(1-42):calmodulin interface as a model for the design of antagonist Aβ peptides and its limitations; (ii) proteolytic degradation as the major source of highly hydrophobic peptides in brain cells; and (iii) brain peptides that have been experimentally demonstrated to bind to Aβ monomers or oligomers, Aβ fibrils, or Aβ plaques. It is highlighted that the hydrophobic amino acid residues of the COOH-terminal segment of Aβ(1-42) play a key role in its interaction with intracellular protein partners linked to its neurotoxicity. The major source of highly hydrophobic endogenous peptides of 8-10 amino acids in neurons is the proteasome activity. Many canonical antigen peptides bound to the major histocompatibility complex class 1 are of this type. These highly hydrophobic peptides bind to Aβ and are likely to be efficient antagonists of the binding of Aβ monomers/oligomers concentrations in the nanomolar range with intracellular proteins. Also, their complexation with Aβ will protect them against endopeptidases, suggesting a putative chaperon-like physiological function for Aβ that has been overlooked until now. Remarkably, the hydrophobic amino acid residues of Aβ responsible for the binding of several neuropeptides partially overlap with those playing a key role in its interaction with intracellular protein partners that mediates its neurotoxicity. Therefore, these latter neuropeptides are also potential candidates to antagonize Aβ peptides binding to target proteins. In conclusion, the analysis performed in this review points out that hydrophobic endogenous brain neuropeptides could be valuable biomarkers to evaluate the risk of the onset of sporadic AD, as well as for the prognosis of AD.
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Affiliation(s)
- Carlos Gutierrez-Merino
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain
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Nguyen PH, Sterpone F, Derreumaux P. Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers. Proteins 2023. [PMID: 37038252 DOI: 10.1002/prot.26495] [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: 12/14/2022] [Revised: 02/15/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023]
Abstract
Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and simulations on Aβ42 monomer point to random coil conformations with either transient helical or β-strand content. Our current conformational description of small Aβ42 oligomers is funneled toward amorphous aggregates with some β-sheet content and rare high energy states with well-ordered assemblies of β-sheets. In this study, we emphasize another view based on metastable α-helix bundle oligomers spanning the C-terminal residues, which are predicted by the machine-learning AlphaFold2 method and supported indirectly by low-resolution experimental data on many amyloid polypeptides. This finding has consequences in developing novel chemical tools and to design potential therapies to reduce aggregation and toxicity.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut Universitaire de France (IUF), Paris, 75005, France
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Zhu M, Tang M, Du Y. Identification of TAC1 Associated with Alzheimer's Disease Using a Robust Rank Aggregation Approach. J Alzheimers Dis 2023; 91:1339-1349. [PMID: 36617784 DOI: 10.3233/jad-220950] [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: 01/07/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) brings heavy burden to society and family. There is an urgent need to find effective methods for disease diagnosis and treatment. The robust rank aggregation (RRA) approach that could aggregate the resulting gene lists has been widely utilized in genomic data analysis. OBJECTIVE To identify hub genes using RRA approach in AD. METHODS Seven microarray datasets in frontal cortex from GEO database were used to identify differential expressed genes (DEGs) in AD patients using RRA approach. STRING was performed to explore the protein-to-protein interaction (PPI). Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses were utilized for enrichment analysis. Human Gene Connectome and Gene Set Enrichment Analysis were used for functional annotation. Finally, the expression levels of hub genes were validated in the cortex of 5xFAD mice by quantitative real-time polymerase chain reaction. RESULTS After RRA analysis, 473 DEGs (216 upregulated and 257 downregulated) were identified in AD samples. PPI showed that DEGs had a total of 416 nodes and 2750 edges. These genes were divided into 17 clusters, each of which contains at least three genes. After functional annotation and enrichment analysis, TAC1 is identified as the hub gene and may be related to synaptic function and inflammation. In addition, Tac1 was found downregulated in cortices of 5xFAD mice. CONCLUSION In the current study, TAC1 is identified as a key gene in the frontal cortex of AD, providing insight into the possible pathogenesis and potential therapeutic targets for this disease.
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Affiliation(s)
- Min Zhu
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, People's Republic of China.,Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Minglu Tang
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, People's Republic of China.,Department of Neurology (Cognitive sleep ward), Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Yifeng Du
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, People's Republic of China.,Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
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