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Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanit S, Thaisakun S, Kumsri N, Arpornsuwan T. Secretomic changes of amyloid beta peptides on Alzheimer's disease related proteins in differentiated human SH-SY5Y neuroblastoma cells. PeerJ 2024; 12:e17732. [PMID: 39035166 PMCID: PMC11260076 DOI: 10.7717/peerj.17732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that causes physical damage to neuronal connections, leading to brain atrophy. This disruption of synaptic connections results in mild to severe cognitive impairments. Unfortunately, no effective treatment is currently known to prevent or reverse the symptoms of AD. The aim of this study was to investigate the effects of three synthetic peptides, i.e., KLVFF, RGKLVFFGR and RIIGL, on an AD in vitro model represented by differentiated SH-SY5Y neuroblastoma cells exposed to retinoic acid (RA) and brain-derived neurotrophic factor (BDNF). The results demonstrated that RIIGL peptide had the least significant cytotoxic activity to normal SH-SY5Y while exerting high cytotoxicity against the differentiated cells. The mechanism of RIIGL peptide in the differentiated SH-SY5Y was investigated based on changes in secretory proteins compared to another two peptides. A total of 380 proteins were identified, and five of them were significantly detected after treatment with RIIGL peptide. These secretory proteins were found to be related to microtubule-associated protein tau (MAPT) and amyloid-beta precursor protein (APP). RIIGL peptide acts on differentiated SH-SY5Y by regulating amyloid-beta formation, neuron apoptotic process, ceramide catabolic process, and oxidative phosphorylation and thus has the potentials to treat AD.
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Affiliation(s)
- Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitithorn Kumsri
- Undergraduate Student of Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumtani, Thailand
| | - Teerakul Arpornsuwan
- Medical Technology Research and Service Unit, Health Care Service Center, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
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Nayak K, Ghosh P, Barman S, Sudhamalla B, Theato P, De P. Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis. Bioconjug Chem 2024; 35:312-323. [PMID: 38420925 DOI: 10.1021/acs.bioconjchem.3c00509] [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
Developing effective amyloidosis inhibitors poses a significant challenge due to the dynamic nature of the protein structures, the complex interplay of interfaces in protein-protein interactions, and the irreversible nature of amyloid assembly. The interactions of amyloidogenic polypeptides with other peptides play a pivotal role in modulating amyloidosis and fibril formation. This study presents a novel approach for designing and synthesizing amyloid interaction surfaces using segments derived from the amyloid-promoting sequence of amyloid β-peptide [VF(Aβ(18-19)/FF(Aβ(19-20)/LVF(Aβ(17-19)/LVFF(Aβ(17-20)], where VF, FF, LVF and LVFF stands for valine phenylalanine dipeptide, phenylalanine phenylalanine dipeptide, leucine valine phenylalanine tripeptide and leucine valine phenylalanine phenylalanine tetrapeptide, respectively. These segments are conjugated with side-chain proline-based methacrylate polymers serving as potent lysozyme amyloidosis inhibitors and demonstrating reduced cytotoxicity of amyloid aggregations. Di-, tri-, and tetra-peptide conjugated chain transfer agents (CTAs) were synthesized and used for the reversible addition-fragmentation chain transfer polymerization of tert-butoxycarbonyl (Boc)-proline methacryloyloxyethyl ester (Boc-Pro-HEMA). Deprotection of Boc-groups from the side-chain proline pendants resulted in water-soluble polymers with defined peptide chain ends as peptide-polymer bioconjugates. Among them, the LVFF-conjugated polymer acted as a potent inhibitor with significantly suppressed lysozyme amyloidosis, a finding supported by comprehensive spectroscopic, microscopic, and computational analyses. These results unveil the synergistic effect between the segment-derived amyloid β-peptide and side-chain proline-based polymers, offering new prospects for targeting lysozyme amyloidosis.
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Affiliation(s)
- Kasturee Nayak
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Pooja Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
- Centre for Interdisciplinary Sciences, JIS Institute of Advanced Studies & Research (JISIASR) Kolkata, JIS University, GP Block, Sector-5, Salt Lake, Kolkata, West Bengal 700091, India
| | - Soumen Barman
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Patrick Theato
- Karlsruhe Institute of Technology (KIT), Institute for Chemical Technology and Polymer Chemistry (ITCP), Engesserstraße 18, Karlsruhe 76131, Germany
- Karlsruhe Institute of Technology (KIT), Soft Matter Synthesis Laboratory,Institute for Biological Interfaces III (IBG-3), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
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Andrikopoulos N, Tang H, Wang Y, Liang X, Li Y, Davis TP, Ke PC. Exploring Peptido-Nanocomposites in the Context of Amyloid Diseases. Angew Chem Int Ed Engl 2024; 63:e202309958. [PMID: 37943171 DOI: 10.1002/anie.202309958] [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: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
Therapeutic peptides are a major class of pharmaceutical drugs owing to their target-binding specificity as well as their versatility in inhibiting aberrant protein-protein interactions associated with human pathologies. Within the realm of amyloid diseases, the use of peptides and peptidomimetics tailor-designed to overcome amyloidogenesis has been an active research endeavor since the late 90s. In more recent years, incorporating nanoparticles for enhancing the biocirculation and delivery of peptide drugs has emerged as a frontier in nanomedicine, and nanoparticles have further demonstrated a potency against amyloid aggregation and cellular inflammation to rival strategies employing small molecules, peptides, and antibodies. Despite these efforts, however, a fundamental understanding of the chemistry, characteristics and function of peptido-nanocomposites is lacking, and a systematic analysis of such strategy for combating a range of amyloid pathogeneses is missing. Here we review the history, principles and evolving chemistry of constructing peptido-nanocomposites from bottom up and discuss their future application against amyloid diseases that debilitate a significant portion of the global population.
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Affiliation(s)
- Nicholas Andrikopoulos
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- College of Mechanics and Materials, Hohai University, Nanjing, 211100, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yue Wang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Xiufang Liang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Yuhuan Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Thomas P Davis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Pu Chun Ke
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
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Kaur A, Goyal B. Identification of new pentapeptides as potential inhibitors of amyloid-β 42 aggregation using virtual screening and molecular dynamics simulations. J Mol Graph Model 2023; 124:108558. [PMID: 37390790 DOI: 10.1016/j.jmgm.2023.108558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease mainly characterized by extracellular accumulation of amyloid-β (Aβ) peptide. Previous studies reported pentapeptide RIIGL as an effective inhibitor of Aβ aggregation and neurotoxicity induced by Aβ aggregates. In this work, a library of 912 pentapeptides based on RIIGL has been designed and assessed for their efficacy to inhibit Aβ42 aggregation using computational techniques. The top hit pentapeptides revealed by molecular docking were further assessed for their binding affinity with Aβ42 monomer using MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method. The MM-PBSA analysis identified RLAPV, RVVPI, and RIAPA, which bind to Aβ42 monomer with a higher binding affinity -55.80, -46.32, and -44.26 kcal/mol, respectively, as compared to RIIGL (ΔGbinding = -41.29 kcal/mol). The residue-wise binding free energy predicted hydrophobic contacts between Aβ42 monomer and pentapeptides. The secondary structure analysis of the conformational ensembles generated by molecular dynamics (MD) depicted remarkably enhanced sampling of helical and no β-sheet conformations in Aβ42 monomer on the incorporation of RVVPI and RIAPA. Notably, RVVPI and RIAPA destabilized the D23-K28 salt bridge in Aβ42 monomer, which plays a crucial role in Aβ42 oligomer stability and fibril formation. The MD simulations highlighted that the incorporation of proline and arginine in pentapeptides contributed to their strong binding with Aβ42 monomer. Furthermore, RVVPI and RIAPA prevented conformational conversion of Aβ42 monomer to aggregation-prone structures, which, in turn, resulted in a lower aggregation tendency of Aβ42 monomer.
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Affiliation(s)
- Apneet Kaur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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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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Shahpasand-Kroner H, Siddique I, Malik R, Linares GR, Ivanova MI, Ichida J, Weil T, Münch J, Sanchez-Garcia E, Klärner FG, Schrader T, Bitan G. Molecular Tweezers: Supramolecular Hosts with Broad-Spectrum Biological Applications. Pharmacol Rev 2023; 75:263-308. [PMID: 36549866 PMCID: PMC9976797 DOI: 10.1124/pharmrev.122.000654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.
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Affiliation(s)
- Hedieh Shahpasand-Kroner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gabriel R Linares
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Magdalena I Ivanova
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Justin Ichida
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Tatjana Weil
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Jan Münch
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Frank-Gerrit Klärner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Thomas Schrader
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
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7
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Ghosh S, Ali R, Verma S. Aβ-oligomers: A potential therapeutic target for Alzheimer's disease. Int J Biol Macromol 2023; 239:124231. [PMID: 36996958 DOI: 10.1016/j.ijbiomac.2023.124231] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The cascade of amyloid formation relates to multiple complex events at the molecular level. Previous research has established amyloid plaque deposition as the leading cause of Alzheimer's disease (AD) pathogenesis, detected mainly in aged population. The primary components of the plaques are two alloforms of amyloid-beta (Aβ), Aβ1-42 and Aβ1-40 peptides. Recent studies have provided considerable evidence contrary to the previous claim indicating that amyloid-beta oligomers (AβOs) as the main culprit responsible for AD-associated neurotoxicity and pathogenesis. In this review, we have discussed the primary features of AβOs, such as assembly formation, the kinetics of oligomer formation, interactions with various membranes/membrane receptors, the origin of toxicity, and oligomer-specific detection methods. Recently, the discovery of rationally designed antibodies has opened a gateway for using synthesized peptides as a grafting component in the complementarity determining region (CDR) of antibodies. Thus, the Aβ sequence motif or the complementary peptide sequence in the opposite strand of the β-sheet (extracted from the Protein Data Bank: PDB) helps design oligomer-specific inhibitors. The microscopic event responsible for oligomer formation can be targeted, and thus prevention of the overall macroscopic behaviour of the aggregation or the associated toxicity can be achieved. We have carefully reviewed the oligomer formation kinetics and associated parameters. Besides, we have depicted a thorough understanding of how the synthesized peptide inhibitors can impede the early aggregates (oligomers), mature fibrils, monomers, or a mixture of the species. The oligomer-specific inhibitors (peptides or peptide fragments) lack in-depth chemical kinetics and optimization control-based screening. In the present review, we have proposed a hypothesis for effectively screening oligomer-specific inhibitors using the chemical kinetics (determining the kinetic parameters) and optimization control strategy (cost-dependent analysis). Further, it may be possible to implement the structure-kinetic-activity-relationship (SKAR) strategy instead of structure-activity-relationship (SAR) to improve the inhibitor's activity. The controlled optimization of the kinetic parameters and dose usage will be beneficial for narrowing the search window for the inhibitors.
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Mallesh R, Juhee khan, Gharai PK, Gupta V, Roy R, Ghosh S. Controlling Amyloid Beta Peptide Aggregation and Toxicity by Protease-Stable Ligands. ACS BIO & MED CHEM AU 2023; 3:158-173. [PMID: 37101809 PMCID: PMC10125337 DOI: 10.1021/acsbiomedchemau.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 02/17/2023]
Abstract
Polymerization of soluble amyloid beta (Aβ) peptide into protease-stable insoluble fibrillary aggregates is a critical step in the pathogenesis of Alzheimer's disease (AD). The N-terminal (NT) hydrophobic central domain fragment 16KLVFF20 plays an important role in the formation and stabilization of β-sheets by self-recognition of the parent Aβ peptide, followed by aggregation of Aβ in the AD brain. Here, we analyze the effect of the NT region inducing β-sheet formation in the Aβ peptide by a single amino acid mutation in the native Aβ peptide fragment. We designed 14 hydrophobic peptides (NT-01 to NT-14) by a single mutation at 18Val by using hydrophobic residues leucine and proline in the natural Aβ peptide fragment (KLVFFAE) and analyzed its effect on the formation of Aβ aggregates. Among all these peptides, NT-02, NT-03, and NT-13 significantly affected the Aβ aggregate formation. When the NT peptides were coincubated with the Aβ peptide, a significant reduction in β-sheet formation and increment in random coil content of Aβ was seen, confirmed by circular dichroism spectroscopy and Fourier transform infrared spectroscopy, followed by the reduction of fibril formation measured by the thioflavin-T (ThT) binding assay. The aggregation inhibition was monitored by Congo red and ThT staining and electron microscopic examination. Moreover, the NT peptides protect the PC-12 differentiated neurons from Aβ-induced toxicity and apoptosis in vitro. Thus, manipulation of the Aβ secondary structure with protease-stable ligands that promote the random coil conformation may provide a tool to control the Aβ aggregates observed in AD patients.
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Affiliation(s)
- Rathnam Mallesh
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan 168, Maniktala Main Road, Kolkata 700054, India
| | - Juhee khan
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Prabir Kumar Gharai
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Varsha Gupta
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Surajit Ghosh
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan 168, Maniktala Main Road, Kolkata 700054, India
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9
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Perugini V, Santin M. The Real-Time Validation of the Effectiveness of Third-Generation Hyperbranched Poly(ɛ-lysine) Dendrons-Modified KLVFF Sequences to Bind Amyloid-β 1-42 Peptides Using an Optical Waveguide Light-Mode Spectroscopy System. SENSORS (BASEL, SWITZERLAND) 2022; 22:9561. [PMID: 36502262 PMCID: PMC9736926 DOI: 10.3390/s22239561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/23/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The aggregation of cytotoxic amyloid peptides (Aβ1-42) is widely recognised as the cause of brain tissue degeneration in Alzheimer's disease (AD). Indeed, evidence indicates that the deposition of cytotoxic Aβ1-42 plaques formed through the gradual aggregation of Aβ1-42 monomers into fibrils determines the onset of AD. Thus, distinct Aβ1-42 inhibitors have been developed, and only recently, the use of short linear peptides has shown promising results by either preventing or reversing the process of Aβ1-42 aggregation. Among them, the KLVFF peptide sequence, which interacts with the hydrophobic region of Aβ16-20, has received widespread attention due to its ability to inhibit fibril formation of full-length Aβ1-42. In this study, hyperbranched poly-L-lysine dendrons presenting sixteen KLVFF at their uppermost molecular branches were designed with the aim of providing the KLVFF sequence with a molecular scaffold able to increase its stability and of improving Aβ1-42 fibril formation inhibitory effect. These high-purity branched KLVFF were used to functionalise the surface of the metal oxide chip of the optical waveguide lightmode spectroscopy sensor showing the more specific, accurate and rapid measurement of Aβ1-42 than that detected by linear KLVFF peptides.
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10
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Davidson DS, Kraus JA, Montgomery JM, Lemkul JA. Effects of Familial Alzheimer's Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide. J Phys Chem B 2022; 126:7552-7566. [PMID: 36150020 PMCID: PMC9547858 DOI: 10.1021/acs.jpcb.2c03520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Familial Alzheimer's disease (FAD) mutations of the amyloid β-peptide (Aβ) are known to lead to early onset and more aggressive Alzheimer's disease. FAD mutations such as "Iowa" (D23N), "Arctic" (E22G), "Italian" (E22K), and "Dutch" (E22Q) have been shown to accelerate Aβ aggregation relative to the wild-type (WT). The mechanism by which these mutations facilitate increased aggregation is unknown, but each mutation results in a change in the net charge of the peptide. Previous studies have used nonpolarizable force fields to study Aβ, providing some insight into how this protein unfolds. However, nonpolarizable force fields have fixed charges that lack the ability to redistribute in response to changes in local electric fields. Here, we performed polarizable molecular dynamics simulations on the full-length Aβ42 of WT and FAD mutations and calculated folding free energies of the Aβ15-27 fragment via umbrella sampling. By studying both the full-length Aβ42 and a fragment containing mutations and the central hydrophobic cluster (residues 17-21), we were able to systematically study how these FAD mutations impact secondary and tertiary structure and the thermodynamics of folding. Electrostatic interactions, including those between permanent and induced dipoles, affected side-chain properties, salt bridges, and solvent interactions. The FAD mutations resulted in shifts in the electronic structure and solvent accessibility at the central hydrophobic cluster and the hydrophobic C-terminal region. Using umbrella sampling, we found that the folding of the WT and E22 mutants is enthalpically driven, whereas the D23N mutant is entropically driven, arising from a different unfolding pathway and peptide-bond dipole response. Together, the unbiased, full-length, and umbrella sampling simulations of fragments reveal that the FAD mutations perturb nearby residues and others in hydrophobic regions to potentially alter solubility. These results highlight the role electronic polarizability plays in amyloid misfolding and the role of heterogeneous microenvironments that arise as conformational change takes place.
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Affiliation(s)
- Darcy S Davidson
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joshua A Kraus
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Julia M Montgomery
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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11
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Sarkar D, Maity NC, Shome G, Varnava KG, Sarojini V, Vivekanandan S, Sahoo N, Kumar S, Mandal AK, Biswas R, Bhunia A. Mechanistic insight into functionally different human islet polypeptide (hIAPP) amyloid: the intrinsic role of the C-terminal structural motifs. Phys Chem Chem Phys 2022; 24:22250-22262. [PMID: 36098073 DOI: 10.1039/d2cp01650h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet Polypeptide (hIAPP) amyloidogenesis for the full-length peptide along with its N- and C-terminal fragments, under different temperatures and sample agitation conditions. This helped us to gain a comprehensive understanding of the intrinsic role of specific functional epitopes in the primary structure of the peptide that regulates amyloidogenesis and subsequent cytotoxicity. Intriguingly, our study involving an array of biophysical experiments and ex vivo data suggests a direct influence of external changes on the C-terminal fibrillating sequence. Furthermore, the observations indicate a possible collaborative role of this segment in nucleating hIAPP amyloidogenesis in a physiological scenario, thus making it a potential target for future therapeutic interventions.
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Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Narayan Chandra Maity
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Gourav Shome
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Kyriakos Gabriel Varnava
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, Texas, 78539, USA
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Ranjit Biswas
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
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12
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Mañas‐Torres MC, Illescas‐Lopez S, Gavira JA, de Cienfuegos LÁ, Marchesan S. Interactions Between Peptide Assemblies and Proteins for Medicine. Isr J Chem 2022. [DOI: 10.1002/ijch.202200018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mari C. Mañas‐Torres
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - Sara Illescas‐Lopez
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR) Avenida de las Palmeras 4 18100 Armilla, UEQ Granada Spain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
- Instituto de Investigación Biosanitaria ibs Granada Spain
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department University of Trieste Via L. Giorgieri 1 Trieste 34127 Italy
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13
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Vezenkov LT, Danalev DL, Iwanov I, Lozanov V, Atanasov A, Todorova R, Vassilev N, Karadjova V. Synthesis and biological study of new galanthamine-peptide derivatives designed for prevention and treatment of Alzheimer 's disease. Amino Acids 2022; 54:897-910. [PMID: 35562605 DOI: 10.1007/s00726-022-03167-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
Abstract
The Alzheimer's disease leads to neurodegenerative processes and affecting negatively million people worldwide. The treatment of the disease is still difficult and incomplete in practice. Galanthamine is one of the most commonly used drugs against the illness. The main aim of this work is design and synthesis of new derivatives of galanthamine comprising peptide moiety as well as study of their β-secretase inhibitory activity and the anti-aggregating effect. All new derivatives of galanthamine containing analogues of Leu-Val-Phe-Phe (Aβ17-Aβ20) were synthesized in solution using fragment and consecutive condensation approaches. The new derivatives were characterized by melting points, NMR, and HPLC/MS. They were tested in vitro for β-secretase inhibition activity by means of fluorescent method and were investigated in vitro for anti-aggregation activity on sheep platelet-rich plasma. Although the new compounds do not contain a structural element responsible for the β-secretase inhibition, five of them show high or good β-secretase inhibitory activity between 19.98 and 51.19% with IC50 between 1.95 and 5.26 nM. Four of the new molecules were able to inhibit platelet aggregation between 55.0 and 90.0% with IC50 between 0.69 and 1.36 µM. Four of the compounds were able to inhibit platelet aggregation and two of them have high anti-aggregating effects.
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Affiliation(s)
| | - Dancho L Danalev
- University of Chemical Technology and Metallurgy, Sofia, 1756, Bulgaria.
| | - Iwan Iwanov
- University of Chemical Technology and Metallurgy, Sofia, 1756, Bulgaria
| | - Valentin Lozanov
- Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, 1000, Bulgaria
| | - Atanas Atanasov
- Medical Faculty, Trakia University, Stara Zagora, 6000, Bulgaria
| | - Rumyana Todorova
- Medical Faculty, Trakia University, Stara Zagora, 6000, Bulgaria
| | - Nikolay Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
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14
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Zhou Y, Hua J, Ding D, Tang Y. Interrogating amyloid aggregation with aggregation-induced emission fluorescence probes. Biomaterials 2022; 286:121605. [DOI: 10.1016/j.biomaterials.2022.121605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/26/2022]
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15
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Mazzaglia A, Di Natale G, Tosto R, Scala A, Sortino G, Piperno A, Casaletto MP, Riminucci A, Giuffrida ML, Mineo PG, Villari V, Micali N, Pappalardo G. KLVFF oligopeptide-decorated amphiphilic cyclodextrin nanomagnets for selective amyloid beta recognition and fishing. J Colloid Interface Sci 2022; 613:814-826. [PMID: 35074707 DOI: 10.1016/j.jcis.2022.01.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 12/19/2022]
Abstract
Recognition and capture of amyloid beta (Aβ) is a challenging task for the early diagnosis of neurodegenerative disorders, such as Alzheimer's disease. Here, we report a novel KLVFF-modified nanomagnet based on magnetic nanoparticles (MNP) covered with a non-ionic amphiphilic β-cyclodextrin (SC16OH) and decorated with KLVFF oligopeptide for the self-recognition of the homologous amino-acids sequence of Aβ to collect Aβ (1-42) peptide from aqueous samples. MNP@SC16OH and MNP@SC16OH/Ada-Pep nanoassemblies were fully characterized by complementary techniques both as solid powders and in aqueous dispersions. Single domain MNP@SC16OH/Ada-Pep nanomagnets of 20-40 nm were observed by TEM analysis. DLS and ζ-potential measurements revealed that MNP@SC16OH nanoassemblies owned in aqueous dispersion a hydrodynamic radius of about 150 nm, which was unaffected by Ada-Pep decoration, while the negative ζ-potential of MNP@SC16OH (-40 mV) became less negative (-30 mV) in MNP@SC16OH/Ada-Pep, confirming the exposition of positively charged KLVFF on nanomagnets surface. The ability of MNP@SC16OH/Ada-Pep to recruit Aβ (1-42) in aqueous solution was evaluated by MALDI-TOF and compared with the ineffectiveness of undecorated MNP@SC16OH and VFLKF scrambled peptide-decorated nanoassemblies (MNP@SC16OH/Ada-scPep), pointing out the selectivity of KLVFF-decorated nanohybrid towards Aβ (1-42). Finally, the property of nanomagnets to extract Aβ in conditioned medium of cells over-producing Aβ peptides was investigated as proof of concept of effectiveness of these nanomaterials as potential diagnostic tools.
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Affiliation(s)
- Antonino Mazzaglia
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno D'Alcontres 31, Messina 98166, Italy.
| | - Giuseppe Di Natale
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia (CNR-IC), Via P. Gaifami 18, 95126 Catania, Italy
| | - Rita Tosto
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia (CNR-IC), Via P. Gaifami 18, 95126 Catania, Italy; International PhD School of Chemical Sciences, University of Catania, 95125 Catania, Italy
| | - Angela Scala
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy
| | - Giuseppe Sortino
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno D'Alcontres 31, Messina 98166, Italy
| | - Anna Piperno
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy
| | - Maria Pia Casaletto
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Via U. La Malfa, 153, 90146 Palermo, Italy
| | - Alberto Riminucci
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Via P. Gobetti 101, 40129 Bologna, Italy
| | - Maria Laura Giuffrida
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia (CNR-IC), Via P. Gaifami 18, 95126 Catania, Italy
| | - Placido G Mineo
- Dipartimento di Scienze Chimiche, Università di Catania, V. le A. Doria 6, 95125 Catania, Italy
| | - Valentina Villari
- Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici (CNR-IPCF), Viale F. Stagno D'Alcontres 37, 98158 Messina, Italy
| | - Norberto Micali
- Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici (CNR-IPCF), Viale F. Stagno D'Alcontres 37, 98158 Messina, Italy.
| | - Giuseppe Pappalardo
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia (CNR-IC), Via P. Gaifami 18, 95126 Catania, Italy.
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16
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Mocanu CS, Niculaua M, Zbancioc G, Mangalagiu V, Drochioiu G. Novel Design of Neuropeptide-Based Drugs with β-Sheet Breaking Potential in Amyloid-Beta Cascade: Molecular and Structural Deciphers. Int J Mol Sci 2022; 23:ijms23052857. [PMID: 35269999 PMCID: PMC8911100 DOI: 10.3390/ijms23052857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
Our work discusses the investigation of 75 peptide-based drugs with the potential ability to break the β-sheet structures of amyloid-beta peptides from senile plaques. Hence, this study offers a unique insight into the design of neuropeptide-based drugs with β-sheet breaker potential in the amyloid-beta cascade for Alzheimer’s disease (AD). We started with five peptides (15QKLVFF20, 16KLVFF20, 17LVFF20, 16KLVF19 and 15QKLV18), to which 14 different organic acids were attached at the N-terminal. It was necessary to evaluate the physiochemical features of these sequences due to the biological correlation with our proposal. Hence, the preliminary analysis of different pharmacological features provided the necessary data to select the peptides with the best biocompatibility for administration purposes. Our approaches demonstrated that the peptides 17LVFF20, NA-17LVFF20, 16KLVF19 and NA-16KLVF19 (NA-nicotinic acid) have the ability to interfere with fibril formation and hence improve the neuro and cognitive functions. Moreover, the peptide conjugate NA-16KLVF19 possesses attractive pharmacological properties, demonstrated by in silico and in vitro studies. Tandem mass spectrometry showed no fragmentation for the spectra of 16KLVF19. Such important results suggest that under the action of protease, the peptide cleavage does not occur at all. Additionally, circular dichroism confirmed docking simulations and showed that NA-16KLVF19 may improve the β-sheet breaker mechanism, and thus the entanglement process of amyloid-beta peptides can be more effective.
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Affiliation(s)
- Cosmin Stefan Mocanu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I Bd., 700506 Iasi, Romania; (C.S.M.); (G.Z.)
| | - Marius Niculaua
- Research Centre for Oenology Iași, Romanian Academy Iași Branch, 8 Carol I, 700505 Iasi, Romania;
| | - Gheorghita Zbancioc
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I Bd., 700506 Iasi, Romania; (C.S.M.); (G.Z.)
| | - Violeta Mangalagiu
- Department of Exact and Natural Sciences–CERNESIM Center, Institute of Interdisciplinary Research, Alexandru Ioan Cuza University of Iasi, 11 Carol I Bd., 700506 Iasi, Romania;
- Faculty of Food Engineering, Stefan cel Mare University of Suceava, 13 Universitatii Str., 720229 Suceava, Romania
| | - Gabi Drochioiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I Bd., 700506 Iasi, Romania; (C.S.M.); (G.Z.)
- Correspondence:
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17
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Sorout N, Chandra A. Interactions of the Aβ(1-42) Peptide with Boron Nitride Nanoparticles of Varying Curvature in an Aqueous Medium: Different Pathways to Inhibit β-Sheet Formation. J Phys Chem B 2021; 125:11159-11178. [PMID: 34605235 DOI: 10.1021/acs.jpcb.1c05805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloid β (Aβ) peptide triggered by its conformational changes leads to the commonly known neurodegenerative disease of Alzheimer's. It is believed that the formation of β sheets of the peptide plays a key role in its aggregation and subsequent fibrillization. In the current study, we have investigated the interactions of the Aβ(1-42) peptide with boron nitride nanoparticles and the effects of the latter on conformational transitions of the peptide through a series of molecular dynamics simulations. In particular, the effects of curvature of the nanoparticle surface are studied by considering boron nitride nanotubes (BNNTs) of varying diameter and also a planar boron nitride nanosheet (BNNS). Altogether, the current study involves the generation and analysis of 9.5 μs of dynamical trajectories of peptide-BNNT/BNNS pairs in an aqueous medium. It is found that BN nanoparticles of different curvatures that are studied in the present work inhibit the conformational transition of the peptide to its β-sheet form. However, such an inhibition effect follows different pathways for BN nanoparticles of different curvatures. For the BNNT with the highest surface curvature, i.e., (3,3) BNNT, the nanoparticle is found to inhibit β-sheet formation by stabilizing the helical structure of the peptide, whereas for planar BNNS, the β-sheet formation is prevented by making more favorable pathways available for transitions of the peptide to conformations of random coils and turns. The BNNTs with intermediate curvatures are found to exhibit diverse pathways of their interactions with the peptide, but in all cases, essentially no formation of the β sheet is found whereas substantial β-sheet formation is observed for Aβ(1-42) in water in the absence of any nanoparticle. The current study shows that BN nanoparticles have the potential to act as effective tools to prevent amyloid formation from Aβ peptides.
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Affiliation(s)
- Nidhi Sorout
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
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18
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Li F, Zhan C, Dong X, Wei G. Molecular mechanisms of resveratrol and EGCG in the inhibition of Aβ 42 aggregation and disruption of Aβ 42 protofibril: similarities and differences. Phys Chem Chem Phys 2021; 23:18843-18854. [PMID: 34612422 DOI: 10.1039/d1cp01913a] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The aggregation of amyloid-β protein (Aβ) into fibrillary deposits is implicated in Alzheimer's disease (AD), and inhibiting Aβ aggregation and clearing Aβ fibrils are considered as promising strategies to treat AD. It has been reported that resveratrol (RSV) and epigallocatechin-3-gallate (EGCG), two of the most extensively studied natural polyphenols, are able to inhibit Aβ fibrillization and remodel the preformed fibrillary aggregates into amorphous, non-toxic species. However, the mechanisms by which RSV inhibits Aβ42 aggregation and disrupts Aβ42 protofibril, as well as the inhibitory/disruptive mechanistic similarities and differences between RSV and EGCG, remain mostly elusive. Herein, we performed extensive all-atom molecular dynamics (MD) simulations on Aβ42 dimers (the early aggregation state of Aβ42) and protofibrils (the intermediate of Aβ42 fibril formation and elongation) in the absence/presence of RSV or EGCG molecules. Our simulations show that both RSV and EGCG can bind with Aβ42 monomers and inhibit the dimerization of Aβ42. The binding of RSV with Aβ42 peptide is mostly viaπ-π stacking interactions, while the binding of EGCG with Aβ42 is mainly through hydrophobic, π-π stacking, and hydrogen-bonding interactions. Moreover, both RSV and EGCG disrupt the β-sheet structure and K28-A42 salt bridges, leading to a disruption of Aβ42 protofibril structure. RSV mainly binds with residues whose side-chains point inwards from the surface of the protofibril, while EGCG mostly binds with residues whose side-chains point outwards from the surface of the protofibril. Furthermore, RSV interacts with Aβ42 protofibrils mostly viaπ-π stacking interactions, while EGCG interacts with Aβ42 protofibrils mainly via hydrogen-bonding and hydrophobic interactions. For comparison, we also explore the effects of RSV/EGCG molecules on the aggregation inhibition and protofibril disruption of the Iowa mutant (D23N) Aβ. Our findings may pave the way for the design of more effective drug candidates as well as the utilization of cocktail therapy using RSV and EGCG for the treatment of AD.
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Affiliation(s)
- Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, 200438, People's Republic of China.
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19
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Breaker peptides against amyloid-β aggregation: a potential therapeutic strategy for Alzheimer's disease. Future Med Chem 2021; 13:1767-1794. [PMID: 34498978 DOI: 10.4155/fmc-2021-0184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder, for which blocking the early steps of extracellular misfolded amyloid-β (Aβ) aggregation is a promising therapeutic approach. However, the pathological features of AD progression include the accumulation of intracellular tau protein, membrane-catalyzed cell death and the abnormal deposition of Aβ. Here, we focus on anti-amyloid breaker peptides derived from the Aβ sequence and non-Aβ-based peptides containing both natural and modified amino acids. Critical aspects of the breaker peptides include N-methylation, conformational restriction through cyclization, incorporation of unnatural amino acid, fluorinated molecules, polymeric nanoparticles and PEGylation. This review confers a general idea of such breaker peptides with in vitro and in vivo studies, which may advance our understanding of AD pathology and develop an effective treatment strategy against AD.
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Marulanda K, Mercel A, Gillis DC, Sun K, Gambarian M, Roark J, Weiss J, Tsihlis ND, Karver MR, Centeno SR, Peters EB, Clemons TD, Stupp SI, McLean SE, Kibbe MR. Intravenous Delivery of Lung-Targeted Nanofibers for Pulmonary Hypertension in Mice. Adv Healthc Mater 2021; 10:e2100302. [PMID: 34061473 PMCID: PMC8273153 DOI: 10.1002/adhm.202100302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Indexed: 01/11/2023]
Abstract
Pulmonary hypertension is a highly morbid disease with no cure. Available treatments are limited by systemic adverse effects due to non-specific biodistribution. Self-assembled peptide amphiphile (PA) nanofibers are biocompatible nanomaterials that can be modified to recognize specific biological markers to provide targeted drug delivery and reduce off-target toxicity. Here, PA nanofibers that target the angiotensin I-converting enzyme and the receptor for advanced glycation end-products (RAGE) are developed, as both proteins are overexpressed in the lung with pulmonary hypertension. It is demonstrated that intravenous delivery of RAGE-targeted nanofibers containing the targeting epitope LVFFAED (LVFF) significantly accumulated within the lung in a chronic hypoxia-induced pulmonary hypertension mouse model. Using 3D light sheet fluorescence microscopy, it is shown that LVFF nanofiber localization is specific to the diseased pulmonary tissue with immunofluorescence analysis demonstrating colocalization of the targeted nanofiber to RAGE in the hypoxic lung. Furthermore, biodistribution studies show that significantly more LVFF nanofibers localized to the lung compared to major off-target organs. Targeted nanofibers are retained within the pulmonary tissue for 24 h after injection. Collectively, these data demonstrate the potential of a RAGE-targeted nanomaterial as a drug delivery platform to treat pulmonary hypertension.
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Affiliation(s)
- Kathleen Marulanda
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Alexandra Mercel
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - David C Gillis
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Kui Sun
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Maria Gambarian
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Joshua Roark
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Jenna Weiss
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Nick D Tsihlis
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Mark R Karver
- Simpson Querrey Institute, Northwestern University, 303 E. Superior Street, Chicago, IL, 60611, USA
| | - S Ruben Centeno
- Department of Pediatrics, University of North Carolina, 260 MacNider Building CB# 7220, Chapel Hill, NC, 27599, USA
| | - Erica B Peters
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Tristan D Clemons
- Simpson Querrey Institute, Northwestern University, 303 E. Superior Street, Chicago, IL, 60611, USA
| | - Samuel I Stupp
- Simpson Querrey Institute, Northwestern University, 303 E. Superior Street, Chicago, IL, 60611, USA
| | - Sean E McLean
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Melina R Kibbe
- Department of Surgery, University of North Carolina, 4041 Burnett Womack, 101 Manning Drive, Chapel Hill, NC, 27599, USA
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Zhang S, Asghar S, Zhu C, Ye J, Lin L, Xu L, Hu Z, Chen Z, Shao F, Xiao Y. Multifunctional nanorods based on self-assembly of biomimetic apolipoprotein E peptide for the treatment of Alzheimer's disease. J Control Release 2021; 335:637-649. [PMID: 34087249 DOI: 10.1016/j.jconrel.2021.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 05/25/2021] [Accepted: 05/30/2021] [Indexed: 12/18/2022]
Abstract
Targeting a single molecule or a single pathway and poor drug delivery to the brain hamper the therapy of Alzheimer's disease (AD) based on abnormal metabolism of amyloid-β (Aβ). To solve these problems, we designed and synthesized a multi - strategy peptide (MOP), an ingenious apolipoprotein E mimetic peptide, which could reduce Aβ deposition via inhibiting Aβ aggregation and at the same time accelerate Aβ clearance. Meanwhile, MOP could be self-assembled into different nanostructure, thus we constructed a multifunctional delivery system (APND-3) based on MOP self-assembled nanorods (aspect ratios of 3) that was a favorable morphology to enhance the permeation across the blood brain barrier (BBB) to address the poor delivery to brain issues. Besides, the drug delivery system introduces polydopamine (PDA) and COG1410 ligand as a shell to keep the favorable morphology of core and enhance the BBB targeting efficiency. As a result, the delivery system significantly enhances the delivery of MOP to the brain, thus reducing Aβ deposition, mitigating the memory deficits, and ameliorating neurologic damage in AD model mice. Our findings suggest that our drug and carrier integrated multifunctional delivery system has the potential for AD treatment.
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Affiliation(s)
- Shanshan Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China; School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Sajid Asghar
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Chenqi Zhu
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Department of Pharmacy, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, PR China
| | - Junxiu Ye
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Ling Lin
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Liu Xu
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Ziyi Hu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Zhipeng Chen
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Feng Shao
- Phase I Clinical Trial Unit, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China.
| | - Yanyu Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China.
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Asadbegi M, Shamloo A. Evaluating the Multifunctionality of a New Modulator of Zinc-Induced Aβ Aggregation Using a Novel Computational Approach. J Chem Inf Model 2021; 61:1383-1401. [PMID: 33617717 DOI: 10.1021/acs.jcim.0c01264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The high concentration of zinc metal ions in Aβ aggregations is one of the most cited hallmarks of Alzheimer's disease (AD), and several substantial pieces of evidence emphasize the key role of zinc metal ions in the pathogenesis of AD. In this study, while designing a multifunctional peptide for simultaneous targeting Aβ aggregation and chelating the zinc metal ion, a novel and comprehensive approach is introduced for evaluating the multifunctionality of a multifunctional drugs based on computational methods. The multifunctional peptide consists of inhibitor and chelator domains, which are included in the C-terminal hydrophobic region of Aβ, and the first four amino acids of human albumin. The ability of the multifunctional peptide in zinc ion chelation has been investigated using molecular dynamics (MD) simulations of the peptide-zinc interaction for 300 ns, and Bennett's acceptance ratio (BAR) method has been used to accurately calculate the chelation free energy. Data analysis demonstrates that the peptide chelating domain can be stably linked to the zinc ion. Besides, the introduced method used for evaluating chelation and calculating the free energy of peptide binding to zinc ions was successfully validated by comparison with previous experimental and theoretical published data. The results indicate that the multifunctional peptide, coordinating with the zinc metal ion, can be effective in Aβ inhibition by preserving the native helical structure of the Aβ42 monomer as well as disrupting the β-sheet structure of Aβ42 aggregates. Detailed assessments of the Aβ42-peptide interactions elucidate that the inhibition of Aβ is achieved by considerable hydrophobic interactions and hydrogen bonding between the multifunctional peptide and the hydrophobic Aβ regions, along with interfering in stable bridges formed inside the Aβ aggregate.
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Affiliation(s)
- Mohsen Asadbegi
- School of Mechanical Engineering, Sharif University of Technology, Tehran 1458889694, Iran
| | - Amir Shamloo
- School of Mechanical Engineering, Sharif University of Technology, Tehran 1458889694, Iran
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Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies. Int J Mol Sci 2021; 22:ijms22031051. [PMID: 33494369 PMCID: PMC7865305 DOI: 10.3390/ijms22031051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Neurodegeneration in Alzheimer's disease (AD) is defined by pathology featuring amyloid-β (Aβ) deposition in the brain. Aβ monomers themselves are generally considered to be nontoxic, but misfold into β-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aβ and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aβ(1-42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aβ in anti-parallel orientation, demonstrated neuroprotection against Aβ(1-42). A third inhibitor, predicted to bind parallel to Aβ, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aβ toxicity.
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Kaur A, Goyal D, Goyal B. An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ 42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:28055-28073. [PMID: 33289734 DOI: 10.1039/d0cp04672h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD), an epidemic growing worldwide due to no effective medical aid available in the market, is a neurological disorder. AD is known to be directly associated with the toxicity of amyloid-β (Aβ) aggregates. In search of potent inhibitors of Aβ aggregation, Hamilton and co-workers reported an α-helix mimetic, ADH-31, which acts as a powerful antagonist of Aβ42 aggregation. To identify the key interactions between protein-ligand complexes and to gain insights into the inhibitory mechanism of ADH-31 against Aβ42 aggregation, molecular dynamics (MD) simulations were performed in the present study. The MD simulations highlighted that ADH-31 showed distinct binding capabilities with residues spanning from the N-terminal to the central hydrophobic core (CHC) region of Aβ42 and restricted the conformational transition of the helix-rich structure of Aβ42 into another form of secondary structures (coil/turn/β-sheet). Hydrophobic contacts, hydrogen bonding and π-π interaction contribute to the strong binding between ADH-31 and Aβ42 monomer. The Dictionary of Secondary Structure of Proteins (DSSP) analysis highlighted that the probability of helical content increases from 38.5% to 50.2% and the turn content reduces from 14.7% to 6.2% with almost complete loss of the β-sheet structure (4.5% to 0%) in the Aβ42 monomer + ADH-31 complex. The per-residue binding free energy analysis demonstrated that Arg5, Tyr10, His14, Gln15, Lys16, Val18, Phe19 and Lys28 residues of Aβ42 are responsible for the favourable binding free energy in Aβ42 monomer + ADH-31 complex, which is consistent with the 2D HSQC NMR of the Aβ42 monomer that depicted a change in the chemical shift of residues spanning from Glu11 to Phe20 in the presence of ADH-31. The MD simulations highlighted the prevention of sampling of amyloidogenic β-strand conformations in Aβ42 trimer in the presence of ADH-31 as well as the ability of ADH-31 to destabilize Aβ42 trimer and protofibril structures. The lower binding affinity between Aβ42 trimer chains in the presence of ADH-31 highlights the destabilization of the Aβ42 trimer structure. Overall, MD results highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptides into helical conformation and destabilized Aβ42 trimer as well as protofibril structures. The present study provides a theoretical insight into the atomic level details of the inhibitory mechanism of ADH-31 against Aβ42 aggregation as well as protofibril destabilization and could be implemented in the structure-based drug design of potent therapeutic agents for AD.
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Affiliation(s)
- Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India.
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Rationally designed peptide-based inhibitor of Aβ42 fibril formation and toxicity: a potential therapeutic strategy for Alzheimer's disease. Biochem J 2020; 477:2039-2054. [PMID: 32427336 PMCID: PMC7293109 DOI: 10.1042/bcj20200290] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
Amyloid beta peptide (Aβ42) aggregation in the brain is thought to be responsible for the onset of Alzheimer's disease, an insidious condition without an effective treatment or cure. Hence, a strategy to prevent aggregation and subsequent toxicity is crucial. Bio-inspired peptide-based molecules are ideal candidates for the inhibition of Aβ42 aggregation, and are currently deemed to be a promising option for drug design. In this study, a hexapeptide containing a self-recognition component unique to Aβ42 was designed to mimic the β-strand hydrophobic core region of the Aβ peptide. The peptide is comprised exclusively of D-amino acids to enhance specificity towards Aβ42, in conjunction with a C-terminal disruption element to block the recruitment of Aβ42 monomers on to fibrils. The peptide was rationally designed to exploit the synergy between the recognition and disruption components, and incorporates features such as hydrophobicity, β-sheet propensity, and charge, that all play a critical role in the aggregation process. Fluorescence assays, native ion-mobility mass spectrometry (IM-MS) and cell viability assays were used to demonstrate that the peptide interacts with Aβ42 monomers and oligomers with high specificity, leading to almost complete inhibition of fibril formation, with essentially no cytotoxic effects. These data define the peptide-based inhibitor as a potentially potent anti-amyloid drug candidate for this hitherto incurable disease.
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26
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Mitra A, Sarkar N. Sequence and structure-based peptides as potent amyloid inhibitors: A review. Arch Biochem Biophys 2020; 695:108614. [PMID: 33010227 DOI: 10.1016/j.abb.2020.108614] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Misfolded and natively disordered globular proteins tend to aggregate together in an interwoven fashion to form fibrous, proteinaceous deposits referred to as amyloid fibrils. Formation and deposition of such insoluble fibrils are the characteristic features of a broad group of diseases, known as amyloidosis. Some of these proteins are known to cause several degenerative disorders in humans, such as Amyloid-Beta (Aβ) in Alzheimer's disease (AD), human Islet Amyloid Polypeptide (hIAPP, amylin) in type 2 diabetes, α-synuclein (α-syn) in Parkinson's disease (PD) and so on. The fact that these proteins do not share any significant sequence or structural homology in their native states make therapy quite challenging. However, it is observed that aggregation-prone proteins and peptides tend to adopt a similar type of secondary structure during the formation of fibrils. Rationally designed peptides can be a potent inhibitor that has been shown to disrupt the fibril structure by binding specifically to the amyloidogenic region(s) within a protein. The following review will analyze the inhibitory potency of both sequence-based and structure-based small peptides that have been shown to inhibit amyloidogenesis of proteins such as Aβ, human amylin, and α-synuclein.
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Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India.
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Shi XL, Yan N, Cui YJ, Liu ZP. A Unique GSK-3β inhibitor B10 Has a Direct Effect on Aβ, Targets Tau and Metal Dyshomeostasis, and Promotes Neuronal Neurite Outgrowth. Cells 2020; 9:cells9030649. [PMID: 32155989 PMCID: PMC7140427 DOI: 10.3390/cells9030649] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023] Open
Abstract
Due to the complicated pathogenesis of Alzheimer's disease (AD), the development of multitargeted agents to simultaneously interfere with multiple pathological processes of AD is a potential choice. Glycogen synthase kinase-3β (GSK-3β) plays a vital role in the AD pathological process. In this study, we discovered a novel 1H-pyrrolo[2,3-b]pyridine derivative B10 as a GSK-3β inhibitor that features with a quinolin-8-ol moiety to target the metal dyshomeostasis of AD. B10 potently inhibited GSK-3β with an IC50 of 66 ± 2.5 nM. At the concentration of 20 μM, B10 increased β-catenin abundance (β-catenin/GAPDH: 0.83 ± 0.086 vs. 0.30 ± 0.016), phosphorylated GSK-3β at Ser9 (p-GSK-3β/GAPDH: 0.53 ± 0.045 vs. 0.35 ± 0.012), and decreased the phosphorylated tau level (p-tau/GAPDH: 0.33 ± 0.065 vs. 0.83 ± 0.061) in SH-SY5Y cells. Unlike other GSK-3β inhibitors, B10 had a direct effect on Aβ by inhibiting Aβ1-42 aggregation and promoting the Aβ1-42 aggregate disassociation. It selectively chelated with Cu2+, Zn2+, Fe3+, and Al3+, and targeted AD metal dyshomeostasis. Moreover, B10 effectively increased the mRNA expression of the recognized neurogenesis markers, GAP43, N-myc, and MAP-2, and promoted the differentiated neuronal neurite outgrowth, possibly through the GSK-3β and β-catenin signal pathways. Therefore, B10 is a potent and unique GSK-3β inhibitor that has a direct on Aβ and serves as a multifunctional anti-AD agent for further investigations.
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Armiento V, Spanopoulou A, Kapurniotu A. Peptide-Based Molecular Strategies To Interfere with Protein Misfolding, Aggregation, and Cell Degeneration. Angew Chem Int Ed Engl 2020; 59:3372-3384. [PMID: 31529602 PMCID: PMC7064928 DOI: 10.1002/anie.201906908] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Indexed: 12/31/2022]
Abstract
Protein misfolding into amyloid fibrils is linked to more than 40 as yet incurable cell- and neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes. So far, however, only one of the numerous anti-amyloid molecules has reached patients. This Minireview gives an overview of molecular strategies and peptide chemistry "tools" to design, develop, and discover peptide-based molecules as anti-amyloid drug candidates. We focus on two major inhibitor rational design strategies: 1) the oldest and most common strategy, based on molecular recognition elements of amyloid self-assembly, and 2) a more recent approach, based on cross-amyloid interactions. We discuss why peptide-based amyloid inhibitors, in particular their advanced generations, can be promising leads or candidates for anti-amyloid drugs as well as valuable tools for deciphering amyloid-mediated cell damage and its link to disease pathogenesis.
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Affiliation(s)
- Valentina Armiento
- Division of Peptide BiochemistryTUM School of Life SciencesTechnische Universität MünchenEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Anna Spanopoulou
- Division of Peptide BiochemistryTUM School of Life SciencesTechnische Universität MünchenEmil-Erlenmeyer-Forum 585354FreisingGermany
- Current address: Coriolis Pharma Research GmbHFraunhoferstrasse 18B82152PlaneggGermany
| | - Aphrodite Kapurniotu
- Division of Peptide BiochemistryTUM School of Life SciencesTechnische Universität MünchenEmil-Erlenmeyer-Forum 585354FreisingGermany
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Sorout N, Chandra A. Effects of Boron Nitride Nanotube on the Secondary Structure of Aβ(1–42) Trimer: Possible Inhibitory Effect on Amyloid Formation. J Phys Chem B 2020; 124:1928-1940. [DOI: 10.1021/acs.jpcb.9b11986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nidhi Sorout
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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Kapadia A, Patel A, Sharma KK, Maurya IK, Singh V, Khullar M, Jain R. Effect of C-terminus amidation of Aβ39–42fragment derived peptides as potential inhibitors of Aβ aggregation. RSC Adv 2020; 10:27137-27151. [PMID: 35515767 PMCID: PMC9055537 DOI: 10.1039/d0ra04788k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/10/2020] [Indexed: 11/21/2022] Open
Abstract
The C-terminus fragment (Val-Val-Ile-Ala) of amyloid-β is reported to inhibit the aggregation of the parent peptide. In an attempt to investigate the effect of sequential amino-acid scan and C-terminus amidation on the biological profile of the lead sequence, a series of tetrapeptides were synthesized using MW-SPPS. Peptide D-Phe-Val-Ile-Ala-NH2 (12c) exhibited high protection against β-amyloid-mediated-neurotoxicity by inhibiting Aβ aggregation in the MTT cell viability and ThT-fluorescence assay. Circular dichroism studies illustrate the inability of Aβ42 to form β-sheet in the presence of 12c, further confirmed by the absence of Aβ42 fibrils in electron microscopy experiments. The peptide exhibits enhanced BBB permeation, no cytotoxicity along with prolonged proteolytic stability. In silico studies show that the peptide interacts with the key amino acids in Aβ, which potentiate its fibrillation, thereby arresting aggregation propensity. This structural class of designed scaffolds provides impetus towards the rational development of peptide-based-therapeutics for Alzheimer's disease (AD). Amidated C-terminal fragment, Aβ39–42 derived non-cytotoxic β-sheet breaker peptides exhibit excellent potency, enhanced bioavailability and improved proteolytic stability.![]()
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Affiliation(s)
- Akshay Kapadia
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
| | - Aesan Patel
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
| | - Krishna K. Sharma
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
| | | | - Varinder Singh
- Post Graduate Institute of Medical Education and Research
- Chandigarh
- India
| | - Madhu Khullar
- Post Graduate Institute of Medical Education and Research
- Chandigarh
- India
| | - Rahul Jain
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
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31
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Armiento V, Spanopoulou A, Kapurniotu A. Peptid‐basierte molekulare Strategien zum Einsatz bei Proteinfehlfaltung, Proteinaggregation und Zelldegeneration. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Valentina Armiento
- Fachgebiet PeptidbiochemieTUM School of Life SciencesTechnische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
| | - Anna Spanopoulou
- Fachgebiet PeptidbiochemieTUM School of Life SciencesTechnische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
- Aktuelle Adresse: Coriolis Pharma Research GmbH Fraunhoferstraße 18B 82152 Planegg Deutschland
| | - Aphrodite Kapurniotu
- Fachgebiet PeptidbiochemieTUM School of Life SciencesTechnische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
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32
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Gaudreault R, Mousseau N. Mitigating Alzheimer’s Disease with Natural Polyphenols: A Review. Curr Alzheimer Res 2019; 16:529-543. [DOI: 10.2174/1567205016666190315093520] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/14/2019] [Accepted: 03/13/2019] [Indexed: 11/22/2022]
Abstract
:According to Alzheimer’s Disease International (ADI), nearly 50 million people worldwide were living with dementia in 2017, and this number is expected to triple by 2050. Despite years of research in this field, the root cause and mechanisms responsible for Alzheimer’s disease (AD) have not been fully elucidated yet. Moreover, promising preclinical results have repeatedly failed to translate into patient treatments. Until now, none of the molecules targeting AD has successfully passed the Phase III trial. Although natural molecules have been extensively studied, they normally require high concentrations to be effective; alternately, they are too large to cross the blood-brain barrier (BBB).:In this review, we report AD treatment strategies, with a virtually exclusive focus on green chemistry (natural phenolic molecules). These include therapeutic strategies for decreasing amyloid-β (Aβ) production, preventing and/or altering Aβ aggregation, and reducing oligomers cytotoxicity such as curcumin, (-)-epigallocatechin-3-gallate (EGCG), morin, resveratrol, tannic acid, and other natural green molecules. We also examine whether consideration should be given to potential candidates used outside of medicine and nutrition, through a discussion of two intermediate-sized green molecules, with very similar molecular structures and key properties, which exhibit potential in mitigating Alzheimer’s disease.
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Affiliation(s)
- Roger Gaudreault
- Department of Physics, Universit�© de Montr�©al, Case Postale 6128, Succursale Centre-ville, Montreal (QC), Canada
| | - Normand Mousseau
- Department of Physics, Universit�© de Montr�©al, Case Postale 6128, Succursale Centre-ville, Montreal (QC), Canada
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Opare SKA, Rauk A. Pseudopeptide Designed to Inhibit Oligomerization and Redox Chemistry in Alzheimer’s Disease. J Phys Chem B 2019; 123:5206-5215. [DOI: 10.1021/acs.jpcb.9b01665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stanley K. A. Opare
- Department of Chemistry, The University of Calgary, Calgary, Alberta Canada, T2N 1N4
| | - Arvi Rauk
- Department of Chemistry, The University of Calgary, Calgary, Alberta Canada, T2N 1N4
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Narang SS, Goyal D, Goyal B. Inhibition of Alzheimer’s amyloid-β42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:1598-1611. [DOI: 10.1080/07391102.2019.1614093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Habtemariam S. Natural Products in Alzheimer's Disease Therapy: Would Old Therapeutic Approaches Fix the Broken Promise of Modern Medicines? Molecules 2019; 24:molecules24081519. [PMID: 30999702 PMCID: PMC6514598 DOI: 10.3390/molecules24081519] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/30/2022] Open
Abstract
Despite extensive progress in understanding the pathology of Alzheimer's disease (AD) over the last 50 years, clinical trials based on the amyloid-beta (Aβ) hypothesis have kept failing in late stage human trials. As a result, just four old drugs of limited clinical outcomes and numerous side effects are currently used for AD therapy. This article assesses the common pharmacological targets and therapeutic principles for current and future drugs. It also underlines the merits of natural products acting through a polytherapeutic approach over a monotherapy option of AD therapy. Multi-targeting approaches through general antioxidant and anti-inflammatory mechanisms coupled with specific receptor and/or enzyme-mediated effects in neuroprotection, neuroregeneration, and other rational perspectives of novel drug discovery are emphasized.
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Affiliation(s)
- Solomon Habtemariam
- Pharmacognosy Research Laboratories & Herbal Analysis Services UK, University of Greenwich, Central Avenue, Chatham-Maritime, Kent ME4 4TB, UK.
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36
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Bisceglia F, Seghetti F, Serra M, Zusso M, Gervasoni S, Verga L, Vistoli G, Lanni C, Catanzaro M, De Lorenzi E, Belluti F. Prenylated Curcumin Analogues as Multipotent Tools To Tackle Alzheimer's Disease. ACS Chem Neurosci 2019; 10:1420-1433. [PMID: 30556996 DOI: 10.1021/acschemneuro.8b00463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Alzheimer's disease is likely to be caused by copathogenic factors including aggregation of Aβ peptides into oligomers and fibrils, neuroinflammation, and oxidative stress. To date, no effective treatments are available, and because of the multifactorial nature of the disease, it emerges the need to act on different and simultaneous fronts. Despite the multiple biological activities ascribed to curcumin as neuroprotector, its poor bioavailability and toxicity limit the success in clinical outcomes. To tackle Alzheimer's disease on these aspects, the curcumin template was suitably modified and a small set of analogues was attained. In particular, derivative 1 turned out to be less toxic than curcumin. As evidenced by capillary electrophoresis and transmission electron microscopy studies, 1 proved to inhibit the formation of large toxic Aβ oligomers, by shifting the equilibrium toward smaller nontoxic assemblies and to limit the formation of insoluble fibrils. These findings were supported by molecular docking and steered molecular dynamics simulations which confirmed the superior capacity of 1 to bind Aβ structures of different complexity. Remarkably, 1 also showed in vitro anti-inflammatory and antioxidant properties. In summary, the curcumin-based analogue 1 emerged as multipotent compound worthy to be further investigated and exploited in the Alzheimer's disease multitarget context.
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Affiliation(s)
- Federica Bisceglia
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Francesca Seghetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Massimo Serra
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Morena Zusso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti 2, 35131 Padua, Italy
| | - Silvia Gervasoni
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Laura Verga
- Department of Molecular Medicine, Unit of Pathology, University of Pavia IRCCS Policlinico S. Matteo Foundation, Via Forlanini 14, 27100 Pavia, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Cristina Lanni
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Michele Catanzaro
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Ersilia De Lorenzi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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Xu J, Yuan Y, Zhang R, Song Y, Sui T, Wang J, Wang C, Chen Y, Guan S, Wang L. A deuterohemin peptide protects a transgenic Caenorhabditis elegans model of Alzheimer’s disease by inhibiting Aβ1–42 aggregation. Bioorg Chem 2019; 82:332-339. [DOI: 10.1016/j.bioorg.2018.10.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/27/2018] [Accepted: 10/31/2018] [Indexed: 01/05/2023]
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Chan KH, Lee WH, Ni M, Loo Y, Hauser CAE. C-Terminal Residue of Ultrashort Peptides Impacts on Molecular Self-Assembly, Hydrogelation, and Interaction with Small-Molecule Drugs. Sci Rep 2018; 8:17127. [PMID: 30459362 PMCID: PMC6244206 DOI: 10.1038/s41598-018-35431-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/06/2018] [Indexed: 12/26/2022] Open
Abstract
Single molecular changes on a tripeptide can have dramatic effects on their self-assembly and hydrogelation. Herein, we explore C-terminal residue variation on two consistent ultrashort peptide backbones, i.e. acetylated-Leu-Ile-Val-Ala-Gly-Xaa and acetylated-Ile-Val-Xaa (Xaa = His, Arg, Asn). The objective of this study is to identify candidates that can form hydrogels for small-molecule drug (SMD) delivery. Haemolysis and cytotoxicity (with human adipose-derived mesenchymal stem cells) assays showed that the new soluble peptides (Xaa = His, Arg) are cytocompatible. Gelation studies showed that all but acetylated-Ile-Val-Arg could gel under physiological conditions. Longer peptidic backbones drive self-assembly more effectively as reflected in field emission scanning electron microscopy (FESEM) and circular dichroism spectroscopy studies. Rheological studies revealed that the resultant hydrogels have varying stiffness and yield stress, depending on the backbone and C-terminal residue. Visible spectroscopy-based elution studies with SMDs (naltrexone, methotrexate, doxorubicin) showed that besides the C-terminal residue, the shape of the SMD also determines the rate and extent of SMD elution. Based on the elution assays, infrared spectroscopy, and FESEM, we propose models for the peptide fibril-SMD interaction. Our findings highlight the importance of matching the molecular properties of the self-assembling peptide and SMD in order to achieve the desired SMD release profile.
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Affiliation(s)
- Kiat Hwa Chan
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore, 138527, Singapore.
| | - Wei Hao Lee
- Department of Chemistry, Krieger School of Arts & Sciences, 3400 North Charles Street, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ming Ni
- School of Biological Sciences & Engineering, Yachay Tech University, Hacienda San José s/n, San Miguel de Urcuquí, 100105, Ecuador
| | - Yihua Loo
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore, 138669, Singapore
| | - Charlotte A E Hauser
- Laboratory for Nanomedicine, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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39
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An Aβ42 variant that inhibits intra- and extracellular amyloid aggregation and enhances cell viability. Biochem J 2018; 475:3087-3103. [DOI: 10.1042/bcj20180247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/02/2018] [Accepted: 09/07/2018] [Indexed: 01/06/2023]
Abstract
Aggregation and accumulation of the 42-residue amyloid β peptide (Aβ42) in the extracellular matrix and within neuronal cells is considered a major cause of neuronal cell cytotoxicity and death in Alzheimer's disease (AD) patients. Therefore, molecules that bind to Aβ42 and prevent its aggregation are therapeutically promising as AD treatment. Here, we show that a non-self-aggregating Aβ42 variant carrying two surface mutations, F19S and L34P (Aβ42DM), inhibits wild-type Aβ42 aggregation and significantly reduces Aβ42-mediated cell cytotoxicity. In addition, Aβ42DM inhibits the uptake and internalization of extracellularly added pre-formed Aβ42 aggregates into cells. This was the case in both neuronal and non-neuronal cells co-expressing Aβ42 and Aβ42DM or following pre-treatment of cells with extracellular soluble forms of the two peptides, even at high Aβ42 to Aβ42DM molar ratios. In cells, Aβ42DM associates with Aβ42, while in vitro, the two soluble recombinant peptides exhibit nano-molar binding affinity. Importantly, Aβ42DM potently suppresses Aβ42 amyloid aggregation in vitro, as demonstrated by thioflavin T fluorescence and transmission electron microscopy for detecting amyloid fibrils. Overall, we present a new approach for inhibiting Aβ42 fibril formation both within and outside cells. Accordingly, Aβ42DM should be evaluated in vivo for potential use as a therapeutic lead for treating AD.
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Savelieff MG, Nam G, Kang J, Lee HJ, Lee M, Lim MH. Development of Multifunctional Molecules as Potential Therapeutic Candidates for Alzheimer’s Disease, Parkinson’s Disease, and Amyotrophic Lateral Sclerosis in the Last Decade. Chem Rev 2018; 119:1221-1322. [DOI: 10.1021/acs.chemrev.8b00138] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Masha G. Savelieff
- SciGency Science Communications, Ann Arbor, Michigan 48104, United States
| | - Geewoo Nam
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Juhye Kang
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyuck Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Misun Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Ryan P, Patel B, Makwana V, Jadhav HR, Kiefel M, Davey A, Reekie TA, Rudrawar S, Kassiou M. Peptides, Peptidomimetics, and Carbohydrate-Peptide Conjugates as Amyloidogenic Aggregation Inhibitors for Alzheimer's Disease. ACS Chem Neurosci 2018; 9:1530-1551. [PMID: 29782794 DOI: 10.1021/acschemneuro.8b00185] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder accounting for 60-80% of dementia cases. For many years, AD causality was attributed to amyloid-β (Aβ) aggregated species. Recently, multiple therapies that target Aβ aggregation have failed in clinical trials, since Aβ aggregation is found in AD and healthy patients. Attention has therefore shifted toward the aggregation of the tau protein as a major driver of AD. Numerous inhibitors of tau-based pathology have recently been developed. Diagnosis of AD has shifted from measuring late stage senile plaques to early stage biomarkers, amyloid-β and tau monomers and oligomeric assemblies. Synthetic peptides and some derivative structures are being explored for use as theranostic tools as they possess the capacity both to bind the biomarkers and to inhibit their pathological self-assembly. Several studies have demonstrated that O-linked glycoside addition can significantly alter amyloid aggregation kinetics. Furthermore, natural O-glycosylation of amyloid-forming proteins, including amyloid precursor protein (APP), tau, and α-synuclein, promotes alternative nonamyloidogenic processing pathways. As such, glycopeptides and related peptidomimetics are being investigated within the AD field. Here we review advancements made in the last 5 years, as well as the arrival of sugar-based derivatives.
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Affiliation(s)
- Philip Ryan
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Bhautikkumar Patel
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Vivek Makwana
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Hemant R. Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Pilani-333031, Rajasthan, India
| | - Milton Kiefel
- Institute for Glycomics, Griffith University, Gold Coast 4222, Australia
| | - Andrew Davey
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
- Quality Use of Medicines Network, Griffith University, Gold Coast 4222, Australia
| | | | - Santosh Rudrawar
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
- Quality Use of Medicines Network, Griffith University, Gold Coast 4222, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, NSW 2006, Australia
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42
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Young SC. A Systematic Review of Antiamyloidogenic and Metal-Chelating Peptoids: Two Structural Motifs for the Treatment of Alzheimer's Disease. Molecules 2018; 23:E296. [PMID: 29385058 PMCID: PMC6017092 DOI: 10.3390/molecules23020296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 11/17/2022] Open
Abstract
Alzheimer's disease (AD) is an incurable form of dementia affecting millions of people worldwide and costing billions of dollars in health care-related payments, making the discovery of a cure a top health, societal, and economic priority. Peptide-based drugs and immunotherapies targeting AD-associated beta-amyloid (Aβ) aggregation have been extensively explored; however, their therapeutic potential is limited by unfavorable pharmacokinetic (PK) properties. Peptoids (N-substituted glycine oligomers) are a promising class of peptidomimetics with highly tunable secondary structures and enhanced stabilities and membrane permeabilities. In this review, the biological activities, structures, and physicochemical properties for several amyloid-targeting peptoids will be described. In addition, metal-chelating peptoids with the potential to treat AD will be discussed since there are connections between the dysregulation of certain metals and the amyloid pathway.
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Affiliation(s)
- Sherri C Young
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, PA 18104, USA.
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43
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Longhena F, Spano P, Bellucci A. Targeting of Disordered Proteins by Small Molecules in Neurodegenerative Diseases. Handb Exp Pharmacol 2018; 245:85-110. [PMID: 28965171 DOI: 10.1007/164_2017_60] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The formation of protein aggregates and inclusions in the brain and spinal cord is a common neuropathological feature of a number of neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and many others. These are commonly referred as neurodegenerative proteinopathies or protein-misfolding diseases. The main characteristic of protein aggregates in these disorders is the fact that they are enriched in amyloid fibrils. Since protein aggregation is considered to play a central role for the onset of neurodegenerative proteinopathies, research is ongoing to develop strategies aimed at preventing or removing protein aggregation in the brain of affected patients. Numerous studies have shown that small molecule-based approaches may be potentially the most promising for halting protein aggregation in neurodegenerative diseases. Indeed, several of these compounds have been found to interact with intrinsically disordered proteins and promote their clearing in experimental models. This notwithstanding, at present small molecule inhibitors still awaits achievements for clinical translation. Hopefully, if we determine whether the formation of insoluble inclusions is effectively neurotoxic and find a valid biomarker to assess their protein aggregation-inhibitory activity in the human central nervous system, the use of small molecule inhibitors will be considered as a cure for neurodegenerative protein-misfolding diseases.
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Affiliation(s)
- Francesca Longhena
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa No. 11, Brescia, 25123, Italy
| | - PierFranco Spano
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa No. 11, Brescia, 25123, Italy
| | - Arianna Bellucci
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa No. 11, Brescia, 25123, Italy.
- Laboratory of Personalized and Preventive Medicine, University of Brescia, Brescia, Italy.
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44
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Suprun EV, Radko SP, Farafonova TE, Mitkevich VA, Makarov AA, Archakov AI, Shumyantseva VV. Application of an Electrochemical Method to Evaluation of Amyloid-β Aggregation Inhibitors: Testing the RGKLVFFGR-NH2Peptide Antiaggregant. ELECTROANAL 2017. [DOI: 10.1002/elan.201700499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Elena V. Suprun
- Institute of Biomedical Chemistry; Pogodinskaya Street 10/8 Moscow 119121 Russia
| | - Sergey P. Radko
- Institute of Biomedical Chemistry; Pogodinskaya Street 10/8 Moscow 119121 Russia
| | | | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Vavilov Street 32 Moscow 119991 Russia
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Vavilov Street 32 Moscow 119991 Russia
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45
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Pseudo-peptide amyloid-β blocking inhibitors: molecular dynamics and single molecule force spectroscopy study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1707-1718. [PMID: 28844735 DOI: 10.1016/j.bbapap.2017.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
Abstract
By combining MD simulations and AFS experimental technique, we demonstrated a powerful approach for rational design and single molecule testing of novel inhibitor molecules which can block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. We designed and tested novel pseudo-peptide amyloid-β (Aβ) inhibitors that bind to the Aβ peptide and effectively prevent amyloid-amyloid binding. First, molecular dynamics (MD) simulations have provided information on the structures and binding characteristics of the designed pseudo-peptides targeting amyloid fragment Aβ (13-23). The binding affinities between the inhibitor and Aβ as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations. Atomic Force Spectroscopy (AFS) was used to experimentally test several proposed inhibitors in their ability to block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. The experimental AFS data are in a good agreement with theoretical MD calculations and demonstrate that three proposed pseudo-peptides bind to amyloid fragment with different affinities and all effectively prevent Aβ-Aβ binding in similar way. We propose that the designed pseudo-peptides can be used as potential drug candidates to prevent Aβ toxicity in Alzheimer's disease.
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46
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Jones MR, Mathieu E, Dyrager C, Faissner S, Vaillancourt Z, Korshavn KJ, Lim MH, Ramamoorthy A, Wee Yong V, Tsutsui S, Stys PK, Storr T. Multi-target-directed phenol-triazole ligands as therapeutic agents for Alzheimer's disease. Chem Sci 2017; 8:5636-5643. [PMID: 28989601 PMCID: PMC5621006 DOI: 10.1039/c7sc01269a] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/04/2017] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is a multifactorial disease that is characterized by the formation of intracellular neurofibrillary tangles and extracellular amyloid-β (Aβ) plaque deposits. Increased oxidative stress, metal ion dysregulation, and the formation of toxic Aβ peptide oligomers are all considered to contribute to the etiology of AD. In this work we have developed a series of ligands that are multi-target-directed in order to address several disease properties. 2-(1-(3-Hydroxypropyl)-1H-1,2,3-triazol-4-yl)phenol (POH), 2-(1-(2-morpholinoethyl)-1H-1,2,3-triazol-4-yl)phenol (PMorph), and 2-(1-(2-thiomorpholinoethyl)-1H-1,2,3-triazol-4-yl)phenol (PTMorph) have been synthesized and screened for their antioxidant capacity, Cu-binding affinity, interaction with the Aβ peptide and modulation of Aβ peptide aggregation, and the ability to limit Aβ1-42-induced neurotoxicity in human neuronal culture. The synthetic protocol and structural variance incorporated via click chemistry, highlights the influence of R-group modification on ligand-Aβ interactions and neuroprotective effects. Overall, this study demonstrates that the phenol-triazole ligand scaffold can target multiple factors associated with AD, thus warranting further therapeutic development.
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Affiliation(s)
- Michael R Jones
- Department of Chemistry , Simon Fraser University , V5A1S6 , Burnaby , BC , Canada .
- Department of Clinical Neurosciences , Hotchkiss Brain Institute , Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Emilie Mathieu
- Department of Chemistry , Simon Fraser University , V5A1S6 , Burnaby , BC , Canada .
| | - Christine Dyrager
- Department of Chemistry , Simon Fraser University , V5A1S6 , Burnaby , BC , Canada .
| | - Simon Faissner
- Department of Clinical Neurosciences , Hotchkiss Brain Institute , Cumming School of Medicine , University of Calgary , Calgary , Canada
- Department of Neurology , St. Josef-Hospital , Ruhr-University , Bochum , Germany
| | - Zavier Vaillancourt
- Department of Chemistry , Simon Fraser University , V5A1S6 , Burnaby , BC , Canada .
| | - Kyle J Korshavn
- Department of Chemistry , University of Michigan , Ann Arbor , USA
| | - Mi Hee Lim
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , Ulsan , Korea
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry , University of Michigan , Ann Arbor , USA
- Department of Biophysics , University of Michigan , Ann Arbor , USA
| | - V Wee Yong
- Department of Clinical Neurosciences , Hotchkiss Brain Institute , Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Shigeki Tsutsui
- Department of Clinical Neurosciences , Hotchkiss Brain Institute , Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Peter K Stys
- Department of Clinical Neurosciences , Hotchkiss Brain Institute , Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Tim Storr
- Department of Chemistry , Simon Fraser University , V5A1S6 , Burnaby , BC , Canada .
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47
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Castelletto V, Ryumin P, Cramer R, Hamley IW, Taylor M, Allsop D, Reza M, Ruokolainen J, Arnold T, Hermida-Merino D, Garcia CI, Leal MC, Castaño E. Self-Assembly and Anti-Amyloid Cytotoxicity Activity of Amyloid beta Peptide Derivatives. Sci Rep 2017; 7:43637. [PMID: 28272542 PMCID: PMC5341572 DOI: 10.1038/srep43637] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
The self-assembly of two derivatives of KLVFF, a fragment Aβ(16-20) of the amyloid beta (Aβ) peptide, is investigated and recovery of viability of neuroblastoma cells exposed to Aβ (1-42) is observed at sub-stoichiometric peptide concentrations. Fluorescence assays show that NH2-KLVFF-CONH2 undergoes hydrophobic collapse and amyloid formation at the same critical aggregation concentration (cac). In contrast, NH2-K(Boc)LVFF-CONH2 undergoes hydrophobic collapse at a low concentration, followed by amyloid formation at a higher cac. These findings are supported by the β-sheet features observed by FTIR. Electrospray ionization mass spectrometry indicates that NH2-K(Boc)LVFF-CONH2 forms a significant population of oligomeric species above the cac. Cryo-TEM, used together with SAXS to determine fibril dimensions, shows that the length and degree of twisting of peptide fibrils seem to be influenced by the net peptide charge. Grazing incidence X-ray scattering from thin peptide films shows features of β-sheet ordering for both peptides, along with evidence for lamellar ordering of NH2-KLVFF-CONH2. This work provides a comprehensive picture of the aggregation properties of these two KLVFF derivatives and shows their utility, in unaggregated form, in restoring the viability of neuroblastoma cells against Aβ-induced toxicity.
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Affiliation(s)
- V. Castelletto
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - P. Ryumin
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - R. Cramer
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - I. W. Hamley
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - M. Taylor
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - D. Allsop
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - M. Reza
- Department of Applied Physics, Aalto University School of Science, Aalto FI-00076, Finland
| | - J. Ruokolainen
- Department of Applied Physics, Aalto University School of Science, Aalto FI-00076, Finland
| | - T. Arnold
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D. Hermida-Merino
- European Synchrotron Radiation Facility, ESRF, 71 avenue des Martyrs, 38000 Grenoble, France
| | - C. I. Garcia
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - M. C. Leal
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - E. Castaño
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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48
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Shuaib S, Goyal B. Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β 42 monomer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:663-678. [PMID: 28162045 DOI: 10.1080/07391102.2017.1291363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β42 (Aβ42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ42. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ42.
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Affiliation(s)
- Suniba Shuaib
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
| | - Bhupesh Goyal
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
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49
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Goyal D, Shuaib S, Mann S, Goyal B. Rationally Designed Peptides and Peptidomimetics as Inhibitors of Amyloid-β (Aβ) Aggregation: Potential Therapeutics of Alzheimer's Disease. ACS COMBINATORIAL SCIENCE 2017; 19:55-80. [PMID: 28045249 DOI: 10.1021/acscombsci.6b00116] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease with no clinically accepted treatment to cure or halt its progression. The worldwide effort to develop peptide-based inhibitors of amyloid-β (Aβ) aggregation can be considered an unplanned combinatorial experiment. An understanding of what has been done and achieved may advance our understanding of AD pathology and the discovery of effective therapeutic agents. We review here the history of such peptide-based inhibitors, including those based on the Aβ sequence and those not derived from that sequence, containing both natural and unnatural amino acid building blocks. Peptide-based aggregation inhibitors hold significant promise for future AD therapy owing to their high selectivity, effectiveness, low toxicity, good tolerance, low accumulation in tissues, high chemical and biological diversity, possibility of rational design, and highly developed methods for analyzing their mode of action, proteolytic stability (modified peptides), and blood-brain barrier (BBB) permeability.
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Affiliation(s)
- Deepti Goyal
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Suniba Shuaib
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Sukhmani Mann
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Bhupesh Goyal
- Department of Chemistry,
School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
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50
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Kouza M, Banerji A, Kolinski A, Buhimschi IA, Kloczkowski A. Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model. Phys Chem Chem Phys 2017; 19:2990-2999. [PMID: 28079198 PMCID: PMC5305032 DOI: 10.1039/c6cp07145g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Preeclampsia, a pregnancy-specific disorder, shares typical pathophysiological features with protein misfolding disorders including Alzheimer's disease. Characteristic for preeclampsia is the involvement of multiple proteins of which fragments of SERPINA1 and β-amyloid co-aggregate in urine and placenta of preeclamptic women. To explore the biophysical basis of this interaction, we investigated the multidimensional efficacy of the FVFLM sequence in SERPINA1, as a model inhibitory agent of β-amyloid aggregation. After studying the oligomerization of FVFLM peptides using all-atom molecular dynamics simulations with the GROMOS43a1 force field and explicit water, we report that FVFLM can aggregate and its aggregation is spontaneous with a remarkably faster rate than that recorded for KLVFF (aggregation "hot-spot" from β-amyloid). The fast kinetics of FVFLM aggregation was found to be driven primarily by core-like aromatic interactions originating from the anti-parallel orientation of complementarily uncharged strands. The conspicuously stable aggregation mechanism observed for FVFLM peptides is found not to conform to the popular 'dock-lock' scheme. We also found high propensity of FVFLM for KLVFF binding. When present, FVFLM disrupts the β-amyloid aggregation pathway and we propose that FVFLM-like peptides might be used to prevent the assembly of full-length Aβ or other pro-amyloidogenic peptides into amyloid fibrils.
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Affiliation(s)
- M Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. and Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Banerji
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - I A Buhimschi
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - A Kloczkowski
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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