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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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2
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Picone P, Sanfilippo T, Vasto S, Baldassano S, Guggino R, Nuzzo D, Bulone D, San Biagio PL, Muscolino E, Monastero R, Dispenza C, Giacomazza D. From Small Peptides to Large Proteins against Alzheimer’sDisease. Biomolecules 2022; 12:biom12101344. [PMID: 36291553 PMCID: PMC9599460 DOI: 10.3390/biom12101344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the elderly. The two cardinal neuropathological hallmarks of AD are the senile plaques, which are extracellular deposits mainly constituted by beta-amyloids, and neurofibrillary tangles formed by abnormally phosphorylated Tau (p-Tau) located in the cytoplasm of neurons. Although the research has made relevant progress in the management of the disease, the treatment is still lacking. Only symptomatic medications exist for the disease, and, in the meantime, laboratories worldwide are investigating disease-modifying treatments for AD. In the present review, results centered on the use of peptides of different sizes involved in AD are presented.
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Affiliation(s)
- Pasquale Picone
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Tiziana Sanfilippo
- Ambulatorio di Nutrizione Clinica ASP Palermo, Via G. Cusmano 24, 90141 Palermo, Italy
- Anestesia e Rianimazione, Presidio Ospedaliero “S. Cimino”, 90141 Termini Imerese, Italy
| | - Sonya Vasto
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Istituti Euro-Mediterranei di Scienza e Tecnologia (IEMEST), Via M. Miraglia 20, 90139 Palermo, Italy
| | - Sara Baldassano
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Rossella Guggino
- Ambulatorio di Nutrizione Clinica ASP Palermo, Via G. Cusmano 24, 90141 Palermo, Italy
- Anestesia e Rianimazione, Presidio Ospedaliero “S. Cimino”, 90141 Termini Imerese, Italy
| | - Domenico Nuzzo
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Correspondence: (D.N.); (D.G.)
| | - Donatella Bulone
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Pier Luigi San Biagio
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Emanuela Muscolino
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Bldg 6, 90128 Palermo, Italy
| | - Roberto Monastero
- Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università degli Studi di Palermo, Via del Vespro 129, 90127 Palermo, Italy
| | - Clelia Dispenza
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Bldg 6, 90128 Palermo, Italy
| | - Daniela Giacomazza
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Correspondence: (D.N.); (D.G.)
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3
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Chakraborty I, Kar RK, Sarkar D, Kumar S, Maiti NC, Mandal AK, Bhunia A. Solvent Relaxation NMR: A Tool for Real-Time Monitoring Water Dynamics in Protein Aggregation Landscape. ACS Chem Neurosci 2021; 12:2903-2916. [PMID: 34292711 DOI: 10.1021/acschemneuro.1c00262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Solvent dynamics strongly induce the fibrillation of an amyloidogenic system. Probing the solvation mechanism is crucial as it enables us to predict different proteins' functionalities, such as the aggregation propensity, structural flexibility, and toxicity. This work shows that a straightforward NMR method in conjunction with phenomenological models gives a global and qualitative picture of water dynamics at different concentrations and temperatures. Here, we study amyloid system Aβ40 and its fragment AV20 (A21-V40) and G37L (mutation at Gly37 → Leu of AV20), having different aggregation and toxic properties. The independent validation of this method is elucidated using all-atom classical MD simulation. These two state-of-the-art techniques are pivotal in linking the effect of solvent environment in the near hydration-shell to their aggregation nature. The time-dependent modulation in solvent dynamics probed with the NMR solvent relaxation method can be further adopted to gain insight into amyloidogenesis and link with their toxicity profiles.
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Affiliation(s)
| | - Rajiv K. Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Dibakar Sarkar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
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4
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Wang W, Zhao G, Dong X, Sun Y. Unexpected Function of a Heptapeptide-Conjugated Zwitterionic Polymer that Coassembles into β-Amyloid Fibrils and Eliminates the Amyloid Cytotoxicity. ACS APPLIED MATERIALS & INTERFACES 2021; 13:18089-18099. [PMID: 33829756 DOI: 10.1021/acsami.1c01132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fibrillogenesis of amyloid β-protein (Aβ) is pathologically associated with Alzheimer's disease (AD), so modulating Aβ aggregation is crucial for AD prevention and treatment. Herein, a zwitterionic polymer with short dimethyl side chains (pID) is synthesized and conjugated with a heptapeptide inhibitor (Ac-LVFFARK-NH2, LK7) to construct zwitterionic polymer-inhibitor conjugates for enhanced inhibition of Aβ aggregation. However, it is unexpectedly found that the LK7@pID conjugates remarkably promote Aβ fibrillization to form more fibrils than the free Aβ system but effectively eliminate Aβ-induced cytotoxicity. Such an unusual behavior of the LK7@pID conjugates is unraveled by extensive mechanistic studies. First, the hydrophobic environment within the assembled micelles of LK7@pID promotes the hydrophobic interaction between Aβ molecules and LK7@pID, which triggers Aβ aggregation at the very beginning, making fibrillization occur at an earlier stage. Second, in the aggregation process, the LK7@pID micelles disassemble by the intensive interactions with Aβ, and LK7@pID participates in the fibrillization by being embedded in the Aβ fibrils, leading to the formation of hybrid and heterogeneous fibrillar aggregates with a different structure than normal Aβ fibrils. This unique Trojan horse-like feature of LK7@pID conjugates has not been observed for any other inhibitors reported previously and may shed light on the design of new modulators against β-amyloid cytotoxicity.
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Affiliation(s)
- Wenjuan Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Guangfu Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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5
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Siwy CM, Delfing BM, Lockhart C, Smith AK, Klimov DK. Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer. J Phys Chem B 2021; 125:2658-2676. [PMID: 33656350 DOI: 10.1021/acs.jpcb.0c11253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.
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Affiliation(s)
- Christopher M Siwy
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Amy K Smith
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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6
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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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7
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Vijayan D, Chandra R. Amyloid Beta Hypothesis in Alzheimer's Disease: Major Culprits and Recent Therapeutic Strategies. Curr Drug Targets 2021; 21:148-166. [PMID: 31385768 DOI: 10.2174/1389450120666190806153206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/13/2019] [Accepted: 07/26/2019] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease (AD) is one of the most common forms of dementia and has been a global concern for several years. Due to the multi-factorial nature of the disease, AD has become irreversible, fatal and imposes a tremendous socio-economic burden. Even though experimental medicines suggested moderate benefits, AD still lacks an effective treatment strategy for the management of symptoms or cure. Among the various hypotheses that describe development and progression of AD, the amyloid hypothesis has been a long-term adherent to the AD due to the involvement of various forms of Amyloid beta (Aβ) peptides in the impairment of neuronal and cognitive functions. Hence, majority of the drug discovery approaches in the past have focused on the prevention of the accumulation of Aβ peptides. Currently, there are several agents in the phase III clinical trials that target Aβ or the various macromolecules triggering Aβ deposition. In this review, we present the state of the art knowledge on the functional aspects of the key players involved in the amyloid hypothesis. Furthermore, we also discuss anti-amyloid agents present in the Phase III clinical trials.
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Affiliation(s)
- Dileep Vijayan
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Remya Chandra
- Department of Biotechnology and Microbiology, Thalassery Campus, Kannur University, Kerala Pin 670 661, India
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8
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Kapadia A, Sharma KK, Maurya IK, Singh V, Khullar M, Jain R. Structural and mechanistic insights into the inhibition of amyloid-β aggregation by Aβ 39-42 fragment derived synthetic peptides. Eur J Med Chem 2020; 212:113126. [PMID: 33395622 DOI: 10.1016/j.ejmech.2020.113126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
The inhibition of amyloid-β (Aβ) aggregation is a promising approach towards therapeutic intervention for Alzheimer's disease (AD). Thirty eight tetrapeptides based upon Aβ39-42C-terminus fragment of the parent Aβ peptide were synthesized. The sequential replacement/modification employing unnatural amino acids imparted scaffold diversity, augmented activity, enhanced blood brain barrier permeability and offered proteolytic stability to the synthetic peptides. Several peptides exhibited promising protection against Aβ aggregation-mediated-neurotoxicity in PC-12 cells at doses ranged between 10 μM and 0.1 μM, further confirmed by the thioflavin-T fluorescence assay. CD study illustrate that these peptides restrict the β-sheet formation, and the non-appearance of Aβ42 fibrillar structures in the electron microscopy confirm the inhibition of Aβ42 aggregation. HRMS and ANS fluorescence spectroscopic analysis provided additional mechanistic insights. Two selected lead peptides 5 and 16 depicted enhanced blood-brain penetration and stability against serum and proteolytic enzyme. Structural insights into ligand-Aβ interactions on the monomeric and proto-fibrillar units of Aβ were computationally studied. Promising inhibitory potential and short sequence of the lead peptides offers new avenues for the advancement of peptide-derived therapeutics for AD.
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Affiliation(s)
- Akshay Kapadia
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India
| | - Indresh Kumar Maurya
- Department of Microbial Biotechnology, Punjab University, Sector 25, Chandigarh, 160 014, India
| | - Varinder Singh
- Post Graduate Institute of Medical Education and Research, Sector 11, Chandigarh, 160 014, India
| | - Madhu Khullar
- Post Graduate Institute of Medical Education and Research, Sector 11, Chandigarh, 160 014, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India.
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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: 11] [Impact Index Per Article: 2.8] [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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Kumar S, Tyagi YK, Kumar M, Kumar S. Synthesis of novel 4-methylthiocoumarin and comparison with conventional coumarin derivative as a multi-target-directed ligand in Alzheimer's disease. 3 Biotech 2020; 10:509. [PMID: 33184595 PMCID: PMC7644673 DOI: 10.1007/s13205-020-02481-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is a multifactorial disorder characterized by cognitive deficit and memory loss. The pathological feature of the disease involves β-amyloid senile plaques, reduced levels of acetylcholine neurotransmitter, oxidative stress and neurofibrillary tangles formation within the brain of AD patients. The present study aims to screen the inhibitory activity of newly synthesized and existing novel 4-methylthiocoumarin derivative against acetylcholinesterase, butyrylcholinesterase, BACE1, β-amyloid aggregation and oxidative stress involved in the AD pathogenesis. The in vitro assays used in this study were Ellman's assay, FRET assays, Thioflavin T, transmission electron microscopy, circular dichroism, FRAP, and TEAC. Molecular docking and dynamics studies were performed to correlate the results. C3 and C7 (thiocoumarin derivatives) were found to be the most potent inhibitors of acetylcholinesterase (IC50-5.63 µM) and butyrylcholinesterase (IC50-3.40 µM) using Ellman's assays. Enzyme kinetic studies showed that C3 and C7 compounds followed by the mixed mode of inhibition using LB plot. C3 also moderately inhibited the BACE1 using FRET assay. C3 inhibited the fibrillization of β-amyloid peptides in a concentration-dependent manner as observed by Thioflavin T, TEM studies and Circular dichroism data. Molecular modeling studies were performed to understand the probable mode of binding of C3 and C7 in the binding pocket of acetylcholinesterase, butyrylcholinesterase, BACE1 and amyloid β peptides. This indicates the important role of hydrophobic interactions between C3 and acetylcholinesterase. C3 also exhibited significant antioxidant potential by FRAP and TEAC assays. Hence, C3 might serve as a promising lead for developing novel multi target-directed ligand for the treatment of AD.
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Affiliation(s)
- Shivani Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi, 110078 India
| | - Yogesh Kumar Tyagi
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi, 110078 India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Suresh Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi, 110078 India
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11
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Tandem-Homodimer of a β-Sheet-Forming Short Peptide Inhibits Random-to-β Structural Transition of Its Original Monomer. Processes (Basel) 2020. [DOI: 10.3390/pr8111421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is an increasing interest in designing fibrillogenesis modulators for treating amyloid β (Aβ)-peptide-associated diseases. The use of Aβ fragment peptides and their derivatives, as well as nonpeptidyl natural products, is one promising approach to prevent Aβ fibrillation. In this study, we demonstrate that tandem-homodimers (TDs) of a β-sheet-forming short peptide in which the amino acid sequence is duplicated in series and joined via an amino alkanoic acid linker of different chain lengths, preventing the random-to-β structural transition of the original monomer. Ape5-TD, containing 5-amino pentanoate, most potently prevented this transition for at least five days by generating disordered aggregates with reduced tryptic stability. The linkers in the TDs generated this inhibitory activity, probably due to their bent conformations and hydrophobicity, appropriate for accommodating and twisting the monomers, resulting in irregular arrangements of the peptides. The present study could allow the design of a new class of protein/peptide fibrillogenesis modulators.
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12
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Mason AJ, Hurst I, Malik R, Siddique I, Solomonov I, Sagi I, Klärner FG, Schrader T, Bitan G. Different Inhibitors of Aβ42-Induced Toxicity Have Distinct Metal-Ion Dependency. ACS Chem Neurosci 2020; 11:2243-2255. [PMID: 32559370 DOI: 10.1021/acschemneuro.0c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Oligomers of amyloid β-protein (Aβ) are thought to be the proximal toxic agents initiating the neuropathologic process in Alzheimer's disease (AD). Therefore, targeting the self-assembly and oligomerization of Aβ has been an important strategy for designing AD therapeutics. In parallel, research into the metallobiology of AD has shown that Zn2+ can strongly modulate the aggregation of Aβ in vitro and both promote and inhibit the neurotoxicity of Aβ, depending on the experimental conditions. Thus, successful inhibitors of Aβ self-assembly may have to inhibit the toxicity not only of Aβ oligomers themselves but also of Aβ-Zn2+ complexes. However, there has been relatively little research investigating the effects of Aβ self-assembly and toxicity inhibitors in the presence of Zn2+. Our group has characterized previously a series of Aβ42 C-terminal fragments (CTFs), some of which have been shown to inhibit Aβ oligomerization and neurotoxicity. Here, we asked whether three CTFs shown to be potent inhibitors of Aβ42 toxicity maintained their activity in the presence of Zn2+. Biophysical analysis showed that the CTFs had different effects on oligomer, β-sheet, and fibril formation by Aβ42-Zn2+ complexes. However, cell viability experiments in differentiated PC-12 cells incubated with Aβ42-Zn2+ complexes in the absence or presence of these CTFs showed that the CTFs completely lost their inhibitory activity in the presence of Zn2+ even when applied at 10-fold excess relative to Aβ42. In light of these results, we tested another inhibitor, the molecular tweezer CLR01, which coincidentally had been shown to have a high affinity for Zn2+, suggesting that it could disrupt both Aβ42 oligomerization and Aβ42-Zn2+ complexation. Indeed, we found that CLR01 effectively inhibited the toxicity of Aβ42-Zn2+ complexes. Moreover, it did so at a lower concentration than needed for inhibiting the toxicity of Aβ42 alone. In agreement with these results, CLR01 inhibited β-sheet and fibril formation in Aβ42-Zn2+ complexes. Our data suggest that, for the development of efficient therapeutic agents, inhibitors of Aβ self-assembly and toxicity should be examined in the presence of relevant metal ions and that molecular tweezers may be particularly attractive candidates for therapy development.
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Affiliation(s)
- Ashley J. Mason
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ian Hurst
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Frank-Gerrit Klärner
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
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13
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Yang F, Zhang W, Jiang Y, Yin F, Han W, Li Z. Targeting the Amyloid-β Fibril Surface with a Constrained Helical Peptide Inhibitor. Biochemistry 2020; 59:290-296. [PMID: 31702899 DOI: 10.1021/acs.biochem.9b00800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β (Aβ) oligomers are well-known toxic molecular species associated with Alzheimer's disease. Recent discoveries of the ability of amyloid fibril surfaces to convert soluble proteins into toxic oligomers suggested that these surfaces could serve as therapeutic targets for intervention. We have shown previously that a short helical peptide could be a key structural motif that can specifically recognize the K16-E22 region of the Aβ40 fibril surface with an affinity at the level of several micromolar. Here, we demonstrate that in-tether chiral center-induced helical stabilized peptides could also recognize the fibril surfaces, effectively inhibiting the surface-mediated oligomerization of Aβ40. Moreover, through extensive computational sampling, we observed two distinct ways in which the peptide inhibitors recognize the fibril surface. Apart from a binding mode that, in accord with the original design, involves hydrophobic side chains at the binding interface, we observed much more frequently another binding mode in which the hydrophobic staple interacts directly with the fibril surface. The affinity of the peptides for the fibril surface could be adjusted by tuning the hydrophobicity of the staple. The best candidate investigated here exhibits a submicromolar affinity (∼0.75 μM). Collectively, this work opens an avenue for the rational design of candidate drugs with stapled peptides for amyloid-related disease.
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Affiliation(s)
- Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Wan Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China.,Shenzhen Bay Laboratory , Shenzhen 518055 , China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China.,Shenzhen Bay Laboratory , Shenzhen 518055 , China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China.,Shenzhen Bay Laboratory , Shenzhen 518055 , China
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14
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Jakubowski J, Orr AA, Le DA, Tamamis P. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:289-305. [PMID: 31809572 PMCID: PMC7732148 DOI: 10.1021/acs.jcim.9b00561] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 12/24/2022]
Abstract
The aggregation of amyloid-β (Aβ) peptides into senile plaques is a hallmark of Alzheimer's disease (AD) and is hypothesized to be the primary cause of AD related neurodegeneration. Previous studies have shown the ability of curcumin to both inhibit the aggregation of Aβ peptides into oligomers or fibrils and reduce amyloids in vivo. Despite the promise of curcumin and its derivatives to serve as diagnostic, preventative, and potentially therapeutic AD molecules, the mechanism by which curcumin and its derivatives bind to and inhibit Aβ fibrils' formation remains elusive. Here, we investigated curcumin and a set of curcumin derivatives in complex with a hexamer peptide model of the Aβ1-42 fibril using nearly exhaustive docking, followed by multi-ns molecular dynamics simulations, to provide atomistic-detail insights into the molecules' binding and inhibitory properties. In the vast majority of the simulations, curcumin and its derivatives remain firmly bound in complex with the fibril through primarily three different principle binding modes, in which the molecules interact with residue domain 17LVFFA21, in line with previous experiments. In a small subset of these simulations, the molecules partly dissociate the outermost peptide of the Aβ1-42 fibril by disrupting β-sheets within the residue domain 12VHHQKLVFF20. A comparison between binding modes leading or not leading to partial dissociation of the outermost peptide suggests that the latter is attributed to a few subtle key structural and energetic interaction-based differences. Interestingly, partial dissociation appears to be either an outcome of high affinity interactions or a cause leading to high affinity interactions between the molecules and the fibril, which could partly serve as a compensation for the energy loss in the fibril due to partial dissociation. In conjunction with this, we suggest a potential inhibition mechanism of Αβ1-42 aggregation by the molecules, where the partially dissociated 16KLVFF20 domain of the outermost peptide could either remain unstructured or wrap around to form intramolecular interactions with the same peptide's 29GAIIG33 domain, while the molecules could additionally act as a patch against the external edge of the second outermost peptide's 16KLVFF20 domain. Thereby, individually or concurrently, these could prohibit fibril elongation.
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Affiliation(s)
| | | | - Doan A. Le
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Phanourios Tamamis
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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15
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Asadbegi M, Shamloo A. Identification of a Novel Multifunctional Ligand for Simultaneous Inhibition of Amyloid-Beta (Aβ 42) and Chelation of Zinc Metal Ion. ACS Chem Neurosci 2019; 10:4619-4632. [PMID: 31566950 DOI: 10.1021/acschemneuro.9b00468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn2+ chelating domain, derived from rapeseed meal, merge with a linker. The multifunctionality of the ligand was evaluated using a comprehensive set of MD simulations spanning up to 3.2 μs including Aβ relaxation, ligand-Zn2+ bilateral interaction, and, more importantly, ligand-Zn2+-Aβ42 trilateral interactions. Analysis of the results strongly indicated that the bifunctional ligand can chelate zinc metal ion and avoid Aβ aggregation simultaneously. The present study illustrated that the proposed ligand has considerable hydrophobic interactions and hydrogen bonding with monomeric Aβ in the presence of zinc metal ion. Therefore, in light of these considerable interactions and contacts, the α-helical structure of Aβ has been enhanced, while the β-sheet formation is prevented and the α-helix native structure is protected. Furthermore, the analysis of interactions between Aβ and ligand-zinc complex revealed that the zinc metal ion is coordinated to Met13, the ending residue of the ligand and merely one residue in Aβ. The results have proven the previous experimental and theoretical findings in the literature about Aβ interactions with zinc metal ion and also Aβ interactions with the first domain of the proposed ligand. Moreover, the current research has evaluated the chelation using MD simulation and linear interaction energy (LIE) methods, and the result has been satisfactorily verified with previous experimental and theoretical (DFT) studies.
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Affiliation(s)
- Mohsen Asadbegi
- Sharif University of Technology, School of Mechanical Engineering, Tehran 94305, Iran
| | - Amir Shamloo
- Sharif University of Technology, School of Mechanical Engineering, Tehran 94305, Iran
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16
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Multi-target-directed triazole derivatives as promising agents for the treatment of Alzheimer’s disease. Bioorg Chem 2019; 87:572-584. [DOI: 10.1016/j.bioorg.2019.03.058] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 03/06/2019] [Accepted: 03/19/2019] [Indexed: 12/17/2022]
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17
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ADS-J1 disaggregates semen-derived amyloid fibrils. Biochem J 2019; 476:1021-1035. [PMID: 30877194 DOI: 10.1042/bcj20180886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 11/17/2022]
Abstract
Semen-derived amyloid fibrils, comprising SEVI (semen-derived enhancer of viral infection) fibrils and SEM1 fibrils, could remarkably enhance HIV-1 sexual transmission and thus are potential targets for the development of an effective microbicide. Previously, we found that ADS-J1, apart from being an HIV-1 entry inhibitor, could also potently inhibit seminal amyloid fibrillization and block fibril-mediated enhancement of viral infection. However, the remodeling effects of ADS-J1 on mature seminal fibrils were unexplored. Herein, we investigated the capacity of ADS-J1 to disassemble seminal fibrils and the potential mode of action by applying several biophysical and biochemical measurements, combined with molecular dynamic (MD) simulations. We found that ADS-J1 effectively remodeled SEVI, SEM186-107 fibrils and endogenous seminal fibrils. Unlike epigallocatechin gallate (EGCG), a universal amyloid fibril breaker, ADS-J1 disaggregated SEVI fibrils into monomeric peptides, which was independent of oxidation reaction. MD simulations revealed that ADS-J1 displayed strong binding potency to the full-length PAP248-286 via electrostatic interactions, hydrophobic interactions and hydrogen bonds. ADS-J1 might initially bind to the fibrillar surface and then occupy the amyloid core, which eventually lead to fibril disassembly. Furthermore, the binding of ADS-J1 with PAP248-286 might induce conformational changes of PAP248-286 Disassembled PAP248-286 might not be favorable to re-aggregate into fibrils. ADS-J1 also exerts abilities to remodel a panel of amyloid fibrils, including Aβ1-42, hIAPP1-37 and EP2 fibrils. ADS-J1 displays promising potential to be a combination microbicide and an effective lead-product to treat amyloidogenic diseases.
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18
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Pandey G, Morla S, Nemade HB, Kumar S, Ramakrishnan V. Modulation of aggregation with an electric field; scientific roadmap for a potential non-invasive therapy against tauopathies. RSC Adv 2019; 9:4744-4750. [PMID: 35514655 PMCID: PMC9060620 DOI: 10.1039/c8ra09993f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/22/2019] [Indexed: 11/21/2022] Open
Abstract
Toxic aggregation of tau protein to neurofibrillary tangles (NFTS) is a central pathological event involved in tauopathies. Inhibition of tau protein aggregation can serve as a straightforward therapeutic strategy. However, tau-based therapeutic solutions are not very common. Phenothiazine methylene blue (tau protein inhibitor) is currently the only drug under phase III clinical trials. In this work, a non-invasive strategy is presented for modulating the aggregation of core peptide segments of tau protein (VQIVYK and VQIINK) by using electric fields of varying strengths. We use thioflavin T staining, tyrosine fluorescence assay, electron microscopy, IR, dynamic and static light scattering, and neuronal toxicity estimation, for verifying the effect of electric field on the aggregation kinetics, morphology, conformational state and cellular toxicity of peptide systems. Our observations suggest that electric field arrests the self-assembly of VQIVYK and VQIINK fibrils thereby reducing the neurotoxicity instigated by them. Based on our observations, we propose a prospective scheme for a futuristic non-invasive therapeutic device.
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Affiliation(s)
- Gaurav Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Sudhir Morla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Harshal B Nemade
- Department of Electronics and Electrical Engineering, Indian Institute of Technology Guwahati Guwahati-781039 India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
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19
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20
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Ismail T, Vancha SR, Kanapathipillai M. L‐proline and betaine inhibit extracellular enzymes mediated abeta 1‐42 aggregation, oxidative stress, and toxicity. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Tania Ismail
- University of Michigan‐DearbornDepartment of Mechanical Engineering Dearborn Michigan
| | - Sushma Reddy Vancha
- University of Michigan‐DearbornDepartment of Mechanical Engineering Dearborn Michigan
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21
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Kamp F, Scheidt HA, Winkler E, Basset G, Heinel H, Hutchison JM, LaPointe LM, Sanders CR, Steiner H, Huster D. Bexarotene Binds to the Amyloid Precursor Protein Transmembrane Domain, Alters Its α-Helical Conformation, and Inhibits γ-Secretase Nonselectively in Liposomes. ACS Chem Neurosci 2018; 9:1702-1713. [PMID: 29717863 DOI: 10.1021/acschemneuro.8b00068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bexarotene is a pleiotropic molecule that has been proposed as an amyloid-β (Aβ)-lowering drug for the treatment of Alzheimer's disease (AD). It acts by upregulation of an apolipoprotein E (apoE)-mediated Aβ clearance mechanism. However, whether bexarotene induces removal of Aβ plaques in mouse models of AD has been controversial. Here, we show by NMR and CD spectroscopy that bexarotene directly interacts with and stabilizes the transmembrane domain α-helix of the amyloid precursor protein (APP) in a region where cholesterol binds. This effect is not mediated by changes in membrane lipid packing, as bexarotene does not share with cholesterol the property of inducing phospholipid condensation. Bexarotene inhibited the intramembrane cleavage by γ-secretase of the APP C-terminal fragment C99 to release Aβ in cell-free assays of the reconstituted enzyme in liposomes, but not in cells, and only at very high micromolar concentrations. Surprisingly, in vitro, bexarotene also inhibited the cleavage of Notch1, another major γ-secretase substrate, demonstrating that its inhibition of γ-secretase is not substrate specific and not mediated by acting via the cholesterol binding site of C99. Our data suggest that bexarotene is a pleiotropic molecule that interfere with Aβ metabolism through multiple mechanisms.
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Affiliation(s)
- Frits Kamp
- Biomedical Center - BMC, Metabolic Biochemistry, Ludwig-Maximilians University, Munich 80539, Germany
| | - Holger A. Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Edith Winkler
- Biomedical Center - BMC, Metabolic Biochemistry, Ludwig-Maximilians University, Munich 80539, Germany
| | - Gabriele Basset
- Biomedical Center - BMC, Metabolic Biochemistry, Ludwig-Maximilians University, Munich 80539, Germany
| | - Hannes Heinel
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - James M. Hutchison
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Loren M. LaPointe
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Charles R. Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Harald Steiner
- Biomedical Center - BMC, Metabolic Biochemistry, Ludwig-Maximilians University, Munich 80539, Germany
- German Center for Neurodegenerative Diseases (DZNE)−Munich, Feodor-Lynen-Str. 17, D-81377 Munich, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
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22
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Heid C, Sowislok A, Schaller T, Niemeyer F, Klärner FG, Schrader T. Molecular Tweezers with Additional Recognition Sites. Chemistry 2018; 24:11332-11343. [DOI: 10.1002/chem.201801508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Christian Heid
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Andrea Sowislok
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Torsten Schaller
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Felix Niemeyer
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Frank-Gerrit Klärner
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Thomas Schrader
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
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23
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Goyal D, Kaur A, Goyal B. Benzofuran and Indole: Promising Scaffolds for Drug Development in Alzheimer's Disease. ChemMedChem 2018; 13:1275-1299. [DOI: 10.1002/cmdc.201800156] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/27/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib 140406 Punjab India
| | - Amandeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib 140406 Punjab India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry; Thapar Institute of Engineering & Technology; Patiala 147004 Punjab India
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24
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Nieznanska H, Bandyszewska M, Surewicz K, Zajkowski T, Surewicz WK, Nieznanski K. Identification of prion protein-derived peptides of potential use in Alzheimer's disease therapy. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2143-2153. [DOI: 10.1016/j.bbadis.2018.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/27/2018] [Accepted: 03/26/2018] [Indexed: 12/01/2022]
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25
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Das P, Matysiak S, Mittal J. Looking at the Disordered Proteins through the Computational Microscope. ACS CENTRAL SCIENCE 2018; 4:534-542. [PMID: 29805999 PMCID: PMC5968442 DOI: 10.1021/acscentsci.7b00626] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.
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Affiliation(s)
- Payel Das
- IBM Thomas J.
Watson Research Center, Yorktown Heights, New York 10598, United States
- E-mail:
| | - Silvina Matysiak
- Fischell
Department of Bioengineering, University
of Maryland, College Park, Maryland 20742, United States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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26
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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27
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Liu Y, Xu LP, Wang Q, Yang B, Zhang X. Synergistic Inhibitory Effect of GQDs-Tramiprosate Covalent Binding on Amyloid Aggregation. ACS Chem Neurosci 2018; 9:817-823. [PMID: 29244487 DOI: 10.1021/acschemneuro.7b00439] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Inhibiting the amyloid aggregation is considered to be an effective strategy to explore possible treatment of amyloid-related diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Herein, a new high-efficiency and low-cytotoxicity Aβ aggregation inhibitors, GQD-T, was designed through the combination of two Aβ aggregation inhibitors, graphene quantum dots (GQDs) and tramiprosate. GQD-T showed the capability of efficiently inhibiting the aggregation of Aβ peptides and rescuing Aβ-induced cytotoxicity due to the synergistic effect of the GQDs and tramiprosate. In addition, the GQD-T has the characteristics of low toxicity and great biocompatibility. It is believed that GQD-T may be a potential candidate for an Alzheimer's drug and this work provides a new strategy for exploring Aβ peptide aggregation inhibitors.
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Affiliation(s)
- Yibiao Liu
- Institute of Nanostructured Functional Materials, Huanghe Science & Technology College, Zhengzhou 450006, P.R. China
- Henan Provincial Key Laboratory of Nano-composite Materials and Applications, Huanghe Science & Technology College, Zhengzhou 450006, P.R. China
| | - Li-Ping Xu
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Qiang Wang
- State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, The Chinese Academy of Sciences, Taiyuan 030001, P.R. China
| | - Baocheng Yang
- Institute of Nanostructured Functional Materials, Huanghe Science & Technology College, Zhengzhou 450006, P.R. China
- Henan Provincial Key Laboratory of Nano-composite Materials and Applications, Huanghe Science & Technology College, Zhengzhou 450006, P.R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P.R. China
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28
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Han X, He G. Toward a Rational Design to Regulate β-Amyloid Fibrillation for Alzheimer's Disease Treatment. ACS Chem Neurosci 2018; 9:198-210. [PMID: 29251488 DOI: 10.1021/acschemneuro.7b00477] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The last decades have witnessed a growing global burden of Alzheimer's disease (AD). Evidence indicates that the onset and progression of AD is associated with β-amyloid (Aβ) peptide fibrillation. As such, there is a strong passion with discovering potent Aβ fibrillation inhibitors that can be developed into anti-amyloiddogenic agents for AD treatment. Current challenges that have arisen with this development involve with Aβ oligomer toxicity suppression and Blood Brain Barrier penetration capability. Considering most natural or biological events, one would observe that there is usually a "seed" to direct natural materials to assemble in response to a certain stimulation. Inspired by this, several materials or compounds, including nanoparticle, peptide or peptide mimics, and organic molecules, have been designed for the purpose of redirecting or impeding Aβ aggregation. Achieving these tasks requires comprehensive understanding on (1) initial Aβ assembly into insoluble deposits, (2) main concerns with fibrillation inhibition, and (3) current major methodologies to disrupt the aggregation. Herein, the objective of this review is to address these three areas, and enable the pathway for a promising therapeutic agent design for AD treatment.
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Affiliation(s)
- Xu Han
- Huston Labs, 1951 NW Seventh
Avenue, Suite 600, Miami, Florida 33136, United States
| | - Gefei He
- East China Normal University, 3663 Zhongshan N Road, Putuo District, Shanghai 200062, China
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29
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Cheng B, Li Y, Ma L, Wang Z, Petersen RB, Zheng L, Chen Y, Huang K. Interaction between amyloidogenic proteins and biomembranes in protein misfolding diseases: Mechanisms, contributors, and therapy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1876-1888. [PMID: 29466701 DOI: 10.1016/j.bbamem.2018.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/14/2022]
Abstract
The toxic deposition of misfolded amyloidogenic proteins is associated with more than fifty protein misfolding diseases (PMDs), including Alzheimer's disease, Parkinson's disease and type 2 diabetes mellitus. Protein deposition is a multi-step process modulated by a variety of factors, in particular by membrane-protein interaction. The interaction results in permeabilization of biomembranes contributing to the cytotoxicity that leads to PMDs. Different biological and physiochemical factors, such as protein sequence, lipid composition, and chaperones, are known to affect the membrane-protein interaction. Here, we provide a comprehensive review of the mechanisms and contributing factors of the interaction between biomembranes and amyloidogenic proteins, and a summary of the therapeutic approaches to PMDs that target this interaction. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Biao Cheng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430023, China; Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430023, China
| | - Yang Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Ma
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhuoyi Wang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mt. Pleasant, MI 48858, USA
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan 430072, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Chakraborty S, Das P. Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors. Sci Rep 2017; 7:9941. [PMID: 28855598 PMCID: PMC5577341 DOI: 10.1038/s41598-017-10212-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023] Open
Abstract
Alzheimer’s disease (AD) is characterized by deposition of amyloid beta (Aβ) peptides into senile plaques in the brain. While most familial mutations are associated with early-onset AD, recent studies report the AD-protective nature of two genetic human Aβ variants, i.e. A2T and A2V, in the heterozygous state. The mixture of A2V Aβ1-6 (Aβ6) hexapeptide and WT Aβ1–42 (Αβ42) is also found neuroprotective. Motivated by these findings, in this study we investigate the effects of WT, A2V, and A2T Aβ6 hexapeptide binding on the monomeric WT Aβ42 landscape. For this purpose, we have performed extensive atomistic Replica Exchange Molecular Dynamics simulations, elucidating preferential binding of Aβ42 with the A2V and A2T hexapeptides compared to WT Aβ6. A notable reorganization of the Aβ42 landscape is revealed due to hexapeptide association, as manifested by lowering of transient interactions between the central and C-terminal hydrophobic patches. Concurrently, Aβ6-bound Aβ42 monomer exhibits alternative structural features that are strongly dependent on the hexapeptide sequence. For example, a central helix is more frequently populated within the A2T-bound monomer, while A2V-bound Aβ42 is often enhanced in overall disorder. Taken together, the present simulations offer novel molecular insights onto the effect of the N-terminal hexapeptide binding on the Aβ42 monomer structure, which might help in explaining their reported amyloid inhibition properties.
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Affiliation(s)
| | - Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA.
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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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Shuaib S, Saini RK, Goyal D, Goyal B. Insights into the Inhibitory Mechanism of Dicyanovinyl-Substituted J147 Derivative against Aβ42
Aggregation and Protofibril Destabilization: A Molecular Dynamics Simulation Study. ChemistrySelect 2017. [DOI: 10.1002/slct.201601970] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Suniba Shuaib
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib- 140406, Punjab India
| | - Rajneet Kaur Saini
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib- 140406, Punjab India
| | - Deepti Goyal
- 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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