1
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Maity D. Recent advances in the modulation of amyloid protein aggregation using the supramolecular host-guest approaches. Biophys Chem 2023; 297:107022. [PMID: 37058879 DOI: 10.1016/j.bpc.2023.107022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Misfolding of proteins is associated with many incurable diseases in human beings. Understanding the process of aggregation from monomers to fibrils, the characterization of all intermediate species, and the origin of toxicity is very challenging. Extensive research including computational and experimental shed some light on these tricky phenomena. Non-covalent interactions between amyloidogenic domains of proteins play a major role in their self-assembly which can be disrupted by designed chemical tools. This will lead to the development of inhibitors of detrimental amyloid formations. In supramolecular host-guest chemistry approaches, different macrocycles function as hosts for encapsulating hydrophobic guests, i.e. phenylalanine residues of proteins, in their hydrophobic cavities via non-covalent interactions. In this way, they can disrupt the interactions between adjacent amyloidogenic proteins and prevent their self-aggregation. This supramolecular approach has also emerged as a prospective tool to modify the aggregation of several amyloidogenic proteins. In this review, we discussed recent supramolecular host-guest chemistry-based strategies for the inhibition of amyloid protein aggregation.
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Affiliation(s)
- Debabrata Maity
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Dahri M, Miri Jahromi A, Nikzad A, Mohammadgholian M, Rahmanian M, Abolmaali SS, Maleki R. Novel bioengineered MBenes for the treatment of Alzheimer's disease: An in-Sillico study. J Biomol Struct Dyn 2022; 40:12268-12276. [PMID: 34427178 DOI: 10.1080/07391102.2021.1969288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease is a neurodegenerative disease caused by the deposition and accumulation of amyloid-β (Aβ) peptides in the brain neurons. Current medications are not a definitive cure for this disease, but they can hamper the signs and symptoms of Alzheimer's disease. Therefore, prevention is the best way to deal with this disease. In this study, the novel structures based on MBenes (such as Cd2B, Mo2B, Cu2B, and Ta2B) are proposed to prevent amyloid-β accumulation in Alzheimer's disease. Regarding the remarkable MBene properties such as tunability, biocompatibility, and low manufacturing cost, the effect of these structures on amyloid-β deformation was explored using molecular dynamics simulation. To provide an atomic analysis of Beta-amyloid behavior in the presence of these structures, the compaction, contact area, and stability of Beta-amyloid were investigated. The results indicated the satisfactory performance of MBenes on the destabilization of amyloid-β structures. Moreover, given the higher interactions between Cd2B and amyloid-β, the instability, compaction, and the contact area of amyloid-β particles were investigated in this complex. The findings confirmed Cd2B as the best structure to prevent amyloid-β accumulation. The results of this investigation paved the way for the development of these structures as a medicinal agent to prevent Alzheimer's disease.
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Affiliation(s)
- Mohammad Dahri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran.,Center for Nanotechnology in Drug Delivery, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Miri Jahromi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran
| | - Arash Nikzad
- The University of British Columbia, Vancouver, Canada
| | - Maryam Mohammadgholian
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran
| | - Mohammad Rahmanian
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Sadat Abolmaali
- Center for Nanotechnology in Drug Delivery, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran
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3
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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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4
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Kaur R, Kaur Saini R, Singh P, Goyal B. Unveiling the inhibitory mechanism of peptidomimetic inhibitor against Aβ42 aggregation and protofibril disaggregation by molecular dynamics. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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5
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Jarmuła A, Ludwiczak J, Stępkowski D. β-sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β-amyloid fibrils. Proteins 2021; 89:762-780. [PMID: 33550630 DOI: 10.1002/prot.26057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/31/2021] [Indexed: 12/27/2022]
Abstract
β-sheet breakers (BSB) constitute a class of peptide inhibitors of amyloidogenesis, a process which is a hallmark of many diseases called amyloidoses, including Alzheimer's disease (AD); however, the molecular details of their action are still not fully understood. Here we describe the results of the computational investigation of the three BSBs, iaβ6 (LPFFFD), iaβ5 (LPFFD), and iaβ6_Gly (LPFGFD), in complex with the fibril model of Aβ42 and propose the kinetically probable mechanism of their action. The mechanism involves the binding of BSB to the central hydrophobic core (CHC) region (LVFFA) of Aβ fibril and the π-stacking of its Phe rings both internally and with the Aβ fibril. In the process, the Aβ fibril undergoes distortion accumulating on the side of chain A (located on the odd tip of the fibril). In a single replica of extended molecular dynamics run of one of the iaβ6 poses, the distortion concludes in a dissociation of chain A from the fibril model of Aβ42. Altogether, we postulate that including consecutive Phe residues into BSBs docked around Phe 20 in the CHC region of Aβ42 improve their potency for dissolution of fibrils.
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Affiliation(s)
- Adam Jarmuła
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology PAS, Warszawa, Poland
| | - Jan Ludwiczak
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology PAS, Warszawa, Poland.,Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warszawa, Poland
| | - Dariusz Stępkowski
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology PAS, Warszawa, Poland
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6
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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: 3] [Impact Index Per Article: 0.8] [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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7
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Sun Y, Ding F. αB-Crystallin Chaperone Inhibits Aβ Aggregation by Capping the β-Sheet-Rich Oligomers and Fibrils. J Phys Chem B 2020; 124:10138-10146. [PMID: 33119314 DOI: 10.1021/acs.jpcb.0c07256] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inhibiting the cytotoxicity of amyloid aggregation by endogenous proteins is a promising strategy against degenerative amyloid diseases due to their intrinsically high biocompatibility and low immunogenicity. In this study, we investigated the inhibition mechanism of the structured core region of αB-crystallin (αBC) against Aβ fibrillization using discrete molecular dynamics simulations. Our computational results recapitulated the experimentally observed Aβ binding sites in αBC and suggested that αBC could bind to various Aβ aggregate species during the aggregation process-including monomers, dimers, and likely other high molecular weight oligomers, protofibrils, and fibrils-by capping the exposed β-sheet elongation surfaces. Thus, the nucleation of Aβ oligomers into fibrils and the fibril growth could be inhibited. Mechanistic insights obtained from our systematic computational studies may aid in the development of novel therapeutic strategies to modulate the aggregation of pathological, amyloidogenic protein in degenerative diseases.
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Affiliation(s)
- Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.,Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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8
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Zou Y, Yu L, Fang X, Zheng Y, Yang Y, Wang C. Position-coded multivalent peptide-peptide interactions revealed by tryptophan-scanning mutagenesis. J Pept Sci 2020; 26:e3273. [PMID: 32583616 DOI: 10.1002/psc.3273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 11/08/2022]
Abstract
We demonstrate in this contribution the evidence that significant cooperative binding effect can be identified for the amino acid sites that are determinant to the binding characteristics in peptide-peptide interactions. The analysis of tryptophan-scanning mutagenesis of the 14-mer peptide consisting only of glycine provides a mapping of position-dependent contributions to the binding energy. The pronounced tryptophan-associated peptide-peptide interactions are originated from the indole moieties with the main chains of 14-mer glycines containing N-H and CO moieties. Specifically, with the presence of two tryptophans as determinant amino acids, cooperative binding can be observed, which are dependent on relative positions of the two tryptophans with a "volcano"-like characteristics. An optimal separation of 6-10 amino acids between two adjacent binding sites can be identified to achieve maximal binding interactions.
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Affiliation(s)
- Yimin Zou
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, CAS Center for Excellence in Brain Science, National Center for Nanoscience and Technology, Beijing, China.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Lanlan Yu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, CAS Center for Excellence in Brain Science, National Center for Nanoscience and Technology, Beijing, China.,State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiaocui Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, CAS Center for Excellence in Brain Science, National Center for Nanoscience and Technology, Beijing, China
| | - Yongfang Zheng
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, CAS Center for Excellence in Brain Science, National Center for Nanoscience and Technology, Beijing, China.,Department of Chemistry, Tsinghua University, Beijing, China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, CAS Center for Excellence in Brain Science, National Center for Nanoscience and Technology, Beijing, China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, CAS Center for Excellence in Brain Science, National Center for Nanoscience and Technology, Beijing, China
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9
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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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10
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Pilkington AW, Schupp J, Nyman M, Valentine SJ, Smith DM, Legleiter J. Acetylation of Aβ 40 Alters Aggregation in the Presence and Absence of Lipid Membranes. ACS Chem Neurosci 2020; 11:146-161. [PMID: 31834770 DOI: 10.1021/acschemneuro.9b00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A hallmark of Alzheimer's disease (AD) is the formation of senile plaques comprised of the β-amyloid (Aβ) peptide. Aβ fibrillization is a complex nucleation-dependent process involving a variety of metastable intermediate aggregates and features the formation of inter- and intramolecular salt bridges involving lysine residues, K16 and K28. Cationic lysine residues also mediate protein-lipid interactions via association with anionic lipid headgroups. As several toxic mechanisms attributed to Aβ involve membrane interactions, the impact of acetylation on Aβ40 aggregation in the presence and absence of membranes was determined. Using chemical acetylation, varying mixtures of acetylated and nonacetylated Aβ40 were produced. With increasing acetylation, fibril and oligomer formation decreased, eventually completely arresting fibrillization. In the presence of total brain lipid extract (TBLE) vesicles, acetylation reduced the interaction of Aβ40 with membranes; however, fibrils still formed at near complete levels of acetylation. Additionally, the combination of TBLE and acetylated Aβ promoted annular aggregates. Finally, toxicity associated with Aβ40 was reduced with increasing acetylation in a cell culture assay. These results suggest that in the absence of membranes that the cationic character of lysine plays a major role in fibril formation. However, acetylation promotes unique aggregation pathways in the presence of lipid membranes.
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Affiliation(s)
- Albert W. Pilkington
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Jane Schupp
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Morgan Nyman
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Stephen J. Valentine
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - David M. Smith
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
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11
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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: 5] [Impact Index Per Article: 1.3] [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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12
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Liu Z, Zou Y, Zhang Q, Chen P, Liu Y, Qian Z. Distinct Binding Dynamics, Sites and Interactions of Fullerene and Fullerenols with Amyloid-β Peptides Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2019; 20:E2048. [PMID: 31027286 PMCID: PMC6514889 DOI: 10.3390/ijms20082048] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/21/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
The pathology Alzheimer's disease (AD) is associated with the self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. A promising treatment strategy is focused on the inhibition of amyloid fibrillization of Aβ peptide. Fullerene C60 is proved to effectively inhibit Aβ fibrillation while the poor water-solubility restricts its use as a biomedicine agent. In this work, we examined the interaction of fullerene C60 and water-soluble fullerenol C60(OH)6/C60(OH)12 (C60 carrying 6/12 hydroxyl groups) with preformed Aβ40/42 protofibrils by multiple molecular dynamics simulations. We found that when binding to the Aβ42 protofibril, C60, C60(OH)6 and C60(OH)12 exhibit distinct binding dynamics, binding sites and peptide interaction. The increased number of hydroxyl groups C60 carries leads to slower binding dynamics and weaker binding strength. Binding free energy analysis demonstrates that the C60/C60(OH)6 molecule primarily binds to the C-terminal residues 31-41, whereas C60(OH)12 favors to bind to N-terminal residues 4-14. The hydrophobic interaction plays a critical role in the interplay between Aβ and all the three nanoparticles, and the π-stacking interaction gets weakened as C60 carries more hydroxyls. In addition, the C60(OH)6 molecule has high affinity to form hydrogen bonds with protein backbones. The binding behaviors of C60/C60(OH)6/C60(OH)12 to the Aβ40 protofibril resemble with those to Aβ42. Our work provides a detailed picture of fullerene/fullerenols binding to Aβ protofibril, and is helpful to understand the underlying inhibitory mechanism.
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Affiliation(s)
- Zhiwei Liu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Peijie Chen
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Yu Liu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
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13
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Zou Y, Qian Z, Chen Y, Qian H, Wei G, Zhang Q. Norepinephrine Inhibits Alzheimer's Amyloid-β Peptide Aggregation and Destabilizes Amyloid-β Protofibrils: A Molecular Dynamics Simulation Study. ACS Chem Neurosci 2019; 10:1585-1594. [PMID: 30605312 DOI: 10.1021/acschemneuro.8b00537] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The abnormal self-assembly of amyloid-β (Aβ) peptides into toxic fibrillar aggregates is associated with the pathogenesis of Alzheimer's disease (AD). The inhibition of β-sheet-rich oligomer formation is considered as the primary therapeutic strategy for AD. Previous experimental studies reported that norepinephrine (NE), one of the neurotransmitters, is able to inhibit Aβ aggregation and disaggregate the preformed fibrils. Moreover, exercise can markedly increase the level of NE. However, the underlying inhibitory and disruptive mechanisms remain elusive. In this work, we performed extensive replica-exchange molecular dynamic (REMD) simulations to investigate the conformational ensemble of Aβ1-42 dimer with and without NE molecules. Our results show that without NE molecules, Aβ1-42 dimer transiently adopts a β-hairpin-containing structure, and the β-strand regions of this β-hairpin (residues 15QKLVFFA21 and 33GLMVGGVV40) strongly resemble those of the Aβ fibril structure (residues 15QKLVFFA21 and 30AIIGLMVG37) reported in an electron paramagnetic resonance spectroscopy study. NE molecules greatly reduce the interpeptide β-sheet content and suppress the formation of the above-mentioned β-hairpin, leading to a more disordered coil-rich Aβ dimer. Five dominant binding sites are identified, and the central hydrophobic core 16KLVFFA21 site and C-terminal 31IIGLMV36 hydrophobic site are the two most favorable ones. Our data reveal that hydrophobic, aromatic stacking, hydrogen-bonding and cation-π interactions synergistically contribute to the binding of NE molecules to Aβ peptides. MD simulations of Aβ1-42 protofibril show that NE molecules destabilize Aβ protofibril by forming H-bonds with residues D1, A2, D23, and A42. This work reveals the molecular mechanism by which NE molecules inhibit Aβ1-42 aggregation and disaggregate Aβ protofibrils, providing valuable information for developing new drug candidates and exercise therapy against AD.
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Affiliation(s)
- Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, People’s Republic of China
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, People’s Republic of China
| | - Yujie Chen
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
| | - Hongsheng Qian
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, People’s Republic of China
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14
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Townsend D, Hughes E, Stewart KL, Griffin JM, Radford SE, Middleton DA. Orientation of a Diagnostic Ligand Bound to Macroscopically Aligned Amyloid-β Fibrils Determined by Solid-State NMR. J Phys Chem Lett 2018; 9:6611-6615. [PMID: 30354142 DOI: 10.1021/acs.jpclett.8b02448] [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: 06/08/2023]
Abstract
With amyloid diseases poised to become a major health burden in countries with aging populations, diagnostic molecules that aid the detection of amyloid in vitro and in vivo are of considerable clinical value. Understanding how such ligands recognize their amyloid targets would help to design diagnostics that target specific amyloid types associated with a particular disease, but methods to provide comprehensive information are underdeveloped. Here, solid-state NMR is used to determine the molecular orientation of the amyloid diagnostic 1-fluoro-2,5-bis[( E)-3-carboxy-4-hydroxystyryl]-benzene (FSB) when bound to fibrils of the Alzheimer's amyloid-β polypeptide aligned on a planar substrate. The 19F NMR spectrum of the aligned complex reveals that FSB is oriented approximately parallel with the fibril long axis and bridges four hydrogen-bonded β-sheets. In addition to providing atomic details to aid the design of amyloid-specific diagnostics, this approach will also illuminate the molecular mechanisms of accessory molecules in amyloid disease.
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Affiliation(s)
- David Townsend
- Department of Chemistry , Lancaster University , Lancaster LA1 4YB , United Kingdom
| | - Eleri Hughes
- Department of Chemistry , Lancaster University , Lancaster LA1 4YB , United Kingdom
| | - Katie L Stewart
- Department of Physics , Emory University , Atlanta , Georgia 30322 , United States
| | - John M Griffin
- Materials Science Institute , Lancaster University , Lancaster LA1 4YB , United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology , Faculty of Biological Sciences, University of Leeds , Leeds LS2 9JT , United Kingdom
| | - David A Middleton
- Department of Chemistry , Lancaster University , Lancaster LA1 4YB , United Kingdom
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15
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Kokotidou C, Jonnalagadda SVR, Orr AA, Seoane-Blanco M, Apostolidou CP, van Raaij MJ, Kotzabasaki M, Chatzoudis A, Jakubowski JM, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Llamas-Saiz AL, Tamamis P, Mitraki A. A novel amyloid designable scaffold and potential inhibitor inspired by GAIIG of amyloid beta and the HIV-1 V3 loop. FEBS Lett 2018; 592:1777-1788. [PMID: 29772603 DOI: 10.1002/1873-3468.13096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
The GAIIG sequence, common to the amyloid beta peptide (residues 29-33) and to the HIV-1 gp120 (residues 24-28 in a typical V3 loop), self-assembles into amyloid fibrils, as suggested by theory and the experiments presented here. The longer YATGAIIGNII sequence from the V3 loop also self-assembles into amyloid fibrils, of which the first three and the last two residues are outside the amyloid GAIIG core. We postulate that this sequence, with suitably selected modifications at the flexible positions, can serve as a designable scaffold for novel amyloid-based materials. Moreover, we report the single crystal X-ray structure of the beta-breaker peptide GAIPIG at 1.05 Å resolution. The structural information provided in this study could serve as the basis for structure-based design of potential inhibitors of amyloid formation.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | | | - Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Mateo Seoane-Blanco
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Chrysanthi Pinelopi Apostolidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Marianna Kotzabasaki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Apostolos Chatzoudis
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Joseph M Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Estelle Mossou
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - V Trevor Forsyth
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - Edward P Mitchell
- Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK.,European Synchrotron Radiation Facility, Grenoble Cedex 9, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble, France.,Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Antonio L Llamas-Saiz
- X-Ray Unit, RIAIDT, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
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16
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Wójcik S, Birol M, Rhoades E, Miranker AD, Levine ZA. Targeting the Intrinsically Disordered Proteome Using Small-Molecule Ligands. Methods Enzymol 2018; 611:703-734. [DOI: 10.1016/bs.mie.2018.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Zhang YX, Wang SW, Lu S, Zhang LX, Liu DQ, Ji M, Wang WY, Liu RT. A mimotope of Aβ oligomers may also behave as a β-sheet inhibitor. FEBS Lett 2017; 591:3615-3624. [DOI: 10.1002/1873-3468.12871] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/16/2017] [Accepted: 09/23/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Yang-xin Zhang
- School of Life Science; Anhui Agricultural University; Hefei China
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
| | - Shao-wei Wang
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
| | - Shuai Lu
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
| | - Ling-xiao Zhang
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
| | - Dong-qun Liu
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
| | - Mei Ji
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
| | - Wei-yun Wang
- School of Life Science; Anhui Agricultural University; Hefei China
| | - Rui-tian Liu
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing China
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18
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Datta A, Yadav V, Ghosh A, Choi J, Bhattacharyya D, Kar RK, Ilyas H, Dutta A, An E, Mukhopadhyay J, Lee D, Sanyal K, Ramamoorthy A, Bhunia A. Mode of Action of a Designed Antimicrobial Peptide: High Potency against Cryptococcus neoformans. Biophys J 2017; 111:1724-1737. [PMID: 27760359 DOI: 10.1016/j.bpj.2016.08.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/11/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
There is a significant need for developing compounds that kill Cryptococcus neoformans, the fungal pathogen that causes meningoencephalitis in immunocompromised individuals. Here, we report the mode of action of a designed antifungal peptide, VG16KRKP (VARGWKRKCPLFGKGG) against C. neoformans. It is shown that VG16KRKP kills fungal cells mainly through membrane compromise leading to efflux of ions and cell metabolites. Intracellular localization, inhibition of in vitro transcription, and DNA binding suggest a secondary mode of action for the peptide, hinting at possible intracellular targets. Atomistic structure of the peptide determined by NMR experiments on live C. neoformans cells reveals an amphipathic arrangement stabilized by hydrophobic interactions among A2, W5, and F12, a conventional folding pattern also known to play a major role in peptide-mediated Gram-negative bacterial killing, revealing the importance of this motif. These structural details in the context of live cell provide valuable insights into the design of potent peptides for effective treatment of human and plant fungal infections.
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Affiliation(s)
- Aritreyee Datta
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | - Vikas Yadav
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anirban Ghosh
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | - Jaesun Choi
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul, Korea
| | | | - Rajiv K Kar
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | - Humaira Ilyas
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | | | - Eunseol An
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul, Korea
| | | | - Dongkuk Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul, Korea
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Anirban Bhunia
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India.
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19
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Song M, Zhu Y, Wei G, Li H. Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1321757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Menghua Song
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, P.R. China
- College of Energy and Mechanical Engineering, Shanghai University of Electric Power, Shanghai, P.R. China
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, P.R. China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences(Ministry of Education), and Department of Physics, Fudan University, Shanghai, P.R. China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, P.R. China
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences(Ministry of Education), and Department of Physics, Fudan University, Shanghai, P.R. China
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20
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Zhao J, Ma B, Nussinov R. Compilation and Analysis of Enzymes, Engineered Antibodies, and Nanoparticles Designed to Interfere with Amyloid-β Aggregation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program; National Cancer Institute; Frederick Maryland 21702 USA
| | - Buyong Ma
- Basic Science Program; Leidos Biomedical Research, Inc.; Cancer and Inflammation Program; National Cancer Institute; Frederick Maryland 21702 USA
| | - Ruth Nussinov
- Basic Science Program; Leidos Biomedical Research, Inc.; Cancer and Inflammation Program; National Cancer Institute; Frederick Maryland 21702 USA
- Sackler Institute of Molecular Medicine; Department of Human Genetics and Molecular Medicine; Sackler School of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
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21
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Mehrazma B, Petoyan A, Opare SK, Rauk A. Interaction of the N-AcAβ(13–23)NH2 segment of the beta amyloid peptide with beta-sheet-blocking peptides: site and edge specificity. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The region encompassing residues 13–23 of the amyloid beta peptide (Aβ(13–23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization and also is the site of interaction of Aβ with many other proteins. We describe herein a study by molecular dynamics of the complexes formed by R (= N-AcAβ(13–23)NH2(N-CH3C(O)HHQKLVFFAEDNH2)) with several pseudopeptides designed to form β-sheets with Aβ(1-40,42) and prevent oligomer and fibril formation. Adhesion to both edges of the R β-strand is examined by structure analysis. Umbrella sampling along a dissociation pathway reveals approximate free energies of binding in the submicromolar range. One of the three pseudopeptides binds strongly to one edge of the R β-strand and another to the opposite edge, while the third displays strong binding to both edges. It is desirable to block both edges of the self-recognition site of Aβ to prevent oligomer formation. The study reveals that this may be accomplished by a single pseudopeptide or two in combination. Thus the pseudopeptides, used singly or in pairs, may be competitive inhibitors of Aβ oligomerization at stoichiometric concentrations.
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Affiliation(s)
- Banafsheh Mehrazma
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Anahit Petoyan
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Stanley K.A. Opare
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Arvi Rauk
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
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22
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Amino acid substitutions [K16A] and [K28A] distinctly affect amyloid β-protein oligomerization. J Biol Phys 2016; 42:453-76. [PMID: 27155979 DOI: 10.1007/s10867-016-9417-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/28/2016] [Indexed: 10/21/2022] Open
Abstract
Amyloid β-protein (A β) assembles into oligomers that play a seminal role in Alzheimer's disease (AD), a leading cause of dementia among the elderly. Despite undisputed importance of A β oligomers, their structure and the basis of their toxicity remain elusive. Previous experimental studies revealed that the [K16A] substitution strongly inhibits toxicity of the two predominant A β alloforms in the brain, A β 40 and A β 42, whereas the [K28A] substitution exerts only a moderate effect. Here, folding and oligomerization of [A16]A β 40, [A28]A β 40, [A16]A β 42, and [A28]A β 42 are examined by discrete molecular dynamics (DMD) combined with a four-bead implicit solvent force field, DMD4B-HYDRA, and compared to A β 40 and A β 42 oligomer formation. Our results show that both substitutions promote A β 40 and A β 42 oligomerization and that structural changes to oligomers are substitution- and alloform-specific. The [K28A] substitution increases solvent-accessible surface area of hydrophobic residues and the intrapeptide N-to-C terminal distance within oligomers more than the [K16A] substitution. The [K16A] substitution decreases the overall β-strand content, whereas the [K28A] substitution exerts only a modest change. Substitution-specific tertiary and quaternary structure changes indicate that the [K16A] substitution induces formation of more compact oligomers than the [K28A] substitution. If the structure-function paradigm applies to A β oligomers, then the observed substitution-specific structural changes in A β 40 and A β 42 oligomers are critical for understanding the structural basis of A β oligomer toxicity and correct identification of therapeutic targets against AD.
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23
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Sun Y, Qian Z, Wei G. The inhibitory mechanism of a fullerene derivative against amyloid-β peptide aggregation: an atomistic simulation study. Phys Chem Chem Phys 2016; 18:12582-91. [PMID: 27091578 DOI: 10.1039/c6cp01014h] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease (AD) is associated with the pathological self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. Aβ dimers formed in the initial step of Aβ aggregation were reported to be the smallest toxic species. Inhibiting the formation of β-sheet-rich oligomers and fibrils is considered as the primary therapeutic strategy for AD. Previous studies reported that fullerene derivatives strongly inhibit Aβ fibrillation. However, the underlying inhibitory mechanism remains elusive. As a first step to understand fullerene-modulated full-length Aβ aggregation, we investigated the conformational ensemble of the Aβ1-42 dimer with and without 1,2-(dimethoxymethano)fullerene (DMF) - a more water-soluble fullerene derivative - by performing a 340 ns explicit-solvent replica exchange molecular dynamics simulation. Our simulations show that although disordered states are the most abundant conformations of the Aβ1-42 dimer, conformations containing diverse extended β-hairpins are also populated. The first most-populated β-hairpins involving residues L17-D23 and A30-V36 strongly resemble the engineered β-hairpin which is a building block of toxic Aβ oligomers. We find that the interaction of DMFs with Aβ peptides greatly impedes the formation of such β-hairpins and inter-peptide β-sheets. Binding energy analyses demonstrate that DMF preferentially binds not only to the central hydrophobic motif LVFFA of the Aβ peptide as suggested experimentally, but also to the aromatic residues including F4 and Y10 and the C-terminal hydrophobic region I31-V40. This study reveals a complete picture of the inhibitory mechanism of full-length Aβ1-42 aggregation by fullerenes, providing theoretical insights into the development of drug candidates against AD.
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Affiliation(s)
- Yunxiang Sun
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China.
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24
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Kundaikar HS, Degani MS. Insights into the Interaction Mechanism of Ligands with Aβ42 Based on Molecular Dynamics Simulations and Mechanics: Implications of Role of Common Binding Site in Drug Design for Alzheimer's Disease. Chem Biol Drug Des 2015; 86:805-12. [PMID: 25763767 DOI: 10.1111/cbdd.12555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/02/2015] [Accepted: 03/02/2015] [Indexed: 12/13/2022]
Abstract
Aggregation of β-amyloid (Aβ) into oligomers and further into fibrils is hypothesized to be a key factor in pathology of Alzheimer's disease (AD). In this study, mapping and docking were used to study the binding of ligands to protofibrils. It was followed by molecular simulations to understand the differences in interactions of known therapeutic agents such as curcumin, fluorescence-based amyloid staining agents such as thioflavin T, and diagnostic agents such as florbetapir (AV45), with Aβ protofibrils. We show that therapeutic agents bind to and distort the protofibrils, thus causing destabilization or prevention of oligomerization, in contrast to diagnostic agents which bind to but do not distort such structures. This has implications in the rational design of ligands, both for diagnostics and therapeutics of AD.
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Affiliation(s)
- Harish S Kundaikar
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Mumbai, 400 019, India
| | - Mariam S Degani
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Mumbai, 400 019, India
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25
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Sun Y, Xi W, Wei G. Atomic-Level Study of the Effects of O4 Molecules on the Structural Properties of Protofibrillar Aβ Trimer: β-Sheet Stabilization, Salt Bridge Protection, and Binding Mechanism. J Phys Chem B 2015; 119:2786-94. [DOI: 10.1021/jp508122t] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yunxiang Sun
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
| | - Wenhui Xi
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
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26
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Aoraha E, Candreva J, Kim JR. Engineering of a peptide probe for β-amyloid aggregates. MOLECULAR BIOSYSTEMS 2015; 11:2281-9. [DOI: 10.1039/c5mb00280j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A non-self-aggregating peptide ligand for β-amyloid aggregates created by simple point mutation of an β-amyloid-derived segment.
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Affiliation(s)
- Edwin Aoraha
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering
- New York University
- Brooklyn
- USA
| | - Jason Candreva
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering
- New York University
- Brooklyn
- USA
| | - Jin Ryoun Kim
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering
- New York University
- Brooklyn
- USA
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27
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Cabrele C, Martinek TA, Reiser O, Berlicki Ł. Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry. J Med Chem 2014; 57:9718-39. [DOI: 10.1021/jm5010896] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Chiara Cabrele
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Tamás A. Martinek
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6., H-6720 Szeged, Hungary
| | - Oliver Reiser
- Institute
of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Łukasz Berlicki
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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28
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Shi H, Kang B, Lee JY. Zn2+ Effect on Structure and Residual Hydrophobicity of Amyloid β-Peptide Monomers. J Phys Chem B 2014; 118:10355-61. [DOI: 10.1021/jp504779m] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hu Shi
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon 440-746, South Korea
| | - Baotao Kang
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon 440-746, South Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon 440-746, South Korea
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29
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Zhang T, Xu W, Mu Y, Derreumaux P. Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity. ACS Chem Neurosci 2014; 5:148-59. [PMID: 24246047 DOI: 10.1021/cn400197x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12-28 and 17-42, none of these studies were conducted on the full-length Aβ1-42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1-42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1-42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1-42 dimer against AD.
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Affiliation(s)
- Tong Zhang
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- State Key Laboratory of Precision Spectroscopy, Department
of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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30
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Loureiro JA, Rocha S, Pereira MDC. Charged surfactants induce a non-fibrillar aggregation pathway of amyloid-beta peptide. J Pept Sci 2013; 19:581-7. [PMID: 23922329 DOI: 10.1002/psc.2535] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/30/2013] [Accepted: 06/17/2013] [Indexed: 01/21/2023]
Abstract
The amyloid β-peptide with a sequence of 42 amino acids is the major constituent of extracellular amyloid deposits in Alzheimer's disease plaques. The control of the peptide self-assembly is difficult to achieve because the process is fast and is affected by many variables. In this paper, we describe the effect of different charged and non-charged surfactants on Aβ(₁₋₄₂) fibrillation to define common alternate aggregation pathways. The characterization of the peptide-surfactant interactions by ultra-structural analysis, thioflavin T assay and secondary structure analysis, suggested that charged surfactants interact with Aβ(₁₋₄₂) through electrostatic interactions. Charged micelles slow down the aggregation process and stabilize the peptide in the oligomeric state, whereas non-charged surfactants promote the Aβ(₁₋₄₂) fibril formation.
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Affiliation(s)
- Joana A Loureiro
- LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Roberto Frias, Porto, Portugal
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31
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GhattyVenkataKrishna PK, Uberbacher EC, Cheng X. Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates. FEBS Lett 2013; 587:2649-55. [PMID: 23845280 DOI: 10.1016/j.febslet.2013.06.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/16/2013] [Accepted: 06/21/2013] [Indexed: 11/16/2022]
Abstract
Various structural models for amyloid β fibrils have been derived from a variety of experimental techniques. However, these models cannot differentiate between the relative position of the two arms of the β hairpin called the stagger. Amyloid fibrils of various hierarchical levels form left-handed helices composed of β sheets. However it is unclear if positive, negative and zero staggers all form the macroscopic left-handed helices. To address this issue we have conducted extensive molecular dynamics simulations of amyloid β sheets of various staggers and shown that only negative staggers lead to the experimentally observed left-handed helices while positive staggers generate the incorrect right-handed helices. This result suggests that the negative staggers are physiologically relevant structure of the amyloid β fibrils.
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32
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Jarmuła A, Stępkowski D. Theβ-sheet breakers and π-stacking. J Pept Sci 2013; 19:345-9. [DOI: 10.1002/psc.2506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Adam Jarmuła
- Department of Biochemistry; Nencki Institute of Experimental Biology; Warsaw; Poland
| | - Dariusz Stępkowski
- Department of Biochemistry; Nencki Institute of Experimental Biology; Warsaw; Poland
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33
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Ward JM, Skrynnikov NR. Very large residual dipolar couplings from deuterated ubiquitin. JOURNAL OF BIOMOLECULAR NMR 2012; 54:53-67. [PMID: 22828737 DOI: 10.1007/s10858-012-9651-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/25/2012] [Indexed: 06/01/2023]
Abstract
Main-chain (1)H(N)-(15)N residual dipolar couplings (RDCs) ranging from approximately -200 to 200 Hz have been measured for ubiquitin under strong alignment conditions in Pf1 phage. This represents a ten-fold increase in the degree of alignment over the typical weakly aligned samples. The measurements are made possible by extensive proton-dilution of the sample, achieved by deuteration of the protein with partial back-substitution of labile protons from 25 % H(2)O / 75 % D(2)O buffer. The spectral quality is further improved by application of deuterium decoupling. Since standard experiments using fixed-delay INEPT elements cannot accommodate a broad range of couplings, the measurements were conducted using J-resolved and J-modulated versions of the HSQC and TROSY sequences. Due to unusually large variations in dipolar couplings, the trosy (sharp) and anti-trosy (broad) signals are often found to be interchanged in the TROSY spectra. To distinguish between the two, we have relied on their respective (15)N linewidths. This strategy ultimately allowed us to determine the signs of RDCs. The fitting of the measured RDC values to the crystallographic coordinates of ubiquitin yields the quality factor Q = 0.16, which confirms the perturbation-free character of the Pf1 alignment. Our results demonstrate that RDC data can be successfully acquired not only in dilute liquid crystals, but also in more concentrated ones. As a general rule, the increase in liquid crystal concentration improves the stability of alignment media and makes them more tolerant to variations in sample conditions. The technical ability to measure RDCs under moderately strong alignment conditions may open the door for development of alternative alignment media, including new types of media that mimic biologically relevant systems.
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Affiliation(s)
- Joshua M Ward
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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34
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Fülöp L, Mándity IM, Juhász G, Szegedi V, Hetényi A, Wéber E, Bozsó Z, Simon D, Benkő M, Király Z, Martinek TA. A foldamer-dendrimer conjugate neutralizes synaptotoxic β-amyloid oligomers. PLoS One 2012; 7:e39485. [PMID: 22859942 PMCID: PMC3408453 DOI: 10.1371/journal.pone.0039485] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/21/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND AIMS Unnatural self-organizing biomimetic polymers (foldamers) emerged as promising materials for biomolecule recognition and inhibition. Our goal was to construct multivalent foldamer-dendrimer conjugates which wrap the synaptotoxic β-amyloid (Aβ) oligomers with high affinity through their helical foldamer tentacles. Oligomeric Aβ species play pivotal role in Alzheimer's disease, therefore recognition and direct inhibition of this undruggable target is a great current challenge. METHODS AND RESULTS Short helical β-peptide foldamers with designed secondary structures and side chain chemistry patterns were applied as potential recognition segments and their binding to the target was tested with NMR methods (saturation transfer difference and transferred-nuclear Overhauser effect). Helices exhibiting binding in the µM region were coupled to a tetravalent G0-PAMAM dendrimer. In vitro biophysical (isothermal titration calorimetry, dynamic light scattering, transmission electron microscopy and size-exclusion chromatography) and biochemical tests (ELISA and dot blot) indicated the tight binding between the foldamer conjugates and the Aβ oligomers. Moreover, a selective low nM interaction with the low molecular weight fraction of the Aβ oligomers was found. Ex vivo electrophysiological experiments revealed that the new material rescues the long-term potentiation from the toxic Aβ oligomers in mouse hippocampal slices at submicromolar concentration. CONCLUSIONS The combination of the foldamer methodology, the fragment-based approach and the multivalent design offers a pathway to unnatural protein mimetics that are capable of specific molecular recognition, and has already resulted in an inhibitor for an extremely difficult target.
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Affiliation(s)
- Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - István M. Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
| | - Gábor Juhász
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Viktor Szegedi
- Bay Zoltán Foundation for Applied Research – BAYGEN, Szeged, Hungary
| | | | - Edit Wéber
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
| | - Zsolt Bozsó
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Dóra Simon
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Mária Benkő
- Department of Physical Chemistry and Materials Science, University of Szeged, Szeged, Hungary
| | - Zoltán Király
- Department of Physical Chemistry and Materials Science, University of Szeged, Szeged, Hungary
| | - Tamás A. Martinek
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
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35
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Sinha S, Lopes DHJ, Bitan G. A key role for lysine residues in amyloid β-protein folding, assembly, and toxicity. ACS Chem Neurosci 2012; 3:473-81. [PMID: 22860216 DOI: 10.1021/cn3000247] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Accepted: 03/16/2012] [Indexed: 12/25/2022] Open
Abstract
A combination of hydrophobic and electrostatic interactions is important in initiating the aberrant self-assembly process that leads to formation of toxic oligomers and aggregates by multiple disease-related proteins, including amyloid β-protein (Aβ), whose self-assembly is believed to initiate brain pathogenesis in Alzheimer's disease. Lys residues play key roles in this process and participate in both types of interaction. They also are the target of our recently reported molecular tweezer inhibitors. To obtain further insight into the role of the two Lys residues in Aβ assembly and toxicity, here we substituted each by Ala in both Aβ40 and Aβ42 and studied the impact of the substitution on Aβ oligomerization, aggregation, and toxicity. Our data show that each substitution has a major impact on Aβ assembly and toxicity, with significant differences depending on peptide length (40 versus 42 amino acids) and the position of the substitution. In particular, Lys16→Ala substitution dramatically reduces Aβ toxicity. The data support the use of compounds targeting Lys residues specifically as inhibitors of Aβ toxicity and suggest that exploring the role of Lys residues in other disease-related amyloidogenic proteins may help understanding the mechanisms of aggregation and toxicity of these proteins.
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Affiliation(s)
- Sharmistha Sinha
- Department of Neurology, David Geffen School of Medicine, ‡Brain Research Institute, and §Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Dahabada H. J. Lopes
- Department of Neurology, David Geffen School of Medicine, ‡Brain Research Institute, and §Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, ‡Brain Research Institute, and §Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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36
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Wang C, Yang A, Li X, Li D, Zhang M, Du H, Li C, Guo Y, Mao X, Dong M, Besenbacher F, Yang Y, Wang C. Observation of molecular inhibition and binding structures of amyloid peptides. NANOSCALE 2012; 4:1895-909. [PMID: 22334382 DOI: 10.1039/c2nr11508e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.
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Affiliation(s)
- Chenxuan Wang
- National Center for Nanoscience and Technology, Beijing, 100190, PR China
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37
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SivakamaSundari C, Rukmani S, Nagaraj R. Effect of introducing a short amyloidogenic sequence from the Aβ peptide at the N-terminus of 18-residue amphipathic helical peptides. J Pept Sci 2012; 18:122-8. [DOI: 10.1002/psc.1424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 09/10/2011] [Accepted: 09/13/2011] [Indexed: 12/16/2022]
Affiliation(s)
| | - Sridharan Rukmani
- CSIR-Centre for Cellular and Molecular Biology; Uppal Road; Hyderabad ; 500 007; India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology; Uppal Road; Hyderabad ; 500 007; India
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38
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Lopez del Amo JM, Fink U, Dasari M, Grelle G, Wanker EE, Bieschke J, Reif B. Structural properties of EGCG-induced, nontoxic Alzheimer's disease Aβ oligomers. J Mol Biol 2012; 421:517-24. [PMID: 22300765 DOI: 10.1016/j.jmb.2012.01.013] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/10/2012] [Accepted: 01/13/2012] [Indexed: 10/14/2022]
Abstract
The green tea compound epigallocatechin-3-gallate (EGCG) inhibits Alzheimer's disease β-amyloid peptide (Aβ) neurotoxicity. Solution-state NMR allows probing initial EGCG-Aβ interactions. We show that EGCG-induced Aβ oligomers adopt a well-defined structure and are amenable for magic angle spinning solid-state NMR investigations. We find that EGCG interferes with the aromatic hydrophobic core of Aβ. The C-terminal part of the Aβ peptide (residues 22-39) adopts a β-sheet conformation, whereas the N-terminus (residues 1-20) is unstructured. The characteristic salt bridge involving residues D23 and K28 is present in the structure of these oligomeric Aβ aggregates as well. The structural analysis of small-molecule-induced amyloid aggregates will open new perspectives for Alzheimer's disease drug development.
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Affiliation(s)
- Juan Miguel Lopez del Amo
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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39
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Buell AK, Esbjörner EK, Riss PJ, White DA, Aigbirhio FI, Toth G, Welland ME, Dobson CM, Knowles TPJ. Probing small molecule binding to amyloid fibrils. Phys Chem Chem Phys 2011; 13:20044-52. [PMID: 22006124 DOI: 10.1039/c1cp22283j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.
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Affiliation(s)
- Alexander K Buell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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40
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Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature 2011; 475:96-100. [PMID: 21677644 DOI: 10.1038/nature10154] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 04/21/2011] [Indexed: 12/25/2022]
Abstract
Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies as well as with normal cellular functions, and frequently form during protein denaturation. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-D-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer's disease, and a non-natural L-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-β-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers.
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Affiliation(s)
- Stuart A Sievers
- Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Box 951970, Los Angeles, California 90095-1570, USA
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41
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Bruinsma IB, Karawajczyk A, Schaftenaar G, de Waal RMW, Verbeek MM, van Delft FL. A rational design to create hybrid β-sheet breaker peptides to inhibit aggregation and toxicity of amyloid-β. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00213e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Functionalization of gold nanoparticles with amino acid, β-amyloid peptides and fragment. Colloids Surf B Biointerfaces 2010; 81:235-41. [DOI: 10.1016/j.colsurfb.2010.07.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Revised: 05/18/2010] [Accepted: 07/07/2010] [Indexed: 11/20/2022]
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43
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Bett CK, Ngunjiri JN, Serem WK, Fontenot KR, Hammer RP, McCarley RL, Garno JC. Structure-activity relationships in peptide modulators of β-amyloid protein aggregation: variation in α,α-disubstitution results in altered aggregate size and morphology. ACS Chem Neurosci 2010; 1:608-26. [PMID: 22778850 DOI: 10.1021/cn100045q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 06/25/2010] [Indexed: 12/20/2022] Open
Abstract
Neuronal cytotoxicity observed in Alzheimer's disease (AD) is linked to the aggregation of β-amyloid peptide (Aβ) into toxic forms. Increasing evidence points to oligomeric materials as the neurotoxic species, not Aβ fibrils; disruption or inhibition of Aβ self-assembly into oligomeric or fibrillar forms remains a viable therapeutic strategy to reduce Aβ neurotoxicity. We describe the synthesis and characterization of amyloid aggregation mitigating peptides (AAMPs) whose structure is based on the Aβ "hydrophobic core" Aβ(17-20), with α,α-disubstituted amino acids (ααAAs) added into this core as potential disrupting agents of fibril self-assembly. The number, positional distribution, and side-chain functionality of ααAAs incorporated into the AAMP sequence were found to influence the resultant aggregate morphology as indicated by ex situ experiments using atomic force microscopy (AFM) and transmission electron microscopy (TEM). For instance, AAMP-5, incorporating a sterically hindered ααAA with a diisobutyl side chain in the core sequence, disrupted Aβ(1-40) fibril formation. However, AAMP-6, with a less sterically hindered ααAA with a dipropyl side chain, altered fibril morphology, producing shorter and larger sized fibrils (compared with those of Aβ(1-40)). Remarkably, ααAA-AAMPs caused disassembly of existing Aβ fibrils to produce either spherical aggregates or protofibrillar structures, suggesting the existence of equilibrium between fibrils and prefibrillar structures.
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Affiliation(s)
- Cyrus K. Bett
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Johnpeter N. Ngunjiri
- NanoInk, Inc., Illinois Science & Technology Park, 8025 Lamon Ave, Skokie, Illinois 60077
| | - Wilson K. Serem
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Krystal R. Fontenot
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Robert P. Hammer
- New England Peptide LLC, 65 Zub Lane, Gardner, Massachusetts 01440
| | - Robin L. McCarley
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Jayne C. Garno
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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44
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Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010; 110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
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45
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Ostapchenko VG, Sawaya MR, Makarava N, Savtchenko R, Nilsson KPR, Eisenberg D, Baskakov IV. Two amyloid States of the prion protein display significantly different folding patterns. J Mol Biol 2010; 400:908-21. [PMID: 20553730 DOI: 10.1016/j.jmb.2010.05.051] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/27/2010] [Accepted: 05/21/2010] [Indexed: 12/16/2022]
Abstract
It has been well established that a single amino acid sequence can give rise to several conformationally distinct amyloid states. The extent to which amyloid structures formed within the same sequence are different, however, remains unclear. To address this question, we studied two amyloid states (referred to as R- and S-fibrils) produced in vitro from highly purified full-length recombinant prion protein. Several biophysical techniques including X-ray diffraction, CD, Fourier transform infrared spectroscopy (FTIR), hydrogen-deuterium exchange, proteinase K digestion, and binding of a conformation-sensitive fluorescence dye revealed that R- and S-fibrils have substantially different secondary, tertiary, and quaternary structures. While both states displayed a 4. 8-A meridional X-ray diffraction typical for amyloid cross-beta-spines, they showed markedly different equatorial profiles, suggesting different folding pattern of beta-strands. The experiments on hydrogen-deuterium exchange monitored by FTIR revealed that only small fractions of amide protons were protected in R- or S-fibrils, an argument for the dynamic nature of their cross-beta-structure. Despite this fact, both amyloid states were found to be very stable conformationally as judged from temperature-induced denaturation monitored by FTIR and the conformation-sensitive dye. Upon heating to 80 degrees C, only local unfolding was revealed, while individual state-specific cross-beta features were preserved. The current studies demonstrated that the two amyloid states formed by the same amino acid sequence exhibited significantly different folding patterns that presumably reflect two different architectures of cross-beta-structure. Both S- and R-fibrils, however, shared high conformational stability, arguing that the energy landscape for protein folding and aggregation can contain several deep free-energy minima.
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Affiliation(s)
- Valeriy G Ostapchenko
- Center for Biomedical Engineering and Technology, University of Maryland, Baltimore, MD 21201, USA
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46
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Chen D, Martin ZS, Soto C, Schein CH. Computational selection of inhibitors of Abeta aggregation and neuronal toxicity. Bioorg Med Chem 2009; 17:5189-97. [PMID: 19540126 PMCID: PMC2743868 DOI: 10.1016/j.bmc.2009.05.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/13/2009] [Accepted: 05/18/2009] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease (AD) is characterized by the cerebral accumulation of misfolded and aggregated amyloid-beta protein (Abeta). Disease symptoms can be alleviated, in vitro and in vivo, by 'beta-sheet breaker' pentapeptides that reduce plaque load. However the peptide nature of these compounds, made them biologically unstable and unable to penetrate membranes with high efficiency. The main goal of this study was to use computational methods to identify small molecule mimetics with better drug-like properties. For this purpose, the docked conformations of the active peptides were used to identify compounds with similar activities. A series of related beta-sheet breaker peptides were docked to solid state NMR structures of a fibrillar form of Abeta. The lowest energy conformations of the active peptides were used to design three dimensional (3D)-pharmacophores, suitable for screening the NCI database with Unity. Small molecular weight compounds with physicochemical features and a conformation similar to the active peptides were selected, ranked by docking and biochemical parameters. Of 16 diverse compounds selected for experimental screening, 2 prevented and reversed Abeta aggregation at 2-3microM concentration, as measured by Thioflavin T (ThT) fluorescence and ELISA assays. They also prevented the toxic effects of aggregated Abeta on neuroblastoma cells. Their low molecular weight and aqueous solubility makes them promising lead compounds for treating AD.
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Affiliation(s)
- Deliang Chen
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
| | - Zane S. Martin
- George and Cynthia Mitchell Center for Neurodegenerative diseases, Department of Neurology, Neurosciences & Cell Biology UTMB, Galveston TX 77555-1045, USA
| | - Claudio Soto
- George and Cynthia Mitchell Center for Neurodegenerative diseases, Department of Neurology, Neurosciences & Cell Biology UTMB, Galveston TX 77555-1045, USA
- Department of Neurology, University of Texas Medical School at Houston. Houston, TX 77030, USA
| | - Catherine H. Schein
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
- Department of Microbiology and Immunology, and Sealy Center for Vaccine Development, UTMB, Galveston, TX 77555-0857, USA
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47
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Benaki D, Stathopoulou K, Leondiadis L, Ferderigos N, Pelecanou M, Mikros E. Detection of interactions of the β-amyloid peptide with small molecules employing transferred NOEs. J Pept Sci 2009; 15:435-41. [DOI: 10.1002/psc.1138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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48
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Chebaro Y, Derreumaux P. Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study. Proteins 2009; 75:442-52. [PMID: 18837034 DOI: 10.1002/prot.22254] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aggregation of the Abeta1-40/Abeta1-42 peptides is a key factor in Alzheimer's disease. Though the inhibitory effect of N-methylated Abeta16-22 (mAbeta16-22) peptides is well characterized in vitro, there is little information on how they disassemble full-length Abeta fibrils or block fibril formation. Here, we report coarse-grained implicit solvent molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulations on Abeta16-22 and mAbeta16-22 monomers, and then a preformed six-chain Abeta16-22 bilayer with either four copies of Abeta16-22 or four copies of mAbeta16-22. Our simulations show that the effect of N-methylation on mAbeta16-22 monomer is to reduce the density of compact forms. While 100 ns MD trajectories do not reveal any significant differences between the two ten-chain systems, the REMD simulations totaling 1 micros help understand the first steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors. Notably, we find that mAbeta16-22 preferentially interacts with Abeta16-22 by blocking both beta-sheet extension and lateral association of layers, but also by intercalation of the inhibitors allowing sequestration of Abeta16-22 peptides. This third binding mode is particularly appealing for blocking Abeta fibrillogenesis.
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Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie, Physico Chimique et Université Paris 7 Denis Diderot, 13 rue Pierre et Marie Curie, Paris 75005, France
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Chini MG, Scrima M, D'Ursi AM, Bifulco G. Fibril aggregation inhibitory activity of the beta-sheet breaker peptides: a molecular docking approach. J Pept Sci 2009; 15:229-34. [PMID: 19090016 DOI: 10.1002/psc.1095] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the present study, we used a molecular docking as a rapid, interactive method to study the inhibition of fibrillogenesis process by beta-sheet breaker peptide (BSB) (Ac-L(1)-V(2)-(NMet)F(3)-F(4)-A(5)-NH(2)). Our aim was to find the complex (Abeta:BSB) that blocks the aggregation of the fibrils, and to identify the binding sequences for the small peptides on Abeta(1-42). An NMR structure solved by Lührs et al. in 2005 was used to study the interaction of BSB with the amyloid aggregated forms. From our preliminary step-by-step docking studies, the L(17)-D(23) sequence seems to be one of the most common active sites of Abeta(1-42), and critical in amyloid fibril formation. We note that a single molecule of BSB does not influence the interaction between the two fibrils, while a little excess of BSB (two molecules) with respect to the amyloid does not completely block but undoubtedly obstructs the aggregation process.
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Affiliation(s)
- Maria Giovanna Chini
- Department of Pharmaceutical Sciences, University of Salerno, Fisciano (SA), Italy
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Hetényi A, Fülöp L, Martinek TA, Wéber E, Soós K, Penke B. Ligand-Induced Flocculation of Neurotoxic Fibrillar Aβ(1–42) by Noncovalent Crosslinking. Chembiochem 2008; 9:748-57. [DOI: 10.1002/cbic.200700351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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