1
|
Zahraee H, Arab SS, Khoshbin Z, Bozorgmehr MR. A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer's disease insignia. J Biomol Struct Dyn 2023; 41:10830-10839. [PMID: 36576270 DOI: 10.1080/07391102.2022.2158939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/10/2022] [Indexed: 12/29/2022]
Abstract
Amyloid-β peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-β(1-42) (Aβ1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aβ1-42 fibrils. The present study provides molecular insight to clarify the inhibitory mechanisms of the EGCG and NQTrp ligands on the Aβ1-42 assemblies by using molecular dynamics (MD) simulation. Hence, nine different Aβ1-42-containing systems including the monomer, dimer, and hexamer of Aβ1-42 considering each of them in a media with no ligands, in the presence of one EGCG ligand, and in the presence of one EGCG ligand were studied with a simulation time of 1 µs for each system. The precise investigation of the peptide-ligand distance, conformational factor (Pi), solvent accessible surface area (SASA), dictionary of secondary structure (DSSP), and Lys28-Ala42 salt bridge analyses confirmed that the hydroxyl-rich structure of the EGCG ligand applied its inhibitory effect on the aggregation of the peptides indirectly by involving water molecules. While the hydroxyl-free structure of the NQTrp ligand exposed its inhibitory effect through a direct interaction with the Aβ1-42 peptides. Besides, reduced density gradient (RDG) analysis clarified the hydrogen bonding interactions as the dominant ones for the peptide-EGCG systems, and also, steric and van der Waals interactions for the peptide-NQTrp systems.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | | |
Collapse
|
2
|
Zahraee H, Mohammadi F, Parvaee E, Khoshbin Z, Arab SS. Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: molecular dynamics simulation exploration. J Biomol Struct Dyn 2023:1-15. [PMID: 37599504 DOI: 10.1080/07391102.2023.2247086] [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: 03/09/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
Amyloid-β peptide, the predominant proteinaceous component of senile plaques, is responsible for the incidence of Alzheimer's disease (AD), an age-associated neurodegenerative disorder. Specifically, the amyloid-β(1-42) (Aβ1-42) isoform, known for its high toxicity, is the predominant biomarker for the preliminary diagnosis of AD. The aggregation of the Aβ1-42 peptides can be affected by the components of the cellular medium through changing their structures and molecular interactions. In this study, we investigated the effect of sodium dodecyl sulfate (SDS) at much lower concentrations than the critical micelle concentration (CMC) on Aβ1-42 aggregation. For this purpose, we studied mono-, di-, tri- and tetramers of Aβ1-42 peptide in two different concentrations of SDS molecules (10 and 40 molecules) using a 300 ns molecular dynamics simulation for each system. The distance between the center of mass (COM) of Aβ1-42 peptides confirms that an increase in the number of SDS molecules decreases their aggregation probability due to greater interaction with SDS molecules. Besides, the less compactness parameter reveals the reduced aggregation probability of Aβ1-42 peptides. Based on the energetic FEL landscapes, SDS molecules with the concentration closer to the CMC are an effective inhibitory agent to prevent the formation of Aβ1-42 fibrils. Also, the aggregation direction of the peptide pairs can be predicted by determining the direction of the accumulation-deterrent forces.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Mohammadi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elahe Parvaee
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
3
|
Rahman A, Saikia B, Gogoi CR, Baruah A. Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:31-48. [PMID: 36044970 DOI: 10.1016/j.pbiomolbio.2022.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Aberrant protein folding known as protein misfolding is counted as one of the striking factors of neurodegenerative diseases. The extensive range of pathologies caused by protein misfolding, aggregation and subsequent accumulation are mainly classified into either gain of function diseases or loss of function diseases. In order to seek for novel strategies for treatment and diagnosis of neurodegenerative diseases, insights into the mechanism of misfolding and aggregation is essential. A comprehensive knowledge on the factors influencing misfolding and aggregation is required as well. An extensive experimental study on protein aggregation is somewhat challenging due to the insoluble and noncrystalline nature of amyloid fibrils. Thus there has been a growing use of computational approaches including Monte Carlo simulation, docking simulation, molecular dynamics simulation in the study of protein misfolding and aggregation. The review presents a discussion on molecular dynamics simulation alone as to how it has emerged as a promising tool in the understanding of protein misfolding and aggregation in general, detailing upon three different aspects considering four misfold prone proteins in particular. It is noticeable that all four proteins considered in this review i.e prion, superoxide dismutase1, huntingtin and amyloid β are linked to chronic neurodegenerative diseases with debilitating effects. Initially the review elaborates on the factors influencing the misfolding and aggregation. Next, it addresses our current understanding of the amyloid structures and the associated aggregation mechanisms, finally, summarizing the contribution of this computational tool in the search for therapeutic strategies against the respective protein-deposition diseases.
Collapse
Affiliation(s)
- Aziza Rahman
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Chimi Rekha Gogoi
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
| |
Collapse
|
4
|
Dehabadi MH, Caflisch A, Ilie IM, Firouzi R. Interactions of Curcumin's Degradation Products with the Aβ 42 Dimer: A Computational Study. J Phys Chem B 2022; 126:7627-7637. [PMID: 36148988 DOI: 10.1021/acs.jpcb.2c05846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid-β (Aβ) dimers are the smallest toxic species along the amyloid-aggregation pathway and among the most populated oligomeric accumulations present in the brain affected by Alzheimer's disease (AD). A proposed therapeutic strategy to avoid the aggregation of Aβ into higher-order structures is to develop molecules that inhibit the early stages of aggregation, i.e., dimerization. Under physiological conditions, the Aβ dimer is highly dynamic and does not attain a single well-defined structure but is rather characterized by an ensemble of conformations. In a recent study, a highly heterogeneous library of conformers of the Aβ dimer was generated by an efficient sampling method with constraints based on ion mobility mass spectrometry data. Here, we make use of the Aβ dimer library to study the interaction with two curcumin degradation products, ferulic aldehyde and vanillin, by molecular dynamics (MD) simulations. Ensemble docking and MD simulations are used to provide atomistic detail of the interactions between the curcumin degradation products and the Aβ dimer. The simulations show that the aromatic residues of Aβ, and in particular 19FF20, interact with ferulic aldehyde and vanillin through π-π stacking. The binding of these small molecules induces significant changes on the 16KLVFF20 region.
Collapse
Affiliation(s)
- Maryam Haji Dehabadi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Pajohesh Boulevard, 1496813151 Tehran, Iran
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ioana M Ilie
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Pajohesh Boulevard, 1496813151 Tehran, Iran
| |
Collapse
|
5
|
Optimization of IL-1RA structure to achieve a smaller protein with a higher affinity to its receptor. Sci Rep 2022; 12:7483. [PMID: 35523814 PMCID: PMC9076856 DOI: 10.1038/s41598-022-11100-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/12/2022] [Indexed: 01/01/2023] Open
Abstract
Interleukine-1 family cytokines are key orchestrators of innate and adaptive immunity. In particular, up-regulation of IL-1R1 via its agonistic ligands consisting of IL-1β and IL-1α is implicated in a variety of human diseases, such as rheumatoid arthritis, psoriasis, type I diabetes, amyotrophic lateral sclerosis, and dry-eye disease. Until now, there are no small-molecule inhibitors of the IL-1R1 with increased antagonistic potency to be used for the treatment of peripheral inflammation. The objective of this study was to engineer a low-molecular-weight version of IL-1RA with increased affinity and enhanced antagonistic activity for potential therapeutic use. To develop a smaller protein–ligand with a better affinity to IL-1R, we used bioinformatics studies and in silico simulations to anticipate non-binding areas on IL-1RA. In this study, we have identified a 41aa (F57-F98) non-binding site of IL-1RA. Overall RMSF of the Truncated complex (1.5 nm) was lower than the Native complex (2 nm), which could prove higher stability of the Truncated complex. The free binding energy of the T-IL-1RA (− 1087.037 kJ/mol) was significantly lower than the IL-1RA (− 836.819 kJ/mol) which could demonstrate a higher binding affinity of the truncated ligand with its receptor as a result of new important interactions. These findings have demonstrated a higher binding affinity of the T-IL-1RA with its receptor than the native protein. These results should: have an impact on the development of new treatments that block IL-1 signaling, although more research is needed in vitro and in vivo.
Collapse
|
6
|
Mishra P, Basak S, Mukherjee A, Basu A. Design and Study of In Silico Binding Dynamics of Certain Isoxazole Bearing Leads Against Aβ-42 and BACE-1 Loop in Protein Fibrillation. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210813120444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
Design isoxazole bearing leads as dual inhibitors against Amyloid β and BACE-1 loop
in protein fibrillation.
Background:
Protein fibrillation is one of the key reasons for several diseases, namely Alzheimer’s, Parkinson’s,
and many others. One of the key strategies of preventing protein fibrillation is destabilizing the
protein fibrils themselves or inhibiting the amyloid fibril-forming pathway in the initial stage.
Introduction:
Attempts have been taken to design newer leads to inhibit protein fibrillation by targeting
the β-amyloidogenesis pathway in the brain. To exploit interfenestration between Amyloid β -42 protein
and BACE-1 (β-site amyloid precursor protein cleaving enzyme) for amyloidogenesis, studies are undertaken
to design dual inhibitors against the same.
Method:
In vitro binding interactions were found using docking, de novo ligand design, and MD simulation
study.
Results:
Three compounds bearing an isoxazole heterocyclic nucleus were designed which could successfully
bind to the hydrophobic raft and salt bridge residues Asp 23-Lys-26 of Amyloid β, destabilizing the
growing fibril. Additionally, one of our candidate compounds exhibited force of interaction with Thr232
at the S3 pocket of BACE-1, interacted with key residue Asp228, Tyr71, and Thr72 of the β-hairpin flap
and hydrogen bonding with Gly11 at loop 10s.
Conclusion:
Protein flexibility dynamics of the Aβ-42 protein revealed that there is a considerable conformational
change of the same with or without ligand binding. The lower RMSF of the bound region and
reprogramming residual contacts within the Aβ-42 protein suggested successful binding of the ligand with
the protein, lowering the access for further β-β dimerization.
Collapse
Affiliation(s)
- Puja Mishra
- Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India
| | - Souvik Basak
- Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India
| | - Arup Mukherjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, WB, India
| | - Anindya Basu
- School of Pharmaceutical Sciences, Rajiv
Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
| |
Collapse
|
7
|
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]
|
8
|
Mladenova K, Stavrakov G, Philipova I, Atanasova M, Petrova S, Doumanov J, Doytchinova I. A Galantamine-Curcumin Hybrid Decreases the Cytotoxicity of Amyloid-Beta Peptide on SH-SY5Y Cells. Int J Mol Sci 2021; 22:ijms22147592. [PMID: 34299209 PMCID: PMC8307467 DOI: 10.3390/ijms22147592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Misfolded amyloid beta (Aβ) peptides aggregate and form neurotoxic oligomers. Membrane and mitochondrial damages, calcium dysregulation, oxidative stress, and fibril deposits are among the possible mechanisms of Aβ cytotoxicity. Galantamine (GAL) prevents apoptosis induced by Aβ mainly through the ability to stimulate allosterically the α7 nAChRs and to regulate the calcium cytosolic concentration. Here, we examined the cytoprotective effects of two GAL derivatives, namely compounds 4b and 8, against Aβ cytotoxicity on the human neuroblastoma cell line SH-SY5Y. The protective effects were tested at simultaneous administration, pre-incubation and post-incubation, with Aβ. GAL and curcumin (CU) were used in the study as reference compounds. It was found that 4b protects cells in a similar mode as GAL, while compound 8 and CU potentiate the toxic effects of Aβ. Allosteric stimulation of α7 nAChRs is suggested as a possible mechanism of the cytoprotectivity of 4b. These and previous findings characterize 4b as a prospective non-toxic multi-target agent against neurodegenerative disorders with inhibitory activity on acetylcholinesterase, antioxidant, and cytoprotective properties.
Collapse
Affiliation(s)
- Kirilka Mladenova
- Faculty of Biology, Sofia University, 1164 Sofia, Bulgaria; (K.M.); (S.P.); (J.D.)
| | - Georgi Stavrakov
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (G.S.); (M.A.)
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Irena Philipova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Mariyana Atanasova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (G.S.); (M.A.)
| | - Svetla Petrova
- Faculty of Biology, Sofia University, 1164 Sofia, Bulgaria; (K.M.); (S.P.); (J.D.)
| | - Jordan Doumanov
- Faculty of Biology, Sofia University, 1164 Sofia, Bulgaria; (K.M.); (S.P.); (J.D.)
| | - Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (G.S.); (M.A.)
- Correspondence:
| |
Collapse
|
9
|
Effects of Curcumin and Ferulic Acid on the Folding of Amyloid-β Peptide. Molecules 2021; 26:molecules26092815. [PMID: 34068636 PMCID: PMC8126156 DOI: 10.3390/molecules26092815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 11/17/2022] Open
Abstract
The polyphenols curcumin (CU) and ferulic acid (FA) are able to inhibit the aggregation of amyloid-β (Aβ) peptide with different strengths. CU is a strong inhibitor while FA is a weaker one. In the present study, we examine the effects of CU and FA on the folding process of an Aβ monomer by 1 µs molecular dynamics (MD) simulations. We found that both inhibitors increase the helical propensity and decrease the non-helical propensity of Aβ peptide. They prevent the formation of a dense bulk core and shorten the average lifetime of intramolecular hydrogen bonds in Aβ. CU makes more and longer-lived hydrogen bonds, hydrophobic, π–π, and cation–π interactions with Aβ peptide than FA does, which is in a good agreement with the observed stronger inhibitory activity of CU on Aβ aggregation.
Collapse
|
10
|
Curcumin Inhibits the Primary Nucleation of Amyloid-Beta Peptide: A Molecular Dynamics Study. Biomolecules 2020; 10:biom10091323. [PMID: 32942739 PMCID: PMC7563689 DOI: 10.3390/biom10091323] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/07/2020] [Accepted: 09/12/2020] [Indexed: 12/11/2022] Open
Abstract
The amyloid plaques are a key hallmark of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease. Amyloidogenesis is a complex long-lasting multiphase process starting with the formation of nuclei of amyloid peptides: a process assigned as a primary nucleation. Curcumin (CU) is a well-known inhibitor of the aggregation of amyloid-beta (Aβ) peptides. Even more, CU is able to disintegrate preformed Aβ firbils and amyloid plaques. Here, we simulate by molecular dynamics the primary nucleation process of 12 Aβ peptides and investigate the effects of CU on the process. We found that CU molecules intercalate among the Aβ chains and bind tightly to them by hydrogen bonds, hydrophobic, π–π, and cation–π interactions. In the presence of CU, the Aβ peptides form a primary nucleus of a bigger size. The peptide chains in the nucleus become less flexible and more disordered, and the number of non-native contacts and hydrogen bonds between them decreases. For comparison, the effects of the weaker Aβ inhibitor ferulic acid (FA) on the primary nucleation are also examined. Our study is in good agreement with the observation that taken regularly, CU is able to prevent or at least delay the onset of neurodegenerative disorders.
Collapse
|
11
|
Jia L, Wang W, Yan Y, Hu R, Sang J, Zhao W, Wang Y, Wei W, Cui W, Yang G, Lu F, Zheng J, Liu F. General Aggregation-Induced Emission Probes for Amyloid Inhibitors with Dual Inhibition Capacity against Amyloid β-Protein and α-Synuclein. ACS APPLIED MATERIALS & INTERFACES 2020; 12:31182-31194. [PMID: 32584021 DOI: 10.1021/acsami.0c07745] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amyloid self-assembly is pathologically linked to many neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD). While many inhibitors have been developed individually for specific amyloid proteins, there are a few effective platforms to screen on a large scale general amyloid inhibitors against different amyloid proteins. Herein, we developed a new class of amyloid inhibitor probes by site-specific conjugation of aggregation-induced emission (AIE) molecules with amyloid proteins (i.e., AIE@amyloid probes) to realize a high-throughput screening of small-molecule inhibitors. Optimization of site-specific AIE conjugation with two amyloid proteins, amyloid-β protein (Aβ) and α-synuclein (αSN), enabled us to retain their high amyloidogenic properties; i.e., AIE-amyloid probes alone exhibited strong fluorescence due to amyloid-like aggregation, but they showed no fluorescence in the presence of amyloid inhibitors to prevent amyloid aggregation. From integration of AIE@amyloid probes and computational virtual screening from a large drug database, it was found that tolcapone possessed a dual inhibition against the aggregation and cytotoxicity of both Aβ and αSN. More importantly, tolcapone significantly improved the spatial cognition and recognition of Aβ-treated mice. This work represents an innovative attempt to design an AIE-based anti-amyloid drug platform for identifying new small-molecule inhibitors against amyloidogenesis in both AD and PD or other amyloid diseases.
Collapse
Affiliation(s)
- Longgang Jia
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Wenjuan Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yushan Yan
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Zhejiang 315211, China
| | - Rui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jingcheng Sang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenping Zhao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Ying Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Wei
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Cui
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Zhejiang 315211, China
| | - Guoqiang Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| |
Collapse
|
12
|
Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
Collapse
Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| |
Collapse
|
13
|
Şahİn K, DurdaĞi S. Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors. Turk J Chem 2020; 44:574-588. [PMID: 33488178 PMCID: PMC7671205 DOI: 10.3906/kim-1911-57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/03/2020] [Indexed: 11/26/2022] Open
Abstract
The excessive activity of acetylcholinesterase enzyme (AChE) causes different neuronal problems, especially dementia and neuronal cell deaths. Food and Drug Administration (FDA) approved drugs donepezil, rivastigmine, tacrine and galantamine are AChE inhibitors and in the treatment of Alzheimer’s disease (AD) these drugs are currently prescribed. However, these inhibitors have various adverse side effects. Therefore, there is a great need for the novel selective AChE inhibitors with fewer adverse side effects for the effective treatment. In this study, combined ligand-based and structure-based virtual screening approaches were used to identify new hit compounds from small molecules library of National Cancer Institute (NCI) containing approximately 265,000 small molecules. In the present study, we developed a computational pipeline method to predict the binding affinities of the studied compounds at the specific target sites. For this purpose, a text mining study was carried out initially and compounds containing the keyword “indol” were considered. The therapeutic activity values against AD were screened using the binary quantitative structure activity relationship (QSAR) models. We then performed docking, molecular dynamics (MD) simulations and free energy analysis to clarify the interactions between selected ligands and enzyme. Thus, in this study we identified new promising hit compounds from a large database that may be used to inhibit the enzyme activity of AChE.
Collapse
Affiliation(s)
- Kader Şahİn
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul Turkey
| | - Serdar DurdaĞi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul Turkey
| |
Collapse
|
14
|
Sharma S, Singh N, Nepovimova E, Korabecny J, Kuca K, Satnami ML, Ghosh KK. Interaction of synthesized nitrogen enriched graphene quantum dots with novel anti-Alzheimer’s drugs: spectroscopic insights. J Biomol Struct Dyn 2019; 38:1822-1837. [DOI: 10.1080/07391102.2019.1619625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Srishti Sharma
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, India
| | - Namrata Singh
- Ramrao Adik Institute of Technology, DY Patil University, Navi Mumbai, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- National Institute of Mental Health, Klecany, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Manmohan L. Satnami
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, India
| | - Kallol K. Ghosh
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, India
| |
Collapse
|
15
|
Narang SS, Goyal D, Goyal B. Inhibition of Alzheimer’s amyloid-β42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:1598-1611. [DOI: 10.1080/07391102.2019.1614093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| |
Collapse
|
16
|
Chaudhary M, Kumar N, Baldi A, Chandra R, Babu MA, Madan J. 4-Bromo-4’-chloro pyrazoline analog of curcumin augmented anticancer activity against human cervical cancer, HeLa cells: in silico-guided analysis, synthesis, and in vitro cytotoxicity. J Biomol Struct Dyn 2019; 38:1335-1353. [DOI: 10.1080/07391102.2019.1604266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Monika Chaudhary
- IKG Punjab Technical University, Jalandhar, Punjab, India
- Department of Medicinal Chemistry, Hindu College of Pharmacy, Sonepat, Haryana, India
| | - Neeraj Kumar
- Department of Chemistry, University of Delhi, Delhi, India
| | - Ashish Baldi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi, India
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
| | - M. Arockia Babu
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, Punjab, India
| | - Jitender Madan
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, Punjab, India
| |
Collapse
|
17
|
Saravanan K, Hunday G, Kumaradhas P. Binding and stability of indirubin-3-monoxime in the GSK3β enzyme: a molecular dynamics simulation and binding free energy study. J Biomol Struct Dyn 2019; 38:957-974. [DOI: 10.1080/07391102.2019.1591301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| |
Collapse
|
18
|
Jeyaraman P, Alagarraj A, Natarajan R. In silico and in vitro studies of transition metal complexes derived from curcumin-isoniazid Schiff base. J Biomol Struct Dyn 2019; 38:488-499. [PMID: 30767624 DOI: 10.1080/07391102.2019.1581090] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A series of transition metal complexes have been synthesized from biologically active curcumin and isoniazid Schiff base. They are characterized by various spectral techniques like UV-Vis, Fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR) and mass spectroscopies. Moreover, elemental analysis, magnetic susceptibility and molar conductivity measurements are also carried out. All these data evidence that the metal complexes acquire square planar except zinc(II) which adopts a tetrahedral geometry, and they are non-electrolytic in nature. Groove mode of binding between the calf thymus DNA (CT DNA) and metal complexes is confirmed by electronic absorption titration, viscosity and cyclic voltammetry studies. In addition to that, all the metal complexes are able to cleave pUC 19 DNA. Optimized geometry and ground-state electronic structure calculations of all the synthesized compounds are established out by density functional theory (DFT) using B3LYP method which theoretically reveals that copper(II) complex explores higher stability and higher biological accessibility. This is experimentally corroborated by antimicrobial studies. In silico Absorption, Distribution, Metabolism, Excretion (ADME) studies reveal the biological potential of all synthesized complexes, and also biological activity of the ligand is predicted by PASS online biological activity prediction software. Molecular docking studies are also carried out to confirm the groove mode of binding and receptor-complex interactions.
Collapse
Affiliation(s)
- Porkodi Jeyaraman
- Research Department of Chemistry, VHNSN College, Virudhunagar, Tamil Nadu, India
| | - Arunadevi Alagarraj
- Research Department of Chemistry, VHNSN College, Virudhunagar, Tamil Nadu, India
| | - Raman Natarajan
- Research Department of Chemistry, VHNSN College, Virudhunagar, Tamil Nadu, India
| |
Collapse
|
19
|
Reddy PH, Manczak M, Yin X, Grady MC, Mitchell A, Tonk S, Kuruva CS, Bhatti JS, Kandimalla R, Vijayan M, Kumar S, Wang R, Pradeepkiran JA, Ogunmokun G, Thamarai K, Quesada K, Boles A, Reddy AP. Protective Effects of Indian Spice Curcumin Against Amyloid-β in Alzheimer's Disease. J Alzheimers Dis 2019; 61:843-866. [PMID: 29332042 DOI: 10.3233/jad-170512] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The purpose of our article is to assess the current understanding of Indian spice, curcumin, against amyloid-β (Aβ)-induced toxicity in Alzheimer's disease (AD) pathogenesis. Natural products, such as ginger, curcumin, and gingko biloba have been used as diets and dietary supplements to treat human diseases, including cancer, cardiovascular, respiratory, infectious, diabetes, obesity, metabolic syndromes, and neurological disorders. Products derived from plants are known to have protective effects, including anti-inflammatory, antioxidant, anti-arthritis, pro-healing, and boosting memory cognitive functions. In the last decade, several groups have designed and synthesized curcumin and its derivatives and extensively tested using cell and mouse models of AD. Recent research on Aβ and curcumin has revealed that curcumin prevents Aβ aggregation and crosses the blood-brain barrier, reach brain cells, and protect neurons from various toxic insults of aging and Aβ in humans. Recent research has also reported that curcumin ameliorates cognitive decline and improves synaptic functions in mouse models of AD. Further, recent groups have initiated studies on elderly individuals and patients with AD and the outcome of these studies is currently being assessed. This article highlights the beneficial effects of curcumin on AD. This article also critically assesses the current limitations of curcumin's bioavailability and urgent need for new formulations to increase its brain levels to treat patients with AD.
Collapse
Affiliation(s)
- P Hemachandra Reddy
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Speech, Language and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Public Health, Graduate School of Biomedical Studies, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Maria Manczak
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Xiangling Yin
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Mary Catherine Grady
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Andrew Mitchell
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Sahil Tonk
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Chandra Sekhar Kuruva
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jasvinder Singh Bhatti
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Biotechnology and Bioinformatics, Sri Guru Gobind Singh College, Chandigarh, India
| | - Ramesh Kandimalla
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Murali Vijayan
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Subodh Kumar
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Rui Wang
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | | | - Gilbert Ogunmokun
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kavya Thamarai
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kandi Quesada
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Annette Boles
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Arubala P Reddy
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| |
Collapse
|
20
|
Saini RK, Shuaib S, Goyal D, Goyal B. Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aβ42 aggregation and protofibril destabilization: A molecular dynamics simulation study. J Biomol Struct Dyn 2018; 37:3183-3197. [DOI: 10.1080/07391102.2018.1511475] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, India
| | - Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, India
| |
Collapse
|
21
|
Shruti SR, Rajasekaran R. Identification of protegrin-1 as a stable and nontoxic scaffold among protegrin family - a computational approach. J Biomol Struct Dyn 2018; 37:2430-2439. [PMID: 30047844 DOI: 10.1080/07391102.2018.1491418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Achieving both, nontoxicity and stability in antimicrobial peptides (AMP) is a challenge. This study predicts a structurally stable, nontoxic scaffold among the protegrin family, for future therapeutic peptide analogs. Protegrins (PG) are a class of pharmaceutically approved, in demand AMPs, which require further improvement in terms of nontoxicity and stability. Out of five protegrins viz., PG1, PG2, PG3, PG4 and PG5, PG1 has been predicted as best scaffold. Prediction was based upon sequential elimination of other protegrins, using computational methods to assess the extracellular bacterial membrane penetrability, nontoxicity and structural stability by geometric observables. Initially, PG2 and PG4 showing the lowest membrane penetrability and highest toxicity respectively, were screened out. Among the remaining three protegrins, PG1 displayed both lowest root mean square deviation and radius of gyration, with a considerable occupancy of seven H-bonds and established uniform secondary structure profile throughout its ensembles. Therefore, the authors claim the superiority of PG1 as a nontoxic stable scaffold among its family. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- S R Shruti
- a Department of Biotechnology, Bioinformatics lab, School of Biosciences and Technology , VIT (Deemed to be University) , Vellore , Tamil Nadu , India
| | - R Rajasekaran
- a Department of Biotechnology, Bioinformatics lab, School of Biosciences and Technology , VIT (Deemed to be University) , Vellore , Tamil Nadu , India
| |
Collapse
|
22
|
Kamshad M, Jahanshah Talab M, Beigoli S, Sharifirad A, Chamani J. Use of spectroscopic and zeta potential techniques to study the interaction between lysozyme and curcumin in the presence of silver nanoparticles at different sizes. J Biomol Struct Dyn 2018; 37:2030-2040. [PMID: 29757090 DOI: 10.1080/07391102.2018.1475258] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This article describes, for the first time, the effect of three different sizes of silver nanoparticles on the binding of curcumin to lysozyme as examined by spectroscopic and zeta potential techniques at physiological conditions. The binding constants of curcumin to lysozyme in the presence of silver nanoparticles were measured. Based on the results of synchronous fluorescence and three-dimensional fluorescence spectroscopy, the presence of the different sizes of silver nanoparticles caused conformational changes in lysozyme during the binding of curcumin. Such changes were also observed when increasing the curcumin concentration. The results of fluorescence resonance energy transfer theory indicated that different sizes of silver nanoparticles could change the binding distance between curcumin and lysozyme. Based on the red edge excitation shift approach, we concluded that the limited mobility around the Trp residues decreased in the presence of silver nanoparticles with bigger size. Under resonance light scattering, the aggregation of curcumin on lysozyme in the presence of silver nanoparticles can play a major role in functional proteins. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Maryam Kamshad
- a Department of Biology, Faculty of Sciences , Mashhad Branch, Islamic Azad University , Mashhad , Iran
| | - Mahtab Jahanshah Talab
- a Department of Biology, Faculty of Sciences , Mashhad Branch, Islamic Azad University , Mashhad , Iran
| | - Sima Beigoli
- b Endoscopic and Minimally Invasive Surgery Research Center, Mashhad University of Medical Sciences , Mashhad , Iran
| | - Atena Sharifirad
- c Department of Biology, Faculty of Sciences , Neyshabur Branch, Islamic Azad University , Neyshabur , Iran
| | - Jamshidkhan Chamani
- a Department of Biology, Faculty of Sciences , Mashhad Branch, Islamic Azad University , Mashhad , Iran
| |
Collapse
|
23
|
Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils. Molecules 2018; 23:molecules23061320. [PMID: 29857500 PMCID: PMC6100107 DOI: 10.3390/molecules23061320] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/31/2022] Open
Abstract
One of the principal hallmarks of Alzheimer’s disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists of either blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-epigallocatechin-3-gallate, quercetin, and rosmarinic acid) with amyloid-β(1–40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulates the double-layered structure stability.
Collapse
|
24
|
Niu X, Gao Y, Yu Y, Yang Y, Wang G, Sun L, Wang H. Molecular Modelling reveals the inhibition mechanism and structure-activity relationship of curcumin and its analogues to Staphylococcal aureus Sortase A. J Biomol Struct Dyn 2018; 37:1220-1230. [PMID: 29546799 DOI: 10.1080/07391102.2018.1453380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182 and ILE-199 are key residues in Sortase A-inhibitor complexes. Furthermore, interactions between the methoxyl group on the benzene ring in the conjugated molecule (curcumin, demethoxycurcumin, bisdemethoxycurcumin) and VAL-168, LEU-169 and GLN-172 induce the inhibitory activity based on the energy decomposition and distance analyses between the whole residues and inhibitors. However, because of its coiled structure, the non-conjugated molecule, tetrahydrocurcumin, with key residues in the binding sites of Sortase A, interacted weakly with SrtA, leading to the loss of inhibitory activity. Based on these results, the methoxyl group on the benzene ring in the conjugated molecule largely influenced the inhibitory activity of the Sortase A inhibitors.
Collapse
Affiliation(s)
- Xiaodi Niu
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Yawen Gao
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Yiding Yu
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Yanan Yang
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Guizhen Wang
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Lin Sun
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Hongsu Wang
- a College of Food Science and Engineering , Jilin University , Changchun , China
| |
Collapse
|
25
|
Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| |
Collapse
|
26
|
Azam F, Alabdullah NH, Ehmedat HM, Abulifa AR, Taban I, Upadhyayula S. NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer's disease: an investigation by docking, molecular dynamics, and DFT studies. J Biomol Struct Dyn 2017; 36:2099-2117. [PMID: 28571516 DOI: 10.1080/07391102.2017.1338164] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Aggregation of amyloid beta (Aβ) protein considered as one of contributors in development of Alzheimer's disease (AD). Several investigations have identified the importance of non-steroidal anti-inflammatory drugs (NSAIDs) as Aβ aggregation inhibitors. Here, we have examined the binding interactions of 24 NSAIDs belonging to eight different classes, with Aβ fibrils by exploiting docking and molecular dynamics studies. Minimum energy conformation of the docked NSAIDs were further optimized by density functional theory (DFT) employing Becke's three-parameter hybrid model, Lee-Yang-Parr (B3LYP) correlation functional method. DFT-based global reactivity descriptors, such as electron affinity, hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated to inspect the expediency of these descriptors for understanding the reactive nature and sites of the molecules. Few selected NSAID-Aβ fibrils complexes were subjected to molecular dynamics simulation to illustrate the stability of these complexes and the most prominent interactions during the simulated trajectory. All of the NSAIDs exhibited potential activity against Aβ fibrils in terms of predicted binding affinity. Sulindac was found to be the most active compound underscoring the contribution of indene methylene substitution, whereas acetaminophen was observed as least active NSAID. General structural requirements for interaction of NSAIDs with Aβ fibril include: aryl/heteroaryl aromatic moiety connected through a linker of 1-2 atoms to a distal aromatic group. Considering these structural requirements and electronic features, new potent agents can be designed and developed as potential Aβ fibril inhibitors for the treatment of AD.
Collapse
Affiliation(s)
- Faizul Azam
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Nada Hussin Alabdullah
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Hadeel Mohammed Ehmedat
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Abdullah Ramadan Abulifa
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Ismail Taban
- b School of Pharmacy and Pharmaceutical Sciences , Cardiff University , Cardiff , UK
| | - Sreedevi Upadhyayula
- c Department of Chemical Engineering , Indian Institute of Technology , New Delhi , India
| |
Collapse
|