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Nie RZ, Zhang SS, Yan XK, Feng K, Lao YJ, Bao YR. Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study. Int J Biol Macromol 2023; 253:127002. [PMID: 37729983 DOI: 10.1016/j.ijbiomac.2023.127002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.
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Affiliation(s)
- Rong-Zu Nie
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Shan-Shuo Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xiao-Ke Yan
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Kun Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yan-Jing Lao
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Ya-Ru Bao
- Science and Technology Division, Zhengzhou University of Light Industry, Zhengzhou 450002, China.
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Effect of Antihypertensive Drug (Chlorothiazide) on Fibrillation of Lysozyme: A Combined Spectroscopy, Microscopy, and Computational Study. Int J Mol Sci 2023; 24:ijms24043112. [PMID: 36834523 PMCID: PMC9959601 DOI: 10.3390/ijms24043112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest that diuretics prevent amyloid-related diseases and reduce amyloid aggregation. Thus, in this study we examine the effects of CTZ on hen egg white lysozyme (HEWL) aggregation using spectroscopic, docking, and microscopic approaches. Our results showed that under protein misfolding conditions of 55 °C, pH 2.0, and 600 rpm agitation, HEWL aggregated as evidenced by the increased turbidity and Rayleigh light scattering (RLS). Furthermore, thioflavin-T, as well as trans electron microscope (TEM) analysis confirmed the formation of amyloid structures. An anti-aggregation effect of CTZ is observed on HEWL aggregations. Circular dichroism (CD), TEM, and Thioflavin-T fluorescence show that both CTZ concentrations reduce the formation of amyloid fibrils as compared to fibrillated. The turbidity, RLS, and ANS fluorescence increase with CTZ increasing. This increase is attributed to the formation of a soluble aggregation. As evidenced by CD analysis, there was no significant difference in α-helix content and β-sheet content between at 10 µM CTZ and 100 µM. A TEM analysis of HEWL coincubated with CTZ at different concentrations validated all the above-mentioned results. The TEM results show that CTZ induces morphological changes in the typical structure of amyloid fibrils. The steady-state quenching study demonstrated that CTZ and HEWL bind spontaneously via hydrophobic interactions. HEWL-CTZ also interacts dynamically with changes in the environment surrounding tryptophan. Computational results revealed the binding of CTZ to ILE98, GLN57, ASP52, TRP108, TRP63, TRP63, ILE58, and ALA107 residues in HEWL via hydrophobic interactions and hydrogen bonds with a binding energy of -6.58 kcal mol-1. We suggest that at 10 µM and 100 μM, CTZ binds to the aggregation-prone region (APR) of HEWL and stabilizes it, thus preventing aggregation. Based on these findings, we can conclude that CTZ has antiamyloidogenic activity and can prevent fibril aggregation.
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Nie RZ, Cai S, Yu B, Fan WY, Li HH, Tang SW, Huo YQ. Molecular insights into the very early steps of Aβ1-42 pentameric protofibril disassembly by PGG: A molecular dynamics simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Screening inhibitor to prevent the psychrotrophic growth of Pseudomonas fluorescens by using molecular simulation. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau Fragment 171IPAKTPPAPK 180 Using Molecular Dynamic Simulation and the Markov State Model. Int J Mol Sci 2022; 23:ijms23052399. [PMID: 35269542 PMCID: PMC8910285 DOI: 10.3390/ijms23052399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
The formation of neurofibrillary tangles (NFT) with β-sheet-rich structure caused by abnormal aggregation of misfolded microtubule-associated protein Tau is a hallmark of tauopathies, including Alzheimer’s Disease. It has been reported that acetylation, especially K174 located in the proline-rich region, can largely promote Tau aggregation. So far, the mechanism of the abnormal acetylation of Tau that affects its misfolding and aggregation is still unclear. Therefore, revealing the effect of acetylation on Tau aggregation could help elucidate the pathogenic mechanism of tauopathies. In this study, molecular dynamics simulation combined with multiple computational analytical methods were performed to reveal the effect of K174 acetylation on the spontaneous aggregation of Tau peptide 171IPAKTPPAPK180, and the dimerization mechanism as an early stage of the spontaneous aggregation was further specifically analyzed by Markov state model (MSM) analysis. The results showed that both the actual acetylation and the mutation mimicking the acetylated state at K174 induced the aggregation of the studied Tau fragment; however, the effect of actual acetylation on the aggregation was more pronounced. In addition, acetylated K174 plays a major contributing role in forming and stabilizing the antiparallel β-sheet dimer by forming several hydrogen bonds and side chain van der Waals interactions with residues I171, P172, A173 and T175 of the corresponding chain. In brief, this study uncovered the underlying mechanism of Tau peptide aggregation in response to the lysine K174 acetylation, which can deepen our understanding on the pathogenesis of tauopathies.
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Li J, Li Y, Zhong J, Wang Y, Liu X, Qin X. Effect of cellulose nanocrystals on the formation and stability of oil-in-water emulsion formed by octenyl succinic anhydride starch. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jing J, Tu G, Yu H, Huang R, Ming X, Zhan H, Zhan F, Xue W. Copper (Cu 2+) ion-induced misfolding of tau protein R3 peptide revealed by enhanced molecular dynamics simulation. Phys Chem Chem Phys 2021; 23:11717-11726. [PMID: 33982037 DOI: 10.1039/d0cp05744d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tau misfolding plays a significant role in some neurodegenerative diseases such as Alzheimer's disease (AD). It is intrinsically disordered and highly soluble under normal physiological conditions. While the protein will aggregate to form paired helical filaments (PHFs) under copper homeostasis at pathological conditions, which is the main substance of neurofibrillary tangles (NFTs) in the brain of AD patients. However, the molecular mechanism underlying the copper (Cu2+) ion-induced tau misfolding is not fully understood. In this study, using the 1/2 third repeat fragment (R3 peptide) of tau protein (residues 318-335: VTSKCGSLGNIHHKPGGG) as a model, a Gaussian accelerated molecular dynamics (GaMD) method followed by efficient trajectory analysis was carried out to investigate the influences of Cu2+ on the tau about the protein fold and the free energy landscape along the simulation. The two-dimensional potential of mean force (PMF) profiles obtained from reweighting of the GaMD simulations as well as clustering analysis revealed the Cu2+ ion induced α-helix fold R3 peptide located at the low-energy wells of free energy map, which is in agreement with the reported experimental result. In contrast, there is no α-helix fold of R3 peptide that appeared during the GaMD simulation without Cu2+ ion existing. Furthermore, the definition of secondary structure of protein (DSSP) analysis indicated that the R3 peptide with Cu2+ ion forms a stable structure of the helix (Lys321-His330 interval of the peptide) at between 400 and 500 ns. Therefore, the structures and free energy profiles from GaMD simulations proposed that Cu2+ triggers the aggregation of R3 peptide into toxic PHFs through a stable α-helix fold form.
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Affiliation(s)
- Jing Jing
- The Key Laboratory of Nonferrous Metal Materials and New Processing Technology of Ministry of Education, Guangxi University, Nanning 530004, China. and School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China.
| | - Gao Tu
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China.
| | - Hongyan Yu
- The Key Laboratory of Nonferrous Metal Materials and New Processing Technology of Ministry of Education, Guangxi University, Nanning 530004, China. and School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China.
| | - Rong Huang
- Central Nervous System Drug Key Laboratory of Sichuan Province, Luzhou 646106, China and Sichuan Credit Pharmaceutical Co., Ltd., Luzhou 646106, China
| | - Xianquan Ming
- CITIC Dameng Mining Industries Ltd., Nanning 530028, China
| | - Haiqing Zhan
- CITIC Dameng Mining Industries Ltd., Nanning 530028, China
| | - Feng Zhan
- The Key Laboratory of Nonferrous Metal Materials and New Processing Technology of Ministry of Education, Guangxi University, Nanning 530004, China.
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China. and Central Nervous System Drug Key Laboratory of Sichuan Province, Luzhou 646106, China
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Nie RZ, Dang MZ, Ge ZZ, Huo YQ, Yu B, Tang SW. Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations. Biophys Chem 2021; 274:106592. [PMID: 33887572 DOI: 10.1016/j.bpc.2021.106592] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 02/09/2023]
Abstract
Previous studies suggested that naturally occurring EGCG primarily acted on the bacterial cell membrane then damaged the membrane and the gallate moiety in EGCG was very important to its anti-bacterial activity. However, the detailed mechanisms were still poorly understood. In this paper, EGCG and EGC were selected to study the great contribution of gallate moiety on the anti-bacterial activities of polyphenols. The results indicated that EGCG could penetrate deeper into the POPG lipid bilayer and possess more potent structure-perturbing potency on the POPG lipid bilayer than EGC. We also found that EGCG had the ability to form hydrogen bonds with the deeper inside oxygen atoms in the POPG lipid bilayer and the gallate moiety was the key functional group for EGCG forming hydrogen bonds with the POPG lipid bilayer. Moreover, results from the binding free energy analysis demonstrated that the gallate moiety made great contribution to the high affinity between EGCG and the POPG lipid bilayer. We believed that these findings could yield useful insights into the influence mechanisms of gallate moiety on the anti-bacterial activities of polyphenols.
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Affiliation(s)
- Rong-Zu Nie
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Mei-Zhu Dang
- School of Energy and Intelligence Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450002, China
| | - Zhen-Zhen Ge
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Yin-Qiang Huo
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Bo Yu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Shang-Wen Tang
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China.
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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.
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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
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Nie RZ, Huo YQ, Yu B, Liu CJ, Zhou R, Bao HH, Tang SW. Molecular insights into the inhibitory mechanisms of gallate moiety on the Aβ 1-40 amyloid aggregation: A molecular dynamics simulation study. Int J Biol Macromol 2020; 156:40-50. [PMID: 32275992 DOI: 10.1016/j.ijbiomac.2020.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease is the most common form of neurodegenerative disease and the formation of Aβ amyloid aggregates has been widely demonstrated to be the principal cause of Alzheimer's disease. Our previous study and other studies suggested that the gallate moiety played an obligatory role in the inhibition process of naturally occurring polyphenols on Aβ amyloid fibrils formation. However, the detailed mechanisms were still unknown. Thus, in the present study, the gallic acid (GA) was specially selected and the molecular recognition mechanisms between GA molecules and Aβ1-40 monomer were examined and analyzed by molecular dynamics simulation. The in silico experiments revealed that GA significantly prevented the conformational changes of Aβ1-40 monomer with no β-sheet structure during the whole 100 ns. By analyzing the binding sites of GA molecules to Aβ1-40 monomer, we found that both hydrophilic and hydrophobic amino acid residues were participated in the binding of GA molecules to Aβ1-40 monomer. Moreover, results from the binding free energy analysis further demonstrated that the strength of polar interactions was significantly stronger than that of nonpolar interactions. We believed that our results could help to elucidate the underlying mechanisms of gallate moiety on the anti-amyloidogenic effects of polyphenols at the atomic level.
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Affiliation(s)
- Rong-Zu Nie
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Yin-Qiang Huo
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Bo Yu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Chuan-Ju Liu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Rui Zhou
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Hong-Hui Bao
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Shang-Wen Tang
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China.
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Liu H, Zhong H, Liu X, Zhou S, Tan S, Liu H, Yao X. Disclosing the Mechanism of Spontaneous Aggregation and Template-Induced Misfolding of the Key Hexapeptide (PHF6) of Tau Protein Based on Molecular Dynamics Simulation. ACS Chem Neurosci 2019; 10:4810-4823. [PMID: 31661961 DOI: 10.1021/acschemneuro.9b00488] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The microtubule-associated protein tau is critical for the development and maintenance of the nervous system. Tau dysfunction is associated with a variety of neurodegenerative diseases called tauopathies, which are characterized by neurofibrillary tangles formed by abnormally aggregated tau protein. Studying the aggregation mechanism of tau protein is of great significance for elucidating the etiology of tauopathies. The hexapeptide 306VQIVYK311 (PHF6) of R3 has been shown to play a vital role in promoting tau aggregation. In this study, long-term all-atom molecular dynamics simulations in explicit solvent were performed to investigate the mechanisms of spontaneous aggregation and template-induced misfolding of PHF6, and the dimerization at the early stage of nucleation was further specifically analyzed by the Markov state model (MSM). Our results show that PHF6 can spontaneously aggregate to form multimers enriched with β-sheet structure and the β-sheets in multimers prefer to exist in a parallel way. It is observed that PHF6 monomer can be induced to form a β-sheet structure on either side of the template but in a different way. In detail, the β-sheet structure is easier to form on the left side but does not extend well, but on the right side, the monomer can form the extended β-sheet structure. Furthermore, MSM analysis shows that the formation of dimer mainly occurs in three steps. First, the separated monomers collide with each other at random orientations, and then a dimer with short β-sheet structure at the N-terminal forms; finally, β-sheets elongate to form an extended parallel β-sheet dimer. During these processes, multiple intermediate states are identified and multiple paths can form a parallel β-sheet dimer from the disordered coil structure. Moreover, the residues I308, V309, and Y310 play an essential role in the dimerization. In a word, our results uncover the aggregation and misfolding mechanism of PHF6 from the atomic level, which can provide useful theoretical guidance for rational design of effective therapeutic drugs against tauopathies.
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Affiliation(s)
| | | | | | - Shuangyan Zhou
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | | | | | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
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Molecular insights into the inhibitory mechanism of bi-functional bis-tryptoline triazole against β-secretase (BACE1) enzyme. Amino Acids 2019; 51:1593-1607. [PMID: 31654211 DOI: 10.1007/s00726-019-02797-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The β-site amyloid precursor protein-cleaving enzyme 1 (β-secretase, BACE1) is involved in the formation of amyloid-β (Aβ) peptide that aggregates into soluble oligomers, amyloid fibrils, and plaques responsible for the neurodegeneration in Alzheimer disease (AD). BACE1 is one of the prime therapeutic targets for the design of inhibitors against AD as BACE1 participate in the rate-limiting step in Aβ production. Jiaranaikulwanitch et al. reported bis-tryptoline triazole (BTT) compound as a potent inhibitor against BACE1, Aβ aggregation as well as possessing metal chelation and antioxidant activity. However, the molecular mechanism of BACE1 inhibition by BTT remains unclear. Thus, molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of BTT against BACE1. MD simulations highlight that BTT interact with catalytic aspartic dyad residues (Asp32 and Asp228) and active pocket residues of BACE1. The hydrogen-bond interactions, hydrophobic contacts, and π-π stacking interactions of BTT with flap residues (Val67-Asp77) of BACE1 confine the movement of the flap and help to achieve closed (non-active) conformation. The PCA analysis highlights lower conformational fluctuations for BACE1-BTT complex, which suggests enhanced conformational stability in comparison to apo-BACE1. The results of the present study provide key insights into the underlying inhibitory mechanism of BTT against BACE1 and will be helpful for the rational design of novel inhibitors with enhanced potency against BACE1.
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Narang SS, Shuaib S, Goyal D, Goyal B. In silico-guided identification of potential inhibitors against β2m aggregation in dialysis-related amyloidosis. J Biomol Struct Dyn 2019; 38:3927-3941. [DOI: 10.1080/07391102.2019.1668852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Suniba Shuaib
- 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 and Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Narang SS, Goyal D, Goyal B. Inhibition of Alzheimer’s amyloid-β42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:1598-1611. [DOI: 10.1080/07391102.2019.1614093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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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
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Shao Z, Fang S, Li Y, Chen J, Meng Y. Physicochemical properties and formation mechanism of electrostatic complexes based on ε-polylysine and whey protein: Experimental and molecular dynamics simulations study. Int J Biol Macromol 2018; 118:2208-2215. [DOI: 10.1016/j.ijbiomac.2018.07.086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/30/2023]
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