1
|
Chen J, Warner MJ, Sikora B, Kiddle D, Coverdell D, Allam O, Kohl PA, Jang SS. The selective heating effect of microwave irradiation on a binary mixture of water and polyethylene oxide: a molecular dynamics simulation approach. Phys Chem Chem Phys 2023; 25:12522-12531. [PMID: 37133822 DOI: 10.1039/d3cp00349c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this study, we investigate the molecular mechanisms of a microwave-driven selective heating process by performing molecular dynamics simulations for three different systems including pure water, pure polyethylene oxide (PEO), and water-PEO mixed systems in the presence of a microwave with two different intensities of electric field such as 0.001 V Å-1 and 0.01 V Å-1 at a frequency of 100 GHz. First, from performing molecular dynamics simulations of CO and CO2 in the presence of the microwave, it is confirmed that the molecular dipole moment is responsible for the rotational motion induced by the oscillating electric field. Second, by analyzing the MD simulations of the pure water system, we discover that the dipole moment of water exhibits a time lag with respect to the microwave. During the heating process, however, the temperature, kinetic, and potential energies increase synchronously with the oscillating electric field of the microwave, showing that the heating of the water system is caused by the molecular reaction of water to the microwave. Comparing the water-PEO mixed system to the pure water and pure PEO systems, the water-PEO mixed system has a higher heating rate than the pure PEO system but a lower heating rate than the pure water system. Therefore, we conclude that heating the water-PEO mixed system is driven by water molecules selectively activated by microwave irradiation. We also calculate the diffusion coefficients of water molecules and PEO chains by describing their mean square displacements, demonstrating that the diffusion coefficients are increased in the presence of microwaves for both water and PEO in pure and mixed systems. Lastly, during the microwave heating process, the structures of the water-PEO mixed system are altered as a function of the intensity of electric field, which is mainly driven by the response of water molecules.
Collapse
Affiliation(s)
- Junhe Chen
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, 30332-0245, USA.
| | - Matthew J Warner
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332-0100, USA
| | - Benjamin Sikora
- Department of Energy's Kansas City National Security Campus managed by Honeywell, 14520 Botts Road, Kansas City, MO 64147, USA
| | - Daniel Kiddle
- Department of Energy's Kansas City National Security Campus managed by Honeywell, 14520 Botts Road, Kansas City, MO 64147, USA
| | - Danielle Coverdell
- Department of Energy's Kansas City National Security Campus managed by Honeywell, 14520 Botts Road, Kansas City, MO 64147, USA
| | - Omar Allam
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, 30332-0245, USA.
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801 Ferst Drive NW, Atlanta, Georgia 30332-0405, USA
| | - Paul A Kohl
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332-0100, USA
| | - Seung Soon Jang
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, 30332-0245, USA.
| |
Collapse
|
2
|
Gao W, Li Y, Xu W, Mei J, Wang C, Sajjad A, Ai H. Inhibitory Mechanisms of Three Modified Small Molecules on the Misfolding of Cu
2+
‐Aβ42 Complex in Different pH Conditions: Insights from MD/QM Studies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wenqi Gao
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Ye Li
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Wen Xu
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Jinfei Mei
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Chuanbo Wang
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Ahmad Sajjad
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| |
Collapse
|
3
|
Picone P, Sanfilippo T, Vasto S, Baldassano S, Guggino R, Nuzzo D, Bulone D, San Biagio PL, Muscolino E, Monastero R, Dispenza C, Giacomazza D. From Small Peptides to Large Proteins against Alzheimer’sDisease. Biomolecules 2022; 12:biom12101344. [PMID: 36291553 PMCID: PMC9599460 DOI: 10.3390/biom12101344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the elderly. The two cardinal neuropathological hallmarks of AD are the senile plaques, which are extracellular deposits mainly constituted by beta-amyloids, and neurofibrillary tangles formed by abnormally phosphorylated Tau (p-Tau) located in the cytoplasm of neurons. Although the research has made relevant progress in the management of the disease, the treatment is still lacking. Only symptomatic medications exist for the disease, and, in the meantime, laboratories worldwide are investigating disease-modifying treatments for AD. In the present review, results centered on the use of peptides of different sizes involved in AD are presented.
Collapse
Affiliation(s)
- Pasquale Picone
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Tiziana Sanfilippo
- Ambulatorio di Nutrizione Clinica ASP Palermo, Via G. Cusmano 24, 90141 Palermo, Italy
- Anestesia e Rianimazione, Presidio Ospedaliero “S. Cimino”, 90141 Termini Imerese, Italy
| | - Sonya Vasto
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Istituti Euro-Mediterranei di Scienza e Tecnologia (IEMEST), Via M. Miraglia 20, 90139 Palermo, Italy
| | - Sara Baldassano
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Rossella Guggino
- Ambulatorio di Nutrizione Clinica ASP Palermo, Via G. Cusmano 24, 90141 Palermo, Italy
- Anestesia e Rianimazione, Presidio Ospedaliero “S. Cimino”, 90141 Termini Imerese, Italy
| | - Domenico Nuzzo
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Correspondence: (D.N.); (D.G.)
| | - Donatella Bulone
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Pier Luigi San Biagio
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Emanuela Muscolino
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Bldg 6, 90128 Palermo, Italy
| | - Roberto Monastero
- Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università degli Studi di Palermo, Via del Vespro 129, 90127 Palermo, Italy
| | - Clelia Dispenza
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Bldg 6, 90128 Palermo, Italy
| | - Daniela Giacomazza
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Correspondence: (D.N.); (D.G.)
| |
Collapse
|
4
|
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]
|
5
|
Mei J, Yang H, Sun B, Liu C, Ai H. Small-Molecule Targeted Aβ 42 Aggregate Degradation: Negatively Charged Small Molecules Are More Promising than the Neutral Ones. ACS Chem Neurosci 2021; 12:1197-1209. [PMID: 33687193 DOI: 10.1021/acschemneuro.1c00047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heavy evidence has confirmed that Aβ42 oligomers are the most neurotoxic aggregates and play a critical role in the occurrence and development of Alzheimer's disease by causing functional neuron death, cognitive damage, and dementia. Disordered Aβ42 oligomers are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, a negatively charged molecule (ER), rather than the neutral TS1 one, is identified by a molecular dynamics simulation method to be more capable of binding and sequestering the intrinsically disordered amyloid-β peptide Aβ42 in its soluble pentameric state as well as its monomeric components. Results reveal that the ERs interact with Aβ and inhibit the primary nucleation pathways in its aggregation process in entropic expansion mechanism for both Aβ42 and Aβ40 oligomers but with opposite characteristics of hydrophobic surface area (HSA). The interaction between Aβ42 oligomer and either charged ER or neutral TS1/TS0 characterizes decreased HSA, and the decrease in ER-involved case is highly visible, consistent with the observations from in silico and in vitro studies. By contrast, the presence of these inhibitors causes the HSA of Aβ40 oligomer to change undetectably and there is even a bit of increase in the histidine isomerized Aβ40 oligomer. The HSA distinction between Aβ42 and Aβ40 oligomer is possibly derived from the different effects of M35-inhibitor interaction, which is analogous to the effect of M35 oxidation. In comparison with the neutral TS1/TS0 inhibitors, ER is more prone to bind the residues located in the central (β1) and C-terminal (β2) regions of Aβ42 peptide, two key nucleation regions for Aβ intramolecular folding, intermolecular aggregation, and assembly. Notably, ER can strongly bind the charged residues, such as K16, K28, D23, to greatly disturb the potential stabilizer (e.g., salt-bridge, etc.) in metastable Aβ42 oligomers and protofibrils. These results illustrate the strategy of overcoming Alzheimer's disease from inhibiting its early stage Aβ aggregation with two kinds of small molecules to alter their behavior for therapeutic purposes and strongly recommend paying more attention to the engineering and development of negatively charged inhibitors, the long-term underappreciated ones, targeting the early stage Aβ aggregates.
Collapse
Affiliation(s)
- Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Bo Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| |
Collapse
|
6
|
Jokar S, Erfani M, Bavi O, Khazaei S, Sharifzadeh M, Hajiramezanali M, Beiki D, Shamloo A. Design of peptide-based inhibitor agent against amyloid-β aggregation: Molecular docking, synthesis and in vitro evaluation. Bioorg Chem 2020; 102:104050. [PMID: 32663672 DOI: 10.1016/j.bioorg.2020.104050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 12/30/2022]
Abstract
Formation of the amyloid beta (Aβ) peptide aggregations represents an indispensable role in appearing and progression of Alzheimer disease. β-sheet breaker peptides can be designed and modified with different amino acids in order to improve biological properties and binding affinity to the amyloid beta peptide. In the present study, three peptide sequences were designed based on the hopeful results of LIAIMA peptide and molecular docking studies were carried out onto the monomer and fibril structure of amyloid beta peptide using AutoDock Vina software. According to the obtained interactions and binding energy from docking, the best-designed peptide (d-GABA-FPLIAIMA) was chosen and synthesized in great yield (%96) via the Fmoc solid-phase peptide synthesis. The synthesis and purity of the resulting peptide were estimated and evaluated by Mass spectroscopy and Reversed-phase high-performance liquid chromatography (RP-HPLC) methods, respectively. Stability studies in plasma and Thioflavin T (ThT) assay were performed in order to measure the binding affinity and in vitro aggregation inhibition of Aβ peptide. The d-GABA-FPLIAIMA peptide showed good binding energy and affinity to Aβ fibrils, high stability (more than 90%) in human serum, and a reduction of 20% in inhibition of the Aβ aggregation growth. Finally, the favorable characteristics of our newly designed peptide make it a promising candidate β-sheet breaker agent for further in vivo studies.
Collapse
Affiliation(s)
- Safura Jokar
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Erfani
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, Tehran, Iran.
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, Iran.
| | - Saeedeh Khazaei
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sharifzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy; Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - Malihe Hajiramezanali
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Beiki
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
| |
Collapse
|
7
|
Xing X, Liu C, Ali A, Kang B, Li P, Ai H. Novel Disassembly Mechanisms of Sigmoid Aβ 42 Protofibrils by Introduced Neutral and Charged Drug Molecules. ACS Chem Neurosci 2020; 11:45-56. [PMID: 31697060 DOI: 10.1021/acschemneuro.9b00550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by fibrillar deposits of amyloid-β (Aβ) peptides and neurofibrillary tangles of Tau proteins. Aβ peptides are composed of 37-49 residues, among which the Aβ42 isoform is particularly toxic and aggregation-prone and is enriched in the plaques of AD brains and thus considered central to the development of AD. Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. Here we capture the atomic-level details of the interactions between sigmoid Aβ42 fibril 2MXU or 5KK3 and either natural tanshinone compounds TS1 or TS0 or negatively charged ER, proposing two unprecedented disassembly mechanisms. Natural TS1 or TS0 prefers to insert into the cavity together with part at the surface of the 2MXU to open up the mouth and twist the conformation, destroying the ordered growth of subsequent monomers along the fibril axis. For the more compact two-fold 5KK3 , attachment of TS1 or TS0 at the surface including some inserted in cavity results in the separation of the two folds. In the two sigmoid fibril systems, it is no longer applicable for the routine criteria to assess Aβ42 fibril disassembly by introduction of these drugs, such as either reduced H-bond number, decreased β-sheet contents, or both. ER, like-charged to Aβ42 fibril, is especially exceptional, and departs utterly from the neutral ones to disassemble Aβ42 fibril. Besides the inapplicable routine criteria, positive binding energy between ER and Aβ42 fibril also deviates from the hypotheses of "ligands exhibiting greater affinity for the β-amyloid peptide are effective at altering its aggregation and inhibiting cell toxicity" ( Cairo et al. , Biochemistry 2002 , 41 , 8620 - 8629 ) but results in stronger disassembly effect on the two kinds of sigmoid Aβ42 fibrils than neutral TS0 or TS1. The disassembly power of charged ER molecules derives from its stronger deformation ability to the conformation of Aβ42 fibril than the neutral ones, twisting the one-fold 2MXU into tapered-shape and separating two-fold 5KK3 in two parts further, which is in great agreement with experimental observations ( Irwin et al. Biomacromolecules 2013 , 14 ( 1 ), 264 - 274 ). The unusual disassembly mechanisms fill the gaps and offer an alternative direction in engineering new inhibitors to treat AD.
Collapse
Affiliation(s)
- Xiaofeng Xing
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Aqsa Ali
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Ping Li
- Key Laboratory of Life-Organic Analysis, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| |
Collapse
|
8
|
Gupta S, Dasmahapatra AK. Caffeine destabilizes preformed Aβ protofilaments: insights from all atom molecular dynamics simulations. Phys Chem Chem Phys 2019; 21:22067-22080. [PMID: 31565708 DOI: 10.1039/c9cp04162a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The aggregation and deposition of neurotoxic Aβ fibrils are key in the etiology of Alzheimer's disease (AD). It has been clinically recognized as a major form of dementia across the globe. Finding and testing various natural compounds to target Aβ fibrils to disrupt their stable structures seems to be a promising and attractive therapeutic strategy. The destabilization effects of caffeine on Aβ fibrils are investigated via in silico studies, where a series of molecular dynamics (MD) simulations, each of 100 ns, was conducted. The simulation outcomes obtained henceforth clearly indicated the drift of the terminal chains from the protofibrils, leading to disorganization of the characteristically organized cross-β structures of Aβ fibrils. The structural instability of Aβ17-42 protofibrils is explained through enhanced fluctuations in the RMSD, radius of gyration and RMSF values in the presence of caffeine. The key interactions providing stability, comprising D23-K28 salt bridges, intra- and inter-chain hydrogen bonding and hydrophobic interactions involving interchain A21-V36 and F19-G38 and intrachain L34-V36, were found to be disrupted due to increases in the distances between the participating components. The loss of β-sheet structure with the introduction of turns and α-helices in terminal chains may further inhibit the formation of higher order aggregates, which is necessary to stop the progression of the disease. The atomistic details obtained via MD studies relating to the mechanism behind the underlying destabilization of Aβ17-42 protofibrils by caffeine encourage further investigations exploring the potency of natural compounds to treat AD via disrupting preformed neurotoxic Aβ protofibrils.
Collapse
Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering and Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
| | | |
Collapse
|
9
|
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
|
10
|
Saini RK, Shuaib S, Goyal B. Molecular insights into Aβ42protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Suniba Shuaib
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Bhupesh Goyal
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| |
Collapse
|
11
|
Dong M, Zhao W, Hu D, Ai H, Kang B. N-Terminus Binding Preference for Either Tanshinone or Analogue in Both Inhibition of Amyloid Aggregation and Disaggregation of Preformed Amyloid Fibrils-Toward Introducing a Kind of Novel Anti-Alzheimer Compounds. ACS Chem Neurosci 2017; 8:1577-1588. [PMID: 28406293 DOI: 10.1021/acschemneuro.7b00080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Amyloid-β (Aβ40/Aβ42) peptide with a length of 40 or 42 residues is naturally secreted as cleavage product of the amyloid precursor protein, and formation of Aβ aggregates in a patient's brain is a hallmark of Alzheimer's disease (AD). Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. The disaggregation/inhibition effect of the inhibitors applies generally to both Aβ40 and Aβ42 aggregations. Here we capture the atomic-level details of the interaction between Aβ40/Aβ42 and either natural tanshinone compound TS1 or its derivative TS0, and observe novel results by using molecular dynamics simulations. We observe that the natural TS1 indeed inhibits the monomolecular Aβ42 (mAβ42) aggregation and disaggregates Aβ42 amyloid fibrils, being in good agreement with the experimental results. TS1 is favorable to stabilize mAβ40 and even Aβ40 fibril, playing an opposite role to that in the Aβ42 counterpart, however. TS0 can inhibit the misfolding of either mAβ40 or mAβ42 and disaggregate Aβ42 fibril but stabilize the Aβ40 fibril. Using a combination of secondary structural analysis, MM-PBSA binding energy calculations, and radial distribution functions computations, we find that both TS0 and TS1, especially the former, prefer to bind at the charged residues within disordered N-terminus with a scarce positive binding energy and disappear the characteristic C-terminal bend region of Aβ42 fibril, as well as twist the Aβ42 fibril seriously. It turns out to destabilize the Aβ42 fibril and enable the conversion of U-shaped Aβ42 fibril from the onefold to the twofold morphologies. The N-terminal binding preference helps us to identify N-terminal region as the specific epitope for specific inhibitors/drugs (such as TS0 and analogues), heralding unusual inhibition/disaggregation or stabilization mechanisms, and offering an alternative direction in engineering new inhibitors to treat AD.
Collapse
Affiliation(s)
- Mingyan Dong
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Wei Zhao
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Dingkun Hu
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Hongqi Ai
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Baotao Kang
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| |
Collapse
|
12
|
Shuaib S, Goyal B. Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β 42 monomer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:663-678. [PMID: 28162045 DOI: 10.1080/07391102.2017.1291363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β42 (Aβ42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ42. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ42.
Collapse
Affiliation(s)
- Suniba Shuaib
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
| | - Bhupesh Goyal
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
| |
Collapse
|
13
|
Goyal B, Kumar A, Srivastava KR, Durani S. Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides. J Biomol Struct Dyn 2016; 35:1923-1935. [DOI: 10.1080/07391102.2016.1199972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| |
Collapse
|
14
|
Goyal B, Kumar A, Srivastava KR, Durani S. Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Adv 2016. [DOI: 10.1039/c6ra10934a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N-Terminal l- to d-residue mutation nucleate helical fold in Ac–DAla–LAla3–NHMe (Ib, m2), Ac–DPro–LAla3–NHMe (IIb, m1), and Ac–DPro–LPro–LAla2–NHMe (IIIb, m2) peptides.
Collapse
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| |
Collapse
|