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Chen C, Yan ZS, Ma YQ, Ding HM. Effect of Terahertz Waves on the Structure of the Aβ42 Monomer, Dimer, and Protofibril: Insights from Molecular Dynamics Simulations. ACS Chem Neurosci 2023; 14:4128-4138. [PMID: 37983764 DOI: 10.1021/acschemneuro.3c00485] [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] [Indexed: 11/22/2023] Open
Abstract
Amyloid-β (Aβ) and its assemblies play important roles in the pathogenesis of Alzheimer's disease (AD). Recent studies conducted by experimental and computational researchers have extensively explored the structure, assembly, and influence of biomolecules and cell membranes on Aβ. However, the impact of terahertz waves on the structures of Aβ monomers and aggregates remains largely unexplored. In this study, we systematically investigate the molecular mechanisms by which terahertz waves affect the structure of the Aβ42 monomer, dimer, and tetramer through all-atom molecular dynamics (MD) simulations. Our findings indicate that terahertz waves at a specific frequency (42.55 THz) can enhance intramolecular and intermolecular interactions in the Aβ42 monomer and dimer, respectively, by resonating with the symmetric stretching mode of the -COO- groups and the symmetric bending/stretching mode of -CH3 groups. Consequently, the β-structure content of the Aβ42 monomer is greatly increased, and the binding energy between the monomers in the Aβ42 dimer is significantly enhanced. Additionally, our observations suggest that terahertz waves can mildly stabilize the structure of tetrameric protofibrils by enhancing the interactions among peripheral peptides. Furthermore, we also investigated the effect of the frequency of terahertz waves on the structure of Aβ42. The present study contributes to a better understanding of the impact of external fields on the biobehavior of Aβ42 peptides and may shed some light on the potential risks associated with electromagnetic field radiation.
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Affiliation(s)
- Chen Chen
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Zeng-Shuai Yan
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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Garg P, Priyadarshi N, Ambule MD, Kaur G, Kaul S, Gupta R, Sagar P, Bajaj G, Yadav B, Rishi V, Goyal B, Srivastava AK, Singhal NK. Multiepitope glycan based laser assisted fluorescent nanocomposite with dual functionality for sensing and ablation of Pseudomonas aeruginosa. NANOSCALE 2023; 15:15179-15195. [PMID: 37548288 DOI: 10.1039/d3nr02983b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) infection is becoming a severe health hazard and needs early diagnosis with high specificity. However, the non-specific binding of a biosensor is a challenge to the current bacterial detection system. For the first time, we chemically synthesized a galactose tripod (GT) as a P. aeruginosa-specific ligand. We conjugated GT to a photothermally active fluorescent nanocomposite (Au@SiO2-TCPP). P. aeruginosa can be detected using Au@SiO2-TCPP-GT, and additionally ablated as well using synergistic photothermal and photodynamic therapy. Molecular dynamics and simulation studies suggested better binding of GT (binding energy = -6.6 kcal mol-1) with P. aeruginosa lectin than that of galactose monopod (GM) (binding energy = -5.9 kcal mol-1). Furthermore, a binding study was extended to target P. aeruginosa, which has a galactose-binding carbohydrate recognition domain receptor. The colorimetric assay confirmed a limit of detection (LOD) of 104 CFU mL-1. We also looked into the photosensitizing property of Au@SiO2-TCPP-GT, which is stimulated by laser light (630 nm) and causes photoablation of bacteria by the formation of singlet oxygen in the surrounding media. The cytocompatibility of Au@SiO2-TCPP-GT was confirmed using cytotoxicity assays on mammalian cell lines. Moreover, Au@SiO2-TCPP-GT also showed non-hemolytic activity. Considering the toxicity analysis and efficacy of the synthesized glycan nanocomposites, these can be utilized for the treatment of P. aeruginosa-infected wounds. Furthermore, the current glycan nanocomposites can be used for bacterial detection and ablation of P. aeruginosa in contaminated food and water samples as well.
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Affiliation(s)
- Priyanka Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
- Department of Biotechnology, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Nitesh Priyadarshi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
| | - Mayur D Ambule
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Gurmeet Kaur
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India.
| | - Sunaina Kaul
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
- Department of Biotechnology, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Ritika Gupta
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
| | - Poonam Sagar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
| | - Geetika Bajaj
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
- Department of Biotechnology, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Binduma Yadav
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
- Regional Center for Biotechnology (RCB), Faridabad, 121001, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India.
| | - Ajay Kumar Srivastava
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Nitin Kumar Singhal
- National Agri-Food Biotechnology Institute (NABI), Sector-81, S.A.S. Nagar, Mohali, Punjab, India.
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Kaur R, Narang SS, Singh P, Goyal B. Structural and molecular insights into tacrine-benzofuran hybrid induced inhibition of amyloid-β peptide aggregation and BACE1 activity. J Biomol Struct Dyn 2023; 41:13211-13227. [PMID: 37013977 DOI: 10.1080/07391102.2023.2191722] [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: 08/05/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023]
Abstract
Amyloid-β (Aβ) aggregation and β-amyloid precursor protein cleaving enzyme 1 (BACE1) are the potential therapeutic drug targets for Alzheimer's disease (AD). A recent study highlighted that tacrine-benzofuran hybrid C1 displayed anti-aggregation activity against Aβ42 peptide and inhibit BACE1 activity. However, the inhibition mechanism of C1 against Aβ42 aggregation and BACE1 activity remains unclear. Thus, molecular dynamics (MD) simulations of Aβ42 monomer and BACE1 with and without C1 were performed to inspect the inhibitory mechanism of C1 against Aβ42 aggregation and BACE1 activity. In addition, a ligand-based virtual screening followed by MD simulations was employed to explore potent new small-molecule dual inhibitors of Aβ42 aggregation and BACE1 activity. MD simulations highlighted that C1 promotes the non aggregating helical conformation in Aβ42 and destabilizes D23-K28 salt bridge that plays a vital role in the self-aggregation of Aβ42. C1 displays a favourable binding free energy (-50.7 ± 7.3 kcal/mol) with Aβ42 monomer and preferentially binds to the central hydrophobic core (CHC) residues. MD simulations highlighted that C1 strongly interacted with the BACE1 active site (Asp32 and Asp228) and active pockets. The scrutiny of interatomic distances among key residues of BACE1 highlighted the close flap (non-active) position in BACE1 on the incorporation of C1. The MD simulations explain the observed high inhibitory activity of C1 against Aβ aggregation and BACE1 in the in vitro studies. The ligand-based virtual screening followed by MD simulations identified CHEMBL2019027 (C2) as a promising dual inhibitor of Aβ42 aggregation and BACE1 activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajdeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Pritpal Singh
- 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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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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