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Kaur A, Goyal B. Identification of new pentapeptides as potential inhibitors of amyloid-β 42 aggregation using virtual screening and molecular dynamics simulations. J Mol Graph Model 2023; 124:108558. [PMID: 37390790 DOI: 10.1016/j.jmgm.2023.108558] [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: 05/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease mainly characterized by extracellular accumulation of amyloid-β (Aβ) peptide. Previous studies reported pentapeptide RIIGL as an effective inhibitor of Aβ aggregation and neurotoxicity induced by Aβ aggregates. In this work, a library of 912 pentapeptides based on RIIGL has been designed and assessed for their efficacy to inhibit Aβ42 aggregation using computational techniques. The top hit pentapeptides revealed by molecular docking were further assessed for their binding affinity with Aβ42 monomer using MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method. The MM-PBSA analysis identified RLAPV, RVVPI, and RIAPA, which bind to Aβ42 monomer with a higher binding affinity -55.80, -46.32, and -44.26 kcal/mol, respectively, as compared to RIIGL (ΔGbinding = -41.29 kcal/mol). The residue-wise binding free energy predicted hydrophobic contacts between Aβ42 monomer and pentapeptides. The secondary structure analysis of the conformational ensembles generated by molecular dynamics (MD) depicted remarkably enhanced sampling of helical and no β-sheet conformations in Aβ42 monomer on the incorporation of RVVPI and RIAPA. Notably, RVVPI and RIAPA destabilized the D23-K28 salt bridge in Aβ42 monomer, which plays a crucial role in Aβ42 oligomer stability and fibril formation. The MD simulations highlighted that the incorporation of proline and arginine in pentapeptides contributed to their strong binding with Aβ42 monomer. Furthermore, RVVPI and RIAPA prevented conformational conversion of Aβ42 monomer to aggregation-prone structures, which, in turn, resulted in a lower aggregation tendency of Aβ42 monomer.
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Affiliation(s)
- Apneet Kaur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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Luo K, Chen J, Li H, Wu D, Du Y, Zhao S, Liu T, Li L, Dai Z, Li Y, Zhao Y, Tang L, Fu X. Design, synthesis and biological evaluation of new multi-target scutellarein hybrids for treatment of Alzheimer's disease. Bioorg Chem 2023; 138:106596. [PMID: 37186997 DOI: 10.1016/j.bioorg.2023.106596] [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: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
Scutellarein hybrids were designed, synthesized and evaluated as multifunctional therapeutic agents for the treatment of Alzheimer's disease (AD). Compounds 11a-i, containing a 2-hydroxymethyl-3,5,6-trimethylpyrazine fragment at the 7-position of scutellarein, were found to have balanced and effective multi-target potencies against AD. Among them, compound 11e exhibited the most potent inhibition of electric eel and human acetylcholinesterase enzymes with IC50 values of 6.72 ± 0.09 and 8.91 ± 0.08 μM, respectively. In addition, compound 11e displayed not only excellent inhibition of self- and Cu2+-induced Aβ1-42 aggregation (91.85% and 85.62%, respectively) but also induced disassembly of self- and Cu2+-induced Aβ fibrils (84.54% and 83.49% disaggregation, respectively). Moreover, 11e significantly reduced tau protein hyperphosphorylation induced by Aβ25-35, and also exhibited good inhibition of platelet aggregation. A neuroprotective assay demonstrated that pre-treatment of PC12 cells with 11e significantly decreased lactate dehydrogenase levels, increased cell viability, enhanced expression of relevant apoptotic proteins (Bcl-2, Bax and caspase-3) and inhibited RSL3-induced PC12 cell ferroptosis. Furthermore, hCMEC/D3 and hPepT1-MDCK cell line permeability assays indicated that 11e would have optimal blood-brain barrier and intestinal absorption characteristics. In addition, in vivo studies revealed that compound 11e significantly attenuated learning and memory impairment in an AD mice model. Toxicity experiments with the compound did not reveal any safety concerns. Notably, 11e significantly reduced β-amyloid precursor protein (APP) and β-site APP cleaving enzyme-1 (BACE-1) protein expression in brain tissue of scopolamine-treated mice. Taken together, these outstanding properties qualified compound 11e as a promising multi-target candidate for AD therapy, worthy of further studies.
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Affiliation(s)
- Keke Luo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Jiao Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Hui Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Dirong Wu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Yuanjiang Du
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Shanshan Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550025, China
| | - Ting Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China
| | - Li Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Zeqin Dai
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Yongjun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Yonglong Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China
| | - Lei Tang
- State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550025, China.
| | - Xiaozhong Fu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Pharmacy, Guizhou Medical University, Guiyang 550004, China; National Engineering Research Center of Miao's Medicines & Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guiyang 550004, Guizhou, China.
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Liu F, Wang W, Xuan Z, Jiang L, Chen B, Dong Q, Zhao F, Cui W, Li L, Lu F. Fast green FCF inhibits Aβ fibrillogenesis, disintegrates mature fibrils, reduces the cytotoxicity, and attenuates Aβ-induced cognitive impairment in mice. Int J Biol Macromol 2020; 170:33-41. [PMID: 33352157 DOI: 10.1016/j.ijbiomac.2020.12.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022]
Abstract
Fast green FCF (FGF) is often used in foods, pharmaceuticals, and cosmetics. However, little is known about the interactions of FGF with amyloid-β protein (Aβ) associated with Alzheimer's disease. In this study, the inhibitory effects of FGF on Aβ fibrillogenesis, the disruption of preformed Aβ fibrils, the reduction of Aβ-induced cytotoxicity, and the attenuation of Aβ-induced learning and memory impairments in mice were investigated. FGF significantly inhibited Aβ fibrillogenesis and disintegrated the mature fibrils as evidenced by thioflavin T fluorescence and atomic force microscopy studies. Co-incubation of Aβ with FGF greatly reduced Aβ-induced cytotoxicity in vitro. Moreover, FGF showed a protective effect against cognitive impairment in Aβ-treated mice. Molecular dynamics simulations further showed that FGF could synergistically interact with the Aβ17-42 pentamer via electrostatic interactions, hydrogen bonds and π-π interactions, which reduced the β-sheet content, and disordered random coils and bend structures of the Aβ17-42 pentamer. This study offers a comprehensive understanding of the inhibitory effects of FGF against Aβ neurotoxicity, which is critical for the search of effective food additives that can combat amyloid-associated disease.
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Affiliation(s)
- Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Wenjuan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhenquan Xuan
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Luying Jiang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Beibei Chen
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Qinchen Dong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of 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, Ningbo 315211, China
| | - Li Li
- College of Marine and Environmental Science, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
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Iraji A, Khoshneviszadeh M, Firuzi O, Khoshneviszadeh M, Edraki N. Novel small molecule therapeutic agents for Alzheimer disease: Focusing on BACE1 and multi-target directed ligands. Bioorg Chem 2020; 97:103649. [PMID: 32101780 DOI: 10.1016/j.bioorg.2020.103649] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/05/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that effects 50 million people worldwide. In this review, AD pathology and the development of novel therapeutic agents targeting AD were fully discussed. In particular, common approaches to prevent Aβ production and/or accumulation in the brain including α-secretase activators, specific γ-secretase modulators and small molecules BACE1 inhibitors were reviewed. Additionally, natural-origin bioactive compounds that provide AD therapeutic advances have been introduced. Considering AD is a multifactorial disease, the therapeutic potential of diverse multi target-directed ligands (MTDLs) that combine the efficacy of cholinesterase (ChE) inhibitors, MAO (monoamine oxidase) inhibitors, BACE1 inhibitors, phosphodiesterase 4D (PDE4D) inhibitors, for the treatment of AD are also reviewed. This article also highlights descriptions on the regulator of serotonin receptor (5-HT), metal chelators, anti-aggregants, antioxidants and neuroprotective agents targeting AD. Finally, current computational methods for evaluating the structure-activity relationships (SAR) and virtual screening (VS) of AD drugs are discussed and evaluated.
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Affiliation(s)
- Aida Iraji
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsima Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Liu F, Ma Z, Sang J, Lu F. Edaravone inhibits the conformational transition of amyloid-β42: insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:2377-2388. [PMID: 31234720 DOI: 10.1080/07391102.2019.1632225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method to address the issue. MD simulations confirmed that edaravone inhibits the conformational transition of the Aβ42 monomer in a dose-dependent manner. It was found that the direct interactions between edaravone and Aβ42 are responsible for its inhibiting effects. The analysis of binding free energy using the MM-PBSA method demonstrated that the nonpolar interactions provide favourable contributions (about -71.7 kcal/mol). Conversely, the polar interactions are unfavourable for the binding process. A total of 14 residues were identified as greatly contributing to the binding free energy between edaravone and the Aβ42 monomer. In addition, the intra-peptide hydrophobic interactions were weakened and the salt bridge D23-K28 was interrupted by edaravone. Therefore, the conformational transition was inhibited. Our studies provide molecular-level insights into how edaravone molecules inhibit the conformational transition of the Aβ42 monomer, which may be useful for designing amyloid inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin, PR China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Zheng Ma
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Jingcheng Sang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin, PR China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
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