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Trans-channel fluorescence learning improves high-content screening for Alzheimer’s disease therapeutics. NAT MACH INTELL 2022; 4:583-595. [DOI: 10.1038/s42256-022-00490-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Khan MI, Taehwan P, Cho Y, Scotti M, Priscila Barros de Menezes R, Husain FM, Alomar SY, Baig MH, Dong JJ. Discovery of novel acetylcholinesterase inhibitors through integration of machine learning with genetic algorithm based in silico screening approaches. Front Neurosci 2022; 16:1007389. [PMID: 36937207 PMCID: PMC10020350 DOI: 10.3389/fnins.2022.1007389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/08/2022] [Indexed: 03/06/2023] Open
Abstract
Introduction Alzheimer's disease (AD) is the most studied progressive eurodegenerative disorder, affecting 40-50 million of the global population. This progressive neurodegenerative disease is marked by gradual and irreversible declines in cognitive functions. The unavailability of therapeutic drug candidates restricting/reversing the progression of this dementia has severed the existing challenge. The development of acetylcholinesterase (AChE) inhibitors retains a great research focus for the discovery of an anti-Alzheimer drug. Materials and methods This study focused on finding AChE inhibitors by applying the machine learning (ML) predictive modeling approach, which is an integral part of the current drug discovery process. In this study, we have extensively utilized ML and other in silico approaches to search for an effective lead molecule against AChE. Result and discussion The output of this study helped us to identify some promising AChE inhibitors. The selected compounds performed well at different levels of analysis and may provide a possible pathway for the future design of potent AChE inhibitors.
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Affiliation(s)
- Mohd Imran Khan
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Park Taehwan
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Yunseong Cho
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Marcus Scotti
- Postgraduate Program in Bioactive Natural and Synthetic Products, Federal University of Paraíba, João Pessoa, Brazil
| | | | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suliman Yousef Alomar
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Mohammad Hassan Baig,
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Jae-June Dong,
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Bagri K, Kumar A, Manisha, Kumar P. Computational Studies on Acetylcholinesterase Inhibitors: From Biochemistry to Chemistry. Mini Rev Med Chem 2021; 20:1403-1435. [PMID: 31884928 DOI: 10.2174/1389557520666191224144346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
Abstract
Acetylcholinesterase inhibitors are the most promising therapeutics for Alzheimer's disease treatment as these prevent the loss of acetylcholine and slows the progression of the disease. The drugs approved for the management of Alzheimer's disease by the FDA are acetylcholinesterase inhibitors but are associated with side effects. Consistent and stringent efforts by the researchers with the help of computational methods opened new ways of developing novel molecules with good acetylcholinesterase inhibitory activity. In this manuscript, we reviewed the studies that identified the essential structural features of acetylcholinesterase inhibitors at the molecular level as well as the techniques like molecular docking, molecular dynamics, quantitative structure-activity relationship, virtual screening, and pharmacophore modelling that were used in designing these inhibitors.
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Affiliation(s)
- Kiran Bagri
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Manisha
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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Mahomoodally F, Abdallah HH, Suroowan S, Jugreet S, Zhang Y, Hu X. In silico Exploration of Bioactive Phytochemicals Against Neurodegenerative Diseases Via Inhibition of Cholinesterases. Curr Pharm Des 2021; 26:4151-4162. [PMID: 32178608 DOI: 10.2174/1381612826666200316125517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
Neurodegenerative disorders are estimated to become the second leading cause of death worldwide by 2040. Despite the widespread use of diverse allopathic drugs, these brain-associated disorders can only be partially addressed and long term treatment is often linked with dependency and other unwanted side effects. Nature, believed to be an arsenal of remedies for any illness, presents an interesting avenue for the development of novel neuroprotective agents. Interestingly, inhibition of cholinesterases, involved in the breakdown of acetylcholine in the synaptic cleft, has been proposed to be neuroprotective. This review therefore aims to provide additional insight via docking studies of previously studied compounds that have shown potent activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) in vitro. Indeed, the determination of potent plant-based ligands for this purpose through in silico methods enables the elimination of lengthy and costly traditional methods of drug discovery. Herein, a literature search was conducted to identify active phytochemicals which are cholinesterase inhibitors. Following which in silico docking methods were applied to obtain docking scores. Compound structures were extracted from online ZINC database and optimized using AM1 implemented in gaussian09 software. Noteworthy ligands against AChE highlighted in this study include: 19,20-dihydroervahanine A and 19, 20-dihydrotabernamine. Regarding BChE inhibition, the best ligands were found to be 8-Clavandurylkaempferol, Na-methylepipachysamine D; ebeiedinone; and dictyophlebine. Thus, ligand optimization between such phytochemicals and cholinesterases coupled with in vitro, in vivo studies and randomized clinical trials can lead to the development of novel drugs against neurodegenerative disorders.
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Affiliation(s)
- Fawzi Mahomoodally
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
| | - Hassan H Abdallah
- Chemistry Department, College of Education, Salahaddin University, 44002 Erbil, Iraq
| | - Shanoo Suroowan
- Department of Health Sciences, Faculty of Science, University of Mauritius, Mauritius
| | - Sharmeen Jugreet
- Department of Health Sciences, Faculty of Science, University of Mauritius, Mauritius
| | - Yansheng Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Xuebo Hu
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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Shakil S. Molecular interaction of investigational ligands with human brain acetylcholinesterase. J Cell Biochem 2019; 120:11820-11830. [PMID: 30746750 DOI: 10.1002/jcb.28461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/09/2018] [Accepted: 12/13/2018] [Indexed: 01/24/2023]
Abstract
Alzheimer's disease, a neurodegenerative disorder continues to be an area of investigation by the international researchers' fraternity. Despite all the ongoing efforts, the effective set of promising cholinesterase inhibitors available in the market for patients' use is limited. Furthermore, the currently available drugs could provide only a palliative type of treatment instead of providing a complete cure or foolproof prevention. Hence, design/discovery of fresh drug molecules as acetylcholinesterase (AChE) inhibitors still remains an urgent requirement. The drug discovery platform, MCULE in the "structure-based virtual screening" (SBVS) mode was used for high throughput ligand screening of over five million structures targeted against the AChE catalytic site. A stepwise query was made for the SBVS input. The number of hits was narrowed down in consecutive succession via varied filtration criteria as AutoDock-Vina rankings, MCULE toxicity filtration, exclusion of ligands having less than four H-bond acceptors, filtration by ΔG cutoff, rule-of-five violation and SWISS ADME profiling. This was followed by holistic analysis of all the results, thereby leading to one promising ligand. The screened out drug molecule, MCULE-5872671137-0-1 exhibited a robust interaction with the AChE catalytic site involving 20 amino acid residues, an acceptable binding free energy of -10.2 kcal/mol in addition to a favorable SWISS ADME-profie showing no harmful effects on the human body. It can be carefully stated that the molecule, MCULE-5872671137-0-1, which is chemically (3S)-N-{4-[(4-chlorophenyl)sulfanyl]phenyl}-3-hydroxypyrrolidine-1-carboxamide could function as a significant "seed" ligand for future design of potent AChE inhibitors and/or novel neuro drugs built upon the seed-scaffold.
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Affiliation(s)
- Shazi Shakil
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Ece A. Towards more effective acetylcholinesterase inhibitors: a comprehensive modelling study based on human acetylcholinesterase protein–drug complex. J Biomol Struct Dyn 2019; 38:565-572. [DOI: 10.1080/07391102.2019.1583606] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul, Turkey
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Doytchinova I, Atanasova M, Valkova I, Stavrakov G, Philipova I, Zhivkova Z, Zheleva-Dimitrova D, Konstantinov S, Dimitrov I. Novel hits for acetylcholinesterase inhibition derived by docking-based screening on ZINC database. J Enzyme Inhib Med Chem 2018; 33:768-776. [PMID: 29651876 PMCID: PMC6010092 DOI: 10.1080/14756366.2018.1458031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/23/2018] [Accepted: 03/23/2018] [Indexed: 11/08/2022] Open
Abstract
The inhibition of the enzyme acetylcholinesterase (AChE) increases the levels of the neurotransmitter acetylcholine and symptomatically improves the affected cognitive function. In the present study, we searched for novel AChE inhibitors by docking-based virtual screening of the standard lead-like set of ZINC database containing more than 6 million small molecules using GOLD software. The top 10 best-scored hits were tested in vitro for AChE affinity, neurotoxicity, GIT and BBB permeability. The main pharmacokinetic parameters like volume of distribution, free fraction in plasma, total clearance, and half-life were predicted by previously derived models. Nine of the compounds bind to the enzyme with affinities from 0.517 to 0.735 µM, eight of them are non-toxic. All hits permeate GIT and BBB and bind extensively to plasma proteins. Most of them are low-clearance compounds. In total, seven of the 10 hits are promising for further lead optimisation. These are structures with ZINC IDs: 00220177, 44455618, 66142300, 71804814, 72065926, 96007907, and 97159977.
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Affiliation(s)
- Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
- Drug Design and Development Lab, Sofia Tech Park, Sofia, Bulgaria
| | | | - Iva Valkova
- Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
- Drug Design and Development Lab, Sofia Tech Park, Sofia, Bulgaria
| | - Georgi Stavrakov
- Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irena Philipova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | | | - Ivan Dimitrov
- Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
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