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Integration of System Biology Tools to Investigate Huperzine A as an Anti-Alzheimer Agent

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Title: Integration of System Biology Tools to Investigate Huperzine A as an Anti-Alzheimer Agent
Authors: Pukar Khanal, Farshid Zargari, Bahareh Farasati Far, Dharmendra Kumar, Mogana R, Yasir K. Mahdi, Najwan K. Jubair, Shailendra K. Saraf, Parveen Bansal, Ranjit Singh, Malarvili Selvaraja, Yadu Nandan Dey
Source: Frontiers in Pharmacology, Vol 12 (2021)
Publisher Information: Frontiers Media S.A., 2021.
Publication Year: 2021
Collection: LCC:Therapeutics. Pharmacology
Subject Terms: Alzheimer’s disease, huperzine A, system biology, donepezil, ligand–receptor interactions, Therapeutics. Pharmacology, RM1-950
More Details: Aim: The present study aimed to investigate huperzine A as an anti-Alzheimer agent based on the principle that a single compound can regulate multiple proteins and associated pathways, using system biology tools.Methodology: The simplified molecular-input line-entry system of huperzine A was retrieved from the PubChem database, and its targets were predicted using SwissTargetPrediction. These targets were matched with the proteins deposited in DisGeNET for Alzheimer disease and enriched in STRING to identify the probably regulated pathways, cellular components, biological processes, and molecular function. Furthermore, huperzine A was docked against acetylcholinesterase using AutoDock Vina, and simulations were performed with the Gromacs package to take into account the dynamics of the system and its effect on the stability and function of the ligands.Results: A total of 100 targets were predicted to be targeted by huperzine A, of which 42 were regulated at a minimum probability of 0.05. Similarly, 101 Kyoto Encyclopedia of Genes and Genomes pathways were triggered, in which neuroactive ligand–receptor interactions scored the least false discovery rate. Also, huperzine A was predicted to modulate 54 cellular components, 120 molecular functions, and 873 biological processes. Furthermore, huperzine A possessed a binding affinity of −8.7 kcal/mol with AChE and interacted within the active site of AChE via H-bonds and hydrophobic interactions.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1663-9812
Relation: https://www.frontiersin.org/articles/10.3389/fphar.2021.785964/full; https://doaj.org/toc/1663-9812
DOI: 10.3389/fphar.2021.785964
Access URL: https://doaj.org/article/b4ffcdfb1bca4b078f09270d9500cf46
Accession Number: edsdoj.b4ffcdfb1bca4b078f09270d9500cf46
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  Data: Integration of System Biology Tools to Investigate Huperzine A as an Anti-Alzheimer Agent
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  Data: <searchLink fieldCode="AR" term="%22Pukar+Khanal%22">Pukar Khanal</searchLink><br /><searchLink fieldCode="AR" term="%22Farshid+Zargari%22">Farshid Zargari</searchLink><br /><searchLink fieldCode="AR" term="%22Bahareh+Farasati+Far%22">Bahareh Farasati Far</searchLink><br /><searchLink fieldCode="AR" term="%22Dharmendra+Kumar%22">Dharmendra Kumar</searchLink><br /><searchLink fieldCode="AR" term="%22Mogana+R%22">Mogana R</searchLink><br /><searchLink fieldCode="AR" term="%22Yasir+K%2E+Mahdi%22">Yasir K. Mahdi</searchLink><br /><searchLink fieldCode="AR" term="%22Najwan+K%2E+Jubair%22">Najwan K. Jubair</searchLink><br /><searchLink fieldCode="AR" term="%22Shailendra+K%2E+Saraf%22">Shailendra K. Saraf</searchLink><br /><searchLink fieldCode="AR" term="%22Parveen+Bansal%22">Parveen Bansal</searchLink><br /><searchLink fieldCode="AR" term="%22Ranjit+Singh%22">Ranjit Singh</searchLink><br /><searchLink fieldCode="AR" term="%22Malarvili+Selvaraja%22">Malarvili Selvaraja</searchLink><br /><searchLink fieldCode="AR" term="%22Yadu+Nandan+Dey%22">Yadu Nandan Dey</searchLink>
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  Data: Frontiers in Pharmacology, Vol 12 (2021)
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  Data: <searchLink fieldCode="DE" term="%22Alzheimer%27s+disease%22">Alzheimer’s disease</searchLink><br /><searchLink fieldCode="DE" term="%22huperzine+A%22">huperzine A</searchLink><br /><searchLink fieldCode="DE" term="%22system+biology%22">system biology</searchLink><br /><searchLink fieldCode="DE" term="%22donepezil%22">donepezil</searchLink><br /><searchLink fieldCode="DE" term="%22ligand–receptor+interactions%22">ligand–receptor interactions</searchLink><br /><searchLink fieldCode="DE" term="%22Therapeutics%2E+Pharmacology%22">Therapeutics. Pharmacology</searchLink><br /><searchLink fieldCode="DE" term="%22RM1-950%22">RM1-950</searchLink>
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  Data: Aim: The present study aimed to investigate huperzine A as an anti-Alzheimer agent based on the principle that a single compound can regulate multiple proteins and associated pathways, using system biology tools.Methodology: The simplified molecular-input line-entry system of huperzine A was retrieved from the PubChem database, and its targets were predicted using SwissTargetPrediction. These targets were matched with the proteins deposited in DisGeNET for Alzheimer disease and enriched in STRING to identify the probably regulated pathways, cellular components, biological processes, and molecular function. Furthermore, huperzine A was docked against acetylcholinesterase using AutoDock Vina, and simulations were performed with the Gromacs package to take into account the dynamics of the system and its effect on the stability and function of the ligands.Results: A total of 100 targets were predicted to be targeted by huperzine A, of which 42 were regulated at a minimum probability of 0.05. Similarly, 101 Kyoto Encyclopedia of Genes and Genomes pathways were triggered, in which neuroactive ligand–receptor interactions scored the least false discovery rate. Also, huperzine A was predicted to modulate 54 cellular components, 120 molecular functions, and 873 biological processes. Furthermore, huperzine A possessed a binding affinity of −8.7 kcal/mol with AChE and interacted within the active site of AChE via H-bonds and hydrophobic interactions.
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  Data: https://www.frontiersin.org/articles/10.3389/fphar.2021.785964/full; https://doaj.org/toc/1663-9812
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