In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved]
Background Alzheimer’s disease (AD) is a neurological condition that primarily affects older people. Currently available AD drugs are associated with side effects and there is a need to develop natural drugs from plants. Aquilaria is as an endangered medicinal plant genus (commonly called agarwood p...
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2024-12-01
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| author | Tewin Tencomnao Krishna Swamy V. K. D Prem Kumar Borugadda Vishwambar Vishnu Bhandare Vishal S. Patil Phaniendra Alugoju |
| author_facet | Tewin Tencomnao Krishna Swamy V. K. D Prem Kumar Borugadda Vishwambar Vishnu Bhandare Vishal S. Patil Phaniendra Alugoju |
| author_sort | Tewin Tencomnao |
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| description | Background Alzheimer’s disease (AD) is a neurological condition that primarily affects older people. Currently available AD drugs are associated with side effects and there is a need to develop natural drugs from plants. Aquilaria is as an endangered medicinal plant genus (commonly called agarwood plants) and various products of Aquilaria plant spp. including resinous heartwood, leaves, bark, and stem have been widely used in various traditional medicine systems. Research on agarwood plants is sparse and only a few previous studies demonstrated their neuroprotective properties in vitro. Owing to the presence of a plethora of secondary metabolites in agarwood plants, it is imperative not only to protect these plants but also evaluate the bioactivity of agarwood phytochemicals. Methods This study used Molsoft tools to predict the physicochemical properties of agarwood ligands, including the number of H-bond donors and acceptors, polar surface area, lipophilicity, solubility, and the molecular polar surface area and volume of agarwood ligands. Additionally, ADMET (absorption, digestion, metabolism, excretion, and toxicity) properties were predicted using ADMETlab 2.0. Computational methods such as AutoDock Vina and molecular dynamic (MD) simulations were employed for the docking of 41 selected agarwood compounds with AD-related molecular targets. Results and Conclusion According to docking data, three compounds aquilarisin (ASN), aquilarisinin (ANN), aquilarixanthone (AXN) showed highest binding affinity to selected AD targets compared to their known inhibitors. MD simulation studies revealed that, selected agarwood compounds’ protein-ligand complexes showed remarkable structural stability throughout 100ns simulation. The agarwood chemicals aquilarisin, aquilarisinin, aquilarixanthone, pillion (PLN), and agarotetrol (AGT) are consequently suggested as some of the found hits against AD targets, however, additional experimental validation is required to establish their effectiveness. |
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| institution | Kabale University |
| issn | 2046-1402 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | F1000 Research Ltd |
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| spelling | doaj-art-566abeed15a3463b99446850d08b735d2025-01-04T01:00:00ZengF1000 Research LtdF1000Research2046-14022024-12-0112175226In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved]Tewin Tencomnao0https://orcid.org/0000-0003-4177-2165Krishna Swamy V. K. D1Prem Kumar Borugadda2Vishwambar Vishnu Bhandare3Vishal S. Patil4https://orcid.org/0000-0002-1219-1962Phaniendra Alugoju5Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, 10330, ThailandPhytomedicine and Ageing laboratory, Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, Puducherry, 605014, IndiaDepartment of Computer Science, School of Engineering and Technology, Pondicherry University (A Central University), Karaikal Campus, Karaikal, Puducherry, 609605, IndiaDepartment of Microbiology, Shivaji University, Kolhapur, Maharashtra, 416004, IndiaICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, 590010, IndiaNatural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, 10330, ThailandBackground Alzheimer’s disease (AD) is a neurological condition that primarily affects older people. Currently available AD drugs are associated with side effects and there is a need to develop natural drugs from plants. Aquilaria is as an endangered medicinal plant genus (commonly called agarwood plants) and various products of Aquilaria plant spp. including resinous heartwood, leaves, bark, and stem have been widely used in various traditional medicine systems. Research on agarwood plants is sparse and only a few previous studies demonstrated their neuroprotective properties in vitro. Owing to the presence of a plethora of secondary metabolites in agarwood plants, it is imperative not only to protect these plants but also evaluate the bioactivity of agarwood phytochemicals. Methods This study used Molsoft tools to predict the physicochemical properties of agarwood ligands, including the number of H-bond donors and acceptors, polar surface area, lipophilicity, solubility, and the molecular polar surface area and volume of agarwood ligands. Additionally, ADMET (absorption, digestion, metabolism, excretion, and toxicity) properties were predicted using ADMETlab 2.0. Computational methods such as AutoDock Vina and molecular dynamic (MD) simulations were employed for the docking of 41 selected agarwood compounds with AD-related molecular targets. Results and Conclusion According to docking data, three compounds aquilarisin (ASN), aquilarisinin (ANN), aquilarixanthone (AXN) showed highest binding affinity to selected AD targets compared to their known inhibitors. MD simulation studies revealed that, selected agarwood compounds’ protein-ligand complexes showed remarkable structural stability throughout 100ns simulation. The agarwood chemicals aquilarisin, aquilarisinin, aquilarixanthone, pillion (PLN), and agarotetrol (AGT) are consequently suggested as some of the found hits against AD targets, however, additional experimental validation is required to establish their effectiveness.https://f1000research.com/articles/12-230/v2agarwood neurodegeneration docking molecular dynamic simulation. eng |
| spellingShingle | Tewin Tencomnao Krishna Swamy V. K. D Prem Kumar Borugadda Vishwambar Vishnu Bhandare Vishal S. Patil Phaniendra Alugoju In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved] F1000Research agarwood neurodegeneration docking molecular dynamic simulation. eng |
| title | In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved] |
| title_full | In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved] |
| title_fullStr | In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved] |
| title_full_unstemmed | In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved] |
| title_short | In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease [version 2; peer review: 2 approved, 1 not approved] |
| title_sort | in silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of alzheimer s disease version 2 peer review 2 approved 1 not approved |
| topic | agarwood neurodegeneration docking molecular dynamic simulation. eng |
| url | https://f1000research.com/articles/12-230/v2 |
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