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

ABSTRACT: 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.

SUBMITTER: Khanal P

PROVIDER: S-EPMC8710610 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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

Khanal Pukar P Zargari Farshid F Far Bahareh Farasati BF Kumar Dharmendra D R Mogana M Mahdi Yasir K YK Jubair Najwan K NK Saraf Shailendra K SK Bansal Parveen P Singh Ranjit R Selvaraja Malarvili M Dey Yadu Nandan YN

Frontiers in pharmacology 20211213

<b>Aim:</b> 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. <b>Methodology:</b> 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 en ...[more]

PMID: 34966281

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Project description:Orchids are commercially important flowers, comprising one of the largest families of plants. Model plants such as Arabidopsis do not contain all plant genes. In this study, several molecular biology tools were integrated to isolate the flower-specific gene promoters of Oncidium Gower Ramsey (GR). A cDNA library of reproductive tissues was constructed and a microarray was established and used to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues and the subcellular locations of the corresponding proteins were identified using fluorescent protein-fusion protein lip transient transformation, and related to their putative functions. BAC clones of the five genes, together with nine previously published flower and reproductive growth specific genes in Onc. GR, were identified and promoter regions were cloned by screening an Onc. GR BAC library. Interestingly, three of the five novel flower-abundant genes were putative trypsin inhibitor (TI) genes, OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable Arabidopsis transformation analyses. In conclusion, a combination of tools including a cDNA microarray, a BAC library, and a bombardment assay can be successfully employed to identify orchid genes and promoters. A total of 960 cDNAs derived from the Onc. GR flower cDNA library were amplified using PCR incorporating the T3 and M13 reverse universal primers. The PCR products were purified using the QIAquick PCR Purification kit (Qiagen, Germantown, MD) and eluted into 100 M-BM-5l of 0.1M-CM-^W Tris-EDTA buffer, pH 8.0. Purified PCR products were printed on GAPS II-coated slides (Corning, New York, NY) using the OmniGrid 100 microarray (Genomic Solutions, Ann Arbor, MI), and arranged into 1.8 M-CM-^W 1.8-cm arrays (spot size: 100 M-NM-<m) twice. These DNAs were cross-linked to the slide by baking the array at 80M-BM-0C for 2 h. After printing, the slides were left to dry overnight. The total RNA from leaves and flowers (25 M-NM-<g) was used for cDNA synthesis with either Cy3 or Cy5 dye molecules, using the 3DNA Expression Array Detection kit for microarrays (Array 50, version 2, Genisphere, Hatfield, PA). cDNA hybridization and washing procedures were performed according to the manufacturer's instructions. All experiments were carried out in triplicate, with repeats of each dye combination (n = 3).

Dataset Information

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

Publications

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

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