| Literature DB >> 27199743 |
Gesivaldo Santos1, Lisandro Diego Giraldez-Alvarez2, Marco Ávila-Rodriguez3, Francisco Capani4, Eduardo Galembeck5, Aristóteles Gôes Neto6, George E Barreto7, Bruno Andrade1.
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders. A theoretical approach of our previous experiments reporting the cytoprotective effects of the Valeriana officinalis compounds extract for PD is suggested. In addiction to considering the PD as a result of mitochondrial metabolic imbalance and oxidative stress, such as in our previous in vitro model of rotenone, in the present manuscript we added a genomic approach to evaluate the possible underlying mechanisms of the effect of the plant extract. Microarray of substantia nigra (SN) genome obtained from Allen Brain Institute was analyzed using gene set enrichment analysis to build a network of hub genes implicated in PD. Proteins transcribed from hub genes and their ligands selected by search ensemble approach algorithm were subjected to molecular docking studies, as well as 20 ns Molecular Dynamics (MD) using a Molecular Mechanic Poison/Boltzman Surface Area (MMPBSA) protocol. Our results bring a new approach to Valeriana officinalis extract, and suggest that hesperidin, and probably linarin are able to relieve effects of oxidative stress during ATP depletion due to its ability to binding SUR1. In addition, the key role of valerenic acid and apigenin is possibly related to prevent cortical hyperexcitation by inducing neuronal cells from SN to release GABA on brain stem. Thus, under hyperexcitability, oxidative stress, asphyxia and/or ATP depletion, Valeriana officinalis may trigger different mechanisms to provide neuronal cell protection.Entities:
Keywords: GABAA; Parkinson disease; SUR1; Valeriana officinalis; neuroprotection
Year: 2016 PMID: 27199743 PMCID: PMC4852538 DOI: 10.3389/fnagi.2016.00097
Source DB: PubMed Journal: Front Aging Neurosci ISSN: 1663-4365 Impact factor: 5.750
Figure 1Hierarchical clustering used to get insight about gene hub from microarray list.
Figure 2Pathway association between TH and metabolic process via ABCC8 (Kir6.2) (A). The six hub genes obtained from Allen Brain Atlas via yEd application (B).
Figure 3Docking between alpha-synuclein (SNCA) and Apigenin (green) and valerenic acid inside active site, while linarin and hesperidin appears out.
Affinity energies for docking calculations between alpha-synuclein and tyrosine hydroxylase with .
| Target | RMSD | Affinity energy (Kcal/mol) | |
|---|---|---|---|
| SNCA | Apigenin | 9.019 | −5.1 |
| Valerenic acid | 9.548 | −4.4 | |
| Valerenic acid | 0 | −7.4 | |
| TH | Apigenin | 0 | −8.9 |
| Linarin | 0 | −9.3 | |
| Hesperidin | 0 | −9.4 |
Similarity Ensemble Approach (SEA) search results for .
| Known drug | Max TC | |
|---|---|---|
| Methylpredinisolone | Acid valenenic | 0.60 |
| Norethynodrel | Acid valenenic | 0.59 |
| Androsterone | Acid valenenic | 0.52 |
| Menadione | Apigenin | 0.51 |
| Atractyloside | Hesperidin | 0.47 |
| Atractyloside | Linarin | 0.45 |
| Resveratrol | Apigenin | 0.45 |
| Menadione | Linarin | 0.42 |
Figure 4In this docking, apigenin (green), valerenic acid (yellow), hesperidin (cyan) and linarin (orange), all the molecules interacting with TH active site.
Figure 7Twenty nanoseconds Molecular Dynamics (MD) Molecular Mechanic Poison/Boltzman Surface Area (MMPBSA) for complexes between GABAA with apigenin and valerenic acid. (A) Root mean square deviation (RMSD) fluctuations for GABAA-Apigenin complex; (B) RMSD fluctuations for valerenic acid; (C) Apigenin RMSD variation; (D) valerenic acid RMSD variations; (E) hydrogen bonds fluctuations for apigenin inside GABAA active site; (F) hydrogen bonds fluctuations for valerenic acid inside GABAA active site.
Figure 8GABAA receptor docked with Flurazepan and Apigenin (yellow) and valerenic acid docked in the same site of Flurazepan (red).
Affinity energies for docking calculations between Kir and SUR1 with .
| Target | RMSD | Affinity energy (Kcal/Mol) | |
|---|---|---|---|
| SUR | Hesperidin | 0 | −6.3 |
| Linarin | 0 | −5.9 | |
| Apigenin | 0 | −5.2 | |
| Valerenic acid | 0 | −4.5 | |
| Kir | Apigenin | 0 | −6.5 |
| Valerenic acid | 0 | −5.5 |
Figure 9MMPBSA simulation results for the complex SUR1 with hesperidin and 2D interaction map. (A) RMSD fluctuations for SUR1-Hesperidin complex; (B) RMSD fluctuations for hesperidin; (C) hydrogen bonds fluctuations for hesperidin inside SUR1 active site; (D) 2D interaction map for hesperidin inside SUR1 active pocket.
Figure 6Apigenin (cyan), valerenic acid (green), hesperidin (yellow) and linarin (orange) complexed with SUR1.