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Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes

OBJECTIVE: The main aim of this scientific report was to investigate a series of phytochemicals in silico and the pharmacology of four plants found at higher altitude in the ginger family, Zingiberaceae (incl. Costaceae) from North-East India, particularly Sikkim. First, the goal was to determine th...

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Autores principales: Usha, Talambedu, Pradhan, Sushen, Goyal, Arvind Kumar, Dhivya, Shanmugarajan, Kumar, H. P. Prashanth, Singh, Manoj Kumar, Joshi, Neelu, Basistha, Bharat Chandra, Murthy, K. R. Siddalinga, Selvaraj, Saravanakumar, Middha, Sushil Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Medknow Publications & Media Pvt Ltd 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669121/
https://www.ncbi.nlm.nih.gov/pubmed/29142438
http://dx.doi.org/10.4103/pm.pm_82_17
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author Usha, Talambedu
Pradhan, Sushen
Goyal, Arvind Kumar
Dhivya, Shanmugarajan
Kumar, H. P. Prashanth
Singh, Manoj Kumar
Joshi, Neelu
Basistha, Bharat Chandra
Murthy, K. R. Siddalinga
Selvaraj, Saravanakumar
Middha, Sushil Kumar
author_facet Usha, Talambedu
Pradhan, Sushen
Goyal, Arvind Kumar
Dhivya, Shanmugarajan
Kumar, H. P. Prashanth
Singh, Manoj Kumar
Joshi, Neelu
Basistha, Bharat Chandra
Murthy, K. R. Siddalinga
Selvaraj, Saravanakumar
Middha, Sushil Kumar
author_sort Usha, Talambedu
collection PubMed
description OBJECTIVE: The main aim of this scientific report was to investigate a series of phytochemicals in silico and the pharmacology of four plants found at higher altitude in the ginger family, Zingiberaceae (incl. Costaceae) from North-East India, particularly Sikkim. First, the goal was to determine the biological activities of the four herbs (used under Zingiberaceae family) using antioxidant assays to identify the best species. Second, previously reported compounds in litero were subsequently screened for their anticancerous activities using in silico methods. MATERIALS AND METHODS: Using the methanolic extracts of herbs, quantitative detection of phytochemicals such as total phenols and total flavonoids was detected, and the free radical scavenging activity was also studied using 2,2-diphenyl-1-picryl-hydrazyl (DPPH) assay. Docking process was studied, using Discovery Studio version 3.5, to identify suitable molecules at the protein-binding sites through annealing and genetic simulation algorithms. Grids centered on active sites were obtained with spacing of 54 × 55 × 56, and 0.503 grid spacing was calculated. The methods adopted and used in this study were comparisons of Global and Local Search Methods to determine the parameters such as maximum number of 250,000 energy evaluations as well as generations of 27,000, followed by mutation and crossover rates of 0.02 and 0.80. The number of docking runs was set to 10. Molecular dynamics study was done to check the stability of the complex. RESULTS: Among all the genus of Zingiberaceae family investigated in this study, Curcuma angustifolia and Hedychium sp. exhibited the highest 537 ± 12.45; 292 ± 9.16 mg gallic acid equivalent/g total polyphenols and 38 ± 1.54; 75 ± 6.75 mg quercetin equivalent/g flavonoids, respectively. Depending on the concentration, the Hedychium sp. extract exerted the highest scavenging activity on DPPH radical (IC(50) 36.4 μg/mL). In silico result demonstrated that the synergetic effects of β-phellandrene with other compounds might be responsible for its anticancerous activity. β-phellandrene and farnesene epoxide showed bonding with Leu(298), Ala(302), Met(336), Leu(339), Leu(343), Phe(356), Ala(302), Glu(305), Met(340), Leu(343), Arg(346), Phe(356), Ile(373), Ile(376), Leu(380), His(475), Leu(476), and Leu(491). CONCLUSION: Based on the current available literature, this is the first study to understand the interaction of compounds found in the rhizomes of Zingiberaceae family. SUMMARY: The aqueous methanolic extract of Zingiberaceae family Curcuma angustifolia and Hedychium sp. has potent antioxidant activity as assessed by 2,2-diphenyl-1-picryl-hydrazyl assays. Hedychium sp. is understood to possess more active compounds than other varieties. In silico studies indicated synergetic effects of β-phellandrene and other compounds for its anticancerous activity. [Image: see text] Abbreviations used: CADD: Computer-aided drug designing; ROS: Reactive oxygen species; ADMET: Absorption, distribution, metabolism, and excretion-toxicity; FeCl(3): Ferric chloride; DPPH: 2,2-diphenyl-1-picryl-hydrazyl; NaNO(2): Sodium nitrite; TCA: Trichloroacetic acid; K(2)HPO(4): Di-potassium hydrogen phosphate; H(2)O(2): Hydrogen peroxide; KH(2)PO(4): Potassium di-hydrogen phosphate, K(2)Fe (CN)(6): Potassium ferricyanide; KOH: Potassium hydroxide; NaOH: Sodium hydroxide; Na(2)CO(3): Sodium carbonate; CH(3)COONa: Sodium acetate; AlCl(3): Aluminum chloride.
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spelling pubmed-56691212017-11-15 Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes Usha, Talambedu Pradhan, Sushen Goyal, Arvind Kumar Dhivya, Shanmugarajan Kumar, H. P. Prashanth Singh, Manoj Kumar Joshi, Neelu Basistha, Bharat Chandra Murthy, K. R. Siddalinga Selvaraj, Saravanakumar Middha, Sushil Kumar Pharmacogn Mag Original Article OBJECTIVE: The main aim of this scientific report was to investigate a series of phytochemicals in silico and the pharmacology of four plants found at higher altitude in the ginger family, Zingiberaceae (incl. Costaceae) from North-East India, particularly Sikkim. First, the goal was to determine the biological activities of the four herbs (used under Zingiberaceae family) using antioxidant assays to identify the best species. Second, previously reported compounds in litero were subsequently screened for their anticancerous activities using in silico methods. MATERIALS AND METHODS: Using the methanolic extracts of herbs, quantitative detection of phytochemicals such as total phenols and total flavonoids was detected, and the free radical scavenging activity was also studied using 2,2-diphenyl-1-picryl-hydrazyl (DPPH) assay. Docking process was studied, using Discovery Studio version 3.5, to identify suitable molecules at the protein-binding sites through annealing and genetic simulation algorithms. Grids centered on active sites were obtained with spacing of 54 × 55 × 56, and 0.503 grid spacing was calculated. The methods adopted and used in this study were comparisons of Global and Local Search Methods to determine the parameters such as maximum number of 250,000 energy evaluations as well as generations of 27,000, followed by mutation and crossover rates of 0.02 and 0.80. The number of docking runs was set to 10. Molecular dynamics study was done to check the stability of the complex. RESULTS: Among all the genus of Zingiberaceae family investigated in this study, Curcuma angustifolia and Hedychium sp. exhibited the highest 537 ± 12.45; 292 ± 9.16 mg gallic acid equivalent/g total polyphenols and 38 ± 1.54; 75 ± 6.75 mg quercetin equivalent/g flavonoids, respectively. Depending on the concentration, the Hedychium sp. extract exerted the highest scavenging activity on DPPH radical (IC(50) 36.4 μg/mL). In silico result demonstrated that the synergetic effects of β-phellandrene with other compounds might be responsible for its anticancerous activity. β-phellandrene and farnesene epoxide showed bonding with Leu(298), Ala(302), Met(336), Leu(339), Leu(343), Phe(356), Ala(302), Glu(305), Met(340), Leu(343), Arg(346), Phe(356), Ile(373), Ile(376), Leu(380), His(475), Leu(476), and Leu(491). CONCLUSION: Based on the current available literature, this is the first study to understand the interaction of compounds found in the rhizomes of Zingiberaceae family. SUMMARY: The aqueous methanolic extract of Zingiberaceae family Curcuma angustifolia and Hedychium sp. has potent antioxidant activity as assessed by 2,2-diphenyl-1-picryl-hydrazyl assays. Hedychium sp. is understood to possess more active compounds than other varieties. In silico studies indicated synergetic effects of β-phellandrene and other compounds for its anticancerous activity. [Image: see text] Abbreviations used: CADD: Computer-aided drug designing; ROS: Reactive oxygen species; ADMET: Absorption, distribution, metabolism, and excretion-toxicity; FeCl(3): Ferric chloride; DPPH: 2,2-diphenyl-1-picryl-hydrazyl; NaNO(2): Sodium nitrite; TCA: Trichloroacetic acid; K(2)HPO(4): Di-potassium hydrogen phosphate; H(2)O(2): Hydrogen peroxide; KH(2)PO(4): Potassium di-hydrogen phosphate, K(2)Fe (CN)(6): Potassium ferricyanide; KOH: Potassium hydroxide; NaOH: Sodium hydroxide; Na(2)CO(3): Sodium carbonate; CH(3)COONa: Sodium acetate; AlCl(3): Aluminum chloride. Medknow Publications & Media Pvt Ltd 2017-10 2017-10-11 /pmc/articles/PMC5669121/ /pubmed/29142438 http://dx.doi.org/10.4103/pm.pm_82_17 Text en Copyright: © 2017 Pharmacognosy Magazine http://creativecommons.org/licenses/by-nc-sa/3.0 This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as the author is credited and the new creations are licensed under the identical terms.
spellingShingle Original Article
Usha, Talambedu
Pradhan, Sushen
Goyal, Arvind Kumar
Dhivya, Shanmugarajan
Kumar, H. P. Prashanth
Singh, Manoj Kumar
Joshi, Neelu
Basistha, Bharat Chandra
Murthy, K. R. Siddalinga
Selvaraj, Saravanakumar
Middha, Sushil Kumar
Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes
title Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes
title_full Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes
title_fullStr Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes
title_full_unstemmed Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes
title_short Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes
title_sort molecular simulation-based combinatorial modeling and antioxidant activities of zingiberaceae family rhizomes
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669121/
https://www.ncbi.nlm.nih.gov/pubmed/29142438
http://dx.doi.org/10.4103/pm.pm_82_17
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