scholarly journals Bioactive Flavonoids from the Stem Bark of Cordia dichotoma Forst.: Identification, Docking and ADMET Studies

2021 ◽  
Author(s):  
Nazim Hussain ◽  
Bibhuti Bhushan Kakoti ◽  
Mithun Rudrapal ◽  
Khomendra Kumar Sarwa ◽  
Ismail Celik ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Mass Spectroscopy ◽  
Stem Bark ◽  
Antidiabetic Activity ◽  
Bark Extract ◽  
Computational Studies ◽  
Autodock Vina ◽  
Online Tool ◽  
Alpha Glucosidase

Cordia dichotoma Forst. (F. Boraginaceae) has been traditionally used for the management of a variety of human ailments. In our earlier work, the antidiabetic activity of methanolic bark extract of C. dichotoma (MECD) has been reported. In this paper, two flavonoid molecules were isolated (by column chromatography) and identified (by IR, NMR and Mass spectroscopy/spectrometry) from the MECD with an aim to investigate their antidiabetic effectiveness. Molecular docking and ADMET studies were carried out using AutoDock Vina software and Swiss ADME online tool, respectively. The isolated flavonoids were identified as 3,5,7,3’,4’-tetrahydroxy-4-methoxyflavanone-3-O-L-rhamnopyranoside and 5,7,3’-trihydroxy-4-methoxyflavanone-7-O-L-rhamnopyranoside (quercitrin). Docking and ADMET studies revealed the promising binding affinity of flavonoid molecules for human lysosomal alpha-glucosidase and human pancreatic alpha-amylase with acceptable ADMET properties. Based on computational studies, our study reports the antidiabetic potential of the isolated flavonoids with predictive pharmacokinetics profile.

scholarly journals Bioactive Antidiabetic Flavonoids from the Stem Bark of Cordia dichotoma Forst.: Identification, Docking and ADMET Studies

Molbank ◽  
10.3390/m1234 ◽  
2021 ◽  
Vol 2021 (2) ◽  
pp. M1234
Author(s):  
Nazim Hussain ◽  
Bibhuti Bhushan Kakoti ◽  
Mithun Rudrapal ◽  
Khomendra Kumar Sarwa ◽  
Ismail Celik ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Mass Spectroscopy ◽  
Column Chromatography ◽  
Stem Bark ◽  
Antidiabetic Activity ◽  
Bark Extract ◽  
Computational Studies ◽  
Autodock Vina ◽  
Online Tool

Cordia dichotoma Forst. (F. Boraginaceae) has been traditionally used for the management of a variety of human ailments. In our earlier work, the antidiabetic activity of methanolic bark extract of C. dichotoma (MECD) has been reported. In this paper, two flavonoid molecules were isolated (by column chromatography) and identified (by IR, NMR and mass spectroscopy/spectrometry) from the MECD with an aim to investigate their antidiabetic effectiveness. Molecular docking and ADMET studies were carried out using AutoDock Vina software and Swiss ADME online tool, respectively. The isolated flavonoids were identified as 3,5,7,3′,4′-tetrahydroxy-4-methoxyflavone-3-O-L-rhamnopyranoside and 5,7,3′-trihydroxy-4-methoxyflavone-7-O-L-rhamnopyranoside (quercitrin). Docking and ADMET studies revealed the promising binding affinity of flavonoid molecules for human lysosomal α-glucosidase and human pancreatic α-amylase with acceptable ADMET properties. Based on computational studies, our study reports the antidiabetic potential of the isolated flavonoids with predictive pharmacokinetics profile.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Inhibitory Effect of the Stem Bark Extracts of Albizia chevalieri Harms on the Activity of Alpha-glucosidase Obtained from Aspergillus niger

2019 ◽  
pp. 1-10
Author(s):  
Abdulhafiz Damilola Oso ◽  
Idris Bello ◽  
Yusuf Sa’idu ◽  
Onu Andrew
Keyword(s):  
Ethyl Acetate ◽  
Competitive Inhibition ◽  
Stem Bark ◽  
Inhibitory Effect ◽  
Acetate Buffer ◽  
Bark Extract ◽  
Methanol Extracts ◽  
Glucosidase Activity ◽  
Alpha Glucosidase

The aim of the current study is to evaluate the inhibition of α-glucosidase activity by stem bark extract of Albizia chevalieri. The activity of alpha glucosidase was assayed in vitro using 50 mM acetate buffer pH 6.0 (prepared from acetic acid and sodium acetate) and various concentration of maltose (0.5 mM to 10 mM). Five test tubes, labeled TA – TE, each containing 1.5 ml of acetate buffer, 0.5 ml of alpha glucosidase and 0.5 ml of a known concentration of plant extract and control tubes (CA – CE) were assessed for Alpha glucosidase activity. The results showed that hexane, ethyl acetate and methanol extracts inhibited α-glucosidase activity. The results further indicated that the extracts act by competitive inhibition with inhibition constant of 232 mg/ml, 157 mg/ml and 67 mg/ml for hexane, ethyl acetate and methanol extracts, respectively. The value for the inhibition constants shows that there is a strong binding of the enzyme to the inhibitor as the polarity of solvent increases. The inhibitory activity of Albizia chevalieri may be due one or more of the phytochemicals present in the extracts.

scholarly journals A COMPARATIVE STUDY OF STEREOCHEMICAL EFFECTS OF ANTI-PROSTATE AGENTS BY MOLECULAR DOCKING

2018 ◽  
Vol 11 (14) ◽  
pp. 76 ◽  
Author(s):  
Oluwaseun S Osanyinpeju ◽  
Roqia Bashary ◽  
Amit Mittal ◽  
Manish Vyas ◽  
Surendra Kumar Nayak ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Docking ◽  
Comparative Study ◽  
Binding Affinity ◽  
Energy Minimization ◽  
Receptor Protein ◽  
Autodock Vina ◽  
Androgen Receptor Protein ◽  
The Right ◽  
3D Software

Objective: A comparative study of anti-prostate agents to investigate the stereochemical influences on binding affinity by molecular docking.Methods: Structures of enantiomers (R and S stereoisomers) for known anti-prostate cancer (PCa) agents were drawn using ChemBioDraw 2D software. Thereafter, they were converted to 3D structures using the ChemBioDraw 3D software in which they were subjected to energy minimization using the MM2 method and then saved as PDB extension files which can be accessed using the ADT interface. AutoDock Vina (ADT) 1.5.6 software version was used for molecular docking study.Results: A total of 12 different anti-PCa agents were selected and drawn including well-known drug R-bicalutamide. All molecules showed the binding affinity with respect to the nature of stereochemistry. R-stereoisomers showed better interaction as well as binding affinity toward 1z95 (mutated androgen receptor protein involved in the progression of PCa) whereas their S-stereoisomers were found inferior in comparison.Conclusion: This study showed that CB1-R and R-bicalutamide (with R-stereochemistry) were better in binding affinity comparative to their counterpart CB1-S and S-Bicalutamide (with S-stereochemistry). All the selected anti-PCa agents were showing the effect of stereochemical center; therefore, we must choose the right kind of stereochemistry while planning to develop the newer anti-PCa agents.

scholarly journals IDENTIFICATION OF NOVEL 5-STYRYL-1,2,4-OXADIAZOLE/TRIAZOLE DERIVATIVES AS THE POTENTIAL ANTI-ANDROGENS THROUGH MOLECULAR DOCKING STUDY

2016 ◽  
Vol 8 (10) ◽  
pp. 72 ◽  
Author(s):  
Paranjeet Kaur ◽  
Gopal L. Khatik
Keyword(s):  
Molecular Docking ◽  
Androgen Receptor ◽  
Binding Affinity ◽  
Docking Study ◽  
Molecular Structures ◽  
The Novel ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Triazole Derivatives ◽  
Better Than

<p class="Default"><strong>Objective: </strong>To identify the novel and simple bioactive antiandrogens, that can overcome to side effects as well as drug resistance.</p><p class="Default"><strong>Methods: </strong>The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes. The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by MM2 method and converted to pdb extension file which is readable at the ADT interface.</p><p class="Default"><strong>Results: </strong>Total ten compounds from both series were shown better binding affinity than <em>R</em>-bicalutamide including oxadiazole and triazole series. Among these pk42 and pk46 were studied in-depth which showed best binding affinity to the androgen receptor. The <em>cis</em>-isomers were found better than their <em>trans</em>-isomer.</p><p><strong>Conclusion: </strong>Novel 5-styryl-1,2,4-oxadiazole/triazole derivatives were studied through molecular modeling using Autodock Vina. The potent compounds which showed better binding affinity than <em>R</em>-bicalutamide like pk24 and 46 were further analyzed for their interactions. The conformational effect also found significant in binding to the androgen receptor.</p>

scholarly journals IDENTIFICATION OF POSSIBLE MOLECULAR TARGETS OF POTENTIAL ANTI-PARKINSON DRUGS BY PREDICTING THEIR BINDING AFFINITIES USING MOLECULAR DOCKING TECHNIQUE

2018 ◽  
Vol 11 (14) ◽  
pp. 28
Author(s):  
Maguemga Homsi Chanceline Dorice ◽  
Navneet Khurana ◽  
Neha Sharma ◽  
Gopal L Khatik
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Energy Minimization ◽  
Molecular Targets ◽  
Mechanistic Study ◽  
Binding Affinities ◽  
Autodock Vina ◽  
3D Structures ◽  
Mao B ◽  
3D Software

Objective: Mechanistic study of newly reported anti-Parkinson agents by molecular docking to predict possible target.Methods: Structures of newer drugs known anti-Parkinson agents were drawn using ChemBioDraw 2D software. Thereafter, they were converted to 3D structures using ChemBioDraw 3D software in which they were subjected to energy minimization using the MM2 method and then saved as PDB extension files, which can be accessed using the AutoDock Vina (ADT) interface. ADT 1.5.6 software version was used for molecular docking study.Results: Various molecular targets were selected (D2/D3, D2, A2A, and MAO-B) and studied for Pardoprunox, Istradefylline, Rasagiline, and Bromocriptine. Pardoprunox, Istradefylline, and Bromocriptine had more affinity with their corresponding receptor with −6.9, −8.5, and −9.4 kcal/mol binding affinity, respectively, except Rasagiline, who has less affinity with its corresponding receptor (−6.4kcal/mol) and shown better affinity with 3pbl receptor (−6.7 kcal/mol).Conclusion: Pardoprunox, Istradefylline, and Bromocriptine were found to act on D2/D3 (3pbl), A2A (3pwh), and D2 (4yyw), respectively, whereas Rasagiline found to be act on D2/D3 (3pbl) receptor. The results help in prediction of mechanism and interaction to various Parkinson’s disease targets.

scholarly journals Evaluation of the Antioxidant, Antidiabetic, and Antiplasmodial Activities of Xanthones Isolated from Garcinia forbesii and Their In Silico Studies

Biomedicines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1380
Author(s):  
Johanis Wairata ◽  
Edwin Risky Sukandar ◽  
Arif Fadlan ◽  
Adi Setyo Purnomo ◽  
Muhammad Taher ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Molecular Docking ◽  
In Silico ◽  
Stem Bark ◽  
Docking Studies ◽  
Antidiabetic Activity ◽  
In Silico Studies ◽  
Dehydrogenase Enzyme ◽  
Ch2cl2 Extract

This study aimed to isolate xanthones from Garcinia forbesii and evaluated their activity in vitro and in silico. The isolated compounds were evaluated for their antioxidant activity by DPPH, ABTS and FRAP methods. The antidiabetic activity was performed against α-glucosidase and α-amylase enzymes. The antiplasmodial activity was evaluated using Plasmodium falciparum strain 3D7 sensitive to chloroquine. Molecular docking analysis on the human lysosomal acid-alpha-glucosidase enzyme (5NN8) and P. falciparum lactate dehydrogenase enzyme (1CET) and prediction of ADMET for the active compound, were also studied. For the first time, lichexanthone (1), subelliptenone H (2), 12b-hydroxy-des-D-garcigerrin A (3), garciniaxanthone B (4) and garcigerin A (5) were isolated from the CH2Cl2 extract of the stem bark of G. forbesii. Four xanthones (Compounds 2–5) showed strong antioxidant activity. In vitro α-glucosidase test showed that Compounds 2 and 5 were more active than the others, while Compound 4 was the strongest against α-amylase enzymes. In vitro antiplasmodial evaluation revealed that Compounds 2 and 3 showed inhibitory activity on P. falciparum. Molecular docking studies confirmed in vitro activity. ADMET predictions suggested that Compounds 1–5 were potential candidates for oral drugs. The isolated 2–5 can be used as promising phytotherapy in antidiabetic and antiplasmodial treatment.

scholarly journals Computational analysis of the interaction of limonene with the fat mass and obesity-associated protein

2021 ◽  
Vol 8 (1) ◽  
pp. 154-160
Author(s):  
Muhammad Zeeshan Ahmed ◽  
Shahzeb Hameed ◽  
Mazhar Ali ◽  
Ammad Zaheer
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Fat Mass ◽  
Computational Analysis ◽  
Physical Interaction ◽  
Autodock Vina ◽  
Inhibitory Interaction ◽  
Protein Association ◽  
Discovery Studio ◽  
Bioinformatic Tool

This study aimed to predict the binding affinity, orientation, and physical interaction between limonene and fat mass and obesity-associated protein. The mechanism of limonene and protein association was explored by molecular docking, a bioinformatic tool. The results of association were compared with the reported results of the anti-obesity drug such as orlistat and with the flavonoids. AutoDock Vina tools were used for the molecular docking of limonene with fat mass and obesity-associated protein. PyMol and Discovery Studio Visualizer were used to visualize the results of this docking. The binding affinity of limonene was higher (Least negative G) than the orlistat and flavonoids such as Daidzein, Exemestane, Kaempherol, Letrozole, And Rutin. It is conducted in this study that the Limonene can alleviate obesity by making an interaction with the fat mass and obesity-associated protein. This inhibitory interaction was greater as compared to other reported phytochemicals and drugs.

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