Molecular Docking, Drug-Likeness and ADMET Analysis, Application of Density Functional Theory (DFT) and Molecular Dynamics (MD) Simulation to the Phytochemicals from Withania Somnifera as a Potential Antagonist of Estrogen Receptor Alpha (ER-α)

2020 ◽  
Vol 16 ◽  
Author(s):  
Alamgir Hossain
Keyword(s):  
Breast Cancer ◽  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Estrogen Receptor ◽  
Molecular Docking ◽  
Density Functional ◽  
Estrogen Receptor Alpha ◽  
Md Simulation ◽  
Withania Somnifera ◽  
Functional Theory

Introduction: Breast cancer is one of the leading causes of death of women every year. Estrogen receptor alpha (ER-α) is an important pathway that is responsible for the development of breast cancer. Tamoxifen is the most commonly used to treat breast cancer. But the main drawback of using the drug is that it increases the risk of uterine cancer, stroke,and pulmonary embolism. Methods: In this research, the in-silico approach was followed to get the anticancer agent from Withania somnifera as the root extract of the plant is active against breast cancer. For this, 15 bioactive molecules were subjected to molecular docking and got 9 molecules comparing the consensus binding affinity of H3B-9224. Results: After rescoring, drug-likeness analysis, and ADMET analysis of the molecules were done and 3 molecules remained. These 3 molecules showed good ADMET properties which arecrucial requirements in the drug discovery process. Their activity was checked by applying density functional theory (DFT) and all of them showed good reactivity. Their binding interaction was also evaluated. Conclusion: Finally, the stability of those molecules checked by applying molecular dynamics (MD) simulation. After this simulation, 2 molecules remained that had good stability with the protein during the simulation period.

scholarly journals Evolution of Dirac Cone in Disclinated Graphene

2018 ◽  
Vol 57 (2) ◽  
pp. 137-142 ◽  
Author(s):  
M.A. Rozhkov ◽  
A.L. Kolesnikova ◽  
I. Hussainova ◽  
M.A. Kaliteevskii ◽  
T.S. Orlova ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Band Structure ◽  
Density Functional ◽  
Md Simulation ◽  
Dirac Cone ◽  
Electronic Band ◽  
Functional Theory ◽  
Periodic Distribution ◽  
Electronic Band Structures

Abstract Graphene crystals, containing arrays of disclination defects, are modeled and their energies are calculated using molecular dynamics (MD) simulation technique. Two cases are analyzed in details: (i) pseudo-graphenes, which contain the alternating sign disclination ensembles and (ii) graphene with periodic distribution of disclination quadrupoles. Electronic band structures of disclinated graphene crystals are calculated in the framework of density functional theory (DFT) approach. The evolution of the Dirac cone and magnitude of band gap in the band structure reveal a dependence on the density of disclination quadrupoles and alternating sign disclinations. The electronic properties of graphene with disclination ensembles are discussed.

scholarly journals Molecular Dynamics Simulation Estrogen Receptor Alpha againts Andrographolide as Anti Breast Cancer

2019 ◽  
Vol 6 (2) ◽  
pp. 65
Author(s):  
Doni Dermawan ◽  
Riyadi Sumirtanurdin ◽  
Deti Dewantisari
Keyword(s):  
Breast Cancer ◽  
Molecular Dynamics ◽  
Estrogen Receptor ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Estrogen Receptor Alpha ◽  
Docking Simulation ◽  
Dynamics Simulation ◽  
Receptor Alpha ◽  
A Value

Breast cancer is the most common cancer suffered by women with 1.67 million new cases in the world by 2012 with a mortality rate of 12.9%. Tamoxifen is a standard therapy for breast cancer but can cause endometrial and thromboembolic cancer. Andrografolid is an active compound from  Andrographis paniculata which has antiproliferation activity of MCF-7 breast cancer cells with IC50 was 61.11 μM. The purpose of this study was to design andrographolide modification structures as human estrogen receptor alpha (hER-α) antagonists. Molecular docking simulation results showed that the andrographolide and AND5 (best andrographolide derivative) have free binding energy (ΔG) values were -9.65 kcal/mol and -12.43 kcal/mol, respectively, and hydrogen bonds were formed with Gly521, Asp351, and Met343. The ΔG value of ANDS was lower than tamoxifen (-11.40 kcal/mol). Pharmacophore modeling results showed that andrographolide and AND5 had a high pharmacophore-fit value of 46.39% and 63.47%, respectively. Molecular dynamics simulation using MM-PBSA calculation method, showed that the hERα-AND5 system has a value of ΔGTOTAL = -50.52 kcal/mol compared to the hERα-estradiol system as an agonist with a value of ∆GTOTAL = -40.86 kcal/mol . These results suggested that AND5 has better affinity for hERα compared to estradiol so that AND5 is a very promising anti breast cancer agent.Keywords: Andrographolide, molecular dynamics, breast cancer, molecular docking, estrogen receptor alpha

scholarly journals A method to calculate redox potentials relative to the normal hydrogen electrode in nonaqueous solution by using density functional theory-based molecular dynamics

2015 ◽  
Vol 17 (40) ◽  
pp. 27103-27108 ◽  
Author(s):  
Ryota Jono ◽  
Yoshitaka Tateyama ◽  
Koichi Yamashita
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Md Simulation ◽  
Redox Potentials ◽  
Hydrogen Electrode ◽  
Functional Theory ◽  
Normal Hydrogen Electrode ◽  
Normal Hydrogen

We demonstrate the redox potential calculations relative to the normal hydrogen electrode (NHE) in non-aqueous solution by density functional theory based molecular dynamics (DFT-MD) simulation.

scholarly journals Density functional theory calculations and molecular docking of 2-phenylbenzimidazoles with estrogen receptor for quantitative structure-activity relationship studies

2021 ◽  
pp. 44-44
Author(s):  
Mahani Madadi ◽  
Sayed Mohammadi ◽  
Khadije Anjomshoa
Keyword(s):  
Density Functional Theory ◽  
Estrogen Receptor ◽  
Dipole Moment ◽  
Molecular Docking ◽  
Anticancer Agents ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Pharmaceutical Chemistry ◽  
Benzimidazole Derivatives ◽  
Functional Theory

Benzimidazole derivatives, especially 2-phenylbenzimidazole with various substituents on the C-5, C-2, and C-6 positions, are so important in pharmaceutical chemistry. Multiple linear regression was applied to predict the activity of 27 novel 2-phenylbenzimidazole derivatives as anticancer agents. At first, we effort to create a QSAR model for a selected series of novel 2-phenyl-benzimidazole with density functional theory and molecular docking descriptors. Then, we tried to investigate the nature of the interactions between 2-pheny-lbenzimidazole derivatives and the Estrogen Receptor by using the molecular docking method. Six descriptors of MATS4e, GATS5e, R6v, R1v+, dipole moment, and torsional free energy were selected for modelling. Due to docking results, increasing the binding energy, and decreasing the dipole moment could be increasing of inhibitor activity.

Graphene adlayer growth between nonepitaxial graphene and Ni(111) substrate: a promising theoretical scheme

2020 ◽  
Author(s):  
Lijuan Meng ◽  
Jinlian Lu ◽  
Yujie Bai ◽  
Lili Liu ◽  
Tang Jingyi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Chemical Vapor Deposition ◽  
Molecular Dynamics Simulations ◽  
Vapor Deposition ◽  
Density Functional ◽  
Chemical Vapor ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Dynamics Simulations

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

scholarly journals Molecular docking and density functional theory studies on creatine, guanidinoacetic acid, and their phosphorylated analogues binding to muscle creatine kinase

2020 ◽  
pp. 174751982097858
Author(s):  
M Vraneš ◽  
S Ostojić ◽  
Č Podlipnik ◽  
A Tot
Keyword(s):  
Density Functional Theory ◽  
Creatine Kinase ◽  
Molecular Docking ◽  
Density Functional ◽  
Creatine Phosphate ◽  
Docking Studies ◽  
Muscle Creatine Kinase ◽  
Functional Theory ◽  
Guanidinoacetic Acid ◽  
Muscle Creatine

Comparative molecular docking studies on creatine and guanidinoacetic acid, as well as their phosphorylated analogues, creatine phosphate, and phosphorylated guanidinoacetic acid, are investigated. Docking and density functional theory studies are carried out for muscle creatine kinase. The changes in the geometries of the ligands before and after binding to the enzyme are investigated to explain the better binding of guanidinoacetic acid and phosphorylated guanidinoacetic acid compared to creatine and creatine phosphate.

Sign in / Sign up

Export Citation Format

Share Document