scholarly journals Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

RSC Advances ◽  
2019 ◽  
Vol 9 (20) ◽  
pp. 11465-11475 ◽  
Author(s):  
Xingchun Li ◽  
Zhenhua Chu ◽  
Xianyuan Du ◽  
Youli Qiu ◽  
Yu Li
Keyword(s):  
Density Functional Theory ◽  
Molecular Docking ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Density Functional ◽  
Homology Modelling ◽  
Metabolic Enzyme ◽  
Naphthalene Dioxygenase ◽  
Functional Theory

To promote the biodegradation of aromatic hydrocarbons in petroleum-contaminated soils, naphthalene dioxygenase (NDO), which is the key metabolic enzyme that degrades aromatic hydrocarbons, was modified using molecular docking and homology modelling.

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.

Vibrational spectral, density functional theory and molecular docking analysis on 4-nitrobenzohydrazide

2021 ◽  
Vol 1223 ◽  
pp. 128948
Author(s):  
H. Marshan Robert ◽  
D Usha ◽  
M. Amalanathan ◽  
R. Racil Jeya Geetha ◽  
M. Sony Michael Mary
Keyword(s):  
Density Functional Theory ◽  
Molecular Docking ◽  
Spectral Density ◽  
Density Functional ◽  
Functional Theory ◽  
Docking Analysis ◽  
Molecular Docking Analysis
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