scholarly journals Molecular docking study of the phytol and its derivatives against COX-2 induced inflammation: A combined density functional study

2020 ◽  
pp. 1-5
Author(s):  
Muhammad Torequl Islam ◽  
Pranta Ray ◽  
Abul Bashar Ripon Khalipha ◽  
SM Hafiz Hassan ◽  
Md. Roich Khan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Docking Study ◽  
Functional Study ◽  
Molecular Docking Study ◽  
Study Results ◽  
Homo And Lumo ◽  
Cox 2

This study aimed to determine the activity of PYT and its derivatives against COX-2, including 5IKR protein induced inflammation by using the computational tools. PYT and its derivatives have been designed by utilizing density functional theory (DFT) and the performance of the drugs was also evaluated by molecular docking study. Results suggest that the NH2 derivative of PYT (D-NH2) showed binding energy -6.4 (Kcal/mol) with protein 5IKR of COX-2 compared to the main drug (D) that showed binding energy -5.1 (Kcal/mol) with the same protein. HOMO and LUMO energy values were also calculated to determine the chemical reactivity of all the modified drugs. Non-covalent interactions of PYT and its derivatives were essential in improving the performance. In conclusion, D-NH2 showed better preference in inhibiting to the protein 5IKR of COX-2 compared to other modified drugs and it can be claimed that D-NH2 will be the best conformer for COX-2 induced inflammation.

scholarly journals Molecular Docking Study on Several Benzoic Acid Derivatives against SARS-CoV-2

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5828
Author(s):  
Amalia Stefaniu ◽  
Lucia Pirvu ◽  
Bujor Albu ◽  
Lucia Pintilie
Keyword(s):  
Molecular Docking ◽  
Benzoic Acid ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Principal Component ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Alkyl Gallates ◽  
Main Protease

Several derivatives of benzoic acid and semisynthetic alkyl gallates were investigated by an in silico approach to evaluate their potential antiviral activity against SARS-CoV-2 main protease. Molecular docking studies were used to predict their binding affinity and interactions with amino acids residues from the active binding site of SARS-CoV-2 main protease, compared to boceprevir. Deep structural insights and quantum chemical reactivity analysis according to Koopmans’ theorem, as a result of density functional theory (DFT) computations, are reported. Additionally, drug-likeness assessment in terms of Lipinski’s and Weber’s rules for pharmaceutical candidates, is provided. The outcomes of docking and key molecular descriptors and properties were forward analyzed by the statistical approach of principal component analysis (PCA) to identify the degree of their correlation. The obtained results suggest two promising candidates for future drug development to fight against the coronavirus infection.

scholarly journals In silico Drug Repurposing of FDA-Approved Artemisinins as Potent Chemotherapeutics Targeting Bcl-2, CDK-6 & VEGFR-2: Density Functional Exploration and Molecular Docking Study

2020 ◽  
Vol 11 (2) ◽  
pp. 9604-9618
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Chemical Reactivity ◽  
Lethal Dose ◽  
Drug Repurposing ◽  
Cancer Therapeutics ◽  
Docking Study ◽  
Molecular Docking Study

The strategy of using existing drugs originally developed for one disease to treat other indications has found success across medical fields. This paper focuses on drug repurposing of artemisinin and its derivatives (artenimol, artemether, artemotil, and artesunate) that kill malaria parasites for anticancer agents, specifically targeting Bcl-2, CDK-6, and VEGFR-2. The Artemisinins 1-5 were analyzed for compliance with Lipinski’s drug-likeness rule and optimum ADME parameters. The results of which revealed all calculated physicochemical descriptors and pharmacokinetic properties are within the expected thresholds. Toxicity in terms of predicted median lethal dose (LD50) in mg/kg weight of investigated Artemisinins 1-5 is also reported. Artemisinins 1-5 were subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of Bcl-2, CDK-6, and VEGFR-2. The molecular docking study revealed that Artemisinins 1-5 were able to target CDK-6 and VEGFR-2. DFT/B3LYP theoretical calculations for optimization, DFT, frequency, and HOMO/LUMO were performed to obtain electronic and structural properties, chemical reactivity descriptors. Hence, these findings will be highly beneficial in optimizing the utility of the development of Artemisinins 1-5 for cancer therapeutics, specifically targeting CDK-6 and VEGFR-2.

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).

Density Functional Study of H2S Adsorption on Small Agn (n = 1–5)

2013 ◽  
Vol 634-638 ◽  
pp. 47-51 ◽  
Author(s):  
Jun Qing Wen ◽  
A Ping Yang ◽  
Guo Xiang Chen ◽  
Chen Jun Zhang
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Global Minimum ◽  
Electronic States ◽  
Functional Study ◽  
Functional Theory ◽  
Energy Gaps ◽  
Single Fold ◽  
Homo And Lumo

The global-minimum geometries and electronic states of AgnH2S (n=1-5) clusters have been calculated using density-functional theory. Our calculations predicate that the stable geometries of AgnH2S clusters can be got by directly adding the H2S molecule on different site of Agn clusters, Agn (n=1-5) clusters would like to bond with sulfur atom and the H2S molecule is partial to hold the top location and single fold coordination site in the clusters. After adsorption, the structures of Agn clusters and H2S molecule keep the original structures and are only distorted slightly. The averaged binding energy reveals that adsorption of H2S molecule can strengthen the stabilities of AgnH2S clusters. The second difference in energy and the energy gaps between the HOMO and LUMO of Agn and AgnH2S have been studied.

COX-1/COX-2 inhibition activities and molecular docking study of newly designed and synthesized pyrrolo[3,4-c]pyrrole Mannich bases

2019 ◽  
Vol 27 (17) ◽  
pp. 3918-3928 ◽  
Author(s):  
Aleksandra Redzicka ◽  
Łukasz Szczukowski ◽  
Andrzej Kochel ◽  
Benita Wiatrak ◽  
Katarzyna Gębczak ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Mannich Bases ◽  
Molecular Docking Study ◽  
Cox 2 ◽  
Cox 1

scholarly journals MOLECULAR DOCKING STUDY OF NATURALLY OCCURRING COMPOUNDS AS INHIBITORS OF COVID -19

2021 ◽  
pp. 69-71
Author(s):  
SREEDEVI A ◽  
MALAR RETNA A ◽  
ROBIN KUMAR SAMUEL
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Discovery Studio ◽  
Naturally Occurring ◽  
Short Period ◽  
The Right ◽  
Native Ligand ◽  
Made In

Objectives: The worldwide spread of COVID-19 is an emergent issue to be tackled. Currently, several works in various field have been made in rather short period. The present study aimed to assess bioactive compounds found in medicinal plants as potential COVID-19 Mpro inhibitors using molecular docking study. Methods: The docking analyses were performed by using Autodock, Discovery Studio Visualiser and Igemdock. Results: The binding energy obtained from the docking of 6LU7 with native ligand cupressuflavone is -8.9 kcal/mol. Conclusion: These findings will provide the opportunities to identify the right drug to combat COVID-19.

scholarly journals DFT and Molecular Docking Study of 2-[2-(4-Chlorophenylaminothiazol-5-yl]benzothiazole

2019 ◽  
Vol 31 (3) ◽  
pp. 695-698
Author(s):  
N.S. Femila Nirmal ◽  
T.F. Abbs Fen Reji
Keyword(s):  
Molecular Docking ◽  
Atomic Charge ◽  
Molecular Geometry ◽  
Docking Study ◽  
Vibrational Frequencies ◽  
Molecular Docking Study ◽  
B3lyp Method ◽  
Homo And Lumo ◽  
Charge Analysis ◽  
Vibrational Bands

The title compound was computed by means of DFT chemical quantum calculations to obtain optimized molecular geometry, harmonic vibrational frequencies and atomic charges. Vibrational bands to the various structural groups and their importance were predicted by analyzing the vibrational spectra. The data showed that B3LYP method provide satisfactory data for assigning vibrational frequencies and structural properties.The HOMO and LUMO energies calculated permit the determination of atomic and molecular parameters and they also represented the transfer of charge in the molecule. Mulliken atomic charge analysis was also done. A comprehensive molecular picture of 2-[2-(4-chlorophenylaminothiazol-5-yl]benzothiazole and its interactions were got from NBO investigations. The molecular docking study indicates that benzothiazole derivative may possess inhibitory activity against BCL2 pancreatic cancer cell lines.

Sign in / Sign up

Export Citation Format

Share Document