MOLECULAR DOCKING ANALYSES OF SOME CYCLOHEXADIENE DERIVATIVES

2021 ◽  
Author(s):  
Jelena Đorović Jovanović ◽  
◽  
Dušan Dimić ◽  
Marijana Stanojević Pirković ◽  
Svetlana Jeremić ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Inhibitory Potency ◽  
Docking Simulations ◽  
Type Plasminogen Activator ◽  
Urokinase Type Plasminogen Activator ◽  
Autodock 4.0 ◽  
Free Energy Of Binding

The molecular docking study was performed with aim to examine the inhibitory potency of two selected cyclohexadiene derivatives (cis-(1S)-3-Fluoro-3,5-cyclohexadiene-1,2-diol (1), and 1,1′-(3,5-Cyclohexadiene-1,3-diyl)dibenzene (2)). The inhibitory potency of compounds 1 and 2 was investigated toward Urokinase Type Plasminogen Activator (uPa). For this purpose AutoDock 4.0 software was used. The thermodynamic parameters achieved from molecular docking simulations, free energy of binding (ΔGbind) and inhibition constant (Ki), are analyzed and discussed. The compound 2 shows better inhibitory potency through uPa, than compound 1.

scholarly journals BETWEEN ARTEMISININ AND DERIVATIVES WITH NEURAMINIDASE: A DOCKING STUDY INSIGHT

2017 ◽  
Vol 10 (8) ◽  
pp. 304 ◽  
Author(s):  
Mohammad Rizki Fadhil Pratama ◽  
Tutus Gusdinar
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Docking Study ◽  
Basis Sets ◽  
Molecular Docking Study ◽  
Oseltamivir Resistance ◽  
Hartree Fock ◽  
In Silico Molecular Docking ◽  
Free Energy Of Binding ◽  
The Relationship

Objectives: This study aims to find the relationship between artemisinins and neuraminidase (NA) with molecular docking study and also to determine the most potent NA inhibitor from artemisinin and derivatives.Methods: All ligands were sketched and optimized using Gaussian 03W with Hartree-Fock method basis sets 6-311G. Molecular docking was performed using AutoDock 4.2.3 toward NA in complexes with oseltamivir as co-crystal ligand. The main parameters used were the free energy of binding (ΔG) and dissociation constant (Ki) as affinity marker.Results: Artesunate provided most negative free ΔG and lowest Ki toward NA with −9.55 kcal/mol and 100.66 nM, respectively. Artesunate shows higher affinity than oseltamivir with interactions between artesunate and amino acids at position 246 had important influences on artesunate affinity toward NA from H5N1.Conclusion: In silico molecular docking results indicated that artesunate could be considered as NA inhibitor and should be potential to be developed as anti-influenza particularly to H5N1 with oseltamivir resistance.

Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors

2006 ◽  
Vol 14 (17) ◽  
pp. 6001-6011 ◽  
Author(s):  
Fernanda G. Oliveira ◽  
Carlos M.R. Sant’Anna ◽  
Ernesto R. Caffarena ◽  
Laurent E. Dardenne ◽  
Eliezer J. Barreiro
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Binding Free Energy ◽  
Docking Study ◽  
Energy Model ◽  
Molecular Docking Study ◽  
Phosphodiesterase 4 ◽  
Phosphodiesterase 4 Inhibitors ◽  
Free Energy Model

scholarly journals Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

2020 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Sefren Geiner Tumilaar ◽  
Nurdjannah Jane Niode ◽  
Fatimawali Fatimawali ◽  
Billy Johnson Kepel ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Bioactive Compounds ◽  
Binding Free Energy ◽  
Epigallocatechin Gallate ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Ligand Complex ◽  
Main Protease ◽  
Glycoprotein Inhibitors

Since the outbreak of the COVID-19 (Coronavirus Disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit the Main Protease (Mpro) and Spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. A rule of five (RO5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was done by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding / ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development lead compounds to treat infections caused by SARS-CoV-2.

scholarly journals In Silico Study on N-Ferrocenylmethyl-N-Phenylpropionohydrazide and N-Ferrocenylmethyl-N-Pheylbenzohydrazide as Anticancer Drugs for Breast and Prostate Cancer

2018 ◽  
Vol 11 ◽  
pp. 17-25 ◽  
Author(s):  
Zegheb Nadjiba ◽  
Boubekri Chérifa ◽  
Touhami Lanez ◽  
Elhafnaoui Lanez
Keyword(s):  
Prostate Cancer ◽  
Free Energy ◽  
Molecular Docking ◽  
Hydrogen Bonds ◽  
Binding Free Energy ◽  
Docking Study ◽  
Dominant Mode ◽  
Molecular Docking Study ◽  
Docking Calculations ◽  
Breast And Prostate Cancer

Molecular docking calculations were used to evaluate the antitumor activities of N-ferrocenylmethyl-N-phenylpropanamide (FP) and N-ferrocenylmethyl-N-pheylbenzohydrazide (FH) against the enzymes of breast cancer 17-beta-hydroxysteroid dehydrogenase type 1 (17β-HSD1) and human steroidogenic cytochrome P450 17A1 prostate cancer mutant A105L (CYP17A1). The molecular docking study was performed using the open source AutoDock 4.2 software. The obtained results showed that both FP and FH bind with 17β-HSD1 and CYP17A1 via hydrogen bonds, binding free energy values for the adducts FH-17β-HSD1 and FH-CYP17A1 were respectively equal to-27.67 and-27.55 KJmol-1, while for the adducts FP-17β-HSD1 and FP-CYP17A1 they were respectively equal to-29.13 and 29.18 KJmol-1. The negative values and the magnitude of the obtained binding free energy indicated respectively the spontaneity and the electrostatic interaction of both ligands FP and FH with 17β-HSD1 and CYP17A1 receptors as the dominant mode. Finally the ligand FP binds more strongly to the receptor CYP17A1 and forms two respective hydrogen bonds with Arg96 and His373; this finding clearly indicate that FP is best qualified as potential drug candidature for breast and prostate cancer.

scholarly journals Analysis of flavonoid compounds of Orange (Citrus sp.) peel as anti-main protease of SARS-CoV-2: A molecular docking study

2022 ◽  
Vol 951 (1) ◽  
pp. 012078
Author(s):  
N B Maulydia ◽  
T E Tallei ◽  
B Ginting ◽  
R Idroes ◽  
D N illian ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Binding Free Energy ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Flavonoid Compounds ◽  
Global Pandemic ◽  
Main Protease ◽  
New Type ◽  
The City

Abstract SARS-CoV-2 is a new type of coronavirus that causes COVID-19. This virus was first detected in the city of Wuhan, China, at the end of 2019, and until now, it has become a global pandemic. The FDA recently approved Vekluty (remdesivir) for adults and certain pediatric patients who have COVID-19 and are sick enough to require hospitalization. One of the potential drug target candidates for SARS-CoV-2 is the main protease (Mpro). The purpose of this study was to analyze the flavonoid compounds found in orange (Citrus sp.) peel to determine its potential as anti-Mpro through a molecular docking study. The compounds were initially screened for drug-like properties and then docked using Autodock Vina in the PyRx emulator software. The docking results were visualized using the BIOVIA Discovery Visualizer 2020. The result showed that the binding free energy of hesperidin (-8.6 kcal/mol) was higher than nelfinavir (-8.5 kcal/mol). In addition, hesperitin (-7.3 kcal/mol), sakuranetin (-7.1 kcal/mol), isosacuranetin (-7.2 kcal/mol) and tetra-o-methylscutallerin (-6.8 kcal/mol) exhibited lower binding free energy value than control. Based on these results, hesperidin has the potential as an inhibitor of the main protease’s SARS-CoV-2.

scholarly journals MOLECULAR DOCKING STUDY OF NEUROPROTECTIVEPLANT-DERIVED BIOMOLECULES IN PARKINSON’S DISEASE

2017 ◽  
Vol 9 (9) ◽  
pp. 149 ◽  
Author(s):  
Saurabh Kumar Jha ◽  
Pravir Kumar
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Docking Studies ◽  
Neuroprotective Activity ◽  
Therapeutic Window ◽  
Molecular Docking Study ◽  
Altered Expression ◽  
Lipinski’S Rule ◽  
Lipinski’S Rule Of Five ◽  
Free Energy Of Binding

Objective: The objective of this study was to explore the therapeutic role of biomolecules in targeting the altered expression of Parkin in PD pathogenesis.Methods: We employed various in silico tools such as drug-likeness parameters, namely, Lipinski filter analysis, Muscle tool for phylogenetic analysis, Castp Server for active site prediction, molecular docking studies using AutoDock 4.2.1 and LIGPLOT1.4.5 were carried out.Results: Our results show that neuroprotective activity of Quercetin to be most effective and can provide their possible clinical relevance in PD. Further, initial screenings of the molecules were done based on Lipinski’s rule of five. CastP server used to predict the ligand binding site suggests that this protein can be utilized as a potential drug target. Finally, we have found Quercetin to be most effective amongst four biomolecules in modulating Parkin based on minimum inhibition constant, Ki and highest negative free energy of binding with the maximum interacting surface area in a course of docking studies.Conclusion: This research could provide a potential therapeutic window for the treatment of PD.

scholarly journals Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

2020 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Sefren Geiner Tumilaar ◽  
Nurdjannah Jane Niode ◽  
Fatimawali Fatimawali ◽  
Billy Johnson Kepel ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Bioactive Compounds ◽  
Binding Free Energy ◽  
Biological Activities ◽  
Epigallocatechin Gallate ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Glycoprotein Inhibitors

Background: Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the cause of COVID-19. The search for plant-based antivirals against the SARS-CoV-2 is promising, as several plants have been shown to possess antiviral activities against betacoronaviruses (beta-CoVs) Objective: The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit Main Protease (Mpro) (PDB code: 6LU7) and Spike (S) Glycoprotein (PDB code: 6VXX) of SARS-CoV-2. Methods: Evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. For each compound that was docked, a rule of five was calculated to determine whether a compound with certain pharmacological or biological activities might have chemical and physical properties that would make it an active drug orally in humans. Determination of the docking score was done by selecting the conformation of the ligand that has the lowest binding free energy (best pose). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. Results: The results showed that hesperidine, cannabinoids, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and cannabinoids had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Conclusion: Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19.

scholarly journals Synthesis, In Silico and In Vitro Assessment of New Quinazolinones as Anticancer Agents via Potential AKT Inhibition

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4780 ◽  
Author(s):  
Ahmed A. Noser ◽  
Mohamed El-Naggar ◽  
Thoria Donia ◽  
Aboubakr H. Abdelmonsef
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
Homo Sapiens ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Docking Simulations ◽  
Ic50 Values ◽  
Quinazolinone Derivatives ◽  
Mcf 7

A series of novel quinazolinone derivatives (2–13) was synthesized and examined for their cytotoxicity to HepG2, MCF-7, and Caco-2 in an MTT assay. Among these derivatives, compounds 4 and 9 exhibited significant cytotoxic activity against Caco-2, HepG2, and MCF-7 cancer cells. Compound 4 had more significant inhibitory effects than compound 9 on Caco-2, HepG2, and MCF-7 cell lines, with IC50 values of 23.31 ± 0.09, 53.29 ± 0.25, and 72.22 ± 0.14µM, respectively. The AKT pathway is one of human cancer’s most often deregulated signals. AKT is also overexpressed in human cancers such as glioma, lung, breast, ovarian, gastric, and pancreas. A molecular docking study was performed to analyze the inhibitory action of newly synthetic quinazolinone derivatives against Homo sapiens AKT1 protein. Molecular docking simulations were found to be in accordance with in vitro studies, and hence supported the biological activity. The results suggested that compounds 4 and 9 could be used as drug candidates for cancer therapy via its potential inhibition of AKT1 as described by docking study.

scholarly journals METHYLCYTISINE ALCALOID POTENTIALLY ACTIVE AGAINST DENGUE VIRUS: A MOLECULAR DOCKING STUDY AND ELECTRONIC STRUCTURAL CHARACTERIZATION

2020 ◽  
Vol 8 (1) ◽  
pp. 221-236 ◽  
Author(s):  
Francisco Nithael Melo Lucio ◽  
José Elieudo Da Silva ◽  
Emanuelle Machado Marinho ◽  
Francisco Rogênio Da Silva Mendes ◽  
Marcia Machado Marinho ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dengue Virus ◽  
Acetylcholine Receptors ◽  
Chemical Reactivity ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Stable Conformation ◽  
Docking Simulations ◽  
Reactivity Descriptors ◽  
Biological Targets

Dengue fever is a serious disease acquired from the Aedes aegypti mosquito present in tropical and subtropical regions, deeply impacting the population's quality of life. Its control requires combating the virus, and the use of substances that do not cause damage to the environment is of fundamental importance. The present work was carried out in silico to perform the structural-electronic characterization of the alkaloid Methylcytisine, a tricyclic quinolizidine alkaloid that has insecticidal activities, identifying the molecular boundary orbitals and descriptors of global chemical reactivity and assessing the inhibitory potential of methylcytisine on NS5 methyltransferase enzyme dengue virus, as well as identifying possible biological targets in humans. Methylcytisine was geometrically optimized through semi-empirical quantum calculations with thermodynamically more stable conformation, characterizing its structure (atoms, angles and bonds) and its reactivity descriptors. The analysis of the molecular docking simulations showed that methylcytisine is coupled in the same active site of the NS5 enzyme methyltransferase DENV, very similar to the complexed ligand S-adenosyl-L-homocysteine. The intermolecular interactions found for the complex formed and the distance values of the enzyme residues, indicate that methylcytisine has potential application as a new inhibitor of the dengue virus, however it has a high possibility of interaction with human neuronal acetylcholine receptors.

scholarly journals Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

2020 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Sefren Geiner Tumilaar ◽  
Nurdjannah Jane Niode ◽  
Fatimawali Fatimawali ◽  
Billy Johnson Kepel ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Bioactive Compounds ◽  
Binding Free Energy ◽  
Biological Activities ◽  
Epigallocatechin Gallate ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Glycoprotein Inhibitors

Background: Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the cause of COVID-19. The search for plant-based antivirals against the SARS-CoV-2 is promising, as several plants have been shown to possess antiviral activities against betacoronaviruses (beta-CoVs) Objective: The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit Main Protease (Mpro) (PDB code: 6LU7) and Spike (S) Glycoprotein (PDB code: 6VXX) of SARS-CoV-2. Methods: Evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. For each compound that was docked, a rule of five was calculated to determine whether a compound with certain pharmacological or biological activities might have chemical and physical properties that would make it an active drug orally in humans. Determination of the docking score was done by selecting the conformation of the ligand that has the lowest binding free energy (best pose). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. Results: The results showed that hesperidine, cannabinoids, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and cannabinoids had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro/3CLpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Conclusion: Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19.

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