scholarly journals POTENTIAL ANTIVIRAL OF CATECHINS AND THEIR DERIVATIVES TO INHIBIT SARS-COV-2 RECEPTORS OF M pro PROTEIN AND SPIKE GLYCOPROTEIN IN COVID-19 THROUGH THE IN SILICO APPROACH

2020 ◽  
Vol 14 (3) ◽  
Author(s):  
Frengki Frengki ◽  
Deddi Prima Putra ◽  
Fatma Sri Wahyuni ◽  
Daan Khambri ◽  
Henni Vanda ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Pharmacokinetic Profile ◽  
Spike Glycoprotein ◽  
Software Application ◽  
Better Than

Catechin and their derivatives have been studied to have antiviral potential against COVID-19 through in silico method “pharmacokinetics screening and molecular docking”. Pharmacokinetics and toxicity profiles were obtained through the ADMETSAR server and SwissADME server. Then proceed with the prediction of affinity through the method molecular docking using the software application MOE 2007.09. The testmaterial is in the form of a 3D catechin structure and its derivatives as well as several control ligands downloaded via Pubmed. While templatethe Receptor M pro protein and the Spike glycoprotein are downloaded from pdb.org (PDB ID: 6LU7 and 6LXT). The pharmacokinetic profile of catechins is relatively better than all control ligands with the lowest toxicity. Molecular docking results also show that catechins and theirderivatives have a stronger affinity than control ligands. This research proves that catechin has antiviral potential through inhibition of Mpro protein and Spike glycoprotein COVID-19 virus.

scholarly journals In Silico Effects of Steviol on Depression, Inflammation and Cancer Biomarkers

2021 ◽  
Vol 12 (6) ◽  
pp. 8385-8393
Keyword(s):  
Electron Transfer ◽  
Molecular Docking ◽  
In Silico ◽  
Cancer Biomarkers ◽  
Md Simulations ◽  
Monoamine Oxidase A ◽  
Transfer Processes ◽  
Cox 2 ◽  
Electron Transfer Processes ◽  
Better Than

Steviol (ST1), a known natural product, and methylated models (ST2-ST4) were investigated in this in silico work to see their effects were examined on each of depression, inflammation, and cancer biomarkers by participating in interactions with each of monoamine oxidase-A (MAO-A), cyclooxygenase-2 (COX-2), methyltransferase (MTN) enzymes, respectably. The stabilized structures of ST1-ST4 were achieved by performing optimization calculations. Subsequently, formations of interacting ligand-target complexes were examined by molecular docking (MD) simulations. The evaluated molecular orbital features showed a different tendency of ST1-ST4 models for contributing to electron transfer processes. Accordingly, the interacting ligand-target complexes showed differential interactions of each ligand towards each target, making ST1-ST4 as appropriate compounds for the detection of targets. The methylated ST2-ST4 models worked even better than the original ST1 model to affirm the benefit of steviol modification to achieve desired results. Meaningful interactions of ST1-ST4 with the targets also showed the possible application of steviol for the medication of each of depression, inflammation, and cancer cases.

scholarly journals Computational Approach Revealed Potential Affinity of Antiasthmatics Against Receptor Binding Domain of 2019n-Cov Spike Glycoprotein

2020 ◽  
Author(s):  
LAMIAE ELKHATTABI ◽  
Hicham Charoute ◽  
Rachid Saile ◽  
Abdelhamid Barakat
Keyword(s):  
Molecular Docking ◽  
Receptor Binding ◽  
In Silico ◽  
Cyclic Peptide ◽  
Direct Interaction ◽  
Binding Domain ◽  
Binding Energies ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Pubchem Database

The novel COVID-19 pandemic is now a health threat, with a deep-felt impact worldwide. The new coronavirus 2019 (2019 n-Cov) binds to host human receptors through Receptor Binding Domain RBD of Spike glycoprotein (S), making it a prominent drug target. The present study aims to identify new potential hits that can inhibit the S protein using in silico approaches. Several natural and synthetics compounds (antiasthmatics, Antiviral, Antimalarial, Antibacterial, Anti-Inflammatory, cyclic peptide, and cyclic bis) were screened by molecular docking using AutoDock Vina. Additionally, we tested calcitriol and three known drugs (Azithromycin, HydroxyChloroquine, and Chloroquine ) against the spike protein to found if they have any direct interaction.<br>Our finding consists of 4 potential synthetic compounds from PubChem database, known for their antiasthmatic effects, that show highly binding energies each (-8.6 kcal/mol, 7.7kcal/mol, -7.2 kcal/mol and -7.0 kcal/mol). Another 5 natural compounds from the South African natural sources database (SANCDB) that bind to RBD of Spike with significant energy each: (Marchantin C with -7.3 kcal/mol, Riccardin C with -7.0 kcal/mol, Digitoxigenin-glucoside with -6.9 kcal/mol, D-Friedoolean-14-en-oic acid with -6.8 kcal/mol and, Spongotine A with -6.7 kcal/mol). The FaF-Drugs server was used to evaluate the drug-like properties of the identified compounds. Additionally, Calcitriol, Azithromycin, and HydroxyChloroquine have an appreciable binding affinity to 2019-nCoV S, suggesting a possible mechanism of action. Using in silico approaches like molecular docking and pharmacokinetic properties, we showed new potential inhibitors. Our findings need further analysis, and chemical design for more effective derivatives of these compounds speculated to disrupt the viral recognition of host receptors.

In silico discovery of novel phytoconstituents of Amyris pinnata as mitotic spindle kinase inhibitor

2020 ◽  
Vol 12 ◽  
Author(s):  
Ghanshyam R. Parmar ◽  
Ashish P. Shah ◽  
Girish U. Sailor ◽  
Avinash Kumar Seth
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Mitotic Spindle ◽  
In Silico ◽  
Kinase Inhibitor ◽  
Pharmacokinetic Profile ◽  
Docking Studies ◽  
Chemotherapeutic Agents ◽  
Cancer Disease ◽  
Molecular Docking Studies

Background: Despite of many successes in discovery of numerous cancer chemotherapeutic agents from natural sources, some of the moieties were dropped because of its inefficiency or serious toxicity. Mitosis is an ordered series of fundamentally mechanical events in which identical copies of the genome are moved to two discrete locations within the dividing cell. The crucial role of the mitotic spindle in cell division has identified which is an important target in cancer chemotherapy. In the present study we are reporting molecular docking studies and in silico pharmacokinetic profile of selected phytoconstituents obtained from Amyris pinnata. Methods: Molecular docking studies of selected phytoconstituents were performed using iGEMDOCK. The crystal structure of protein was exported from protein data bank (PDB id: 4C4H). In silico pharmacokinetic profile of selected phytoconstituents were performed using SWISSADME server. Results: Compound AMNP6 showed higher binding affinity as compared to standard ligand. All the selected phytoconstituents has passed Lipinski rule of five and shown no violations. Conclusion: Good binding affinity and drug likeliness of the AMNP6 suggest that it can be further investigated and explored as mitotic spindle kinase inhibitor in cancer disease.

scholarly journals Antimalarial Properties of Isoquinoline Derivative from Streptomyces hygroscopicus subsp. Hygroscopicus: An In Silico Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Rivo YB. Nugraha ◽  
Icha FD. Faratisha ◽  
Kana Mardhiyyah ◽  
Dio G. Ariel ◽  
Fitria F. Putri ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Antimalarial Activity ◽  
Pharmacokinetic Profile ◽  
Streptomyces Hygroscopicus ◽  
Protein Targets ◽  
Pharmacokinetic Profiles ◽  
Bond Interaction ◽  
In Silico Studies ◽  
Isoquinoline Derivative

Malaria is one of the life-threatening diseases in the world. The spread of resistance to antimalarial drugs is a major challenge, and resistance to artemisinin has been reported in the Southeast Asian region. In the previous study, the active compound of Streptomyces hygroscopicus subsp. Hygroscopicus (S. hygroscopicus), eponemycin, has been shown to have antimalarial effects. To further analyze the effects of other active compounds on the Plasmodium parasite, identifying and analyzing the effectiveness of compounds contained in S. hygroscopicus through instrumentation of liquid chromatography/mass spectrometry (LC/MS) and in silico studies were very useful. This study aimed at identifying other derivative compounds from S. hygroscopicus and screening the antimalarial activity of the compound by assessing the binding affinity, pharmacokinetic profile, and bond interaction. The derivative compounds were identified using LC/MS. Protein targets for derivative compounds were found through literature studies, and the results of identification of compounds and protein targets were reconstructed into three-dimensional models. Prediction of pharmacokinetic profiles was carried out using Swiss ADME. Screening of protein targets for the derivative compound was carried out using the reverse molecular docking method. Analyzing bond interaction was done by LigPlot. One compound from S. hygroscopicus, i.e., 6,7-dinitro-2-[1, 2, 4]triazole-4-yl-benzo[de]isoquinoline-1,3-dione, was successfully identified using LC/MS. This compound was an isoquinoline derivative compound. Through literature studies with inclusion criteria, thirteen protein targets were obtained for reverse molecular docking. This isoquinoline derivative had the potential to bind to each protein target. The pharmacokinetic profile showed that this compound had the drug-likeness criteria. Conclusion. 6,7-Dinitro-2-[1, 2, 4]triazole-4-yl-benzo[de]isoquinoline-1,3-dione has antimalarial activity as shown by reverse molecular docking studies and pharmacokinetic profiles. The best inhibitory ability of compounds based on bond affinity is with adenylosuccinate synthetase.

scholarly journals Sterols from Jatropha tanjorensis leaves exhibit anti-inflammatory potential: in vitro and in silico studies

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Damilola Alex Omoboyowa
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Diclofenac Sodium ◽  
Ethanol Extract ◽  
Pharmacokinetic Profile ◽  
Gas Chromatography Mass Spectrometry ◽  
Toxicity Screening ◽  
In Silico Studies ◽  
Anti Inflammatory

Abstract Background Inflammation has continued to raise global challenges and Jatropha tanrogenesis (JT) is used traditionally for its management. In this study, the in silico and in vitro anti-inflammatory potential of bioactive sterols were investigated. The active compounds of ethanol extract of JT leaves were identified using Gas chromatography-mass spectrometry (GC.MS) followed by molecular docking against COX-1 and COX-2 using maestro Schrödinger and pharmacokinetic profile prediction using webserver tools. The in vitro anti-inflammatory and anti-oxidantive potentials were investigated using standard protocols. Results GC–MS analysis of ethanol extract of JT leaves revealed the presence of eight (8) compounds, the molecular docking analysis of these compounds demonstrated varying degrees of binding affinities against the target proteins. The extract exhibit concentration dependent anti-oxidant activity with IC50 of 106.383 and 6.00 Fe2+E/g for DPPH and FRAP respectively. The extract showed significant (P < 0.05) reduction in percentage inhibition of hemolysis at 200 µg/ml while non-significant (P > 0.05) increase was observed at 600 and 1000 µg/ml compared to 200 µg/ml of diclofenac sodium. At lower concentration of 25 and 50 µg/ml, percentage inhibition of albumin denaturation was significantly (P < 0.05) higher compared to 200 µg/ml of diclofenac sodium. Drug likeness prediction and ADME/toxicity screening showed that the bioactive compounds possess no side effects. Conclusion The results obtained in this study suggested that, JT leaves possess anti-inflammatory activity and could be used as a source of new drug.

scholarly journals Computational Approach Revealed Potential Affinity of Antiasthmatics Against Receptor Binding Domain of 2019n-Cov Spike Glycoprotein

2020 ◽  
Author(s):  
LAMIAE ELKHATTABI ◽  
Hicham Charoute ◽  
Rachid Saile ◽  
Abdelhamid Barakat
Keyword(s):  
Molecular Docking ◽  
Receptor Binding ◽  
In Silico ◽  
Cyclic Peptide ◽  
Direct Interaction ◽  
Binding Domain ◽  
Binding Energies ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Pubchem Database

The novel COVID-19 pandemic is now a health threat, with a deep-felt impact worldwide. The new coronavirus 2019 (2019 n-Cov) binds to host human receptors through Receptor Binding Domain RBD of Spike glycoprotein (S), making it a prominent drug target. The present study aims to identify new potential hits that can inhibit the S protein using in silico approaches. Several natural and synthetics compounds (antiasthmatics, Antiviral, Antimalarial, Antibacterial, Anti-Inflammatory, cyclic peptide, and cyclic bis) were screened by molecular docking using AutoDock Vina. Additionally, we tested calcitriol and three known drugs (Azithromycin, HydroxyChloroquine, and Chloroquine ) against the spike protein to found if they have any direct interaction.<br>Our finding consists of 4 potential synthetic compounds from PubChem database, known for their antiasthmatic effects, that show highly binding energies each (-8.6 kcal/mol, 7.7kcal/mol, -7.2 kcal/mol and -7.0 kcal/mol). Another 5 natural compounds from the South African natural sources database (SANCDB) that bind to RBD of Spike with significant energy each: (Marchantin C with -7.3 kcal/mol, Riccardin C with -7.0 kcal/mol, Digitoxigenin-glucoside with -6.9 kcal/mol, D-Friedoolean-14-en-oic acid with -6.8 kcal/mol and, Spongotine A with -6.7 kcal/mol). The FaF-Drugs server was used to evaluate the drug-like properties of the identified compounds. Additionally, Calcitriol, Azithromycin, and HydroxyChloroquine have an appreciable binding affinity to 2019-nCoV S, suggesting a possible mechanism of action. Using in silico approaches like molecular docking and pharmacokinetic properties, we showed new potential inhibitors. Our findings need further analysis, and chemical design for more effective derivatives of these compounds speculated to disrupt the viral recognition of host receptors.

EVALUATION OF IN-SILICO ANTICANCER POTENTIAL OF PYRETHROIDS: A COMPARATIVE MOLECULAR DOCKING STUDY

2015 ◽  
Author(s):  
Manik Ghosh ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Padma Behera ◽  
Naresh Rangra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study
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