Computational Exploration of Anti-Cancer Potential of Guaiane Dimers from Xylopia vielana by Targeting B-Raf Kinase Using Chemo-Informatics, Molecular Docking and MD Simulation Studies

2021 ◽  
Vol 21 ◽  
Author(s):  
Syed Shams ul Hassan ◽  
Syed Qamar Abbas ◽  
Mubashir Hassan ◽  
Hui-Zi Jin
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Md Simulations ◽  
Binding Potential ◽  
Anticancer Activities ◽  
Raf Kinase ◽  
Anti Cancer ◽  
In Silico Study ◽  
Computational Exploration ◽  
Future Drug

Background: Natural products from herbs are prolific to display robust anticancer activities. Objectives: In the current study, B-Raf kinase protein (PDB: 3OG7), a potent target for melanoma, was tested against two guaiane-type sesquiterpene dimers, xylopin E-F, obtained from Xylopia vielana. Methods: In this work, a systematic in silico study using ADMET analysis, bioactivity score forecasts, molecular docking, and its simulations were conducted to understand compounds' pharmacological properties. Results: During ADMET predictions of both the compounds, Xylopin E-F has displayed a safer profile in hepatotoxicity, cytochrome inhibition, and only xylopin F displayed as non-cardiotoxic compared to FDA approved drug vemurafenib. Both the compounds were proceeded to molecular docking experiments using Autodock docking software and both the compounds Xylopin E-F have displayed higher binding potential with -11.5Kcal/mol energy compared to control vemurafenib -10.2 Kcal/mol. All the compounds were further evaluated for their MD simulations and their molecular interactions with the B-Raf kinase complex displayed precise interactions with the active gorge of the enzyme by hydrogen bonding. Conclusions: Overall, xylopin F had a better profile relative to xylopin E and vemurafenib, and these findings indicated that this bio-molecule could be used as an anti-melanoma agent and as a possible anticancer drug in the future. Therefore, this is a systematic optimized in silico approach to creating an anticancer pathway for guaiane dimers against the backdrop of its potential for future drug development.

scholarly journals Synthesis, in Silico Study, and Anti-Cancer Activity of Thiosemicarbazone Derivatives

Biomedicines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1375
Author(s):  
Belay Zeleke Sibuh ◽  
Piyush Kumar Gupta ◽  
Pankaj Taneja ◽  
Sonia Khanna ◽  
Paratpar Sarkar ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Cell Lines ◽  
Anticancer Activities ◽  
Standard Drug ◽  
Drug Candidates ◽  
Anti Cancer ◽  
In Silico Study ◽  
Assay Result ◽  
Tgf Β1

Thiosemicarbazones are known for their biological and pharmacological activities. In this study, we have synthesized and characterized 3-Methoxybenzaldehyde thiosemicarbazone (3-MBTSc) and 4-Nitrobenzaldehyde thiosemicarbazone (4-NBTSc) using IR, 1HNMR and 13C NMR. The compound’s in vitro anticancer activities against different cell lines were evaluated. Molecular docking, Insilco ADMET, and drug-likeness prediction were also done. The test compounds showed a comparative IC50 and growth inhibition with the standard drug Doxorubicin. The IC50 ranges from 2.82 µg/mL to 14.25 µg/mL in 3-MBTSc and 2.80 µg/mL to 7.59 µg/mL in 4-NBTSc treated cells. The MTT assay result revealed, 3-MBTSc inhibits 50.42 and 50.31 percent of cell growth in B16-F0 and EAC cell lines, respectively. The gene expression showed that tumor suppressor genes such as PTEN and BRCA1 are significantly upregulated in 7.42 and 5.33 folds, and oncogenes, PKC, and RAS are downregulated −7.96 and −7.64 folds, respectively in treated cells. The molecular docking performed on the four targeted proteins (PARP, VEGFR-1, TGF-β1, and BRAFV600E) indicated that both 4-NBTSc and 3-MBTSc potentially bind to TGF-β1 with the best binding energy of −42.34 Kcal/mol and −32.13 Kcal/mol, respectively. In addition, the test compound possesses desirable ADMET and drug-likeness properties. Overall, both 3-MBTSc and 4-NBTSc have the potential to be multitargeting drug candidates for further study. Moreover, 3-MBTSc showed better activity than 4-NBTSc.

Molecular Docking of some Neem Constituents with COX-2 and NOs: An in silico Study

2020 ◽  
Vol 10 (3) ◽  
pp. 134-135
Author(s):  
Sambhav Jain ◽  
Aditya Ganeshpurkar ◽  
Nazneen Dubey
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
In Silico Study ◽  
Cox 2

Combined Pharmacophore and Molecular Docking-based In silico Study of Some Pyrrolyl 1,3,4-oxadiazole benzothioate Derivatives

2015 ◽  
Vol 5 (2) ◽  
pp. 69-80
Author(s):  
Shrinivas Dattatraya Joshi ◽  
Uttam Ashok More ◽  
Manoj Shripad Kulkarni ◽  
Kirankumar Nelaguddad ◽  
Venkatrao Hanumanthrao Kulkarni
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
In Silico Study

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 In-silico Study of the Developed Hydroxychloroquine-based ACE2 Inhibitor Molecules Against COVID-19: Molecular Modeling and Docking

2021 ◽  
Vol 11 (4) ◽  
pp. 7336-7342
Author(s):  
K. Zaher ◽  
N. E. Masango ◽  
W. Sobhi ◽  
K. E. Kanouni ◽  
A. Semmeq ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Modeling ◽  
In Silico ◽  
Viral Proteins ◽  
In Silico Study ◽  
Docking Calculations ◽  
Portal Of Entry ◽  
Molecular Modeling And Docking ◽  
Materials Studio

In the present study, we will verify the action of hydroxychloroquine-based derivatives on ACE2 which is considered to be the main portal of entry of the SARS-CoV-2 virus and constitutes an exciting target given its relative genetic stability compared to viral proteins. Thus, 81 molecules derived from hydroxychloroquine by substitutions at 4 different positions were generated in-silico and then studied for their affinity for ACE2 by molecular docking. Only 4 molecules were retained because of their affinity and bioavailability demonstrated by molecular dynamics and molecular docking calculations using COSMOtherm and Materials Studio software.

scholarly journals In silico Study of the Interactions between Schiff Base Polyphenols and HPV 16 E6/E6AP/p53 complex

2021 ◽  
pp. 3973-3980
Author(s):  
Jeremiah I. Ogah ◽  
Olatunji M. Kolawole ◽  
Steven O. Oguntoye ◽  
Muhammed Mustapha Suleiman
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
In Silico ◽  
In Silico Analysis ◽  
Docking Study ◽  
Hydrogen Atoms ◽  
Molecular Docking Study ◽  
Hpv 16 ◽  
In Silico Study

The rise in the incidence of cervical cancer globally has accentuate attention to the potential role of polyphenols as anticancer agents. Different studies have demonstrated the role of some polyphenols in altering Human Papillomavirus (HPV) carcinogenesis. Thus, this study was aimed at establishing the potentials of Schiff-based polyphenols from imesatin and satin as anticancer agents through in silico analysis. The polyphenols were synthesized and characterized using elemental analyses, spectroscopic analyses, UV-visible, Infrared, and Nuclear Magnetic Resonance (1H NMR and 13C, NMR). Molecular docking study of the polyphenols was carried out using Auto Dock Vina. The oncogenic E6 protein structure of HPV 16 was obtained from the protein bank (ID: 4XR8). The E6 proteins were prepared using AutoDock tools. Water molecules were removed from the protein molecules while hydrogen atoms were added. Also, the structures of Curcumin and Isomericitrin were obtained from PubChem. Results showed that three different Schiff based polyphenols were obtained from the synthesis; 3-(2’,4’-dimethoxy benzylidene hydrazono) indoline-2-one (DMBH), 3-(2’-hydroxy-4’-methoxy benzylidene hydrazono) indoline-2-one (HMBD), and 3-((4-4’-((2’’, 4’’-dimethoxy benzylidene amino) benzyl)phenyl)imino) indoline-2-one (DMBP). Higher ability of the docked polyphenols to bind to the E6/E6AP/p53 complex when compared to Curcumin was revealed. Also, results showed that the binding energy of Curcumin and Isomericitrin were -7.1kcal/mol and -8.4kcal/mol respectively while that of the polyphenols ranged from -7.4kcal/mol to -7.9kcal/mol. The molecular docking results of the polyphenols used in this study further confirm their potentials as strong anti-cancer agents.

scholarly journals The Comparison Between the Mutated HuIFN-β 27-101 and the WildType Interferon β: the Comprehensive In Silico Study to Evaluate theEffect of Mutations on IFN-β

2019 ◽  
Vol 9 (4) ◽  
pp. 640-648
Author(s):  
Sayed Sharif Balkhi ◽  
Zohreh Hojati
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Interferon Beta ◽  
Human Interferon ◽  
Meaningful Relationship ◽  
Significant Difference ◽  
In Silico Study ◽  
The Impact ◽  
Life Function

Purpose: Interferon beta (IFN-β) is used to combat multiple sclerosis (MS) disease. CreatingR27T and V101F mutations (mHuIFN-β-27 and mHuIFN-β-101) is one of the tasks performedto improve human interferon beta (HuIFN-β) half-life, function and expression. In this work,the impact of R27T and V101F mutations in recombinant IFN-β on its binding to interferonreceptors were studied by molecular docking.Methods: This work was performed through in silico study. The simulation of mutation wasperformed using the online Rosetta Backrub software and checked using server verify3D.Comparison of access to the solvent of the amino acids in the structures created was performedusing the asaview online server. Also, the effect of mutations on the fold of the protein wasreviewed by the online HOPE server. The molecular docking was performed between HuIFN-βand the external region of IFNAR receptor using the online ClusPro2 protein-protein dockingserver.Results: The comparison of the values of the negative binding energy (ΔGbind) obtained fromprotein-protein molecular docking between IFNAR receptor and HuIFN-β, mHuIFN-β-27,mHuIFN-β-101 and mHuIFN-β-27-101 ligands did not show a significant difference, and thesedifferences do not see any meaningful relationship between them (P > 0.9999).Conclusion: Regarding these results, it can be concluded that these mutations do not have anegative effect on the composition of the complex rHuIFN-β/IFNAR. So, they do not interferewith the binding of the IFN-β to the receptor. It is concluded that the quality of the rHuIFN-β isimproved by introducing these two mutations.<br />

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating that they are potentials candidates for muti-target drugs for COVID-19.

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