Molecular Docking of Phytochemicals Targeting GFRs as Therapeutic Sites for Cancer: an In Silico Study

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.

Download Full-text

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

Nigerian Journal of Pure and Applied Sciences ◽

10.48198/njpas/21.a19 ◽

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.

Download Full-text

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

Advanced Pharmaceutical Bulletin ◽

10.15171/apb.2019.074 ◽

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 />

Download Full-text

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

10.26434/chemrxiv.12100968 ◽

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.

Download Full-text

In Silico Study of Metoclopramide as A Small Molecule of Dopamine D2 Receptor: a Quantum-Mechanical (QM) Based Molecular Docking Treatment

Chemical Methodologies ◽

10.33945/sami/chemm.2020.1.2 ◽

2020 ◽

Vol 4 (1) ◽

pp. 19-33

Keyword(s):

Molecular Docking ◽

Small Molecule ◽

In Silico ◽

Dopamine D2 Receptor ◽

D2 Receptor ◽

Quantum Mechanical ◽

Dopamine D2 ◽

In Silico Study

Download Full-text

Synthesis, Molecular Docking and Evaluation of Library of 3-Mercapto-1,2,4-Triazole Derivatives as Antimicrobial Agents

Asian Journal of Chemistry ◽

10.14233/ajchem.2021.23472 ◽

2021 ◽

Vol 33 (12) ◽

pp. 3039-3046

Author(s):

Swarnagowri Nayak ◽

Santosh L. Gaonkar ◽

Sushruta S. Hakkimane ◽

Swapna B ◽

Nitinkumar S. Shetty

Keyword(s):

Antimicrobial Activity ◽

Molecular Docking ◽

In Silico ◽

Structural Modification ◽

Antimicrobial Agents ◽

Antifungal Drugs ◽

Aromatic Acids ◽

Triazole Derivatives ◽

In Silico Study ◽

Antibacterial And Antifungal

Due to the increasing microbial resistance to antibacterial and antifungal drugs, the development of new antimicrobial agents is an urgent priority. In search of newer antimicrobial agents, a series of 4,5-disubstituted-3-mercapto-1,2,4-triazole derivatives were synthesized from aromatic acids and substituted isothiocyanates. The in silico study was performed to study the binding interactions of the synthesized compounds with the active pocket of CYP51. Among the synthesized 3-mercapto-triazole derivatives, compounds 6r, 6s and 6u exhibited promising antimicrobial activity comparable to standard drugs. The results suggested that the structural modification to 3-mercapto-1,2,4-triazole derivatives could lead to promising antimicrobial scaffolds.

Download Full-text

In Silico Study of The Potential of Naturally Caffeoylquinic Acids From Lentinus Crinitus Basidiocarp With Zika Virus Inhibition Targets

10.21203/rs.3.rs-1011019/v1 ◽

2021 ◽

Author(s):

Aluísio Marques da Fonseca ◽

Neidelenio Baltazar Soares ◽

Regilany Paulo Colares ◽

Ethanielda de Lima Coelho ◽

Paulo Riceli Vasconcelos Ribeiro ◽

...

Keyword(s):

Molecular Docking ◽

Zika Virus ◽

In Silico ◽

Total Mortality ◽

Docking Simulation ◽

Biologically Active ◽

Biological Assays ◽

Virus Inhibition ◽

In Silico Study ◽

First Time

Abstract The methanolic extract of the fungus Lentinus crinitus was submitted to biological assays, identification of the chemical composition by LC-MS, and in silico study by molecular docking with all identified compounds. The test against Artemis salina reached LD50 > 1000 μg/mL within 24h, and total mortality within 48 hours; the antioxidant test 62.4% inhibition in 1.0 mg/mL was obtained. Only 16 compounds were identified from the LC-MS analysis based on the comparison of reports already recorded in the literature. Most of the compounds identified here are described for the first time in the genus Lentinus. These results showed that the fungus is a producer of different classes of secondary metabolites biologically active. The results of the molecular docking simulation of the identified phytochemicals presented 1,13,4-di-O-Caffeoylquinic, as the leading promising candidate in the inhibition of the Zika virus.

Download Full-text