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

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.

scholarly journals In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents

2020 ◽  
Vol 3 (4) ◽  
pp. 989-1000
Author(s):  
Mustapha Abdullahi ◽  
Shola Elijah Adeniji
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Density Functional ◽  
Docking Simulation ◽  
Basis Set ◽  
Hybrid Functional ◽  
Standard Drug

AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.

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 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 />

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