Molecular docking, molecular dynamics simulation, biological evaluation and 2D QSAR analysis of flavonoids from Syzygium alternifolium as potent anti-Helicobacter pylori agents

Two novel oxidovanadium(IV) complexes with a new bidentate (O- and N-) imine-based ligand 2-((E)-(6-fluorobenzo[d]thiazol-2-ylimino)methyl)-6-methoxyphenol (HL) were synthesized under in situ experimental condition where VOSO4 acts as a kinetic template in the ratio 2 : 1 (L : M) and mixed ligand complex using 1,10-phenanthroline (phen) in 1 : 1 : 1 (L : M : phen) ratio. The synthesized compounds were structurally characterized by microanalysis, magnetic susceptibility, FTIR, electronic spectra, TG/DTA, ESR, and molar conductance studies. Based on the spectral studies, the complexes have the general composition [VO(L)2] (C1) and [VO(L)phen] (C2) in a square pyramid geometrical fashion. The synthesized compounds were primarily screened for their in vitro growth inhibiting activity against different strains of bacteria, namely, E. coli, B. subtilis, S. aureus, and P. aeruginosa by the disc diffusion method. Also, the antifungal activity was determined against C. albicans and A. niger by the Bateman poisoned technique. The in vitro antioxidant activity of all the compounds was determined by DPPH free radical-scavenging assay. Intercalative mode of DNA-binding properties of the oxidovanadium(IV) complexes with calf-thymus DNA (CT-DNA) was investigated using UV, fluorescence spectra, and viscosity measurements.

show abstract

“…The experiment was performed in triplicate. The rate and extent of killing were expressed as mean log 10 ·CFU·mL −1 against time [ 12 ].…”

Section: Methodsmentioning

confidence: 99%

Synthesis and Characterization of Oxidovanadium(IV) Complexes of 2-((E)-(6-Fluorobenzo[d]thiazol-2-ylimino)methyl)-6-methoxyphenol and Their Antimicrobial, Antioxidant, and DNA-Binding Studies

Savithri

Revanasiddappa

2018

Bioinorganic Chemistry and Applications

View full text Add to dashboard Cite

show abstract

“…Research from previous studies suggest that, combinatorial dynamics and docking approaches can be employed to get structural information as well as impact of protein structure stability upon ligand binding (Dasgupta et al, 2003;Nagasundaram & George Priya Doss, 2013). Also, different studies give indications that concordance between experimental and computational studies (Abu-Aisheh et al, 2019;Chandra Babu et al, 2017). However, we run molecular dynamics simulation for both of Apo and ligand bound complexes to understand the structural change of the protein upon ligand binding.…”

Section: Discussionmentioning

confidence: 99%

Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2

Mahmud

Uddin

Zaman

et al. 2020

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

Newly emerged SARS-CoV-2 made recent pandemic situations across the globe is accountable for countless unwanted death and insufferable panic associated with co-morbidities among mass people. The scarcity of appropriate medical treatment and no effective vaccine or medicine against SARS-CoV-2 has turned the situation worst. Therefore, in this study, we made a deep literature review to enlist plant-derived natural compounds and considered their binding mechanism with the main protease of SARS-CoV-2 through combinatorial bioinformatics approaches. Among all, a total of 14 compounds were filtered where Carinol, Albanin, Myricetin were had better binding profile than the rest of the compounds with having binding energy of-8.476,-8.036,-8.439 kcal/mol, respectively. Furthermore, MM-GBSA calculations were also considered in this selection process to support docking studies. Besides, 100 ns molecular dynamics simulation endorsed the rigid nature, less conformational variation and binding stiffness. As this study, represents a perfect model for SARS-CoV-2 main protease inhibition through bioinformatics study, these potential drug candidates may assist the researchers to find a superior and effective solution against COVID-19 after future experiments.

show abstract

“…Root-mean-square deviation (RMSD) and intermolecular interactions were also analyzed and discussed. The typical procedure of a molecular docking simulation followed three steps [ 19 , 20 , 21 , 22 ]:…”

Section: Methodsmentioning

confidence: 99%

“…This might help to mitigate the amount of glucose catalytically synthesized and excreted into the bloodstream. Regarding ligand–protein inhibition simulated by molecular docking simulation, an associated docking score (DS) under −3.2 kcal·mol −1 indicates good binding capacity [ 19 , 20 , 21 , 22 ]. In principle, the figure is calculated by a sum of all intermolecular-interaction free energy.…”

Section: Introductionmentioning

confidence: 99%

On the Inhibitability of Natural Products Isolated from Tetradium ruticarpum towards Tyrosine Phosphatase 1B (PTP1B) and α-Glucosidase (3W37): An In Vitro and In Silico Study

Bui

Nhung

et al. 2021

Molecules

View full text Add to dashboard Cite

Folk experiences suggest natural products in Tetradium ruticarpum can be effective inhibitors towards diabetes-related enzymes. The compounds were experimentally isolated, structurally elucidated, and tested in vitro for their inhibition effects on tyrosine phosphatase 1B (PTP1B) and α-glucosidase (3W37). Density functional theory and molecular docking techniques were utilized as computational methods to predict the stability of the ligands and simulate interaction between the studied inhibitory agents and the targeted proteins. Structural elucidation identifies two natural products: 2-heptyl-1-methylquinolin-4-one (1) and 3-[4-(4-methylhydroxy-2-butenyloxy)-phenyl]-2-propenol (2). In vitro study shows that the compounds (1 and 2) possess high potentiality for the inhibition of PTP1B (IC50 values of 24.3 ± 0.8, and 47.7 ± 1.1 μM) and α-glucosidase (IC50 values of 92.1 ± 0.8, and 167.4 ± 0.4 μM). DS values and the number of interactions obtained from docking simulation highly correlate with the experimental results yielded. Furthermore, in-depth analyses of the structure–activity relationship suggest significant contributions of amino acids Arg254 and Arg676 to the conformational distortion of PTP1B and 3W37 structures overall, thus leading to the deterioration of their enzymatic activity observed in assay-based experiments. This study encourages further investigations either to develop appropriate alternatives for diabetes treatment or to verify the role of amino acids Arg254 and Arg676.

show abstract

Molecular docking, molecular dynamics simulation, biological evaluation and 2D QSAR analysis of flavonoids from Syzygium alternifolium as potent anti-Helicobacter pylori agents

Abstract: The present study was carried out with the specific aim to evaluate anti-Helicobacter pylori(Hp) and urease inhibitory activities of three flavonoids from Syzygium alternifolium through thein vitroand bio-computational approaches.

Cited by 64 publications

References 40 publications

Synthesis and Characterization of Oxidovanadium(IV) Complexes of 2-((E)-(6-Fluorobenzo[d]thiazol-2-ylimino)methyl)-6-methoxyphenol and Their Antimicrobial, Antioxidant, and DNA-Binding Studies

Synthesis and Characterization of Oxidovanadium(IV) Complexes of 2-((E)-(6-Fluorobenzo[d]thiazol-2-ylimino)methyl)-6-methoxyphenol and Their Antimicrobial, Antioxidant, and DNA-Binding Studies

Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2

On the Inhibitability of Natural Products Isolated from Tetradium ruticarpum towards Tyrosine Phosphatase 1B (PTP1B) and α-Glucosidase (3W37): An In Vitro and In Silico Study

Contact Info

Product

Resources

About