Are Pro8/Pro18 really critical for functional dynamic behavior of human endostatin N-terminal peptide? A comparative molecular dynamics study

Rasouli, Hassan; Mehrabi, Masomeh; Arab, Seyed Shahriar; Khodarahmi, Reza

doi:10.1007/s13738-017-1140-y

Cited by 6 publications

(4 citation statements)

References 76 publications

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“…Recent progresses on computational assays for unraveling the possible interaction of natural products and cellular receptors provided a new way to easily predict the molecular action of plant secondary metabolites. Among applied computational methods, docking analysis is one of the most important and handy methods because of its simple application to predict the inhibitory mode of action of chemical ligands against their favorable receptors (Rasouli et al 2017(Rasouli et al , 2020. It is not exaggerating if we say at least half one-third of our knowledge regarding the inhibitory properties of EOs and purified metabolites against a variety of receptors directly generated from docking analyses.…”

Section: Introductionmentioning

confidence: 99%

Decoding antibacterial and antibiofilm properties of cinnamon and cardamom essential oils: a combined molecular docking and experimental study

2021

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This study sets out to compare the antibacterial and antibiofilm profiles of Ci/Ca EOs alone and in combination together against infectious bacterial strains. MIC assay was carried out to survey the effectiveness of prepared EOs by two-fold serial dilution method and MTT evaluation. Synergic antibacterial properties of EOs against target strains were studied by using checkerboard titration method. Biofilm growth and development were evaluated using CV and XTT reduction assays. Antibacterial activity was observed for EOs against both bacterial strains with stronger activity for CiEO against both bacteria. The synergistic antibacterial effect was observed only against B. subtilis. Based on the FIC index, combinations could not inhibit the growth of E. coli. The pure EOs and their combination inhibited cell attachment for both studied bacteria with stronger effect on E. coli. CV and XTT reduction assays results showed that Ci EO and its combination with CaEO had the highest antibiofilm activity at lowest MIC value 0.08% and 0.04/0.02% against biofilm formed by E. coli and B. subtilis respectively, indicating a high antibiofilm potential. Computational docking analyses also postulated that the active constituents of evaluated EOs have the potential to interact with different bacterial targets, suggested binding mode of action of EOs metabolites. By and large, synergistic anti-biofilm properties of EOs may provide further options for developing novel formula to inhibit a variety of infectious clinical and industrial strains without (or less) toxicity effects on human body. Graphical Abstract

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Section: Introductionmentioning

confidence: 99%

Decoding antibacterial and antibiofilm properties of cinnamon and cardamom essential oils: a combined molecular docking and experimental study

2021

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“… 16 , 31 - 33 At the molecular level, the binding mode of small ligands to large protein targets plays an important role at numerous biological processes. 33 , 34 Though the accurate prediction of interaction between ligand and receptor is a major problem in experimental assays, however, molecular docking simulation (especially fully blind docking approach) can give useful information about the behavior of ligands towards the suspected peripheral, inner/outer and catalytic residues of protein active sites. In this regard, to interpret the results obtained from experimental assays molecular docking can be used as a valuable method to decide about the observed interactions.…”

Section: Resultsmentioning

confidence: 99%

Comparative in vitro/theoretical studies on the anti-angiogenic activity of date pollen hydro-alcoholic extract: Highlighting the important roles of its hot polyphenols

et al. 2018

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Introduction: Date palm pollen (DPP) is the male reproductive soft powder from date flowers widely used as the valuable dietary supplement to fortify the size of testis and ovarian to increase the power of sex. This part of date palm significantly exhibited anti-diabetic, anti-inflammation and protective effects against male and female infertility. Though the anticancer activity of date fruits was previously reported, the DPP anti-angiogenic effects were not reported, and as the first study, its inhibitory effects were examined in the current study. Methods: The DPP soft powder was collected to prepare its hydro-alcoholic extract to examine its anti-angiogenic activity in an in vitro model. At different concentrations, the cytotoxicity of the prepared extract was examined on human umbilical vein endothelial cells (HUVECs) using lactate dehydrogenase method. Cell proliferation was determined using the MTT assay and cytodex-3D model in collagen gel was used to assay its possible anti-angiogenic activity. The expression of VEGF, MMP-2 and MMP-9 genes was measured using real-time polymerase chain reaction (PCR). Finally, molecular docking simulation was used to highlight the possible role of DPP polyphenols to interact with the associated receptors. Results: The prepared hydro-alcoholic extract exhibited significant anti-angiogenic activity in a dose-dependent manner and decreased the endothelial cell proliferation. The calculated IC50 value for the examined extract in angiogenesis model was 260 µg·mL, respectively. Also, the expression of VEGF, MMP-2 and MMP-9 genes were significantly decreased. Docking simulation results unveiled that the isolated DPP polyphenols have the affinity to interact with ctDNA, VEGF and its receptors. Conclusion: The DPP is the new source of non-toxic anti-cancer agents to use as a dietary supplement in the pre-treatment of cancer.

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“…11 Collectively, the MD simulation method illustrates either the molecular mechanism of interactions or the effect of the support on the structure and function of enzymes, complies with the experimental results, and represents reliable output. 8,38,72,73 Nevertheless, some studies indicated that MD is insufficient to justify what is happening in the experimental phase. One reason is an initial mistaken assumption.…”

Section: And Nosementioning

confidence: 99%

“…The method employed to lead to a proper answer relies completely on the question. [35][36][37][38] The metal ion binding site prediction (MIB) server is another tool that primarily estimates enzyme immobilization. The server was established to predict the protein binding regions for twelve metal ions, including Ca 2+ , Cu 2+ , Cu + , Fe 3+ , Fe 2+ , Mg 2+ , Zn 2+ , Cd 2+ , Mn 2+ , Hg 2+ , Ni 2+ , and Co 2+ .…”

Section: Introductionmentioning

confidence: 99%

In silico approaches to investigate enzyme immobilization: a comprehensive systematic review

Barati,

Hosseini,

Vafaee

et al. 2024

Phys. Chem. Chem. Phys.

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Are Pro8/Pro18 really critical for functional dynamic behavior of human endostatin N-terminal peptide? A comparative molecular dynamics study

Cited by 6 publications

References 76 publications

Decoding antibacterial and antibiofilm properties of cinnamon and cardamom essential oils: a combined molecular docking and experimental study

Decoding antibacterial and antibiofilm properties of cinnamon and cardamom essential oils: a combined molecular docking and experimental study

Comparative in vitro/theoretical studies on the anti-angiogenic activity of date pollen hydro-alcoholic extract: Highlighting the important roles of its hot polyphenols

In silico approaches to investigate enzyme immobilization: a comprehensive systematic review

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