In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach.

Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes

In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach

Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+ . Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+ . The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes

Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach.

Calprotectin is a heterodimeric protein complex with two subunits called S100A8/A9. The protein has an essential role in inflammation process and various human diseases. It has the ability to bind to unsaturated fatty acids including Arachidonic acid, Oleic acid and etc., which could be considered as a major carrier for fatty acids. In this study we aimed to appraise the thermodynamics and structural changes of Calprotectin in presence of Arachidonic acid/Oleic acid) using docking and molecular dynami simulation method. To create the best conformation of Calprotectin-Oleic acid/Arachidonic acid complexes, the docking process was performed. The complexes with the best binding energy were selected as the models for molecular dynamics simulation process. Furthermore, the structural and thermodynamics properties of the complexes were evaluated too. The Root Mean Square Deviation and Root Mean Square Fluctuation results showed that the binding of Arachidonic acid/Oleic acid to Calprotectin can cause the protein structural changes which was confirmed by Define Secondary Structure of Proteins results. Accordingly, the binding free energy results verified that binding of Oleic acid to Calprotectin leads to instability of S100A8/A9 subunits in the protein. Moreover, the electrostatic energy contribution of the complexes (Calprotectin-Oleic acid/Arachidonic acid) was remarkably higher than van der Waals energy. Thus, the outcome of this study confirm that Oleic acid has a stronger interaction with Calprotectin in comparison with Arachidonic acid. Our findings indicated that binding of unsaturated fatty acids to Calprotectin leads to structural changes of the S100A8/A9 subunits which could be beneficial to play a biological role in inflammation process

In silico assessment of the inhibitory effect of four flavonoids (Chrysin, naringin, quercetin, kaempferol) on tyrosinase activity using the md simulation approach

Tyrosinase is a tetrameric enzyme that plays an important role in pigment production. Overproduction of melanin, which may lead to several skin disorders, is a result of tyrosinase activity. Hence, tyrosinase inhibitors are of key importance in the treatment of these disorders. In the present study, four flavonoid inhibitors, namely chrysin, naringin, quercetin, and kaempferol, were evaluated physiochemically, and the inhibitory effects of these compounds on tyrosinase activity were evaluated using the molecular dynamics (MD) simulation method. To create the best conformation of the enzyme-substrate/inhibitor, the docking process for enzyme-substrate, i.e., enzymechrysin, enzyme-quercetin, enzyme-naringin, and enzyme-kaempferol, was performed. The complexes with the best binding energies were selected as the models for the MD simulation process. Furthermore, the structural (RMSD, Rg, RMSF, and Distance) and the thermodynamics properties of the complexes were evaluated. Additionally, the PMF was conducted to calculate the binding free energies. The results showed that chrysin, quercetin and the substrate were at similar distances to the amino acids of the active site, but naringin and kaempferol were closer to the active site of the enzyme than the substrate. Moreover, the analysis of the binding energy revealed that the substrates, chrysin, kaempferol, quercetin, and naringin bound to the enzyme with binding energies of !7.8, !3.1, !7.1, !3.9, and !8.4 kcal/mol, respectively, which confirms that naringin has the highest inhibitory effect on tyrosinase among other inhibitors, which makes it an appropriate candidate as a whitening agent in skin disorders

Study of HSA interactions with arachidonic acid using spectroscopic methods revealing molecular dynamics of HSA-AA interactions

The interaction between human serum albumin (HSA) and arachidonic acid (AA) as an unsaturated fatty acid were investigated in the present study using methods including UV-VIS spectrophotometry, fluorescence and circular dichroism (CD) spectroscopy, lifetime measurements, fluorescence anisotropy measurements and visual molecular dynamics(MD). The thermodynamic parameters were assessed from HSA thermal and chemical denaturation in the presence and absence of AA. From the thermal denaturation, the Tm and ΔG˚(298K) magnitudes obtained were 327.7 K and 88 kJ/mol, respectively, for HSA alone, and 323.4 K and 85 kJ/mol, respectively, following treatment with a 10 µM AA concentration. The same manner of reduction in Gibbs free energy as a criterion of protein stability was achieved during chemical denaturation by urea in the presence of AA. The present study investigates HSA binding nature through MD approaches, and the results indicated that the binding affinity of AA to the subdomain IIA of HSA is greater compared with that of subdomain IIIA. Although the HSA regular secondary structure evaluation by CD exhibited a minor change following incubation with AA, its tertiary structure revealed an observable fluctuation. Thus, it appears that the interaction between AA and HSA requires minor instability and partial structural changes

ACE2-Inhibitory Effects of Bromelain and Ficin in Colon Cancer Cells

Background and Objectives: Bromelain and ficin are aqueous extracts from fruits of Ananas comosus and Ficus carcia plants, used widely for medical applications. Angiotensin-converting enzyme 2 (ACE2) is a homolog of ACE, degrading Ang II to angiotensin 1-7 and decreasing the cellular concentration of Ang II. Materials and Methods: In this study, we investigated the ACE2-inhibitory, antiproliferative, and apoptosis-inducing effects of ficin and bromelain on caco-2 cells. Results: We found that bromelain and ficin significantly reduced the viability of human colon cancer cells with IC50 value concentrations of 8.8 and 4.2 mg/mL for bromelain after 24 and 48 h treatments, and 8.8 and 4.2 mg/mL for ficin after 24 and 48 h treatments, respectively. The apoptosis of the caco-2 cell line treated with bromelain was 81.04% and 56.70%, observed after 24 and 48 h. Total apoptotic proportions in caco-2 cells treated with ficin after 24 and 48 h were 83.7% and 73.0%. An amount of 1.6 mg/mL of bromelain and ficin treatments on caco-2 cells after 24 h revealed a higher decrease than that of other concentrations in the expression of ACE2 protein. Conclusions: In conclusion, bromelain and ficin can dose-dependently decrease the expression of ACE2 protein in caco-2 cells