A nano-liposomal carrier containing p-coumaric acid for induction of targeted apoptosis on melanoma cells and kinetic modeling.

There has been a growth in the use of plant compounds as biological products for the prevention and treatment of various diseases, including cancer. As a phenolic compound, p-Coumaric acid (p-CA) demonstrates preferrable biological effects such as anti-cancer activities. A nano-liposomal carrier containing p-CA was designed to increase the anticancer effectiveness of this compound on melanoma cells (A375). To determine the characteristics of synthesized liposomes, encapsulation efficiency was measured. In addition, the particle size was measured utilizing DLS, FTIR, and morphology examination using SEM. In vitro release was also studied through the dialysis method, while toxicity was evaluated using the MTT assay. To determine apoptotic characteristics, biotechnology tools like flow cytometry, real time PCR, and atomic force microscopy (AFM) were employed. The findings indicated that in the cells treated with the liposomal form of p-CA, the amount of elastic modulus was higher compared to its free form. Kinetic modeling indicated that the best fitting model was zero-order.

The anticancer impacts of free and liposomal caffeic acid phenethyl ester (CAPE) on melanoma cell line (A375).

The deadliest type of skin cancer, malignant melanoma, is also the reason for the majority of skin cancer-related deaths. The objective of this article was to investigate the efficiency of free caffeic acid phenethyl ester (CAPE) and liposomal CAPE in inducing apoptosis in melanoma cells (A375) in in vitro. CAPE was loaded into liposomes made up of hydrogenated soybean phosphatidylcholine, cholesterol, and 1,2-distearoyl-sn-glycero-3 phosphoethanolamine-N-[methoxy (polyethylene glycol)-2000], and their physicochemical properties were assessed. (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test was performed for comparing the cytotoxicity of free CAPE and liposomal CAPE at dosages of 10, 15, 25, 50, 75 and the highest dose of 100 µg/mL for period of 24 and 48 h on A375 cell line to calculate IC50. Apoptosis and necrosis were evaluated in A375 melanoma cancer cells using flow cytometry. Atomic force microscopy was utilized to determine the nanomechanical attributes of the membrane structure of A375 cells. To determine whether there were any effects on apoptosis, the expression of PI3K/AKT1 and BAX/BCL2 genes was analyzed using the real-time polymerase chain reaction technique. According to our results, the maximum amount of drug release from nanoliposomes was determined to be 91% and the encapsulation efficiency of CAPE in liposomes was 85.24%. Also, the release of free CAPE was assessed to be 97%. Compared with liposomal CAPE, free CAPE showed a greater effect on reducing the cancer cell survival after 24 and 48 h. Therefore, IC50 values of A375 cells treated with free and liposomal CAPE were calculated as 47.34 and 63.39 µg/mL for 24 h. After 48 h of incubation of A375 cells with free and liposomal CAPE, IC50 values were determined as 30.55 and 44.83 µg/mL, respectively. The flow cytometry analysis revealed that the apoptosis induced in A375 cancer cells was greater when treated with free CAPE than when treated with liposomal CAPE. The highest nanomechanical changes in the amount of cell adhesion forces, and elastic modulus value were seen in free CAPE. Subsequently, the greatest decrease in PI3K/AKT1 gene expression ratio occurred in free CAPE.

Finding epitopes of Klebsiella pneumoniae outer membrane protein-K17 (OMPK17) and introducing a 25-mer peptide of it as a vaccine candidate.

No approved vaccine exists for Klebsiella pneumoniae yet. Outer membrane protein-K17 (OMPK17) is involved in K. pneumoniae pathogenesis. No information has been found about OMPK17 dominant epitopes in the literature. Therefore, this study aimed to predict both T cell and B cell epitopes of K. pneumoniae OMPK17 via immunoinformatics approaches. Both T cell (class-I and II) and B cell (linear and discontinuous) epitopes of OMPK17 were predicted. Several screening analyses were performed including clustering, immunogenicity, human similarity, toxicity, allergenicity, conservancy, docking, and structural/physicochemical suitability. The results showed that some regions of OMPK17 have more potential as epitopes. The most possible epitopes were found via several analyses including the selection of higher-scoring epitopes, the epitopes predicted with more tools, more immunogenic epitopes, the epitopes capable of producing interferon-gamma, the epitopes with more dissimilarity to human peptides, and non-toxic and non-allergenic epitopes. By comparing the best T cell and B cell epitopes, we reached a 25-mer peptide containing both T cell (class-I and class-II) and B cell (linear) epitopes and comprising appropriate physicochemical characteristics that are required for K. pneumoniae vaccine development. The in vitro/in vivo study of this peptide is recommended to clarify its actual efficiency and efficacy. Supplementary information: The online version contains supplementary material available at 10.1007/s11756-023-01371-0.

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.

Affinity enhancement of CR3022 binding to RBD; in silico site directed mutagenesis using molecular dynamics simulation approaches.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a disease which caused by a novel beta coronavirus. Structural and non-structural proteins are expressed by the virus gene fragments. The RBD of the S1 protein of the virus has the ability to interact with potent antibodies including CR3022, which was characterized to target the S protein of the virus which can efficiently neutralize the SARS-CoV in vitro and in vivo. In current study, we aimed to design CR3022 based antibody with high affinity compared with wild-type CR3022 using MD simulation method. Two variants were designed based on the amino acid binding conformation and the free binding energy of the critical amino acids which involved in CR3022-RBD interactions were evaluated. In this study three complexes were evaluated; CR3022-RBD, V1-RBD and V2-RBD using molecular dynamics simulations carried out for 100 ns in each case. Then, all the complexes were simulated for 100 ns. In the next step, to calculate the free binding affinity of the wild CR3022 and mutant antibody (V1 and V2) with RBD, the PMF method was performed. The RMSD profile demonstrated that all three complexes were equilibrated after 85 ns. Furthermore, the free binding energy results indicated that the V2-RBD complex has the higher binding affinity than V1-RBD and CR3022-RBD complexes. It should be noted that in above variants, the electrostatic energy and the number of H-bonds between the antibody and RBD increased. Thus, it is suggested that both designed antibodies could be considered as appropriate candidates for covid-19 disease treatment.Communicated by Ramaswamy H. Sarma.

Biomolecular interactions and binding dynamics of inhibitor arachidonic acid, with tyrosinase enzyme.

Hyperpigmentation is a disorder caused by increased melanin deposition and changes in skin pigmentation. Inhibition of tyrosinase activity contributes to the control of food browning and skin pigmentation diseases. The effects of arachidonic acid (AA) on tyrosinase activity were examined using different spectroscopy methods including UV-VIS spectrophotometry, fluorescence spectroscopy, circular dichroism (CD) differential scanning calorimetry, and molecular dynamics (MD) simulations. Based on the kinetic results, arachidonic acid showed mixed-type of inhibition with Ki = 4.7 µM. Fluorescence and CD studies showed changes of secondary and tertiary structures of enzyme and a reduction of α-helix* amino acids after its incubation with different concentrations of AA, which is also confirmed by DSSP analysis. In addition, differential scanning calorimetry (DSC) studies showed a decrease in thermodynamic stability of enzyme from Tm = 338.65k for sole enzyme after incubation with AA in comparison with complex enzyme with Tm= 334.26k, ΔH =7.52 kJ/mol, and ΔS = 0.15 kJ/mol k. Based on the theoretical methods, it was found that the interaction between enzyme and AA follows an electrostatic manner with ΔG = -8.314 kJ/mol and ΔH = -12.9 kJ/mol. The MD results showed the lowest flexibility in the complex amino acids and minimal fluctuations in AA interaction with tyrosinase in Residue 240 to 260 and 66 to 80. Thus, AA inhibitory and structural and thermodynamic instability of tyrosinase supported advantages of this fatty acid for prevention of medical hyperpigmentation. Therefore, it is a good candidate for cosmetic applications. Communicated by Ramaswamy H. Sarma.

A comprehensive review on methotrexate containing nanoparticles; an appropriate tool for cancer treatment.

For more than seven decades, methotrexate has been used all over the world for treatment of different diseases such as: cancer, autoimmune diseases, and rheumatoid arthritis. Several studies have addressed its formula, efficacy, and delivery methods in recent years. These studies have been focused on the effectiveness of different nanoparticles on drug delivery, delivery of the drug to the target cells, and attenuation of harm to the host cell. Whereas, the main usages of methotrexate are in cancer treatment field, this review provided a brief perspective into using different nanoparticles and their role in the treatment of different cancers.

Activation of apoptosis and G0/G1 cell cycle arrest along with inhibition of melanogenesis by humic acid and fulvic acid: BAX/BCL-2 and Tyr genes expression and evaluation of nanomechanical properties in A375 human melanoma cell line.

Objectives: Humic acid (HA) and Fulvic acid (FA) are major members of humic substances, which are extracted from organic sources including soil and peat. The pro-apoptotic and anti-melanogenic effects of HA and FA at the cellular and molecular levels in the A375 human melanoma cell line were examined in this study. Materials and Methods: The cytotoxicity effect of HA and FA were evaluated by cell viability assay. Apoptosis and cell cycle were investigated by flow cytometry. Real-time PCR was carried out to measure the expression of BAX, BCL-2, and Tyr genes. Moreover, the changes in nanomechanical properties were determined through atomic force microscopy (AFM). Results: It was found that HA and FA decrease cell viability with an IC50 value of 50 µg/ml (dose-dependent) for 14 hr, arrested cells in the G0/G1 phase, and increased the sub-G1 phase (induce apoptosis). Based on the AFM analysis, Young's modulus and adhesion force values were increased, also ultrastructural characteristics of cells were changed. Results of Real-time PCR revealed that HA and FA lead to a decrease in the expressions of BCL-2 and Tyr genes, and increase the BAX gene expression. Conclusion: These results exhibited that HA and FA possess pro-apoptotic effects through increasing the BAX/ BCL-2 expression in A375 cells. These molecular reports were confirmed by cellular nanomechanical assessments using AFM and flow cytometry. In addition, HA and FA inhibited melanogenesis by decreasing the expression of the Tyr gene. It is worthwhile to note that, HA and FA can be regarded to design new anti-cancer and anti-melanogenesis products.

Anticancer Properties of Probiotic Saccharomyces boulardii Supernatant on Human Breast Cancer Cells.

Saccharomyces boulardii, a variety of S. cerevisiae, is used as a probiotic yeast in food and drug industries. However, S. boulardii is an opportunistic pathogen, and the supernatant of this organism has recently been recommended for its health-promoting benefits. Breast cancer is the most frequent cancer disease in women worldwide. The objective of this study was to investigate the effects of S. boulardii supernatant (SBS) on cell viability, inducing apoptosis and suppression of survivin gene expression in MCF-7 and MCF-7/MX as human non-drug-resistant and multidrug-resistant breast cancer cells respectively. The IC50 value of SBS against MCF-7 was calculated 1037, 542, and 543 µg/mL for 24, 48, and 72 h treatments, respectively. Also, this value against MCF-7/MX cells were measured 1242, 616, and 444 µg/mL after 24, 48, and 72 h respectively. We found that suppression of survivin gene expression should be one of the main molecular antitumor mechanisms which is contributed to apoptosis in breast cancer cells. However, anticancer activity of SBS was observed more efficient against MCF-7 than that against MCF-7/MX cells. SBS is suggested to be considered as one of the prospective anticancer drugs to treat human breast carcinoma. More investigations especially in vivo studies are strongly recommended to be implemented to characterize other antitumor mechanisms of SBS against breast carcinoma.

Immunoinformatics and molecular dynamics studies to predict T-cell-specific epitopes of four Klebsiella pneumoniae fimbriae antigens.

Klebsiella pneumoniae (K. pneumoniae) is a causative agent of severe infections in humans. There is no publically available vaccine for K. pneumoniae infections yet. Here, using comprehensive immunoinformatics methods, T-cell-specific epitopes of four type 1 fimbriae antigens of K. pneumoniae were predicted and evaluated as potential vaccine candidates. Both CD8+ (class I) and CD4+ (class II) T-cell-specific epitopes were predicted and the epitopes similar to human proteome were excluded. Subsequently, the windows of class-II epitopes containing class-I epitopes were determined. The immunogenicity, IFN-γ production and population coverage were also estimated. Using the 3D structure of HLA and epitopes, molecular docking was carried out. Two best epitopes were selected for molecular dynamics studies. Our prediction and analyses resulted in the several dominant epitopes for each antigen. The docking results showed that all selected epitopes can bind to their restricted HLA molecules with high affinity. The molecular dynamics results indicated the stability of system with minimum possible deviation, suggesting the selected epitopes can be promising candidates for stably binding to HLA molecules. Altogether, our results suggest that the selected T-cell-specific epitopes of K. pneumoniae fimbriae antigens, particularly the two epitopes confirmed by molecular dynamics, can be applied for vaccine development. However, the in vitro and in vivo studies are required to authenticate the results of the present study.Communicated by Ramaswamy H. Sarma.

Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study.

Regarding the urgency of therapeutic measures for coronavirus disease 2019 (COVID-19) pandemic, the use of available drugs with FDA approval is preferred because of the less time and cost required for their development. In silico drug repurposing is an accurate way to speed up the screening of the existing FDA-approved drugs to find a therapeutic option for COVID-19. The similarity in SARS-CoV-2 and HIV-1 fusion mechanism to host cells can be a key point for Inhibit SARS-CoV-2 entry into host cells by HIV fusion inhibitors. Accordingly, in this study, an HIV-1 fusion inhibitor called Enfuvirtide (Enf) was selected. The affinity and essential residues involving in the Enf binding to the S2 protein of SARS-CoV-2, HIV-1 gp41 protein and angiotensin-converting enzyme 2 (ACE-2) as a negative control, was evaluated using molecular docking. Eventually, Enf-S2 and Enf-gp41 protein complexes were simulated by molecular dynamics (MD) in terms of binding affinity and stability. Based on the most important criteria such as docking score, cluster size, energy and dissociation constant, the strongest interaction was observed between Enf with the S2 protein. In addition, MD results confirmed that Enf-S2 protein interaction was remarkably stable and caused the S2 protein residues to undergo the fewest fluctuations. In conclusion, it can be stated that Enf can act as a strong SARS-CoV-2 fusion inhibitor and demonstrates the potential to enter the clinical trial phase of COVID-19. Communicated by Ramaswamy H. Sarma.

The effects of the esterified Quercetin with omega3 and omega6 fatty acids on viability, nanomechanical properties, and BAX/BCL-2 gene expression in MCF-7 cells.

Quercetin is one of the major flavonoids and it appears to have cytotoxic effects on various cancer cells through regulating the apoptosis pathway genes such as BAX and BCL2. Combination of Quercetin (Q) with other compounds can increase its effectiveness. In the present study, the effects of the Quercetin and its esterified derivatives on viability, nanomechanical properties of cells, and BAX/BCL-2 gene expression were investigated. Using the MTT and flow cytometry assays, the cytotoxic potential, apoptosis, and necrosis were investigated. The AFM assay was performed to find the nanomechanical properties of cells as the elastic modulus value and cellular adhesion forces. The BAX/BCL2 gene expression was investigated through the Real-Time PCR. The results showed that the esterification of Quercetin with linoleic acid (Q-LA) and α-linolenic acid (Q-ALA) increased the cytotoxic potential of Q. The elastic modulus value and cellular adhesion forces were increased using the esterified derivatives and the highest ratio of BAX/BCL2 gene expression was observed in Q-LA. Esterified Quercetin derivatives have a higher cytotoxic effect than the un-esterified form in a dose-dependent manner. Esterified derivatives caused the nanomechanical changes and pores formation on the cytoplasmic membrane. One of the internal apoptosis pathway regulation mechanisms of these compounds is increasing the BAX/BCL2 gene expression ratio.

Probiotic Saccharomyces cerevisiae var. boulardii supernatant inhibits survivin gene expression and induces apoptosis in human gastric cancer cells.

Natural anticancer drug and compounds with other great benefits are of interest recently due to lower side effects than chemotherapy for cancer treatment and prevention. Different natural and synthetic drugs have been suggested to be used for treatment of gastric cancers, the second deadly cancer worldwide. The aim of this study was to investigate anticancer activity of SBS including inducing apoptosis and inhibition of survivin gene expression in gastric cancer cells. We evaluated cell viability, inducing apoptosis and change in survivin gene expression of EPG85-257P (EPG) and EPG85-257RDB (resistant to Daunorubicin, RDB) cell lines under exposure of SBS after 24, 48, and 72 hr. We found that SBS decreased cell viability, induced apoptosis, and reduced survivin gene expression in treated EPG and RDB cells (with the significant IC50 values of 387 and 575 µg/ml after 72 and 48 hr for EPG and RDB cells respectively). However, we observed SBS was more efficient to induce apoptosis in EPG than RDB cells. We strongly suggest SBS be considered as a prospective anticancer agent or in formulation of complementary medication to treat and prevent gastric cancers.

Design and Characterization of Liposomal Methotrexate and Its Effect on BT-474 Breast Cancer Cell Line.

Background: Breast cancer is the most common type of cancer among women worldwide. Traditional treatments, including chemotherapy, surgery, mastectomy, and radiotherapy, are commonly used. Because of the limitation of the aforementioned methods, novel treatment strategies are needed. Methotrexate is a chemotherapeutic drug, which is commonly used to treat breast cancer. Because of the side effects of the free drug, the liposomal form of the drug is suggested. Methods: Liposomal methotrexate was prepared and the encapsulation efficiency was measured. Moreover, the particle size and the zeta potential were measured. The liposome morphology was confirmed using transmission electron microscopy. The MTT assay was done to examine the cytotoxicity of free and encapsulated methotrexate on BT-474 cell line. The Annexin-V/PI dual staining assay was performed to assess the apoptosis in BT-474 breast cancer cells via the flow cytometry method. Results: The transmission electron microscopy results confirmed the integrated and spherical structure of the nanoparticles. The results of drug release showed that in acidic pH (5.4), more than 90% of the drug was released after 24 hours, which was higher than 2 other pHs. Furthermore, the IC50 value of liposomal methotrexate was determined as 2.15 and 0.82 mg/mL for 24 and 48 hours. The flow cytometry results confirmed that liposomal methotrexate had a greater cytotoxic effect on cancer cells compared with free methotrexate. Conclusion: Because of the advantages of liposomal based nanocarriers, in this study, liposomal methotrexate could be suggested as an appropriate candidate to treat breast cancer.

Antibacterial Assessment of Zinc Sulfide Nanoparticles against Streptococcus pyogenes and Acinetobacter baumannii.

BACKGROUND: Due to the appearance of resistant bacterial strains against the antimicrobial drugs and the reduced efficiency of these valuable resources, the health of a community and the economies of countries have been threatened. OBJECTIVE: In this study, the antibacterial assessment of zinc sulfide nanoparticles (ZnS NPs) against Streptococcus pyogenes and Acinetobacter baumannii has been performed. METHODS: ZnS NPs were synthesized through a co-precipitation method using polyvinylpyrrolidone (PVP), polyvinyl alcohol (PVA) and polyethylene glycol (PEG-4000). The size and morphology of the synthesized ZnS NPs were determined by a scanning electron microscope (SEM) and it was found that the average size of the applied NPs was about 70 nm. In order to evaluate the antibacterial effect of the synthesized ZnS NPs, various concentrations (50µg/mL, 100 µg/mL and 150 µg/mL) of ZnS NPs were prepared. Antibacterial assessments were performed through the disc diffusion method in Mueller Hinton Agar (MHA) culture medium and also the optical density (OD) method was performed by a UV-Vis spectrophotometer in Trypticase™ Soy Broth (TSB) medium. Then, in order to compare the antibacterial effects of the applied NPs, several commercial antibiotics including penicillin, amikacin, ceftazidime and primaxin were used. RESULTS: The achieved results indicated that the antibacterial effects of ZnS NPs had a direct relation along with the concentrations and the concentration of 150 µg/mL showed the highest antibacterial effect in comparison with others. In addition, the ZnS NPs were more effective on Acinetobacter baumannii. CONCLUSION: The findings of this research suggest a novel approach against antibiotic resistance.

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.

Updates on Novel Erythropoiesis-Stimulating Agents: Clinical and Molecular Approach.

Erythropoietin (EPO) is an important hormone responsible for the stimulation of hematopoiesis which is impaired in a variety of diseases, such as chronic kidney disease, cancer chemotherapy, and the use of some anti-HIV drugs. Difficulties in the purification of endogenous EPO due to problems such as technical limitations, heterogeneity of target cells, inadequate amount and immunogenicity of the resultant product, had limited the entry of endogenous EPO in the clinical applications. The integration of medical biotechnology and hematology has introduced novel procedures for the production of human recombinant erythropoietin (rHuEPO), and other erythropoiesis-stimulating agents (ESAs). To investigate and produce rHuEPO, the first step is to recognize the molecular biology and functional pathways, structure, metabolism, and basic physiology of EPO. In this review, all clinical indications, side effects, challenges and notable points regarding EPO, rHuEPO, and other ESAs have also been addressed along with its molecular characterization, such as the modifications needed to optimize their rHuEPO biosynthesis.

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.

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.

Identification of HLA-I restricted epitopes in six vaccine candidates of Leishmania tropica using immunoinformatics and molecular dynamics simulation approaches.

In spite of numerous studies on vaccination for various species of Leishmania, research on the development of an effective vaccine for L. tropica is very scarce. In silico epitope prediction is a new way to survey the best vaccine candidates. Here, we predicted the best epitopes of six L. tropica antigens with vaccine capability against this pathogen, using highly frequent HLA-I alleles. Based on the frequent HLA alleles, the protein sequences were screened individually using four different MHC prediction applications, namely SYFPEITHI, ProPredI, BIMAS, and IEDB. Several in silico assays including clustering, human similarity exclusion, epitope conservancy prediction, investigating in experimental records, immunogenicity prediction, and prediction of population coverage were performed to narrow the results and to find the best epitopes. The selected epitopes and their restricted HLA-I alleles were docked and the final epitopes with the lowest binding energy (the highest binding affinity) were chosen. Finally, the stability and the binding properties of the best epitope-HLA-I combinations were analyzed using molecular dynamics simulation studies. We found ten potential peptides with strong binding affinity to highly frequent HLA-I alleles that can be further evaluated as vaccine targets against L. tropica.