Different aspects in explaining how mutations could affect the binding mechanism of receptor binding domain of SARS-CoV-2 spike protein in interaction with ACE2.

During replication, some mutations occur in SARS-CoV-2, the causal agent of COVID-19, leading to the emergence of different variants of the virus. The mutations that accrue in different variants of the virus, influence the virus' ability to bind to human cell receptors and ability to evade the human immune system, the rate of viral transmission, and effectiveness of vaccines. Some of these mutations occur in the receptor binding domain (RBD) of the spike protein that may change the affinity of the virus for the ACE2 receptor. In this study, several in silico techniques, such as MD and SMD simulations, were used to perform comparative studies to deeply understand the effect of mutation on structural and functional details of the interaction of the spike glycoprotein of SARS-CoV-2, with the ACE2 receptor. According to our results, the mutation in the RBD associated with the Omicron variant increase binding affinity of the virus to ACE2 when compared to wild type and Delta variants. We also observed that the flexibility of the spike protein of the Omicron variant was lower than in comparison to other variants. In summary, different mutations in variants of the virus can have an effect on the binding mechanism of the receptor binding domain of the virus with ACE2.

In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS-CoV-2 infected millions of people in the world and immediately became a pandemic in March 2020. SARS-CoV-2 belongs to the beta-coronavirus genus of the large family of Coronaviridae. It is now known that its surface spike glycoprotein binds to the angiotensin-converting enzyme-2 (ACE2), which is expressed on the lung epithelial cells, mediates the fusion of the cellular and viral membranes, and facilitates the entry of viral genome to the host cell. Therefore, blocking the virus-cell interaction could be a potential target for the prevention of viral infection. The binding of SARS-CoV-2 to ACE2 is a protein-protein interaction, and so, analyzing the structure of the spike glycoprotein of SARS-CoV-2 and its underlying mechanism to bind the host cell receptor would be useful for the management and treatment of COVID-19. In this study, we performed comparative in silico studies to deeply understand the structural and functional details of the interaction between the spike glycoprotein of SARS-CoV-2 and its cognate cellular receptor ACE2. According to our results, the affinity of the ACE2 receptor for SARS-CoV-2 was higher than SARS-CoV. According to the free energy decomposition of the spike glycoprotein-ACE2 complex, we found critical points in three areas which are responsible for the increased binding affinity of SARS-CoV-2 compared with SARS-CoV. These mutations occurred at the receptor-binding domain of the spike glycoprotein that play an essential role in the increasing the affinity of coronavirus to ACE2. For instance, mutations Pro462Ala and Leu472Phe resulted in the altered binding energy from - 2 kcal mol-1 in SARS-COV to - 6 kcal mol-1 in SARS-COV-2. The results demonstrated that some mutations in the receptor-binding motif could be considered as a hot-point for designing potential drugs to inhibit the interaction between the spike glycoprotein and ACE2.

Targeting cell cycle protein in gastric cancer with CDC20siRNA and anticancer drugs (doxorubicin and quercetin) co-loaded cationic PEGylated nanoniosomes.

BACKGROUND AND PURPOSE: In a past study, we developed and optimized a novel cationic PEGylated niosome containing anticancer drugs (doxorubicin or quercetin) and siRNA. This study intended to evaluate the anti-tumor effects of the combination therapy to target both the proteins and genes responsible for the development of gastric cancer. CDC20, known as an oncogene, is a good potential therapeutic candidate for gastric cancer. METHODS: In order to increase the loading capacity of siRNA and achieve appropriate physical properties, we optimized the cationic PEGylated niosome in terms of the amount of the cationic lipids. Drugs (doxorubicin and quercetin) and CDC20siRNA were loaded into the co-delivery system, and physical characteristics, thermosensitive controlled-release, gene silencing efficiency, and apoptosis rate were determined. RESULTS: The results showed that the designed co-delivery system for the drugs and gene silencer had an appropriate size and a high positive charge for loading siRNA, and also showed a thermosensitive drug release behavior, which successfully silenced the CDC20 expression when compared with the single delivery of siRNA or the drug. Moreover, the co-delivery of drugs and CDC20siRNA exhibited a highly inhibitory property for the cell growth of gastric cancer cells. CONCLUSION: It seems that the novel cationic PEGylated niosomes co-loaded with anticancer drug and CDC20siRNA has a promising application for the treatment of gastric cancer.

Gene expression profile evaluation of integrins in 3T3-L1 cells differentiated to adipocyte, insulin resistant and hypertrophied cells.

Integrins are cell attachment receptors that function in the communication between the intracellular and extracellular compartments. Integrins and extra cellular matrix (ECM) collaborate to regulate gene expression by extracellular signal-regulated kinases (ERKs). Integrins as regulators, have critical role in ECM remodeling. Fibrosis is the hallmark of obesity and insulin resistance originated by aberrant ECM remodeling. Therefore deciphering integrins' expression profile in cells at different conditions is worthy. The aim of this study is evaluation of integrins' gene expression profile changes in mouse 3T3-L1 preadipocytes, adipocytes, insulin resistant and hypertrophic adipocytes. For this purpose, we differentiated mouse 3T3-L1 preadipocytes to adipocytes, insulin resistant and hypertrophied adipocytes and assayed integrins' gene expression in four conditions by real time-PCR. Also the proteins expression changes of ERK and collagen VI assayed by Western blotting. Data analysis has shown that integrins' gene expression changes throughout adipocyte differentiation and pathological processes. The expressions of many integrins genes were significantly up- or down-regulated by >1.5-fold during differentiation, insulin resistant, and hypertrophic adipocytes. In addition to changes in the type of integrin, the integrins expression levels were different. Integrins, on the whole were more expressed in pathological processes relative to normal adipocytes. Also, phosphorylation of ERK 1,2 was increased >1.5-fold in differentiated, insulin resistant and hypertrophied adipocytes versus preadipocytes. Collagen VI only increased 2-fold in hypertrophied adipocytes. Examination of the total integrin gene family expression during adipocyte differentiation and pathological processes, leads to the identification of differential integrin gene expression. These results suggest that the type of integrin may not only play a role in adipocyte differentiation but also in pathological processes which may associate to increased ERK pathway activity in these conditions.

Novel Peptide Inhibitors for Lactate Dehydrogenase A (LDHA): A Survey to Inhibit LDHA Activity via Disruption of Protein-Protein Interaction.

Lactate dehydrogenase A (LDHA) is a critical metabolic enzyme belonging to a family of 2-hydroxy acid oxidoreductases that plays a key role in anaerobic metabolism in the cells. In hypoxia condition, the overexpression of LDHA shifts the metabolic pathway of ATP synthesis from oxidative phosphorylation to aerobic glycolysis and the hypoxia condition is a common phenomenon occurred in the microenvironment of tumor cells; therefore, the inhibition of LDHA is considered to be an excellent strategy for cancer therapy. In this study, we employed in silico methods to design inhibitory peptides for lactate dehydrogenase through the disturbance in tetramerization of the enzyme. Using peptide as an anti-cancer agent is a novel approach for cancer therapy possessing some advantages with respect to the chemotherapeutic drugs such as low toxicity, ease of synthesis, and high target specificity. So peptides can act as appropriate enzyme inhibitor in parallel to chemical compounds. In this study, several computational techniques such as molecular dynamics (MD) simulation, docking and MM-PBSA calculation have been employed to investigate the structural characteristics of the monomer, dimer, and tetramer forms of the enzyme. Analysis of MD simulation and protein-protein interaction showed that the N-terminal arms of each subunit have an important role in enzyme tetramerization to establish active form of the enzyme. Hence, N-terminal arm can be used as a template for peptide design. Then, peptides were designed and evaluated to obtain best binders based on the affinity and physicochemical properties. Finally, the inhibitory effect of the peptides on subunit association was measured by dynamic light scattering (DLS) technique. Our results showed that the designed peptides which mimic the N-terminal arm of the enzyme can successfully target the C-terminal domain and interrupt the bona fide form of the enzyme subunits. The result of this study makes a new avenue to disrupt the assembly process and thereby oppress the function of the LDHA.

Immobilization of the Alkaline Phosphatase on Collagen Surface via Cross-Linking Method.

BACKGROUND: Collagen, the most abundant protein in the human body, and as an extracellular matrix protein, has an important role in the fiber formation. This feature of the collagen renders establishment of the structural skeleton in tissues. Regarding specific features associated with the collagen, such as, formation of the porous structure, permeability and hydrophilicity, it can also be used as a biocompatible matrix in the enzyme engineering. OBJECTIVES: The aim of the present study was to investigate the application of the type I collagen as a matrix for alkaline phosphatase immobilization using cross-linking method. MATERIALS AND METHODS: The Alkaline phosphatase was covalently immobilized on collagen matrix by using 1-ethyl-3- (dimethylaminopropyl) carbodiimide hydrochloride (EDC). The source of the alkaline phosphatase was from the bovine intestinal mucous. After that, the activity of the immobilized enzyme was assayed under different experimental conditions. RESULTS: The optimum pH was similar to that of the free enzyme, whereas the optimum temperature and thermal stability were shown some increments. The surface topography of the collagen matrix containing immobilized enzyme and ALP (Alkaline phosphatase) deficient was investigated by Atomic-force microscopy (AFM). Images that have been obtained applying AFM show significant differences between uncovered and immobilized enzyme- matrix surface topography. CONCLUSIONS: Our findings suggest that type I collagen can be utilized as a matrix for alkaline phosphatase immobilization via cross-linking method.

Comparison of Phenotypic Characterization between Differentiated Osteoblasts from Stem Cells and Calvaria Osteoblasts In vitro.

BACKGROUND: Characteristics of differentiated osteoblasts from adipose derived stem cells (ADSCs) in compared with isolated osteoblasts from normal bone such as calvaria are unknown. The aim of this study was determination and comparison of phenotypic characterization between differentiated osteoblasts from stem cells and calvaria osteoblasts in vitro. METHODS: In this study, mesenchymal stem cells were isolated from adipose tissue of human by enzymatic digestion and were differentiated into osteoblasts using osteogenic medium. Characteristics of these cells at first, second, third and fourth weeks were comprised with calvaria osteoblasts that were isolated from human calvaria by explanation culture method. To screen the characteristics of both calvaria and the differentiated osteoblasts, we used western blot to identify protein levels, von Kossa staining for mineral matrix detection and alkaline phosphatase (ALP) assay kit (Sigma) for ALP activity measurement. Difference between calvaria and differentiated osteoblast cells were analyzed by one-way ANOVA and P < 0.05 was considered as statistically significant. RESULTS: Alkaline phosphatase activity, collagen and mineral material production in differentiated osteoblasts at third week were more significantly than calvaria cells (P < 0.05). Our results indicated that there was no significant different in osteocalcin (OC) production between differentiated osteoblast at first, second and third weeks and calvaria cells but declined at fourth week (P < 0.05). CONCLUSIONS: Our survey showed that cellular traits of differentiated osteoblasts presented better than calvaria osteoblasts in vitro conditions. Therefore, we suggest that ADSCs could be used in next studies for bone tissue engineering.

Stability improvement of immobilized lactoperoxidase using polyaniline polymer.

Enzyme engineering via immobilization techniques is perfectly compatible against the other chemical or biological approximate to improve enzyme functions and stability. In this study lactoperoxidase was immobilized onto polyaniline polymer activated with glutaraldehyde as a bifunctional agent, to improve enzyme properties. Polyaniline polymer was used due its unique physical and chemical properties to immobilize lactoperoxidase (LPO). The optimum activity of immobilized LPO was observed at pH 6 and 55 °C, which has been increased about 10 °C for the immobilized enzyme. The immobilized enzyme maintained absolutely active for 60 days whereas the native enzyme lost 80 % of its initial activity within this period of time. Moreover, the immobilized enzyme can be reused for several times without loss of activity. The kinetic parameter studies showed slight differences between free and immobilized enzymes. The K(m) and K(m.app) were calculated to be 0.6 and 0.4; also V(max) and V(max.app) were 1.3 and 0.9 respectively.

Association between mismatch repair gene MSH3 codons 1036 and 222 polymorphisms and sporadic prostate cancer in the Iranian population.

The mismatch repair system (MMR) is a post-replicative DNA repair mechanism whose defects can lead to cancer. The MSH3 protein is an essential component of the system. We postulated that MSH3 gene polymorphisms might therefore be associated with prostate cancer (PC). We studied MSH3 codon 222 and MSH3 codon 1036 polymorphisms in a group of Iranian sporadic PC patients. A total of 60 controls and 18 patients were assessed using the polymerase chain reaction and single strand conformational polymorphism. For comparing the genotype frequencies of patients and controls the chi-square test was applied. The obtained result indicated that there was significantly association between G/A genotype of MSH3 codon 222 and G/G genotype of MSH3 codon 1036 with an increased PC risk (P=0.012 and P=0.02 respectively). Our results demonstrated that MSH3 codon 222 and MSH3 codon 1036 polymorphisms may be risk factors for sporadic prostate cancer in the Iranian population.