In silico Evaluation of PLAC1-fliC As a Chimeric Vaccine against Breast Cancer

Designing of a Multi-Epitope Antigen for Toxocariasis Diagnosis: An in Silico Approach

BACKGROUND

Toxoariasis is recognized as one of the most widespread diseases affecting both animals and humans, exhibiting a global distribution. In light of the public health challenges it poses, particularly for children infected with Toxocara canis, the development of effective diagnostic tests or vaccines is of paramount importance. Serological methods are routinely employed to detect specific anti-Toxocara antibodies in infected individuals. This bioinformatics study aims to formulate a multi-epitope protein for Toxocara canis, leveraging various immunoinformatics web servers to enhance the accuracy of serodiagnosis.

METHODS

The identification of linear and conformational B-cell epitopes for the antigens TES-26, TES-30, and TES-120 was conducted using the ABCpred and BepiPred servers. Various web servers were employed to evaluate antigenicity, solubility, and physicochemical properties, as well as to examine secondary and tertiary structures, enhance the three-dimensional model, and confirm the findings.

RESULTS

This process led to the identification of conformational B-cell epitopes, aimed at exploring possible protein-antibody interactions.

CONCLUSION

Ultimately, further experimental investigations are essential for this multi-epitope construct before it can be incorporated into commercial serodiagnosis kits.

Designing a Secretory form of RTX-A as an Anticancer Toxin: An In Silico Approach

BACKGROUND

Cancer is a leading cause of death and a significant public health issue worldwide. Standard treatment methods such as chemotherapy, radiotherapy, and surgery are only sometimes effective. Therefore, new therapeutic approaches are needed for cancer treatment. Sea anemone actinoporins are pore-forming toxins (PFTs) with membranolytic activities. RTX-A is a type of PFT that interacts with membrane phospholipids, resulting in pore formation. The synthesis of recombinant proteins in a secretory form has several advantages, including protein solubility and easy purification. In this study, we aimed to discover suitable signal peptides for producing RTX-A in Bacillus subtilis in a secretory form.

METHODS

Signal peptides were selected from the Signal Peptide Web Server. The probability and secretion pathways of the selected signal peptides were evaluated using the SignalP server. ProtParam and Protein-sol were used to predict the physico-chemical properties and solubility. AlgPred was used to predict the allergenicity of RTX-A linked to suitable signal peptides. Non-allergenic, stable, and soluble signal peptides fused to proteins were chosen, and their secondary and tertiary structures were predicted using GOR IV and I-TASSER, respectively. The PROCHECK server performed the validation of 3D structures.

RESULTS

According to bioinformatics analysis, the fusion forms of OSMY_ECOLI and MALE_ECOLI linked to RTX-A were identified as suitable signal peptides. The final proteins with signal peptides were stable, soluble, and non-allergenic for the human body. Moreover, they had appropriate secondary and tertiary structures.

CONCLUSION

The signal above peptides appears ideal for rationalizing secretory and soluble RTX-A. Therefore, the signal peptides found in this study should be further investigated through experimental researches and patents.

MicroRNA electrochemical biosensors for pancreatic cancer

Pancreatic cancer (PC) is one of the deadliest cancers worldwide. MicroRNAs (miRs) are sensitive molecular diagnostic tools that can serve as highly accurate biomarkers in many disease states in general and cancer specifically. MiR-based electrochemical biosensors can be easily and inexpensively manufactured, making them suitable for clinical use and mass production for point-of-care use. This paper reviews nanomaterial-enhanced miR-based electrochemical biosensors in pancreatic cancer detection, analyzing both labeled and label-free approaches, as well as enzyme-based and enzyme-free methods.

Laccase: Various types and applications

Laccase belongs to the polyphenol oxidase family and is very important in removing environmental pollutants due to its structural and functional properties. Recently, the ability of laccase to oxidize phenolic and nonphenolic substances has been considered by many researchers. This enzyme's application scope includes a broad range of chemical processes and industrial usages, such as bioremediation, nanobiotechnology, woodworking industries, bleaching of paper pulp, dyeing in the textile industry, biotechnological uses in food industries, biorefining, detoxification from wastewater, production of organic matter from phenolic and amine substrates, and biofuels. Although filamentous fungi produce large amounts of laccase, high-yield industrial-scale production of laccase is still faced with many problems. At present, researchers are trying to increase the efficiency and productivity and reduce the final price of laccase by finding suitable microorganisms and improving the process of production and purification of laccase. This article reviews the introduction of laccase, its properties, production processes, and the effect of various factors on the enzyme's stability and activity, and some of its applications in various industries.

Designing a Multi-Epitope Antigen for Serodiagnosis of Strongyloides stercoralis Based on L3Nie.01 and IgG Immunoreactive Epitopes

BACKGROUND

Serological diagnosis of Strongyloides stercoralis (S. stercoralis) is fre-quently challenging because of cross-reactivity with other parasitic nematodes. Therefore, it is necessary to introduce novel serological tests with high performance to properly diagnose this neglected parasitic infection. The purpose of the current study was to design a multi-epitope construct for the diagnosis of S. stercoralis.

METHODS

For the purpose of this study, first, highly antigenic segments and potential immunodominant epitopes of S. stercoralis were identified from two antigenic proteins, and then all of the selected parts were linked by an appropriate linker. Next, the physicochemical features of the designed construct were analyzed. Then, tertiary structures of the construct were built and evaluated to find out the best one. Lastly, the amino acid sequence was reverse-translated and optimized for over-expression in Escherchia coli (E. coli).

RESULTS

The bioinformatic evaluation indicated that the designed protein construct could be hydrophilic, thermostable, and acidic and the estimated half-life was more than 10 hr in E. coli.

CONCLUSION

According to the results of the study, the designed construct could be used as an efficient antigen in the ELISA system for serological diagnosis of human strong-yloidiasis.

Design of a new multi-epitope peptide vaccine for non-small cell Lung cancer via vaccinology methods: an in silico study

Lung cancer is the most common type of tumor worldwide. Non-small-cell lung carcinoma (NSCLC) is considered any epithelial cell-related lung cancer, which includes more than 85% of all lung cancer cases. NSCLC is less responsive to chemotherapy than SCLC. Therefore, the need for other treatments has become more pronounced and immunotherapy has gained increasing attention as a promising therapy in recent years. The current study aimed to design a multi-epitope peptide vaccine targeting main cancer/testis antigens of SP17, AKAP4, and PTTG1, which have a major function in tumor cell proliferation invasion. The protein vaccine was constructed using the rigorous immunoinformatics analysis and investigation of several immune system parameters, considering B cell epitopes and CD4 and CD8 induced epitopes as the most important cells to respond to cancer cells. Inverse translation and optimization of codons were performed to have the designed protein's cloning as well as expression potential in E.coli. Physicochemical, antigenic, and allergenic features were assessed to confirm the safety and immunogenicity of the vaccine. The secondary and tertiary structures were predicted. Finally, intrinsic disorder and 3D model refinement and validation were performed to eliminate structural problems. The designed construct had a stable structure that could be an antigen and stimulate the immune system and not be an allergen. The built model 3D structure was valid and stable. Further investigations are needed to approve the safety and immunogenic property of this new vaccine for NSCLC before it can be used in patients.

Finding Appropriate Signal Peptides for Secretory Production of Recombinant Glucarpidase: An In SilicoMethod

BACKGROUND

Methotrexate (MTX) is a general chemotherapeutic agent utilized to treat a variety of malignancies, woefully, its high doses can cause nephrotoxicity and subsequent defect in the process of MTX excretion. The recombinant form of glucarpidase is produced by engineered E. coli and is a confirmed choice to overcoming this problem.

OBJECTIVE

In the present study, in silico analyses were performed to select suitable SPs for the secretion of recombinant glucarpidase in E. coli.

METHODS

The signal peptide website and UniProt database were employed to collect the SPs and protein sequences. In the next step, SignalP-5.0 helped us to predict the SPs and the position of cleavage sites. Moreover, physicochemical properties and solubility were evaluated using Prot- Param and Protein-sol online software, and finally, ProtCompB was used to predict the final subcellular localization.

RESULTS

Luckily, all SPs could form soluble fusion proteins. At last, it was found that PPB and TIBA could translocate the glucarpidase into the extracellular compartment.

CONCLUSION

This study showed that there are only 2 applicable SPs for the extracellular translocation of glucarpidase. Although the findings were remarkable with high degrees of accuracy and precision based on the utilization of bioinformatics analyses, additional experimental assessments are required to confirm and validate it. Recent patents revealed several inventions related to the clinical aspects of vaccine peptides against human disorders.

Placenta-specific protein 1 promotes cell proliferation via the AKT/GSK-3β/cyclin D1 signaling pathway in gastric cancer

Gastric cancer is a malignant tumor with a poor prognosis. Therefore, it is important to search for molecules that play a vital role in the development, diagnosis, and treatment of this disease. Placenta-specific 1 (PLAC1) is one of the cancer-testis antigens; it plays an important role in both placental development and tumorigenesis. However, the role of PLAC1 in gastric cancer has not been fully investigated, and its underlying mechanism needs further study. We first explored the expression and clinical relevance of PLAC1 in gastric cancer and performed gene set enrichment analysis of PLAC1-related genes using online databases. Subsequently, we studied the function and mechanism of PLAC1 in gastric cancer cells through in vitro experiments. Our results showed that PLAC1 is highly expressed in gastric cancer, is associated with poor prognosis, and can promote gastric cancer cell proliferation through the AKT/GSK-3β/cyclin D1 signaling pathway. Moreover, we discovered that AKTi attenuates the effect of PLAC1. Our study further revealed the role and mechanism of PLAC1 in gastric cancer and suggested that this antigen might be a useful molecular marker for gastric cancer diagnosis, prognosis, and treatment.

Glucose oxidase: Applications, sources, and recombinant production

Glucose oxidase is a subset of oxidoreductase enzymes that catalyzes the transfer of electrons from an oxidant to a reductant. Glucose oxidases use oxygen as an external electron acceptor that releases hydrogen peroxide (H₂ O₂ ). Glucose oxidase has many applications in commercial processes, including improving the color and taste, increasing the persistence of food materials, removing the glucose from the dried egg, and eliminating the oxygen from different juices and beverages. Moreover, glucose oxidase, along with catalase, is used in glucose testing kits (especially in biosensors) to detect and measure the presence of glucose in industrial and biological solutions (e.g., blood and urine specimens). Hence, glucose oxidase is a valuable enzyme in the industry and medical diagnostics. Therefore, evaluating the structure and function of glucose oxidase is crucial for modifying as well as improving its catalytic properties. Finding different sources of glucose oxidase is an effective way to find the type of enzyme with the desired catalysis. Besides, the recombinant production of glucose oxidase is the best approach to produce sufficient amounts of glucose oxidase for various uses. Accordingly, the study of various aspects of glucose oxidase in biotechnology and bioprocessing is crucial.