Younes Ghasemi

Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus

Staphylococcus aureus is a pathogen that causes a variety of infections in humans. Methicillin-resistant S. aureus, which is an antibiotic-resistant form, is responsible for nosocomial staphylococcal infections, whose frequency is increasing in healthy people. Thereby, the development of novel techniques is required to overcome this bacterial infection. In this context, the use of vaccines to control infections is an appropriate alternative. In this study, immunoinformatics analysis is used on three antigenic determinants as vaccine candidates, and a novel multi-epitope vaccine is designed to induce cellular, humoral, and innate immune responses against S. aureus. Alpha-enolase, clumping factor A, and iron surface determinant B were selected as the protective antigens; and phenol-soluble modulin alpha 4was applied as the adjuvant. Epitopes identification was done for each antigen using various immunoinformatics servers. Moreover, the tertiary structure of our protein vaccine was predicted and validated. Subsequently, the best-modeled protein structure was used for the refinement process. There fined model was then applied for docking studies with Toll-like receptor 2 (TLR2).In the next step, molecular dynamics (MD) simulation was used to evaluate the stability of vaccine molecule and TLR2-vaccine complex. The high ranked epitopes were selected from the mentioned antigens. The selected epitopes and the adjuvant were fused together by proper linkers. Then, the modeled protein structure was selected and validated. Validation results indicated that the initial model needs refinement. After a refinement process, the final model was generated. Finally, the best-docked model of vaccine and TLR2 complex was selected. In this research, we attempted to design an efficient subunit vaccine, which could stimulate humoral and cellular immune responses. Therefore, we expect that our designed vaccine could defeat antibiotic-resistant staphylococcal infections.

In Silico Sub-unit Hexavalent Peptide Vaccine Against an Staphylococcus aureus Biofilm-Related Infection

Staphylococcus aureus is responsible for significant and increasing number of hospital-and community-acquired infections worldwide. A pool of pathogenesis factors helps the bacterium to cause the range of mild to severe infections leading the high mortality and morbidity. Staphylococcus aureus and Candida albicans can be co-isolated from all human mucosal sites and are responsible for diverse infections. Vaccine design for related polymicrobial infections should consider the consortia of microorganisms responsible for the disease. In this study we considered biofilm mode of growth and polymicrobial nature of the infections caused by S. aureus. In the first phase of study the prediction of putative antigenic targets of S. aureus and C. albicans was conducted based on data mining and bioinformatic characterization of their proteins. Various properties of proteins were evaluated such as subcellular localization, hydrophilicity, repeat containing modules, beta turns, surface accessibility and number of antigenic determinants. The second phase includes various immunoinformatics analyses on six proteins include ALS, ClfA, FtmB, SdrE, Spa and Bap leading to design a novel sub-unit hexavalent vaccine. Several potential T cell and B-cell epitopes are present in our vaccine. Also the vaccine is expected to strongly induce IFN-gamma production. The amino acid sequence introduced here is expected to enhance cell-mediated and humoral responses against S. aureus biofilm-related infections to clear biofilm communities of S. aureus and intracellular colonies of pathogen as well as planktonic cells and thus reduces colonization and persistence.

Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) system is a novel type of innate defense system in prokaryotes for destruction of exogenous elements. To gain further insight into behavior and organization of the system, the extensive analysis of the available sequenced genomes is necessary. The dynamic nature of CRISPR loci is possibly valuable for typing and relative analyses of strains and microbial population. There are a few orderly bioinformatics investigations about the structure of CRISPR sequences in the Escherichia coli strains. In this study, 57 CRISPR loci were selected from 32 Escherichia coli strains to investigate their structural characteristics and potential functions using bioinformatics tools. Our results showed that most strains contained several loci that mainly included conserved direct repeats, while the spacers were highly variable. Moreover, RNA analysis of the sequences indicated that all loci could form stable RNA secondary structures and showed homology mostly with phages compared to plasmids. Only three strains included cas genes around their loci.

A novel HPV prophylactic peptide vaccine, designed by immunoinformatics and structural vaccinology approaches

Human papillomavirus (HPV)-caused cervical cancer is the fourth common female cancer globally. Despite availability of three effective vaccines in market, development of HPV prophylactic vaccines is still pursued due to affordability issues and type-restricted protection of the marketed vaccines. Investigational second generation prophylactic HPV vaccines are mostly exploiting epitopes from the virus minor capsid protein (L2), which despite many advantages suffer from low immunogenicity, a common problem of epitope vaccines. Adjuvants such as TLR agonists may overcome this drawback. In this study, different immunoinformatics and computational tools were employed to design a novel peptide vaccine for protection against cervical cancer. Two immunodominant epitope domains (amino acids 10-36 and 65-89) from the L2 protein of HPV 16 with potential to promote Th1, Th2, CTL, B-cell, and INF-gamma responses were selected. Flagellin, as a TLR5 agonist, a short synthetic TLR4 agonist, and two universal T-helper agonists (PADRE and TpD) were added to ensure strong induction of immune responses. Different segments were joined by proper linkers, and the physicochemical, structural, and immunological characteristics of the resultant construct were evaluated. Modeling, refinement, and validation were done to achieve a high quality 3D structure of the vaccine protein. Docking and molecular dynamics (MD) studies demonstrated an appropriate and stable interaction between the vaccine and TLR5 during the simulation period. Totally, a potential vaccine candidate with proper immunological and physicochemical properties was designed for HPV prophylaxis. The designed vaccine is expected to be capable of generating humoral and cellular responses, which are vital for protection against HPV.

Production of a novel multi-epitope peptide vaccine for cancer immunotherapy in TC-1 tumor-bearing mice

In our previous research, several bioinformatic strategies were utilized to design an efficient multi-epitope peptide vaccine (MEV) against cancer. The designed vaccine consists of Wilms tumor-1 (WT-1) and human papillomavirus (HPV) E7 cytotoxic T lymphocyte (CTL) epitopes, tetanus toxin fragment C (TTFrC) and HLA-DR epitope (PADRE) helper T lymphocyte (HTL) epitopes and heparin-binding hemagglutinin (HBHA) as an immunostimulatory adjuvant. All segments were fused together by suitable linkers. In the current study, we cloned and expressed the designed MEV in E. coli. We subsequently performed in vivo preventative and therapeutic assays to evaluate antitumor efficacy of the vaccine against the HPV-16 E7-expressing murine tumor cell line TC-1 as a model for cancer immunotherapy. The results showed that in preventive experiments, vaccination with MEV significantly augmented the IgG antibody titer and the percentage of tumor-free mice compared to control groups (PBS and E7). Moreover, in therapeutic experiments, vaccination with MEV led to a reduction in the number of metastatic nodules, lung weights and the ratio of lung weights to body weights compared to other groups. In sum, our epitope vaccine could efficiently induce preventive and therapeutic antitumor immunity in TC-1 tumor bearing mice.

Modification in Media Composition to Obtain Secretory Production of STxB-based Vaccines using Escherichia coli

Shiga toxin B-subunit (STxB) from Shigella dysenteriae targets in vivo antigen to cancer cells, dendritic cells (DC) and B cells, which preferentially express the globotriaosylceramide (Gb3) receptor. This pivotal role has encouraged scientists to investigate fusing STxB with other clinical antigens. Due to the challenges of obtaining a functional soluble form of the recombinant STxB, such as formation of inclusion bodies during protein expression, scientists tend to combine STxB with vaccine candidates rather than using their genetically fused forms. In this work, we fused HPV16 E7 as a vaccine candidate to the recombinantly-produced STxB. To minimize the formation of inclusion bodies, we investigated a number of conditions during the expression procedure. Then various strategies were used in order to obtain high yield of soluble recombinant protein from E. coli which included the use of different host strains, reduction of cultivation temperature, as well as using different concentrations of IPTG and different additives (Glycin, Triton X-100, ZnCl2). Our study demonstrated the importance of optimizing incubation parameters for recombinant protein expression in E. coli; also showed that the secretion production can be achieved over the course of a few hours when using additives such as glycine and Triton X-100. Interestingly, it was shown that when the culture mediums were supplemented by additives, there was an inverse ratio between time of induction (TOI) and the level of secreted protein at lower temperatures. This study determines the optimal conditions for high yield soluble E7-STxB expression and subsequently facilitates reaching a functionally soluble form of STxB-based vaccines, which can be considered as a potent vaccine candidate for cervical cancer.

New Developments in Pichia pastoris Expression System, Review and Update

BACKGROUND Although Pichia pastoris is an outstanding host among conventional expression systems for production of recombinant proteins, a new interest has been emerged to this system due to the inherent advantages and new developments in this expression host. The potential for secretory and soluble expression of heterologous glycoproteins in P. pastoris proposed this system as a candidate for the production of complex eukaryotic proteins. METHODS Several new developments have occurred in different areas related to P. pastoris expression system including hosts, vectors, glycosylation pattern and fermentation technology. Strain engineering using Crispr/Cas9 technology to produce human-like glycoproteins and protease deficient strains are two new areas of development with high importance. RESULTS This review is dedicated to discuss the most important characteristics of P. pastoris with emphasis on new developments, especially in the field of glycoengineering, efficient expression vectors and promoters. CONCLUSION New developments that occurred in the P. pastoris expression system converted this system to a versatile host for the production of complex proteins. This progress paved the way for several proteins to enter the clinical trials or industrial processes with this valuable expression host.

Microbial calcium carbonate precipitation with high affinity to fill the concrete pore space: nanobiotechnological approach

Despite the advantages of concrete, it has a pore structure and is susceptible to cracking. The initiated cracks as well as pores and their connectivity accelerate the structure degradation by permitting aggressive substances to flow into the concrete matrix. This phenomenon results in a considerable repair and maintenance costs and decreases the concrete lifespan. In recent years, biotechnological approach through immobilization of bacteria in/or protective vehicles has emerged as a viable solution to address this issue. However, the addition of macro- or micro scale size particles can decrease the integrity of matrix. In this study, the immobilization of bacteria with magnetic iron oxide nanoparticle (ION) was proposed to protect the bacterial cell and evaluate their effect on healing the concrete pore space. The results show that the addition of immobilized bacteria with IONs resulted in a lower water absorption and volume of permeable pore space. Crystal analysis using scanning electron microscope (SEM) and energy dispersive X-ray spectroscopy (EDS) revealed that CaCO3 was precipitated in bio-concrete specimen as a result of microbial biosynthesis.

Chemical and biological approaches for the synthesis of iron based nanoparticles

Iron based nanoparticles are one of the most applicable and studied nanostructures in various sciences and technologies. These nanoparticles are also introduced to the pharmaceutical and biomedical sciences due to their unique physicochemical properties such as super par magnetism, ease of synthesis, and biocompatibility. Several techniques are now developed and available for the preparation of iron based nanoparticles. Including chemical synthesis and biological synthesis which can be divided into microbial synthesis and plant mediated synthesis. Coprecipitation reaction is introduced as the main chemical method for the synthesis of magnetite nanoparticles as one of the most applied iron nanoparticle. The main approaches in biosynthesis of iron nanoparticles are also reviewed as microbial and plant mediated synthesis. In this mini review we are going to have an over view upon the main approaches for the synthesis of iron nanoparticles.