Rupal Ojha

Immunoinformatics approaches to design a novel multi-epitope subunit vaccine against HIV infection

The end goal of HIV vaccine designing requires novel strategies to elicit a strong humoral and cell-mediated immune response. The emergence of drug resistance and the requirement of next line treatment necessitate the finding of the potential and immunogenic vaccine candidate. This study employed a novel immunoinformatics approach to design multi-epitope subunit vaccine against HIV infection. Here, we designed the subunit vaccine by the combination of CTL, HTL and BCL epitopes along with suitable adjuvant and linkers. Physiochemical characterization of subunit vaccine was assessed to ensure its thermostability, theoretical PI, and amphipathic behavior. In further assessment, subunit vaccine was found to be immunogenic with the capability to generate humoral and cell-mediated immune response. Further, homology modeling and refinement was performed and the refined modeled structure was used for molecular docking with the immune receptor (TLR-3) present on lymphocyte cells. Consequently, molecular dynamics simulation ensured the molecular interaction between TLR-3 and subunit vaccine candidate. Disulfide engineering was performed by placing the cysteine residues in the region of high mobility to enhance the vaccine stability. At last, in silico cloning was performed to warrant the translational efficiency and microbial expression of the designed vaccine.

Development of multi-epitope driven subunit vaccine in secretory and membrane protein of Plasmodium falciparum to convey protection against malaria infection

Malaria infection is the severe health concern for a long time. As per the WHO reports, the malarial infection causes huge mortality all around the world and is incomparable with any other infectious diseases. The absence of effective treatment options and increasing drug resistance to the available therapeutics like artemisinin and other derivatives demand an efficient alternative to overcome this death burden. Here, we performed the literature survey and sorted the Plasmodium falciparum secretory and membrane proteins to design multi-epitope subunit vaccine using an adjuvant, B-cell- and T-cell epitopes. Every helper T-lymphocyte (HTL) epitope was IFN-γ positive and IL-4 non-inducer. The physicochemical properties, allergenicity, and antigenicity of designed vaccine were analyzed for the safety concern. Homology modeling and refinement were performed to obtain the functional tertiary structure of vaccine protein followed by its molecular docking with the toll-like receptor-4 (TLR-4) immune receptor. Molecular dynamics simulation was performed to check the interaction and stability of the receptor-ligand complex. Lastly, in silico cloning was performed to generate the restriction clone of designed vaccine for the futuristic expression in a microbial expression system. This way, we designed the multi-epitope subunit vaccine to serve the people living in the global endemic zone.

Scrutinizing Mycobacterium tuberculosis membrane and secretory proteins to formulate multiepitope subunit vaccine against pulmonary tuberculosis by utilizing immunoinformatic approaches

Tuberculosis is a menacing disease caused eminently to the people inhabiting the tropical and sub-tropical nations. A holistic approach is required to generate T and B memory cells to effectuate a long-term exemption from the pulmonary tuberculosis. In this study, immunoinformatic approaches were used to design a multi-epitope-based subunit vaccine for pulmonary tuberculosis which may improve human immune system. The various B-cell, TH cell and TC cell binding epitopes were predicted for selected 2 membrane and 12 secretory proteins of Mycobacterium tuberculosis. The final vaccine construct was assembled by merging the predicted epitope sequences and an adjuvant at the N-terminal of the construct. Furthermore, the physiochemical characterization was done to check the molecular weight, aliphatic index, theoretical PI, hydropathicity and thermostable nature of the designed vaccine. The construct was a potential antigen while wasnt allergenic in nature. Tertiary modeling was performed, by filtering them a refined model was chosen and was docked with TLR-4 (immune receptor). Molecular docking and dynamic simulation was performed and the microscopic interaction between the vaccine construct (ligand) and TLR-4 receptor complex was verified. In silico cloning was used to fortify the expression and translation efficiency of the vaccine within an expression vector.

Conglomeration of novel Culex quinquefasciatus salivary proteins to contrive multi-epitope subunit vaccine against infections caused by blood imbibing transmitter

The southern house vector, Culex quinquefasciatus is the paramount cause of Japanese encephalitis, West Nile fever and Lymphatic Filariasis, which is globally affecting the worldwide population. Many attempts were made by researchers with different perceptions to discover regimen against these aforementioned ailments but the output was not that effectual. Consequently, there is an imminent need to develop very effective and potential treatment against these perilous diseases. Employing immunoinformatic approaches, we have designed the multi-epitope subunit vaccine by exploring salivary proteins of Culex quinquefasciatus, which possess both antigenic and potent immunogenic behaviour. The immunogenic epitopes from the immune cells (B-cell, CTL, and HTL) were predicted and linked together with the help of linkers. Apart from this, at the N-terminal of the construct, an adjuvant was added in order to enhance the immunogenicity of the vaccine. The physiological parameters, antigenicity and allergenicity were also evaluated for the designed vaccine construct. Molecular docking between ligand (vaccine construct) and TLR-4 receptor was performed. Molecular dynamics simulation of the docked complex was performed to identify the stability, patterns, macromolecules interactions and their behaviour. Finally, to ensure the translation and gene expression efficiency of designed construct, insilico restriction cloning was executed into suitable expression vector pET28a.

Chemical system biology based molecular interactions to identify inhibitors against Q151M mutant of HIV-1 reverse transcriptase

The emergence of mutations leading to drug resistance is the main cause of therapeutic failure in the human HIV infection. Chemical system biology approach has drawn great attention to discover new antiretroviral hits with high efficacy and negligible toxicity, which can be used as a prerequisite for HIV drug resistance global action plan 2017-21. To discover potential hits, we docked 49 antiretroviral analogs (nu202f=u202f6294) against HIV-1 reverse transcriptase Q151M mutant & its wild-type form and narrow downed their number in three sequential modes of docking using Schrödinger suite. Later on, 80 ligands having better docking score than reference ligands (tenofovir and lamivudine) were screened for ADME, toxicity prediction, and binding energy estimation. Simultaneously, the area under the curve (AUC) was estimated using receiver operating characteristics (ROC) curve analysis to validate docking protocols. Finally, single point energy and molecular dynamics simulation approaches were performed for best two ligands (L3 and L14). This study reveals the antiretroviral efficacy of obtained two best ligands and delivers the hits against HIV-1 reverse transcriptase Q151M mutant.

Designing B- and T-cell multi-epitope based subunit vaccine using immunoinformatics approach to control Zika virus infection: PANDEY et al.

The Zika virus is a rapidly spreading Aedes mosquito‐borne sickness, which creates an unanticipated linkage birth deformity and neurological turmoil. This study represents the use of the combinatorial immunoinformatics approach to develop a multiepitope subunit vaccine using the structural and nonstructural proteins of the Zika virus. The designed subunit vaccine consists of cytotoxic T‐lymphocyte and helper T‐lymphocyte epitopes accompanied by suitable adjuvant and linkers. The presence of humoral immune response specific B‐cell epitopes was also confirmed by B‐cell epitope mapping among vaccine protein. Further, the vaccine protein was characterized for its allergenicity, antigenicity, and physiochemical parameters and found to be safe and immunogenic. Molecular docking and molecular dynamics studies of the vaccine protein with the toll‐like receptor‐3 were performed to ensure the binding affinity and stability of their complex. Finally, in silico cloning was performed for the effective expression of vaccine construct in the microbial system (Escherichia coli K12 strain). Aforementioned approaches result in the multiepitope subunit vaccine which may have the ability to induce cellular as well as humoral immune response. Moreover, this study needs the experimental validation to prove the immunogenic and protective behavior of the developed subunit vaccine.

Examination of antigenic proteins of Trypanosoma cruzi to fabricate an epitope-based subunit vaccine by exploiting epitope mapping mechanism

Chagas disease is a protozoan parasitic disease caused by Trypanosoma cruzi. This injurious disease spread by the circulation of the blood sucking triatomine insects and transmitted to humans. Chagas disease is endemic in Latin America and also known as American trypanosomasis. Currently, 7 million people are infected by T. cruzi infection and about 22,000 death cases were reported per year throughout the Americas. Various immunization approaches against T. cruzi infection have been examined and some of the developed vaccine showed efficacy in animal models but there is no effective and safe vaccines for humans have been developed yet. Since, the drug resistance is increasing day by day because the developed drug (nifurtimox and benznidazole) to control T. cruzi infection, failed to activate a prodrug and still no drug and vaccine have been established. To control the infection of chagas disease, here in this study we use immunoinformatics method to design multi-epitope subunit vaccine against T. cruzi infection. Moreover, on the basis of immunogenicity B and T cell epitopes were evaluated. The allergenicity, antigenicity was predicted to ensure the safety of vaccine constructs whereas, the physiochemical property showing the stable nature of final vaccine model. Further, molecular docking was performed to optimize the interaction between TLR-2 and TLR-4 (receptor) and vaccine model (ligand) complex. Molecular dynamics simulation was performed to evaluate the energy minimization; RMSD and RMSF plot which confirm the stability of TLR-2 and TLR-4 (receptor) present on immune cells and vaccine model (ligand) complex. This study needed the experimental validation for the safety and immunogenic behavior of designed vaccine protein and it may be helpful in future to control T. cruzi infection.

Emerging Role of Circular RNAs as Potential Biomarkers for the Diagnosis of Human Diseases

In the eukaryotic transcriptome, the evolutionary conserved circular RNAs naturally occur from the family of noncoding RNAs. Circular RNAs possess a unique feature to interact with nucleic acids and ribonucleoproteins and are establishing themselves as an obligatory composition for the regulatory messages which are encoded by the genome. The back-splicing mechanism leads to the formation of circularized RNA, and because of this they become resistant to exonuclease-mediated degradation. The differential and aberrant expression of circular RNAs can be detected with the help of various profiling methods by using serum, plasma, and tissue samples. In this chapter, we have highlighted the role of circular RNAs as putative biomarker for the detection of various human diseases along with its profiling methods. Here we have discussed the differentially expressed circular RNAs in neurological disorders and infectious diseases along with cancer diseases. For instance, in case of pulmonary tuberculosis, hsa_circRNA_001937 was upregulated, while hsa_circRNA_102101 got downregulated; Hsa_circ_000178 was depicted to get upregulated in breast cancer which is associated with disease progression. Furthermore, it has been observed that circRNAs are abundantly present within the mammalian brain tissues. In epileptic condition, Circ-EFCAB2 was observed to get notably upregulated within patients. Taking the above conditions into consideration, circular RNAs have proven themselves as promising noninvasive biomarker for the detection of human diseases.

Emerging role of circulating microRNA in the diagnosis of human infectious diseases: OJHA et al.

The endogenic microRNAs (miRNA) are evolutionary, conserved, and belong to a group of small noncoding RNAs with a stretch of 19–24 nucleotides. The miRNAs play an indispensable role in gene modulation at the posttranscriptional level, inclusive of stem‐cell differentiation, embryogenesis, hematopoiesis, metabolism, immune responses, or infections. The miRNAs secreted from the cells and their presence in the biological fluids signifies the regulatory role of circulating miRNAs in the pathogenesis. The phenomenal expression levels of circulating miRNAs in serum or plasma during infection makes them the potential therapeutic biomarkers for the diagnosis of assorted human infectious diseases. In this article, we have accentuated the methods for the profiling of circulating miRNA as well as the importance of miRNA as biomarkers for the diagnosis of human infectious diseases. To date, numerous biomarkers have been identified for the diagnostic or prognostic purpose; for instance, miR‐182, miR‐486, and miR15a in sepsis; miR‐320 and miR505 in inflammatory bowel disease; miR‐155 and miR‐1260 in influenza; miR‐12, miRVP‐3p, and miR‐184 in arboviruses; and miR‐29b and miR‐125 in hepatitis infection. Nevertheless, the noninvasive diagnostic approach, with the aid of biomarkers, currently plays a decisive role in the untimely diagnosis of human infections. So, in the near future, the exploitation of circulating miRNAs as therapeutic biomarkers for the diagnosis of human infections will help us to cure the associated diseases promptly and effectively.

Contriving multiepitope subunit vaccine by exploiting structural and nonstructural viral proteins to prevent Epstein-Barr virus-associated malignancy: OJHA et al.

Cancer is one of the common lifestyle diseases and is considered to be the leading cause of death worldwide. Epstein–Barr virus (EBV)‐infected individuals remain asymptomatic; but under certain stress conditions, EBV may lead to the development of cancers such as Burkitt’s and Hodgkin’s lymphoma and nasopharyngeal carcinoma. EBV‐associated cancers result in a large number of deaths in Asian and African population, and no effective cure has still been developed. We, therefore, tried to devise a subunit vaccine with the help of immunoinformatic approaches that can be used for the prevention of EBV‐associated malignancies. The epitopes were predicted through B‐cell, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) from the different oncogenic proteins of EBV. A vaccine was designed by combining the B‐cell and T‐cell (HTL and CTL) epitopes through linkers, and for the enhancement of immunogenicity, an adjuvant was added at the N‐terminal. Further, homology modeling was performed to generate the 3D structure of the designed vaccine. Moreover, molecular docking was performed between the designed vaccine and immune receptor (TLR‐3) to determine the interaction between the final vaccine construct and the immune receptor complex. In addition, molecular dynamics was performed to analyze the stable interactions between the ligand final vaccine model and receptor TLR‐3 molecule. Lastly, to check the expression of our vaccine construct, we performed in silico cloning. This study needed experimental validation to ensure its effectiveness and potency to control malignancy.