Immunoinformatics Patterns and Characteristic of Epitope-Based Peptide Vaccine candidates against COVID-19

Vaccination as defined by the WHO is “the administration of agent-specific, but safe, antigenic components that in vaccinated individuals can induce protective immunity against the corresponding infectious agent”. Regardless of their debated history, the standard vaccine approaches have been unsuccessful in providing vaccines for numerous infectious organisms. In the recent three decades, an enormous amount of immunological data was retrieved from clinical studies  due to the advancement in human genome sequencing. These data are being deposited in databases and numerous scientific literature. The development of several bioinformatics tools to analyze this rapidly increasing immunological databank has given rise to the field of immunoinformatics. This approach allows the selection of immunogenic residues from the pathogen genomes. The ideal residues could be industrialized as vaccine candidates to provide protective immune responses in the hosts. This methodology will significantly decrease the time and cost needed for the vaccine development.  This review focus on  published articles that proposed as vaccine candidates through immunoinformatics analysis. The reviewed  Published immunoinformatics studies provided vaccine peptide candidates against SARS-COV-2, which is based on functional and non functional immunogenic proteins like open reading frame , spike protein, envelope protein and membranous protein .All of which  are designed by unique strategies like reverse vaccinology . Spike protein was the most common used target with different suggeststed B and T cell peptides  due to the difference in methodology between the findings

Cytokine Storm in COVID-19 Patients, their Impact on Organs and the Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors

The novel coronavirus in not only causing respiratory problems, it may also damage the heart, kidneys, liver and other organs; in Wuhan 14 to 30% of COVID-19 patients have lost their kidney function and now require either dialysis or kidney transplants. The novel coronavirus gains entry into humans by targeting ACE2 receptor that found on lung cells, which destroy human lungs through cytokine storms, this leads to hyper-inflammation, forcing the immune cells to destroy healthy cells. This is why some COVID-19 patients need intensive care. The inflammatory chemicals released during COVID-19 infection cause the liver to produce proteins that defend the body from infections. However, these proteins can cause blood clotting, which can clog blood vessels in the heart and other organs; as a result, the organs are deprived from oxygen and nutrients which could ultimately lead to multi-organ failure and subsequent progression to acute lung injury, acute respiratory distress syndrome and often death. However, a novel protein modification tool called the QTY code, that are similar in their structure to antibodies, which could provide a solution to excess cytokines, these synthetic proteins can be injected into the body to blind the excess cytokines generated by the cytokine storm; this will eventually remove the excessive cytokines and inhibit the severe symptoms caused by the COVID-19 infection. In this review we will focuses on cytokine storm in COVID-19 patients, their impact on the organs and the potential treatment by QTY code-designed detergent-free chemokine receptors

Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors

The novel coronavirus is not only causing respiratory problems, but it may also damage the heart, kidneys, liver, and other organs; in Wuhan, 14 to 30% of COVID-19 patients have lost their kidney function and now require either dialysis or kidney transplants. The novel coronavirus gains entry into humans by targeting the ACE2 receptor that found on lung cells, which destroy human lungs through cytokine storms, and this leads to hyperinflammation, forcing the immune cells to destroy healthy cells. This is why some COVID-19 patients need intensive care. The inflammatory chemicals released during COVID-19 infection cause the liver to produce proteins that defend the body from infections. However, these proteins can cause blood clotting, which can clog blood vessels in the heart and other organs; as a result, the organs are deprived of oxygen and nutrients which could ultimately lead to multiorgan failure and consequent progression to acute lung injury, acute respiratory distress syndrome, and often death. However, there are novel protein modification tools called the QTY code, which are similar in their structure to antibodies, which could provide a solution to excess cytokines. These synthetic proteins can be injected into the body to bind the excess cytokines created by the cytokine storm; this will eventually remove the excessive cytokines and inhibit the severe symptoms caused by the COVID-19 infection. In this review, we will focus on cytokine storm in COVID-19 patients, their impact on the body organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors

Extensive In Silico Analysis of ATL1 Gene : Discovered Five Mutations That May Cause Hereditary Spastic Paraplegia Type 3A

Background. Hereditary spastic paraplegia type 3A (SPG3A) is a neurodegenerative disease inherited type of Hereditary spastic paraplegia (HSP). It is the second most frequent type of HSP which is characterized by progressive bilateral and mostly symmetric spasticity and weakness of the legs. SPG3A gene mutations and the phenotype-genotype correlations have not yet been recognized. The aim of this work was to categorize the most damaging SNPs in ATL1 gene and to predict their impact on the functional and structural levels by several computational analysis tools. Methods. The raw data of ATL1 gene were retrieved from dbSNP database and then run into numerous computational analysis tools. Additionally; we submitted the common six deleterious outcomes from the previous functional analysis tools to I-mutant 3.0 and MUPro, respectively, to investigate their effect on the structural level. The 3D structure of ATL1 was predicted by RaptorX and modeled using UCSF Chimera to compare the differences between the native and the mutant amino acids. Results. Five nsSNPs out of 249 were classified as the most deleterious (rs746927118, rs979765709, rs119476049, rs864622269, and rs1242753115). Conclusions. In this study, the impact of nsSNPs in the ATL1 gene was investigated by various in silico tools that revealed five nsSNPs (V67F, T120I, R217Q, R495W, and G504E) are deleterious SNPs, which have a functional impact on ATL1 protein and, therefore, can be used as genomic biomarkers specifically before 4 years of age; also, it may play a key role in pharmacogenomics by evaluating drug response for this disabling disease

Design of a Multiepitope-Based Peptide Vaccine against the E Protein of Human COVID-19: An Immunoinformatics Approach

BACKGROUND: A new endemic disease has spread across Wuhan City, China, in December 2019. Within few weeks, the World Health Organization (WHO) announced a novel coronavirus designated as coronavirus disease 2019 (COVID-19). In late January 2020, WHO declared the outbreak of a “public-health emergency of international concern” due to the rapid and increasing spread of the disease worldwide. Currently, there is no vaccine or approved treatment for this emerging infection; thus, the objective of this study is to design a multiepitope peptide vaccine against COVID-19 using an immunoinformatics approach. METHOD: everal techniques facilitating the combination of the immunoinformatics approach and comparative genomic approach were used in order to determine the potential peptides for designing the T-cell epitope-based peptide vaccine using the envelope protein of 2019-nCoV as a target. RESULTS: Extensive mutations, insertion, and deletion were discovered with comparative sequencing in the COVID-19 strain. Additionally, ten peptides binding to MHC class I and MHC class II were found to be promising candidates for vaccine design with adequate world population coverage of 88.5% and 99.99%, respectively. CONCLUSION: The T-cell epitope-based peptide vaccine was designed for COVID-19 using the envelope protein as an immunogenic target. Nevertheless, the proposed vaccine rapidly needs to be validated clinically in order to ensure its safety and immunogenic profile to help stop this epidemic before it leads to devastating global outbreaks