International Journal for Computational Biology (IJCB)
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Recent challenges and progress of potential vaccines for Coronavirus disease 2019 (COVID-19)
No full textThe pandemic of COVID-19 emerged at the end of 2019 and spread rapidly in almost all the countries around the world. This has become a severe global health concern. COVID-19 pandemic is still spreading and reoccurring, so vaccines are urgently needed to control the spreading of this epidemic. Facts have shown that vaccines are the most successful and efficient way to combat and manage infectious diseases. Enormous efforts have been made by government, industry, and academia to develop successful vaccines in a few months span. Some vaccines have been evaluated for efficiency in animal and preliminary clinical trials. This brief review summarizes the approaches used in the vaccines design and focuses on the progress of COVID-19 vaccine development. We have also highlighted the challenges faced in the development of COVID-19 vaccines
Treatment Strategies for COVID 19: New Insights from Comparative Genome Analysis, Pathophysiology, Host-Virus Interaction and Immune Response
No full textThe recent outbreak of Coronavirus (SARS-CoV-2, earlier known as 2019-nCoV) in Wuhan City, China and its subsequent spread in other countries have posed a big threat to human health. The speed with which this virus has spread across the globe was unimaginably fast that within a span of 2 months, more than 100 countries became victims of its vicious trap. As of today, there is no potent therapeutic regime available in any form (drug, vaccine or other) for effective treatment of COVID19. In this review, we have presented therapeutic solution of COVID 19 based of understanding drawn from comparative genome analysis, pathophysiology, host-virus interaction and immune response. Herein, we have presented the genomic and structural organization of the virus have been studied which pose an immense resemblance with the previously reported coronaviruses. The SARS-CoV-2 is highly contagious and its infectivity is unimaginably high as compared to all previously known coronaviruses such as SARS-CoV-1, MERS-CoV, CoV-NL63, CoV-229E, CoV-HUK1, CoV-OC43 and others. Further, we aimed to describe the complex etiology, deregulated immune response and other pathophysiological outcomes of SARS-CoV-2 infection so as to define their unimaginable high infectivity and transmission properties. In addition, we discuss about the current status of screening tests, drugs, reprofiled drugs, vaccines and other therapies that are under different stages of development. The biorhythm and host response on infection have also been studied which can sanguinely open the door for treatment of the disease. No vaccination or drug candidate has been identified yet but the use of the repurposed drug of its ancestors and other related causal organisms have shown promising results and recovery of the patients
Machine Learning Analysis of National Vaccination Schedules and Rates of Compliance Reveals Correlation with COVID19 Mortality
No full textWe questioned whether previous vaccination histories, as reflected by the national vaccination schedules and compliance rates, might correlate with mortality rates from COVID-19. Using a machine learning algorithm, we aligned the WHO data on national vaccinations schedules and compliance rates with national mortality rates, as published daily by official health authorities and posted on the WHO website. Vaccination schedule and the national rates of compliance were significantly associated with national mortality rates. The five most influential vaccines were Rubella, inactivated Polio, DTP (Diphtheria, Tetanus, Pertussis) and the Pneumococcal vaccine. These vaccinations are more likely to be associated with younger generations whereas mortality is reported mainly in older people. Our findings suggest that further studies exploring the possible mechanism(s) underlying this association with vaccination may provide important information in dealing with an ongoing pandemic. Supporting our conclusions, a recent computational study predicted an epitope similarity between the viruses causing COVID_19, measles, and rubella, the latter two covered by the triple vaccine MMR identified in our studies. This suggests that childhood vaccinations contribute to the differential clinical presentation of COVID_19 in young and older populations. Some recent publication also hypothesized that there would be a non-specific protective effect for the MMR vaccine
Revisiting Prostate Cancer in India: A Genomic View
Get PDFIn the recent past, there has been a rise in Prostate Cancer (PCa) in Asia, particularly India. Although systematic reviews on PCa have dealt on the genetics, genomics and the environmental influence in causal of PCa, no predictive analytics in comparing the PCa from Caucasian, American to Asian population was attempted. In this review article, we have attempted to elaborate this aspect of PCa and deliberated on challenges related to next generation sequencing methods of PCa’s manifestation when compared to the west
A Molecular Docking and Pharmacokinetic Prediction of Thiazolidine-2, 4-dione Derivatives: Toward Novel Therapeutic Targets for Type-2 Diabetes Mellitus
Get PDFType 2 diabetes mellitus (T2DM) is a leading endocrine disorder that affects millions of people worldwide. It is characterized by hyperglycemia and high insulin resistance. The commonly prescribed oral therapeutic for insulin resistance in T2DM is Thiazolidine-2, 4-diones (TZDs). TZDs are a class of oral hypoglycemic agents that act on Peroxisome proliferator activating receptor-γ (PPAR-γ) receptors and are mainly expressed in the adipose tissues. In this work, we derive novel classes of TZDs and predict the nature of structural affinity using docking studies against the PPAR-γ.
ATPase Domain of Heat Shock protein 70—isoform 2—(Hsp70-2) and their role in activating the adaptive immune response: An in silico approach
No full textA lot of molecules play fundamental roles in neoplasic processes and cancer. Heat shock proteins may enhance these pathologies and favor the protumoral milieu. However, a look at the literature tells us that these molecules intervene in both to promote or attack cancer cells. In the case of breast cancer is known that Hsp70 (isoform 2) improve its establishment and progression in the patient, and is possible that the ATPase domain of Hsp70-2 favors this disease. Thus, is relevant to know if this molecular region has immunogenic activity as well as which epitopes are essential to stimulate immune cells, and whether could induce the attack of the tumor mass. In this aim, the immunogenicity of ATPase domain of Hsp70-2 was studied in silico. The results suggest that the majority of the molecule had immunogenic epitopes that boosts the immune response through activation of B cells and T cells. However, in vitro synthesis and in vivo experimental studies to evaluate the efficacy of this therapeutic candidate are required to ensure safety in people
Combined gene expression analysis in HIV Associated Dementia, Alzheimer’s disease and Parkinson’s disease- An in-silico approach
No full textHuman immunodeficiency virus (HIV) Type 1 infection predominantly affects the immune system. Nevertheless, scientific studies have proven its association with the Central Nervous system (CNS) causing several neurological complications leading to HIV Associated Dementia (HAD). HAD is characterized by a progressive, disabling decline in essential CNS functions such as cognition, motor control and behavior. These are the general characteristics of the most common Neuro degenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). The genetics of AD and PD is widely studied and clinical studies have shown cohesion in the pathology of HAD, AD and PD. Analysing the concurrent expression patterns of large number of genes amongst these related diseases will aid in establishing correlations between the genes and their functions.We have analysed the gene expression datasets of HAD, AD and PD from GEO database to determine the overlapping genes and transcription factors involved. The datasets were normalized using R-Bioconductor, and statistical analysis was performed to identify the significant genes using limma and related packages in R. Although substantial amount of common proteins among HAD and other Neuro degenerative diseases have been previously reported, our findings can help in expanding the pool of target genes and further enhancing the knowledge about the convergent pathways among HAD, AD and PD. These common markers identified will provide insights into parallel pathways of disease mechanisms and further assist in the understanding of progression of HAD pathogenesis
FrameOUT and FrameOUTDB: A web based application and repository for the identification and analysis of frameshift mutations
Get PDFFrameshift, one of the three classes of recoding, leads to waste of energy, resources and activity of biosynthetic machinery. In addition, some peptides, probably cycotoxic synthesized after frameshifts, results in diseases and disorders like muscular dystrophies, lysosomal storage disorders, and cancer. Hidden Stop Codons that occur naturally in coding sequences among all organisms, are associated with the early termination of translation for incorrect reading frame selection and help to reduce the metabolic cost related to the frame-shift events. Hidden stop codons and their association with numerous diseases. These codons are associated with the early termination of translation for incorrect reading frame selection and help to reduce the metabolic cost related to the frame-shift events. There are lots of appearances of hidden stops in mitochondrial genomes and we tried to study this putative event in mitochondrial genomes of vertebrates. To reduce this gap, this work presents an algorithmic web based tool to study hidden stops in frame-shifted translation for vertebrate mitochondrial genomes through respective genetic code system. FrameOUT (FO), an algorithmic web based application, predicts mutations in a user input sequence, be it a diseased or a normal sequence by implementation of Hidden Markov Model. FODB is a collection of all available Frameshift events and their association with various diseases
Effect of C-terminal truncations on the aggregation propensity of A53E, a familial mutant of α-Synuclein: An Insilico Study
Get PDFα-Synuclein, an intrinsically disordered protein, is well known for its role on the onset of Parkinson’s Disease (PD), a neurodegenerative disorder. In α-synuclein, several mutations have been known to cause genetic forms of PD. Recently a new familial mutant, A53E of α-synuclein was discovered in a family and found to accelerate the α-synuclein gene, SNCA. But the molecular details about the A53E α-synuclein aggregation were not well studied. It has been recently suggested that two C-terminally truncated α-synuclein (αS C-X): 120 and 123, along with the A53E mutation would cause a more aggressive pathology and an increase in aggregation. So here we demonstrate the effect of C-terminal truncations along with A53E mutation on the aggregation propensity of α-synuclein by comparing the conformational dynamics of A53E full length protein and its C-terminal truncations using molecular dynamics simulation methods. In A53E full length protein we observed stability to be more and also hydrophobic surface (NAC (non-amyloid β component) region), number of molecular interactions and interface area between monomeric units to be relatively less than αS C-X. Our findings in this study suggest that more the residues removed from the C-terminal along with A53E mutation have significant effect on the aggregation propensity of α-synuclein
ATPase Domain of Heat Shock protein 70—isoform 2—(Hsp70-2) and their role in activating the adaptive immune response: An in silico approach
Get PDFA lot of molecules play fundamental roles in neoplasic processes and cancer. Heat shock proteins may enhance this severe pathology and favor the protumoral milieu. However, a look at the literature tells us that these molecules intervene in both to promote or attack cancer cells. In the case of breast cancer is known that Hsp70 (isoform 2) improve this establishment and progression in the patient, and is possible that the ATPase domain of Hsp70-2 favors this disease. Thus, is relevant to know if this molecular region has immunogenic activity as well as which epitopes are essential to stimulate immune cells, and whether could induce the attack of the tumor mass. In this aim, the immunogenicity of ATPase domain of Hsp70-2 was studied in silico. The results suggest that the majority of the molecule had immunogenic epitopes that boosts the immune response through activation of B cells and T cells. However, in vitro synthesis and in vivo experimental studies to evaluate the efficacy of this therapeutic candidate are required to ensure efficacy and safety in people.