Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection results in the development of a highly contagious respiratory ailment known as new coronavirus disease (COVID-19). Despite the fact that the prevalence of COVID-19 continues to rise, it is still unclear how people become infected with SARS-CoV-2 and how patients with COVID-19 become so unwell. Detecting biomarkers for COVID-19 using peripheral blood mononuclear cells (PBMCs) may aid in drug development and treatment. This research aimed to find blood cell transcripts that represent levels of gene expression associated with COVID-19 progression. Through the development of a bioinformatics pipeline, two RNA-Seq transcriptomic datasets and one microarray dataset were studied and discovered 102 significant differentially expressed genes (DEGs) that were shared by three datasets derived from PBMCs. To identify the roles of these DEGs, we discovered disease-gene association networks and signaling pathways, as well as we performed gene ontology (GO) studies and identified hub protein. Identified significant gene ontology and molecular pathways improved our understanding of the pathophysiology of COVID-19, and our identified blood-based hub proteins TPX2, DLGAP5, NCAPG, CCNB1, KIF11, HJURP, AURKB, BUB1B, TTK, and TOP2A could be used for the development of therapeutic intervention. In COVID-19 subjects, we discovered effective putative connections between pathological processes in the transcripts blood cells, suggesting that blood cells could be used to diagnose and monitor the disease’s initiation and progression as well as developing drug therapeutics.

Bioinformatics and System Biology Approach to Reveal the Interaction Network and the Therapeutic Implications for Non-Small Cell Lung Cancer Patients With COVID-19

“…It is generally believed that TOP2A is a prognostic indicator of NSCLC, and its level is negatively correlated with the prognosis ( Hou et al, 2017 ; Ma et al, 2019 ). In consistence with the result of our study, TOP2A has been identified as a hub gene that could govern many cellular processes by protein–protein interactions in COVID-19 patients ( Hasan et al, 2022 ).…”

SARS-CoV-2 potential drugs, drug targets, and biomarkers: a viral-host interaction network-based analysis

“…TOP2A (AUC = 0.842) is a crucial gene in the DNA replication process during the cell cycle. It was identified as a central hub gene in a study on comparing the gene expression profiles of blood samples from patients with COVID-19 with healthy controls 64 . According to the drug-gene network constructed, it was inhibited by different classes of anti-cancers such as anthracyclines, mitotic inhibitors, anti-tumor antibiotics, and topoisomerase II inhibitors.…”

Screening of Phytochemicals against Osteoporosis: Molecular Docking and Simulation-Based Computational Approaches

“…In-silico approaches are not only less time-consuming but also cost-effective as compared to conventional drug design [29,30]. With the advancements in the field of Bioinformatics, different tools and algorithms have been advised that identify and discover the drug targets [31]. Molecular docking is one of the popular and modern in silico approaches in the field of medical research that led to the invention of new compounds by observing the pattern of the small molecule's binding to the target and hence discovering the new drug that combats the deadly diseases [32,33].…”