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In Silico Pharmacol ; 10(1): 12, 2022.
Article in English | MEDLINE | ID: covidwho-1959193


Despite the availability of COVID-19 vaccines, additional more potent vaccines are still required against the emerging variations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the present investigation, we have identified a promising vaccine candidate against the Omicron (B.1.1.529) using immunoinformatics approaches. Various available tools like, the Immune Epitope Database server resource, and NetCTL-1.2, have been used for the identification of the promising T-cell and B-cell epitopes. The molecular docking was performed to check the interaction of TLR-3 receptors and validated 3D model of vaccine candidate. The codon optimization was done followed by cloning using SnapGene. Finally, In-silico immune simulation profile was also checked. The identified T-cell and B-cell epitopes have been selected based on their antigenicity (VaxiJen v2.0) and, allergenicity (AllerTOP v2.0). The identified epitopes with antigenic and non-allergenic properties were fused with the specific peptide linkers. In addition, the 3D model was constructed by the PHYRE2 server and validated using ProSA-web. The validated 3D model was further docked with the Toll-like receptor 3 (TLR3) and showed good interaction with the amino acids which indicate a promising vaccine candidate against the Omicron variant of SARS-CoV-2. Finally, the codon optimization, In-silico cloning and immune simulation profile was found to be satisfactory. Overall, the designed vaccine candidate has a potential against variant of SARS-Cov-2. However, further experimental studies are required to confirm.

EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-331033


Background: It has been almost 2 years since the first SARS-CoV-2 virus was first reported in the city of Wuhan. So far, 8 drugs are approved against Covid-19 by FDA, however, an active drug against multi-mutational Covid-19 is still missing. In this present study, we aim to identify the most crucial and highly correlated protein targets from the publicly available transcriptomics datasets. Methods Transcriptomics datasets were retrieved from Geo Omnibus (GEO). We use relevant datasets to identify the most significant and differentially expressed genes and integrated them into a Research graph called CovInt (a network of Covid-19) that includes all biological molecules associated in the network with their directionalities collected from publicly available and patient-derived multi-omics datasets from millions of unstructured and structured datasets such as publications, patents, grants, preclinical and clinical reports. CovInt utilizes powerful traversal, clustering and centrality algorithms to identify key connections in the pathophysiology of the disease and its treatments. Results Leveraging 3M + connections, important interactions among key 42 drugs, 962 biological processes and molecular functions, 926 pathways, 897 phenotypes, 7103 proteins, 61 tissues were identified. This narrowed interactome was explored further using PageRank, lovain detection & strongly connected components (SSC) algorithms. In our analysis 63, strongly connected communities were identified which gives us an understanding of hidden underlying mechanisms. We further explored this network to identify and triangulate the key proteins, metabolic pathways and associated risk factors that can regulate moderate to severe Covid-19 infections. Conclusions Our study suggests that CREB3L1, SOX2, UBR4, FLNC, ITPA, DLG3, ING4, TECR, NADH, SMAD, HUWE1, DDX17, CREBBP, RELA, HPSE, TRIM33, TNFSF13B are the key regulator proteins and involved in ER-stress, cytokine signaling, T-Cell activation, Activation of NLRP3 Inflammation by SARS-CoV-2, JAK-STAT, IL-4, IL-13 pathways, MAPK signaling pathways, Activation of NMDA receptor & postsynaptic events and TGF-β signaling pathways.

J Thromb Haemost ; 19(6): 1585-1588, 2021 06.
Article in English | MEDLINE | ID: covidwho-1202119


Vaccine administration is under way worldwide to combat the current COVID-19 pandemic. The newly developed vaccines are highly effective with minimal adverse effects. Recently, the AstraZeneca ChadOx1 nCov-19 vaccine has raised public alarm with concerns regarding the rare, but serious, development of thrombotic events, now known as vaccine-induced immune thrombotic thrombocytopenia (VITT). These thrombotic events appear similar to heparin-induced thrombocytopenia, both clinically and pathologically. In this manuscript, the ISTH SSC Subcommittee on Platelet Immunology outlines guidelines on how to recognize, diagnose and manage patients with VITT.

COVID-19 , Vaccines , COVID-19 Vaccines , Clinical Laboratory Techniques , Communication , Humans , Pandemics , SARS-CoV-2