Browsing by Author "Rao, Abhishek"

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    Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection
    (Springer, 2022-12-17T00:00:00) Singh, Satyendra; Chauhan, Priya; Sharma, Vinita; Rao, Abhishek; Kumbhar, Bajarang Vasant; Prajapati, Vijay Kumar
    SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100�ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic. � 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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    Mechanism of cell cycle regulation and cell proliferation during human viral infection
    (Academic Press Inc., 2023-02-01T00:00:00) Panda, Mamta; Kalita, Elora; Rao, Abhishek; Prajapati, Vijay Kumar
    Over the history of the coevolution of Host viral interaction, viruses have customized the host cellular machinery into their use for viral genome replication, causing effective infection and ultimately aiming for survival. They do so by inducing subversions to the host cellular pathways like cell cycle via dysregulation of important cell cycle checkpoints by viral encoded proteins, arresting the cell cycle machinery, blocking cytokinesis as well as targeting subnuclear bodies, thus ultimately disorienting the cell proliferation. Both DNA and RNA viruses have been active participants in such manipulation resulting in serious outcomes of cancer. They achieve this by employing different mechanisms�Protein-protein interaction, protein-phosphorylation, degradation, redistribution, viral homolog, and viral regulation of APC at different stages of cell cycle events. Several DNA viruses cause the quiescent staged cells to undergo cell cycle which increases nucleotide pools logistically significantly persuading viral replication whereas few other viruses arrest a particular stage of cell cycle. This allows the latter group to sustain the infection which allows them to escape host immune response and support viral multiplication. Mechanical study of signaling such viral mediated pathways could give insight into understanding the etiology of tumorigenesis and progression. Overall this chapter highlights the possible strategies employed by DNA/RNA viral families which impact the normal cell cycle but facilitate viral infected cell replication. Such information could contribute to comprehending viral infection-associated disorders to further depth. � 2023 Elsevier Inc.
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    Translational vaccinomics and structural filtration algorithm to device multiepitope vaccine for catastrophic monkeypox virus
    (Elsevier Ltd, 2022-12-30T00:00:00) Singh, Satyendra; Rao, Abhishek; Kumar, Ketan; Mishra, Amit; Prajapati, Vijay Kumar
    Recent outbreak of monkeypox disease commenced in April 2022, and on May 7, the first confirmed case was reported. The world health organization then designated monkeypox disease as a public health emergency of international outrage on July 23, after it spread to 70 non-endemic nations in less than 15 days. This catastrophic viral infection encourages the development of antiviral therapeutics due to the lack of specific treatments with negligible adverse effects. This analysis developed a highly immunogenic multiepitope subunit vaccine against the monkeypox virus using an in silico translational vaccinomics technique. Highly antigenic B cell and T cell (HTL and CTL) epitopes were predicted and conjugated with the help of unique linkers. An adjuvant (?-defensin) and a pan-HLA DR sequence were attached at the vaccine construct's N-terminal to invoke a robust immunological response. Additionally, physiochemical, allergic, toxic, and antigenic properties were anticipated. Interactions between the vaccine candidate and the TLR3 demonstrated that the vaccine candidate triggers a robust immunological response. Finally, the stability is confirmed by the molecular dynamics study. In contrast, the modified vaccine candidate's ability to produce a protective immune response were verified by an immune dynamics simulation study conducted via C-ImmSim server. This study validates the generation of B cell, Th cell, and Tc cell populations as well as the production of IFN??. � 2022 Elsevier Ltd