Browsing by Author "Singh, Satyendra"

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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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    Multi-pathogen based chimeric vaccine to fight against COVID-19 and concomitant coinfections
    (Springer Science and Business Media B.V., 2023-05-06T00:00:00) Ojha, Rupal; Singh, Satyendra; Gupta, Nidhi; Kumar, Ketan; Padhi, Aditya K.; Prajapati, Vijay Kumar
    Background: COVID-19 has proved to be a fatal disease of the year 2020, due to which thousands of people globally have lost their lives, and still, the infection cases are at a high rate. Experimental studies suggested that SARS-CoV-2 interacts with various microorganisms, and this coinfection is accountable for the augmentation of infection severity. Methods and results: In this study, we have designed a multi-pathogen vaccine by involving the immunogenic proteins from S. pneumonia, H. influenza, and M. tuberculosis, as they are dominantly associated with SARS-CoV-2. A total of 8 antigenic protein sequences were selected to predict B-cell, HTL, and CTL epitopes restricted to the most prevalent HLA alleles. The selected epitopes were antigenic, non-allergenic, and non-toxic and were linked with adjuvant and linkers to make the vaccine protein more immunogenic, stable, and flexible. The tertiary structure, Ramachandran plot, and discontinuous B-cell epitopes were predicted. Docking and MD simulation study has shown efficient binding of the chimeric vaccine with the TLR4 receptor. Conclusion: The in silico immune simulation analysis has shown a high level of cytokines and IgG after a three-dose injection. Hence, this strategy could be a better way to decrease the disease's severity and could be used as a weapon to prevent this pandemic. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.
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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