Developing cost-efficient vaccine candidates against arboviruses
Developing cost-efficient vaccine candidates against arboviruses
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movie4.mp4The outbreaks caused by arboviruses such as Chikungunya Virus (CHIKV), Japanese Encephalitis Virus (JEV), and Zika Virus (ZV) are expected to intensify globally due to increased vector proliferation and dissemination triggered by climate change, and Ineffective vector control strategies. We are working on developing a subunit or VLP-based vaccine candidate against arboviruses by using the AI/ML approach of protein engineering to redesign viral glycoprotein.
movie2.mp4Therapeutic potential of neutralizing antibodies
Therapeutic potential of neutralizing antibodies
The neutralizing monoclonal antibodies (mAbs) have recently shown huge therapeutic/diagnostic potential against viral infections. Neutralizing mAbs is also critical for designing novel antigenic epitopes for developing next-generation vaccine candidates. Using X-ray crystallography and cryo-EM methods, we characterize the complex structures of neutralizing monoclonal antibodies against pathogenic RNA viruses in complex with viral antigens or virus-like particles (VLPs). We will harness the information gathered from structures of viral transcription, capping assemblies, and Ag-Ab complexes to engineer antivirals and test their efficacy in cell culture and animal models.
movie5.mp4Viral replication and transcription complexes
Viral replication and transcription complexes
The heterogeneity in viral transcription and mRNA capping machinery provides a promising avenue, largely ignored due to the complexities associated with the viral transcription and capping process. Advances in cryo-EM methods allow us to explore the atomic details of viral transcription and capping assemblies in greater detail. We are currently exploring the transcription and capping process in paramyxoviruses containing contagious human and animal pathogens such as Newcastle Disease virus, Hendra virus, Henipah virus, and Measles virus etc.
Structural and functional elucidation of Prolyl hydroxylases
Structural and functional elucidation of Prolyl hydroxylases
In collaboration with Dr. Trayambk Basak's Lab (Lab Webpage) and Bhaskar Mondal's lab (Lab Webpage) at IIT Mandi, we are exploring the structural and functional characterization of prolyl hydroxylases and their binding partners.
Selected publications:
Ghosh, S., Kumar, D., Mondal, B. et al. Enzymatic craftsmanship in collagen glycosylation. Nat Communications 16, 7252 (2025). https://doi.org/10.1038/s41467-025-62768-w
Kumar et. al., 2.7 Å Cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity. Science Advances, 15 Apr 2020: Vol. 6, no. 16, eaay6410.
Lawson, C.L., Kryshtafovych, A., Pintilie, G.D. et al. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature Methods (2024). https://doi.org/10.1038/s41592-024-02321-7
Dodd-O et. al., Antiviral fibrils of self-assembled peptides with tunable compositions. Nature Communications, 2024 Feb 7;15(1):1142. doi: 10.1038/s41467-024-45193-3.
Catherine L Lawson et. al., Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods, 18, pages 156–164 (2021).
Covered in news and views: https://www.nature.com/articles/s41592-021-01062-1.
Mallick D, Yadav U, Gupta M, Kumar D, Kumar R. The evolving landscape of Chandipura virus: A comprehensive account of outbreaks to recent advances. Virology. 2025 Apr 15;608:110541. doi: 10.1016/j.virol.2025.110541. Epub ahead of print. PMID: 40311237.
Madhukalya, R., Yadav, U., Parray, H.A. et al. Nipah virus: pathogenesis, genome, diagnosis, and treatment. Appl Microbiol Biotechnol 109, 158 (2025). https://doi.org/10.1007/s00253-025-13474-6.
Gupta R, Sharma S, Saroj A, Madhukalya R, Kumar V, Agarwal V, Kumar D, Mangala Prasad V, Kumar R. Kyasanur Forest disease virus non-structural protein NS1 forms multimers in solution, with a distinctly identifiable tetrameric state. Biochimie. 2025 Apr 17;234:89-94. doi: 10.1016/j.biochi.2025.04.005. Epub ahead of print. PMID: 40252820.
Gupta M, Mallick D, Kumar D*, Kumar R*. Genomic and Structural Insights into Chandipura Virus: A Comparative in Silico Analysis of Indian and West African Strains and Potential Host Receptor Interactions. Curr Microbiol. 2025 May 9;82(6):286. doi: 10.1007/s00284-025-04258-2. PMID: 40346308
Mallick et. al., Optimized high-yield expression of envelope glycoprotein domain III from dengue virus serotypes 1 to 4. Biochimie. 2024 Dec 11:S0300-9084(24)00296-7. doi: 10.1016/j.biochi.2024.12.003. PMID: 39672456.
Das et. al., Purification and characterization of kyasanur forest disease virus EDIII domain of major envelope glycoprotein. J Virol Methods. 2024 Dec 3;333:115089. doi: 10.1016/j.jviromet.2024.115089. Epub ahead of print. PMID: 39638261.
Das, M., Kumar, V., Madhukalya, R. et al. Purification, refolding, and pH-dependent stability evaluation of Zika virus EDIII protein. Int Microbiol (2025). https://doi.org/10.1007/s10123-025-00679-y.
Chiranjivi et. al., Generation of soluble, cleaved, well-ordered, native-like dimers of dengue virus 4 envelope protein ectodomain (sE) suitable for vaccine immunogen design. International Journal of Biological Macromolecules, 217 (2022) 19–26.\
Mitra et. al., Influenza A virus protein NS1 exhibits strain-independent conformational plasticity. Journal of Virology, 2019 Aug 2. 917-919. doi: 10.1128/JVI.00917-19.
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