Dr.-Sanjukta-Mukherjee

Dr. Sanjukta Mukherjee

Ph.D., CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata; Post-doc, SANKEN (or ISIR), Osaka University, Japan
Associate Professor, School of Bioscience

Dr. Sanjukta Mukherjee

Ph.D., CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata; Post-doc, SANKEN (or ISIR), Osaka University, Japan
sanjukta.m@chanakyauniversity.edu.in
Chemical Biology of Nucleic Acids, Organic chemistry, Medicinal chemistry and Drug discovery

My research lies at the interface of chemistry and biology, driven by the premise that fundamental chemical events underpin most biological processes. I am particularly interested in harnessing the power of small molecules as chemical probes to interrogate and manipulate complex biological systems, with strong translational relevance to biomedical research and drug discovery. My work focuses on the rational design and discovery of unique organic molecules that selectively target nucleic acids, with a specific emphasis on RNA. RNA represents a largely unexplored yet highly privileged chemical space for small-molecule recognition. A central goal of my research is to understand how RNA structure and dynamics can be exploited to develop selective, high-affinity RNA-binding ligands. To achieve this, I employ an interdisciplinary approach that integrates synthetic chemistry, chemical biology, biophysics, and cell biology. In parallel, my laboratory is developing innovative experimental strategies and analytical tools to elucidate RNA–small molecule interactions and their functional consequences in cellular contexts. A major current focus of my research is the development of RNA-specific chemical probes for super-resolution imaging of RNA in live cells. These probes enable direct visualization of RNA localization, dynamics, and organization at the nanoscale. Using these tools, I aim to perturb and study RNA–protein interactions to uncover their roles in RNA–protein phase separation, protein aggregation, and higher-order cellular organization, processes that are increasingly recognized as critical regulators of cell physiology. The biological relevance of this work is underscored by its strong connection to age-related neurodegenerative diseases. Despite significant advances in our understanding of these diseases, effective disease-modifying therapies remain unavailable, and there is a critical lack of drug-like molecules capable of targeting pathogenic RNA–protein assemblies. Through my ongoing research, I aim to develop bespoke RNA-binding small molecules as chemical probes to dissect pathogenic RNA–protein interactions and to unravel their mechanistic roles in toxic aggregate formation. By bridging fundamental chemical principles with biological complexity, my long-term goal is to establish new paradigms for RNA-targeted chemical biology and to lay the groundwork for innovative therapeutic strategies to combat neurodegenerative diseases and cancer.

Dr. Sanjukta Mukherjee joined the School of Biosciences, Chanakya University, in April 2025. She earned her Master’s degree in Applied Chemistry from the Indian Institute of Engineering Science and Technology (IIEST), Howrah. Following early pre-doctoral industry exposure, she completed her PhD in Organic Chemistry at CSIR–Indian Institute of Chemical Biology (IICB), Kolkata. She then pursued postdoctoral research at ISIR (SANKEN), Osaka University, Japan, where she was promoted to Assistant Professor after two and a half years. Motivated to return to India for personal reasons, Dr. Mukherjee subsequently held research positions at several premier Indian institutions. She was awarded a Campus Fellow position at TIFR–National Centre for Biological Sciences (NCBS), Bengaluru, where she conducted independent research while maintaining a concurrent adjunct appointment as a specially appointed researcher and Assistant Professor at Osaka University until the COVID-19 pandemic. She later served as a Visiting Scientist at DBT–Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, and as a BIRAC-BIG Innovator and incubatee at the Centre for Cellular and Molecular Platforms (C-CAMP). Prior to joining Chanakya University, she was a DBT/Wellcome Trust India Alliance Intermediate Fellow at the DBT–National Centre for Cell Science (NCCS), Pune. Dr. Mukherjee is actively engaged in translational research and biomedical entrepreneurship, aiming to translate fundamental discoveries into clinical applications. She is also involved in teaching engineering chemistry and postgraduate biosciences courses and has authored several publications in leading peer-reviewed journals.

  • Ph.D., CSIR-Indian Institute of Chemical Biology, 2012, Jadavpur University
  • M.Sc., 2003, Indian Institute of Engineering Science and Technology (IIEST), Shibpur
  • B.Sc., Chemistry (H), 2000, Scottish Church College, University of Calcutta

  1. P. Nayim, A. T. Mbaveng, K. Sudhir, B. E. N. Wamba, S. Mukherjee*, and V. Kuete*, “Phytochemistry and pharmacology of Imperata cylindrica: A comprehensive review,” Invest. Med. Chem. Pharmacol., vol. 6, no. 1, p. 76, 2023.
  2. R. Arora, L. Dohadwala, B. Nanavati, V. Lakshmanan, and S. Mukherjee, “Merkel cell polyomavirus regulates miR183 cluster and piR62011 in Merkel cell carcinoma,” bioRxiv, preprint, 2022, doi: 10.1101/2022.01.18.476776.
  3. S. Mukherjee*, A. Murata, R. Ishida, A. Sugai, C. Dohno, M. Hamada, S. Krishna, and K. Nakatani*, “HT-SELEX-based identification of binding pre-miRNA hairpin loop motifs for small-molecule ligands,” Mol. Ther. Nucleic Acids, vol. 27, pp. 165–174, 2022.
  4. S. Mukherjee*, B. Shelar, and S. Krishna*, “Versatile roles of miR-24/24-1*/24-2* expression in cancer and other human diseases,” Am. J. Transl. Res., vol. 14, pp. 20–54, 2022.
  5. P. Nayim, K. Sudhir, A. T. Mbaveng*, V. Kuete*, and S. Mukherjee*, “In vitro anticancer activity of Imperata cylindrica root extract against human cervical cancer and identification of potential bioactive compounds,” Biomed. Res. Int., vol. 2021, Art. ID 4259777, 2021.
  6. P. Konieczny#, S. Mukherjee#, E. Stepniak-Konieczna, K. Taylor, D. Niewiadomska, A. Piasecka, A. Walczak, A. Baud, C. Dohno, K. Nakatani, and K. Sobczak, “Cyclic mismatch-binding ligands interact with disease-associated CGG trinucleotide repeats in RNA and suppress their translation,” Nucleic Acids Res., vol. 49, pp. 9479–9495, 2021.
  7. P. Nayim, A. T. Mbaveng, S. Mukherjee*, R. Jain, V. Kuete*, and S. Krishna, “CD24 gene inhibition and TIMP-4 gene upregulation by Imperata cylindrica root extract prevent metastasis of CaSki cells via inhibition of PI3K/Akt/Snail signaling and EMT,” J. Ethnopharmacol., vol. 275, p. 114111, 2021.
  8. S. Mukherjee#, L. Błaszczyk#, W. Rypniewski, C. Falschlunger, R. Micura, A. Murata, C. Dohno, K. Nakatani, and A. Kiliszek, “Structure-based insights into RNA recognition by small molecules,” Nucleic Acids Res., vol. 47, pp. 10906–10913, 2019.
  9. T. Ohshiro, R. K. Verma, K. Yokota, M. Tsutsui, S. Mukherjee, T. Kawai, K. Nakatani, and M. Taniguchi, “Electrical nucleotide sensor based on synthetic guanine-receptor-modified electrodes,” ChemistrySelect, vol. 3, pp. 3819–3824, 2018.
  10. P. Konieczny#, S. Mukherjee#, C. Dohno, K. Nakatani, and K. Sobczak, “Cyclic naphthyridine dimers as therapeutic agents for fragile X-associated tremor/ataxia syndrome,” Acta Neurobiol. Exp., vol. 77, Suppl. 1, p. 72, 2017.
  11. K. Nakatani, N. Natsuhara, Y. Mori, S. Mukherjee, B. Das, and A. Murata, “Synthesis of naphthyridine dimers with conformational restriction and their binding to DNA and RNA,” Chem. Asian J., vol. 12, pp. 3077–3087, 2017.
  12. S. Mukherjee*, C. Dohno, and K. Nakatani*, “Design and synthesis of cyclic mismatch-binding ligands with variable linkers by ring-closing metathesis and their photophysical and DNA repeat-binding properties,” Chem. Eur. J., vol. 23, pp. 11385–11396, 2017.
  13. S. Mukherjee, C. Dohno, K. Asano, and K. Nakatani, “Cyclic mismatch-binding ligand CMBL4 binds to the 5′-T-3′/5′-GG-3′ site by inducing thymine base flipping,” Nucleic Acids Res., vol. 44, pp. 7090–7099, 2016.
  14. B. Chakraborty, D. Dutta, S. Mukherjee, S. Das, N. C. Maiti, P. Das, and C. Chowdhury, “Synthesis and biological evaluation of a novel betulinic acid derivative as an inducer of apoptosis in human colon carcinoma cells,” Eur. J. Med. Chem., vol. 102, pp. 93–105, 2015.
  15. C. Chowdhury, S. Mukherjee, B. Das, and B. Achari, “Palladium-catalyzed synthesis of (E)-2-arylmethylidene-N-tosylindolines and tetrahydroquinolines: Access to 2-substituted indoles and quinolines,” J. Org. Chem., vol. 77, pp. 5108–5119, 2012.
  16. C. Chowdhury, S. Mukherjee, B. Chakraborty, and B. Achari, “A rapid and facile synthesis of 3-aryl-substituted tetrahydro[1,2,3]triazolo[1,5-a]pyrazines and fused analogues,” Org. Biomol. Chem., vol. 9, pp. 5856–5862, 2011.
  17. C. Chowdhury, K. Brahma, S. Mukherjee, and A. K. Sasmal, “Regio- and stereoselective synthesis of (E)-3-arylidene-3,4-dihydro-2H-1,4-benzoxazines under palladium catalysis,” Tetrahedron Lett., vol. 51, pp. 2859–2861, 2010.
  18. C. Chowdhury, S. Mukherjee, B. Das, and B. Achari, “Expedient synthesis of 1,2,3-triazolo[5,1-c]morpholines through palladium–copper catalysis,” J. Org. Chem., vol. 74, pp. 3612–3615, 2009.

Project 1

  • Title: Recognition of RNA structural motifs by bespoke small-molecules to interrogate and alter RNA-RBP interactions associated with phase-separated toxic aggregate formation
  • Duration: 2024-29
  • Granting Agency: DBT/Wellcome Trust India Alliance [Grant for Intermediate Fellowship]
  • PIs/Co PIs: Sanjukta Mukherjee
  • Purpose: we aim to develop bespoke RNA-binding small molecules as chemical probing tools to interrogate RPIs and unravel their role in toxic aggregate formation in neurological disorders.
  • Short Description: One of the key drivers of neurodegenerative disorder is the accumulation of toxic RNA foci—abnormal aggregates formed through aberrant RNA–protein interactions (RPIs) in neurons—which disrupt critical cellular processes and ultimately lead to neuronal death. Despite intensive research efforts, there are still no effective treatments for NDs, apart from a few symptomatic therapies that offer only limited relief and benefit. Critically, we also lack potent drug-like molecules capable of disrupting these pathogenic aggregates.
  • Status: Ongoing
  • Grant Amount: 3.6 Crores

Project 2

  • Title: Pharmacological evaluation of novel class of small molecule regulator of miRNA as anti-cancer drug and validation of the hit molecule
  • Duration: two years
  • Granting Agency: BIRAC Biotechnology Ignition Grant (BIG-19)
  • PIs/Co PIs: Sanjukta Mukherjee
  • Purpose: Validation of anti-carcinogenic properties of new class of molecules
  • Short Description: Evaluation of anti-carcinogenic properties and Pharmacological evaluation of small molecule regulator of oncogenic miRNA in cervical cancer
  • Status: Ongoing
  • Grant Amount: Rs. 50 Lakhs

Project 3

  • Title: Small molecule mediated regulation of Notch targeted genes to develop targeted cancer therapy miRNA as anti-cancer drug and validation of the hit molecule
  • Duration: one year
  • Granting Agency: Osaka University/ Osaka University’s International Joint Research Promotion Program 2020
  • PIs/Co PIs: Sanjukta Mukherjee & Asako Murata
  • Purpose: Development of Notch targeted anti-cancer therapeutics
  • Short Description: Screening of small molecule library to regulate Notch targeted genes in cancer oncogenic miRNA in cervical cancer
  • Status: Completed
  • Grant Amount: JYP 18,62,540.00 /-

Project 4

  • Title: Exploring the therapeutic potential of Cyclic Mismatch Binding Ligands (CMBLs) in cervical cancer Sub-Sets
  • Duration: Two years
  • Granting Agency: DST and JSPS/ Indo-Japan Bilateral Cooperative Science Program (IJCSP)
  • PIs/Co PIs: Chikara Dohno (PI, Japan side), Sudhir Krishna (PI, Indian side),) Sanjukta Mukherjee (co-PI, Indian Side), Asako Murata (co-PI, Japan side)
  • Purpose: Anti-cancer therapeutics development
  • Short Description: Evaluation of the anti-cancer activity of small-molecule library
  • Status: Completed
  • Grant Amount: Rs. 9,40,000.00/-

Project 5

  • Title: Evaluation of therapeutic potential of CMBLs targeting cervical cancer via new approach based on SELEX technology and dicer cleavage reaction (SELEX-Dicer strategy)
  • Duration: 4.5 years
  • Granting Agency: TIFR-NCBS
  • PIs/Co PIs: Sanjukta Mukherjee
  • Purpose: Anti-cancer therapeutics development
  • Short Description: Evaluation of the anti-cancer activity of small-molecule library
  • Status: Completed
  • Grant Amount: Rs. 90,000/- (fellowship) & USD5000 (contingency/year for 4 years)

  • DBT/Wellcome Trust India Alliance Intermediate Fellowship Award, 2024-till
  • BIRAC-Biotechnology Ignition Grant (BIG), 2022
  • Osaka University’s International Joint Research Promotion Program Grant as Assistant Professor, 2020-2021
  • Indo-Japan (DST and JSPS) Bilateral Cooperative Science Program (IJCSP) grant, 2018-2020
  • TIFR-NCBS Campus Fellowship, 2017-2021
  • UGC-CSIR/ National Eligibility Test (NET), 2006

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