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Design and Synthesis of New Benzimidazole–Carbazole Conjugates for the Stabilization of Human Telomeric DNA, Telomerase Inhibition, and Their Selective Action on Cancer Cells

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Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560 012, India
§ Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
*E-mail: [email protected]. Phone: (91)-80-2293 2664. Fax: (91)-80-2293 0529.
Cite this: J. Med. Chem. 2014, 57, 16, 6973–6988
Publication Date (Web):July 25, 2014
Copyright © 2014 American Chemical Society

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    Cell-permeable small molecules that enhance the stability of the G-quadruplex (G4) DNA structures are currently among the most intensively pursued ligands for inhibition of the telomerase activity. Herein we report the design and syntheses of four novel benzimidazole–carbazole conjugates and demonstrate their high binding affinity to G4 DNA. S1 nuclease assay confirmed the ligand mediated G-quadruplex DNA protection. Additional evidence from Telomeric Repeat Amplification Protocol (TRAP-LIG) assay demonstrated efficient telomerase inhibition activity by the ligands. Two of the ligands showed IC50 values in the sub-micromolar range in the TRAP-LIG assay, which are the best among the benzimidazole derivatives reported so far. The ligands also exhibited cancer cell selective nuclear internalization, nuclear condensation, fragmentation, and eventually antiproliferative activity in long-term cell viability assays. Annexin V-FITC/PI staining assays confirm that the cell death induced by the ligands follows an apoptotic pathway. An insight into the mode of ligand binding was obtained from the molecular dynamics simulations.

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    Synthesis of compounds 1116, characterization of the key compounds, additional UV–vis titration, fluorescence, CD spectroscopic data, telomerase inhibition data, cytotoxicity data, and computational results. This material is available free of charge via the Internet at

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