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Play of molecular host: guest assembly on a G-quadruplex binder

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Abstract

Benzimidazoles are known G-quadruplex binding molecules. G-quadruplex-selective binding is relevant in the target-based design of the molecules for treating certain diseases, including cancer. Herein, we present the synthesis of a new benzimidazolyl guanidine and its binding association with various nucleic acids viz., calf thymus DNA (duplex), kit22, myc22, and telo (G-quadruplexes). The synthesized compound is characterized by IR, NMR, and mass spectrometric techniques. The binding titration is carried out utilizing UV–vis and fluorescence spectroscopy. The conformational changes of DNAs on the ligand binding are monitored using circular dichroism. Further, the compound inclusion complex with a porphyrin-β-cyclodextrin host molecule. The binding strengths of the guanidine and its Ppy-CD inclusion complex are compared. The inclusion complexes bind stronger to G-quadruplexes than CT-DNA. The binding constants value is the largest for the interaction of the guanidine: porphyrin-β-cyclodextrin inclusion complex with the G-quadruplex kit22, which possesses a parallel conformation. The difference in the binding strengths is articulated and compared between duplex and G-quadruplex bindings.

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Acknowledgements

This work was supported by the Board of Research in Nuclear Science (Department of Atomic Energy), New Delhi. Project Number: 37(2)/14/17/2018-BRNS/37147. HP is grateful to the Department of Atomic Energy, for the reward of the Raja Ramanna Fellowship.

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Board of Research in Nuclear Sciences, 37(2)/14/17/2018-BRNS/37147.

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Authors and Affiliations

  1. Centre for Nanoscience and Genomics, Karunya Deemed University, Coimbatore, Tamil Nadu, 641114, India

    Aleyamma Alexander, Archana Sumohan Pillai & Israel Vijayaraj Muthu Vijayan Enoch

  2. Department of Applied Chemistry, Karunya Deemed University, Coimbatore, Tamil Nadu, 641114, India

    Sudhaker Raboni Grace, Nallamuthu Ananthi & Israel Vijayaraj Muthu Vijayan Enoch

  3. Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai, 400085, India

    Haridas Pal & Mhejabeen Sayed

  4. Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India

    Mhejabeen Sayed

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Credit authorship contribution statement Aleyamma Alexander: Data curation, Formal analysis. Archana Sumohan Pillai: Data curation, Formal analysis. Sudhaker Raboni Grace: Data curation, Formal analysis. Nallamuthu Ananthi: Data curation, Formal analysis. Haridas Pal: Conceptualization, Funding acquisition. Israel VMV Enoch: Conceptualization, Funding acquisition. Mhejabeen Sayed: Conceptualization, Funding acquisition.

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Correspondence to Israel Vijayaraj Muthu Vijayan Enoch or Mhejabeen Sayed.

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Alexander, A., Pillai, A.S., Grace, S.R. et al. Play of molecular host: guest assembly on a G-quadruplex binder. J Incl Phenom Macrocycl Chem 103, 147–159 (2023). https://doi.org/10.1007/s10847-023-01185-2

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