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DNA Binding and Molecular Dynamic Studies of Polycyclic Tetramate Macrolactams (PTM) with Potential Anticancer Activity Isolated from a Sponge-Associated Streptomyces zhaozhouensis subsp. mycale subsp. nov.

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Abstract

A sponge-associated actinomycete (strain MCCB267) was isolated from a marine sponge Mycale sp. collected in the Indian Ocean off the Southeast coast of India. Phylogenetic studies of this strain using 16S rRNA gene sequencing showed high sequence similarity to Streptomyces zhaozhouensis. However, strain MCCB267 showed distinct physiological and biochemical characteristic features and was thus designated as S. zhaozhouensis subsp. mycale. subsp. nov. A cytotoxicity-guided fractionation of the crude ethyl acetate extract of strain MCCB267 culture medium yielded four pure compounds belonging to the polycyclic tetramate macrolactam (PTM) family of natural products: ikarugamycin (IK) (1), clifednamide A (CF) (2), 30-oxo-28-N-methylikarugamycin (OI) (3), and 28-N-methylikarugamycin (MI) (4). The four compounds exhibited promising cytotoxic activity against NCI-H460 lung carcinoma cells in vitro, by inducing cell death via apoptosis. Flow cytometric analysis revealed that 1, 3, and 4 induced cell cycle arrest during G1 phase in the NCI-H460 cell line, whereas 2 induced cell arrest in the S phase. A concentration-dependent accumulation of cells in the sub-G1 phase was also detected upon treatment of the cancer cell line with compounds 1–4. The in vitro cytotoxicity studies were supported by molecular docking and molecular dynamic simulation analyses. An in silico study revealed that the PTMs can bind to the minor groove of DNA and subsequently induce the apoptotic stimuli leading to cell death. The characterization of the isolated actinomycete, the study of the mode of action of the four PTMs, 1–4, and the molecular docking and molecular dynamic simulations analyses are herein described.

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Funding

DM would like to thank the Kerala State Council for Science, Technology and Environment, Government of Kerala, India for project funding under best paper award scheme (292/2016/KSCSTE dated 7 July 2016) and Cochin University of Science and Technology and Kerala State Council for Science, Technology and Environment, Government of Kerala, India for funding.

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Authors and Affiliations

  1. National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682 016, India

    M. Dhaneesha & T. P. Sajeevan

  2. Raymond and Beverly Sackler School of Chemistry and Faculty of Exact Sciences, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel

    O. Hasin & S. Carmeli

  3. Bioinformatics Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India

    K. C. Sivakumar

  4. Department of Aquatic Biology and Fisheries, University of Kerala, Thiruvananthapuram, Kerala, 695581, India

    R. Ravinesh

  5. Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315211, China

    C. Benjamin Naman

  6. Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA

    C. Benjamin Naman

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  1. M. Dhaneesha
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Correspondence to T. P. Sajeevan.

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Electronic supplementary material

Online Resource 1

Cultural characteristics of Streptomyces sp. MCCB267 on various media after 2 weeks of growth at 28 °C. (PDF 153 kb)

Online Resource 2

Carbon source utilization pattern of Streptomyces sp. MCCB267. (PDF 148 kb)

Online Resource 3

NMR data of the ikarugamycin derivatives 1–4. (PDF 196 kb)

Online Resource 4

Probit regression line for the determination of IC50 of a) CF, b) OI, c) IK and d) MI on NCI-H460 cells. (PDF 184 kb)

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Dhaneesha, M., Hasin, O., Sivakumar, K.C. et al. DNA Binding and Molecular Dynamic Studies of Polycyclic Tetramate Macrolactams (PTM) with Potential Anticancer Activity Isolated from a Sponge-Associated Streptomyces zhaozhouensis subsp. mycale subsp. nov.. Mar Biotechnol 21, 124–137 (2019). https://doi.org/10.1007/s10126-018-9866-9

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