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.
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.
KeywordsStreptomyces Polycyclic tetramate macrolactams Ikarugamycin Clifednamide Anticancer Apoptosis
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.
Compliance with Ethical Standards
Conflict of Interest
The authors declare that they have no competing interests.
- ChemAxon (2013) Marvin Sketch. https://www.chemaxon.com/products/marvin/
- DeLano WL (2002) The PyMOL user’s manual. DeLano Scientific, San CarlosGoogle Scholar
- Kelly KL (1964) Inter-Society Color Council—National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. US Government Printing Office, Washington, D.CGoogle Scholar
- Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897CrossRefPubMedGoogle Scholar
- Mori T, Cahn JKB, Wilson MC, Meoded RA, Wiebach V, Martinez AFC, Helfrich EJN, Albersmeier A, Wibberg D, Dätwyler S, Keren R, Lavy A, Rückert C, Ilan M, Kalinowski J, Matsunaga S, Takeyama H, Piel J (2018) Single-bacterial genomics validates rich and varied specialized metabolism of uncultivated Entotheonella sponge symbionts. Proc Natl Acad Sci 115:1718–1723CrossRefPubMedGoogle Scholar
- Yang XW, Zhang GY, Ying JX, Yang B, Zhou XF, Steinmetz A, Liu YH, Wang N (2013) Isolation, characterization, and bioactivity evaluation of 3-((6-methylpyrazin-2-yl)methyl)-1H-indole, a new alkaloid from a deep-sea-derived actinomycete Serinicoccus profundi sp. nov. Mar Drugs 11:33–39CrossRefGoogle Scholar