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Structure elucidation and in silico docking studies of a novel furopyrimidine antibiotics synthesized by endolithic bacterium Actinomadura sp. AL2

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Abstract

On screening of endolithic actinobacteria from a granite rock sample of Meghalaya for antibacterial compound, a novel antibacterial compound CCp1 was isolated from the fermentation broth of Actinomadura sp. AL2. On purification of the compound based on chromatographic techniques followed by characterization with FT-IR, UV–visible, 1H NMR, 13C NMR and mass spectrometry, the molecular formula of the compound was generated as C20H17N3O2, a furopyrimidine derivative. In vitro antibacterial activity of the compound was evaluated against both Gram positive and negative bacteria by agar well diffusion assay. The compound had lowest MIC (2.00 µg/ml) for Bacillus subtilis and highest MIC (> 64 µg/ml) for Staphylococcus epidermidis and Pseudomonas aeruginosa. The study revealed that the compound has potential antibacterial activity. The mode of action of the antibacterial compound was evaluated through in silico studies for its ability to bind DNA gyrase, 30S RNA molecules, OmpF porins and N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU). The antibacterial compound demonstrated more favorable docking with DNA gyrase, 30S RNA molecules and OmpF porins than GlmU which support the antibacterial compound CCp1 can be as a promising broad spectrum antibiotic agent with “multitarget” characteristics.

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Acknowledgements

The NMR facility was provided by SAIF, N.E.H.U, Shillong. The UV–visible spectroscopic facility was provided by Central Instrumentation Facility, School of Life Sciences, N.E.H.U, Shillong and FT-IR facility was provided by CIF, I.A.S.S.T, Guwahati. We are also grateful to Dr. S. Sangilipandi, Centre for Advanced Studies in Chemistry, N.E.H.U, Shillong for the help during TLC and purification studies.

Authors’ contribution

KB and SJ designed and carried out the experiments, analyzed the data and drafted the manuscript. NP and KR performed the MS experiment and helped in analyzing the spectrometry data and structure elucidation. SK and PP conducted the in silico docking studies. SJ supervised the whole research work and revised the manuscript. All authors read and approved the final manuscript.

Funding

This research was partly supported by the Department of Science & Technology, Government of India FIST programme to the parent department. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. KB is thankful to UGC, New Delhi for providing financial support in the form of research fellowship.

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Authors and Affiliations

  1. Microbiology Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, 793022, India

    Kaushik Bhattacharjee & Santa Ram Joshi

  2. Bioinformatics Center (ICMR), Department of Biochemistry, Pt. Jawaharlal Nehru Memorial Medical College, Raipur, India

    Shakti Kumar

  3. Centre for Advanced Studies in Chemistry, North-Eastern Hill University, Shillong, India

    Narasinga Rao Palepu & Kollipara Mohan Rao

  4. Department of Biochemistry, Pt. Jawaharlal Nehru Memorial Medical College, Raipur, India

    Pradeep Kumar Patra

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  1. Kaushik Bhattacharjee
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Bhattacharjee, K., Kumar, S., Palepu, N.R. et al. Structure elucidation and in silico docking studies of a novel furopyrimidine antibiotics synthesized by endolithic bacterium Actinomadura sp. AL2. World J Microbiol Biotechnol 33, 178 (2017). https://doi.org/10.1007/s11274-017-2343-1

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