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Chemoinformatics-assisted development of new anti-biofilm compounds

Applied Microbiology and Biotechnology volume 87, pages 309–317 (2010)Cite this article

Abstract

Bacterial biofilms are associated with a large number of infections. Biofilm-dwelling bacteria are particularly resistant to antibiotics, making it hard to eradicate biofilm-associated infections. Here, we use a novel cross-disciplinary approach combining microbiology and chemoinformatics to identify new and efficient anti-biofilm drugs. We found that ellagic acid (present in green tea) significantly inhibited biofilm formation of Streptococcus dysgalactiae. Based on ellagic acid, we performed in silico screening of the Chinese Natural Product Database to predict a 2nd-generation list of compounds with similar characteristics. One of these, esculetin, proved to be more efficient in preventing biofilm formation by Staphylococcus aureus. From esculetin a 3rd-generation list of compounds was predicted. One of them, fisetin, was even better to abolish biofilm formation than the two parent compounds. Fisetin dramatically inhibited biofilm formation of both S. aureus and S. dysgalactiae. The compounds did not affect planktonic growth in concentrations where they affected biofilm formation and appeared to be specific antagonists of biofilms. Arguably, since all three compounds are natural ingredients of dietary plants, they should be well-tolerated by humans. Our results indicate that such small plant components, with bacterial lifestyle altering properties are promising candidates for novel generations of antimicrobial drugs. The study underlines the potential in combining chemoinformatics and biofilm research.

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Acknowledgements

We thank Birthe Jul Jørgensen for expert technical assistance and Olivier Taboureau for fruitful discussions and critical comments. This work was supported by grants from the Danish Medical Research Council (Grant 271-07-0291), the Danish Research Council for Technology and Production Sciences (Grant 274-06-0301), and Lundbeckfonden (Grant R19-A2191).

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Affiliations

  1. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark

    Anna Dürig, Irene Kouskoumvekaki, Rebecca M. Vejborg & Per Klemm

  2. Microbial Genomics Group, Center for Biological Sequence Analysis, Bldg. 301, Technical University of Denmark, DK-2800, Lyngby, Denmark

    Per Klemm

Authors
  1. Anna Dürig
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  2. Irene Kouskoumvekaki
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  3. Rebecca M. Vejborg
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  4. Per Klemm
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Corresponding author

Correspondence to Per Klemm.

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Fig. S1
figure 5

1st-generation hits from CNPD with a higher than 90% similarity to query natural compound ellagic acid (Tanimoto coefficient ≥0.9).CAS registry numbers in brackets [] correspond to hits with chemical structures that are close analogs to the structure depicted. (GIF 263 kb)

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Fig. S2
figure 6

2nd-generation hits from CNPD with a higher than 90% similarity to query natural compound esculetin (Tanimoto coefficient ≥0.9). CAS registry numbers in brackets [] correspond to chemical structures that are close analogs to the structure depicted. (When more than two analog compounds are found, their CAS registry numbers are given as footnote.) (GIF 296 kb)

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Dürig, A., Kouskoumvekaki, I., Vejborg, R.M. et al. Chemoinformatics-assisted development of new anti-biofilm compounds. Appl Microbiol Biotechnol 87, 309–317 (2010). https://doi.org/10.1007/s00253-010-2471-0

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Keywords

  • Anti-biofilm drugs
  • Bacterial biofilms
  • Chemoinformatics
  • Dietary plant components
  • Staphylococcus aureus
  • Streptococcus dysgalactiae