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Virtual screening and in silico design of novel inhibitors of bacterial lectins

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Bacterium Pseudomonas aeruginosa is a human opportunistic pathogen. It can cause infection of immunocompromised people or people suffering from cystic fibrosis, which is often fatal. Bacterial colonization of human tissues is mediated by interaction of bacterial surface proteins – lectins – with cellular surface carbohydrates. PA-IIL is Pseudomonas aeruginosa tetrameric lectin, which contains two calcium ions in each binding site and recognizes fucosylated oligosaccharides [1]. Saturation of bacterial surface lectins by specially designed compounds might prevent adhesion to host tissues and thus suppress the infection. In this work, virtual screening and docking were used for identification of compounds that might inhibit this interaction and be potentially used as a new generation of antibiotics.

Two different approaches for identification of promising compounds were employed. Subset of drug-like molecules was docked into the PA-IIL binding site by Autodock Vina [2] and Dock 6 [3]. Interesting ligands were then selected by identifying those with highest score provided by both programs. In the second approach, we focused on the identification of interesting molecular fragments, which should be attached to already pre-docked carbohydrate. The carbohydrate serves as a targeting agent and newly identified fragments increase its interaction with the lectin. In both approaches, ZINC library [4] was the source of ligands and fragments.

References

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    Adam J, et al: Engineering of PA-IIL lectin from Pseudomonas aeruginosa - Unravelling the role of the specificity loop for sugar preference. BMC Struct Biol. 2007, 7: 36-10.1186/1472-6807-7-36.

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    Trott O, et al: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010, 31: 455-461.

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    Kuntz ID, et al: A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982, 161: 269-288. 10.1016/0022-2836(82)90153-X.

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    Irwin JJ, et al: ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005, 45: 177-182. 10.1021/ci049714+.

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Acknowledgements

The work is supported by the Ministry of Education (MSM0021622413, LC6030, ME08008), the Czech Science Foundation (GA/303/09/1168, GD301/09/H004) of the Czech Republic, the European Community's Seventh Framework Programme (grant agreement n° 205872) and the project “CEITEC - Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) from European Regional Development Fund.

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Correspondence to Jan Alán.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Keywords

  • Cystic Fibrosis
  • Oligosaccharide
  • Pseudomonas Aeruginosa
  • Dock
  • Virtual Screening