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Probing Riboswitch Binding Sites with Molecular Docking, Focused Libraries, and In-line Probing Assays

  • Francesco Colizzi
  • Anne-Marie Lamontagne
  • Daniel A. Lafontaine
  • Giovanni Bussi
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1103)

Abstract

Molecular docking calculations combined with chemically focused libraries can bring insight in the exploration of the structure–activity relationships for a series of related compounds against an RNA target. Yet, the in silico engine must be fueled by experimental observations to drive the research into a more effective ligand-discovery path. Here we show how molecular docking predictions can be coupled with in-line probing assays to explore the available chemical and configurational space in a riboswitch binding pocket.

Key words

Structure-based Ligand design Virtual screening Structure–activity relationship (SAR) Docking Focused library In-line probing 

Notes

Acknowledgements

This work was supported by the National Sciences and Engineering Research Council of Canada (NSERC). D.A.L. is a Canadian Institutes of Health Research (CIHR) New Investigator Scholar. F.C. was supported by the “Young SISSA Scientist” grant (FISB.647 2011) for independent research development. F.C. and G.B. acknowledge the European Research Council for funding through the Starting Grant S-RNA-S (no. 306662).

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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Francesco Colizzi
    • 1
  • Anne-Marie Lamontagne
    • 2
  • Daniel A. Lafontaine
    • 2
  • Giovanni Bussi
    • 1
  1. 1.Scuola Internazionale Superiore di Studi AvanzatiTriesteItaly
  2. 2.RNA Group, Department of Biology, Faculty of ScienceUniversité de SherbrookeSherbrookeCanada

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