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Chemogenomics pp 195-205 | Cite as

Off-Target Networks Derived from Ligand Set Similarity

  • Michael J. Keiser
  • Jérôme Hert
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 575)

Summary

Chemically similar drugs often bind biologically diverse protein targets, and proteins with similar sequences or structures do not always recognize the same ligands. How can we uncover the pharmacological relationships among proteins, when drugs may bind them in defiance of bioinformatic criteria? Here we consider a technique that quantitatively relates proteins based on the chemical similarity of their ligands. Starting with tens of thousands of ligands organized into sets for hundreds of drug targets, we calculated the similarity among sets using ligand topology. We developed a statistical model to rank the resulting scores, which were then expressed in minimum spanning trees. We have shown that biologically sensible groups of targets emerged from these maps, as well as experimentally validated predictions of drug off-target effects.

Key words

SEA Expectation value Target network Polypharmacology Off-targets 

Notes

Acknowledgments

M.J.K is supported by a National Science Foundation graduate fellowship. J.H. is supported by the sixth Framework Program of the European Commission. We are grateful to MDL Information Systems Inc. for the MDDR database; Daylight Chemical Information Systems Inc.; and OpenEye Scientific Software for software support. We thank John J. Irwin for reading the manuscript and Brian K. Shoichet for mentoring.

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Michael J. Keiser
    • 1
  • Jérôme Hert
    • 1
  1. 1.Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoUSA

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