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Journal of Biomolecular Screening, Vol. 12, No. 7, 972-982 (2007)
DOI: 10.1177/1087057107306759
© 2007 Society for Biomolecular Sciences

A Chemogenomic Analysis of the Human Proteome: Application to Enzyme Families

Paul Bernasconi

BASF Corporation, Research Triangle Park, North Carolina

Min Chen

Amphora Discovery Corporation, Durham, North Carolina

Scott Galasinski

Abbott Laboratories, Abbott Park, Illinois

Ioana Popa-Burke

GSK, Research Triangle Park, North Carolina

Anna Bobasheva

Varian, Inc, Cary, North Carolina

Louis Coudurier

Amphora Discovery Corporation, Durham, North Carolina

Steve Birkos

Amphora Discovery Corporation, Durham, North Carolina

Rhonda Hallam

Amphora Discovery Corporation, Durham, North Carolina

William P. Janzen

Amphora Discovery Corporation, Durham, North Carolina, bill.janzen{at}amphoracorp.com

Sequence-based phylogenies (SBP) are well-established tools for describing relationships between proteins. They have been used extensively to predict the behavior and sensitivity toward inhibitors of enzymes within a family. The utility of this approach diminishes when comparing proteins with little sequence homology. Even within an enzyme family, SBPs must be complemented by an orthogonal method that is independent of sequence to better predict enzymatic behavior. A chemogenomic approach is demonstrated here that uses the inhibition profile of a 130,000 diverse molecule library to uncover relationships within a set of enzymes. The profile is used to construct a semimetric additive distance matrix. This matrix, in turn, defines a sequence-independent phylogeny (SIP). The method was applied to 97 enzymes (kinases, proteases, and phosphatases). SIP does not use structural information from the molecules used for establishing the profile, thus providing a more heuristic method than the current approaches, which require knowledge of the specific inhibitor's structure. Within enzyme families, SIP shows a good overall correlation with SBP. More interestingly, SIP uncovers distances within families that are not recognizable by sequence-based methods. In addition, SIP allows the determination of distance between enzymes with no sequence homology, thus uncovering novel relationships not predicted by SBP. This chemogenomic approach, used in conjunction with SBP, should prove to be a powerful tool for choosing target combinations for drug discovery programs as well as for guiding the selection of profiling and liability targets. (Journal of Biomolecular Screening 2007:972-982)

Key Words: chemogenomic • proteome • enzyme • phylogeny • sequence independent


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