title: Small molecule affinity fingerprinting. A tool for enzyme family subclassification, target identification, and inhibitor design.
abstract: Classifying proteins into functionally distinct families based only on primary sequence information remains a difficult task. We describe here a method to generate a large data set of small molecule affinity fingerprints for a group of closely related enzymes, the papain family of cysteine proteases. Binding data was generated for a library of inhibitors based on the ability of each compound to block active-site labeling of the target proteases by a covalent activity based probe (ABP). Clustering algorithms were used to automatically classify a reference group of proteases into subfamilies based on their small molecule affinity fingerprints. This approach was also used to identify cysteine protease targets modified by the ABP in complex proteomes by direct comparison of target affinity fingerprints with those of the reference library of proteases. Finally, experimental data were used to guide the development of a computational method that predicts small molecule inhibitors based on reported crystal structures. This method could ultimately be used with large enzyme families to aid in the design of selective inhibitors of targets based on limited structural/function information.
authors.affiliation: Department of Pharmaceutical Chemistry, San Francisco, CA 94143, USA.
authors.forename: Doron C
authors.initials: DC
authors.lastname: Greenbaum
authors.forename: William D
authors.initials: WD
authors.lastname: Arnold
authors.forename: Felice
authors.initials: F
authors.lastname: Lu
authors.forename: Linda
authors.initials: L
authors.lastname: Hayrapetian
authors.forename: Amos
authors.initials: A
authors.lastname: Baruch
authors.forename: Jennifer
authors.initials: J
authors.lastname: Krumrine
authors.forename: Samuel
authors.initials: S
authors.lastname: Toba
authors.forename: Kareem
authors.initials: K
authors.lastname: Chehade
authors.forename: Dieter
authors.initials: D
authors.lastname: Brömme
authors.forename: Irwin D
authors.initials: ID
authors.lastname: Kuntz
authors.forename: Matthew
authors.initials: M
authors.lastname: Bogyo
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D016000:Cluster Analysis; D015853:Cysteine Proteinase Inhibitors / Q000737:chemistry* / Q000378:metabolism; D015195:Drug Design; D004353:Drug Evaluation, Preclinical / Q000379:methods; D004852:Epoxy Compounds / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D010206:Papain / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D051381:Rats; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D015853:Cysteine Proteinase Inhibitors; D004852:Epoxy Compounds; D010206:Papain