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Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening

Academic Article
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Overview

related to degree

  • Blankman, Jacqueline, Ph.D. in Chemistry, Scripps Research 2006 - 2012
  • Bachovchin, Daniel A., Ph.D. in Chemistry, Scripps Research 2006 - 2011
  • Li, Weiwei, Ph.D. in Chemical Biology, Scripps Research 2005 - 2010
  • Simon, Gabriel, Ph.D. in Chemistry, Scripps Research 2004 - 2009

authors

  • Bachovchin, Daniel A.
  • Ji, T. Y.
  • Li, Weiwei
  • Simon, Gabriel
  • Blankman, Jacqueline
  • Adibekian, Alexander
  • Hoover, H.
  • Niessen, Sherry
  • Cravatt, Benjamin

publication date

  • December 2010

journal

  • Proceedings of the National Academy of Sciences of the United States of America  Journal

abstract

  • Serine hydrolases (SHs) are one of the largest and most diverse enzyme classes in mammals. They play fundamental roles in virtually all physiological processes and are targeted by drugs to treat diseases such as diabetes, obesity, and neurodegenerative disorders. Despite this, we lack biological understanding for most of the 110+ predicted mammalian metabolic SHs, in large part because of a dearth of assays to assess their biochemical activities and a lack of selective inhibitors to probe their function in living systems. We show here that the vast majority (> 80%) of mammalian metabolic SHs can be labeled in proteomes by a single, active site-directed fluorophosphonate probe. We exploit this universal activity-based assay in a library-versus-library format to screen 70+ SHs against 140+ structurally diverse carbamates. Lead inhibitors were discovered for ?40% of the screened enzymes, including many poorly characterized SHs. Global profiles identified carbamate inhibitors that discriminate among highly sequence-related SHs and, conversely, enzymes that share inhibitor sensitivity profiles despite lacking sequence homology. These findings indicate that sequence relatedness is not a strong predictor of shared pharmacology within the SH superfamily. Finally, we show that lead carbamate inhibitors can be optimized into pharmacological probes that inactivate individual SHs with high specificity in vivo.
  • Serine hydrolases (SHs) are one of the largest and most diverse enzyme classes in mammals. They play fundamental roles in virtually all physiological processes and are targeted by drugs to treat diseases such as diabetes, obesity, and neurodegenerative disorders. Despite this, we lack biological understanding for most of the 110+ predicted mammalian metabolic SHs, in large part because of a dearth of assays to assess their biochemical activities and a lack of selective inhibitors to probe their function in living systems. We show here that the vast majority (> 80%) of mammalian metabolic SHs can be labeled in proteomes by a single, active site-directed fluorophosphonate probe. We exploit this universal activity-based assay in a library-versus-library format to screen 70+ SHs against 140+ structurally diverse carbamates. Lead inhibitors were discovered for ∼40% of the screened enzymes, including many poorly characterized SHs. Global profiles identified carbamate inhibitors that discriminate among highly sequence-related SHs and, conversely, enzymes that share inhibitor sensitivity profiles despite lacking sequence homology. These findings indicate that sequence relatedness is not a strong predictor of shared pharmacology within the SH superfamily. Finally, we show that lead carbamate inhibitors can be optimized into pharmacological probes that inactivate individual SHs with high specificity in vivo.

subject areas

  • Carbamates
  • Catalytic Domain
  • Drug Discovery
  • Drug Evaluation, Preclinical
  • Enzyme Inhibitors
  • Fluorides
  • Humans
  • Hydrolases
  • Molecular Probes
  • Phosphates
  • Protein Binding
  • Proteome
  • Serine
  • Small Molecule Libraries
  • Substrate Specificity
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Research

keywords

  • enzymology
  • mass spectrometry
  • profiling
  • proteomics
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Identity

PubMed Central ID

  • PMC3000285

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.1011663107

PubMed ID

  • 21084632
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Additional Document Info

start page

  • 20941

end page

  • 20946

volume

  • 107

issue

  • 49

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