Discovery metabolite profiling of the prolyl peptidases

Summary

Principal Investigator: Alan Saghatelian
Abstract: Abstract Elucidation of the molecular mechanisms that underlie disease is crucial for the development of new therapeutic agents. Researchers have recently developed a number of methods to identify the genes, proteins, and metabolites associated with disease. However, complementary methods that define connections between these molecules[unreadable]connections that are the foundation of biological models of disease and targeted medicine[unreadable]have proven much more difficult to develop. As a result, there remains a tremendous need for innovative new approaches that reveal interactions between the molecular components of disease in vivo. The following proposal outlines the continued development and application of one such method, termed discovery metabolite profiling (DMP), for the assignment of endogenous substrates to the prolyl peptidase family of enzymes. DMP integrates an array of biological and chemical methods, including genetics, pharmacology, and analytical chemistry to identify bona fide physiological enzyme-substrate interactions. Importantly, by using DMP to study a family of enzymes that are virtually lacking in known endogenous substrates, but regulate phenotypes of tremendous biomedical interest, this research will begin to realize the incredible potential of the prolyl peptidases in medicine. Furthermore, the application of DMP to peptidases will demonstrate the generality of this approach for the future characterization of medically relevant enzymes and signaling pathways.
Funding Period: 2007-09-30 - 2012-08-31
more information: NIH RePORT

Top Publications

  1. pmc Peptidase substrates via global peptide profiling
    Debarati M Tagore
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Chem Biol 5:23-5. 2009
  2. pmc Analysis of the proteolysis of bioactive peptides using a peptidomics approach
    Yun Gon Kim
    Department of Chemical Engineering, Soongsil University, Seoul, South Korea
    Nat Protoc 8:1730-42. 2013
  3. pmc Proteolysis controls endogenous substance P levels
    Andrew J Mitchell
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS ONE 8:e68638. 2013
  4. pmc Peptidomics methods for the identification of peptidase-substrate interactions
    Anna Mari Lone
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Curr Opin Chem Biol 17:83-9. 2013
  5. pmc Peptidomic discovery of short open reading frame-encoded peptides in human cells
    Sarah A Slavoff
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:59-64. 2013
  6. pmc Peptidomics approach to elucidate the proteolytic regulation of bioactive peptides
    Yun Gon Kim
    Department of Chemical Engineering, Soongsil University, Seoul 156 743, South Korea
    Proc Natl Acad Sci U S A 109:8523-7. 2012
  7. pmc Deletion of PREPl causes growth impairment and hypotonia in mice
    Anna Mari Lone
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS ONE 9:e89160. 2014
  8. pmc Peptidomics of prolyl endopeptidase in the central nervous system
    Whitney M Nolte
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Biochemistry 48:11971-81. 2009
  9. pmc Investigating endogenous peptides and peptidases using peptidomics
    Arthur D Tinoco
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
    Biochemistry 50:7447-61. 2011
  10. pmc A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors
    Anna Mari Lone
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    J Am Chem Soc 133:11665-74. 2011

Detail Information

Publications13

  1. pmc Peptidase substrates via global peptide profiling
    Debarati M Tagore
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Chem Biol 5:23-5. 2009
    ..Together, these studies elucidate specific aspects of DPP4-regulated metabolism and, more generally, highlight the utility of global peptide profiling for studying peptide metabolism in vivo...
  2. pmc Analysis of the proteolysis of bioactive peptides using a peptidomics approach
    Yun Gon Kim
    Department of Chemical Engineering, Soongsil University, Seoul, South Korea
    Nat Protoc 8:1730-42. 2013
    ..The protocol is valuable because it expedites the characterization of mammalian peptidases, such as IDE, which in certain instances can be used to develop novel therapeutics. ..
  3. pmc Proteolysis controls endogenous substance P levels
    Andrew J Mitchell
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS ONE 8:e68638. 2013
    ..Administration of GM6001 to mice results in a greater-than-three-fold increase in the spinal cord levels of SP, which validates the hypothesis that proteolysis controls physiological SP levels...
  4. pmc Peptidomics methods for the identification of peptidase-substrate interactions
    Anna Mari Lone
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Curr Opin Chem Biol 17:83-9. 2013
    ..Since peptidases are of great biomedical interest, these approaches will begin to impact our ability to identify new drug targets that regulate important bioactive peptides...
  5. pmc Peptidomic discovery of short open reading frame-encoded peptides in human cells
    Sarah A Slavoff
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:59-64. 2013
    ..In addition, coding sORFs are present in a small fraction (8 out of 1,866) of long intergenic noncoding RNAs. Together, these results provide strong evidence that the human proteome is more complex than previously appreciated...
  6. pmc Peptidomics approach to elucidate the proteolytic regulation of bioactive peptides
    Yun Gon Kim
    Department of Chemical Engineering, Soongsil University, Seoul 156 743, South Korea
    Proc Natl Acad Sci U S A 109:8523-7. 2012
    ..More generally, this work suggests that this may be an effective general strategy for characterizing these pathways and peptidases moving forward...
  7. pmc Deletion of PREPl causes growth impairment and hypotonia in mice
    Anna Mari Lone
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS ONE 9:e89160. 2014
    ..These animals provide a valuable asset in deciphering the underlying biochemical, cellular and physiological pathways that link PREPL to HCS, and this may eventually lead to new insights in the treatment of this disease. ..
  8. pmc Peptidomics of prolyl endopeptidase in the central nervous system
    Whitney M Nolte
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Biochemistry 48:11971-81. 2009
    ..The discovery of Prep-regulated peptides implicates Prep in new biological pathways and provides insights into the biochemistry of this enzyme...
  9. pmc Investigating endogenous peptides and peptidases using peptidomics
    Arthur D Tinoco
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
    Biochemistry 50:7447-61. 2011
    ....
  10. pmc A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors
    Anna Mari Lone
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    J Am Chem Soc 133:11665-74. 2011
    ..The application of fluopol-ABPP has led to the first reported PREPL inhibitors, and these inhibitors will be of great value in studying the biochemistry of PREPL and in eventually understanding the link between PREPL and HCS...
  11. pmc A peptidomics strategy to elucidate the proteolytic pathways that inactivate peptide hormones
    Arthur D Tinoco
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
    Biochemistry 50:2213-22. 2011
    ..Moreover, integrating this peptidomics approach with bioassays (i.e., GSIS) provides a general strategy to reveal proteolytic pathways that may regulate the activity of peptide hormones...
  12. pmc Expanding the dipeptidyl peptidase 4-regulated peptidome via an optimized peptidomics platform
    Arthur D Tinoco
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    J Am Chem Soc 132:3819-30. 2010
    ..Together these results strengthen our ability to identify endogenous peptide substrates through improved peptidome coverage and demonstrate a broader potential of this peptidomics platform...
  13. ncbi Functional analysis of protein targets by metabolomic approaches
    Yun Gon Kim
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, USA
    Top Curr Chem 324:137-62. 2012
    ..Metabolomics approaches are useful in characterizing proteins that regulate or bind metabolites. Here, we provide examples of the development and use of metabolomics approaches to elucidate protein-metabolite interactions...