John R Somoza

Summary

Affiliation: Celera Genomics
Country: USA

Publications

  1. ncbi The structure of the extracellular region of human hepsin reveals a serine protease domain and a novel scavenger receptor cysteine-rich (SRCR) domain
    John R Somoza
    Celera, Inc, 180 Kimball Road, South San Francisco, CA 94080, USA
    Structure 11:1123-31. 2003
  2. ncbi Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases
    John R Somoza
    Celera, 180 Kimball Way, South San Francisco, CA 94080 USA
    Structure 12:1325-34. 2004
  3. ncbi Expression, purification, crystallization and preliminary X-ray diffraction studies of human cathepsin F complexed with an irreversible vinyl sulfone inhibitor
    Joseph D Ho
    Celera Inc, 180 Kimball Way, South San Francisco, CA 94080, USA
    Acta Crystallogr D Biol Crystallogr 58:2187-90. 2002
  4. ncbi Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA)
    Bradley A Katz
    Celera, 180 Kimball Way, South San Francisco, CA 94080, USA
    J Mol Biol 344:527-47. 2004
  5. ncbi Design of novel, potent, and selective human beta-tryptase inhibitors based on alpha-keto-[1,2,4]-oxadiazoles
    Chang Sun Lee
    Department of Chemistry, Celera, 180 Kimball Way, South San Francisco, CA 94080, USA
    Bioorg Med Chem Lett 16:4036-40. 2006
  6. ncbi Design and synthesis of tri-ring P3 benzamide-containing aminonitriles as potent, selective, orally effective inhibitors of cathepsin K
    James T Palmer
    Celera Genomics, Inc, 180 Kimball Way, South San Francisco, California 94080, USA
    J Med Chem 48:7520-34. 2005
  7. ncbi Peptide ketobenzoxazole inhibitors bound to cathepsin K
    Mary E McGrath
    Celera, South San Francisco, California 94080, USA
    Biochemistry 42:15018-28. 2003
  8. ncbi Structure-guided design of peptide-based tryptase inhibitors
    Mary E McGrath
    Celera Genomics, Inc, 180 Kimball Way, South San Francisco, California 94080, USA
    Biochemistry 45:5964-73. 2006
  9. ncbi The crystal structure of human cathepsin F and its implications for the development of novel immunomodulators
    John R Somoza
    Department of Medicinal and Structural Chemistry, Celera, 180 Kimball Way, 94080, South San Francisco, CA, USA
    J Mol Biol 322:559-68. 2002
  10. ncbi Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV
    Todd C Appleby
    Department of Structural Chemistry, Gilead Sciences, Inc, 333 Lakeside Drive, Foster City, CA 94404, USA
    J Mol Biol 405:1139-53. 2011

Detail Information

Publications12

  1. ncbi The structure of the extracellular region of human hepsin reveals a serine protease domain and a novel scavenger receptor cysteine-rich (SRCR) domain
    John R Somoza
    Celera, Inc, 180 Kimball Road, South San Francisco, CA 94080, USA
    Structure 11:1123-31. 2003
    ..The structure suggests how the extracellular region of hepsin may be positioned with respect to the plasma membrane...
  2. ncbi Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases
    John R Somoza
    Celera, 180 Kimball Way, South San Francisco, CA 94080 USA
    Structure 12:1325-34. 2004
    ..This work sheds light on the catalytic mechanism of the HDACs, and on differences in substrate specificity across the HDAC family. The structure also suggests how phosphorylation of Ser39 affects HDAC8 activity...
  3. ncbi Expression, purification, crystallization and preliminary X-ray diffraction studies of human cathepsin F complexed with an irreversible vinyl sulfone inhibitor
    Joseph D Ho
    Celera Inc, 180 Kimball Way, South San Francisco, CA 94080, USA
    Acta Crystallogr D Biol Crystallogr 58:2187-90. 2002
    ..A complete data set to a resolution of 2.5 A has been collected at room temperature. The Laue group was determined to be orthorhombic, space group P2(1)2(1)2, with unit-cell parameters a = 68.9, b = 104.8, c = 68.5 A...
  4. ncbi Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA)
    Bradley A Katz
    Celera, 180 Kimball Way, South San Francisco, CA 94080, USA
    J Mol Biol 344:527-47. 2004
    ..The 6-fluoro-5-amidinobenzimidzole, CA-11, is more than 1000-fold selective against natural Ala190 protease anti-targets, and more than 100-fold selective against other Ser190 anti-targets...
  5. ncbi Design of novel, potent, and selective human beta-tryptase inhibitors based on alpha-keto-[1,2,4]-oxadiazoles
    Chang Sun Lee
    Department of Chemistry, Celera, 180 Kimball Way, South San Francisco, CA 94080, USA
    Bioorg Med Chem Lett 16:4036-40. 2006
    ..The inhibitor design is focused on using a prime-side hydrophobic pocket and the S2 pocket of beta-tryptase to achieve inhibition potency and selectivity over other serine proteases...
  6. ncbi Design and synthesis of tri-ring P3 benzamide-containing aminonitriles as potent, selective, orally effective inhibitors of cathepsin K
    James T Palmer
    Celera Genomics, Inc, 180 Kimball Way, South San Francisco, California 94080, USA
    J Med Chem 48:7520-34. 2005
    ..Inhibition of collagen breakdown by cathepsin K inhibitors suggests this mechanism of action may be useful in osteoporosis and other indications involving bone resorption...
  7. ncbi Peptide ketobenzoxazole inhibitors bound to cathepsin K
    Mary E McGrath
    Celera, South San Francisco, California 94080, USA
    Biochemistry 42:15018-28. 2003
    ..X-ray crystal structures of cathepsin K both unbound and complexed with inhibitors provide detailed information on protease/inhibitor interactions and suggestions for the design of tight-binding, selective molecules...
  8. ncbi Structure-guided design of peptide-based tryptase inhibitors
    Mary E McGrath
    Celera Genomics, Inc, 180 Kimball Way, South San Francisco, California 94080, USA
    Biochemistry 45:5964-73. 2006
    ..Thus, replacement of Lys/Arg at P1 in a peptide-like scaffold does not need to be accompanied by a loss in target affinity...
  9. ncbi The crystal structure of human cathepsin F and its implications for the development of novel immunomodulators
    John R Somoza
    Department of Medicinal and Structural Chemistry, Celera, 180 Kimball Way, 94080, South San Francisco, CA, USA
    J Mol Biol 322:559-68. 2002
    ..This structure provides a basis for understanding cathepsin F's substrate specificity, and suggests ways of identifying potent and selective inhibitors of this enzyme...
  10. ncbi Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV
    Todd C Appleby
    Department of Structural Chemistry, Gilead Sciences, Inc, 333 Lakeside Drive, Foster City, CA 94404, USA
    J Mol Biol 405:1139-53. 2011
    ....
  11. ncbi Beta-substituted cyclohexanecarboxamide: a nonpeptidic framework for the design of potent inhibitors of cathepsin K
    Sheldon N Crane
    Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec, Canada, H9H 3L1
    J Med Chem 49:1066-79. 2006
    ..28 nM; >800-fold selectivity vs Cat B, L, and S; PK data in dogs: F 55%, t(1/2) = 15 h) exhibit great potential for development as an orally bioavailable therapeutic for treatment of diseases that involve bone loss...
  12. ncbi Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease
    Stephanie X Wang
    Department of Pathology and the Sandler Center, San Francisco General Hospital, University of California, CA 94143, USA
    Proc Natl Acad Sci U S A 103:11503-8. 2006
    ..Motifs similar to FP2(nose) and FP2(arm) are found only in related plasmodial proteases, suggesting that they confer malaria-specific functions...