A Specific Mechanism for Non-Specific Inhibition

Summary

Principal Investigator: Brian K Shoichet
Abstract: DESCRIPTION (provided by applicant): Many bioactive molecules form colloidal aggregates at micromolar and sub-micromolar concentrations. These colloids inhibit soluble proteins without specificity but with shared mechanism: adsorbing and partially denaturing them;they are the dominant artifact in early drug discovery and chemical biology. Surprisingly, the colloids are stable in cell culture, serum, and apparently even in vivo. Whereas we have previously focused on the impact of aggregates on soluble proteins in biochemical assays, we increasingly turn our attention to cell- based assays, tissue penetration and animal pharmacokinetics. The specific aims are: 1. to investigate the affect of colloids in cell culture, tissue penetration, and pharmacokinetics. We investigate the impact of aggregates on biology at increasing levels of complexity, beginning with a. Membrane-bound receptors, focusing on GPCR signaling, and continue with b. a simple, web-based tool to predict compound aggregation. These goals reflect the ongoing importance of detecting aggregation in early discovery. More ambitiously, we investigate c. Tumor penetration. Anti-neoplastic drugs like Fulvestrant aggregate not only in buffer but also in serum. Do these colloids affect the cellular activity of these drugs, and might they actually be exploited for delivery, targeting high vascular permeability of tumors? d. In vivo pharmacokinetics. Colloids of several BCS II and IV oral drugs are stable in simulated intestinal fluids. We explore their stability in the gut, and their affects on in vivo pharmacokinetics and distribution. 2. To investigate the structure and mechanism of colloidal aggregates. We continue to believe that progress and understanding will depend on fundamental physical and mechanistic studies. Key unanswered questions include: a. Thermodynamic driving forces and association kinetics. Is colloid formation driven simply by the hydrophobic effect, or are other forces at play? b. Stability and denaturation. Since colloids denature proteins, does protein stability affect the potential for colloidal inhibition? c. Mixed inhibition. Can inhibitors be wel- behaved at lower concentrations, but switch to a colloidal mechanism above some threshold? Does this lead to the common, but physically undefined, "mixed" inhibition mechanism? d. How might aggregators pack, and what separates them from non-aggregators? To investigate this, we will determine the small molecule crystal structures of aggregators and of close analogs that do not aggregate
Funding Period: 2004-08-01 - 2016-01-31
more information: NIH RePORT

Top Publications

  1. pmc Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures
    Brian Y Feng
    Department of Pharmaceutical Chemistry and Graduate Group in Chemistry and Chemical Biology, University of California San Francisco, 1700 4th Street, California 94143 2550, USA
    J Med Chem 49:2151-4. 2006
  2. pmc Colloid formation by drugs in simulated intestinal fluid
    Allison K Doak
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158 2550, USA
    J Med Chem 53:4259-65. 2010
  3. pmc Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors
    Rafaela S Ferreira
    Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, California 94158, USA
    J Med Chem 53:4891-905. 2010
  4. pmc Ligand discovery from a dopamine D3 receptor homology model and crystal structure
    Jens Carlsson
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Chem Biol 7:769-78. 2011
  5. pmc Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4
    Michael M Mysinger
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 109:5517-22. 2012
  6. pmc Novel cruzain inhibitors for the treatment of Chagas' disease
    Kathleen E Rogers
    Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, 92093, USA
    Chem Biol Drug Des 80:398-405. 2012
  7. pmc Colloidal aggregation affects the efficacy of anticancer drugs in cell culture
    Shawn C Owen
    Donnelly Centre, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, Department of Chemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
    ACS Chem Biol 7:1429-35. 2012
  8. pmc Colloidal aggregation causes inhibition of G protein-coupled receptors
    Maria F Sassano
    Department of Pharmacology and the NIMH Psychoactive Drug Screening Program, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina 27759, USA
    J Med Chem 56:2406-14. 2013
  9. pmc Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)
    Ryan T Cameron
    Institute of Cardiovascular and Medical Sciences, CMVLS, Glasgow University, Glasgow G12 8QQ, UK
    Biochem Pharmacol 85:1297-305. 2013
  10. pmc Divergent modes of enzyme inhibition in a homologous structure-activity series
    Rafaela S Ferreira
    Small Molecule Discovery Center, Sandler Center for Basic Research in Parasitic Diseases, and Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    J Med Chem 52:5005-8. 2009

Detail Information

Publications20

  1. pmc Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures
    Brian Y Feng
    Department of Pharmaceutical Chemistry and Graduate Group in Chemistry and Chemical Biology, University of California San Francisco, 1700 4th Street, California 94143 2550, USA
    J Med Chem 49:2151-4. 2006
    ..Synergistic effects on aggregation predominated, although antagonism was also observed. These results suggest that screening mixtures can increase aggregation-based inhibition in a nonadditive manner...
  2. pmc Colloid formation by drugs in simulated intestinal fluid
    Allison K Doak
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158 2550, USA
    J Med Chem 53:4259-65. 2010
    ..Six formed colloids at concentrations equal to or lower than the concentrations reached in the gut, suggesting that aggregation may have an effect on the absorption and distribution of these drugs, and potentially others, in vivo...
  3. pmc Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors
    Rafaela S Ferreira
    Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, California 94158, USA
    J Med Chem 53:4891-905. 2010
    ..Prioritizing molecules that are both predicted by docking and are HTS-active yields well-behaved molecules, relatively unobscured by the false-positives to which both techniques are individually prone...
  4. pmc Ligand discovery from a dopamine D3 receptor homology model and crystal structure
    Jens Carlsson
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Chem Biol 7:769-78. 2011
    ..3 to 3.0 μM. One of the new ligands from the homology model screen was optimized for affinity to 81 nM. The feasibility of docking screens against modeled GPCRs more generally is considered...
  5. pmc Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4
    Michael M Mysinger
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 109:5517-22. 2012
    ..36, and with efficacy in cellular chemotaxis. The potency and efficiency of these molecules has few precedents among protein-protein interface inhibitors, and supports structure-based efforts to discover leads for chemokine GPCRs...
  6. pmc Novel cruzain inhibitors for the treatment of Chagas' disease
    Kathleen E Rogers
    Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, 92093, USA
    Chem Biol Drug Des 80:398-405. 2012
    ..Further optimization of these chemical scaffolds could lead to the development of novel drugs useful in the treatment of Chagas' disease...
  7. pmc Colloidal aggregation affects the efficacy of anticancer drugs in cell culture
    Shawn C Owen
    Donnelly Centre, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, Department of Chemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
    ACS Chem Biol 7:1429-35. 2012
    ....
  8. pmc Colloidal aggregation causes inhibition of G protein-coupled receptors
    Maria F Sassano
    Department of Pharmacology and the NIMH Psychoactive Drug Screening Program, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina 27759, USA
    J Med Chem 56:2406-14. 2013
    ..These observations suggest that some GPCRs may be artifactually antagonized by colloidal aggregates, an effect that merits the attention of investigators in this field...
  9. pmc Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)
    Ryan T Cameron
    Institute of Cardiovascular and Medical Sciences, CMVLS, Glasgow University, Glasgow G12 8QQ, UK
    Biochem Pharmacol 85:1297-305. 2013
    ..Our data suggest that moexipril is a bona fide PDE4 inhibitor that may provide the starting point for development of novel PDE4 inhibitors with an improved therapeutic window...
  10. pmc Divergent modes of enzyme inhibition in a homologous structure-activity series
    Rafaela S Ferreira
    Small Molecule Discovery Center, Sandler Center for Basic Research in Parasitic Diseases, and Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    J Med Chem 52:5005-8. 2009
    ....
  11. pmc Promiscuous aggregate-based inhibitors promote enzyme unfolding
    Kristin E D Coan
    Department of Pharmaceutical Chemistry and Graduate Group in Chemistry and Chemical Biology, University of CaliforniaSan Francisco, San Francisco, California 94158 2550, USA
    J Med Chem 52:2067-75. 2009
    ..Combined, these results suggest that the mechanism of action of aggregate-based inhibitors proceeds via partial protein unfolding when bound to an aggregate particle...
  12. pmc Screening in a spirit haunted world
    Brian K Shoichet
    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, Byers Hall Room 508D, San Francisco, CA 94158, USA
    Drug Discov Today 11:607-15. 2006
    ..The range of molecules that behave this way, their rapid detection in a screening environment and their possible biological implications will be considered here...
  13. ncbi Interpreting steep dose-response curves in early inhibitor discovery
    Brian K Shoichet
    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, USA
    J Med Chem 49:7274-7. 2006
    ..Most steep dose-response curves in screening may be due to this effect...
  14. pmc A detergent-based assay for the detection of promiscuous inhibitors
    Brian Y Feng
    Department of Pharmaceutical Chemistry, and Graduate Group in Chemistry and Chemical Biology, University of California San Francisco, 1700 4th Street, California 94158 2330, USA
    Nat Protoc 1:550-3. 2006
    ..Furthermore, we also describe simple experiments that can offer additional confirmation of aggregate-based inhibition...
  15. ncbi Stability and equilibria of promiscuous aggregates in high protein milieus
    Kristin E D Coan
    Dept of Pharmaceutical Chemistry, University of California San Francisco, Byers Hall, San Francisco, CA 94158, USA
    Mol Biosyst 3:208-13. 2007
    ..These results suggest that enzyme is bound to aggregate so tightly as to prevent any noticeable dissociation and that furthermore, aggregates are stable at physiologically relevant concentrations of protein...
  16. pmc Small-molecule aggregates inhibit amyloid polymerization
    Brian Y Feng
    Department of Pharmaceutical Chemistry and Graduate Group in Chemistry and Chemical Biology, University of California San Francisco, 1700 4th Street, San Francisco, California 94158 2330, USA
    Nat Chem Biol 4:197-9. 2008
    ..They also blocked infection of yeast cells with Sup35 prions, which suggests that colloidal inhibition may be relevant in more biological milieus...
  17. pmc Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase
    Kerim Babaoglu
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158 2330, USA
    J Med Chem 51:2502-11. 2008
    ..Structure-based methods may prioritize weak-but-novel chemotypes in unbiased library screens...
  18. ncbi Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening
    Jui Hua Hsieh
    Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill, CB 7360, Beard Hall, Chapel Hill, NC, 27599 7360, USA
    J Comput Aided Mol Des 22:593-609. 2008
    ..Our studies suggest that validated QSAR models could complement structure based docking and scoring approaches in identifying promising hits by virtual screening of molecular libraries...
  19. pmc Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors
    Kristin E D Coan
    Department of Pharmaceutical Chemistry and Graduate Group in Chemistry and Chemical Biology, 1700 Fourth Street, University of California at San Francisco, San Francisco, California 94158 2550, USA
    J Am Chem Soc 130:9606-12. 2008
    ..Finally, given their size and enzyme stoichiometry, all sequestered enzyme can be comfortably accommodated on the surface of the aggregate...
  20. pmc Colloidal drug formulations can explain "bell-shaped" concentration-response curves
    Shawn C Owen
    Donnelly Centre, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, Department of Chemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
    ACS Chem Biol 9:777-84. 2014
    ..We found that colloidal species are excluded from cells, which may explain the mechanism behind toxicological screens that use Evans blue, Trypan blue, and related dyes. ..

Research Grants30

  1. The Shelf Live Evaluation of Investigational Dosage Forms
    Jonathan White; Fiscal Year: 2013
    ..This contract is essential for continued assurance of the quality of drugs undergoing clinical investigation for different types of cancer by Cancer Therapeutics Evaluation Program. ..
  2. Genomics of Kidney Transplantation Admin
    Arthur J Matas; Fiscal Year: 2013
    ..The Administrative Core will also facilitate interaction between Sites, Cores, and Projects. ..
  3. Interdisciplinary center of excellence for the study of pain and sensory function
    Ian D Meng; Fiscal Year: 2013
    ..Completion of these Aims will develop the research careers of a multidisciplinary group of junior investigators, and establish the core facilities and equipment necessary to constitute a competitive research center. ..
  4. Fundamental Mechanobiology of Tumor Progression
    JAN T LIPHARDT; Fiscal Year: 2013
    ..We have also recruited clinical investigators from 2 outside institutions to compliment existing expertise and to extend the translational scope of our projects. ..
  5. BARRIER FUNCTION OF THE GI TRACT IN HEALTH AND DISEASE
    W Allan Walker; Fiscal Year: 2013
    ..abstract_text> ..
  6. The Discovering Healthcare Innovations to Address Disparties in Stroke (DIADS) pr
    Stephen Sidney; Fiscal Year: 2013
    ....
  7. Caloric Restricted Rodent Colony
    RICK MORIN; Fiscal Year: 2013
    ..The purpose of this project is to develop, maintain and distribute a standing colony ofaged, calorically restricted rodents ofdefined strains for use by investigators in studies of aging. ..
  8. Impact of Lipids on Compound Absorption: Mechanistic Studies and Modeling
    Rebecca L Carrier; Fiscal Year: 2013
    ....
  9. DEGENERATIVE AND DEMENTING DISEASES OF AGING
    Stanley B Prusiner; Fiscal Year: 2013
    ..The ultimate goal of all the proposed studies is to define the molecular events that feature in the formation of human prions in order to develop therapeutics that cure the human prion diseases. ..
  10. Pacific NorthWest Regional Center of Excellence (PNWRCE)
    Jay A Nelson; Fiscal Year: 2013
    ..pseudomallei host pathogen response during both the septicemic as well as the intracellular phases of the disease. ..
  11. LIAI Epitope Validation Center: Characterization of Allergen specific T Cells
    ALESSANDRO D SETTE; Fiscal Year: 2013
    ..abstract_text> ..
  12. Center for Gene Therapy of Cystic Firbosis
    John F Engelhardt; Fiscal Year: 2013
    ..These efforts have led to numerous basic and applied research findings that have enhanced the utility of gene therapies to both study and treat genetic diseases. ..
  13. TOXIC SUBSTANCES IN THE ENVIRONMENT
    Martyn T Smith; Fiscal Year: 2013
    ..The program will be overseen and coordinated by an Administration core (A). ..
  14. Pacific Southwest RCE for Biodefense &Emerging Infectious Diseases Research
    Alan G Barbour; Fiscal Year: 2013
    ..abstract_text> ..
  15. Rocky Mountain Regional Center of Excellence or Biodefense and Emerging Infectiou
    John T Belisle; Fiscal Year: 2013
    ..abstract_text> ..