Genomics Research Institute University of Cincinnati Compound Library Wm. L. Seibel


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Genomics Research Institute University of Cincinnati Compound Library

  • Wm. L. Seibel

  • January 10, 2007


Overview

  • Library Overview

  • Compound Characteristics

    • Design Concepts
    • Drug-Like
  • Library Screening Options

  • Summary of Library Advantages



Compound Repository

  • Haystack Neat Compound Storage

    • Capacity = 200,000 bottles
    • Current = 207,000 bottles
    • Freezer storage when appropriate
  • Solar (Solution Archive) – DMSO solutions

    • Capacity = 1.8 million tubes, 10,000 deep well (96) plates, 13,600 shallow well (384) plates
    • Current = 325,000 unique compounds
  • Related Compound Handling and Dissolution instruments.

  • Housed at P&G’s Mason Business Center in ca. 3000 sf lab space



Haystack® Neat Chemical Storage



Haystack® Neat Chemical Storage



Haystack® Neat Chemical Storage



Solar® Solution Storage



Solar® Solution Storage



Solar® Solution Storage



Library Design Principles





Library Compounds

  • The UC/GRI Compound Library is comprised of compounds from four general categories:

    • 1. Compounds purchased from numerous sources selected to provide a diverse representation across “drug-like” structural properties.
    • 2. Compounds purchased that specifically target kinases and GPCRs
    • 3. Compounds prepared in-house specifically for projects in kinases, GPCRs, phosphatases, ion channels and proteases donated from P&G Pharmaceuticals.
    • 4. Combinatorial Chemistry contract syntheses (Lower Priority Cmpds).
  • This screening library is broadly diverse across drug-like space, with enhanced concentrations in areas of key biological relevance, including notably, kinases and GPCRs.



P&G Pharma Selected Compounds

  • Chemically Diverse

    • Represented uniformly across drug-like space.
    • Want to ensure uniform, comprehensive and diverse representation of compounds across the structural & property types that are typical of drugs and lead structures.
  • Compounds selected based on drug like properties (within “Drug-Like Space”)

  • Total P&G investment to assemble repository = $22 M (over past 10 years)



Chemical Property Filters



Diversity Analysis



Describing Molecular Structure



Diversity Assessment Methodology

  • Used BCUT descriptors *

    • R.S. Pearlman, UT at Austin
    • DiverseSolutions (now available from Tripos)
  • Computed ~120 BCUTs

  • Selected a best subset of 6 BCUTs

    • 6D space – visualization is a challenge


Pearlman’s BCUT descriptors *

  • 6D Chem-space (structure-space)

    • 2 atomic partial-charge descriptors
    • 2 atomic polarizability descriptors
    • a hydrogen-bond acceptor descriptor
    • a hydrogen-bond donor descriptor


Concept of Chemistry Space



Defining Drug Space

  • Based on structures of “drug-like” compounds from

      • The World Drug Index (WDI)
      • The Nation Cancer Institute Open Database


Diverse Subset Selection



Compound Supply

  • External Suppliers (20+ vendors)

    • Brokerage Houses
      • Individual Compounds (Diversity)
      • Target Directed Libraries
    • Combinatorial Chemistry Companies
  • Corporate Suppliers

    • P&G Pharmaceuticals
      • Focus Areas - Medicinal Chemistry
      • Lead ID – Combinatorial Chemistry


Vendor “Dependability”



On the Other Hand…

  • Even within Drug-like space, certain classes can be somewhat clustered.

  • This library therefore has added “focused libraries” from internal synthesis and external vendors emphasizing compounds relevant to:

    • GPCRs
    • Kinases


P&G Pharma Selected Compounds

  • Defined by experienced medicinal chemists

    • Broad, uniform distribution across Drug Space with concentrations of density in key areas from directed purchase and in house synthesis.
  • Compare to 5 vendor screening collections

    • 3,000 to 500,000 compounds
    • 27% - 56% of vendors’ compound collections do NOT meet criteria for drug-like
    • UC Compound collection is 2X to 100X more chemically diverse across Drug Space.
  • Vendor Libraries are inherently predisposed to clustered groupings.

  • We can pick the best, most relevant compounds from each.



Screening Library Options



Screening Library Design Options

  • Diverse broad collections

    • Comprehensive screening against all available compounds (ca. 250,000 cmpds)
    • Screening against a representative subset of available compounds (e.g. 5000 cmpds)
  • Class-associated compounds

    • Compounds with structural features often associated with a particular target (e.g. kinases).
  • Structure-based compound selection

    • Virtual Screening of a crystal structure or high quality homology model to identify the most likely inhibitors (ca. 2000 cmpds), followed by assay of these compounds.
    • Virtual Screening as above based on pharmacophore models from known ligands of the target.


Diverse Subset Selection



Diverse Subset Selection



Diverse Subset Selection



Diverse Subset Selection





Iterative Cycling



Diverse Subset Selection



Class-Associated Compounds



Virtual Screening



Iterative Cycling



Hit to Lead Follow-up (H2L)



Hit to Lead Follow-up (H2L)

  • How to determine optimal hits for follow-up

    • Confirm ID and activity of hits
    • Cluster into groups of related compounds
    • Develop preliminary SAR info on each cluster
    • Assess Each Cluster for optmization
      • “Which compounds have fewest problems?”
      • Synthetic Ease
      • Proprietary Assessment
      • Selectivity Issues
      • Physical Properties
      • Metabolic Handles
      • Cellular Activity


Summary



UC/P&GP Library Advantages

  • Quality Advantages

    • Library carefully constructed to span drug-like space.
    • Compounds restricted to those with properties consistent with clinical materials.
    • Proven to produce viable hits for follow-up programs.
    • Comparisons have uniformly been favorable relative to commercial vendor sets.
    • Includes targeted subsets of compounds for key areas: GPCRs, Kinases, Phosphatases, Ion channels.
  • Practical Advantages

    • SD file of structures and ID tags furnished for unrestricted use.
    • Many compounds from commercial sources, so resupply likely to be easy.
    • Materials supplied in microtiter plates (96 or 384) as requested.
    • Solution Stores made from local dry stores, so follow-up assays will be rapid.
  • Technical Advantages

    • Act as Liaison with screening group (internal or external).
    • Participate in advisory committee for compound acquisition decisions.


Library Use and Data Interpretation

  • Library Design Assistance

    • Computational assistance in selecting diverse subsets or directed subsets.
    • Computational assistance in selecting compounds similar to known leads (Nearest Neighbor).
    • Computational assistance in virtual screening by pharmacophore or protein docking.


Library Use and Data Interpretation

  • Follow-up Assistance

    • Resupply assistance, synthesis info, supplier info
    • Assistance in obtaining related available compounds (Similarity, substructure, Unity, Pharmacophore).
    • Provide preliminary lit search info (known info, IP, etc) on prominent hits.
    • Clustering of hits into chemical/pharmacophore classes included.
    • Provide help identifying chemistry groups with related interests for collaborations
    • Provide assistance in connecting with contract chemistry services (consult).


Questions



Thank you



Acknowledgements

  • Operations

    • Stacey Frazier
    • Kathy Gibboney
  • Computational

    • Matt Wortman
    • David Stanton
    • Prakash Madhav



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