Mel Reichman on Pool Shark’s Cues for More Efficient Drug Discovery


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Mel Reichman, senior investigator and director of the LIMR Chemical Genomics Center at the Lankenau Institute for Medical Research presents at the chemistry department at Drexel University on November 12, 2009.

Modern drug discovery by high-throughput screening (HTS) begins with testing hundreds of thousands of compounds in biological assays. The confirmed hit rate for typical HTS is less than 0.5%; therefore, 99.5% of the costs of HTS are for generating null data. Orthogonal convolution of compound libraries (OCL) is 500% more efficient than present HTS practice. The OCL method combines 10 compounds per well. An advantage of this method is that each compound is represented twice in two separately arrayed pools. The potential for the approach to better enable academic centers of excellence to validate medicinally relevant biological targets is discussed.

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Mel Reichman on Pool Shark’s Cues for More Efficient Drug Discovery

  1. 1. Accelerating Exploration of Chemical and Biological Space for Academic Drug Discovery [email_address] . (see research Services—LCGC)
  2. 2. Lankenau Institute for Medical Research (LIMR). Wynnewood, PA is an non-profit organization of ~22 independent faculty and other principal investigators who conduct basic and clinical research in cancer, diabetes, and cardiovascular disease. Founded in 1927. “ In medicine, hope springs from research”
  3. 3. Summary <ul><li>Origins of NIH Roadmap </li></ul><ul><li>Accelerate Lead Discovery 500% </li></ul><ul><li>New Models for Pharma-Academia Discovery </li></ul>
  4. 4. American Academia: A Golden Goose of Innovation? $100 Billion $500 Billion Bayh-Dole Act 1980
  5. 5. Strangling a Golden Goose The COX-2 Story
  6. 6. Greasy Aryl Polar Celebrex Greasy Aryl Alkyl Acidic Ibuprofen
  7. 7. The COX-2 Story: Timeline 1992: Patent filed 1992: Merck and Searle begin COX-2 program 1998: Celebrex approved, 6 months later Vioxx approved 4/11/2000: U.S. Patent No. 6,048,850 (the '850 patent) issues (‘kitchen sink’) 4/12/2000: UR initiates suit against Searle (Pfizer) 3/5/2003: UR looses up to Supreme Court October, 2003: NIH Roadmap announced
  8. 8. Why UR Lost “ Because the inventors here simply failed to take the last critical step of actually isolating a compound, or even developing a process through which one of skill would be directly led to such a compound, this patent involves &quot;little more than a research plan,&quot; the court concluded. ( ). ‘ The University had claimed a method requiring, yet provided no written description of, a compound that could inhibit COX-2 and, therefore, the patent was invalid.’
  9. 9. &quot;We are the National Institutes of Health, not the National Institutes of Biology,&quot; Elias A. Zerhouni, M.D. says. &quot;We need to reengineer how we apply our research to humans.&quot; ( ) New Roadmap for 21 st Century Translational Research
  10. 10. Harbinger of Change
  11. 12. Proboscis for Probes? volume 5 number 7 JUly 2009 nature chemical biology
  12. 13. With New Models In place
  13. 14. ‘ High Throughput’ Screening? <ul><li>>99.5% of the cost is to generate null data </li></ul><ul><ul><ul><li>HTS is binary; 0.5% hit rate, 99.5% inert rate </li></ul></ul></ul><ul><li>Positive confirmation rates from HTS = ca. 30%-80% </li></ul><ul><ul><ul><li>False negatives rate > 0 </li></ul></ul></ul><ul><ul><ul><li>No other bioassay field runs n = 1 assays </li></ul></ul></ul><ul><li>Goal of HTS is to find the best leads faster </li></ul><ul><ul><ul><li>500% faster; with 80% fewer resources? </li></ul></ul></ul>
  14. 15. Self Deconvoluting Compressed Libraries <ul><li>Pooled sample testing dates to WWII </li></ul><ul><li>Used in developing economies for blood safety testing </li></ul><ul><li>NAT pooling trials ongoing in US (HIV, HCV) </li></ul>
  15. 16. Important Product Usage and Safety Information The ABBOTT PRISM HIV O Plus test (Human Immunodeficiency Virus Types 1 and 2 (E. coli, B. megaterium, Recombinant) Antigen and Synthetic Peptide) can be used by laboratory professionals to screen individual donations of blood for antibodies to HIV-1 (anti-HIV-1) Groups M and O and /or antibodies to HIV-2 (anti-HIV-2). ABBOTT PRISM HIV O Plus can also be used as an aid in the diagnosis of HIV-1/HIV-2 infection. This assay has not been validated for use with pooled specimens and is not intended for use on cord blood specimens.
  16. 17. <ul><li>Hughes-Oliver, JM. Pooling experiments for blood screening and drug discovery. In: Screening Methods for Experimentation in Industry, Drug Discovery, and Genetics. Dean, Angela; Lewis, Susan (Eds.), 21-47. Springer 2006 </li></ul><ul><li>Motlekar N, Diamond SL, Napper AD. Evaluation of an orthogonal pooling strategy for rapid high-throughput screening of proteases. Assay. Drug. Dev. Technol. (2008) 395-405. </li></ul><ul><li>  Ferrand S, Schmid A, Engeloch C, Glickman JF. Statistical evaluation of a self-deconvoluting matrix strategy for high-throughput screening of the CXCR3 receptor. Assay Drug. Dev. Technol. (2005) 395-405. </li></ul><ul><li>Devlin, J.; Lian, A.; Trinh, L.; Polokoff, M.; Senator, D.; Zheng, W.; Kondracki, J.; Kretschmer, P.; Morser, J.; Lipson, S.; Spann, R.; Loughlin, J.; Dunn, K.; Morrissey, M. High capacity screening of pooled compounds: Identification of the active compound without re-assay of pool members. Drug DeV. Res. (1996) 80-85. </li></ul><ul><li>Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J. Med. Chem. (2006) 2151-4. </li></ul><ul><li>Chung, T. Screen Compounds Singly: Why Muck It Up? J. Biomol. Screening (1998) 171-173. </li></ul><ul><li>Konings DA, Wyatt JR, Ecker DJ, Freier SM. Strategies for Rapid Deconvolution of Combinatorial Libraries: Comparative Evaluation Using a Model System. J. Med. Chem. (1997) 4386-95.  </li></ul><ul><li>Snider, M. Screening of Compound Libraries: Consomme or Gumbo? J. Biomol. Screening (1998) 169-170.  </li></ul><ul><li>Oprea, TI. Chemoinformatics in Drug Discovery. In: Chemoinformatics in Drug Discovery Oprea, TI (Ed.) 25-42, Wiley 2005.  </li></ul><ul><li>Cummins, D. Pharmaceutical drug discovery: hunting the blockbuster drug. In: Screening Methods for Experimentation in Industry, Drug Discovery, and Genetics. Dean, Angela; Lewis, Susan (Eds.) 69-114. Springer 2006.  </li></ul><ul><li>Zhang JH, Wu X, Sills MA. Probing the primary screening efficiency by multiple replicate testing: a quantitative analysis of hit confirmation and false screening results of a biochemical assay. J. Biomol. Screen. (2005) 695-704.   </li></ul><ul><li>Hann, M., Hudson, B., Lewell, X., Lifely, R., Miller, L., Ramsden, N. Strategic Pooling of Compounds for High-Throughput Screening. J. Chem. Inf. Comput. Sci. 1999, 39, 897-902.  </li></ul><ul><li>von Ahsen O, Schmidt A, Klotz M, Parczyk K. Assay concordance between SPA and TR-FRET in high-throughput screening. J Biomol Screen. (2006) 606-  </li></ul><ul><li>Leach AR, Bradshaw J, Green DV, Hann MM, Delany JJ 3rd. Implementation of a system for reagent selection and library enumeration, profiling, and design. J. Chem. Inf. Comput. Sci. (1999) 1161-72. </li></ul><ul><li>Spencer R. W. High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. Biotechnol. Bioeng. (1998) 61-67. </li></ul> Relevant References Suggest Productive Paths Forward
  17. 18. MX 1-10 epsilon delta gamma beta alpha
  18. 19. New Approaches, Software and Data Mining www. ceuticalsoft .com
  19. 20. The retinoblastoma tumor suppressor pathway contains multiple oncogenes (green) and tumor suppressors (red) and is dysfunctional in almost every human tumor Münger K PNAS 2003;100:2165-2167
  20. 21. <ul><li>ELISA assay was adapted to 384-well format to do a HTS of >80,000 compounds </li></ul><ul><li>Assay measures the amount of E2F bound to pRb upon addition of 16E7 (CR2/CR3) +/- compound </li></ul><ul><li>prevent E7-mediated E2F displacement from pRb </li></ul>Kindly provided by D. Ferra, Wistar Institute) High Signal Add E2F – specific 1° Ab Wash Add HRP-linked 2° Ab Wash Add luminescence substrate Wash
  21. 22. Pilot Run Library OCL009 9 E7-inhibitors—pRB/E2F
  22. 23. Trends Observed for Hit Categories E7/pRB-E2F    Conf. Rate
  23. 24. Fructosamine –3-Kinase Pathway in Diabetes Fructoselysine Glucose + Lysine Fructoselysine-3- Phosphate FRUCTOSAMINE- 3- KINASE 3DG + LYSINE + Pi Glycated Protein DIET DIABETICS Fructoselysine Glucose + Lysine Fructoselysine-3- Phosphate 3DG + LYSINE + Pi Glycated Protein NON-DIABETICS Diabetic complications Nephropathy Retinopathy Neuropathy Kindly provided by Dynamis Therapeutics Inc.
  24. 25. ADP
  25. 26. Universal Kinase Assay
  26. 27. Pilot Run Library OCL009 9 FN3K Inhibitor Screen
  27. 28. Pilot HTS Results Library LCGC-OCL-009 HTS Results 8 x 8,000 compounds = 64K
  28. 29. Advanced, Innovative Compound Management Strategies
  29. 31. NanoTube Automated Repository System <ul><li>10,000,000 sample capacity </li></ul><ul><li>Single-shot repository—no freeze thawing </li></ul><ul><li>Raw pick rate of 10,000 samples per day </li></ul><ul><li>Support HTS follow-up or focused library ‘screening on the fly’ </li></ul><ul><li>$$Multimillion infrastructure available at reasonable fee-for-service model </li></ul><ul><li>Pricing for long-term cost-recovery costs plus reasonable margin </li></ul><ul><li>Hybrid business model of support-service and academic research collaboration </li></ul>
  30. 32. Indelible Audit Trail -20 o C Operation Consolidate Molecular Diversity Collections Maxiprep genomic DNA extractions for molecular epidemiology studies and biorepositories. CA Garcia-Sepulveda et al., Mol Biol Rep. 2009 Jul 17 Toward noninvasive genomic screening of lung cancer patients. L V Sequist et al., Journal of Clinical Oncology, Vol 27, No 16 (June 1), 2009 epsilon delta gamma beta alpha Abbreviated HTS
  31. 33. FIGURE 3
  32. 34. Present Biorepository Practice
  33. 36. Summary <ul><li>HTS has become an accepted translational research approach in academia </li></ul><ul><li>Far more published support for method than anecdotal evidence against </li></ul><ul><li>NARS support helps ensure a finer net for capturing new leads </li></ul><ul><li>New software tools helps ensure a finer net for capturing new leads </li></ul><ul><li>LCGC can enable ANY lab for true HTS—better than present practice? </li></ul><ul><li>Resources at Drexel can become recruited within emerging collaborative research networks, especially in greater Philly region </li></ul>
  34. 37. Acknowledgements <ul><li>George Prendergast, Todd Abrams Tam Nguyen (LIMR) </li></ul><ul><li>Scott Donover Amanda Schabdach (LCGC) </li></ul><ul><li>Chip Allee (CeuticalSoft Inc.) </li></ul><ul><li>Marlin Yohn et al (Istech) and Ron Miller et al (REMS)—et al. </li></ul><ul><li>Dave Schultz and Danelia Fera (Wistar), Seth Goldenberg (Progenra), Ricardo Macaroon, Dwight Morrow and Snehal Bhat (GSK), Mike Schwartz and Alice Marcy (Dynamis) </li></ul>