Accelerating Exploration of Chemical and Biological Space for Academic Drug Discovery

reichmanm@mlhs.orgreichmanm@mlhs.org. . www.limr.orgwww.limr.org (see research Services— (see research Services—LCGC)LCGC)

Lankenau Institute for Medical Research (LIMR). Lankenau Institute for Medical Research (LIMR). Wynnewood, PAWynnewood, PAis an non-profit organization of ~22 independent faculty and other is an non-profit organization of ~22 independent faculty and other principal investigators who conduct basic and clinical research in principal investigators who conduct basic and clinical research in cancer, diabetes, and cardiovascular disease. Founded in 1927.cancer, diabetes, and cardiovascular disease. Founded in 1927.

“In medicine, hope springs from research”

SummarySummary

• Origins of NIH RoadmapOrigins of NIH Roadmap

• Accelerate Lead Discovery 500%Accelerate Lead Discovery 500%

• New Models for Pharma-Academia DiscoveryNew Models for Pharma-Academia Discovery

American Academia: A Golden Goose of Innovation?American Academia: A Golden Goose of Innovation?

$100 Billion

$500 Billion

All Respondents 2003 2001 % ChangeLicense Options Executed

4995 4058 23

Gross Licensing Income $1.5 Billion 1.1 Billion 36

Total Patents Filed 13995 11265 24New Patents Filed 8346 6812 23Patents Issued 4,112 3721 11

Startups Formed 432 494 -13

Bayh-Dole Act 1980

Strangling a Golden GooseStrangling a Golden Goose

The COX-2 StoryThe COX-2 Story

Greasy Aryl

Polar

NN

Br

SNH2 O

O

F

F

F

Celebrex

Greasy Aryl Alkyl Acidic

Ibuprofen

O

O

The COX-2 Story: TimelineThe COX-2 Story: Timeline

1992: Patent filed1992: Merck and Searle begin COX-2 program 1998: Celebrex approved, 6 months later Vioxx approved4/11/2000: 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

Why UR LostWhy 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 "little more than a research plan," the court concluded.

(http://pub.bna.com/ptcj/006161.pdf).

‘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.’

"We are the National Institutes of Health, not the "We are the National Institutes of Health, not the National Institutes of Biology," Elias A. Zerhouni, National Institutes of Biology," Elias A. Zerhouni,

M.D. says. M.D. says.

"We need to reengineer how we apply our research to "We need to reengineer how we apply our research to humans." humans."

((http://www.the-scientist.com/2004/2/16/44/1http://www.the-scientist.com/2004/2/16/44/1))

New Roadmap for 21st Century Translational Research

Harbinger of ChangeHarbinger of Change

Proboscis for Probes?

volume 5 number 7 JUly 2009 nature chemical biology

http://genome.gov/Pages/About/OD/ReportsPublications/AustinHHT060806.pdf

With New Models

In place

‘‘High Throughput’ Screening?High Throughput’ Screening?

• >99.5% of the cost is to generate null data>99.5% of the cost is to generate null data

– HTS is binary; 0.5% hit rate, 99.5% inert rateHTS is binary; 0.5% hit rate, 99.5% inert rate

• Positive confirmation rates from HTS = ca. 30%-80%Positive confirmation rates from HTS = ca. 30%-80%

– False negatives rate > 0False negatives rate > 0

– No other bioassay field runs n = 1 assaysNo other bioassay field runs n = 1 assays

• Goal of HTS is to find the best leads fasterGoal of HTS is to find the best leads faster

500% faster; with 80% fewer resources?500% faster; with 80% fewer resources?

Self Deconvoluting Compressed LibrariesSelf Deconvoluting Compressed Libraries

• Pooled sample testing dates to WWIIPooled sample testing dates to WWII

• Used in developing economies for blood safety testingUsed in developing economies for blood safety testing

• NAT pooling trials ongoing in US (HIV, HCV)NAT pooling trials ongoing in US (HIV, HCV)

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.

■ 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

■ 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.

■ 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.

■ 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.

■ Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J. Med. Chem. (2006) 2151-4.

■ Chung, T. Screen Compounds Singly: Why Muck It Up? J. Biomol. Screening (1998) 171-173.

■ 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.

■ Snider, M. Screening of Compound Libraries: Consomme or Gumbo? J. Biomol. Screening (1998) 169-170.

■ Oprea, TI. Chemoinformatics in Drug Discovery. In: Chemoinformatics in Drug Discovery Oprea, TI (Ed.) 25-42, Wiley 2005.

■ 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.

■ 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.

■ 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.

■ 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-

■ 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.

■ Spencer R. W. High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. Biotechnol. Bioeng. (1998) 61-67.

1

Relevant References Suggest Productive Paths Forward

MX 1-10

epsilon

delta

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New Approaches, Software and Data Mining

www.ceuticalsoft.com

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

• ELISA assay was adapted to 384-well format to do a HTS of >80,000 compounds

• Assay measures the amount of E2F bound to pRb upon addition of 16E7 (CR2/CR3) +/- compound

prevent E7-mediated E2F displacement from pRb

High Signal

Add E2F – specific 1° Ab

Wash

Add HRP-linked 2° Ab

Wash

Add luminescence substrate

Wash

Kindly provided by D. Ferra, Wistar Institute)

Pilot Run Library OCL009 9 E7-inhibitors—pRB/E2FPilot Run Library OCL009 9 E7-inhibitors—pRB/E2F

-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

0.8

1

0 200 400 600 800 1000 1200 1400 1600 1800

Experiment Data ID

Samples

Positive

Negative

Trends Observed for Hit Categories E7/pRB-E2FTrends Observed for Hit Categories E7/pRB-E2FResult Dependency on Cutoff

Assay 703.04

0

10

20

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40

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0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Cutoff

Nu

mb

er

of

Re

su

lts

Actives

Ambiguous

Orphans

Ac + Am

77%73%

74%

Conf. Rate

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 complicationsNephropathyRetinopathyNeuropathy

Fructosamine –3-Kinase Pathway in DiabetesFructosamine –3-Kinase Pathway in Diabetes

Kindly provided by Dynamis Therapeutics Inc.

ADP

Universal Kinase AssayUniversal Kinase Assay

Pilot Run Library OCL009 9 FN3K Inhibitor Screen

0

20

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60

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0 200 400 600 800 1000 1200 1400 1600 1800

Experiment Data ID

mP

s A

bo

ve A

vera

ge

Po

siti

ve C

on

tro

l

Samples

Positive

Negative

Pilot HTS Results Library LCGC-OCL-009Pilot HTS Results Library LCGC-OCL-009

Assay Z' Cutoff Actives AmbiguousOverall Retest Rate

Ambiguous Retest Rate

Active Retest Rate

W06192009 0.72 10% 13 37 74% 73% 77%Dlcgc011 0.45 96% 13 4 88% 50% 100%Gbio004 0.74 50% 11 10 77% 83% 100%Gcell005 (Fura-2) 0.72 50% 2 0

Assay Z' Cutoff ActivesBest Potency

Active Retest Rate Format

W06192009 0.72 50% 63 < 1 µM 77% ELISA

Dlcgc011 0.45 80% 48 < 10 µM 72% FP

Gbio004 0.74 50% 64 5 nM 88% FPGcell005 (Fura-2) 0.72 50% 7 5 nM 100% FURA-2

HTS Results 8 x 8,000 compounds = 64KHTS Results 8 x 8,000 compounds = 64K

Advanced, Innovative Compound Management Strategies

NanoTube Automated Repository SystemNanoTube Automated Repository System

• 10,000,000 sample capacity10,000,000 sample capacity

• Single-shot repository—no freeze thawingSingle-shot repository—no freeze thawing

• Raw pick rate of 10,000 samples per dayRaw pick rate of 10,000 samples per day

• Support HTS follow-up or focused library ‘screening on the fly’Support HTS follow-up or focused library ‘screening on the fly’

• $$Multimillion infrastructure available at reasonable fee-for-service model$$Multimillion infrastructure available at reasonable fee-for-service model

• Pricing for long-term cost-recovery costs plus reasonable marginPricing for long-term cost-recovery costs plus reasonable margin

• Hybrid business model of support-service and academic research collaborationHybrid business model of support-service and academic research collaboration

Indelible Audit TrailIndelible Audit Trail-20 -20 ooC OperationC 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

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Abbreviated HTS

FIGURE 3

Present Biorepository Practice Present Biorepository Practice

SummarySummary• HTS has become an accepted translational research approach in academiaHTS has become an accepted translational research approach in academia

• Far more published support for method than anecdotal evidence againstFar more published support for method than anecdotal evidence against

• NARS support helps ensure a finer net for capturing new leadsNARS support helps ensure a finer net for capturing new leads

• New software tools helps ensure a finer net for capturing new leadsNew software tools helps ensure a finer net for capturing new leads

• LCGC can enable ANY lab for true HTS—better than present practice?LCGC can enable ANY lab for true HTS—better than present practice?

• Resources at Drexel can become recruited within emerging collaborative Resources at Drexel can become recruited within emerging collaborative research networks, especially in greater Philly regionresearch networks, especially in greater Philly region

AcknowledgementsAcknowledgements• George Prendergast, Todd Abrams Tam Nguyen George Prendergast, Todd Abrams Tam Nguyen (LIMR)(LIMR)

• Scott Donover Amanda Schabdach (LCGC)Scott Donover Amanda Schabdach (LCGC)

• Chip Allee (CeuticalSoft Inc.)Chip Allee (CeuticalSoft Inc.)

• Marlin Yohn et al (Istech) and Ron Miller et al (REMS)—et al.Marlin Yohn et al (Istech) and Ron Miller et al (REMS)—et al.

• Dave Schultz and Danelia Fera (Wistar), Seth Goldenberg Dave Schultz and Danelia Fera (Wistar), Seth Goldenberg (Progenra), Ricardo Macaroon, Dwight Morrow and Snehal Bhat (Progenra), Ricardo Macaroon, Dwight Morrow and Snehal Bhat (GSK), Mike Schwartz and Alice Marcy (Dynamis)(GSK), Mike Schwartz and Alice Marcy (Dynamis)