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Functional Proteomic Profiling for Biomarker and Drug Discovery
BioPartnering 2011
May 23, 2011
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About ProFACT Proteomics, Inc. 1 Deer Park Drive, Suite P
Monmouth Junction, NJ 08852 www.profactproteomics.com
• Founded in 2004
• 3 Patents Pending
• 5 NJ Commission on Science and Technology Grants, 2006-09; QTDC Grants, 2009, 2010
• High Throughput Functional Proteomics Infrastructure
• Molecular Profiling and Discovery Services with transferable protocols & Consumable Reagents
• One Major Biopharma Service Agreement
• Three Institutional Consortium arrangements
• Seeking client-sponsored research, collaborations, partnerships
• Ongoing public and private (one-on-one) tech webinars by subscription.
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Lack of Productivity in BioPharma
An Opportunity for Functional Proteomics
• A wealth of cellular response-based pre-clinical drugs are not well-characterized vis mechanism of action and off-target effects.
• Proteomics platforms reliant on sequence annotation do not provide functional characterization.
BioPharma needs new means to amass productive early stage proteomic data that:
• can access natural cellular sources
• functionally characterize protein-drug interaction
• functionally discriminate to the level of conformational variants
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Competitive Advantages
• Specificity, the Functional Proteomics Advantage: - A sufficiently functionally characterized and enriched protein can yield
a Sequence ID whereas Sequence Annotation cannot be
reconciled to a functioning protein. - Key to specificity is the quality and manner of separations.
• ProFACT Drug Discovery and Development Advantages:
- Drug discovery from natural cellular sources, not recombinant
proteins
- Conformational variant compartmentalization and characterization
- Dimension: Multiple (a customizable number) sub-proteomic comparisons at once, then drill-down by analysis and iterative redistribution and then target enrichment vs single-ply pattern generation platforms
- Pattern Profiling and Drug Responsiveness in one platform
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ProFACT New Functional Proteomics Strategies for Drug Discovery and
Functional Biomarkers
Conformerics™ Bioactive Target/Drug Assays
- Compartmentalize functional variants
- Challenge variants with small molecules - Kinetics-based drug response from natural cellular sources
Functional Proteome Prospecting™
- Find drug targets and functional biomarkers from some or no
foreknowledge. - Enrich and optimize discoveries for further characterization, screening, and sequence annotation.
Rational Genome to Proteome Prospecting™
- Reconcile gene and protein expression for biomarker discovery.
DeepSee™
- SeraFILE™-based kits for entry level functional profiling.
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Conformerics™ screens small molecules against the most kinetically responsive (disease specific) enzyme
variants
Recombinant strategies do not consider the transitions of enzymes in their natural
environment
Hyperactive Conformer
Attenuated Conformer
Active Conformer
Conformerics™ Bioactive Target/Drug Assays
- Compartmentalize functional variants - Challenge specifically pooled variants with small molecules
- Kinetics-based drug response indexing from natural cellular sources
Catalytic Rate Constant
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Binding buffer
Pre-equilibrated
surfaces [A-L]
Flow through Beads
Elution
buffer I
Elution I
Mix
Beads
Beads
Cell lysate
Tissue
homogenate
CleanasciteTM Clarified
sample
Enzyme activity
SeraFILETM
Profiling & Cataloging
Sample
enrichment
(Optional)
Separate
Mix
Separate
Mix
Separate
Protein content Explore, Enrich
Globally or
specifically
Post-translational
features
Incl. allosteric
regulation Elution
buffer II
Elution II
SAMPLE PRETREATMENT
SERAFILE™ SEPARATION
SUB-PROTEOME
Beads
Mix
Separate
Elution
buffer n
Elution n
ANALYSIS
Parent proteomes profiling
Daughter sub-proteomes
cataloguing
Intra-sample analysis
Inter-sample analysis
Sub-proteome A
Challenge 1
Challenge 2
Sub-proteome B
DATA GENERATED
kinetics,
compartmentalization
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SeraFILE™ Comparison of Parent Proteomes
Profiles of cyclic AMP hydrolysis activity modulated by cyclic GMP in Phosphodiesterase
RBH: Rat Brain Homogenate
BBH: Bovine Brain Homogenate
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SeraFILE™ Comparison of Derivative Proteomes
Profiles of cyclic AMP hydrolysis activity modulated by cyclic GMP in Phosphodiesterase
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0
50
100
150
200
250
300
A B C D E F G H I Sample
Un
its/
ml o
f e
nzy
me
act
ivit
y
Subproteomes
Cyclic AMP hydrolysis activity in SeraFILE subproteomes
Basal cyclic AMP hydrolysis
Calmodulin activated cAMPhydrolysis
SeraFILE™ Functional Profiles of Phosphodiesterase
PDE 1 Activation with Calmodulin
SeraFILE™ generates a profile of enzyme activities and compartmentalizes those activities in subproteomes.
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SeraFILE™ Functional Profiles of PDE Activity
0
5
10
15
20
25
30
35
40
Sample A B C
Un
its/
ml a
ctiv
ity
Subproteomes
Inhibition of cyclic AMP hydrolysis with rolipram
no inhibitor
with rolipram
Inhibition of cyclic AMP hydrolysis activity in bovine brain homogenate (BBH) with rolipram, a PDE4 specific inhibitor.
SeraFILE™ generates a profile of enzyme activities and compartmentalizes those activities in subproteomes.
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ERK PI3 cAMP Regulation
Low cAMP Essential for cancer
PDE inhibitors, though clinically promising, often fail due to adverse events and toxicity generally
attributable to lack of specificity
Functional Phosphodiesterase Variants Could Be Significant Cancer Targets
with the assistance of ProFACT’s proteomics strategies
ProFACT A Commercial Direction For Cancer Targets
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SeraFILE™ Proteomic connections to function, small molecule
modulation, and gene expression
Enrichment Strategies Specific Activity • Immunological
• Catalytic Rates
• Conformation Variants
• Cellular Response
Purification Identification/Characterization
Discovery Comparisons - Cell Models • Environmental Stimuli
• Oxygen Stress
• Interfering RNA
• Drugs
Comparison of Normal/Disease
• Tissue
• Blood/Serum
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Call to Action
Collaborations & Partnerships
Biomarker Discovery Gene Expression to Protein Reconciliation
Functional Protein Profiling Targeted Enrichment
Drug Discovery Protein classes in progress:
Phosphodiesterases Kinases Proteasome p53 Platform is open to others Allosteric Regulation and Kinetics Enzyme Variant Cataloging/Characterization Small Molecule Screening/Indexing Drug Responsiveness
We invite you to help build ProFACT’s vision for new candidates functionally optimized at the cellular, mechanistic and clinical levels.
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1 Deer Park Drive, Suite P Monmouth Junction, NJ 08852 www.profactproteomics.com
Contact: Matthew Kuruc, President 732-230-3021 [email protected]