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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 mkuruc@profactproteomics.com