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Compugen Ltd

Establishing a New Paradigm for

Drug and Diagnostic Discovery

1st Quarter 2011 Conference Call

May 11, 2011

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Safe Harbor Statement

This presentation contains "forward-looking statements" within the

meaning of the Private Securities Litigation Reform Act of 1995. These

statements include words like "may," "expects," "believes," and

"intends," and describe opinions about future events. These forward-

looking statements involve known and unknown risks and uncertainties

that may cause the actual results, performance or achievements of

Compugen to be materially different from any future results,

performance or achievements expressed or implied by such forward-

looking statements. These risks are more fully explained under the

heading "Risk Factors" in Compugen's annual reports filed on form 20Fthat are filed with the Securities and Exchange Commission.

2

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Agenda

Welcome

Update Presentations:

Status of Pipeline Program

Why & HowA Quick Review Financial Status and Outlook

Questions and Answers Session

3

Compugen Participants: Martin Gerstel Chairman Anat Cohen-Dayag, PhD President & CEO Dikla Czaczkes-Axselbrad CFO

[email protected]

www.compugen.co.il or www.cgen.com

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Agenda

Welcome

Update Presentations:


4

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Pipeline Program - Introduction

Initiated in 2010

Currently >30 product candidates in variousstages of validation

Continuing discovery runs

Market Driven Selection Pathways, protein families and targets of

high industry interest

5

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Therapeutic Fields:

Oncology

Immunology

Drug Classes:

Therapeutic Monoclonal Antibodies (mAbs)

Therapeutic Proteins

Therapeutic Peptides

Pipeline Program: Current Focus

6

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Pipeline Program - Introduction

Initiated in 2010



Market Driven Selection Pathways, protein families and targets of

high industry interest

Moving selected candidates further indevelopment post animal disease model

Initially 12-18 months post animal diseasemodel to pre-IND stage

7

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Pipeline Program: Oncology

8

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC/Target

Validation

(IHC)

Lead

Candidate

/mAb & in

vivo POC

Lead

Candidate/

Pre-IND

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9

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND

CGEN-928 mAb TargetMultiple

Myeloma

Uncharacterized

gene

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CGEN 928: For Multiple Myeloma

Affect on cell viability- combination with Bortezomib

Field: Oncology

Biologic Type: Novel Drug Target (and Diagnostic)

Potential use in multiple myeloma, specifically in advanced stagesand drug-resistant subtypes

Plus synergism with standard-of-care MM therapies Potentially enhanced clinical response with combination therapy

10

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11

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND


Myeloma

Uncharacterized

gene

Six

undisclosedmAb Targets Epithelial Cancers

Splice variants of

known cancer

targets or

proteins

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Compugen

mAb Targets Discovery Platform

12

MED: Disease Exp Database

Integrating >70,000Microarray experiments

Product Candidates: Novel proteins and Drug Targets

LEADS: Human Transcriptome,

Proteome & Peptidome

Specialized algorithms:

Disease specific, protein family,

pathway analysis, splice

variants, protein-proteininteractions, transcriptional

regulation and more

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13

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND


Myeloma

Uncharacterized

gene

Six


Splice variants of

known cancer

targets or

proteins

CGEN-15001T mAb TargetSCLC, Cancer

Immunotherapy Novel B7-like

N M b f P t i F ili Di

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New Members of Protein Families Discovery

Platform

ExperimentalValidation

Further refinedprioritization criteria

Proteins expressed ondiseased cells

Proteins with family characteristics

All human proteins

Multiple Novel

Protein FamilyMembers

In Silico

Prediction

& Selection

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15

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND


Myeloma

Uncharacterized

gene

Six


Splice variants of

known cancer

targets or

proteins



CGEN-671 mAb Target Epithelial CancersSplice variant of

CD55

Two

undisclosedmAb Targets

Epithelial

Cancers

Uncharacterized

genes

Two


Lung & Ovarian

CancerNovel B7-like

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Multiple mAb Target candidates targetingepithelial cancers

Epithelial tumors, also referred to ascarcinomas, account for approximately 85%

of all cancers including the ten most prevalent cancers in the

Western world, such as breast, colorectal, lung,

ovary and prostate

16

Large Unmet Clinical Need

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17

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND


Myeloma

Uncharacterized

gene

Six


Splice variants of

known cancer

targets or

proteins




CD55

Two


Epithelial

Cancers

Uncharacterized

genes

Two


Lung & Ovarian

CancerNovel B7-like

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-25017 peptide OncologyAng-2/Tie2

pathway

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Field: Oncology and Other (e.g. Inflammatory and Ocular)

Biologic Type: Peptide Therapeutic

A novel peptide antagonist of angiopoietins/Tie2 pathway

Inhibits generation of new blood vessels

Potential use in various cancers, inflammatory disorders andretinal disorders

CGEN-25017: For Angiogenesis Related Diseases

18

Tiran et al. in prep.

Potent reduction of neovascularization(in vivo model of retinopathy)

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19

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND


Myeloma

Uncharacterized

gene

Six


Splice variants of

known cancer

targets or

proteins




CD55

Two


Epithelial

Cancers

Uncharacterized

genes

Two


Lung & Ovarian

CancerNovel B7-like

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND


pathway

Four

undisclosedpeptides Oncology Cancer pathways

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20

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

Target

Validation

(IHC)

mAb & in

vivo POC

Lead

Candidate

& Pre-IND


Myeloma

Uncharacterized

gene

Six


Splice variants of

known cancer

targets or

proteins




CD55

Two


Epithelial

Cancers

Uncharacterized

genes

Two


Lung & Ovarian

CancerNovel B7-like

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND


pathway

Four

undisclosedpeptides Oncology Cancer pathways

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Pipeline Program: Immunology and Other

21

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-15001Protein

therapeutic

Multiple Sclerosis,

Rheumatoid

Arthritis

Novel B7-like

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3 times/wk

6 daily

CGEN-15001: For Multiple Sclerosis

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Field: Immunology : Autoimmune diseases

Biologic Type: Protein Therapeutic

Potential use in various autoimmune diseases including multiple sclerosisrheumatoid arthritis, inflammatory bowel disease and type 1 diabetes

Short-term treatment resulted in long-term amelioration of

disease symptoms and complete abolishment of relapses(in vivo model of MS)

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CGEN-15001: For Rheumatoid Arthritis

Potent reduction in disease symptoms with similar efficacyas Enbrel (Etanercept) and potentially less adverse events

(in vivo model of RA)23

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24

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-15001Protein

therapeutic

Multiple Sclerosis,

Rheumatoid

Arthritis

Novel B7-like

Eight

undisclosed

Protein

therapeutics

Autoimmune and

Inflammatory

diseases

8 Novel B7-

like

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Pipeline Program: Immunology

Compugen Announces Discovery Platform for

New Members of Protein Families withKnown Therapeutic Applications (Nov 2010)

Platform development resulted in nine predicted

novel members of B7/CD28 Protein Family

Molecules to be further researchedunder expanded arrangement with Northwestern

University

25

Significant Clinical Potential inAutoimmune Diseases and Cancer

i li l d h

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26

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-15001Protein

therapeutic

Multiple Sclerosis,

Rheumatoid

Arthritis

Novel B7-like

Eight

undisclosed

Protein

therapeutics

Autoimmune and

Inflammatory

diseases

8 Novel B7-

like

CGEN-25007 peptide Inflammatorydiseases (IBD)

gp96 (HSP)

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DAC Blockers Discovery Platform

27

Inactive state

Active state

Blocked state

Pi li P I l d O h

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28

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-15001Protein

therapeutic

Multiple Sclerosis,

Rheumatoid

Arthritis

Novel B7-like

Eight

undisclosed

Protein

therapeutics

Autoimmune and

Inflammatory

diseases

8 Novel B7-

like


gp96 (HSP)

CGEN-856 peptideFibrosis (Cardiac,

Renal),

Hypertension

Ang1-7/Mas

(RAS system)

CGEN-25009 peptidePulmonary

Fibrosis

LGR7

(RXFP1)

CGEN-855 peptide

Inflammatory

diseases (IBD) and

Cardiovascular

(I/R)

FPRL-1

d d l f

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GPCR Peptide Ligand Platform

Modeling the Peptidome: Endogenous Peptides

Signal

peptide

Signal

peptide

Prediction of

novel

cleavage sites

Proteome

Scoring system

ranking

possible

peptides

29

Novel GPCR Ligand PredictorIn silico

modeling and

scoring system

of GPCR ligands

Pi li P I l d Oth
http://www.jbc.org/

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30

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-15001Protein

therapeutic

Multiple Sclerosis,

Rheumatoid

Arthritis

Novel B7-like

Eight

undisclosed

Protein

therapeutics

Autoimmune and

Inflammatory

diseases

8 Novel B7-

like


gp96 (HSP)


Renal),

Hypertension

Ang1-7/Mas

(RAS system)


Fibrosis

LGR7

(RXFP1)

CGEN-855 peptide

Inflammatory

diseases (IBD) and

Cardiovascular

(I/R)

FPRL-1

CGEN-25017 peptideOcular diseases

and Oncology

Angiopoeitin-

2/Tie2

pathway

Pi li P I l d Oth

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31

CGEN#Type of

Biologic

Therapeutic

IndicationPathway

Prediction

and

Selection

In vitro

validation

In vivo

POC

Lead

CandidatePre-IND

CGEN-15001Protein

therapeutic

Multiple Sclerosis,

Rheumatoid

Arthritis

Novel B7-like

Eight

undisclosed

Protein

therapeutics

Autoimmune and

Inflammatory

diseases

8 Novel B7-

like


gp96 (HSP)


Renal),

Hypertension

Ang1-7/Mas

(RAS system)


Fibrosis

LGR7

(RXFP1)

CGEN-855 peptide

Inflammatory

diseases (IBD) and

Cardiovascular

(I/R)

FPRL-1

CGEN-25017 peptideOcular diseases

and Oncology

Angiopoeitin-

2/Tie2

pathway

Pi li P

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Pipeline Program

Initiated in 2010



Market Driven Selection

Pathways, protein families and targets ofhigh industry interest

Moving selected candidates further indevelopment post animal disease model

Initially 12-18 months post animal diseasemodel to pre-IND stage

32

A d

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Agenda


Why & HowA Quick Review Only One Key Need for the Industry

33

Ph I d t Sit ti i 2011

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Pharma Industry Situation in 2011

Still very profitable, but

Facing Blockbuster patent expirations

With limited late stage pipelines

Few clinical stage products available for licensing-in

Pricing pressures on Me-Too products with high

margins being a thing of the past

Cutting back on R&D expenses

34

O l O K N d f th I d t

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Only One Key Need for the Industry

Pharma Industry Situation in 2011

The Underlying Cause:

Long-term reliance largely on high through-put based

discovery methodologies

After finding the easy ones first it gets harder and

harder

35

The Missing Link: Systematic, constantlyimproving, discovery methodology has never

existed in the drug industry

A d

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Agenda



Compugen Mission and Business Model

36

Mi i d B i M d l

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Mission:

To provide an increasing flow ofsuperior drug and

diagnostic product candidates to the industry through

leadership in science driven predictive discovery

Mission and Business Model

37

CGEN 928 f M lti l M l

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Dr. James R. Berenson (The Institute for Myeloma & Bone

Cancer Research):

These early results obtained with CGEN-928 are very encouraging,

especially given the fact that this protein is showing high levels of

expression in manymultiple myeloma tumors that are very drug

resistant and highly aggressive.The results we obtained with CGEN-928 in multiple myeloma

provide a basis for development of antibody-based therapy against

this target for MM, which shows promise both as a single therapy

as well as a combination therapywhich improves the activity of

other antimyeloma drugs. In addition, this novel target may be anew marker for this common blood-based malignancy especially for

the unmet medical need ofdetecting and treating cells that are

most aggressive and resistant to currently available drugs.

38

CGEN-928 for Multiple Myeloma

CGEN 15001 f Rh t id A th iti

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Dr. Richard Williams (Imperial College London UK):

Thesepreliminary results are very impressive with CGEN-15001

showing the same level of efficacy as Enbrel. Furthermore, by testing

CGEN-15001 in established disease we are setting the bar quite high, as

not many compounds are effective in this setting. Therefore, based onthe results seen to date, this molecule definitely should be further studied

as a potential therapy for multiple autoimmune diseases.

CGEN-15001 for Rheumatoid Arthritis

CGEN 15001 for Multiple Sclerosis

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Professor Stephen Miller (Northwestern University):

The capacity of CGEN-15001 toprevent the development of

disease in this well-recognized animal model for multiple sclerosis,

and more significantlyto ameliorate its progression when

administered in the presence of pre-existing disease is quite

dramatic.Furthermore, these beneficial effects were shown to be long

lasting and persisted through the study, indicating that CGEN-

15001 may prevent disease progression as efficiently as immune

tolerance induction, a process whereby the immune system no

longer attacks the self antigens that cause the disease.These findings, together with those demonstrated in our earlier

studies, are unique among the molecules targeting the B7 family

of co-stimulatory molecules that have been published to date.

40

CGEN-15001 for Multiple Sclerosis

CGEN 25017 for Angiogenesis Related Diseases

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Professor John S. Penn (Vanderbilt University School ofMedicine):

The efficacy achieved with CGEN- 25017 is afairly rare finding in

this model. Based upon our past experience conducting efficacy

trials of this type, CGEN-25017falls within the top 10% of all testcompounds that have passed through our hands. Thus, in my

opinion, CGEN-25017warrants further development and study

as a potential therapy for angiogenesis-related diseases."

41

CGEN-25017 for Angiogenesis-Related Diseases

CGEN 25007 for IBD

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Professor Markus F. Neurath (University of Erlangen,Germany):

The results achieved with CGEN- 25007 are very impressive. In the

past, we have evaluated numerous molecules in this model but

never saw such dramatic effects.If these results continue to be confirmed in further studies, this

molecule should represent a very exciting drug candidate for this

substantial, and largely unmet medical need."

42

CGEN-25007 for IBD


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Mission:

To provide an increasing flow ofsuperior drug and

diagnostic product candidates to the industry through

leadership in science driven predictive discovery

Business Model:To maximize the number of our product candidates in

development pipelines of, or under co-development with

drug and diagnostic companies worldwide, pursuant to

milestone/royalty, or other revenue sharing agreements


43

Product Candidates for the Industrys Future

Agenda

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Agenda



Compugen Mission and Business Model Science Driven Predictive Discovery

44

Science Driven Predictive Discovery

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45

Synthesis &

Experimental

Validation

In Silico

MultipleProduct

Candidates

Unmet Medical

Need of Interest

Prediction of:Possible Candidates

Selection of:

Most Probable Candidates

The New Paradigm for Drug Discovery

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The New Paradigm for Drug Discovery

46

Synthesis &

Experimental

Validation

In Silico

MultipleProduct

Candidates

Unmet Medical

Need of Interest

Easy to say, very difficult to do.Many have tried in the past and failed

Prediction of:Possible Candidates

Selection of:


The Required Scientific Infrastructure

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47

For more than a decade, Compugens research teamfocused on deeper understandings

of key biological phenomena at the molecular level


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48

48

For more than a decade, Compugens research team

focused on deeper understandings,predictive modeling and integration of

of key biological phenomena at the molecular level


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49

49

UnmetMedical Need

of Interest

MultipleProduct

Candidates

Prediction of:

Possible Candidates

Selection of:


Synthesis &Experimental

Validation

The Proof is In the Pudding

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The Proof is In the Pudding

0

5

10

15

20

25

30

CumulativeProductCandidates

Product Candidates

demonstrating positivedisease animal model*

Increasing discovery rate over time

50

* or equivalent experimental validation

50

Agenda

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Agenda


Why & How A Quick Review Only One Key Need for the Industry



The Obvious Advantages

51

Advantages of Compugen Approach

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Largely random Hypothesis Driven andSystematic


ExperimentalHit or Miss

The CompugenApproach

52


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Largely random

Learn very little from

failures

Hypothesis Driven andSystematic

Gain knowledge from

successes and failures




53


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Largely random

Learn very little from

failures

More difficult overtime

Innovative, HypothesisDriven and Systematic

Gain knowledge from

successes and failures

Easier with each discoveryround




54

Systematic and Continuously Improving

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Systematic and Continuously Improving

New

Product

Candidates

Model and

Algorithm

Improvement

55

Synthesis &Experimental

Validation

Data

Prediction of:

Possible CandidatesSelection of:


UnmetMedical Need

of interest

Agenda

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Agenda





A New Paradigm for Drug Discovery

56

A New Paradigm in Drug Discovery

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A New Paradigm in Drug Discovery

Systematic, constantly improving

Provides flexibility in selecting unmet medical

needs and targets

Deals with biological complexity

Allows powerful Integration of different discoveryapproaches and platforms

Results in novel product candidates

First-in-Class or Best-in-Class

57

Potentially better drugs, higher success rate, strong IPCombined with a low-risk, high reward, business model

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Financial Status and Outlook

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Projected 2011 Cash Expenditures = ~$10 million*

* Net Burn for year would be reduced by any revenues received

59

Extremely Cost Efficient

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Extremely Cost Efficient

New Platforms:

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Projected 2011 Cash Expenditures = ~$10 million*

Available Resources at 03/31/11: >$30 million**

Market Cap: ~$160 million

* Net Burn for year would be reduced by any revenues received

** Includes ~$25.5 million in cash and ~$5.5 million in EVGN (Evogene Ltd) shares

61


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Projected 2011 Cash Expenditures = ~$10 million

Available Resources at 03/31/11: >$30 million

Market Cap: ~$160 million

Outlook:

Expenditures: Largely dependent on Pipeline Programproducts and arrangements

Revenues: Potential sources of short term revenues in

the amounts required for cash breakeven include

upfront fees from licenses, research revenues, andpayments related to strategic-type arrangements.

Possible timing for such revenues based on current

expectations and discussions is later this year or first half

2012

62

Agenda

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g

Welcome Update Presentations:


Why & HowA Quick Review


Questions and Answers Session

63

Compugen Participants: Martin Gerstel Chairman Anat Cohen-Dayag, PhD President & CEO Dikla Czaczkes Axselbrad CFO

[email protected] or www.cgen.com

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Compugen Ltd

Establishing a New Paradigm for

Drug and Diagnostic Discovery

1st Quarter 2011 Conference CallMay 11, 2011

1st q 2011 v15

Documents