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PREDICTIVE DISCOVERY OF FIRST-IN-CLASS BIOLOGICS Primary focus on immuno-oncology Corporate Overview www.cgen.com Ari Krashin Chief Financial and Operating Officer www.cgen.com Jefferies June 2016 1 Safe Harbor Statement This presentation contains “forward-looking statements” within the meaning of the Private Securities Litigation Reform Act of 1995. Forward-looking statements can be identified by the use of terminology such as “will,” “may,” “expects,” “anticipates,” “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. Among these risks: Compugen’s business model is substantially dependent on entering into collaboration agreements with third parties and may not be successful in generating revenues, and the development and commercialization of therapeutic products include many inherent risks, including failure to progress to clinical trials or, if they progress to or enter clinical trials, failure to receive regulatory approval. These and other factors are more fully discussed in the "Risk Factors" section of Compugen’s most recent Annual Report on Form 20-F as filed with the Securities and Exchange Commission as well as other documents that may be subsequently filed by Compugen from time to time with the Securities and Exchange Commission. In addition, any forward-looking statements represent Compugen’s views only as of the date of this presentation and should not be relied upon as representing its views as of any subsequent date. Compugen does not assume any obligation to update any forward-looking statements unless required by law. Certain studies and data presented herein have been conducted for us by other entities as indicated where relevant. 2 Company Overview Leader in Predictive Drug Discovery Mission Discover high value novel targets and develop first-in-class biologics for unmet medical needs Business Model commercialization at various stages, revenue sharing agreements Broad Early Stage Pipeline - Next Wave of Immuno-Oncology Internal discoveries High priority internal programs Two programs partnered with Bayer HealthCare Additional targets for antibody-drug conjugate (ADC) therapy and one program for autoimmune diseases 3 Company Fact Sheet Strong Intellectual Property Landscape Proprietary algorithms and computational biology platforms 61 issued and allowed patents, 137 pending patent applications, in all major countries Experienced Multidisciplinary Teams ~95 employees, 70% R&D Algorithm development, computer sciences, biology and drug development Financial Strength (NASDAQ: CGEN; TASE: CGEN.TA) Cash balance ~$81 million (March 31, 2016) No debt Partners Bayer HealthCare, mAb drugs targeting two novel immune checkpoints Merck-Serono, JV for biomarker discovery 4 Two Centers of Excellence Compugen Ltd. Compugen USA, Inc. Holon, Israel South San Francisco, USA Headquarters Wholly-Owned Subsidiary Predictive Target Discovery & Experimental Validation Therapeutic mAb Research & Development 5 Scientific Advisory Board Renowned Oncologists and Immunologists Drew Pardoll, MD, PhD (Chairman of the SAB; Director - Compugen USA, Inc.) Professor of Oncology, Medicine, Pathology, and Molecular Biology and Genetics and Director of the Bloomberg~Kimmel Institute for Cancer Immunotherapy at the Sidney Kimmel Cancer Center at Johns Hopkins University of Medicine Charles G. Drake, MD, PhD Professor of Oncology, Immunology and Urology at Johns Hopkins School of Medicine, the Sidney Kimmel Comprehensive Cancer Center Iain B. McInnes, MD, PhD Director of the Institute of Infection, Immunity, and Inflammation at the University of Glasgow Antoni Ribas, MD, PhD Professor at the Department of Medicine, Hematology/Oncology, University of California, Los Angeles Howard R. Soule, PhD Executive Vice President and Chief Science Officer, Prostate Cancer Foundation 6 Pipeline Program Focus Areas Multiple Novel Target Candidates for First-in-Class Opportunities Oncology Novel immune checkpoint target candidates Novel Antibody Drug Conjugate target candidates Immunology One program for autoimmune diseases based on a novel immune checkpoint target Diverse portfolio based on Compugen’s predictive discovery capabilities B7/CD28 Immune Checkpoints for Cancer Immunotherapy Harnessing the immune system to destroy cancer cells Breakthrough approach to cancer therapy Impressive, long-lasting clinical benefits Still, the majority of cancer patients do not respond New checkpoints, drug combinations and drug modalities required Checkpoint-based drugs expected to become the largest drug class in history 8 Targeting of Immune Checkpoints Today Crowded Competition on Same Targets PI PC PIII PIII PII PI PC ? M PC PC PC M PII PC PI PC PI PI M PI PI PII PC PI PC PI PC PC PI PC PC PC PC PC PC PC From the Genome to the Clinic An Integrated Approach PREDICTIVE PREDICTIVE DISCOVERY DISCOVERY PIPELINE PROGRAM STRATEGIC PARTNERSHIPS 10 Pharma’s Observational Path to Novel Targets COLLECTION OF KNOWN GENES / PROTEINS DISEASE SAMPLES EXPERIMENTAL CHARACTERIZATION DATA ANALYSIS NOVEL TARGETS FIRST-IN-CLASS Known proteins/genes, disease-specific, assay systems limitation No learning Immune Checkpoint Platform Genomic Detection Leading to Diverse Set of Novel Candidates Diversified portfolio of immuno-oncology targets CGEN candidate Shown for illustrative purpose only 12 Applying Our Predictive Approach First Focused Discovery Program: Novel Immune Checkpoint Target CGEN-15001T CGEN-15052 CGEN-15022 CGEN-15092 CGEN-15049 CGEN - 15029 Undisclosed Targets Partial data sources shown for illustrative purposes B7 refers to B7/CD28 13 From the Genome to the Clinic An Integrated Approach PREDICTIVE DISCOVERY PIPELINE PIPELINE PROGRAM PROGRAM STRATEGIC PARTNERSHIPS 14 Pipeline Program Novel Immune Checkpoint Target Candidates CGEN-15029 Lead drug program Shown for illustrative purpose only 15 CGEN-15029 mRNA Is Expressed in Many Cancers Expression in multiple cancer indications Elevated expression in kidney cancers 16 CGEN-15029 Expression Pattern Associated With Tumor Infiltrating Immune Cells (TILs) RNA correlation with CD8 T cells and PD-1 (Kidney Clear Cell Cancer) CD8 vs 15029 Confirmed TIL protein expression (Melanoma) PD-1 vs 15029 17 RNA Expression of CGEN-15029 Highly Correlated With PD-1, TIM-3 and TIGIT in Solid Tumors All tumors (TCGA) Melanoma (TCGA) 18 CGEN-15029 Inhibits T Cell Cytotoxic Activity Inhibition of Cytotoxic T Cell Activation Cohen and Safion, Bar Ilan Univ. 19 CGEN-15029: Binding Partner Identified Binding of hCGEN-15139-Fc to HEK293 cells over expressing hCGEN-15029 Binding of ligand (CGEN-15139) to receptor (CGEN-15029) was confirmed by SPR, ELISA and FACS 20 CGEN-15029 Highest Priority mAb Program High-affinity blocking antibodies have been identified Ongoing functional screening of blocking mAbs to select clinical lead candidate IND anticipated in 2017 21 Pipeline Program Novel Myeloid Expressed Immune Checkpoint Target Candidates CGEN-15029 CGEN candidate Shown for illustrative purposes only Immune checkpoints have relevance for other multiple mechanism not only on T-cells 22 CGEN Myeloid Candidates • Myeloid cells are important components of the tumor microenvironment • Very few therapeutic targets • Promising emerging area of tumor biology • Included in CGEN’s high priority target programs • • May provide new treatment options for patients refractory to existing immune checkpoint inhibitors (mono and combination therapy) Ongoing verification of MoA and direct T cell inhibition 23 CGEN Myeloid Candidate CD68 Expression Induction in Cancer Correlated with Myeloid Specific Markers CGEN Candidate Expression 24 Cell Surface Tumor Antigen Targets Second Focused Discovery Program: Antibody Drug Conjugate – ADC Targets The goal: identify membrane proteins over-expressed on cancer but with little or no expression on normal tissues 25 Example: Expression Profile Analysis High Cancer Expression, Low Toxicity, Low Sink Potential Predictive discovery driven analysis 26 CGEN-15027: A Novel ADC Target High Expression in Ovarian and Lung Cancers Normal Ovary Normal Lung Ovarian Cancer (Endometroid adenocar.) Lung Cancer (Adenocarcinoma.) Ovarian Cancer (Mucinous cystadenocar.) Lung Cancer (Adenocarcinoma) 27 From the Genome to the Clinic An Integrated Approach PREDICTIVE DISCOVERY PIPELINE PROGRAM STRATEGIC STRATEGIC PARTNERSHIP PARTNERSHIPS 28 Targets for First-in-Class Opportunities BayerNovel Partnership Strategic Collaboration Cancer Immunotherapies The Next WavetoinDevelop Immuno-Oncology Two novel immune checkpoint CGEN-15001T and CGEN-15022 Joint preclinical research program Bayer assumes full control over subsequent development and commercialization Terms include: $10M upfront payment Preclinical milestone payments of up to $30M 15001T - To date achieved three milestones totaling $15M 15022 - To date achieved first milestones $0.4M Eligible to receive over $500M in potential milestone payments Eligible to receive mid-to-high single digit royalties on global net sales 29 Targets for First-in-Class Opportunities BayerNovel Partnership: Current Status Next Targets for Anti-Tumor Immunity The Next Wave in Immuno-Oncology • CGEN-15001T and CGEN-15022: Two novel immune checkpoints • Each presents a distinctive differentiation profile compared to known checkpoints • Targets are expressed on numerous types of solid and hematological cancer as well as on immune cells residing in both tumor and normal tissues • CGEN-15001T antibody program: • Recently transferred to the full control of Bayer (achievement 3rd milestone) • From computer prediction to functional activity in preclinical models • CGEN-15022 antibody program: • Novel mechanism of action has been revealed • Further characterization of its role in anti-cancer immune responses 30 Collaboration with Johns Hopkins School of Medicine Multi-Year Immuno-Oncology Collaboration • Focused on the Company’s novel immune checkpoint target candidates • • Led by Johns Hopkins Professors Drew Pardoll and Charles Drake Supports and accelerates translation to the clinic • • Target characterization and differentiation Evaluation of therapeutic potential as monotherapy and combination therapy 31 From the Genome to the Clinic Drivers and Anticipated Milestones hPOC in clinical trials: Partnered and un-partnered programs First IND anticipated in 2017 for CGEN-15029 Continuing progress on Bayer’s programs Multiple programs in various stages of target validation or antibody discovery Product-oriented collaborations Potential collaborations at various development stages Development milestones in collaborations Potential milestones under Bayer collaboration 32 Financial Status • Strong Financial position • • • Gross Cash Expenditures* • • Cash balance ~$81 million (March 31, 2016) No Debt Forecast 2016 ~$31-$33 million Market Capitalization • • • ~$350 million (May 2016) NASDAQ (CGEN); Indices – NBI (Nasdaq Biotech Index) TASE (CGEN.TA); Indices- TA-75, TA-Biomed, TA BlueTech, TA Tech-Elite * Does not include any anticipated cash receipts 36 Thank You! Ari Krashin Chief Financial and Operating Officer www.cgen.com June 2016 www.cgen.com