Developing multi-benefit DARPin® therapies to improve health and advance modern medicine Cowen and Company - 35th Annual Healthcare Conference Boston, March 3, 2015 Disclaimer NEITHER THIS DOCUMENT NOR ANY PART OR COPY OF IT NOR THE INFORMATION CONTAINED IN IT AND ANY RELATED MATERIALS MAY BE TAKEN OR TRANSMITTED INTO THE UNITED STATES OR DISTRIBUTED OR REDISTRIBUTED, DIRECTLY OR INDIRECTLY, IN THE UNITED STATES. This presentation is not an offer to sell or a solicitation of offers to purchase or subscribe for shares of Molecular Partners AG, nor shall it or any part of it nor the fact of its distribution form the basis of, or be relied on in connection with, any contract or investment decision. This presentation is not an offering circular within the meaning of Article 652a of the Swiss Code of Obligations, nor is it a listing prospectus as defined in the listing rules of the SIX Swiss Exchange AG or a prospectus under any other applicable laws. 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Confidential - 2 Corporate overview • Assets in ophthalmology, oncology and immunology • Pipeline of 4 DARPin® product candidates and several research programs • Abicipar (partnered with Allergan) is expected to enter Phase III in wet AMD in Q2 2015 • Proprietary assets in oncology and ophthalmology • DARPin® technology platform • Multiple partnerships with blue chip pharma companies • c.CHF 161 million non-equity funding collected1 • c.CHF 3.0 billion milestone potential2 • Up to double-digit royalties in all partnerships • Financials • Second largest Biotech IPO in Europe in 2014: Raised CHF 106.2 million on SIX Swiss Exchange (MOLN) • CHF 55.8 million venture capital raised pre-IPO • Pre-IPO cash & cash equivalents of CHF 99.0 million with multiple years of runway3 1 up until June 30, 2014; 2 Assumes exercise of all options for additional programs and attainment of all research option fees, preclinical milestones, development milestones and full commercial milestones for the maximum number of products; 3 as of June 30 2014; Confidential - 3 Strong management team includes DARPin creators Christian Zahnd, CEO • Founder, board member • PhD in Molecular Biology from University of Zurich Patrick Amstutz, COO • Founder • PhD in Molecular Biology from University of Zurich Michael Stumpp, CSO • Founder • PhD in Molecular Biology, Postdoc from University of Zurich Andreas Emmenegger, CFO • Previously with Roche and Glycart • Ex-CFO of two listed companies From left to right: Dr. Stumpp, Mr. Emmenegger, Dr. Amstutz, Dr. Zahnd Confidential - 4 Experienced and independent board of directors Jörn Aldag (Chairman) Steve Holtzman (Non-executive director) • CEO uniQure, Ex CEO Evotec • EVP BD Biogen, Founder and Chairman of Infinity, Ex CBO of Millenium Christian Zahnd (CEO) Francesco de Rubertis (Investor) • CEO Molecular Partners, Founder • Index Ventures Göran Ando (Non-executive director) Petri Vainio (Investor) • Chairman Novo Nordisk, Ex CEO Celltech, Ex CSO Pharmacia • Essex Woodlands Ventures Bill Lee (Non-executive director) Andreas Plückthun (Founder) • SVP Research Gilead, part of the Gilead team from the start • Professor UZH, co-founder of Morphosys Confidential - 5 Broad pipeline addressing high value end markets Immunology Oncology Ophthalmology Description Area Target Abicipar wet AMD VEGF Abicipar DME VEGF multi-DARPin® VEGF/PDGF wet AMD 3 programs n.d. n.d. 2 programs n.d. n.d. MP0250 solid tumors VEGF/HGF MP0274 solid tumors HER2 2 Programs immunooncology n.d. Multiple programs DARPin®-Toxins n.d. Program Immunology n.d. Partner Preclinical development Clinical development Discovery Phase I Preclinics Phase II Phase III Expected Phase III start in Q2 2015 Phase II study started in July 2014 VEGF/PDGF Phase I study started in July 2014 Lighter shading indicates research program Confidential - 6 Unlocking value in partnerships • Validation of the DARPin® approach Comments • All partnerships expanded over time • Validation of the technological approach • Upfront: CHF 99.7 million¹ Ophthalmology • Milestones: c.CHF 1.8 billion2,3,4 • Attractive economical value • Royalties: up to double-digit3 • Significant revenue potential • Upfront: up to CHF 55 million • Strong long-term value retention • Milestones: c.CHF 1.0 billion4 • Development costs borne by partner Oncology • Significant upfront and milestones • Potential for further partnerships • Unlock the full potential of DARPins® • Royalties: up to low double-digit Immunology • Royalties: up to low double-digit • Option taken for program in Dec 14 • Use of DARPins® in novel fields • Increase speed to market c.CHF 3.0 billion4 in milestone potential c.CHF 161 million in non-equity funding collected 1 as per audited accounts; USD 45 million (CHF 38.8 million) for Abicipar and USD 62.5 million (CHF 60.9 million) for multi-DARPin® VEGF/PDGF and discovery alliance; 2 Exchange rate as of 31 Dec 2014: CHF/USD: 1.0064; USD 375 million (CHF 373 million) for Abicipar and USD 1.4 billion (CHF 1.4 billion) for multi-DARPin® VEGF/PDGF and discovery alliance; 3 Co-funding option for significant step-up in royalties on multi-DARPin® VEGF/PDGF; 4 Assumes exercise of all options for additional programs and attainment of all research option fees, preclinical milestones, development milestones and full commercial milestones for the maximum number of products Confidential - 7 DARPin™ Technology Platform Confidential - 8 Mono-DARPins®: Next generation biologics • Tailor-made binding proteins derived from natural ankyrin repeat proteins • Fast and robust DARPin® generation process • Selection of mono-DARPins® from large DARPin® libraries (display technologies) mono-DARPin® • Versatile building blocks with pronounced class behavior • Small size (14-18 kDa) good tissue penetration • High potency (<5-100 pM) active at low concentration • High stability long shelf-life • High solubility (> 100 mg/ml) ideal drug properties • Bacterial production (7-15g/L) rapid and low-cost production • PK properties (min – weeks) adjustable to patient need • Class behavior high developability DARPin inhibiting a target Confidential - 9 Abicipar Retinal diseases – Unmet medical need remains • Large and growing market opportunity in wet agerelated macular degeneration (wet AMD) and diabetic macular edema (DME) • Annual sales in 2013: USD 6.0 billion1 • Expected sales in 2016: USD 8.4 billion (12% CAGR)2 wet AMD Normal vision • Standard of care drugs administered by frequent E injection into the eye • 4 wk dosing3 for Lucentis, Avastin4 • 8 wk dosing5 for Eylea • Unmet medical need for new wet AMD/DME F P therapeutics with: T O Z • Less frequent injections L P E D • Greater vision gains P E C F D E • Quality of life issues (travel, lost wages) D F C Z P F E L O P Z D Source: 1 Represents 2013A global sales of Eylea® (USD 2.0 billion) and Lucentis® (USD 3.8 billion) and other products (USD 0.3 billion) in wet AMD and DME as reported by EvaluatePharma® a service of Evaluate Ltd. (UK), www.evaluategroup.com, accessed [28 Aug.2014]; 2 EvaluatePharma® a service of Evaluate Ltd. (UK), www.evaluategroup.com, accessed [28 Aug.2014]; Estimated expected sales in 2016 do not include off-label use of Avastin; 3 PRN dosing under some European labels; 4 off-label use; 5 Dosing interval following 3 initial loading doses Confidential - 11 Abicipar – VEGF blocker with potential for less frequent dosing and higher vision gain Abicipar Product • Mono-DARPin® blocking VEGF • Collaboration with Allergan • Low double digit to mid-teen royalties and up to USD 375 million in additional milestones • USD 225 million in development and regulatory milestones, USD 150 million in sales milestones • Tested in more than 240 patients to-date Indications and markets • Wet AMD and DME Phase and timing • Wet AMD: Initiation of pivotal Phase III study expected in Q2 2015 • DME: Phase II study initiated in July 2014 Differentiation • Potential for less frequent injections than competitors (long intra-vitreal half-life) • Potential for higher efficacy and higher vision gain Confidential - 12 REACH, Stage 3 – Abicipar data presented at ASRS Abicipar Change of best-corrected visual acuity (BCVA) 1,2 Summary of efficacy and safety data Vision gain Safety (letters) # AEs3 of ocular WK16 WK20 inflammation n = 23 n = 25 Abicipar 2.0mg 8.2 9.0 2 Abicipar 1.0mg 6.3 7.1 3 Lucentis 0.5mg 5.3 4.7 0 n = 16 Dosing: Source: Allergan, 12 August 2014 1 Study not powered to reach statistical significance; 2 Mean visual acuity improvement from baseline (letters); 3 AE: adverse event; 4 BCVA: best corrected visual acuity Confidential - 13 Strong support by Allergan and Actavis “I think as you look at the Allergan products specifically, probably DARPin is the one that I don't think gets enough credit and perhaps that's because it comes in at the ending of the planning period and we're looking at” “When I was at Bausch & Lomb, we tried to buy DARPin as well and missed out on it to [Allergan and its CEO David Pyott]. But this is an area that is growing; [AMD is] a horrific disease and if we can reduce the injection burden for patients, then you really could have a potential blockbuster" Brent Saunders, CEO Actavis, 17 November 2014 “Mr. Saunders praised Allergan's R&D pipeline […]. He was particularly impressed with Allergan's ophthalmology portfolio, including the DARPin program for age-related macular degeneration (AMD)“ Mandy Jackson, Scrip Intelligence, 18 November 2014 “DARPin® could provide the next leap in treatment duration & has c. $ 20 billion in potential cumulative 10 year sales (excl. dual-DARPin®)” David Pyott, CEO Allergan, 30 June 2014 Confidential - 14 Multi-Benefit DARPins in Oncology MP0250 – Multi-benefit DARPin® blocking VEGF and HGF (Phase I, proprietary) MP0250 Product • Multi-DARPin®: blocking VEGF and HGF and binding to human serum albumin • Molecular Partners has full commercial rights Indications and markets • Solid tumors such as liver, renal and gastric cancers Phase and timing • Clinical development started in July 2014 in solid tumors (est. recruitment of 54 patients) • Initial top-line safety and efficacy data expected in 2015 Differentiation • First biologic targeting both VEGF and HGF – blocking tumor growth and spreading • Low toxicity of MP0250 expected to allow for combination with chemotherapy or tyrosine kinase inhibitors (TKIs) • Potential PFS (progression free survival) benefit vs. anti-VEGF mAbs Confidential - 16 MP0250 data is equal or superior to clinical standard of care in all tested PDX models1,2 MP0250 Performance of MP0250 vs. Sorafenib as monotherapy Performance of MP0250 in combination with Paclitaxel PDX: Renal cancer PDX: Gastric cancer RXF 2264 GXA 3027 Source: Presented by the company at ASCO, 2014 1 Company preclinical data. Antitumor activity of MP0250, a bispecific VEGF- and HGF-targeting DARPin, in Patient-Derived Xenograft models (Abstract), ASCO, 2014; 2 MP0250 also tested in preclinical models in liver cancer and lung cancer, which are not depicted above Confidential - 17 MP0274 – Multi-benefit DARPin® with broad antiHER activity (proprietary) MP0274 Product • Multi-DARPin® blocking HER2 and HER3 signaling • Molecular Partners has full commercial rights Indications and markets • In HER2+ patients including those with low levels of HER2 expression Phase and timing • In preclinical development • Expected to enter clinical development in 2016 Differentiation • Inhibits downstream-signaling of HER2 and HER3 • Potentially induces tumor apoptosis and blocks proliferation • Potentially higher cancer killing of MP0274 than Herceptin® Confidential - 18 MP0274 – Differentiation potential based on preclinical studies1 MP0274 Tumor cell apoptosis • Higher cell-killing than Herceptin and Perjeta in preclinical models • Increased potency relative to current HER2-targeted therapies • Potential to benefit a broader spectrum of cancer patients Tumor volume • Treatment for low HER2 expressers • Improved treatment for HER2 overexpressers Source: Company information 1 Company preclinical data. Antitumor activity of MP0274, anti-HER2 VEGF- and HGF-targeting DARPin Confidential - 19 DARPins® with potential to go beyond – Expanding our reach into emerging areas • Molecular Partners explores approaches with Immune checkpoint modulators game-changing potential with DARPins® in oncology • Potential to address fields alone or with partners • Immune-oncology as key focus area • Immune checkpoint modulators (ICM) show potential to revolutionize oncology (e.g. monotargeting PD-1) • Multi-benefit DARPin® approach could have the potential to unlock the complex ICM signaling network • DARPin®-toxin fusions • DARPins® allow combination with different toxins DARPin®-toxin conjugate Confidential - 20 Financials Confidential - 21 Financial highlights CHF 322 million funding since inception Financial highlights • CHF 161 million collected from partners so far2 • CHF 160 million equity raised so far2 • Multiple years of cash runway with CHF 104.1 million IPO and CHF 99.0 million pre-IPO cash3 • Debt free balance sheet • Operating Cash Flow positive since inception on a accumulated basis • Net profit positive in the last two audited years (2012/2013) • c.CHF 3.0 billion4 (USD 3.2 billion) combined milestone potential and up to double-digit royalties in all partnerships 1 VC funding as net proceeds; IPO as gross primary proceeds; 2 up until June 30, 2014; 3 as of June 30, 2014; 4 Exchange rate as of 31 Dec 2014: CHF/USD: 1.0064; Assumes exercise of all options for additional programs and attainment of all research option fees, preclinical milestones, development milestones and full commercial milestones for the maximum number of products Confidential - 22 Financial Summary CHF million FY 2011 FY 2012 FY 2013 HY 20144 Revenues1 18.1 35.6 32.4 13.2 R&D expenses2 (17.7) (18.2) (21.8) (9.8) G&A expenses3 (3.1) (3.0) (3.5) (1.9) Net Profit (Loss) (0.7) 13.3 7.1 1.5 Net cash from (used in) operations4 28.5 54.0 (13.6) 3.1 Cash & cash equivalents 64.2 113.2 96.1 99.0 1 Accounting revenues from collaboration agreements with Allergan, Janssen and Roche. Effective cash payments received amounted to CHF 145.8 million over this entire 3.5y period (includes upfront fees, milestone payments, FTE payments and R&D expense re-imbursements); 2 Thereof non cash costs of CHF 1.1 million in FY2011, CHF 0.9 million in FY2012, CHF 0.8 million in FY2013 and CHF 0.5 million in HY2014; 3 thereof non cash costs of CHF 0.6 million in FY2011, CHF 0.2 million in FY2012, CHF 0.1 million in FY2013 and CHF 0.2 million in HY2014; 4 includes payments of CHF 145.8 million over this entire 3.5y period from Allergan, Janssen and Roche (upfront fees, milestone payments, FTE payments and R&D expense re-imbursements); 4 Unaudited Confidential - 23 Shareholder structure • Listed in SIX Swiss Exchange (Ticker: MOLN) since November 2014 • Included in Swiss Performance Index (SPI) • 19.6 million shares outstanding 24% 25% • 2.7 million outstanding stock options (at IPO) • 24% Free Float • Customary lock-up for Management, Board of Directors (12m) and VCs (6m) 51% Free Float (IPO + non-lockup) VC's Management, Board, Founders Confidential - 24 Summary A strong track record of financial and clinical success 2015 IPO on SIX Swiss Exchange 2014 Start Phase I for MP0250 Phase IIb data for Abicipar Extension of Roche alliance 2013 Phase I/II data of Abicipar in DME Extension of Allergan and JNJ alliance 2012 Alliance with Allergan 2011 2010 Series B financing Start Phase I for Abicipar 2009 Alliance with Janssen Roche partnership and Series A Financing First clinical data for Abicipar 2008 Other milestones 2007 Clinical milestones Source: Company information Confidential - 26 Key near term value catalysts • Start of Abicipar Phase III in wet AMD expected in Q2 2015 • Abicipar Phase II data from BAMBOO/CYPRESS study (establish comparability between Japanese and non-Japanese patients) in wet AMD • Abicipar Phase II data from PALM study in DME • Topline safety and initial efficacy data for MP0250 in solid tumors expected in 2015 • Expect to start clinical development for MP0274 in 2016 • Several upcoming milestone events from partnerships Confidential - 27 Key investment highlights • Most advanced product candidate Abicipar partnered with Allergan expected to enter Phase III development in Q2 2015 in wet AMD • Broad pipeline of 4 DARPin® product candidates and several research programs targeting high value indications • Proprietary portfolio of multi-benefit product candidates in oncology with MP0250 in Phase I development for solid tumors • Partnerships with blue chip pharma companies: Roche (oncology), Allergan (ophthalmology) and Janssen (immunology) • Robust compound engine based on highly efficient DARPin® discovery and preclinical development • Entrepreneurial and collaborative management team who are pioneers in the DARPin® space Confidential - 28 Molecular Partners AG Wagistrasse 14 8952 Zürich-Schlieren Switzerland www.molecularpartners.com