INTERIM MANAGEMENT STATEMENT Q3 2017

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INTERIM MANAGEMENT STATEMENT Q3 2017 Significant progress across all clinical programs New pre-clinical immunooncology data to be presented during R&D Day in New York Research & Development highlights: MP0250: Phase 2 study in Multiple Myeloma progressing well and according to plan MP0250: FDA accepted the company s IND (submitted in August 2017) for phase 2 study evaluating MP0250 in EGFR-mutated Non-Small Cell Lung Cancer (EGFR mut NSCLC); on track to dose first patient in Q1 2018 MP0274: First patient dosed in phase 1 trial of this multi-darpin candidate for the treatment of HER2-positive solid tumors Immuno-oncology: Additional pre-clinical data on proprietary programs with focus on tumor restricted T-cell activation to be presented at the company s R&D Day in New York on November 9, 2017 Abicipar: On track for one-year phase 3 efficacy data in wet age-related macular degeneration (wet AMD) in H2 2018 Team highlights: Bill Burns nominated for election to Molecular Partners Board of Directors as Vice- Chairman at Extraordinary General Meeting (EGM) on October 31, 2017; will stand for nomination as Chairman at the company s Annual General Meeting (AGM) in 2018 Molecular Partners CEO and Co-founder Patrick Amstutz also to stand for election to Board at EGM on October 31, 2017 Financial highlights: Financial performance in-line with expectations and guidance Strong financial position with CHF 151.5 million in cash and short-term time deposits as of September 30, 2017 Net cash used in operating activities of CHF 28.5 million over the first nine months of 2017, reflecting scale-up of R&D and clinical development activities Zurich-Schlieren, October 26, 2017. Molecular Partners AG (SIX: MOLN), a clinical-stage biopharmaceutical company developing a new class of drugs known as DARPin therapies*, today announced its Interim Management Statement for the period ending September 30, 2017. We are very pleased with the ongoing progress of all our programs, both in oncology as well as in immuno-oncology, during the first nine months of 2017, said Dr. Patrick Amstutz, Chief Executive Officer of Molecular Partners. Patient recruitment in the running phase 2 trial in Multiple Myeloma is advancing well. The FDA acceptance of the IND to proceed with MP0250 in a phase 2 study in NSCLC will allow us to test the potential of this drug in solid tumors. Further, the dosing of 1/5 *DARPin is a registered trademark owned by Molecular Partners AG.

the first patient in the phase 1 trial of MP0274, our HER2 multi-darpin drug candidate, was a key milestone for our company, marking the second multi-darpin drug candidate to be evaluated in a systemic cancer trial. Finally, we will present promising pre-clinical data from our immunooncology candidates at our R&D Day. Phase 2 study in Multiple Myeloma progressing well and according to plan The phase 2 study of MP0250, Molecular Partners lead oncology asset, is evaluating this agent in combination with bortezomib (Velcade ) and dexamethasone in patients with multiple myeloma who have failed standard therapies. For this study, which will measure the safety and efficacy of MP0250, additional patients have been dosed at centers in Germany, Poland and Italy. The company anticipates initial safety data before year-end 2017, followed by efficacy data in 2018. FDA accepted IND for second phase 2 trial of MP0250 in Non-Small Cell Lung Cancer (NSCLC) In August 2017, Molecular Partners submitted to the FDA an Investigational New Drug Application (IND) for a phase 1b/2 study of MP0250 in combination with osimertinib (Tagrisso ) in patients with EGFR-mutated Non-Small Cell Lung Cancer (NSCLC) pretreated with osimertinib. The FDA has accepted the IND and endorsed the company s first systemic oncology trial in the US. Targeting HGF and VEGF simultaneously, MP0250 administered in combination with osimertinib offers the possibility to target two of the described escape pathways. We are pleased to have received the positive feedback from the FDA on the IND for MP0250 for our first solid tumor indication, commented Dr. Andreas Harstrick, Chief Medical Officer of Molecular Partners. This feedback from the FDA is encouraging, and we look forward to initiating our second phase 2 clinical trial of MP0250 as planned during the first quarter of 2018. First patient enrolled in the phase 1 trial for MP0274 On October 12, 2017, the company announced that the first patient had been enrolled in the phase 1 trial of MP0274, a multi-specific DARPin candidate being developed for the treatment of HER2-positive solid tumors. MP0274 is a proprietary DARPin drug candidate for the treatment of HER2-positive cancer with a completely new mode of action as compared to current standard of care antibodies. MP0274 induces a profound inhibition of specific downstream signaling pathways, providing mechanistic support to the finding that MP0274 directly kills HER2-addicted tumor cells through the induction of apoptosis. Abicipar on track for one-year phase 3 efficacy data in H2 2018 The company anticipates one-year phase 3 efficacy data in wet age-related macular degeneration (wet AMD) in H2 2018. C. David Nicholson, Executive Vice President & Chief R&D Officer of Allergan, will provide an update on abicipar at Molecular Partner s R&D Day. Balance Sheet: Strong cash and equity positions as of September 30, 2017 Molecular Partners financial performance for the first nine months of 2017 was in-line with management s expectations and reflects the ongoing investments to further expand the 2/5

company s proprietary pipeline. Cash and short-term time deposits decreased by CHF 5.4 million to CHF 151.5 million as of September 30, 2017, from CHF 156.9 million as of June 30, 2017. As of September 30, 2017, the company employed 107 FTEs (+3% year-over-year), with approximately 90% of employees serving in R&D functions. During the first nine months of 2017, Molecular Partners financial position continued to develop in line with our expectations, said Andreas Emmenegger, Chief Financial Officer of Molecular Partners. Our strong cash position provides us with the required financial flexibility and strong negotiation position to achieve multiple value-creating inflection points at least through the end of 2019. Bill Burns and Patrick Amstutz nominated for election to the Board on October 31, 2017 EGM The Board of Directors of Molecular Partners has nominated William (Bill) Burns, former CEO of Roche Pharmaceuticals, for election to the Board of Directors at the upcoming EGM on October 31, 2017. Upon his election, the Board plans to appoint Bill Burns as Vice-Chairman. At the AGM in 2018, he will stand for nomination as Chairman. Patrick Amstutz, CEO and Co-founder of Molecular Partners, will also stand for election to the Board at the EGM. Business outlook and priorities For the company s proprietary oncology pipeline, the company expects to report initial safety data from the phase 2 trial of MP0250 in patients with multiple myeloma (MM) in Q4 2017, and efficacy data in 2018. With regard to the phase 1b/2 trial of MP0250 for NSCLC, initial safety data are expected in 2018. For MP0274, the proprietary, single-pathway DARPin drug candidate for the treatment of HER2-positive cancer, the company expects initial safety and activity data 2018. The company will present new research data on its immuno-oncology pipeline at the R&D Day. In this promising field, Molecular Partners is increasingly focusing on activating agonists in a tumorrestricted way. In ophthalmology, Molecular Partners will continue to support its strategic partner Allergan in advancing abicipar through phase 3 trials in patients with wet AMD, and in initiating a phase 3 trial of abicipar in patients with DME, the next retinal indication, in 2018. R&D Day in New York on November 9 (12.00-2.30 pm EDT) Molecular Partners will host an R&D Day for institutional investors, sell-side analysts, investment bankers, and business development professionals, entitled The DARPin Difference - Offering Patients a New Dimension of Protein Therapeutics. Molecular Partners' management team will provide an overview of the company s clinical oncology pipeline and present key data from its preclinical immuno-oncology activities. C. David Nicholson, Executive Vice President & Chief R&D Officer at Allergan will present and discuss the company s wet AMD candidate, abicipar. The event will also feature presentations by key opinion leaders (KOLs) in oncology, including Prof. Angelo Vacca, MD (Multiple Myeloma), Prof. Kathryn A. Gold, MD (Non-Small Cell Lung Cancer) and Dr. Richard Baird, MA MBBS FRCP Ph.D. (HER2+ Breast Cancer). To reserve a seat for the R&D Day, please contact Susan Noonan at susan@sanoonan.com. For those who are unable to attend in person, a live webcast and replay will be accessible. 3/5

Financial outlook 2017 The first nine months of 2017 developed in line with management expectations. For the full year 2017, at constant exchange rates, the company expects total expenses of approximately CHF 50 million, of which approximately CHF 5 million will be non-cash effective costs for share-based payments, IFRS pension accounting and depreciation. This guidance is subject to the progress of the pipeline, mainly driven by manufacturing costs, the speed of enrollment of patients in clinical trials and data from research and development projects. Financial Calendar October 31, 2017 November 9, 2017 February 8, 2018 March 16, 2018 April 18, 2018 Extraordinary General Meeting R&D Day in New York Publication of Full-year Results 2017 (unaudited) Expected Publication of 2017 Annual Report Annual General Meeting http://investors.molecularpartners.com/financial-calendar-and-events/ About the DARPin Difference DARPin therapeutics are a new class of protein therapeutics that open an extra dimension of multi-specificity and multi-functionality. DARPin candidates are potent, specific, safe and very versatile. They can engage more than five targets at once, offering potential benefits over those provided by conventional monoclonal antibodies or other currently available protein therapeutics. The DARPin technology is a fast and cost-effective drug discovery engine, producing drug candidates with ideal properties for development and very high production yields. With their good safety profile, low immunogenicity and long half-life in the bloodstream and the eye, DARPin therapies have the potential to advance modern medicine and significantly improve the treatment of serious diseases, including cancer and sight-threatening disorders. Molecular Partners is partnering with Allergan to advance clinical programs in ophthalmology, and is advancing a proprietary pipeline of DARPin drug candidates in oncology. The most advanced global product candidate is abicipar, a molecule currently in phase 3, in partnership with Allergan. Several DARPin molecules for various ophthalmic indications are also in development. The most advanced systemic DARPin molecule, MP0250, is in a clinical POC study in multiple myeloma. In addition, Molecular Partners will evaluate MP0250 for the treatment of solid tumors in a phase 1b/2 trial in patients with epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC). MP0274, the company s second-most advanced DARPin drug candidate in oncology, has entered into phase 1 clinical development. With its broad anti-her activity, MP0274 inhibits HER1-, HER2- and HER3-mediated downstream signaling via Her2, leading to induction of apoptosis. Molecular Partners is also advancing a growing preclinical pipeline that features several immuno-oncological development programs. DARPin is a registered trademark owned by Molecular Partners AG. 4/5

About Molecular Partners AG Molecular Partners AG is a clinical-stage biopharmaceutical company that is developing a new class of therapies known as DARPin therapies. With a management team that includes many of the company s founding scientists, Molecular Partners continues to attract talented individuals who share a passion for developing breakthrough medicines for serious diseases. Molecular Partners has compounds in various stages of clinical and preclinical development and several more in the research stage, with a current focus on ophthalmology and oncology. The company establishes research and development partnerships with leading pharmaceutical companies and is backed by established biotech investors. For more information regarding Molecular Partners AG, go to: www.molecularpartners.com. For further details, please contact: Patrick Amstutz, CEO Andreas Emmenegger, CFO patrick.amstutz@molecularpartners.com andreas.emmenegger@molecularpartners.com Tel: +41 44 755 77 00 Tel: +41 44 755 77 00 Rolf Schläpfer Susan A. Noonan Hirzel.Neef.Schmid.Counselors S.A. Noonan Communications, LLC rolf.schlaepfer@konsulenten.ch susan@sanoonan.com Tel: +41 43 344 42 42 Tel.: +1 212 966 3650 Disclaimer This communication does not constitute an offer or invitation to subscribe for or purchase any securities of Molecular Partners AG. This publication may contain certain forward-looking statements and assessments or intentions concerning the company and its business. Such statements involve certain risks, uncertainties and other factors which could cause the actual results, financial condition, performance or achievements of the company to be materially different from those expressed or implied by such statements. Readers should therefore not place reliance on these statements, particularly not in connection with any contract or investment decision. The company disclaims any obligation to update these forward-looking statements, assessments or intentions. 5/5