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Neurology Webcast Presentation Neurology Webcast July 14, 2020 Forward Looking Language Statement This presentation includes forward-looking statements regarding our business, financial guidance and the therapeutic and commercial potential of SPINRAZA® (nusinersen) and Ionis' technologies and products in development, including Ionis’ neurology franchise. Any statement describing Ionis’ goals, expectations, financial or other projections, intentions or beliefs is a forward-looking statement and should be considered an at-risk statement. Such statements are subject to certain risks and uncertainties, including those related to the impact COVID-19 could have on our business, and including but not limited to those related to our commercial products and the medicines in our pipeline, and particularly those inherent in the process of discovering, developing and commercializing medicines that are safe and effective for use as human therapeutics, and in the endeavor of building a business around such medicines. Ionis’ forward-looking statements also involve assumptions that, if they never materialize or prove correct, could cause its results to differ materially from those expressed or implied by such forward-looking statements. Although Ionis’ forward-looking statements reflect the good faith judgment of its management, these statements are based only on facts and factors currently known by Ionis. As a result, you are cautioned not to rely on these forward-looking statements. These and other risks concerning Ionis' programs are described in additional detail in Ionis' annual report on Form 10-K for the year ended December 31, 2019 and our most recent Form 10-Q quarterly filing, which are on file with the SEC. Copies of this and other documents are available at www.ionispharma.com. In this presentation, unless the context requires otherwise, “Ionis,” “Company,” “we,” “our,” and “us” refers to Ionis Pharmaceuticals and its subsidiaries. Ionis Pharmaceuticals™ is a trademark of Ionis Pharmaceuticals, Inc. Akcea Therapeutics® is a registered trademark of Akcea Therapeutics, Inc. SPINRAZA® is a registered trademark of Biogen. 2 Today’s Presenters Brett Monia, Ph.D. C. Frank Bennett, Ph.D. Chief Executive Officer Chief Scientific Officer Ionis Pharmaceuticals Ionis Pharmaceuticals Frank Rigo, Ph.D. Holly Kordasiewicz, Ph.D. VP, Functional Genomics & VP, Neurology Research Drug Discovery Ionis Pharmaceuticals Ionis Pharmaceuticals 3 Today’s Agenda Welcome and Introductions Wade Walke Ionis – The Leader in RNA-targeted Drug Discovery and Development Brett Monia Ionis – The Leader in Targeting Neurological Diseases Frank Bennett Amyotrophic Lateral Sclerosis Frank Bennett & Frank Rigo Alzheimer’s Disease and Dementia Holly Kordasiewicz Parkinson’s Disease and Multiple System Atrophy Holly Kordasiewicz Spinocerebellar Ataxias Holly Kordasiewicz Ionis-owned Medicines – Prion, Lafora and Alexander’s Diseases Holly Kordasiewicz Conclusion Brett Monia Q&A All 4 Ionis – The Leader in RNA-targeted Drug Discovery and Development Brett Monia Where We Are Today Our leadership position in RNA-targeted therapeutics continues to grow as our technology advances We have a large, diverse, expanding, and mature pipeline that continues to perform exceptionally well The Ionis-owned pipeline is a key priority, will expand substantially, and investments are underway to enhance our commercial capabilities We have the financial strength to continue advancing our technology and deliver on our pipeline To become the innovation leader in biotech providing hope and Vision transformational benefit to millions of patients living with severe diseases 6 Ionis Delivering Medicines for Most Major Severe Diseases NEUROLOGICAL NEUROMUSCULAR CARDIOVASCULAR METABOLIC UltraPULMONARY-rare to Common Diseases CANCER HEMATOLOGICAL KIDNEY OPHTHALMOLOGY INFECTIOUS DISEASE 7 The Ionis Neurological Disease Pipeline Validated platform • Proof of mechanism • Proof of safety • Proof of efficacy • Commercial success A rapidly expanding premier pipeline tackling the most severe diseases Continued technology advancement • Greater efficacy • Less frequent dosing • Systemic applications (e.g. neuromuscular) 8 Ionis is Cracking the Code in Neurological Diseases SPINRAZA Alexander disease Myotonic dystrophy Spinal muscular atrophy ION373 ATTR amyloidosis Prion disease TEGSEDI for hATTR polyneuropathy Spinocerebellar ataxias ION716 AKCEA-TTR-LRx for all major forms Huntington’s disease Lafora disease Spinal and Bulbar muscle Tominersen (IONIS-HTTRx) ION283 atrophy Alzheimer’s disease Multiple System Atrophy Charcot-Marie-Tooth IONIS-MAPTRx ION464 Amyotrophic lateral sclerosis Angelman syndrome Tofersen (IONIS-SOD1 ), IONIS-C9 , Multiple sclerosis Rx Rx ION581 ION541 (Sporadic), ION363 (FUS) Parkinson’s disease Severe epilepsies Severe pain ION859 Multiple Programs And many more in Centronuclear myopathy Leukodystrophies IONIS-DNM2-2.5Rx research stage 9 Ionis is Cracking the Code in Neurological Diseases Ionis-owned Neurological Programs SPINRAZA Alexander disease Myotonic dystrophy Spinal muscular atrophy ION373 ATTR amyloidosis Prion disease TEGSEDI for hATTR polyneuropathy Spinocerebellar ataxias ION716 AKCEA-TTR-LRx for all major forms Huntington’s disease Lafora disease Spinal and Bulbar muscle Tominersen (IONIS-HTTRx) ION283 atrophy Alzheimer’s disease Multiple System Atrophy Charcot-Marie-Tooth IONIS-MAPTRx ION464 Amyotrophic lateral sclerosis Angelman syndrome Tofersen (IONIS-SOD1 ), IONIS-C9 , Multiple sclerosis Rx Rx ION581 ION541 (Sporadic), ION363 (FUS) Parkinson’s disease Severe epilepsies Severe pain ION859 Multiple Programs And many more in Centronuclear myopathy Leukodystrophies IONIS-DNM2-2.5Rx research stage 10 Ionis – The Leader in Targeting Neurological Diseases Frank Bennett Advancing and Expanding Ionis’ Neurology Pipeline Pre-clinical and Clinical Development Programs* 40 • Tominersen (HD) 35 • Tofersen (ALS) 30 • TTR-LRx (ATTR) • IONIS-MAPT (AD) 25 Rx • IONIS-C9Rx (ALS) 20 • ION859 (PD) • IONIS-DNM2-2.5Rx (Centronuclear 15 Myopathy) 10 • ION373 (AxD) • ION464 (MSA) Neurology Projects Neurology 5 • ION541 (ALS) 0 • ION363 (ALS) 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 * Drug Discovery Preclinical Phase 1/2 Phase 3 Marketed * Projected by year-end 2020 12 Many Neurodegenerative Diseases are Caused by Toxic Proteins Expressed in Different Brain Regions Frontotemporal dementia Cerebral atrophy Huntington’s disease Misfolded TAU Whole brain atrophy HTT protein aggregates Alzheimer’s disease Cerebral and hippocampal atrophy Aβ plaques, TAU tangles Alexander’s disease Loss of myelin predominantly in Parkinson’s disease frontal lobe Loss of dopamine neurons in Rosenthal fibers-GFAP deposits substantia nigra and cortical atrophy Lewy bodies: alpha-synuclein Lewy body disease Amyotrophic lateral sclerosis Cerebral atrophy Atrophy of motor neurons and muscles Lewy bodies: alpha-synuclein Sporadic: TDP43 inclusions SOD1 Patients: Misfolded SOD1 C9 Patients: Dipeptide repeats and RNA foci 13 Ionis’ Neurological Pipeline Targets All Major Brain Regions Tofersen SOD1-Amyotrophic Lateral Sclerosis Spinal muscular atrophy 14 Ionis’ Neurological Pipeline Targets All Major Brain Regions Tominersen IONIS-MAPT Huntington’s Disease Rx Alzheimer’s Disease and ION373 Tauopathies Alexander Disease ION716 ION859 Parkinson’s Disease Prion Disease ION283 Lafora Disease ION464 Parkinson’s Disease and synucleinopathies Tofersen SOD1-Amyotrophic Lateral Sclerosis IONIS-C9Rx C9-Amyotrophic Lateral Sclerosis Spinal muscular atrophy ION541 Sporadic-Amyotrophic Lateral Sclerosis Phase 3 ION363 Phase 1/2 FUS-Amyotrophic Lateral Sclerosis Preclinical 15 Antisense Targets All CNS Cell Types Total cortex RNA Neurons 1 5 0 1 5 0 • Wild type (normal) mice E D : 3 2 g 5 0 E D 5 0 : 2 0 6 g ED50 = 329 5 %µgC I : 2 6 - 4 0 g ED = 206 µg n 50 9 5 % C I : 1 1 5 - 3 6 9 g o n i o s i s • Intracerebroventricular (ICV) bolus injection s e 1 0 0 s r e 1 0 0 ) p r x ) p S x E S of Malat1 antisense drug at a single dose B E B P A P A N % N ( R % ( R 1 5 0 t 1 5 0 a • Analyzed at 2 weeks after the dose by cell t l a a l a M sorting with antibody and qPCR M 0 0 1 0 1 0 0 1 0 0 0 1 0 1 0 0 1 0 0 0 A m o u n t in j e c t e d ( g ) A m o u n t in j e c t e d ( g ) Oligodendrocytes Astrocytes Microglia 1 5 0 1 5 0 1 5 0 E D : 1 7 g E D : 7 1 g E D 5 0 : 3 4 g 5 0 5 0 ED = 349 5 % CµgI : 2 1 - 5 5 g ED = 179 5 %µgC I : 1 3 - 2 3 g ED = 719 5 % C I :µg 5 5 - 9 1 g n n 50 50 n 50 o o o i i i s s s s s s e e e 1 0 0 1 0 0 1 0 0 r r r ) ) p p ) p x x x S S S E E E B B B P P P A A A N N N % % % ( ( ( R R R 1 1 1 5 0 5 0 5 0 t t t a a a l l l a a a M M M 0 0 0 1 0 1 0 0 1 0 0 0 1 0 1 0 0 1 0 0 0 1 0 1 0 0 1 0 0 0 A m o u n t in j e c t e d ( g ) A m o u n t in j e c t e d ( g ) A m o u n t in j e c t e d ( g ) The ED50 is the dose that produces a 50% reduction in the target RNA 16 Ionis’ Neurological Pipeline Also Targets the Peripheral Nervous System and Muscle AKCEA-TTR-LRx All major forms of TTR amyloidosis Polyneuropathy caused by hereditary transthyretin-mediated amyloidosis IONIS-DNM2-2.5Rx Centronuclear myopathy 17 Ionis’ Neurological Disease Pipeline MEDICINES INDICATION PARTNER PRECLINICAL PHASE 1 PHASE 2 PHASE 3 Tominersen (IONIS-HTTRx) Huntington’s disease Roche Tofersen (IONIS-SOD1Rx) ALS Biogen TTR-LRx TTR Amyloidosis Ionis IONIS-MAPTRx Alzheimer’s disease Biogen IONIS-C9Rx ALS Biogen ION859 Parkinson’s disease Biogen Centronuclear IONIS-DNM2-2.5 Dynacure Rx myopathy Multiple System ION464 Biogen Atrophy ION541 ALS Biogen
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