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DISEASES OF THE BODY, BRAIN AND EYE COMPANY PRESENTATION JANUARY 11, 2021Exhibit 99.1 STOPPING CLASSICAL COMPLEMENT AT THE START TREATING DISEASES OF THE BODY, BRAIN AND EYE COMPANY PRESENTATION JANUARY 11, 2021
Disclaimer This presentation contains
"forward looking" statements about Annexon, Inc. and our industry that involve substantial risks a nd uncertainties. All statements other than statements of historical facts, including statements regarding our clinical and
preclinical programs, timing and commencement of future nonclinical studies and clinical trials and research and development programs, timing of clinical results, strategic plans for our business and product candidates, including additional
indications which we may pursue, our financial position and anticipated milestones, are forward looking statements. In some cases, you can identify forward looking statements by terminology such as "aim," "anticipate,"
"assume," "believe," "contemplate," "continue," "could," "design," "due," "estimate," "expect," "goal," "intend,"
"may," "objective," "plan," "positioned," "potential," "predict," "seek," "should," "target," "will," "would" and
other similar expressions that are predictions of or indicate future events and future trends, or the negative of these terms or other comparable terminology. Forward looking statements are not guarantees of future performance and are subject
to risks and uncertainties that could cause actual results and events to differ materially from those anticipated, including, but not limited to, risks and uncertainties related to: our history of net operating losses; our ability to obtain
necessary capital to fund our clinical programs; the early stages of clinical development of our product candidates; the effects of COVID 19 or other public health crises on our clinical programs and business operations; our ability to obtain
regulatory approval of and successfully commercialize our product candidates; any undesirable side effects or other properties of our product candidates; our reliance on third party suppliers and manufacturers; the outcomes of any future
collaboration agreements; and our ability to adequately maintain intellectual property rights for our product candidates. These and other risks are described in greater detail under the section titled "Risk Factors" contained in our
Quarterly Report on Form 10 Q for the quarterly period ended September 30, 2020 filed with the Securities and Exchange Commission (SEC) on November 16, 2020 as well as discussions of potential risks, uncertainties and other important factors
in our other filings with the SEC. All forward looking statements in this presentation speak only as of the date of this presentation. Except as required by law, we undertake no obligation to publicly update any forward looking
statements, whether as a result of new information, future events or otherwise. This presentation concerns drugs that are under clinical investigation and which have not yet been approved for marketing by the U.S. Food and Drug Administration (FDA).
These are currently limited by Federal law to investigational use, and no representation is made as to their safety or effectiveness for the purposes for which they are being investigated. 2Disclaimer This presentation contains
"forward looking" statements about Annexon, Inc. and our industry that involve substantial risks a nd uncertainties. All statements other than statements of historical facts, including statements regarding our clinical and
preclinical programs, timing and commencement of future nonclinical studies and clinical trials and research and development programs, timing of clinical results, strategic plans for our business and product candidates, including additional
indications which we may pursue, our financial position and anticipated milestones, are forward looking statements. In some cases, you can identify forward looking statements by terminology such as "aim," "anticipate,"
"assume," "believe," "contemplate," "continue," "could," "design," "due," "estimate," "expect," "goal," "intend,"
"may," "objective," "plan," "positioned," "potential," "predict," "seek," "should," "target," "will," "would" and
other similar expressions that are predictions of or indicate future events and future trends, or the negative of these terms or other comparable terminology. Forward looking statements are not guarantees of future performance and are subject
to risks and uncertainties that could cause actual results and events to differ materially from those anticipated, including, but not limited to, risks and uncertainties related to: our history of net operating losses; our ability to obtain
necessary capital to fund our clinical programs; the early stages of clinical development of our product candidates; the effects of COVID 19 or other public health crises on our clinical programs and business operations; our ability to obtain
regulatory approval of and successfully commercialize our product candidates; any undesirable side effects or other properties of our product candidates; our reliance on third party suppliers and manufacturers; the outcomes of any future
collaboration agreements; and our ability to adequately maintain intellectual property rights for our product candidates. These and other risks are described in greater detail under the section titled "Risk Factors" contained in our
Quarterly Report on Form 10 Q for the quarterly period ended September 30, 2020 filed with the Securities and Exchange Commission (SEC) on November 16, 2020 as well as discussions of potential risks, uncertainties and other important factors
in our other filings with the SEC. All forward looking statements in this presentation speak only as of the date of this presentation. Except as required by law, we undertake no obligation to publicly update any forward looking
statements, whether as a result of new information, future events or otherwise. This presentation concerns drugs that are under clinical investigation and which have not yet been approved for marketing by the U.S. Food and Drug Administration (FDA).
These are currently limited by Federal law to investigational use, and no representation is made as to their safety or effectiveness for the purposes for which they are being investigated. 2
Annexon: Pioneering Classical Complement Therapies to Treat Autoimmune,
Neurodegenerative and Ophthalmic Diseases Blocking upstream complement to stop disease processes at the start Broad platform potential in orphan and large patient populations in autoimmune, neurodegenerative and ophthalmic diseases
Phase 2 pipeline with 3 drug candidates to deliver near and mid term catalysts Precision medicine approach leveraging complement and disease biomarkers Well capitalized with worldwide rights to development and
commercialization 3Annexon: Pioneering Classical Complement Therapies to Treat Autoimmune, Neurodegenerative and Ophthalmic Diseases Blocking upstream complement to stop disease processes at the start Broad platform potential in
orphan and large patient populations in autoimmune, neurodegenerative and ophthalmic diseases Phase 2 pipeline with 3 drug candidates to deliver near and mid term catalysts Precision medicine approach leveraging
complement and disease biomarkers Well capitalized with worldwide rights to development and commercialization 3
Demonstrated Leadership Advancing Transformative Therapies Doug Love,
Esq. Ted Yednock, Ph.D. President & CEO Chief Scientific Officer Genentech, Amgen, Elan Elan, Prothena, Athena Jennifer Lew Sanjay Keswani, M.D. Michael Overdorf Chief Financial Officer Chief Medical Officer Chief Business Officer Aduro,
Dynavax, Ernst & Young Roche, Eli Lilly, Amgen, Eli Lilly Bristol Meyers Squibb 4Demonstrated Leadership Advancing Transformative Therapies Doug Love, Esq. Ted Yednock, Ph.D. President & CEO Chief Scientific Officer Genentech, Amgen,
Elan Elan, Prothena, Athena Jennifer Lew Sanjay Keswani, M.D. Michael Overdorf Chief Financial Officer Chief Medical Officer Chief Business Officer Aduro, Dynavax, Ernst & Young Roche, Eli Lilly, Amgen, Eli Lilly Bristol Meyers Squibb
Building a Leading Multi-Faceted Complement Company 2020: A Foundational
Year $100M Series D in June and $263M Nasdaq IPO in July Robust ANX005 and ANX007 patient data demonstrating tolerability, full target engagement, biomarker/clinical data 0 Rapidly advancing into multiple Ph2 autoimmune,
neurodegenerative and ophthalmic trials Developing innovative next generation drug candidates ANX009 subcutaneous Firstin H uman trial ongoing Followo n small molecule and monoclonal antibody candidates
advancing to IND 5Building a Leading Multi-Faceted Complement Company 2020: A Foundational Year $100M Series D in June and $263M Nasdaq IPO in July Robust ANX005 and ANX007 patient data demonstrating tolerability, full target
engagement, biomarker/clinical data 0 Rapidly advancing into multiple Ph2 autoimmune, neurodegenerative and ophthalmic trials Developing innovative next generation drug candidates ANX009 subcutaneous Firstin H
uman trial ongoing Followo n small molecule and monoclonal antibody candidates advancing to IND 5
Robust Clinical Pipeline of C1q Inhibitors for Body, Brain & Eye
Multiple clinical stage drug candidates with diverse routes of administration INDICATION PRECLINICAL PHASE 1 PHASE 2 PHASE 2/3 CURRENT STATUS ANX005 (IV) Guillain-Barr Syndrome (GBS) Ph 2/3 Ongoing Warm Autoimmune Hemolytic Ph 2 Initiating
Anemia (wAIHA) Huntington's Disease (HD) Ph 2 Ongoing Amyotrophic Lateral Sclerosis (ALS) Ph 2 Initiating ANX007 (IVT) Geographic Atrophy (GA) Ph 2 Initiating ANX009 (SubQ) Autoimmune Ph 1 Ongoing 6Robust Clinical Pipeline of C1q Inhibitors
for Body, Brain & Eye Multiple clinical stage drug candidates with diverse routes of administration INDICATION PRECLINICAL PHASE 1 PHASE 2 PHASE 2/3 CURRENT STATUS ANX005 (IV) Guillain-Barr Syndrome (GBS) Ph 2/3 Ongoing Warm Autoimmune
Hemolytic Ph 2 Initiating Anemia (wAIHA) Huntington's Disease (HD) Ph 2 Ongoing Amyotrophic Lateral Sclerosis (ALS) Ph 2 Initiating ANX007 (IVT) Geographic Atrophy (GA) Ph 2 Initiating ANX009 (SubQ) Autoimmune Ph 1 Ongoing 6
Significant Catalysts in 2021 and Beyond Sufficient cash-runway to
achieve these milestones INDICATION 1H 2021 2H 2021 2022 2023 ANX005 (IV) Guillain-Barr Syndrome (GBS) DDI data Ph2/3 data Warm Autoimmune Hemolytic Ph2 data Anemia (wAIHA) Ph2 initial data Huntington's Disease (HD) Amyotrophic Lateral
Sclerosis (ALS) Ph2 initial data ANX007 (IVT) Geographic Atrophy (GA) Ph2 data ANX009 (SubQ) Autoimmune Ph1 data Ph2 data 7Significant Catalysts in 2021 and Beyond Sufficient cash-runway to achieve these milestones INDICATION 1H 2021 2H 2021 2022
2023 ANX005 (IV) Guillain-Barr Syndrome (GBS) DDI data Ph2/3 data Warm Autoimmune Hemolytic Ph2 data Anemia (wAIHA) Ph2 initial data Huntington's Disease (HD) Amyotrophic Lateral Sclerosis (ALS) Ph2 initial data ANX007 (IVT) Geographic
Atrophy (GA) Ph2 data ANX009 (SubQ) Autoimmune Ph1 data Ph2 data 7
Why C1q and the Classical Complement Pathway? C1q is key driver of
disease processes for indications Annexon has targeted C1q directly binds to tissue, initiating and anchoring complement in diseases of the body, brain and eye GBS HEMOLYTIC ANEMIA HUNTINGTON'S GEOGRAPHIC ATROPHY C1q C1q C1q C1q C1q Targeting
the C1q Targeting C1q Targeting Striatal C1q Targeting Neuromuscular Junction Red Blood Cells Synapses Photoreceptor Synapses Halstead, et al. 2004 Brain 127: 2109-2123 C1q bound to antibody coated RBC Jiao, et al., 2018 Mol Neurodegen 14:45
C1q bound to photoreceptor cells synapses in Annexon data on file aged mice: Annexon data on file 8Why C1q and the Classical Complement Pathway? C1q is key driver of disease processes for indications Annexon has targeted C1q directly binds to
tissue, initiating and anchoring complement in diseases of the body, brain and eye GBS HEMOLYTIC ANEMIA HUNTINGTON'S GEOGRAPHIC ATROPHY C1q C1q C1q C1q C1q Targeting the C1q Targeting C1q Targeting Striatal C1q Targeting Neuromuscular Junction
Red Blood Cells Synapses Photoreceptor Synapses Halstead, et al. 2004 Brain 127: 2109-2123 C1q bound to antibody coated RBC Jiao, et al., 2018 Mol Neurodegen 14:45 C1q bound to photoreceptor cells synapses in Annexon data on file aged mice:
Annexon data on file 8
Inhibiting C1q Shuts Down Entire Classical Complement Pathway Blocks C1q
binding to tissues and downstream activation of C4, C3, C5 and C9 Lectin pathway C6-C8 C2 FD,FB Classical C1r C1s C1q C4 C3 C5 C9 Pathway Alternative pathway Potential Efficacy Advantages Potential Safety Advantages 1 Anti-C1q stops the
cascade before it starts Inhibiting C1q upstream Selectively targets C1q in indications where the classical cascade is a key driver Shuts down all tissue-damaging components of 1 classical pathway (C1q, C4, C3, C5, C9) Allows
normal immune functions of lectin and 1 2 alternative complement pathways C1q levels similar to C5, and 10-fold lower than C3 1 2 Data on file; Glovsky, Ann Allery Asthma Immunol 2004, 93:513 9Inhibiting C1q Shuts Down Entire Classical
Complement Pathway Blocks C1q binding to tissues and downstream activation of C4, C3, C5 and C9 Lectin pathway C6-C8 C2 FD,FB Classical C1r C1s C1q C4 C3 C5 C9 Pathway Alternative pathway Potential Efficacy Advantages Potential Safety Advantages 1
Anti-C1q stops the cascade before it starts Inhibiting C1q upstream Selectively targets C1q in indications where the classical cascade is a key driver Shuts down all tissue-damaging components of 1 classical pathway (C1q, C4,
C3, C5, C9) Allows normal immune functions of lectin and 1 2 alternative complement pathways C1q levels similar to C5, and 10-fold lower than C3 1 2 Data on file; Glovsky, Ann Allery Asthma Immunol 2004, 93:513 9
Leveraging Biomarkers to Increase Probability of Clinical Success
Measuring objective classical complement and disease markers in patients Right Indication and Optimal Dose and Objective Measures Patient Selection Dosing Regimen of Treatment Effect Target population for initial study - 25% of lupus nephritis
patients - 55% of lupus nephritis patients in flare Higher Classical Complement Activation Inhibition of C1q observed in CSF High Dose ANX005 (18-75 mg/kg) in Patients with Lupus Nephritis, at 18-75 mg/kg Led to Significant Early NfL Reduction
Particularly Those in Flare (Weeks 2 - 4) * Annexon data on file 10Leveraging Biomarkers to Increase Probability of Clinical Success Measuring objective classical complement and disease markers in patients Right Indication and Optimal Dose and
Objective Measures Patient Selection Dosing Regimen of Treatment Effect Target population for initial study - 25% of lupus nephritis patients - 55% of lupus nephritis patients in flare Higher Classical Complement Activation Inhibition of
C1q observed in CSF High Dose ANX005 (18-75 mg/kg) in Patients with Lupus Nephritis, at 18-75 mg/kg Led to Significant Early NfL Reduction Particularly Those in Flare (Weeks 2 - 4) * Annexon data on file 10
IMPROVING PATIENT OUTCOMES IN AUTOIMMUNE DISEASES G u i l l a i
n-Barr Syndrome Warm Autoimmune Hemolytic Anemia 11IMPROVING PATIENT OUTCOMES IN AUTOIMMUNE DISEASES G u i l l a i n-Barr Syndrome Warm Autoimmune Hemolytic Anemia 11
GBS, a Destructive Neuromuscular Autoimmune Disease Severe disease that
causes acute paralysis GUILLAIN-BARR SYNDROME (GBS) Rare orphan disease: 12K patients diagnosed annually in North America/Europe No approved therapy in the U.S. Autoantibody attack on peripheral nerves, triggering complement
(C1q) and neurodegeneration Anti-C1q blocks autoantibody activation of complement and potentially prevents disability 12 0 0GBS, a Destructive Neuromuscular Autoimmune Disease Severe disease that causes acute paralysis GUILLAIN-BARR SYNDROME
(GBS) Rare orphan disease: 12K patients diagnosed annually in North America/Europe No approved therapy in the U.S. Autoantibody attack on peripheral nerves, triggering complement (C1q) and neurodegeneration Anti-C1q blocks
autoantibody activation of complement and potentially prevents disability 12 0 0
ANX005 Well-Tolerated, Achieved Full Target Engagement, Reduced NfL and
Prevented Disability in GBS Phase 1b Dose-Ranging Trial Full Target Engagement in CSF Significant Early NfL Reduction 28% of High Dose Patients Improved by 3 pts on at Higher Doses (18-75 mg/kg) (Weeks 2 - 4) GBS-Disability Scale by Wk
8 ANX005 Placebo n=18 n=8 Dose Dependent Decrease High Dose ANX005 (18-75 mg/kg) vs Placebo High Dose ANX005 (18-75 mg/kg) vs Placebo of CSF Free C1q Annexon data on file 13 Free C1q (ng/ml)ANX005 Well-Tolerated, Achieved Full Target Engagement,
Reduced NfL and Prevented Disability in GBS Phase 1b Dose-Ranging Trial Full Target Engagement in CSF Significant Early NfL Reduction 28% of High Dose Patients Improved by 3 pts on at Higher Doses (18-75 mg/kg) (Weeks 2 - 4)
GBS-Disability Scale by Wk 8 ANX005 Placebo n=18 n=8 Dose Dependent Decrease High Dose ANX005 (18-75 mg/kg) vs Placebo High Dose ANX005 (18-75 mg/kg) vs Placebo of CSF Free C1q Annexon data on file 13 Free C1q (ng/ml)
Ongoing GBS Phase 2/3 Trial with ANX005 Fast Track and Orphan Drug
designations granted Placebo (n=~60) Randomized, double-blind trial (N=~180) Primary endpoint: GBS Disability Scale ANX005 30 mg/kg (n =~60) Patients stratified for baseline muscle strength and time from symptom onset ANX005
75 mg/kg (n =~60) Data expected 2023 Single Dose Treatment 14Ongoing GBS Phase 2/3 Trial with ANX005 Fast Track and Orphan Drug designations granted Placebo (n=~60) Randomized, double-blind trial (N=~180) Primary endpoint:
GBS Disability Scale ANX005 30 mg/kg (n =~60) Patients stratified for baseline muscle strength and time from symptom onset ANX005 75 mg/kg (n =~60) Data expected 2023 Single Dose Treatment 14
Targeting Life Threatening RBC Autoantibody Attack in wAIHA WARM
AUTOIMMUNE HEMOLYTIC ANEMIA (wAIHA) Autoantibodies attack and destroy RBCs, resulting in anemia, can develop rapidly or gradually ~30,000 patients globally No approved therapy in U.S. Complement activation amplifies RBC destruction
in certain patients Targeted strategy to select patients who meet specific biomarker criteria of complement activation 15 0Targeting Life Threatening RBC Autoantibody Attack in wAIHA WARM AUTOIMMUNE HEMOLYTIC ANEMIA (wAIHA) Autoantibodies attack and
destroy RBCs, resulting in anemia, can develop rapidly or gradually ~30,000 patients globally No approved therapy in U.S. Complement activation amplifies RBC destruction in certain patients Targeted strategy to select patients who
meet specific biomarker criteria of complement activation 15 0
Antibody-Mediated Complement Activation in wAIHA Patient Sera -
Identifying an Enriched Patient Population ANX005 inhibits complement activation ACTIVITY FULLY INHIBITED BY ANX005 in wAIHA in vitro (n=1) Detected complementa ctivating antibodies in 4 of 12 wAIHA patients (literature suggests 20
- 30 %) ANX005 Activity fully inhibited by ANX005 in vitro Precision medicine approach will enable appropriate patient selection for Phase 2 study 16Antibody-Mediated Complement Activation in wAIHA Patient Sera -