Glucagon Receptor Antagonist: LGD-6972 Program Overview and Phase 1b Results

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Glucagon Receptor Antagonist: LGD-6972 Program Overview and Phase 1b Results American Diabetes Association s 75th Scientific Sessions June 7, 2015 Boston

2 Safe Harbor Statement The following presentation contains forward-looking statements regarding Ligand s prospects, plans and strategies, drug development programs and collaborations. Forward-looking statements include financial projections, expectations regarding research and development programs, and other statements including words such as will, should, could, plan, etc. Actual events or results may differ from Ligand s expectations. For example, drug development program benefits may not be realized and there can be no assurance that Ligand will achieve its expected financial performance. The forward-looking statements made in the presentation are subject to several risk factors, including, statements regarding intent, belief, or current expectations of the Ligand, its internal programs, including Glucagon, regulatory hurdles facing Ligand's product candidates, uncertainty regarding Ligand's product development costs, the possibility that Ligand's drug candidates might not be proved to be safe and efficacious and commercial performance of Ligand's products, and other risks and uncertainties described in its public filings with the Securities and Exchange Commission, available at www.sec.gov. Additional risks may apply to forward-looking statements made in this presentation. Our trademarks, trade names and service marks referenced herein include Ligand and Captisol. Each other trademark, trade name or service mark appearing in this presentation belongs to its owner. Readers are cautioned not to place undue reliance on these forward-looking statements, which reflect our good faith beliefs (or those of the indicated third parties) and speak only as of the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement, and Ligand undertakes no obligation to revise or update this presentation to reflect events or circumstances or update third party research numbers after the date hereof. This caution is made under the safe harbor provisions of Section 21E of the Securities Exchange Act of 1934.

Presentation Agenda Introduction John Higgins, CEO Glucagon Receptor Program and LGD-6972 Phase 1b Trial Results Eric Vajda, Ph.D., Head of Preclinical R&D Douglas K. Logan, M.D., Sr. Medical Director Medpace Diabetes Landscape & Program Next Steps John Higgins, CEO 3

Introduction Ligand has concluded 18 months of Phase 1 clinical work with its Glucagon Receptor (GCGR) program Favorable safety and promising efficacy positions program competitively LGD-6972 potentially best-in-class molecule in leading field of non-insulin diabetes research The diabetes commercial and regulatory landscape has positively shifted in past few years Numerous clinical and regulatory successes Growing market need for what is defined as a global epidemic Ligand is now advancing the program to conduct a Phase 2 trial 4

Introducing Eric Vajda, Ph.D. Head of Preclinical R&D at Ligand, joined in 2002 Leadership roles in some of Ligand s most successful discovery programs: EPO, GCSF SARM IRAK-4 Glucagon Receptor Antagonist B.S. - Yale University Ph.D. in Bioengineering - University of Utah Author of more than 60 scientific publications and presentations 5

Diabetes Two main types of diabetes: type 1 and type 2 Type 1 occurs when the immune system destroys the pancreatic cells that produce insulin In the U.S., ~5% of cases are type 1 Type 2 diabetes usually starts as insulin resistance, where cells cannot use insulin properly and eventually the pancreas loses its ability to make insulin In the U.S., 90-95% of cases are type 2 6 Source: American Diabetes Association Fast Facts 2015 WHO Diabetes Fact Sheet; International Diabetes Federation Atlas, 2014 Update

Glucagon Antagonism Leading Novel Non-Insulin Mechanism in Development DPP-IV inhibitors, GLP1 agonists and SGTL2 inhibitors are commercially available classes of anti-hyperglycemic drugs that have been effective, but are associated with issues Glucose control remains a problem for many patients Dosing and delivery improvements needed Safety issues (gastrointestinal and renal limitations) The diabetes market is growing and is clearly underserved by existing medications Antagonism of the glucagon pathway is one of the most promising new therapeutic areas Robust glucose reduction has been observed in both preclinical and clinical studies after glucagon receptor antagonism Until recently, identification of drug-like molecules has been a major hurdle 7

Glucagon: History in Diabetes Glucagon is an essential regulator of glucose, recognized as an important pharmacological target for over 30 years Glucagon increases glucose levels, opposing insulin Glucagon antagonism reduces plasma glucose in diabetics Significant advancement of science during last 4 years 1923 1953 1982 2001 2011-15 Insulin discovered and hyperglycemic factor postulated Glucagon purified and crystallized Peptide GCGR antagonist reduces plasma glucose in diabetic rats Small molecule GCGR antagonist first tested in humans Demonstrated glucose and HbA1c reduction in human trials 8

9 Normal Pancreas Function

Diabetic Patients Insulin Signalling is defective 10

Diabetic Patients Glucagon Signalling remains active 11

Diabetic Patients LGD-6972 blocks glucagon action in liver, reducing glucose release 12

Early Findings From LGD-6972 Program

LGD-6972: Overview LGD-6972 is an orally available small molecule that potently binds to the glucagon receptor in vitro and competitively antagonizes the actions of glucagon Glucose reduction has been demonstrated in animal models of both type 1 and type 2 diabetes LGD-6972 has a clean safety profile in preclinical toxicology studies The first-in-human trial demonstrated efficacy after a single dose of LGD- 6972 14

Earlier Studies Significant Glucose Reduction in Diabetes Model in Mice The db/db mouse is an established model of advanced type 2 diabetes Daily oral doses of LGD-6972 for 28 days yielded significant glucose reductions Showed better reduction than sitagliptin American Diabetes Association (ADA) 72nd Scientific Sessions; Philadelphia, PA, USA; June 8-12, 2012 15

Earlier Studies Glucose Reduction Shown in Type 1 Diabetes Model Streptozotocin injection in mice is a model of type 1 diabetes Once daily LGD-6972 significantly reduced blood glucose Glucagon antagonism was effective even in the absence of insulin 16 Vajda, et al., American Diabetes Association 73rd Scientific Sessions; Chicago, IL; June 21-25, 2013

Earlier Studies Positive Phase 1a Clinical Data Double-blind, placebocontrolled, randomized single ascending oral dose evaluating safety, tolerability, PK, and PD in healthy individuals and type 2 diabetes subjects Dose-dependent decreases in fasting plasma glucose after a single dose Favorable safety profile Healthy Individuals Type 2 Diabetics Vajda, et al., American Diabetes Association 74th Scientific Sessions; San Francisco; June 13-17, 2014 17

LGD-6972: Phase 1b Trial

Introducing Dr. Douglas Logan Clinical Lead, Principal Investigator, Sr. Medical Director - Medpace B.A. Stanford University M.D. University of Cincinnati Areas of medical focus: Internal medicine - primary care and hospital settings Cardiovascular and metabolic early clinical development Key investigator in development of novel lipid lowering agents 19

Phase 1b Study Design Phase 1b multiple ascending dose trial in normal healthy volunteers (NHV) and type 2 diabetes mellitus (T2DM) subjects T2DM subjects were on a stable dose of metformin throughout the study 14-day dosing period, evaluated in 4 cohorts: 15 mg per day in NHV 5, 10, and 15 mg per day in T2DM subjects 48 subjects n = 12 per cohort (9 active + 3 placebo); 3 clinical sites LGD-6972 dosed as ready-to-use pharmacy-compounded solution, in a water/captisol mixture Primary Endpoints: Safety and tolerability of LGD-6972 Secondary Endpoints: Pharmacokinetics and plasma glucose influence 20

Subject Demographics Volunteers Healthy Diabetics Placebo 15 mg Placebo 5 mg 10 mg 15 mg Number of subjects 3 9 9 9 9 9 Age (years) (%) 47.3 (8.7) 42.3 (10.8) 52.2 (6.2) 55.1 (6.0) 58.9 (6.7) 53.6 (8.7) Gender (n) Female 0 0 6 2 4 5 Male 3 9 3 7 5 4 Ethnicity (n) Hispanic/Latino 1 3 7 5 6 6 Not Hispanic/Latino 2 6 2 4 3 3 Race (n) White 1 4 8 8 7 6 African American 2 5 1 1 2 3 BMI (Kg/m 2 ) (%) 27.4 (1.7) 24.4 (2.9) 31.0 (4.7) 33.6 (4.2) 32.0 (4.9) 31.3 (5.1) Baseline HbA1c (%) Not taken Not taken 8.5 (0.9) 8.2 (0.7) 8.2 (1.1) 8.5 (0.9) No study discontinuations No adverse events requiring stoppage of dosing 21

Treatment-Emergent Adverse Events Volunteers Healthy Diabetics Placebo 15 mg Placebo 5 mg 10 mg 15 mg Number of subjects 3 9 9 9 9 9 Any TEAE (%) 1 (33.3) 4 (44.4) 4 (44.4) 2 (22.2) 6 (66.7) 4 (44.4) Any study drug related TEAE (%) - 2 (22.2) 1 (11.1) 1 (11.1) 5 (55.6) 2 (22.2) Detail of study drug related TEAE Gastrointestinal disorders (%) - - 1 (11.1) 1 (11.1) 1 (11.1) 1 (11.1) Investigations (%) - - - 1 (11.1)* - - ALT increased - - - 1 (11.1)* - - AST increased - - - 1 (11.1)* - - Blood urine present - - - 1 (11.1)* - - GGT increased - - - 1 (11.1)* - - Neutrophil increased - - - 1 (11.1)* - - WBC increased - - - 1 (11.1)* - - Nervous system disorders Headache (%) - 2 (22.2) - - 3 (33.3) 1 (11.1) Respiratory disorder (%) Oropharyngeal pain - - - - 1 (11.1) - *occurred in a single subject on day 28, 14 days after dosing had ended 22

Favorable Pharmacokinetics of LGD-6972 Well absorbed after oral administration with dose-dependent exposure, suitable for once-daily administration Comparable exposure in normal and T2DM subjects 23

Phase 1b Trial: Pharmacodynamic Data Eric Vajda, Ph.D.

LGD-6972 Reduces Fasting Plasma Glucose Normal Healthy Volunteers LGD-6972 reduces fasting plasma glucose after a single dose and the effect persisted throughout 14-day dosing period 25

LGD-6972 Reduces Fasting Plasma Glucose Type 2 Diabetics LGD-6972 shows a dose-dependent reduction in fasting plasma glucose, with a maximal decrease of 60 mg/dl 26

Glucose is Reduced Throughout the Day Type 2 Diabetics 7 point glucose measurements performed on Day 1 and Day 14 LGD-6972 decreased glucose in both fasting and post-prandial states (approximate decrease in weighted mean glucose > 50 mg/dl) 27

LGD-6972 Increases in Plasma Glucagon Type 2 Diabetics LGD-6972 increased plasma glucagon on Day 2 and Day 14 28

Conclusions LGD-6972 is a promising agent for the potential treatment of type 2 diabetes Safe and well tolerated in a multi-dose study Robust reduction in glucose in both fasting and post-prandial states Efficacy and safety profiles are highly encouraging; potentially a best-in-class molecule Glucose reduction observed with glucagon receptor antagonists is highly competitive with other approved therapeutic classes Glucagon receptor antagonists have the potential for use as monotherapy or in combination with other oral anti-hyperglycemic medications 29

Diabetes Landscape & Next Steps John Higgins

Diabetes: Serious and Growing Epidemic Diabetes is the 7 th leading cause of death in the U.S., and significantly increases risks of other serious heath problems Heart disease, stroke, kidney failure, neuropathy, lower-limb amputations and blindness According to the ADA, $245 billion in annual costs are attributable to diabetes $176 billion in direct costs and $69 billion in indirect costs (e.g., disability, work loss, premature death) Currently affects over 387 million people worldwide, including over 29 million in the U.S. (9.3% of the total population) 1.7 million Americans are diagnosed every year 31 Source: American Diabetes Association Fast Facts 2015 WHO Diabetes Fact Sheet; International Diabetes Federation Atlas, 2014 Update

Diabetes: A Growing Epidemic Non-Diabetics Diabetics 2014 2050 9% 33% By 2050, 1 in 3 adults in U.S. will have diabetes if trend continues 32 Source: American Diabetes Association, James P Boyle, Theodore J Thompson, Edward W Gregg, Lawrence E Barker and David F Williamson. Projection of the year 2050 burden of diabetes in the U.S. adult population: dynamic modeling of incidence, mortality, and prediabetes prevalence. Population Health Metrics. 2010 Oct 22;8:29

Major Global Market for Diabetes Drugs 33 $38 B $68 B 2013 2022E Sources: EvaluatePharma June 2014; Global Data: Type 2 Diabetes-Global Drug Forecast & Market Analysis to 2022 Thomson Reuters Cortellis One of the largest drug categories Global market projected to grow to $68 billion by 2022, over 75% increase in 10 years Significant opportunity for novel treatment mechanisms Over the past 5 years there have been 32 licensing deals (pre-clinical to Phase 3) in diabetes with disclosed deal payments of >$11 billion Combination therapy highly prevalent and necessary to optimize management of the disease

$ Billions Top Selling Non-Insulin Anti-Diabetic Drugs Significant growth associated with new class launches Non-insulin category essentially did not exist in 2005 Now over $12 billion in 2014 sales and seven major new brands $12.0 Forxiga (Novartis) $10.0 Invokana (J&J) $8.0 $6.0 $4.0 Victoza ( Novo Nordisk) Onglyza (AstraZeneca) Janumet (Merck) Galvus (Novartis) $2.0 $0.0 Januvia (Merck) Byetta/Bydureon (AstraZeneca) 34 Source: Thomson Reuters Cortellis

Top 10 Non-Insulin Diabetes Drugs Current Top 10-2014 Sales Mechanism Drug Company 2014 Sales ($ million) DPP-IV Januvia Merck $3,900 GLP-1 Victoza Novo $2,400 DPP-IV Janumet Merck $2,100 DPP-IV Galvus Novartis $1,200 DPP-IV Onglyza Astra $820 GLP-1 Byetta/ Bydureon Astra $767 SGLT-2 Invokana J&J $552 SGLT-2 Forxiga Astra $138 SGLT-2 Jardiance Eli Lilly/BI $15 GLP-1 Trulicity Eli Lilly $10 TOTAL 2014 SALES $12 B Mechanism Drug Company Est. 2020 Sales ($ million) DPP-IV Januvia Merck $4,190 GLP-1 Victoza Novo $3,445 SGLT-2 Invokana J&J $3,300 DPP-IV Janumet Merck $2,800 DPP-IV Galvus Novartis $1,425 SGLT-2 Forxiga Astra $1,300 GLP-1 Trulicity Eli Lilly $1,100 DPP-IV Onglyza Astra $851 GLP-1 Byetta/ Bydureon Market projected to grow over 65% to ~$20 billion in 2020 Top 10 - Estimated 2020 Sales Astra $810 SGLT-2 Jardiance Eli Lilly/BI $620 TOTAL Est. PEAK SALES 7 products in category projected to have sales greater than $1 billion ~$20 B 35 Source: Thomson Reuters Cortellis - 2020 sales based on analyst consensus projections, 2015

Significant Opportunity for GCGR Antagonists Branded treatments have multibillion-dollar sales potential By 2020, existing classes will all have four or more competing agents Class Estimated Peak Sales Potential Potential Drugs in 2020 DPP-IV Inhibitors $12 Billion 5 GLP-1 Agonists $7 Billion 5 SGLT-2 Inhibitors $2 Billion 4 GCGR Antagonists ++++ 3 Source: Thompson Reuters, Annual Reports GCGR antagonist class: Only three companies currently (Ligand, Eli Lilly and Pfizer), could potentially share a multibillion-dollar opportunity 36

Advantages of Potent GCGR Antagonist Product profile and recent clinical data suggest significant market advantages for a safe, highly potent, oral GCGR antagonist Existing Class Product Profile GCGR Advantage GCGR Competitive with Class Potential GCGR Combo with Class DPP-IV Modest reduction of plasma glucose Expected higher glucose reduction GLP-1 Only available as injectables Oral SGLT-2 Contraindicated for renally impaired patients, safety considerations Potentially effective in renally impaired 37

GCGR Antagonist Role in Type 2 Diabetes Diversity of use settings also creates significant opportunity The safety and drug pharmacology suggests LGD-6972 could be effective across a broad population of diabetes Lean & Obese - Elevated hepatic glucose production determinant in early and late disease Renally Impaired Advanced Disease Combination therapy Potential to be prescribed in combination with other diabetes drugs, including the newer classes of treatments 38

Global Diabetes Dance Card $ Ranked by non-insulin based therapies GCGR antagonism is the leading non-insulin diabetes mechanism in development Two major diabetes players now pursuing GCGR, Ligand is the only other company with published data Class 1 Company Merck Novo J&J AZ Lilly BI Novartis Pfizer Takeda Sanofi GSK DPP-IV $7.3B 1 $0.9B $0.9B 2 $0.9B 2 $1.5B $0.5B GLP-1 $3.7B $0.8B $1.1B $0.4B $0.4B SGLT-2 $0.9B 3 $3.3B $1.3B $0.6B 2 $0.6B 2 $0.9B 3 GCGR Phase 2 Phase 1 Total $8.2B $3.7B $3.3B $3.0B $2.6B $1.5B $1.5B $0.9B $0.5B $0.4B $0.4B Source: Thomson Reuters Recap IQ; Commercial or later-stage clinical assets, single region molecules not shown 39 1 - Includes Januvia and Janumet 2 - Co-promotion between Lilly and BI 3 - Co-promotion agreement between Merck and Pfizer

Planned LGD-6972 Phase 2 Clinical Program Ligand advancing program to initiate a Phase 2 trial for LGD-6972 in 2016 Phase 2 trial: multicenter, randomized, double-blind, placebo-controlled, parallelgroup study in patients with T2DM 12-week treatment with a 4-week follow-up Estimate 3 doses tested Randomize ~100 subjects (20-25 per group) Key inclusion criteria Patients treated with diet and exercise in combination with stable dose of metformin for at least 3 months prior to screening, HbA1c 7% - 10%; BMI 25-35 kg/m 2 ~$10 million estimated costs for this Phase 2 trial, target completion in 2017 Goal to maximize value to Ligand, securing a partner for late-stage clinical development and commercialization to come at a later date 40

Glucagon Receptor Antagonist: LGD-6972 Program Overview and Phase 1b Results American Diabetes Association s 75th Scientific Sessions June 7, 2015 Boston