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Third Quarter 2026 Financial Results OCTOBER 29, 2026
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2 2 Safe Harbor Statement and Disclaimers • Thispresentationcontainsforward-lookingstatements,as definedin Section21E of the SecuritiesExchangeAct of 1934, by Ligandand its partnersthatinvolverisksand uncertaintiesand reflectLigand’sand its partners’judgmentas of thedateof thispresentation. Allstatements,otherthanstatementsof historicalfact,couldbe deemedto be forward-lookingstatements,includingstatementsthatexpressLigand’sor its partners’opinions,expectations,objectives,assumptions,plansor projectionsregardingfutureeventsor futureresults.In someinstances,wordssuchas “plans,”“believes,”“expects,”“anticipates,”and“will,”and similarexpressions,areintendedtoidentifyforward-lookingstatements. Readersarecautionednotto placeunduerelianceon theseforward-lookingstatements,whichreflectourgoodfaithbeliefs(orthoseofthe indicatedthirdparties)andspeakonlyas of thedatehereof. Theseforward-lookingstatementsinclude,withoutlimitation: Ligand’sabilityto expanditsportfoliowithlifesciencesroyaltyopportunities; thetimingof clinicaland regulatoryeventsof Ligand’spartnersand othercommercializationand marketingefforts; the timingof the initiationor completionof preclinicalstudiesand clinicaltrialsby Ligandand its partners; the timingof productlaunchesby Ligandor itspartners; andguidanceregardingprojected2026financialresults.Actualeventsor resultsmaydifferfromLigand'sexpectationsdueto risksanduncertaintiesinherentin Ligand’sbusiness,including,withoutlimitation: Ligandrelieson collaborativepartnersfor milestonepayments,royalties,materialsrevenue,contractpaymentsand otherrevenueprojectionsand may not receive expectedrevenue,royaltyrevenueandincomeforpartnersthathadnotreportedproductsalesas ofthedateof thispressreleasearebasedon estimatesthatmaydifferfromactualresultsandif suchresultsdiffer, theywillbe adjustedin futureperiods; LigandmaynotreceiveexpectedrevenuefromCaptisolmaterialsales;Ligandanditspartnersmaynotbe ableto timelyor successfullyadvanceanyproduct(s)in itsinternalor partneredpipelineorreceiveregulatoryapprovalandtheremaynotbea marketfortheproduct(s)evenifsuccessfullydevelopedandapproved; Ligandmaynotachieveitsfinancialguidancefor2026; Ligandfaces competitionin acquiringroyaltiesand locatingsuitableroyaltiesto acquire; Ligandmay not be able to createfuture revenuesand cash flows throughthe acquisitionof royaltiesor by developinginnovative therapeutics; productsunder developmentby Ligandor its partnersmay not receiveregulatoryapproval; the totaladdressablemarketfor our partners’productsmay be smallerthan estimated; Ligandfaces competitionwithrespecttoitstechnologyplatformswhichmaydemonstrategreatermarketacceptanceorsuperiority; Ligandiscurrentlydependentona singlesourcesolesupplierforCaptisolandfailuresbysuch suppliermay resultin delaysor inabilityto meetthe Captisoldemandsof its partners; Ligand’spartnersmay changetheirdevelopmentfocusand may not executeon theirsalesand marketingplansfor marketed productsforwhichLigandhasaneconomicinterest;Ligand’scollaborationpartnersmaybecomeinsolvent; Ligand’sanditspartners’productsmaynotbeprovedtobesafeandefficaciousandmaynotperformas expectedand uncertaintyregardingthe commercialperformanceof such products; Ligand or its partnersmay not be able to protecttheir intellectualpropertyand patentscoveringcertainproductsand technologiesmaybechallengedorinvalidated; cyber-attacksorotherfailuresintelecommunicationsorinformationtechnologysystemscouldresultininformationtheft,datacorruptionand/orsignificantdisruption to Ligand’sbusinessoperations; Ligand’spartnersmay terminateany of theiragreementsor the developmentor commercializationof any of its products; Ligandand its partnersmay experiencedelaysin the commencement,enrollment,completionor analysisofclinicaltestingforitsproductcandidates,or significantissuesregardingtheadequacyofitsclinicaltrialdesignsor theexecutionofitsclinicaltrials,challenges, costs and chargesassociatedwith integratingacquisitionswith Ligand’sexistingbusinesses; Ligandmay not be able to successfullyimplementits strategicgrowthplan and continuethe developmentof its proprietaryprograms; restrictionsunderLigand’screditagreementmay limitits flexibilityin operatingits businessand a defaultunderthe agreementcouldresultin a foreclosureof the collateralsecuringsuch obligations; Ligandmaynotrealizetheanticipatedbenefitsfrominvestmentssuchas convertiblenotes,includingthe2031convertiblenotes; LigandmaynotsuccessfullyintegratetheXOMAportfolioor realizethe anticipatedbenefitsof theXOMAacquisition; changesin generaleconomicconditions,includingas a resultofwar,conflict,epidemicdiseases,theimpositionand/orannouncementof tariffsandongoingorfuture litigationcouldexposeLigandto significantliabilitiesandhavea materialadverseeffecton Ligand; andotherrisksanduncertaintiesdescribedin ourpublicfilingswiththeSecuritiesandExchangeCommission(the “SEC”),availableat www.sec.gov. Informationregardingpartneredproductsand programscomesfrominformationpubliclyreleasedby our partners. Our trademarks,tradenamesand servicemarksreferenced hereinincludeLigand,Captisol,NITRICILandZELSUVMI.Eachothertrademark,tradenameorservicemarkappearinginthispresentationbelongstoitsowner. • Thispresentationpresentscertainnon-GAAPmeasures. A reconciliationbetweenthenon-GAAPadjustedfinancialnumbersandcorrespondingGAAPfiguresis shownin ourquarterlyearningspressreleasesor the fiscalyearannualreport,availableathttps://investor.ligand.com/news-and-events/press-releases/. • Allforwardlookingstatementsarequalifiedin theirentiretyby thiscautionarystatement,andLigandundertakesno obligationtoreviseorupdatethispresentationto reflecteventsorcircumstancesorupdatedthird partyresearchnumbersoccurringafterthedatehereof.ThiscautionismadeunderthesafeharborprovisionsofSection21EoftheSecuritiesExchangeActof1934.
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3 3 Strong Strategic Momentum in Third Quarter 2026 16 PORTFOLIO SCALE Closed XOMA acquisition in July, adding three key commercial assets and 100+ pipeline programs +51% COMMERCIAL MOMENTUM Filspari, Ohtuvayre and Zelsuvmi lead growth; FSGS approval expands Filspari beyond IgAN Vabysmo, Ojemda and Miplyffa now contribute 180+ DISCIPLINED DEPLOYMENT Two new investments: AvenCell (CAR-T) and Ryjunea (pediatric myopia) Scaled investment team expands our deal capacity Up to 7 FUTURE OUTLOOK Five- year outlook update coming in December Foundation set for long-term growth key commercial royalty assets royalty revenue growth Y oY, to ~$70M opportunities reviewed in 2026 pivotal readouts anticipated through 2027
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4 4 Leadership Network Drives Deal Sourcing and Diligence Tavo Espinoza Chief Financial Officer Andrew Reardon Chief Legal Officer Keith Marschke, Ph.D SVP, Biology & Scientific Affairs Karen Reeves, M. D. SVP, Investments & Head of Clinical Strategy; General Manager, Captisol Todd Davis Chief Executive Officer Vince Antle, Ph.D. SVP, Technical Operations & Quality CLINICAL OPERATIONS & TECHNOLOGY Rich Baxter SVP, Investment Operations Paul Hadden SVP, Investments & Business Development Michael Vigilante VP, Investments & Business Development Lauren Hay VP, Portfolio Strategy & Investments Oread Labs CORPORATE MANAGEMENT Pete Renehan, M. D. VP, Investments & Business Development Lee Brow n VP, Investments & Business Development INVESTMENTS
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5 Note: Illustrative, but not comprehensive, overview of breadth of Ligand’s investment flexibility 1 Commitment of up to $47M including equity component 5 Royalty Monetization Project Finance Special Situations $30M Oct '23 $19M Jan '24–Jan '25 $75M May '24 $40M Jul '25 $11M Sep '25 $23M Q3 '26 $47M 1 Q3 '26 $8M Nov ’23−Jul '24 $50M Feb '25 $22M Sep ‘23−Sep ‘26 $73M Sep '23–Nov '25 $20M Nov '23 $100M Jul '24 $739M Jul '26 $1B+ Invested Across 20+ Investments Since 2023
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6 $73M $85M $109M $161M $238M1 2022 2023 2024 2025 2026E $2. 44 $4. 06 $5. 74 $8.13 $9. 631 2022 2023 2024 2025 2026E Royalty revenue +34% CAGR, 2022–2026E Adjusted EPS 2 +41% CAGR, 2022–2026E 1 2026E shown at the midpoint of guidance (royalty revenue $225M–$250M, midpoint $237.5M; adjusted EPS $9.50–$9.75, midpoint $9.63). CAGR measured from 2022 to the 2026E midpoint 2 Adjusted EPS is a non-gaap measure, see reconciliation to GAAP in our earnings release for the corresponding period 3. 3× 3. 9× Royalty Revenue On Track to Triple and EPS to Nearly Quadruple Since 2022
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Financial Update Tavo Espinoza
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8 8 Third Quarter 2026 Highlights ROYALTY REVENUE $70. 3M 1 Third-quarter royalty revenue ADJUSTED EPS $2. 67 2 Adjusted diluted EPS CASH & INVESTMENTS ~$450M Cash, cash equivalents & short-term investments DEPLO Y ABLE CAPIT AL ~$750M Approximate deployable capital +51% year-over-year vs. $3. 09 in Q3 2025 Q3 2025 included $24.5M of one-time Zelsuvmi out- license income vs. $734M at year-end 2025 Decline reflects XOMA acquisition, partly offset by 2031 notes proceeds Factoring in our equity holdings and credit facility 1 Beginning Q3 2026, Ligand reports earlier in the quarterly cycle. Royalty revenue includes estimates for partners that had not reported as of the date of our presentation; differences are trued up in the following quarter. Income on financial royalty assets is driven by long-term forecasts of royalty cash flows rather than a single quarter of partner-reported sales; see our Form 10−K. 2 Adjusted EPS represents a non-GAAP measure. See our Q3 26 earnings release for a reconciliation to the corresponding GAAP measure.
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9 9 Q3 2026 Royalty Revenue Exceeds $70 Million $58.1M $12. 3M $46. 6M $70. 3M Q3 2025 Q3 2026 ROYALTY REVENUE +51% year-over-year growth, to $70.3M LARGEST ROYALTY ASSET $16. 8M 1 Filspari grew 85% from $9.1M in Q3 2025 and overtook Kyprolis at $10.5M LEGACY VS. XOMA - ACQUIRED ($M) Legacy royalties XOMA-acquired Legacy royalties +25% Y oY; XOMA-acquired assets added $12.3M after the July 14 close Q3 2026 PRODUCT MIX ( $M) 2 Filspari $16. 8M 24% Largest royalty asset, includes US and Ex-US Ohtuvayre $7. 0M 10% Includes royalty on net sales plus Ohtuvayre inventors royalty (FRA) income Other $12. 3M 17% Ojemda $7.0M, Vabysmo $3.6M, Miplyffa $1.7M XOMA $34. 2M 49% Includes Kyprolis $10.5M and Qarziba $6.0M NOTE: XOMA-acquired: Vabysmo, Miplyffa and Ojemda (XOMA acquisition closed July 14, 2026). Other includes Kyprolis, Qarziba, Rylaze, Capvaxive, Vaxneuvance, Zelsuvmi, teriparatide and other royalties. Amounts may not sum due to rounding 1 Travere had not reported Q3 2026 Filspari sales as of the date of this presentation. The $16.8M figure is an estimate based on sell-side consensus of ~$170M in U.S. Filspari net product sales (FactSet consensus) plus Ligand’s estimate of~$17M in Filspari net product sales for CSL Vifor Europe (approximately $187 million in Q3 2026 net sales) applying a 9% royalty rate. The estimate may differ from actual results and if such results differ, they will be adjusted in future periods. 2 Certain Q3 royalties are based on Ligand estimates, informed in part by sell-side consensus, and trued up to partner-reported results the following quarter
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10 Third Quarter 2026 Financial Performance 1 Represents a non-GAAP financial measure. See non-GAAP reconciliation in the Q3 26 and Q3 25 earnings press releases. 2 A reconciliation of forward-looking non-GAAP cash operating expenses to the most directly comparable GAAP measure is not available without unreasonable effort, as certain items cannot be reasonably predicted because of their high variability, complexity and low visibility. NOTE: Amounts may not sum due to rounding $ in millions, except for per share amounts (unaudited) Three Months Ended September 30, 2026 2025 Revenues: Royalties $70.3 $46.6 Captisol 7.9 10.7 Contract revenue and income2 0.5 58.2 Total revenues $78.7 $115.5 Less: Gain on sale of Pelthos business - (28.6) Total core revenues 1 $78. 7 $86. 9 Operating costs and expenses: Cost of Captisol 2.7 3.8 Amortization of intangibles 10.2 8.1 R&D Expense 2.8 21.0 G&A Expense 72.6 28.4 Fair value adjustments to contingent liabilities 6.3 (0.5) Fair value adjustments to partner program derivatives - (0.8) Total Operating Expenses 94. 5 60. 1 Operating (Loss) Income (15.8) 55.4 Non-Operating (Expense) Income, net (28.3) 85.8 GAAP Net (Loss) Income (28.5) 117.3 Non- GAAP Net Income 1 $57. 5 $63. 8 GAAP Diluted EPS ($1.43) $5.68 Non- GAAP Diluted EPS 1 $2. 67 $3. 09 • Total core revenue 1 −9% – Driven by $24.5M Zelsuvmi out-license fee recorded in Q3 2025. Excluding the fee, core revenue 1 grew +26% • R&D – Decrease driven by $17.8M charge in Q3 2025 associated with the R&D funding arrangement with Orchestra BioMed • G&A – Increase driven largely by one-time XOMA transaction costs, plus share-based compensation and expanded business development and investment team • 2026 cash operating expenses 2 – expected to approximate $50M • Non- operating expense – Variance driven by mark- to-market adjustments on equity investments • Adjusted EPS of $2. 671 – Excludes stock-based compensation, amortization of intangible and financial assets and certain transaction costs (see non-GAAP reconciliation in press release)
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11 Economic dilution1 GAAP basis2 Ligand share price Shares (M) Diluted shares (M) $250 – 0. 5 $300 <0.1 0. 9 $350 0. 4 1.5 $400 0. 6 2. 2 $450 0. 8 2. 7 $500 1.0 3.1 $550 1.2 3. 5 $600 1.5 4.0 $650 1.7 4.4 $700 1.9 4.7 $750 2.1 5. 0 $460M, 0. 75% convertible senior notes due 2030 $700M, 0% convertible senior notes due 2031 • Principal repaid in cash: only value above the conversion price can be settled in shares • Bond hedge offsets shares issued on conversion • Warrants raise the effective conversion price to $294.02 (2030) and $524.34 (2031), 100% above the share price at pricing • GAAP shows higher dilution because it excludes the bond hedge, which offsets those conversion shares 1 Illustrative only; shares from warrants after the offsetting bond hedge at various share prices which would be expected to add to the diluted share count for future adjusted EPS calculations . 2If-converted method (ASU 2020−06); excludes the bond hedge as anti-dilutive. Illustrative only: based on initial conversion rates and warrant strikes and ~22M shares outstanding; excludes conversion rate adjustments. Not a forecast of share price. Share Dilution From 2030 & 2031 Convertible Transactions At $400, the call spread limits dilution to ~0.6M shares, or ~3% of current shares outstanding
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12 Royalty Revenue $225−250M Includes: Ojemda, Vabysmo and Miplyffa Adjusted EPS 1 $9. 50−9. 75 ( Previously $9. 00−9. 50) Total Revenue $270−310M Non- Royalty Revenue Captisol: $35– 40M Contract: $10−20M 1. Adjusted EPS represents a non-GAAP measure. A reconciliation of forward-looking adjusted EPS is not available without unreasonable effort, as certain items cannot be reasonably predicted because of their high variability, complexity and low visibility. 2026 Financial Guidance Raising Adjusted EPS Guidance and Reaffirming Full-Year Revenue Guidance
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13 5−Y ear Outlook To Be Updated In December 2024 2025 2026 2027 2028 2029 2030 1. Sell-side consensus sales estimates used to arrive at royalty revenue from commercial programs 2. Microcystic lymphatic malformations Ligand Expected Royalty Receipts 1 Current 5 −Year Target From 2025 Investor Day 23% CAGR Positive developments w hich are expected to drive an increase to the long - term outlook include: Acquisition of XOMA is immediately accretive and is expected to drive significant growth First FDA approved treatment in FSGS in April 2026, creating a significant commercial opportunity to expand beyond IgAN. Ligand earns a 9% royalty on net sales of Filspari NDA acceptance and Priority Review of QTORIN rapamycin in MLM 2 with PDUFA date of February 28, 2027. Ligand will earn a tiered 8−9.8% royalty if approved Potential Incremental Grow th To Be Shared At Investor Day
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Portfolio Update Lauren Hay
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15 Marketer Program Indication Royalty Rate Filspari IgA Nephropathy; Focal Segmental Glomerulosclerosis 9% Kyprolis R/R Multiple Myeloma Tiered 1.5% to 3% Qarziba High-Risk Neuroblastoma Tiered mid-teens Vabysmo Wet AMD; Diabetic Macular Edema 0.5% Ohtuvayre Chronic Obstructive Pulmonary Disease 3% Rylaze Acute Lymphoblastic Leukemia Tiered low-single-digit Capvaxive Pneumococcal Disease Low-single-digit Ojemda R/R Pediatric Low-Grade Glioma Mid-single-digit Zelsuvmi Molluscum Contagiosum 13% Miplyffa Niemann-Pick Type C Mid-single-digit Vaxneuvance Pneumococcal Disease Low-single-digit Teriparatide Osteoporosis 25% to 40%* Nexterone Ventricular Fibrillation Low-single-digit Pneumosil Pneumococcal Disease Low-single-digit Tzield Type-1 Diabetes Less than 1% Ryjunea Pediatric Myopia Low double- digit to high - teens * Represents gross profit share, not royalty rate New investments/approvals since 2022 Key Commercial Programs Ryjunea acquisition adds 16th Key Program to Commercial Portfolio
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16 16 Developer( s) Program Indication(s) Phase Royalty Rate QTORIN Rapamycin Microcystic Lymphatic Malformations Cutaneous Venous Malformations Reg Phase 3 Ready 8−9.8% Lasofoxifene Metastatic Breast Cancer Phase 3 6−10% AVIM Virtue SAB Hypertension In-Stent Restenosis Pivotal High-teens<$100M Mid-single-digit >$100M2 Frontline Pediatric Low-Grade Glioma Phase 3 Mid-single-digit Mezagitamab IgA Nephropathy Immune Thrombocytopenia Phase 3 Low-single-digit Osavampator1 Major Depressive Disorder Phase 3 Low-to mid-single-digit Volixibat Primary Sclerosing Cholangitis Primary Biliary Cholangitis Phase 2b Low-to mid-single-digit D-Fi Dystrophic Epidermolysis Bullosa Phase 3 Mid-single-digit Bot/Bal Microsatellite-Stable Colorectal Cancer Phase 3 2.625% OHB-607 Bronchopulmonary Dysplasia Prevention Phase 2b Low-to mid-single-digit Undisclosed Anti-TL1A Ulcerative Colitis/Crohn’s Disease Phase 3 Low-single-digit 1 Osavampator is being developed by Takeda in Japan and by a Takeda partner outside Japan. 2 Royalty based on Orchestra's annual revenues related to the AVIM and Virtue SAB programs All key pipeline programs represent new or follow - on investment activity since 2022 Key Pipeline Partnered Programs
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17 XOMA High-Priority Pipeline Assets Catalyst: Ph 3 Results Late-’27 to Early-’28 Indication: ITP, IgAN Royalty Rate : Low-single-digit Peak Sales1: $1.5B+ Peak Royalty: $30M+ Catalyst: PSC: Potential NDA Submission H1 ’27 PBC: Potentially Pivotal Ph 2b Results Q1 ’27 Indication: PSC and PBC Royalty Rate : Low-to-mid-single-digit Peak Sales2: $1B+ Peak Royalty: $45M+ Mezagitamab Volixibat Catalyst: Phase 3 Results H2 ’27 Indication: Major Depressive Disorder Royalty Rate: Low-to mid-single-digit Peak Sales3: $500M-1.8B Peak Royalty: Up to $80M Osavampator Catalyst: Phase 3 Results ’27 Indication: Frontline pediatric low-grade glioma Royalty Rate: Mid-single-digit Peak Sales4: $500M Peak Royalty: $25M 1 Peak sales estimates provided by our partner in their latest corporate presentation 2 Peak sales consensus estimate per FactSet as of the date of this presentation 3 Limited analyst estimates available in FactSet. Range provided based on available information in FactSet as of the date of this presentation 4 Peak sales estimate for 1L pLGG indication expansion from Day One investor presentation published on 2/28/2026
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18 18 NDA approval & commercial launch in FSGS 2026 Portfolio Activity 2026 Developments Japan approval ✓ ✓ Volixibat Phase 2b potentially registrational readout in primary sclerosing cholangitis✓ QTORIN rapamycin NDA acceptance in microcystic lymphatic malformations✓ New Portfolio Additions Acquisition of XOMA including 3 key commercial assets✓ AvenCell Pipeline✓ Soticlestat✓ Regulatory submission in Japan (Chugai)✓ QTORIN rapamycin Phase 2 initiation in clinically significant angiokeratomas✓ Full enrollment target exceeded in the BACKBEAT trial of AVIM Therapy ✓ Ganaxolone IV✓ Ryjunea✓ New asset additions from portfolio management✓
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19 19 FDA Approval FDA Approval Geographic Ex pansion FDA Approval Potential FDA Approval for QTORIN Rapamycin in MLM Potential Geographic Expansion for Commercial - Stage Products Portfolio Potential Catalysts Through 2027 Pivotal Trial Readouts Phase 3 Trial Readouts Lasofoxifene Mezagitamab Osavampator1 AVIM Up To 7 Pivotal Trial Readouts Anticipated Through 2027 1. Osavampator is being developed by Takeda in Japan and by a Takeda partner outside Japan Ersodetug Volixibat
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Investment Update Paul Hadden
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21 21 >180 Investments reviewed 115 CDAs signed 6 Investments closed ~60% to CDA 3% to close Investments reviewed On track to best prior years CDAs signed Highest in the past four years 2026 closed investments XOMA ZerionAgenus Primrose AvenCellSydnex is High $ Medium $ Small $ NOTE: Agenus and Primrose represent follow-on investments; Zerion represents a small strategic investment 2026 YTD Investment Activity
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22 22 Ryjunea: $23M for Europe’s First Pediatric Myopia Drug $23M Upfront payment for Sydnexis’ royalty rights under its Santen license WHY IT MATTERS 1st First and only approved drug to slow pediatric myopia (nearsightedness) progression EU + UK Approved by the European Commission and UK MHRA 14M Patients in Europe affected in 2025, per Santen, which names myopia a key growth area Royalty Tiered low-double-digit to high-teens on net sales Territory Europe, Middle East and Africa Milestones Certain milestone payments Retained Sydnexis keeps the U.S. and other non- Santen territories
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23 23 AvenCell: up to $47M Royalty on a Next-Gen CAR-T Platform Up to $47M Royalty financing plus a concurrent Series C equity investment Financing Up to $41M royalty financing Equity Up to $6M in AvenCell’s Series C Royalty Mid-single-digit to low-double-digit on worldwide net sales of all future pipeline assets Tranches At closing: $6M royalty +$3M equity Three later tranches: tied to clinical milestones and other conditions PLATFORM CRISPR-engineered allogeneic CAR-T with a switchable CAR for greater activity control; off-the-shelf, with potential in blood cancers and autoimmune disease PIPELINE Ph 1 Ph 2 Ph 3 AVC- 201 Phase 1b · Anti-CD123 CAR-T in R/R AML, which has no approved cell therapy AVC- 203 Phase 1a · B-cell malignancies
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Q&A