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1 A dynamic force in the fight against infectious disease November 2025
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2 Forward-Looking Statement Certain statements regarding SCYNEXIS, Inc. (the “Company”) made in this presentation constitute forward-looking statements, including, but not limited to, statements regarding our business strategies and goals, plans and prospects, market size, adoption rate, potential revenue, clinical validity and utility, growth opportunities, future products and product pipeline. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially from our expectations. These risks and uncertainties include, but are not limited, to: BREXAFEMME may not be accepted by physicians and patients at the rate SCYNEXIS expects; risks inherent in SCYNEXIS’ ability to successfully develop and obtain FDA approval for ibrexafungerp for additional indications; unexpected delays may occur in the timing of acceptance by the FDA of an NDA submission; the anticipated filing of the Company’s request to the FDA to lift the clinical hold on the MARIO study and its filing timing; the expected costs of commercializing BREXAFEMME or of clinical studies and when they might begin or be concluded; the commercial opportunity and timing of clinical development for SCY-247; SCYNEXIS’ need for additional capital resources; and SCYNEXIS’ reliance on third parties to conduct SCYNEXIS’ clinical studies and commercialize its products. The use of words such as “anticipates,” “expects,” “intends,” “plans,” “could,” “should,” “would,” “may,” “will,” “believes,” “estimates,” “potential,” or “continue” and variations or similar expressions are intended to identify forward-looking statements, but not all forward-looking statements may be so identified. These statements are based upon the current expectations and beliefs of management and are subject to certain risks and uncertainties that could cause actual results to differ materially from those described in the forward-looking statements. These risks and uncertainties include, but are not limited to, risks and uncertainties discussed in the Company’s most recent reports filed with the Securities and Exchange Commission (“SEC”), including under the caption “Risk Factors” in the Company’s annual report on Form 10-K for the year ended December 31, 2024, and in the Company’s subsequent quarterly reports on Form 10-Q, which factors are incorporated herein by reference. Readers are cautioned not to place undue reliance on any of these forward-looking statements. The Company undertakes no obligation to update any of these forward-looking statements to reflect events or circumstances after the date of this presentation, or to reflect actual outcomes.
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3 SCYNEXIS Corporate Update – November 2025 * As previously disclosed, GSK disputes these milestone payments; the Company vigorously disagrees with GSK’s position and is working towards resolving this disagreement SCY-247 Update Positive Phase 1 SAD/MAD data announced in September, 2025 The Company expects to initiate a Phase 1 study with the IV formulation as well as a Phase 2 study in invasive candidiasis (IC) in 2026. The Company aims to release proof of concept data in IC in 2026. Next Generation Fungerps In preclinical stages of development. We have selected a few early-stage candidates with significant potential to overcome limitations of the existing antifungal armamentarium Strong Balance Sheet The Company ended Q3, 2025 with cash, cash equivalents and investments of $37.9 million. After receiving the one time payments of $24.8 million from GSK in Q4 of 2025, the company’s cash runway will be greater than two years. Brexafemme/Ibrexafungerp SCYNEXIS to receive one-time payments of $24.8 million from GSK as part of the resolution of the disagreement related to the restart of the MARIO study. SCYNEXIS has agreed to terminate the study. SCYNEXIS proceeding with NDA transfer to GSK in Q4 of 2025, to facilitate Brexafemme commercialization Following GSK’s re-launch, SCYNEXIS stands to receive up to ~$146 million in annual net sales milestones as well as royalties net of payments to Merck in the low to mid single digit range.
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4 Limited Antifungal Development Coupled with Escalating Resistance has Resulted in Substantial Public Health Burden 1960 1970 1980 1990 2000 Emergence of Resistant Fungi Polyenes (amphotericin B) Azoles (Diflucan, Vfend) Echinocandins (Cancidas, Mycamine) Fungerps (BREXAFEMME) Echinocandin resistance Azole resistance Candida auris (MDR) SCYNEXIS aims to address antimicrobial resistance (AMR) by bringing a ground-breaking class of drugs with the strength, safety and versatility to defeat even the most insidious fungal diseases Increase in vulnerable population (immunocompromised, transplant, long ICU stays, oncology Tx) 2010 2020 TODAY Increase in other resistant fungi (e.g., Aspergillus, Mucorales)
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5 WHO Releases First-Ever List of Priority Deadly Fungal Pathogens CDC Identifies Drug Resistant Candida spp. and C. auris as Serious and Urgent Threats BARDA New Priority: Antifungals Fungal Resistance a Growing, Global, Public Health Threat Antifungal development is a well-recognized priority PASTEUR Act renews focus on antimicrobial resistance Fungal Outbreaks Increasing
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6 Fungerps are Well-Suited to Address High Priority Fungal Pathogens Demonstrated activity vs. fungi in both critical and high priority WHO Fungal Priority Pathogens list1 SCY-247 (IV and oral): Significant opportunity based on broad spectrum activity and fungerp-like tolerability Ibrexafungerp: GSK estimated opportunity as >$500M based on broad coverage of key pathogens 2 Fungerps Echinocandin Azole Polyene Companies Peak Sales per Product > $500M (potential)2 ~$370M to $680M3 ~$720M to >$1B3 ~$500M3 (SCY-247) (Ibrexafungerp) 1. www.who.int/news/item/25-10-2022-who-releases-first-ever-list-of-health-threatening-fungi 2. GSK press briefing on SCYNEXIS/BREXAFEMME March 30, 2023 3. Based on company filings and Symphony data (US)
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7 Product/Company Partner Deal Structure Fosmanogepix – 2023 Phase 3 Acquisition Upfront: $37M Dev. Milestones: $110M Prev. Agreement Obligations: $396M Brexafemme – 2023 Marketed Development & Commercialization Upfront: $90M Total Deal Value: $448M + Royalties Olorofim – 2022 Phase 3 EU & Asia Upfront: $100M Milestones: $380M Rezafungin – 2019 Phase 3 Strategic Partnership Upfront: $30M Equity Investment: $9M Co-dev. Funding - Dev. Milestones: $568M + Royalties Cresemba – 2017 & 2017 Marketed EU, Russia, Turkey, Israel + China, 16 Asian Pacific Countries Upfront: $70M CHF Upfront Payment Milestones: $427M + Royalties Amendment Upfront: $3M Upfront Payment Milestones: $223M + Royalties Cresemba – 2010 Phase 3 U.S. Upfront: 75M CHF Milestones: 478M CHF Antifungals Attract Generous Deal Terms
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8 Opportunities to Grow Shareholder Value Advancing proprietary platform of triterpenoid fungerps while evaluating next generation innovations Maximize Ibrexafungerp opportunity Strong balance sheet enhances the opportunity to deliver additional innovative therapies to patients with significant unmet need Partnership with GSK optimizes BREXAFEMME commercial potential in VVC and RVVC Advance next generation fungerp SCY-247 in invasive fungal infections with critical needs Leverages core internal expertise Addresses recognized unmet needs with significant market potential
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9 Ibrexafungerp GSK Licensing Agreement As Amended • Upon re-launch, SCYNEXIS stands to receive up to ~$146 million in annual sales milestones as well as royalties net of payments to Merck in the low to mid single digits range • SCYNEXIS has already received $125 million from GSK in upfront and development milestone payments • SCYNEXIS to receive one-time payments of $24.8 million in Q4 of 2025 as part of the resolution of the disagreement related to the MARIO study. SCYNEXIS has agreed to GSK’s request to terminate the study • SCYNEXIS proceeding with NDA transfer in Q4, 2025 to facilitate Brexafemme commercialization
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10 Fungerp Pipeline A New Class of Antifungals – Powerful - Different IBREXAFUNGERP VVC and Recurrent VVC Phase 3Phase 1 Phase 2 ApprovedPreclinical SCY-247 Treatment and Prevention of Invasive Fungal Infections Oral ® IV 100% commercial rights Fungerp Analogs Treatment of resistant fungi with novel structural analogs Oral/IVOral/IV Partnered with
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11 SCY-247: Second Generation Fungerp
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12 SCY-247 unique attributes address limitations of existing treatment options, allowing for sizable commercial opportunity SCYNEXIS Proprietary Market Assessment (HCP n=100) SCY-247 1- Broad-spectrum of activity 2- IV and Oral Formulations 3- Low risk of DDIs 4- High Tissue Penetration 5- Favorable Safety Treatment of Invasive Candidiasis (IC) - ~70K annual cases Tx in the U.S. - High mortality rate (20-40%) - Glucan Synthase Inhibitors as 1st line - Rising multi-drug resistance - Need for a drug available IV & Oral Prophylaxis of Invasive Fungal Disease - Multiple at-risk populations hematologic malignancies (Heme), HSCT, and solid organ transplant recipients (SOT) - Long Duration of Treatment - Need for an oral drug with favorable DDI profile Sizable Commercial Opportunity in the U.S. estimated > $700 million annually CONFIDENTIAL
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13 Fungicidal against Candida spp. Active against most drug-resistant fungi Including multi-drug-resistant Candida auris and azole- resistant Aspergillus spp Other fungal pathogens Yeasts, molds, Pneumocystis and dimorphic fungi Glucan synthase inhibitor Glucan synthase not found in human cells – low risk for off- target effect Proven MOA Same MOA as echinocandins, with differentiated binding Active against most echinocandin-resistant Candida strains Suitable for IV and oral formulations Low propensity for DDIs Tissue penetration Distributes into tissues often affected by fungal infections SCY-247 – Our Second Generation Fungerp Broad Spectrum of Activity Validated MOA Favorable PK Profile
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14 SCY-247 – In Development Against Resistant Fungal Infections IP wholly owned by SCYNEXIS Development backed by NIH NIH provided ~$3M funding to Case Western University for development of SCY-247 against C. auris Phase 1 Positive Oral Single and Multiple Ascending Dose Trial results announced Phase 1 Intravenous Single and Multiple Ascending Dose Trial anticipated in Q1 2026 Phase 2 study in invasive candidiasis patients to be initiated in 2026 Anticipated Qualified Infectious Disease Product (QIDP) designation, Orphan Drug Designation and Fast Track (regulatory exclusivity of at least 10 years)
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15 SCY-247 Induces Significant Morphological Cell Wall Alterations and Interference with Cell Division in Candida Species The effect of SCY-247 on the morphology and ultrastructure of C. auris was evaluated using scanning electron microscopy (SEM), caspofungin was included as control. Compared to untreated control, SCY-247 treated C. auris showed enlarged, shriveled, cells with extensive budding scars and holes in the cell wall. In addition, their cytokinesis was inhibited, and apoptosis was observed. Chu S, Antimicrob Agents Chemother. 2021 Feb 17;65(3):e01988-20. doi: 10.1128/AAC.01988-20. PMID: 33317999; PMCID: PMC8092514 CONFIDENTIAL Control A Caspofungin B SCY-247 C SCY-247 D Apoptotic & Shriveled cells Multiple bud scarring SCY-247
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16 SCY-247 Achieves Enhanced Dose-Dependent Exposures in Lung and Kidney in a Murine Model of C. glabrata Infection SCY-247 shows a linear relationship and a high distribution in lung and kidney 1 Dose dependent exposure increases in plasma & tissues Exposure in lung and kidney is ~15 to 35 greater than plasma • Supportive of the potential for efficacy in deep seated fungal infections In contrast2: • Azoles including fluconazole, itraconazole, voriconazole, and isavuconazole have demonstrated concentrations in the lungs that are approximately double of those in plasma • Echinocandins historically have had poor lung tissue and ELF penetration 1. Data on file: SCY247-PH-011; Quantitation performed by qualified LC-MSMS method for SCY-247 2. Stover, K.R., Cleary, J.D. Antifungal Penetration and Distribution into Organs and Tissue. Curr Fungal Infect Rep 14, 279–288 (2020). https://doi.org/10.1007/s12281-020-00390-7 CONFIDENTIAL Kidney LungPlasma Tisue and group mg/kg 16 32 48 16 32 48 16 32 48
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17 SCY-247 Activity against echinocandin-resistant C. glabrata Wiederhold, N. et al., TIMM 2025 p-value vs. Vehicle Control. * p<0.05 ** p<0.005 *** p<0.001 **** p<0.0001 **** **** **** *** CONFIDENTIAL SCY-247 significantly reduced fungal burden in kidneys and lungs of in vivo model of invasive candidiasis caused by an echinocandin-resistant Candida glabrata In contrast, caspofungin and fluconazole did not show any significant effect in reducing fungal burden in this model. Murine model of disseminated candidiasis with an echinocandin-resistant strain
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18 SCY-247 – Activity Against Candida glabrata SCY-247 significantly reduced fungal burden in kidneys and lungs of in vivo model of invasive candidiasis caused by Candida glabrata • C. glabrata the 2nd most common Candida species found in patients with invasive disease at many institutions and is often reported to be azole-resistant In contrast, caspofungin significantly lowered fungal burden within the kidneys but not the lungs, while fungal burden in mice treated with fluconazole was similar to controls in both organs Oral presentation at ESCMID 2024 by Nathan P. Wiederhold, PharmD, Fungus Testing Laboratory, UT Health San Antonio Murine model of disseminated candidiasis Significant, dose-dependent reductions in kidney and lung fungal burden in SCY-247-treated mice
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19 *P <0.05 vs. placebo; **P <0.0001 vs. placebo, and all other monotherapy treatments. 0 3 6 9 12 15 18 21 0 20 40 60 80 100 Days post infection Percent survival Placebo SCY-247 16 mg/kg SCY-247 32 mg/kg SCY-247 48 mg/kg LAMB 10 mg/kg SCY-247-32mg/kg +LAMB 10 mg/kg Uninfected ** * * SCY-247 – Activity Against Rhizopus delemar (Mucormycosis) Gebremariam T et al., SCY-247, a novel second-generation IV/oral triterpenoid antifungal, is efficacious in the neutropenic mouse model of pulmonary mucormycosis, AAAM 2024 Murine model of mucormycosis • SCY-247 (mid and high dose) significantly increased survival when compared to placebo • The combination of SCY-247 with liposomal amphotericin B resulted in a significant better survival rate when compared to placebo and all monotherapy treatments
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20 SCYNEXIS Strongly Positioned for Value Creation Demonstrated internal expertise, solid supply chain and long IP protection, and potential for next generation products and partnerships Global urgency to rapidly develop potent antifungals to treat emerging infectious threats The Company ended Q3, 2025 with cash, cash equivalents and investments of $37.9 million. After receiving the one time payments of $24.8 million from GSK in Q4 of 2025, the company’s cash runway will be greater than two years Category leader in the fight against deadly fungal pathogens with new antifungal (SCY-247) completing Phase 1 development