Drug Development and Trials - Bezuclastinib is being developed for Advanced Systemic Mastocytosis (AdvSM) and Non-Advanced Systemic Mastocytosis (Non-AdvSM), with a median survival of less than 3.5 years for AdvSM patients[56]. - The SUMMIT trial for Non-AdvSM completed enrollment in Q3 2023 with 54 patients, and Part 2 is expected to enroll 159 patients, with top-line results anticipated in H2 2025[57]. - In SUMMIT Part 1b, 100% of patients with baseline tryptase ≥20ng/mL achieved <20ng/mL at week 12, compared to 0% in the placebo group[57]. - The APEX trial for AdvSM reported an objective response rate (ORR) of 52% as of September 25, 2023, with a 56% ORR for TKI-treatment-naïve patients[58]. - The PEAK trial for GIST enrolled 413 patients, with a median progression-free survival (mPFS) of 10.2 months and an ORR of 27.5%[60]. - Bezuclastinib has received orphan drug designation from the FDA and EMA for both Mastocytosis and GIST[59][60]. - The SUMMIT Part 1b showed a 51% mean improvement in overall symptom severity for bezuclastinib compared to 18% for placebo[57]. - The majority of treatment-emergent adverse events in clinical trials were low-grade and reversible, with no serious adverse events reported in the SUMMIT trial[57][60]. - The company initiated a Phase 1 study of CGT4859 in patients with FGFR2 mutations, with preliminary results expected in 2025[63]. - CGT4255 demonstrated low nM potency against ErbB2 wild-type and oncogenic mutations with over 100-fold selectivity over wild-type EGFR[64]. - CGT6297, a PI3Kα inhibitor, showed low nM potency in H1047R mutant PI3K cell lines and superior efficacy compared to Alpelisib in preclinical models[66]. - The company is developing a potent KRAS inhibitor, CGT6737, which demonstrated 90% PD inhibition in mouse xenograft models[67]. - The company plans to initiate IND-enabling studies for CGT4255 in mid-2024 and for CGT6297 in 2025[64][66]. Financial Performance - The company reported a net loss of $187.9 million for the nine months ended September 30, 2024, compared to a net loss of $138.0 million for the same period in 2023, with an accumulated deficit of $791.6 million as of September 30, 2024[68]. - The company expects to incur significant expenses and operating losses for at least the next several years, particularly related to ongoing clinical trials and product development[68]. - As of September 30, 2024, the company had cash, cash equivalents, and marketable securities of $345.5 million, expected to fund operations through late 2026[70]. - Total operating expenses for the three months ended September 30, 2024, were $75.4 million, an increase of $15.8 million (26.6%) compared to $59.6 million for the same period in 2023[75]. - Research and development expenses for the three months ended September 30, 2024, were $63.6 million, up $13.5 million (26.9%) from $50.1 million in 2023, driven by higher costs associated with bezuclastinib and increased personnel costs[76][77]. - Net loss for the three months ended September 30, 2024, was $70.6 million, compared to a net loss of $55.4 million for the same period in 2023, reflecting an increase of $15.2 million (27.5%) in losses[75]. - For the nine months ended September 30, 2024, total operating expenses were $202.2 million, an increase of $52.3 million (34.9%) from $149.9 million in 2023[81]. - Research and development expenses for the nine months ended September 30, 2024, totaled $170.6 million, up $45.6 million (36.5%) from $125.0 million in 2023, primarily due to increased costs for bezuclastinib and personnel[83][84]. - Interest income for the nine months ended September 30, 2024, was $14.2 million, compared to $9.2 million in 2023, reflecting an increase of $5.0 million (54.3%) due to higher invested balances[85]. - Other income, net for the nine months ended September 30, 2024, was less than $0.1 million, a decrease of $0.9 million compared to $1.0 million in 2023, primarily due to the expiration of a sublease[86]. - The change in fair value of the CVR liability for the nine months ended September 30, 2024, was nil, compared to a decrease of $1.7 million in 2023, as the CVRs expired on August 6, 2023[87]. - The company has incurred significant operating losses since inception and does not expect to generate revenue from product sales for several years[88]. Funding and Capital Raising - The company filed a shelf registration statement allowing the sale of up to $300.0 million in various securities, with a specific Sales Agreement for $75.0 million in common stock through Guggenheim Securities[89]. - The company completed a public offering of 17,899,698 shares at $8.25 per share, raising approximately $161.9 million in net proceeds[89]. - A subsequent public offering in June 2023 raised approximately $161.8 million from 14,375,000 shares sold at $12.00 per share[89]. - A private placement on February 16, 2024, generated net proceeds of approximately $213.4 million from the sale of 17,717,997 shares at $7.50 each and 12,280 shares of Series B Preferred Stock[89]. - The company expects expenses to increase as it advances clinical development and research activities, with funding requirements dependent on various operational factors[95]. - The company anticipates needing additional funding to support ongoing research and development programs, with potential dilution of existing ownership interests if equity is raised[97]. Operational Insights - The company has focused significant resources on establishing its intellectual property portfolio and conducting R&D since its inception in 2014[68]. - The company anticipates an increase in general and administrative expenses due to expansion of operations to support ongoing discovery and clinical activities[73]. - Operating activities used $147.2 million in cash during the nine months ended September 30, 2024, primarily due to a net loss of $187.9 million[91]. - Net cash provided by financing activities was $214.4 million for the nine months ended September 30, 2024, compared to $163.5 million in the same period of 2023[94]. - The company has no off-balance sheet arrangements and no material changes in critical accounting policies were reported[99][98].

Clinical Trials - Top-line results from the registration-directed SUMMIT, PEAK, and APEX trials are expected in 2025[1] - Enrollment in the Phase 3 PEAK trial for GIST patients was completed with a total of 413 patients, focusing on median progression-free survival (mPFS) as the primary endpoint[3] - A Phase 1 trial for CGT-4859, a reversible FGFR2 inhibitor, was initiated, with preliminary results expected in 2025[6] - The company plans to present updated clinical data from SUMMIT and APEX at the ASH annual meeting in December 2024[5] - Anticipated milestones include completing enrollment in SUMMIT Part 2 in Q1 2025 and delivering top-line results from PEAK by the end of 2025[10] Financial Performance - Research and development expenses for Q3 2024 were $63.6 million, up from $50.1 million in Q3 2023, reflecting increased costs associated with trial enrollments[14] - General and administrative expenses for Q3 2024 were $11.8 million, compared to $9.5 million in Q3 2023, primarily due to organizational growth[15] - Net loss for Q3 2024 was $70.6 million, compared to a net loss of $55.4 million for the same period in 2023[16] - Cash position as of September 30, 2024, was $345.5 million, down from $389.9 million as of June 30, 2024, sufficient to fund operations into late 2026[13] - Total assets as of September 30, 2024, were $384.0 million, compared to $313.4 million as of December 31, 2023[21]

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 Title of each class Trading Symbol(s) Name of each exchange on which registered Common Stock, $0.001 Par Value COGT The Nasdaq Global Select Market FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2024 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission ...

Exhibit 99.1 Cogent Biosciences Reports Recent Business Highlights and Second Quarter 2024 Financial Results SUMMIT, PEAK and APEX registration-directed clinical trial enrollment remains on track; topline results expected from all three studies in 2025 Ended 2Q 2024 with $390 million, suf icient to fund operations into 2027 WALTHAM, Mass. and BOULDER, Colo., August 6, 2024 – Cogent Biosciences, Inc. (Nasdaq: COGT), a biotechnology company focused on developing precision therapies for genetically defined dis ...

SUMMIT is a randomized, global, multicenter, double-blind, placebo-controlled, multi-part phase II study for patients with nonadvanced systemic mastocytosis (Non-AdvSM). The study is designed to explore the safety and efficacy of COGT's most advanced candidate, bezuclastinib, in patients with moderate to severe NonAdvSM, which includes indolent systemic mastocytosis, smoldering systemic mastocytosis and bone marrow mastocytosis. Bezuclastinib is a selective tyrosine kinase inhibitor that is designed to pote ...

Patients treated with 100 mg bezuclastinib showed substantial reduction in their most severe symptoms and mast cell reactions "Nonadvanced systemic mastocytosis is a debilitating hematologic disorder and physicians and patients remain in search of more effective treatment options to fight this disease," said Lindsay Rein, MD, Associate Professor of Medicine in the Division of Hematologic Malignancies and Cellular Therapy at Duke University. "I am impressed with the rapid patient response and reductions seen ...

Patients treated with 100 mg bezuclastinib showed substantial reduction in their most severe symptoms and mast cell reactions "Nonadvanced systemic mastocytosis is a debilitating hematologic disorder and physicians and patients remain in search of more effective treatment options to fight this disease," said Lindsay Rein, MD, Associate Professor of Medicine in the Division of Hematologic Malignancies and Cellular Therapy at Duke University. "I am impressed with the rapid patient response and reductions seen ...

"We are thrilled to welcome Cole to our leadership team, as we begin preparations for commercializing bezuclastinib, a product we believe has clear potential to become a standard of care treatment for patients with systemic mastocytosis and advanced GIST," said Andrew Robbins, the Company's President and Chief Executive Officer. "Cole's broad commercial knowledge and leadership experience will be invaluable in helping Cogent expand from a research and development company to a fully-integrated commercial org ...

"I have been impressed with Cogent's rapid progress developing bezuclastinib in multiple patient populations," said Mr. Pinnow. "I look forward to building a capable commercial team ahead of Cogent's first potential product launch, and to working across the organization to help bring bezuclastinib to patients." Mr. Pinnow has 25 years of global and U.S. commercial experience, including multiple product launches as well as new product planning, sales and acquisitions. Mr. Pinnow joins Cogent from Pfizer, whe ...

Item 6. Exhibits. 3.2 10.2(1) 32.1*† Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 104* The cover page for the Company's Quarterly Report on Form 10-Q has been formatted in Inline XBRL and contained in Exhibit 101 SIGNATURES Date: May 7, 2024 By: /s/ John Green John Green Chief Financial Officer (Principal Accounting and Financial Officer) PART II—OTHER INFORMATION Item 1. Legal Proceedings. We are not cu ...