Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 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, 2025 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-38916 Bicycle Therapeutics plc (Exact Name of Registrant as Specified in its Charter) England and Wales Not Appl ...

Exhibit 99.1 Bicycle Therapeutics Reports Recent Business Progress and Second Quarter 2025 Financial Results Continued advancement across research and development pipeline, with key program updates expected in 2H 2025 Phase 1/2 Duravelo-4 trial for zelenectide pevedotin in NECTIN4-amplified non-small cell lung cancer open and actively recruiting patients Strengthened clinical leadership and bolstered roster of scientific advisors with additions to Board of Directors and creation of Research and Innovation A ...

Bicycle Therapeutics Investor Presentation • May 2025 Forward-looking statements Bicycle® molecules are short peptides chemically constrained with a central scaffold that can induce diverse structures Scaffold Chemical modification with scaffold Short linear peptide + Bicycle® molecule This presentation may contain forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. These statements may be identified by words such as "aims," "antici ...

This presentation may contain forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. These statements may be identified by words such as "aims," "anticipates," "believes," "could," "estimates," "expects," "forecasts", "goal," "intends," "may," "plans," "possible," "potential," "seeks," "will," and variations of these words or similar expressions that are intended to identify forward-looking statements. All statements other than stateme ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 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 March 31, 2025 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-38916 Bicycle Therapeutics plc (Exact Name of Registrant as Specified in its Charter) England and Wales Not App ...

[Q1 2025 Business Progress and Financial Results](index=1&type=section&id=Bicycle%20Therapeutics%20Reports%20Recent%20Business%20Progress%20and%20First%20Quarter%202025%20Financial%20Results) Bicycle Therapeutics highlights Q1 2025 clinical progress, corporate developments, and financial results, projecting a strong cash runway into 2027 [CEO's Remarks](index=1&type=section&id=CEO's%20Remarks) The CEO highlighted significant Q1 progress, validating MT1-MMP as a novel cancer target and advancing clinical trials, supported by a strong financial position - Human imaging data continues to validate MT1-MMP as a novel cancer target and demonstrates the positive properties of Bicycle Radioconjugate (BRC) molecules[2](index=2&type=chunk) - The Phase 1/2 Duravelo-3 trial for NECTIN4 gene-amplified breast cancer has been initiated[2](index=2&type=chunk) - Dose selection in the Phase 2/3 Duravelo-2 trial for metastatic urothelial cancer is on track for the second half of 2025[2](index=2&type=chunk) - The company has an expected financial runway extending to the second half of 2027[2](index=2&type=chunk) [Key Business and Clinical Updates](index=1&type=section&id=First%20Quarter%202025%20and%20Recent%20Events) The company presented positive BRC imaging data, advanced the zelenectide pevedotin program, and strengthened its leadership team with key appointments and promotions [Pipeline Progress](index=1&type=section&id=Pipeline%20Progress) The company presented additional BRC imaging data, advanced zelenectide pevedotin with ASCO abstract acceptances, and initiated the Phase 1/2 Duravelo-3 trial - Presented additional human imaging data for a Bicycle Radioconjugate (BRC) targeting MT1-MMP at the AACR 2025 meeting, reinforcing its potential. Initial human imaging data for EphA2 is expected in 2H 2025[3](index=3&type=chunk) - Two abstracts on zelenectide pevedotin for metastatic urothelial cancer (mUC) were accepted for presentation at ASCO 2025, covering Phase 1 combination data and the ongoing Phase 2/3 Duravelo-2 trial[6](index=6&type=chunk) - The Phase 1/2 Duravelo-3 trial for zelenectide pevedotin in NECTIN4-amplified breast cancer is now open and actively recruiting patients, following FDA Fast Track designation for this indication[6](index=6&type=chunk) [Corporate Developments](index=2&type=section&id=Corporate%20Developments) The company strengthened its leadership team by appointing a new Chairman, adding new Board and Clinical Advisory Board members, and promoting key internal talent - Felix J. Baker, Ph.D., will succeed Pierre Legault as chairman of the Board of Directors[6](index=6&type=chunk) - World-renowned oncology experts Alessandro Riva, M.D., and Fabrice André, M.D., Ph.D., have joined the company's Board of Directors and Clinical Advisory Board, respectively[6](index=6&type=chunk) - Key leadership promotions include Eric Westin, M.D., to Chief Medical Officer and Jim MacDonald-Clink to SVP, Head of Business Development[6](index=6&type=chunk) [Financial Performance](index=2&type=section&id=First%20Quarter%202025%20Financial%20Results) Bicycle Therapeutics reported a Q1 2025 net loss of **$60.8 million**, primarily due to increased R&D expenses and decreased collaboration revenue, while maintaining a strong cash position [Financial Summary](index=2&type=section&id=Financial%20Summary) Key financial metrics for Q1 2025 show an increased net loss and higher R&D and G&A expenses, alongside a decrease in cash and cash equivalents compared to Q4 2024 Q1 2025 Financial Summary (in millions) | Financial Metric | Q1 2025 | Q1 2024 | Change | | :--- | :--- | :--- | :--- | | **Cash & Cash Equivalents** | $793.0M | - | -$86.5M (vs Q4'24) | | **R&D Expenses** | $59.1M | $34.9M | +$24.2M | | **G&A Expenses** | $21.1M | $16.4M | +$4.7M | | **Net Loss** | $60.8M | $26.6M | +$34.2M | | **Net Loss Per Share** | $(0.88) | $(0.62) | +$0.26 | [Statement of Operations](index=4&type=section&id=Condensed%20Consolidated%20Statements%20of%20Operations%20and%20Comprehensive%20Loss) The condensed consolidated statement of operations for Q1 2025 reflects a significant increase in net loss and operating loss, driven by higher expenses and reduced collaboration revenue Q1 2025 Statement of Operations (in thousands) | Metric | Three Months Ended March 31, 2025 | Three Months Ended March 31, 2024 | | :--- | :--- | :--- | | Collaboration revenue | $ 9,977 | $ 19,530 | | Research and development | 59,058 | 34,864 | | General and administrative | 21,123 | 16,382 | | **Loss from operations** | **(70,204)** | **(31,716)** | | **Net loss** | **$ (60,754)** | **$ (26,563)** | | **Net loss per share, basic and diluted** | **$ (0.88)** | **$ (0.62)** | [Balance Sheet Data](index=5&type=section&id=Balance%20Sheets%20Data) The balance sheet highlights a decrease in cash and cash equivalents, working capital, total assets, and total shareholders' equity as of March 31, 2025, compared to December 31, 2024 Balance Sheet Highlights (in thousands) | Metric | March 31, 2025 | December 31, 2024 | | :--- | :--- | :--- | | Cash and cash equivalents | $ 792,973 | $ 879,520 | | Working capital | 798,463 | 861,375 | | Total assets | 883,894 | 956,868 | | Total shareholders' equity | 740,333 | 793,060 | [Outlook and Future Events](index=1&type=section&id=Outlook%20and%20Future%20Events) The company projects a strong financial position with a cash runway into the second half of 2027 and plans to participate in the RBC Capital Markets Global Healthcare Conference - The company possesses cash and cash equivalents of **$793.0 million** as of March 31, 2025, which is expected to fund operations into the second half of 2027[1](index=1&type=chunk)[5](index=5&type=chunk) - Management will participate in a fireside chat at the 2025 RBC Capital Markets Global Healthcare Conference on May 20, 2025[4](index=4&type=chunk)

Company Overview - Bicycle Therapeutics (NASDAQ: BCYC) is a developmental biotech company focused on novel conjugated targeted therapies aimed at exploiting cell surface targets in cancer [1] Analyst Insights - Analysts, including those from Avisol Capital Partners, have been evaluating Bicycle Therapeutics over the past two years, indicating a growing interest in the company's potential within the biotech sector [1]

Financial Performance - The company has incurred net losses of $169.0 million, $180.7 million, and $112.7 million for the years ended December 31, 2024, 2023, and 2022, respectively, with an accumulated deficit of $680.8 million as of December 31, 2024[564]. - The net loss for the year ended December 31, 2024, was $169.031 million, a decrease of $11.633 million from a net loss of $180.664 million in 2023[596]. - The company does not expect to generate revenue from product sales for the foreseeable future, relying instead on collaboration revenue[571]. - The company has not generated revenue from product sales since inception and expects to continue incurring significant operating losses[605]. Revenue and Collaboration - The company has received gross proceeds of $1.4 billion from the sale of ordinary shares and $236.6 million from collaboration agreements since its inception in 2009[563]. - Collaboration revenue increased by $8.3 million in the year ended December 31, 2024, compared to 2023, primarily due to increases from collaborations with Novartis ($6.3 million), Genentech ($2.9 million), and Bayer ($2.2 million)[597]. - Collaboration revenue increased by $8.3 million to $35.3 million in 2024, driven by contributions from collaborations with Novartis, Genentech, and Bayer[596]. - The company has not recognized any sales-based royalty revenue from its collaboration agreements to date[643]. Expenses and Operating Costs - Total operating expenses for 2024 were $245.147 million, an increase of $28.225 million compared to $216.922 million in 2023[596]. - Research and development expenses for the year ended December 31, 2024, were $172.966 million, an increase of $16.470 million from $156.496 million in 2023[596]. - General and administrative expenses rose to $72.181 million in 2024, up by $11.755 million from $60.426 million in 2023[596]. - The company anticipates substantial increases in expenses and capital requirements as it continues its development activities and seeks marketing approvals[565]. - General and administrative expenses are anticipated to rise as the company increases headcount to support research and development and potential commercialization efforts[586]. Cash and Financing - As of December 31, 2024, the company had cash and cash equivalents of $879.5 million, which is expected to fund operations for at least 12 months[570]. - Net cash used in operating activities was $164.72 million in 2024, an increase of $104.1 million compared to 2023, largely due to higher cash payments for ongoing development activities[608]. - Net cash provided by financing activities was $519.75 million in 2024, primarily from net proceeds of $544.1 million from a private placement[610]. - The company expects to finance its cash needs through equity offerings, debt financings, collaborations, and other strategic transactions, which may dilute existing shareholders' ownership[622]. Research and Development - The company is evaluating multiple product candidates, including zelenectide pevedotin and BT5528, in ongoing clinical trials[559]. - The company expects research and development expenses to continue increasing due to an expanded portfolio of product candidates and ongoing clinical trials[579]. - Research and development expenses increased by $16.5 million to $172.97 million in 2024, primarily due to a $38.6 million increase in clinical program expenses for zelenectide pevedotin[599]. - The company incurred approximately $156.6 million in direct external expenses for the development of zelenectide pevedotin since its candidate nomination[600]. Obligations and Liabilities - Total contractual obligations as of December 31, 2024, amounted to $11.18 million, with $6.07 million due within one year[615]. - The company has entered into agreements with third parties for future milestone payments totaling $166.2 million, contingent upon achieving specific milestones[618]. - Future debt financing may involve covenants that restrict the company's operations or ability to incur additional debt[622]. Economic and Market Conditions - High inflation rates and increased costs of clinical trial materials and supplies may adversely affect the company's operating results and cash flows[623]. - The company faces challenges in raising capital due to unfavorable global economic and political conditions, which may impact its development programs[621]. - The company is subject to potential downward pressure on share prices due to economic uncertainty and volatility in capital markets[623].

Financial Performance - The company reported a net loss of $51.9 million, or $(0.75) basic and diluted net loss per share, for the fourth quarter of 2024, compared to a net loss of $49.1 million, or $(1.16) per share, for the same period in 2023[12]. - Collaboration revenue for Q4 2024 was $3.708 million, compared to $5.331 million in Q4 2023, representing a decrease of 30.4%[16]. - Total operating expenses for Q4 2024 were $71.371 million, up from $59.566 million in Q4 2023, an increase of 19.8%[16]. - Net loss for Q4 2024 was $51.854 million, compared to a net loss of $49.099 million in Q4 2023, reflecting an increase in loss of 5.6%[16]. - General and administrative expenses for the year ended December 31, 2024, were $72.2 million, an increase from $60.4 million in 2023, driven by higher personnel-related expenses[12]. - Research and development expenses for the year ended December 31, 2024, were $173.0 million, up from $156.5 million in 2023, primarily due to increased clinical program expenses for zelenectide pevedotin[12]. Cash and Assets - As of December 31, 2024, cash and cash equivalents were $879.5 million, an increase from $526.4 million as of December 31, 2023, providing a financial runway into the second half of 2027[12]. - Cash and cash equivalents increased to $879.520 million as of December 31, 2024, from $526.423 million in 2023, a growth of 67.0%[18]. - Total assets rose to $956.868 million in 2024, compared to $595.344 million in 2023, marking an increase of 60.6%[18]. Clinical Trials and Research - In the Phase 1 Duravelo-1 trial, a 65% overall response rate (ORR) was achieved among 20 efficacy evaluable patients treated with zelenectide pevedotin plus pembrolizumab for first-line metastatic urothelial cancer[3]. - Bicycle Therapeutics is conducting the Phase 2/3 Duravelo-2 trial evaluating the efficacy of zelenectide pevedotin in combination with pembrolizumab versus chemotherapy in first-line metastatic urothelial cancer[4]. - Among 38 breast cancer patients evaluated, a 62.5% ORR was observed in those with NECTIN4 gene amplification compared to a 14.3% ORR in all efficacy-evaluable patients[4]. - Bicycle Therapeutics plans to initiate several additional Phase 1/2 trials for zelenectide pevedotin in NECTIN4 gene-amplified cancers, including breast cancer in 1H 2025 and lung cancer in 2H 2025[6]. - The company received FDA Fast Track designations for zelenectide pevedotin in the treatment of adult patients with previously treated, NECTIN4 gene-amplified, advanced or metastatic triple-negative breast cancer and non-small cell lung cancer[5]. - The company anticipates additional MT1-MMP human imaging data in mid-2025 and initial EphA2 human imaging data in 2H 2025 as part of its radiopharmaceuticals pipeline[7]. Shareholder Information - The company reported a weighted average of 69,051,745 ordinary shares outstanding for Q4 2024, compared to 42,419,326 in Q4 2023, an increase of 62.8%[16]. Strategic Focus - The company anticipates the initiation of clinical trials for its product candidates in various cancers, including breast and lung cancer, in the near future[14]. - Bicycle Therapeutics expects to leverage its technology through partnerships to develop therapies beyond oncology, indicating a strategic expansion of its research focus[14].

Group 1 - Bicycle Therapeutics (NASDAQ: BCYC) presented two sets of data since August 20, with the first set at ESMO in September 2024 from its phase 1/2 trial of BT8009 or zelenectide pevedotin [1] - The second set of data was not detailed in the provided content [1] Group 2 - The Total Pharma Tracker offers tools for DIY investors, including a software for entering any ticker to access extensive curated research material [2] - In-house experts provide hands-on support to find the best investible stocks, along with buy/sell strategies and alerts [2]