BICYCLE THERAPEUTICS PLC

**(Unaudited)

1. Nature of the business and basis of presentation

Bicycle Therapeutics plc (collectively with its subsidiaries, the “Company”) is a clinical-stage pharmaceutical company developing a novel class of medicines, which the Company refers to as Bicycle® molecules, for diseases that are underserved by existing therapeutics. Bicycle molecules are a unique therapeutic modality combining the pharmacology usually associated with a biologic with the manufacturing and pharmacokinetic properties of a small molecule. The Company’s initial internal programs are focused on oncology indications with high unmet medical need. The Company is evaluating zelenectide pevedotin, formerly BT8009, a Bicycle Drug Conjugate (a “BDC®” molecule) targeting Nectin-4, in an ongoing company-sponsored Phase I/II clinical trial in patients with Nectin-4 expressing advanced malignancies and an ongoing company-sponsored Phase II/III registrational trial, called Duravelo-2, in patients with metastatic urothelial cancer. The Company is also evaluating zelenectide pevedotin in ongoing company-sponsored Phase I/II clinical trials to assess the efficacy and safety of zelenectide pevedotin in patients with NECTIN4 amplified advanced breast cancer and NECTIN4 amplified advanced or metastatic non-small cell lung cancer, which commenced recruiting patients in the first and third quarters of 2025, respectively. In addition, the Company is evaluating BT5528, a BDC molecule targeting Ephrin type-A receptor 2 (“EphA2”), in a company-sponsored Phase I/II clinical trial, and BT7480, a Bicycle Tumor-Targeted Immune Cell Agonist® (a “Bicycle TICA®” molecule) targeting Nectin-4 and agonizing CD137, in a company-sponsored Phase I/II clinical trial. The Company’s discovery pipeline in oncology includes next-generation BDC molecules and Bicycle* *Radioconjugates (“BRC®” molecules). Beyond the Company’s wholly owned oncology portfolio, the Company is collaborating with biopharmaceutical companies and organizations in therapeutic areas in which the Company believes its proprietary Bicycle screening platform can identify therapies to treat diseases with significant unmet medical need.

The accompanying condensed consolidated financial statements include the accounts of Bicycle Therapeutics plc and its wholly owned subsidiaries, BicycleTx Limited, BicycleRD Limited and Bicycle Therapeutics Inc. All intercompany balances and transactions have been eliminated on consolidation.

The accompanying condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”).

Liquidity

As of June 30, 2025, the Company had cash and cash equivalents of $721.5 million.

On May 23, 2024, the Company entered into a securities purchase agreement (the “Purchase Agreement”) with purchasers named therein (the “Investors”). Pursuant to the Purchase Agreement, the Company sold 6,764,705 ADSs, representing the same number of ordinary shares, nominal value £0.01 per share, and 19,169,001 non-voting ordinary shares, nominal value £0.01 per share, each at a purchase price equal to $21.42 per share (the “Private Placement”). The Company completed the Private Placement on May 28, 2024. The transaction resulted in gross proceeds to the Company of $555.5 million, and after deducting commissions and offering expenses of $11.4 million, net proceeds to the Company of $544.1 million.

The accompanying condensed consolidated financial statements have been prepared on the basis of continuity of operations, realization of assets and the satisfaction of liabilities and commitments in the ordinary course of business. Since inception, the Company has devoted substantially all of its efforts to business planning, research and development, recruiting management and technical staff, and raising capital. The Company has funded its operations primarily with proceeds from the sale of its ordinary shares, American Depositary Shares representing ordinary shares (“ADSs”), including in offerings pursuant to its at-the-market offering (“ATM”) program, and non-voting ordinary shares, as well as proceeds received from its collaboration arrangements (Note 9) and proceeds from a loan agreement with Hercules Capital, Inc. (“Hercules”) (Note 6).

The Company has incurred recurring losses since inception, including net losses of $79.0 million and $139.7 million for the three and six months ended June 30, 2025, respectively, and $39.8 million and $66.4 million for the three and six months ended June 30, 2024, respectively. As of June 30, 2025, the Company had an accumulated deficit of $820.5 million. The Company expects to continue to generate operating losses in the foreseeable future. The Company expects that its cash and cash equivalents will be sufficient to fund its operating expenses and capital expenditure requirements through at least twelve months from the issuance date of these interim condensed consolidated financial statements.

The Company expects its expenses to increase substantially in connection with ongoing activities, particularly as the Company advances its clinical trials for its product candidates in development and preclinical activities. Accordingly, the Company will need to obtain additional funding in connection with continuing operations. If the Company is unable to raise funding when needed, or on attractive terms, it could be forced to delay, reduce or eliminate its research or drug development programs or any future commercialization efforts. There is no assurance that the Company will be successful in obtaining sufficient funding on terms acceptable to the Company to fund continuing operations, if at all.

The Company is subject to risks common to companies in the biotechnology and pharmaceutical industries, including but not limited to, risks of delays in initiating or continuing research programs and clinical trials, risks of failure of preclinical studies and clinical trials, the need to obtain marketing approval for any drug product candidate that it may identify and develop, the need to successfully commercialize and gain market acceptance of its product candidates, if approved, dependence on key personnel and collaboration partners, protection of proprietary technology, compliance with government regulations, development by competitors of technological innovations, and the ability to secure additional capital to fund operations. Product candidates currently under development will require significant additional research and development efforts, including preclinical and clinical testing and regulatory approval prior to commercialization. Even if the Company’s research and development efforts are successful, it is uncertain when, if ever, the Company will realize significant revenue from product sales.

2. Summary of significant accounting policies

The Company’s significant accounting policies are disclosed in the audited consolidated financial statements for the year ended December 31, 2024 included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024, which was filed with the Securities and Exchange Commission (the “SEC”), on February 25, 2025 (the “2024 Annual Report”). Since the date of such consolidated financial statements, there have been no changes to the Company’s significant accounting policies, other than those disclosed below.

Use of estimates

The preparation of condensed consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these condensed consolidated financial statements include, but are not limited to, revenue recognition, the accrual for research and development expenses and research and development incentives receivable, share-based compensation expense, valuation of right-of-use assets and liabilities and income taxes, including the valuation allowance for deferred tax assets. The Company bases its estimates on historical experience, known trends and other market-specific or other relevant factors that it believes to be reasonable under the circumstances. Estimates are periodically reviewed in light of reasonable changes in circumstances, facts and experience. Changes in estimates are recorded in the period in which they become known. Actual results could differ from those estimates or assumptions.

Significant risks and uncertainties

The Company currently operates in a period of economic uncertainty which has been significantly impacted by domestic and global monetary and fiscal policy, including changes to global trade policies, geopolitical conflicts such as the ongoing wars involving Ukraine and Israel, inflation and interest rates, and fluctuations in monetary exchange rates.

While the Company has experienced limited financial impacts at this time, the Company continues to monitor these factors and events and the potential effects each may have on the Company’s business, financial condition, results of operations and growth prospects.

Unaudited interim financial information

Certain information in the footnote disclosures of these financial statements has been condensed or omitted pursuant to the rules and regulations of the SEC. These unaudited condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and notes thereto for the year ended December 31, 2024 included in the Company’s 2024 Annual Report.

The accompanying condensed consolidated balance sheet as of June 30, 2025, the condensed consolidated statements of operations and comprehensive loss and condensed consolidated statements of shareholders’ equity for the three and six months ended June 30, 2025 and 2024, and condensed consolidated statements of cash flows for the six months ended June 30, 2025 and 2024, and the related financial information disclosed in these notes are unaudited. The unaudited interim financial statements have been prepared on the same basis as the audited annual financial statements for the year ended December 31, 2024, and, in the opinion of management, reflect all adjustments, consisting of normal recurring adjustments, necessary for the fair statement of the Company’s financial position as of June 30, 2025, the results of its operations for the three and six months ended June 30, 2025 and 2024 and its cash flows for the six months ended June 30, 2025 and 2024. The results for the three and six months ended June 30, 2025 are not necessarily indicative of the results to be expected for the year ending December 31, 2025, any other interim periods, or any future year or period.

Research and development incentives and receivable

The Company, through its subsidiaries in the U.K., receives reimbursements of certain research and development expenditures as part of a U.K. government research and development tax reliefs program. For 2024, the Company benefitted from the Small and Medium-sized Enterprises (“SME”) R&D Tax Relief program, under which the Company was able to surrender trading losses that arose from qualifying research and development expenses incurred by the Company’s subsidiaries in the U.K. for a cash rebate of up to 26.97% of qualifying expenditure incurred as long as the Company qualified as “R&D intensive” (broadly, a loss-making SME whose relevant R&D expenditure represents, for 2024,40% of its total expenditure for the accounting period). Such rebate percentage was increased from 18.6% of qualifying expenditure, retroactively applied to expenditures incurred after April 1, 2023, upon the enactment of Finance Act 2024 in February 2024. For accounting periods beginning after April 1, 2024, Finance Act 2024 replaced the legacy research and development expenditure credit and the SME R&D Tax Relief program with a merged research and development expenditure credit scheme (“RDEC”) and an enhanced research and development intensive support scheme (“ERIS”). Therefore, for 2025 the Company qualifies for the ERIS scheme, and is therefore eligible for a cash rebate up to 26.97% of qualifying expenditures, as it remains R&D intensive (for 2025, a loss-making SME whose relevant R&D expenditure represents 30% of its total expenditure for the accounting period). Going forward, if the Company no longer qualifies as an R&D-intensive SME during an accounting period, the Company will be subject to a single 20% gross rebate rate applying to all claims under the RDEC scheme.

Management has assessed the Company’s research and development activities and expenditures to determine which activities and expenditures are likely to be eligible under the research and development incentive program described above. At each period end, management estimates the reimbursement available to the Company based on available information at the time.

The Company recognizes income from the research and development incentives when the relevant expenditure has been incurred, the associated conditions have been satisfied and there is reasonable assurance that the reimbursement will be received. The Company records these research and development incentives as a reduction to research and development expenses in the condensed consolidated statements of operations and comprehensive loss, as the research and development tax credits are not dependent on us generating future taxable income, the Company’s ongoing tax status, or tax position. The research and development incentives receivable represents amounts due in connection with the above program. The Company recorded a reduction to research and development expenses of $11.5 million and

$20.8 million during the three and six months ended June 30, 2025, respectively, and $7.3 million and $22.6 million during the three and six months ended June 30, 2024, respectively. As of June 30, 2025, the Company had research and development incentives receivable of $60.8 million.

Recently adopted accounting pronouncements

In November 2023, the FASB issued ASU No. 2023-07,Segment Reporting (Topic 280) Improvements to Reportable Segment Disclosures, which requires disclosure of incremental segment information on an interim and annual basis. ASU 2023-07 is effective for annual periods beginning after December 15, 2023, and interim periods within annual periods beginning after December 15, 2024, and requires retrospective adoption to all prior periods presented in the consolidated financial statements. The adoption of ASU 2023-07 had no impact on the Company’s reportable segments identified and additional required disclosures have been included in Note 14.

Recently issued accounting pronouncements not yet adopted

In November 2024, the FASB issued ASU No. 2024-03,Income Statement – Reporting Comprehensive Income – Expense Disaggregation Disclosures (Subtopic 220-40), which requires more detailed disclosures about specified categories of expenses included in certain expense captions presented on the face of the consolidated statements of operations and comprehensive loss, including employee compensation, depreciation and amortization. ASU No. 2024-03 is effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments may be applied either prospectively to financial statements issued for reporting periods after the effective date of the ASU or retrospectively to all prior periods presented. The Company is currently evaluating the impact of the adoption of ASU No. 2024-03 on its consolidated financial statement disclosures.

In December 2023, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2023-09,Income Taxes (Topic 740) Improvements to Income Tax Disclosures (“ASU No. 2023-09”), which prescribes standard categories for the components of the effective tax rate reconciliation and requires disclosure of additional information for reconciling items meeting certain quantitative thresholds, requires disclosure of disaggregated income taxes paid, and modifies certain other income tax-related disclosures. ASU No. 2023-09 is effective for annual periods beginning after December 15, 2024 and allows for adoption on a prospective basis, with a retrospective option. The Company is currently evaluating the potential impact of the adoption of ASU No. 2023-09 on its consolidated financial statements and related disclosures.

3. Fair value of financial assets and liabilities

Financial assets and liabilities carried at fair value are to be classified and disclosed in one of the following three levels of the fair value hierarchy, of which the first two are considered observable and the last is considered unobservable: Level 1, quoted prices in active markets for identical assets or liabilities; Level 2, observable inputs (other than Level 1 quoted prices), such as quoted prices in active markets for similar assets or liabilities, quoted prices in markets that are not active for identical or similar assets or liabilities, or other inputs that are observable or can be corroborated by observable market data; Level 3, unobservable inputs that are supported by little or no market activity that are significant to determining the fair value of the assets or liabilities, including pricing models, discounted cash flow methodologies and similar techniques.

The carrying values of cash, cash equivalents and restricted cash, accounts receivable, research and development incentives receivable, prepaid expenses and other current assets, accounts payable and accrued expenses and other current liabilities approximate their fair values due to the short-term nature of these assets and liabilities.

Cash, cash equivalents and restricted cash

The Company considers all highly liquid investments that are readily convertible to known amounts of cash with original maturities of three months or less at the date of purchase to be cash equivalents. As of June 30,2025 and December 31,2024, the Company had cash equivalents of $446.5 million and $664.9 million, consisting of money

market funds that are primarily invested in U.S. Treasury securities, which are considered Level 1 assets. As of June 30, 2025, and December 31, 2024, there wereno other assets or liabilities measured at fair value on a recurring basis.

As of June 30, 2025 and December 31, 2024, the Company had $0.5 million of restricted cash related to a collateralized letter of credit in connection with the Company’s lease for office and laboratory space in Cambridge, Massachusetts, which is included within prepaid expenses and other current assets and within other assets, respectively, in the Company’s condensed consolidated balance sheet.

4. Property and equipment, net

Property and equipment, net consisted of the following (in thousands):

Depreciation and amortization expense was $1.7 million and $3.3 million for the three and six months ended June 30, 2025, respectively, and $1.6 million and $3.3 million for the three and six months ended June 30, 2024, respectively. Depreciation and amortization expense for the three and six months ended June 30, 2025 included amortization expense of $0.1 million and $0.1 million, respectively, related to property and equipment obtained under finance leases. There wasno amortization expense recorded related to property and equipment obtained under finance leases for the three and six months ended June 30, 2024.

5. Accrued expenses and other current liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

In August 2024, the Company consolidated all discovery research activities to the Company’s headquarters in Cambridge, U.K. As a result, at December 31, 2024, the Company had a remaining liability of$0.4 million related to unpaid severance and other one-time termination benefits. During the six months ended June 30, 2025, the Company paid the remaining$0.4 million, and there areno remaining unpaid benefits outstanding as of June 30, 2025.

6. Debt

On September 30, 2020, Bicycle Therapeutics plc and its subsidiaries (the “Borrowers”) entered into a loan and security agreement (the “Loan Agreement”) with Hercules, as amended from time to time, which provided for aggregate maximum borrowings of up to $75.0 million, of which the Company drew down an aggregate of $30.0 million in 2021

and 2020. Payments on borrowings under the Loan Agreement were interest-only until April 1, 2025 and interest was paid at an annual rate of theWall Street Journalprime rate plus 4.55%, with a minimum annual rate of at least 8.05%, capped at a rate no greater than 9.05%, and the Loan Agreement included a 5.0% end-of-term charge payable upon maturity or repayment. The scheduled maturity date was July 1, 2025. On July 9, 2024, the Company repaid all amounts outstanding, including the outstanding borrowings of $30.0 million, accrued and unpaid interest of $0.1 million, an end-of-term charge of $1.5 million and a prepayment charge of $0.3 million, for a total aggregate payment of $31.9 million, and terminated the Loan Agreement. Upon termination of the Loan Agreement, all security interests granted to the secured parties thereunder were terminated and released. No interest expense associated with the Loan Agreement was recognized for either the three or six months ended June 30, 2025. Interest expense associated with the Loan Agreement was $0.8 million and $1.6 million for the three and six months ended June 30, 2024, respectively.

7. Ordinary shares

The Company’s ordinary shares are divided into two classes: (i) ordinary shares and (ii) non-voting ordinary shares. Each holder of ordinary shares is entitled toone vote per ordinary share and to receive dividends when and if such dividends are recommended by the board of directors and declared by the shareholders. Holders of ADSs are not treated as holders of the Company’s ordinary shares, unless they withdraw the ordinary shares underlying their ADSs in accordance with the deposit agreement and applicable laws and regulations. The depositary is the holder of the ordinary shares underlying the ADSs. Holders of ADSs therefore do not have any rights as holders of the Company’s ordinary shares, other than the rights that they have pursuant to the deposit agreement with the depositary.

The non-voting ordinary shares have the same rights and restrictions as the ordinary shares and otherwise rankpari passu in all respects with the ordinary shares except for the following:

As of June 30, 2025, and December 31, 2024, the Company hadnot declared any dividends.

As of June 30, 2025, and December 31, 2024, the Company’s authorized share capital consisted of 159,802,729 and 155,876,645 ordinary shares, respectively, including ordinary shares and non-voting ordinary shares, with a nominal value of £0.01 per share. Authorized share capital, or shares authorized, comprises (i) the currently issued and outstanding ordinary shares and non-voting ordinary shares, (ii) the remaining ordinary shares available for allotment under the existing authority granted to the Board at the annual general meeting held on May 16, 2024, (iii) ordinary shares issuable on the exercise of outstanding options and settlement of vested restricted share units (“RSUs”) and (iv) ordinary shares reserved for issuance under the Bicycle Therapeutics plc 2024 Inducement Plan (the “2024 Inducement

Plan”), the Amended and Restated Bicycle Therapeutics plc 2020 Equity Incentive Plan with Non Employee Sub Plan (as amended from time to time, the “2020 Plan”) and/or the Bicycle Therapeutics plc 2019 Employee Share Purchase Plan (the “ESPP”).

As of June 30, 2025, there were 49,816,000 ordinary shares issued and outstanding and 19,437,944 non-voting ordinary shares issued and outstanding.

8. Share-based compensation

Employee incentive pool

2024 Inducement Plan

In July 2024, the Company’s board of directors approved the 2024 Inducement Plan. The 2024 Inducement Plan allows for the granting of nonqualified share options, RSUs, and other equity awards under the plan to persons not previously an employee or director of the Company, or following a bona fide period of non-employment, as an inducement material to such persons entering into employment with the Company. Share options granted under the 2024 Inducement Plan have a 10-year contractual life and generally vest over afour-year service period with 25% of the award vesting on the first anniversary of the vesting commencement date and the balance thereafter in 36 equal monthly installments.

The Company initially reserved 1,500,000 of its ordinary shares, or the equivalent number of ADSs, for the issuance of awards under the 2024 Inducement Plan. As of June 30, 2025, there were 892,700 shares available for future issuance under the 2024 Inducement Plan.

As of June 30, 2025, there were options outstanding to purchase 607,300 shares under the 2024 Inducement Plan.

2020 Equity Incentive Plan

In June 2020, the Company’s shareholders first approved the 2020 Plan, under which the Company may grant market value options, market value stock appreciation rights or restricted shares, RSUs, performance RSUs and other share-based awards to the Company’s employees. The Company’s non-employee directors and consultants are eligible to receive awards under the 2020 Non-Employee Sub-Plan to the 2020 Plan. All awards under the 2020 Plan, including the 2020 Non-Employee Sub-Plan, will be set forth in award agreements, which will detail the terms and conditions of awards, including any applicable vesting and payment terms, change of control provisions and post-termination exercise limitations. In the event of a change of control of the Company, as defined in the 2020 Plan, any outstanding awards under the 2020 Plan will vest in full immediately prior to such change of control.

The Company initially reserved up to 4,773,557 ordinary shares for future issuance under the 2020 Plan, including shares subject to options that were granted under the Company’s 2019 Share Option Plan (the “2019 Plan”) and that were granted pursuant to option contracts granted prior to the Company’s IPO, in each case that expire, terminate, are forfeited or otherwise not issued from time to time, if any. In June 2022, the Company’s shareholders approved the amended and restated 2020 Plan, which increased the number of ordinary shares reserved for future issuance by 750,000 shares. Additionally, prior to June 2025, the number of ordinary shares reserved for issuance pursuant to the 2020 Plan automatically increased on the first day of January of each year, initially commencing on January 1, 2021 and continuing up to and including January 1, 2032, in an amount equal to 5% of the total number of the Company’s voting ordinary shares outstanding on the last day of the preceding year, or a lesser number of shares determined by the Company’s board of directors (the “Evergreen Increase”). Pursuant to the Evergreen Increase, on January 1, 2025, the number of shares reserved for issuance under the 2020 Plan was increased by 2,378,465 shares. In June 2025, the Company’s shareholders approved Amendment No. 1 to the 2020 Plan, which (i) amended the calculation of the Evergreen Increase to capture the Company’s total issued share capital in order to treat non-voting ordinary shares the same as voting ordinary shares and (ii) increased the number of ordinary shares reserved for future issuance by 1,300,000. As of June 30, 2025, there were 1,608,530 ordinary shares available for issuance under the 2020 Plan.

Share options granted under the 2020 Plan have a 10-year contractual life and generally vest over either athree-year service period inthree equal annual installments for new non-employee director grants, or afour-year service period with 25% of the award vesting on the first anniversary of the vesting commencement date and the balance thereafter in 36 equal monthly installments for employees and consultants. Certain options granted to the Company’s non-employee directors vest over aone-year service period infour equal quarterly installments.

The Company grants RSUs to non-employee directors, consultants and certain employees under the 2020 Plan. Each RSU represents the right to receiveone of the Company’s ordinary shares upon vesting. RSUs granted to employees and consultants vest over afour-year service period with 25% of the award vesting on the first anniversary of the vesting commencement date and the remaining RSUs vesting in 12 equal quarterly installments. Certain RSUs granted to the Company’s non-employee directors either vest over athree-year service period inthree equal annual installments for new non-employee director grants or over aone-year service period infour equal quarterly installments. The Company may also, in its sole discretion, provide for deferred settlement of RSUs granted to the Company’s non-employee directors.

As of June 30, 2025, there were options outstanding to purchase 7,376,622 shares and RSUs outstanding for 1,891,546 shares under the 2020 Plan.

2019 Share Option Plan

In May 2019, the Company adopted the 2019 Plan, which became effective in conjunction with the IPO. As of June 30, 2025, there were 1,773,816 options outstanding to purchase ordinary shares under the 2019 Plan. In conjunction with the adoption of the 2020 Plan, all shares available for future issuance under the 2019 Plan as of June 29, 2020 became available for issuance under the 2020 Plan and the Company ceased making awards under the 2019 Plan. The 2020 Plan is the successor of the 2019 Plan.

Share options previously issued under the 2019 Plan have a 10-year contractual life, and generally either vest monthly over athree-year service period, or over afour-year service period with 25% of the award vesting on the first anniversary of the vesting commencement date and the balance thereafter in 36 equal monthly installments. Certain awards granted to the Company’s non-employee directors were fully vested on the date of grant. The exercise price of share options issued under the 2019 Plan is not less than the fair value of ordinary shares as of the date of grant.

Employee Share Purchase Plan

In May 2019, the Company adopted the ESPP, which became effective in conjunction with the IPO. The Company initially reserved 215,000 ordinary shares for future issuance under this plan. The ESPP provides that the number of shares reserved and available for issuance will automatically increase each January 1, beginning on January 1, 2020 and each January 1 thereafter through January 1, 2029, by the lower of: (i)1% of the outstanding number of ordinary shares on the immediately preceding December 31; (ii)430,000 ordinary shares or (iii) such lesser number of shares as determined by the Compensation Committee. The number of shares reserved under the ESPP is subject to adjustment in the event of a split-up, share dividend or other change in the Company’s capitalization. The number of shares reserved for issuance under the ESPP was increased by 430,000 shares effective January 1, 2025. As of June 30, 2025, the total number of shares available for issuance under the ESPP was 2,007,671 ordinary shares. As of June 30, 2025, there have been no offering periods to employees under ESPP.

Share-based compensation

The Company recorded share-based compensation expense in the following expense categories of its condensed consolidated statements of operations and comprehensive loss (in thousands):

Share options

The following table summarizes the Company’s option activity since December 31, 2024:

The weighted average grant-date fair value of share options granted during the six months ended June 30, 2025 and 2024 was $8.89 per share and $13.08 per share, respectively.

The aggregate intrinsic value of share options is calculated as the difference between the exercise price of the share options and the fair value of the Company’s ordinary shares. The aggregate intrinsic value of share options exercised waszero for each of the three and six months ended June 30, 2025, respectively, and $3.6 million and $4.6 million for the three and six months ended June 30, 2024.

For the three and six months ended June 30, 2025, the Company recorded share-based compensation expense for share options granted of $6.8 million and $13.6 million, respectively, and for the three and six months ended June 30, 2024, the Company recorded share-based compensation expense for share options granted of $7.3 million and $14.8 million, respectively.

The following table presents, on a weighted average basis, the assumptions used in the Black-Scholes option-pricing model to determine the fair value of share options granted to employees and directors:

As of June 30, 2025, total unrecognized compensation expense related to the unvested employee and director share options was $47.5 million, which is expected to be recognized over a weighted average period of 2.4 years.

Restricted share units

The following table summarizes the Company’s RSU activity under the 2020 Plan since December 31, 2024:

The fair value of RSUs that vested during the three and six months ended June 30, 2025 was $0.5 million and $2.7 million, respectively, and during the three and six months ended June 30, 2024 was $0.8 million and $2.3 million, respectively.

Total share-based compensation expense for RSUs granted was $2.7 million and $5.4 million for the three and six months ended June 30, 2025, respectively, and was $1.9 million and $3.7 million for the three and six months ended June 30, 2024, respectively. As of June 30, 2025, the total unrecognized compensation expense related to unvested RSUs was $25.1 million, which is expected to be recognized over a weighted-average period of 2.9 years.

9. Significant agreements

For the three and six months ended June 30, 2025 and 2024, the Company recognized revenue for its collaborations with Bayer Consumer Care AG (“Bayer”), Novartis Pharma AG (“Novartis”), Ionis Pharmaceuticals, Inc. (“Ionis”) and Genentech, Inc. (“Genentech”). The following table summarizes the revenue recognized in the Company’s condensed consolidated statements of operations and comprehensive loss from these arrangements (in thousands):

Except as otherwise disclosed below, there have been no material changes to the contractual terms, or the associated accounting treatments for recognizing revenue, of the Company’s significant agreements during the three and six months ended June 30, 2025 and 2024. Please read Note 9. “Significant agreements” to the Company’s audited consolidated financial statements for the year ended December 31, 2024 included in the Company’s 2024 Annual Report for further details on the Company’s significant agreements.

Bayer Collaboration Agreement

On May 4, 2023, the Company and Bayer entered into a collaboration and license agreement (the “Bayer Collaboration Agreement”), pursuant to which the parties will perform research and discovery activities under a mutually agreed upon research plan during a research term up to a specified number of years per target program to generate radiopharmaceutical compounds incorporating optimized Bicycle constructs directed totwo specified targets, under the oversight of a joint research committee.

During the three and six months ended June 30, 2025, the Company recognized revenue of $1.0 million and $1.9 million, respectively, and during the three and six months ended June 30, 2024, the Company recognized revenue of $0.8 million and $1.7 million, respectively, in connection with the Bayer Collaboration Agreement. As of June 30, 2025 and December 31, 2024, the Company recorded deferred revenue of $42.0 million and $40.0 million, respectively, in connection with the Bayer Collaboration Agreement. Revenue allocated to the identified performance obligations that are recognized over time is expected to be satisfied over a period of approximately four years from contract inception, and the remaining revenue allocated to material rights is expected to be recognized upon exercise or expiration of the associated options within approximately seven years from contract inception.

Novartis Collaboration Agreement

On March 27, 2023, the Company and Novartis entered into a collaboration and license agreement (the “Novartis Collaboration Agreement”), pursuant to which the parties will perform research and discovery activities under a mutually agreed upon research plan during a research term of up to a specified number of years per target program to generate compounds incorporating optimized Bicycle constructs directed totwo specified targets, under the oversight of a joint steering committee.

During the three and six months ended June 30, 2025, the Company recognized revenue of $1.5 million and $2.9 million, respectively, in connection with the Novartis Collaboration Agreement, and during the three and six months ended June 30, 2024, the Company recognized revenue of $3.8 million and $5.0 million, respectively, in connection with the Novartis Collaboration Agreement, including $2.5 million recognized during the second quarter of 2024 upon the expiration of Novartis’ material rights for limited substitution rights for the first and second targets. As of June 30, 2025 and December 31, 2024, the Company recorded deferred revenue of $45.1 million and $44.1 million, respectively, in connection with the Novartis Collaboration Agreement. Revenue allocated to the identified performance obligations that are recognized over time is expected to be satisfied over a period of approximately three years from contract inception and the remaining revenue allocated to material rights is expected to be recognized upon exercise or expiration of the respective options within approximatelysix years from contract inception.

Ionis Agreements

Following the exercise by Ionis of an option granted pursuant to an evaluation and option agreement, on July 9, 2021, the Company and Ionis entered into a collaboration and license agreement, which was subsequently amended in 2021, 2022, 2023 and 2024 (collectively the agreement and all amendments, the “Ionis Agreements”). Pursuant to the Ionis Agreements, the Company granted to Ionis a worldwide exclusive license under the Company’s relevant technology to research, develop, manufacture and commercialize products incorporating Bicycle* *peptides directed to the protein coded by the gene TFRC1 (transferrin receptor) (“TfR1 Bicycle” molecules) intended for the delivery of oligonucleotide compounds directed to targets selected by Ionis for diagnostic, therapeutic, prophylactic and preventative uses in humans. Each party was responsible for optimization of such TfR1 Bicycle molecules and other research and discovery activities related to TfR1 Bicycle molecules, as specified by a research plan which was

substantially completed in the second quarter of 2024, and thereafter Ionis is responsible for all future research, development, manufacture and commercialization activities.

During the first quarter of 2024, the Company updated its estimate of variable consideration for the reimbursement of contract research organization (“CRO”) costs under the arrangement from $0.6 million to $0.4 million, and the transaction price decreased to from $38.0 million to $37.8 million.

As of June 30, 2025, the combined licenses and research and discovery performance obligation is complete, and all revenue allocated to the combined licenses and research and discovery performance obligation has been recognized. No revenue was recognized during either the three or six months ended June 30, 2025 in connection with the Ionis Agreements. For the three and six months ended June 30, 2024, the Company recognized revenue of $3.0 million and $8.9 million, respectively, in connection with the Ionis Agreements. As of June 30, 2025, and December 31, 2024, the Company recorded deferred revenue of $3.9 million and $3.6 million, respectively, in connection with the Ionis Agreements. The remaining revenue allocated to material rights is recorded as deferred revenue and the Company expects to recognize revenue upon exercise of or upon expiry of the respective option after approximately four toseven years from contract execution.

Genentech Collaboration Agreement

On February 21, 2020, the Company entered into a Discovery Collaboration and License Agreement, as amended from time to time (as amended, the “Genentech Collaboration Agreement”), with Genentech. The collaboration focused on the discovery and development of Bicycle peptides directed to biological targets selected by Genentech and aimed at developing up tofour potential development candidates against multiple immuno-oncology targets (Genentech Collaboration Program #1 through #4) suitable for Genentech to advance into further development and commercialization, governed by a joint research committee. Under the Genentech Collaboration Agreement, Genentech also had the option to have the Company perform initial pre-clinical development and optimization activities in exchange for an additional specified milestone payment in the mid single-digit millions for each Genentech Collaboration Program (the “LSR Go Option”).

In January 2024, the joint research committee reached a decision to discontinue research activities associated with Genentech Collaboration Program #3 and, as a result, the Company recognized revenue of $10.4 million during the three months ended March 31, 2024, including $7.5 million related to the expiration of remaining material rights. In January 2025, Genentech provided the Company with a notice of termination for Genentech Collaboration Program #4, effective in March 2025, and the Company recognized revenue of $7.5 million related to the expiration of remaining material rights.

During the three and six months ended June 30, 2025, the Company recognized revenue of $0.4 million and $8.1 million, respectively, and during the three and six months ended June 30, 2024, the Company recognized revenue of $1.7 million and $13.3 million, respectively. As of June 30, 2025 and December 31, 2024, the Company recorded $6.5 million and $14.0 million, respectively, of deferred revenue in connection with the Genentech Collaboration Agreement. In July 2025, Genentech provided the Company with a notice of termination of the Genentech Collaboration Agreement, effective in August 2025. As a result, in the third quarter of 2025, the Company expects to recognize the remaining deferred revenue of approximately $6.5 million, which was allocated to the material right associated with the LSR Go Option for Collaboration Program #1.

Summary of Contract Assets and Liabilities

The following table presents changes in the balances of the Company’s contract liabilities (in thousands):

Contract assets represent research and development services which have been performed but have not yet been billed and are reduced when they are subsequently billed. There wereno contract assets at June 30, 2025 or December 31, 2024.

As of June 30, 2025, the Bayer, Novartis, Ionis, and Genentech deferred revenue balances include $34.8 million, $34.9 million, $3.9 million, and $6.5 million, respectively, allocated to material rights that will commence revenue recognition when the respective option is exercised or when the option expires.

During the three and six months ended June 30, 2025 and 2024, the Company recognized the following revenue as a result of changes in the contract asset and the contract liability balances in the respective periods (in thousands):

10. Income taxes

During the three and six months ended June 30, 2025, the Company recorded an income tax benefit of $0.2 million and $1.3 million, respectively. During the three months ended June 30, 2024, the Company recorded an income tax provision of $0.1 million, and during the six months ended June 30, 2024, the Company recorded an income tax benefit of $0.2 million. The Company is subject to corporate taxation in the U.K. Due to the nature of its business, the Company has generated losses since inception and has therefore not paid U.K. corporation tax. The benefit from income taxes recognized during the three and six months ended June 30, 2025 and the six months ended June 30, 2024 represents the tax impact from operating activities in the United States, which has generated taxable income based on

intercompany service arrangements. The income tax provision recognized during the three months ended June 30, 2024 is due to timing differences associated with discrete items related to share option exercises. Deferred tax assets in the United States do not have a valuation allowance against them because of profits that will be generated by an intercompany service agreement.

The Company regularly assesses its ability to realize its deferred tax assets. Assessing the realization of deferred tax assets requires significant judgment. In determining whether its deferred tax assets are more likely than not realizable, the Company evaluated all available positive and negative evidence, and weighed the evidence based on its objectivity. After consideration of the evidence, including the Company’s history of cumulative net losses in the U.K., the Company has concluded that it is more likely than not that the Company will not realize the benefits of its U.K. deferred tax assets and accordingly the Company has provided a valuation allowance for the full amount of the deferred tax assets in the U.K. as of June 30, 2025 and December 31, 2024. The Company has considered the Company’s history of cumulative net profits in the United States, estimated future taxable income and concluded that it is more likely than not that the Company will realize the benefits of its U.S. deferred tax assets and has not provided a valuation allowance against the deferred tax assets in the United States.

The Company intends to continue to maintain a full valuation allowance on its U.K. deferred tax assets until there is sufficient evidence to support the reversal of all or some portion of these allowances. The release of the valuation allowance would result in the recognition of certain deferred tax assets and an increase to the benefit from income taxes for the period the release is recorded. However, the exact timing and amount of the valuation allowance release are subject to change on the basis of the level of profitability that the Company is able to actually achieve.

The (benefit from) provision for income taxes recorded in the condensed consolidated statements of operations differs from amounts that would result from applying the statutory tax rates to income before taxes primarily because of certain permanent expenses that were not deductible, U.K., federal and state research and development credits, as well as the application of valuation allowances against the U.K. deferred tax assets.

On July 4, 2025, the One Big Beautiful Bill Act (“OBBBA”) was enacted in the United States. The OBBBA includes significant provisions, such as the permanent extension of certain expiring provisions of the Tax Cuts and Jobs Act, modifications to the international tax framework and the restoration of favorable tax treatment for certain business provisions. The legislation has multiple effective dates, with certain provisions effective in 2025 and others implemented through 2027. The Company is currently assessing the OBBBA’s impact on its consolidated financial statements.

11. Commitments and contingencies

Leases

In January 2023, the Company entered into a lease agreement for office and laboratory space in Cambridge, Massachusetts. The lease has a contractual period of approximately three years, which, subject to certain conditions, may have been extended for an additionaltwo years at the Company’s option and the Company concluded that the lease term isthree years, representing the non-cancelable lease period, as it was not reasonably certain that the lease would be extended.

In December 2021, the Company entered into a lease of office and laboratory space in Cambridge, United Kingdom. The lease has a contractual period of 10 years but may be cancelled by the Company on the fifth anniversary of the lease commencement date and the Company concluded that the lease term isfive years, representing the non-cancelable lease period, as it is not reasonably certain that the lease will not be cancelled.

In September 2017, Bicycle Therapeutics Inc. entered into a lease agreement for office and laboratory space in Lexington, Massachusetts, which commenced on January 1, 2018. In March 2022, Bicycle Therapeutics Inc. notified the landlord of its intent to exercise its option to extend the lease, originally set to expire on December 31, 2022, for a successive period through December 31, 2027 which successive period was not included in the original lease term. The Company accounted for the lease extension as a modification of the existing lease and remeasured the operating lease right-of-use asset and operating lease liability by calculating the present value of lease payments, discounted at the

Company’s incremental borrowing rate on the modification date, over the new lease term. In May 2022, the lease was extended.

From time to time, the Company may enter into finance lease agreements for property and equipment. Amortization expense related to finance lease right-of-use assets is recognized on straight-line basis over the earlier of the useful life of the right-of-use asset or the lease term and interest expense for finance leases is recognized based on the effective interest method using the Company’s incremental borrowing rate. As of June 30, 2025 and December 31, 2024, the Company recorded finance lease right-of-use assets of $1.0 million and $1.0 million, respectively, which are included in property and equipment, net, in the condensed consolidated balance sheets. As of June 30, 2025 and December 31, 2024, the Company recorded finance lease liabilities of $1.0 million and $1.0 million, respectively, which are included in accrued expenses and other current liabilities and other long-term liabilities, as applicable, in the condensed consolidated balance sheets.

The components of the Company’s lease expense, which are recorded as a component of research and development expenses and general and administrative expenses in the condensed consolidated statements of operations and comprehensive loss, are as follows (in thousands):

The weighted average remaining operating lease term was 1.6 years and 2.4 years as of June 30, 2025 and 2024, respectively, and the weighted average operating lease discount rate was 7.7% and 7.9% as of June 30, 2025 and 2024, respectively. The weighted average remaining finance lease term was 4.2 years as of June 30, 2025, and the weighted average finance lease discount rate was 9.5% as of June 30, 2025.

The following table summarizes the maturities of the Company’s lease liabilities as of June 30, 2025 (in thousands):

Other commitments

The Company has entered into various agreements with contract research organizations to provide clinical trial services, contract manufacturing organizations to provide clinical trial materials and with vendors for preclinical research studies, synthetic chemistry and other services for operating purposes. These contracts are generally cancelable at any time upon less than 90 days’ prior written notice. The Company is not contractually able to terminate for convenience and avoid any and all future obligations to these vendors. In some cases, the Company is contractually

obligated to make certain minimum payments to the vendors, based on the timing of the termination notification and the exact terms of the agreement.

The Company has also entered into separate agreements with third parties which provide for various future milestone payments upon the achievement of specified development, regulatory, commercial and sales-based milestones with an aggregate total value of$105.9 million, as well as potential future royalty and other payments at percentages ranging from very low to low single digits. These additional milestone payments are contingent upon future events that are not considered probable of achievement as of June 30, 2025. As of June 30, 2025, the Company was unable to estimate the timing or likelihood of achieving any of these milestones.

Legal proceedings

From time to time, the Company or its subsidiaries may become involved in various legal proceedings and claims, either asserted or unasserted, which arise in the ordinary course of business. The Company is currently not subject to any material legal proceedings. At each reporting date, the Company evaluates whether or not a potential loss amount or a potential range of loss is probable and reasonably estimable under the provisions of ASC 450,Contingencies.

Indemnification obligations

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. The Company also has indemnification obligations towards members of its board of directors and officers that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. In addition, the Company has agreed to indemnify certain investors in limited circumstances. The maximum potential amount of future payments the Company could be required to make under these indemnification arrangements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnification obligations. The Company is not aware of any claims under indemnification arrangements, and therefore it has not accrued any liabilities related to such obligations in its condensed consolidated financial statements as of June 30, 2025 and December 31, 2024.

12. Net loss per share

Basic and diluted net loss per share was calculated as follows (in thousands, except share and per share amounts):

The Company’s potentially dilutive securities, which are options to purchase ordinary shares and RSUs, have been excluded from the computation of diluted net loss per share as the effect would be to reduce the net loss per share. Therefore, the weighted average number of ordinary shares outstanding, which includes both ordinary shares and non-voting ordinary shares, used to calculate both basic and diluted net loss per share is the same. The Company excluded the following potentially dilutive ordinary shares, presented based on amounts outstanding at each period end, from the computation of diluted net loss per share for the periods indicated because including them would have had an anti-dilutive effect:

13. Related party transactions

Amendment to Consulting Agreement with Stone Atlanta Estates LLC

Pierre Legault, the former Chairman of the Company’s board of directors is associated with Stone Atlanta Estates LLC, which provided consultancy services to the Company totaling $0.1 million and $0.1 million during the three and six months ended June 30, 2025, respectively, and $47,000 and $0.1 million during the three and six months ended June 30, 2024, respectively. In March 2025, the Company and Mr. Legault entered into an amendment to the consulting agreement, effective as of June 17, 2025, the date of Mr. Legault’s retirement as Chairman. The amendment modifies the compensation payable under the agreement and provides for expiration of the agreement no later than June 30, 2028.

Related Party Participation in Private Placement

The Investors in the Private Placement included certain entities affiliated with Baker Bros. Advisors LP (the “Baker Entities”), an entity which may be deemed a beneficial owner of greater than 10% of the Company’s voting securities. Felix J. Baker, the Chairman of the Company’s board of directors, is a managing member of Baker Bros. Advisors (GP) LLC, the sole general partner of Baker Bros. Advisors LP. In the Private Placement, the Baker Entities purchased an aggregate of 17,114,846 non-voting ordinary shares, nominal value£0.01 per share, for an aggregate purchase price of$366.6 million. The Private Placement was approved in accordance with the Company’s related person transaction policy by the Company’s Related Parties Committee. See Note 11. “Commitments and contingencies” for additional information on indemnities provided to certain investors.

14. Segments and geographic information

The Company operates and manages its business as a single operating segment, which is developing a unique class of chemically synthesized medicines based on its proprietary platform. The Company’s chief operating decision maker (“CODM”) is the Company’s Chief Executive Officer (“CEO”). The CODM reviews consolidated operating results, manages the business on a consolidated basis and utilizes consolidated net loss from the consolidated statements of operations and comprehensive loss as the primary measure of segment profit or loss in making decisions surrounding allocating resources and assessing performance of the Company. The CODM is regularly provided detailed expense information, including expenses by program and expense category, and the CODM makes decisions surrounding capital and personnel allocation using this information on a consolidated basis.

The following table presents information about the Company’s single operating segment, including significant segment expenses, for the three and six months ended June 30, 2025 and 2024 (in thousands):

The Company does not regularly provide the CODM with detailed segment asset information other than what is included in the condensed consolidated balance sheets. Please refer to the condensed consolidated financial statements and the accompanying notes to the condensed consolidated financial statements for segment asset information.

The Company operates intwo geographic regions: the United States and the United Kingdom. Information about the Company’s long-lived assets, including operating and finance lease right-of-use assets, held in different geographic regions is presented in the table below (in thousands):

The Company’s collaboration revenues are attributed to the operations of the Company in the United Kingdom.

15. Subsequent events

Genentech Notice of Termination

In July 2025, Genentech provided the Company with a notice of termination of the Genentech Collaboration Agreement, effective in August 2025. As a result, in the third quarter of 2025, the Company expects to recognize the remaining deferred revenue of approximately $6.5 million, which was allocated to the material right associated with the LSR Go Option for Collaboration Program #1.

Workforce Reduction

In August 2025, the Company announced cost reduction initiatives that are expected to reduce planned operating costs by approximately 30% over the course of the Company’s expected financial runway period, primarily through a workforce reduction that is expected to result in a reduction of approximately 25% of the Company’s current and planned workforce. The Company estimates that it will incur aggregate charges, representing cash expenditure for severance and other employee termination benefits, of approximately $5.3 million, the majority of which is expected to be recognized in the third quarter of 2025.