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Commitments and contingencies | 12 Months Ended
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Dec. 31, 2024
Commitments and contingencies |
Commitments and contingencies | 11. Commitments and contingencies Operating 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 be extended for an additional two years at the Company’s option. The Company concluded that the lease term is three years, representing the non-cancelable lease period, as it is not reasonably certain that the lease will be extended. The annual rent is approximately $2.1 million in the first year of the lease and increases annually with the last year of the lease having annual rent of approximately $2.3 million. The annual rent is payable monthly in advance following a two-month rent-free period. In connection with the lease agreement, the Company has delivered to the landlord a security deposit in the form of a letter of credit of approximately $0.5 million. The Company recorded a right of use asset and lease liability of approximately $5.8 million, respectively, at the lease commencement date, based on the present value of future lease payments, discounted at 9.0%, the Company’s estimated incremental borrowing rate at the commencement of the lease, over the lease term. On December 6, 2021 the Company entered into a lease of new 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. The lease term is five years, representing the non-cancelable lease period, as it is not reasonably certain that the lease will not be cancelled. The Company has a contractual right to renew the lease for a further ten-year period, which also may be cancelled after five years. The annual rent is approximately $3.0 million, payable quarterly in advance beginning in June 2022, following a six-month rent-free period. There was no deposit paid in conjunction with the lease. The Company recorded a ROU asset of approximately $11.6 million and a lease liability of approximately $11.1 million at the lease commencement date, based on the present value of future lease payments, discounted at 6.9%, the Company’s estimated incremental borrowing rate at the commencement of the lease, over the lease term. In October 2017, the Company entered into a lease agreement for office and laboratory space in Building 900, Babraham Research Campus, Cambridge, U.K., which was renewed in December 2021 for five years through December 2026. The annual rent for the lease was approximately $0.6 million. Service charges were also payable based on floor area and are estimated to be approximately $0.2 million per year. In April 2023, the Company entered into a deed of surrender related to the lease, pursuant to which the lease was terminated effective immediately. As a result of the deed, the Company derecognized the lease liability and right of use asset associated with the lease. The Company also paid termination-related fees of $0.3 million in connection with the deed, which were recorded as a loss on lease termination and are included in operating expenses in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2023. 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 conjunction with the lease agreement, Bicycle Therapeutics Inc. paid a security deposit of $0.2 million. The deposit is recorded in other assets in the consolidated balance sheets. 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 change in lease term as a modification of the existing lease and remeasured the ROU asset and lease liability by calculating the present value of lease payments, discounted at 7.0%, the Company’s incremental borrowing rate at the date of the modification of the lease, over the remaining lease term. In May 2022, the lease was extended. The payments for the extended lease are approximately $0.2 million for the remainder of 2022, $0.7 million in 2023, and increases annually pursuant to an escalation clause with the last year of the lease term having a per annum fixed rent obligation of $0.8 million. Finance Leases From time to time, the Company may enter into finance lease agreements for property and equipment. As of December 31, 2024, the Company recorded finance lease right-of-use assets of $1.0 million, which are included in property and equipment, net, in the consolidated balance sheets. As of December 31, 2024, the Company recorded finance lease liabilities of $1.0 million, which are included in accrued expenses and other current liabilities and other long-term liabilities, as applicable, in the consolidated balance sheets. No finance lease right-of-use assets or liabilities were recorded as of December 31, 2023. ​ The components of the Company’s lease expense are as follows (in thousands):
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | Year Ended
​ | December 31,
​ | 2024 |  | 2023 |  | 2022
Operating lease cost | $ | 5,299 |  | $ | 5,408 |  | $ | 3,790
Variable lease cost |  | 2,924 | ​ |  | 2,777 | ​ |  | 1,643
Finance lease cost: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Amortization of finance lease right-of-use assets | ​ | 53 | ​ | ​ | — | ​ | ​ | —
Interest on finance lease liabilities | ​ | 23 | ​ | ​ | — | ​ | ​ | —
Total finance lease cost | $ | 76 | ​ | $ | — | ​ | $ | —
​ The weighted average remaining operating lease term was 2.0 years and 2.9 years as of December 31, 2024 and 2023, respectively, and the weighted average operating lease discount rate was 7.8% and 7.9% as of December 31, 2024 and 2023, respectively. The weighted average remaining finance lease term was 4.7 years as of December 31, 2024, and the weighted average finance lease discount rate was 9.5% as of December 31, 2024. ​ The following table summarizes the maturities of the Company’s lease liabilities as of December 31, 2024 (in thousands): ​
​ | ​ | ​ | ​ | ​ | ​ | ​
Year Ending December 31, |  | Operating Leases |  | Finance Leases
2025 |  | $ | 5,818 |  | $ | 256
2026 |  | ​ | 3,325 |  | ​ | 256
2027 | ​ | ​ | 821 | ​ | ​ | 256
2028 | ​ | ​ | — | ​ | ​ | 256
2029 | ​ | ​ | — | ​ | ​ | 192
Present value adjustment |  | ​ | (646) |  | ​ | (224)
Total lease liabilities | ​ | ​ | 9,318 | ​ | ​ | 992
Less: current lease liabilities | ​ |  | (5,328) | ​ |  | (175)
Long term lease liabilities | ​ | $ | 3,990 | ​ | $ | 817
​ 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 $166.2 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 December 31, 2024. As of December 31, 2024, the Company was unable to estimate the timing or likelihood of achieving 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 not currently 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. In addition, the Company 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 consolidated financial statements as of December 31, 2024 and 2023.

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