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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 September 30, 2025

☐	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 Applicable
(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)

Blocks A & B, Portway Building, Granta Park Great Abington, Cambridge, United Kingdom		CB21 6GS
(Address of principal executive offices)		(Zip Code)

Registrant’s telephone number, including area code: +44 1223 261503

Securities registered pursuant to Section 12(b) of the Act:


Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Ordinary shares, nominal value £0.01 per share*	n/a	The Nasdaq Stock Market LLC
American Depositary Shares, each representing one ordinary share, nominal value £0.01 per share	BCYC	The Nasdaq Stock Market LLC

* Not for trading, but only in connection with the listing of the American Depositary Shares on the Nasdaq Global Select Market.

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ⌧ No ◻

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ⌧ No ◻

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.


Large accelerated filer ⌧	Accelerated filer ◻
Non-accelerated filer ◻	Smaller reporting company ⌧
	Emerging growth company ◻

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ⌧

As of October 27, 2025, the registrant had 49,929,952 ordinary shares, nominal value £0.01 per share, and 19,437,944 non-voting ordinary shares, nominal value £0.01 per share, outstanding.

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		Page
PART I - FINANCIAL INFORMATION		1

Item 1.	Financial Statements (unaudited)	1
	Condensed Consolidated Balance Sheets	1
	Condensed Consolidated Statements of Operations and Comprehensive Loss	2
	Condensed Consolidated Statements of Shareholders’ Equity	3
	Condensed Consolidated Statements of Cash Flows	5
	Notes to Condensed Consolidated Financial Statements	6

Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	25

Item 3.	Quantitative and Qualitative Disclosure About Market Risk	40

Item 4.	Controls and Procedures	41

PART II - OTHER INFORMATION		41

Item 1.	Legal Proceedings	41

Item 1A.	Risk Factors	41

Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	100

Item 3.	Defaults Upon Senior Securities	101

Item 4.	Mine Safety Disclosures	101

Item 5.	Other Information	101

Item 6.	Exhibits	102

SIGNATURES

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SPECIAL NOTE REGARDING FORWARD LOOKING STATEMENTS

This Quarterly Report on Form 10-Q, or this Quarterly Report, contains forward-looking statements which are made pursuant to the safe harbor provisions of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act. These statements may be identified by such forward-looking terminology as “will,” “may,” “should,” “expects,” “intends,” “plans,” “anticipates,” “believes,” “estimates,” “predicts,” “potential,” “continue” or variations of these words or similar expressions that are intended to identify forward-looking statements, although not all forward-looking statements contain these words. Any forward-looking statement involves known and unknown risks, uncertainties and other factors that may cause our actual results, levels of activity, performance or achievements to differ materially from any future results, levels of activity, performance or achievements expressed or implied by such forward-looking statement. Forward-looking statements include statements, other than statements of historical fact, about, among other things:

●

the initiation, timing, progress and results of our preclinical studies and clinical trials, and our research and development programs;

●

our ability to advance our product candidates into, and successfully complete, clinical trials;

●

our reliance on the success of product candidates in our pipeline programs for our Bicycle^® Drug Conjugate, or BDC^® molecules, Bicycle Tumor-Targeted Immune Cell Agonist^®, or Bicycle TICA^®molecules, and Bicycle Radioconjugates, or BRC^® molecules, as well as our other pipeline programs;

●

our ability to utilize our screening platform to identify and advance additional product candidates into clinical development;

●

the timing or likelihood of regulatory filings and approvals;

●

the commercialization of our product candidates, if approved;

●

our ability to develop sales and marketing capabilities;

●

the pricing, coverage and reimbursement of our product candidates, if approved;

●

the implementation of our business model, strategic plans for our business, product candidates and technology;

●

the scope of protection we are able to establish and maintain for intellectual property rights covering our product candidates and technology;

●

our ability to operate our business without infringing the intellectual property rights and proprietary technology of third parties;

●

costs associated with defending intellectual property infringement, product liability and other claims;

●

regulatory development in the United States, the United Kingdom and other jurisdictions and changes to the laws and regulations of England and Wales, and other jurisdictions;

●

estimates of our expenses, future revenues, capital requirements, share performance and our needs for additional financing;

●

the potential benefits of strategic collaboration agreements and our ability to enter into additional strategic arrangements;

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●

our ability to maintain and establish collaborations or obtain additional grant funding;

●

the rate and degree of market acceptance of any approved products;

●

developments relating to our competitors and our industry, including competing therapies;

●

our ability to effectively manage our anticipated growth;

●

our hiring plans and our ability to attract and retain qualified employees and key personnel;

●

the impact of adverse global economic conditions, including those arising from changes in global trade policies, on our operations and the potential disruption in the operations and business of third-party manufacturers, contract research organizations, or CROs, other service providers, and collaborators with whom we conduct business;

●

potential adverse developments affecting the financial services industry;

●

potential business interruptions resulting from geo-political actions, such as war and terrorism, or the perception that such hostilities may be imminent;

●

our failure or perceived failure to comply with existing or future laws, regulations, contracts, self-regulatory schemes, standards, and other obligations related to data privacy and security (including our ability to identify and respond to potential future security incidents); and

●

other risks and uncertainties, including those listed under the caption “Risk Factors.”

Although we believe that we have a reasonable basis for each forward-looking statement contained in this Quarterly Report, these statements are based on our estimates or projections of the future that are subject to known and unknown risks and uncertainties and other important factors that may cause our actual results, level of activity, performance, experience or achievements to differ materially from those expressed or implied by any forward-looking statement. These risks, uncertainties and other factors are described in greater detail under the caption “Risk Factors” in Part II, Item 1A and elsewhere in this Quarterly Report. As a result of the risks and uncertainties, the results or events indicated by the forward-looking statements may not occur. Undue reliance should not be placed on any forward-looking statement.

Statements that “we believe” and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based on information available to us as of the date of this Quarterly Report. While we believe that information provides a reasonable basis for these statements, that information may be limited or incomplete. Our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all relevant information. These statements are inherently uncertain, and investors are cautioned not to unduly rely on these statements.

In addition, any forward-looking statement in this Quarterly Report represents our views only as of the date of this Quarterly Report and should not be relied upon as representing our views as of any subsequent date. We anticipate that subsequent events and developments may cause our views to change. Although we may elect to update these forward-looking statements publicly at some point in the future, we specifically disclaim any obligation to do so, except as required by applicable law. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make.

iii

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PART I - FINANCIAL INFORMATION

Item 1. Financial Statements.

Bicycle Therapeutics plc

Condensed Consolidated Balance Sheets

(In thousands, except share and per share data)

(Unaudited)


	September 30,		December 31,
	2025		2024
Assets
Current assets:
Cash and cash equivalents	$	648,325	$	879,520
Prepaid expenses and other current assets		23,231		13,432
Research and development incentives receivable		67,263		35,653
Total current assets		738,819		928,605
Property and equipment, net		6,861		9,516
Operating lease right-of-use assets		4,562		7,673
Other assets		13,712		11,074
Total assets	$	763,954	$	956,868
Liabilities and shareholders’ equity
Current liabilities:
Accounts payable	$	12,653	$	15,793
Accrued expenses and other current liabilities		44,368		41,246
Deferred revenue, current portion		12,261		10,191
Total current liabilities		69,282		67,230
Operating lease liabilities, net of current portion		981		3,990
Deferred revenue, net of current portion		74,119		91,467
Other long‑term liabilities		1,093		1,121
Total liabilities		145,475		163,808
Commitments and contingencies (Note 11)
Shareholders’ equity:
Ordinary shares, including non-voting ordinary shares, £0.01 nominal value; 159,690,229 and 155,876,645 shares authorized on September 30, 2025 and December 31, 2024, respectively; 69,306,511 and 69,061,418 shares issued and outstanding at September 30, 2025 and December 31, 2024, respectively		894		890
Additional paid-in capital		1,500,653		1,472,842
Accumulated other comprehensive (loss) income		(3,471)		119
Accumulated deficit		(879,597)		(680,791)
Total shareholders’ equity		618,479		793,060
Total liabilities and shareholders’ equity	$	763,954	$	956,868

The accompanying notes are an integral part of the condensed consolidated financial statements

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Bicycle Therapeutics plc

Condensed Consolidated Statements of Operations and Comprehensive Loss

(In thousands, except share and per share data)

(Unaudited)


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Collaboration revenue	$	11,734	$	2,676	$	24,631	$	31,567
Operating expenses:
Research and development		58,426		48,265		188,513		123,188
General and administrative		18,859		18,257		58,475		50,588
Total operating expenses		77,285		66,522		246,988		173,776
Loss from operations		(65,551)		(63,846)		(222,357)		(142,209)
Other income (expense):
Interest and other income		6,700		10,583		22,587		23,981
Interest expense		(44)		(33)		(149)		(1,678)
Loss on extinguishment of debt		—		(954)		—		(954)
Total other income, net		6,656		9,596		22,438		21,349
Net loss before income tax provision		(58,895)		(54,250)		(199,919)		(120,860)
Provision for (benefit from) income taxes		205		(3,448)		(1,113)		(3,683)
Net loss	$	(59,100)	$	(50,802)	$	(198,806)	$	(117,177)
Net loss per share, basic and diluted	$	(0.85)	$	(0.74)	$	(2.87)	$	(2.15)
Weighted average ordinary shares outstanding, basic and diluted		69,303,746		68,988,858		69,251,291		54,566,490

Comprehensive loss:
Net loss	$	(59,100)	$	(50,802)	$	(198,806)	$	(117,177)
Other comprehensive income (loss):
Foreign currency translation adjustment		(108)		(2,093)		(3,590)		(1,881)
Total comprehensive loss	$	(59,208)	$	(52,895)	$	(202,396)	$	(119,058)

The accompanying notes are an integral part of the condensed consolidated financial statements

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Bicycle Therapeutics plc

Condensed Consolidated Statements of Shareholders’ Equity

(In thousands, except share data)

(Unaudited)


						Accumulated
				Additional		Other				Total
	Ordinary Shares			Paid‑in		Comprehensive		Accumulated		Shareholders’
	Shares	Amount		Capital		Income (Loss)		Deficit		Equity
Balance at December 31, 2024	69,061,418	$	890	$	1,472,842	$	119	$	(680,791)	$	793,060
Issuance of ADSs upon settlement of restricted share units	140,937		2		—		—		—		2
Share-based compensation expense	—		—		9,605		—		—		9,605
Foreign currency translation adjustment	—		—		—		(1,580)		—		(1,580)
Net loss	—		—		—		—		(60,754)		(60,754)
Balance at March 31, 2025	69,202,355		892		1,482,447		(1,461)		(741,545)		740,333
Issuance of ADSs upon settlement of restricted share units	51,589		1		—		—		—		1
Share-based compensation expense	—		—		9,435		—		—		9,435
Foreign currency translation adjustment	—		—		—		(1,902)		—		(1,902)
Net loss	—		—		—		—		(78,952)		(78,952)
Balance at June 30, 2025	69,253,944		893		1,491,882		(3,363)		(820,497)		668,915
Issuance of ADSs upon settlement of restricted share units	52,567		1		—		—		—		1
Share-based compensation expense	—		—		8,771		—		—		8,771
Foreign currency translation adjustment	—		—		—		(108)		—		(108)
Net loss	—		—		—		—		(59,100)		(59,100)
Balance at September 30, 2025	69,306,511	$	894	$	1,500,653	$	(3,471)	$	(879,597)	$	618,479

The accompanying notes are an integral part of the condensed consolidated financial statements

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Bicycle Therapeutics plc

Condensed Consolidated Statements of Shareholders’ Equity

(In thousands, except share data)

(Unaudited)


						Accumulated
				Additional		Other				Total
	Ordinary Shares			Paid‑in		Comprehensive		Accumulated		Shareholders’
	Shares	Amount		Capital		Income (Loss)		Deficit		Equity
Balance at December 31, 2023	42,431,766	$	550	$	883,446	$	(1,304)	$	(511,760)	$	370,932
Issuance of ADSs upon exercise of share options	133,735		2		1,868		—		—		1,870
Issuance of ADSs upon settlement of restricted share units	67,096		1		—		—		—		1
Share-based compensation expense	—		—		9,282		—		—		9,282
Foreign currency translation adjustment	—		—		—		526		—		526
Net loss	—		—		—		—		(26,563)		(26,563)
Balance at March 31, 2024	42,632,597		553		894,596		(778)		(538,323)		356,048
Issuance of ADSs upon exercise of share options	351,099		5		4,495		—		—		4,500
Issuance of ADSs and non-voting ordinary shares, net of commissions and offering expenses of $11.4 million	25,933,706		331		543,796		—		—		544,127
Issuance of ADSs upon settlement of restricted share units	23,840		—		—		—		—		—
Share-based compensation expense	—		—		9,264		—		—		9,264
Foreign currency translation adjustment	—		—		—		(314)		—		(314)
Net loss	—		—		—		—		(39,812)		(39,812)
Balance at June 30, 2024	68,941,242		889		1,452,151		(1,092)		(578,135)		873,813
Issuance of ADSs upon exercise of share options	50,866		1		911		—		—		912
Issuance of ADSs upon settlement of restricted share units	23,863		—		—		—		—		—
Share-based compensation expense	—		—		9,202		—		—		9,202
Foreign currency translation adjustment	—		—		—		(2,093)		—		(2,093)
Net loss	—		—		—		—		(50,802)		(50,802)
Balance at September 30, 2024	69,015,971	$	890	$	1,462,264	$	(3,185)	$	(628,937)	$	831,032

The accompanying notes are an integral part of the condensed consolidated financial statements

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Bicycle Therapeutics plc

Condensed Consolidated Statements of Cash Flows

(In thousands)

(Unaudited)


	Nine Months Ended
	September 30,
	2025		2024
Cash flows from operating activities:
Net loss	$	(198,806)	$	(117,177)
Adjustments to reconcile net loss to net cash used in operating activities:
Share-based compensation expense		27,811		27,748
Depreciation and amortization		5,086		5,470
Non-cash interest		—		211
Loss on extinguishment of debt		—		954
Deferred income tax benefit		(1,693)		(4,192)
Other non-cash charges		—		1,036
Changes in operating assets and liabilities:
Research and development incentives receivable		(28,395)		(31,107)
Prepaid expenses and other assets		(9,946)		(5,244)
Operating lease right‑of‑use assets		3,407		3,326
Accounts payable		(3,990)		(7,593)
Accrued expenses and other current liabilities		2,093		5,952
Operating lease liabilities		(4,046)		(3,626)
Deferred revenue		(21,850)		(31,275)
Other long-term liabilities		—		189
Net cash used in operating activities		(230,329)		(155,328)
Cash flows from investing activities:
Purchases of property and equipment		(1,776)		(867)
Net cash used in investing activities		(1,776)		(867)
Cash flows from financing activities:
Payments on debt		—		(31,863)
Proceeds from the issuance of ADSs and non-voting ordinary shares, net of issuance costs		—		544,127
Proceeds from the exercise of share options and settlement of restricted share units		4		7,283
Payments of finance lease obligations		(120)		—
Net cash (used in) provided by financing activities		(116)		519,547
Effect of exchange rate changes on cash, cash equivalents and restricted cash		1,026		1,087
Net (decrease) increase in cash, cash equivalents and restricted cash		(231,195)		364,439
Cash, cash equivalents and restricted cash at beginning of period		880,067		526,970
Cash, cash equivalents and restricted cash at end of period	$	648,872	$	891,409
Reconciliation of cash, cash equivalents and restricted cash
Cash and cash equivalents	$	648,325	$	890,862
Restricted cash in prepaid expenses and other current assets, and other assets, respectively		547		547
Total cash, cash equivalents and restricted cash	$	648,872	$	891,409
Supplemental disclosure of cash flow information
Cash paid for interest on debt	$	—	$	1,373
Cash paid for interest on finance lease obligations	$	58	$	—
Cash (received from) paid for income taxes	$	(888)	$	792
Cash paid for amounts included in the measurement of operating lease liabilities	$	4,461	$	4,333
Changes in purchases of property and equipment in accounts payable and accrued expenses	$	63	$	9
Property and equipment obtained under finance leases	$	—	$	1,102

The accompanying notes are an integral part of the condensed consolidated financial statements

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Bicycle Therapeutics plc

Notes to Condensed Consolidated Financial Statements
(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 September 30, 2025, the Company had cash and cash equivalents of $648.3 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).

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The Company has incurred recurring losses since inception, including net losses of $59.1 million and $198.8 million for the three and nine months ended September 30, 2025, respectively, and $50.8 million and $117.2 million for the three and nine months ended September 30, 2024, respectively. As of September 30, 2025, the Company had an accumulated deficit of $879.6 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 wars involving Ukraine and Israel, inflation and interest rates, and fluctuations in monetary exchange rates. While

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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 September 30, 2025, the condensed consolidated statements of operations and comprehensive loss and condensed consolidated statements of shareholders’ equity for the three and nine months ended September 30, 2025 and 2024, and condensed consolidated statements of cash flows for the nine months ended September 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 September 30, 2025, the results of its operations for the three and nine months ended September 30, 2025 and 2024 and its cash flows for the nine months ended September 30, 2025 and 2024. The results for the three and nine months ended September 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 $7.6 million and $28.5

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million during the three and nine months ended September 30, 2025, respectively, and $8.5 million and $31.1 million during the three and nine months ended September 30, 2024, respectively. As of September 30, 2025, the Company had research and development incentives receivable of $67.3 million. In October 2025, the Company received $38.2 million of research and development incentives related to relevant expenditures incurred in the year ended December 31, 2024.

Recently adopted accounting pronouncements

In November 2023, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“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 No. 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 No. 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 FASB issued ASU No. 2023-09, Income Taxes (Topic 740) Improvements to Income Tax Disclosures, 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 impact of the adoption of ASU No. 2023-09 on its consolidated financial statement 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 September 30, 2025

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and December 31, 2024, the Company had cash equivalents of $396.5 million and $664.9 million, respectively, consisting of money market funds that are primarily invested in U.S. Treasury securities, which are considered Level 1 assets. As of each of September 30, 2025, and December 31, 2024, there were no other assets or liabilities measured at fair value on a recurring basis.

As of each of September 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):


	September 30,		December 31,
	2025		2024
Laboratory equipment	$	17,420	$	14,658
Leasehold improvements		11,708		10,903
Finance lease right-of-use assets		1,106		1,033
Computer equipment and software		635		581
Furniture and office equipment		864		1,290
		31,733		28,465
Less: Accumulated depreciation and amortization		(24,872)		(18,949)
	$	6,861	$	9,516

Depreciation and amortization expense was $1.8 million and $5.1 million for the three and nine months ended September 30, 2025, respectively, and $2.2 million and $5.5 million for the three and nine months ended September 30, 2024, respectively. Depreciation and amortization expense for the three and nine months ended September 30, 2025 included amortization expense of $0.1 million and $0.2 million, respectively, related to property and equipment obtained under finance leases. There was no amortization expense recorded related to property and equipment obtained under finance leases for the three and nine months ended September 30, 2024.

5. Accrued expenses and other current liabilities

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


	September 30,		December 31,
	2025		2024
Accrued employee compensation and benefits	$	14,881	$	16,272
Accrued external research and development expenses		21,493		14,978
Accrued professional fees		3,028		4,196
Current portion of operating lease liabilities		4,563		5,328
Current portion of finance lease liabilities		199		175
Other		204		297
	$	44,368	$	41,246

In August 2025, the Company announced cost reduction initiatives that the Company anticipates will 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 expects the workforce reduction to be substantially completed by the fourth quarter of 2025, and that it will incur aggregate charges, representing cash expenditure for severance and other employee termination benefits, of approximately $5.3 million. During the three months ended September 30, 2025, the Company recognized charges of $4.1 million of which $3.3 million were included in research and development expenses and $0.8 million were included in general and administrative expenses in the Company’s condensed consolidated

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statements of operations and comprehensive loss. Of the charges recognized during the three months ended September 30, 2025, $2.0 million represented cash expenditure for severance and other employee termination benefits paid during the period, and the remaining $2.1 million in unpaid benefits are included in accrued employee compensation and benefits within accrued expenses and other current liabilities in the Company’s condensed consolidated balance sheet as of September 30, 2025.

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 nine months ended September 30, 2025, the Company paid the remaining $0.4 million, and there are no remaining unpaid benefits outstanding as of September 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 the Wall Street Journal prime 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. The Company recognized a loss on extinguishment of debt of $1.0 million during the three and nine months ended September 30, 2024 in connection with the repayment and termination of the Loan Agreement. Upon termination of the Loan Agreement, all security interests granted to the secured parties thereunder were terminated and released.

Interest expense associated with the Loan Agreement was zero and $1.6 million for the three and nine months ended September 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 to one 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 rank pari passu in all respects with the ordinary shares except for the following:

●

a holder of non-voting ordinary shares shall, in relation to the non-voting ordinary shares held, have no right to receive notice of, or to attend or vote at, any general meeting of shareholders save in relation to a variation of class rights of the non-voting ordinary shares;

●

the non-voting ordinary shares shall be re-designated as ordinary shares by the Company’s board of directors, or a duly authorized committee or representative thereof, upon receipt of a re-designation notice and otherwise subject to the terms and conditions set out in the terms of issue. A holder of non-voting ordinary shares shall not be entitled to have any non-voting ordinary shares re-designated as ordinary shares where such re-designation would result in such holder thereof beneficially owning (for purposes of section 13(d) of the Exchange Act), when aggregated with “affiliates” and “group” members with whom

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such holder is required to aggregate beneficial ownership for the purposes of section 13(d) of the Exchange Act, in excess of 9.99% of any class of the Company’s securities registered under the Exchange Act (which percentage may be increased or decreased on a holder-by-holder basis subject to the provisions set out in the terms of issue); and

●

the non-voting ordinary shares shall be re-designated as ordinary shares automatically upon transfer of a non-voting ordinary share by its holder to any person that is not an “affiliate” or “group” member with whom such holder is required to aggregate beneficial ownership for purposes of section 13(d) of the Exchange Act. This automatic re-designation shall only be in respect of the non-voting ordinary shares that are subject to such transfer.

As of September 30, 2025, and December 31, 2024, the Company had not declared any dividends.

As of September 30, 2025, and December 31, 2024, the Company’s authorized share capital consisted of 159,690,229 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 September 30, 2025, there were 49,868,567 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 a four-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. In the event of a change of control of the Company, as defined in the 2024 Inducement Plan, any outstanding awards under the 2024 Inducement Plan will vest in full immediately prior to such change of control.

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 September 30, 2025, there were 879,725 shares available for future issuance under the 2024 Inducement Plan.

As of September 30, 2025, there were options outstanding to purchase 620,275 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

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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 initial public offering (“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 September 30, 2025, there were 1,753,403 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 a three-year service period in three equal annual installments for new non-employee director grants, or a four-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 a one-year service period in four 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 receive one of the Company’s ordinary shares upon vesting. RSUs granted to employees and consultants vest over a four-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 a three-year service period in three equal annual installments for new non-employee director grants or over a one-year service period in four 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 September 30, 2025, there were options outstanding to purchase 7,280,518 shares and RSUs outstanding for 1,790,210 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 September 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 a three-year service period, or over a four-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.

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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 September 30, 2025, the total number of shares available for issuance under the ESPP was 2,007,671 ordinary shares. As of September 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):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Research and development expenses	$	3,645	$	4,444	$	12,150	$	13,574
General and administrative expenses		5,126		4,758		15,661		14,174
	$	8,771	$	9,202	$	27,811	$	27,748

Share options

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


	Number of			Weighted
	Shares	Weighted		Average	Aggregate
	Underlying	Average		Contractual	Intrinsic
	Share Options	Exercise Price		Term	Value
				(in years)	(in thousands)
Outstanding as of December 31, 2024	8,748,726	$	22.41	6.81	$	9,559
Granted	1,896,338		12.51	—		—
Forfeited	(455,268)		22.77	—		—
Outstanding as of September 30, 2025	10,189,796	$	20.57	6.44	$	3,078
Vested and expected to vest as of September 30, 2025	10,189,796	$	20.57	6.44	$	3,078
Options exercisable as of September 30, 2025	6,615,205	$	22.13	5.22	$	2,975

The weighted average grant-date fair value of share options granted during the nine months ended September 30, 2025 and 2024 was $8.56 per share and $13.40 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 was zero for each of the three and nine months ended September 30, 2025, respectively, and $0.3 million and $4.9 million for the three and nine months ended September 30, 2024.

For the three and nine months ended September 30, 2025, the Company recorded share-based compensation expense for share options granted of $6.3 million and $19.9 million, respectively, and for the three and nine months ended September 30, 2024, the Company recorded share-based compensation expense for share options granted of $7.4 million and $22.2 million, respectively.

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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:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Risk-free interest rate	3.9	%	3.9	%	4.3	%	4.0	%
Expected volatility	73.5	%	74.1	%	74.1	%	77.3	%
Expected dividend yield	—		—		—		—
Expected term (in years)	6.0		6.1		6.1		6.1

As of September 30, 2025, total unrecognized compensation expense related to the unvested employee and director share options was $39.1 million, which is expected to be recognized over a weighted average period of 2.3 years.

Restricted share units

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


	Number of Shares	Weighted-Average
	Underlying RSUs	Grant Date Fair Value
Unvested at December 31, 2024	674,262	$	22.96
Granted	1,447,927		13.82
Vested and settled	(245,093)		24.38
Vested and deferred⁽¹⁾	(43,467)		15.49
Forfeited	(128,886)		14.63
Unvested outstanding at September 30, 2025	1,704,743		15.83
Vested but subject to deferred settlement at December 31, 2024⁽¹⁾	42,000		18.07
Vested and deferred⁽¹⁾	43,467		15.49
Vested but subject to deferred settlement at September 30, 2025⁽¹⁾	85,467		16.76
Outstanding at September 30, 2025	1,790,210	$	15.81

(1)

The Company has granted certain RSUs to the Company’s non-employee directors which provide for deferred settlement of the RSUs to a specified date following the first to occur of (i) the date of the director’s separation from service, (ii) the date of the director’s disability, (iii) the date of the director’s death, or (iv) the date of a change in control event.

The fair value of RSUs that vested during the three and nine months ended September 30, 2025 was $0.5 million and $3.1 million, respectively, and during the three and nine months ended September 30, 2024 was $0.8 million and $3.0 million, respectively.

Total share-based compensation expense for RSUs granted was $2.5 million and $7.9 million for the three and nine months ended September 30, 2025, respectively, and was $1.8 million and $5.5 million for the three and nine months ended September 30, 2024, respectively. As of September 30, 2025, the total unrecognized compensation expense related to unvested RSUs was $21.6 million, which is expected to be recognized over a weighted-average period of 2.8 years.

9. Significant agreements

For the three and nine months ended September 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

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condensed consolidated statements of operations and comprehensive loss from these arrangements (in thousands):


	Three Months				Nine Months
	Ended				Ended
	September 30,				September 30,
	2025		2024		2025		2024
Collaboration revenue
Bayer	$	1,016	$	834	$	2,873	$	2,496
Novartis		2,181		1,276		5,077		6,301
Ionis		2,000		—		2,000		8,881
Genentech		6,537		566		14,681		13,889
Total collaboration revenue	$	11,734	$	2,676	$	24,631	$	31,567

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 nine months ended September 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 to two specified targets, under the oversight of a joint research committee.

During the three and nine months ended September 30, 2025, the Company recognized revenue of $1.0 million and $2.9 million, respectively, and during the three and nine months ended September 30, 2024, the Company recognized revenue of $0.8 million and $2.5 million, respectively, in connection with the Bayer Collaboration Agreement. As of September 30, 2025 and December 31, 2024, the Company recorded deferred revenue of $40.4 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 to two specified targets, under the oversight of a joint steering committee.

During the three and nine months ended September 30, 2025, the Company recognized revenue of $2.2 million and $5.1 million, respectively, and during the three and nine months ended September 30, 2024, the Company recognized revenue of $1.3 million and $6.3 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 September 30, 2025 and December 31, 2024, the Company recorded deferred revenue of $42.1 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

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remaining revenue allocated to material rights is expected to be recognized upon exercise or expiration of the respective options within approximately six 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. In July 2025, a product incorporating TfR1 Bicycle molecules under the Ionis Agreements achieved acceptance of an investigational new drug application (“IND”) upon which Ionis paid the Company $2.0 million. As a result, the transaction price increased from $37.8 million to $39.8 million, and the Company recognized revenue of $2.0 million during the third quarter of 2025.

As of September 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. For each of the three and nine months ended September 30, 2025, the Company recognized revenue of $2.0 million in connection with the Ionis Agreements. For the three and nine months ended September 30, 2024, the Company recognized revenue of zero and $8.9 million, respectively, in connection with the Ionis Agreements. As of September 30, 2025, and December 31, 2024, the Company recorded deferred revenue of $3.8 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 to seven 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 to four 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. In July 2025, Genentech provided the Company with a notice of termination of the Genentech Collaboration Agreement, effective in August 2025. As a result, the Company recognized the remaining deferred

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revenue under the arrangement of $6.5 million, which was allocated to the material right associated with the LSR Go Option for Collaboration Program #1, during the three months ended September 30, 2025.

During the three and nine months ended September 30, 2025, the Company recognized revenue of $6.5 million and $14.7 million, respectively, and during the three and nine months ended September 30, 2024, the Company recognized revenue of $0.6 million and $13.9 million, respectively, in connection with the Genentech Collaboration Agreement. As of September 30, 2025 and December 31, 2024, the Company recorded zero and $14.0 million, respectively, of deferred revenue in connection with the Genentech Collaboration Agreement.

Summary of Contract Assets and Liabilities

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


	Beginning Balance						Impact of		Ending Balance
	January 1,						Exchange		September 30,
	2025		Additions		Deductions		Rates		2025
Contract liabilities:
Deferred revenue
Bayer collaboration deferred revenue	$	39,960	$	619	$	(2,873)	$	2,699	$	40,405
Novartis collaboration deferred revenue		44,073		—		(5,077)		3,137		42,133
Ionis collaboration deferred revenue		3,587		—		—		255		3,842
Genentech collaboration deferred revenue		14,038		—		(14,681)		643		—
Total deferred revenue	$	101,658	$	619	$	(22,631)	$	6,734	$	86,380


	Beginning Balance						Impact of		Ending Balance
	January 1,						Exchange		December 31,
	2024		Additions		Deductions		Rates		2024
Contract liabilities:
Deferred revenue
Bayer collaboration deferred revenue	$	43,618	$	296	$	(3,393)	$	(561)	$	39,960
Novartis collaboration deferred revenue		50,008		3,000		(8,161)		(774)		44,073
Ionis collaboration deferred revenue		12,464		90		(8,881)		(86)		3,587
Genentech collaboration deferred revenue		29,104		—		(14,840)		(226)		14,038
Total deferred revenue	$	135,194	$	3,386	$	(35,275)	$	(1,647)	$	101,658

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 were no contract assets at September 30, 2025 or December 31, 2024.

As of September 30, 2025, the Bayer, Novartis and Ionis deferred revenue balances include $34.2 million, $34.2 million and $3.8 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 nine months ended September 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):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Revenue recognized in the period from:
Revenue recognized based on proportional performance	$	3,197	$	2,676	$	8,581	$	21,126
Revenue recognized based on expiration of material rights		6,537		—		14,050		10,576
Revenue recognized based on changes in transaction price		2,000		—		2,000		(135)
Total	$	11,734	$	2,676	$	24,631	$	31,567

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10. Income taxes

During the three months ended September 30, 2025, the Company recorded an income tax provision of $0.2 million and during the nine months ended September 30, 2025, the Company recorded an income tax benefit of $1.1 million. During the three and nine months ended September 30, 2024, the Company recorded an income tax benefit of $3.4 million and $3.7 million, respectively. 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 provision for (benefit from) income taxes recognized during the three and nine months ended September 30, 2025 and 2024, represents the tax impact from operating activities in the United States, which has generated taxable income based on intercompany service arrangements. 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 September 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 provision for (benefit from) 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 provisions of the OBBBA did not have a material impact on the Company’s condensed consolidated financial statements as of and for the three and nine months ended September 30, 2025, and the Company does not expect the future provisions of the OBBBA to have a material 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 Company concluded that the lease term is three years, representing the non-cancelable lease period.

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

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of the lease commencement date. The Company concluded that 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.

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 September 30, 2025 and December 31, 2024, the Company recorded finance lease right-of-use assets of $0.9 million and $1.0 million, respectively, which are included in property and equipment, net, in the condensed consolidated balance sheets. As of September 30, 2025 and December 31, 2024, the Company recorded finance lease liabilities of $0.9 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):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Operating lease cost	$	1,287	$	1,355	$	3,824	$	4,034
Variable lease cost		921		760		2,495		2,104
Finance lease cost:
Amortization of finance lease right-of-use assets		55		—		162		—
Interest on finance lease liabilities		21		—		65		—
Total finance lease cost	$	76	$	—	$	227	$	—

The weighted average remaining operating lease term was 1.4 years and 2.2 years as of September 30, 2025 and 2024, respectively, and the weighted average operating lease discount rate was 7.5% and 7.8% as of September 30, 2025 and 2024, respectively. The weighted average remaining finance lease term was 4.0 years as of September 30, 2025, and the weighted average finance lease discount rate was 9.5% as of September 30, 2025.

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


Year Ending December 31,	Operating Leases		Finance Leases
2025	$	1,505	$	91
2026		3,464		274
2027		821		274
2028		—		274
2029		—		206
Present value adjustment		(246)		(180)
Total lease liabilities		5,544		939
Less: current lease liabilities		(4,563)		(199)
Long term lease liabilities	$	981	$	740

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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 $105.8 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 September 30, 2025. As of September 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 September 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):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Numerator:
Net loss	$	(59,100)	$	(50,802)	$	(198,806)	$	(117,177)
Denominator:
Weighted average ordinary shares outstanding, basic and diluted		69,303,746		68,988,858		69,251,291		54,566,490
Net loss per share, basic and diluted	$	(0.85)	$	(0.74)	$	(2.87)	$	(2.15)

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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:


	September 30,
	2025	2024
RSUs	1,790,210	812,426
Options to purchase ordinary shares	10,189,796	8,856,901
	11,980,006	9,669,327

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 zero and $0.1 million during the three and nine months ended September 30, 2025, respectively, prior to Mr. Legault’s retirement as Chairman of the Company’s board of directors. Stone Atlanta Estates LLC provided consultancy services to the Company totaling $48,000 and $0.1 million during the three and nine months ended September 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 current 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.

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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 nine months ended September 30, 2025 and 2024 (in thousands):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2025		2024		2025		2024
Collaboration revenue	$	11,734	$	2,676	$	24,631	$	31,567
Significant segment expenses
Research and development:
Zelenectide pevedotin (Nectin-4)		27,461		22,006		104,204		55,326
BT5528 (EphA2)		2,295		2,794		6,641		7,011
Bicycle tumor-targeted immune cell agonists		484		1,510		1,596		6,184
Discovery, platform and other expense		11,969		8,033		33,113		22,994
Employee and contractor related expenses		18,375		15,403		53,919		43,001
Share-based compensation		3,645		4,444		12,150		13,574
Facility expenses		1,814		2,617		5,345		6,294
Research and development incentives and government grants		(7,617)		(8,542)		(28,455)		(31,196)
Total research and development		58,426		48,265		188,513		123,188
General and administrative:
Personnel-related costs		7,305		5,837		21,411		17,078
Professional and consulting fees		4,113		4,812		15,114		12,726
Other general and administrative costs		2,473		2,531		6,993		6,463
Share-based compensation		5,126		4,758		15,661		14,174
Effect of foreign exchange rates		(158)		319		(704)		147
Total general and administrative		18,859		18,257		58,475		50,588
Total significant segment expenses		77,285		66,522		246,988		173,776
Other segment items⁽¹⁾		6,451		13,044		23,551		25,032
Segment net loss	$	(59,100)	$	(50,802)	$	(198,806)	$	(117,177)

(1)	Other segment items include interest and other income, interest expense, loss on extinguishment of debt and provision for (benefit from) income taxes.

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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 in two 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):


	September 30,		December 31,
	2025		2024
United States	$	1,430	$	3,037
United Kingdom		9,993		14,152
	$	11,423	$	17,189

The Company’s collaboration revenue is attributed to the operations of the Company in the United Kingdom.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations.

You should read this discussion and analysis of our financial condition and consolidated results of operations together with our unaudited condensed consolidated financial statements and the related notes appearing elsewhere in this Quarterly Report and our audited financial statements and related notes for the year ended December 31, 2024, included in our Annual Report on Form 10-K for the year ended December 31, 2024, or the 2024 Annual Report, which was filed with the Securities and Exchange Commission, or SEC, on February 25, 2025. Some of the information contained in this discussion and analysis or set forth elsewhere in this report, including statements of our plans, objectives, expectations and intentions, contain forward-looking statements that involve risks and uncertainties. As a result of many factors, including those factors set forth in the “Risk Factors” section of this report, our actual results could differ materially from the results described in or implied by the forward-looking statements contained in the following discussion and analysis. Please also see the section titled “Forward-Looking Statements.”

Overview

We are a clinical-stage pharmaceutical company developing a novel class of medicines, which we refer to as Bicycle^® molecules, for diseases that are underserved by existing therapeutics. Bicycle molecules are fully synthetic short peptides constrained to form two loops which stabilize their structural geometry. This constraint facilitates target binding with high affinity and selectivity, making Bicycle molecules attractive candidates for drug development. Bicycle molecules are a unique therapeutic modality combining the pharmacology usually associated with a biologic with the manufacturing and pharmacokinetic, or PK, properties of a small molecule. The relatively large surface area presented by Bicycle molecules allows targets to be drugged that have historically been intractable to non-biological approaches. Bicycle molecules are excreted by the kidney rather than the liver and have shown no significant signs of immunogenicity to date, qualities which we believe explain the molecules’ favorable toxicological profile.

We have a novel and proprietary phage display screening platform which we use to identify Bicycle molecules in an efficient manner. The platform initially displays linear peptides on the surface of engineered bacteriophages, or phages, before “on-phage” cyclization with a range of small molecule scaffolds which can confer differentiated physicochemical and structural properties. Our platform encodes quadrillions of potential Bicycle molecules which can be screened to identify molecules for optimization to potential product candidates. We have used this powerful screening technology to identify our current portfolio of candidates in oncology and intend to use it in conjunction with our collaborators to seek to develop additional future candidates across a range of other disease areas.

Our product candidates zelenectide pevedotin, formerly BT8009, and BT5528 are each a Bicycle Drug Conjugate, or BDC^®molecule. These Bicycle molecules are chemically attached to a toxin that when administered is cleaved from the Bicycle molecule and kills the tumor cells. We are evaluating zelenectide pevedotin, a BDC molecule targeting Nectin-4, in an ongoing company-sponsored Phase I/II clinical trial to assess the safety, pharmacokinetics and clinical activity in patients with Nectin-4 expressing advanced malignancies and an ongoing Phase II/III registrational trial called Duravelo-2, designed to allow for potential accelerated approval in untreated and previously treated metastatic urothelial cancer. We are 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. Enrollment in these trials is ongoing. In addition, we are evaluating BT5528, a BDC molecule targeting Ephrin type A receptor 2, or EphA2, in an ongoing company-sponsored Phase I/II clinical trial. Additionally, our other product candidate, BT7480, is a Bicycle Tumor-Targeted Immune Cell Agonist^®, or Bicycle TICA^®molecule. A Bicycle TICA molecule links immune cell receptor binding Bicycle molecules to tumor antigen binding Bicycle molecules. We are evaluating BT7480, a Bicycle TICA molecule targeting Nectin-4 and agonizing CD137, in a company-sponsored Phase I/II clinical trial. Our discovery pipeline in oncology includes next-generation BDC molecules and Bicycle Radioconjugates, or BRC^®molecules.

Zelenectide pevedotin has been granted Fast Track Designation, or FTD, by the FDA as a monotherapy for the treatment of adult patients with previously treated locally advanced or metastatic urothelial cancer as well as for the treatment of adult patients with previously treated, NECTIN4 gene-amplified, advanced or metastatic triple-negative breast cancer and non-small cell lung cancer. BT5528 has been granted FTD for the treatment of adult patients with

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previously treated, locally advanced or metastatic urothelial cancer. Zelenectide pevedotin has also been selected to participate in the Chemistry, Manufacturing and Controls, or CMC, Development and Readiness Pilot Program launched by the FDA to facilitate CMC development for therapies with expedited clinical development timeframes based on the anticipated clinical benefits of earlier patient access to the therapy.

In September 2024, we announced updated Phase I/II clinical results for zelenectide pevedotin used as a monotherapy in metastatic urothelial cancer at the European Society for Medical Oncology, or ESMO, Congress 2024, and in January 2025, we also announced updated topline results from the ongoing Phase I trial evaluating 5 mg/m² weekly of zelenectide pevedotin plus 200 mg of pembrolizumab once every three weeks. In addition, in December 2024, we announced data showing the enhanced anti-tumor activity of zelenectide pevedotin monotherapy in breast cancer patients with NECTIN4 gene amplification at the 2024 San Antonio Breast Cancer Symposium and shared topline monotherapy data for zelenectide pevedotin in non-small cell lung cancer patients with NECTIN4 gene amplification. We plan to advance development of zelenectide pevedotin in broader indications outside of metastatic urothelial cancer utilizing a NECTIN4 gene amplification strategy to target patients who have the potential for significantly deeper responses.

In addition, at the ESMO Congress 2024, we announced updated Phase I/II clinical results for BT5528 in advanced solid tumors, including metastatic urothelial cancer and ovarian cancer, and updated Phase I/II clinical results for BT7480 in advanced solid tumors. In October 2024, first human imaging data for a BRC molecule targeting MT1-MMP was presented by the German Cancer Consortium, or DKTK, and we presented preclinical data about BRC molecules for radioisotope delivery to solid tumors at the European Association of Nuclear Medicine, or EANM, 2024 Congress. In April 2025, DKTK presented additional human imaging data for a BRC molecule targeting MT1-MMP at the American Association for Cancer Research, or AACR, Annual Meeting 2025. In October 2025, at the EANM 2025 Congress, we presented data outlining the first clinical experience with an early BRC molecule targeting MT1-MMP and DKTK presented preclinical data about BRC molecules demonstrating high specificity and tunability supporting their potential for radiotheranostic use.

Beyond our wholly owned oncology portfolio, we are collaborating with biopharmaceutical companies and organizations in additional therapeutic areas in which we believe our proprietary Bicycle screening platform can identify therapies to treat diseases with significant unmet medical need.

In August 2025, we announced cost reduction initiatives that are expected to reduce planned operating costs by approximately 30% over the course of our expected financial runway period, primarily through a workforce reduction that is expected to result in a reduction of approximately 25% of our current and planned workforce. We expect the workforce reduction to be substantially completed by the fourth quarter of 2025. As a result, we anticipate that we will incur aggregate charges, representing cash expenditure for severance and other employee termination benefits, of approximately $5.3 million, $4.1 million of which was recognized during the three months ended September 30, 2025.

Financial Overview

Since our inception, we have devoted substantially all of our resources to developing our Bicycle platform and our product candidates, conducting research and development of our product candidates and preclinical programs, raising capital and providing general and administrative support for our operations. To date, we have financed our operations primarily with proceeds from the sale of our equity securities; proceeds received from upfront payments, research and development payments, and development milestone payments from our collaboration agreements; and borrowings pursuant to a loan and security agreement, or the Loan Agreement, with Hercules Capital, Inc., or Hercules. From our inception in 2009 through September 30, 2025, we have received gross proceeds of $1.4 billion from the sale of our equity securities; and $239.3 million of cash payments under our collaboration arrangements, including $45.9 million from Bayer, $53.0 million from Novartis, $49.7 million from Ionis, and $56.0 million from Genentech. We do not have any products approved for sale and have not generated any revenue from product sales.

Since our inception, we have incurred significant operating losses. Our ability to generate product revenue sufficient to achieve profitability will depend on the successful development and eventual commercialization of one or more of our product candidates. Our net losses were $59.1 million and $198.8 million for the three and nine months

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ended September 30, 2025, respectively. As of September 30, 2025, we had an accumulated deficit of $879.6 million. These losses have resulted primarily from costs incurred in connection with research and development activities and general and administrative costs associated with our operations. We expect to continue to incur significant expenses and increasing operating losses for the foreseeable future.

We anticipate that our expenses and capital requirements will increase substantially in connection with our ongoing activities, particularly as we advance our product candidates into later-stage clinical trials and continue preclinical activities and clinical trials for our pipeline programs and, if any product candidates are approved, pursue the commercialization of such product candidates by building internal sales and marketing capabilities. We expect that our expenses and capital requirements will increase substantially if and as we:

●

continue our development of our product candidates, including conducting future clinical trials of zelenectide pevedotin and BT5528;

●

seek to identify and develop additional product candidates, including expanding our pipeline of BRC and next-generation BDC molecules;

●

develop the necessary processes, controls and manufacturing data to obtain marketing approval for our product candidates and to support manufacturing to commercial scale;

●

develop, maintain, expand and protect our intellectual property portfolio;

●

seek marketing approvals for our product candidates that successfully complete clinical trials, if any;

●

hire and retain additional personnel, such as non-clinical, clinical, pharmacovigilance, quality assurance, regulatory affairs, manufacturing, distribution, legal, compliance, medical affairs, commercial and scientific personnel;

●

acquire or in-license other products and technologies;

●

expand our infrastructure and facilities to accommodate our growing employee base, including adding equipment and infrastructure to support our research and development; and

●

add operational, financial and management information systems and personnel, including personnel to support our research and development programs and any future commercialization efforts.

We do not expect to generate revenue from product sales unless and until we successfully complete development and obtain marketing approval for one or more of our product candidates, which we expect will take many years and is subject to significant uncertainty. We have no commercial-scale manufacturing facilities of our own, and all of our manufacturing activities have been and are planned to be contracted out to third parties. Additionally, we currently utilize third-party contract research organizations, or CROs, to carry out our clinical development activities. If we seek to obtain marketing approval for any of our product candidates from which we obtain encouraging results in clinical development, we expect to incur significant commercialization expenses as we prepare for product sales, marketing, manufacturing, and distribution.

As a result, we will need substantial additional funding to support our continuing operations and pursue our growth strategy. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through a combination of equity offerings, debt financings, collaborations, strategic alliances, charitable and governmental grants, monetization transactions or licensing arrangements. We may be unable to raise additional funds or enter into such other agreements or arrangements when needed on favorable terms, or at all. If we fail to raise capital or enter into such agreements as, and when, needed, we may have to significantly delay, scale back, or discontinue the development and commercialization of one or more of our product candidates. Because of the numerous risks and uncertainties associated with product development, we are unable to predict the timing or amount of increased

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expenses or when or if we will be able to achieve or maintain profitability. Even if we are able to generate product sales, we may not become profitable. If we fail to become profitable or are unable to sustain profitability on a continuing basis, we may be unable to continue our operations at planned levels and be forced to reduce or terminate our operations.

As of September 30, 2025, we had cash and cash equivalents of $648.3 million. In October 2025, we received $38.2 million of research and development incentives related to relevant expenditures incurred in the year ended December 31, 2024. We believe that our existing cash and cash equivalents will enable us to fund our operating expenses and capital expenditure requirements for at least 12 months from the date of filing of this Quarterly Report. We have based this estimate on assumptions that may prove to be wrong, and we could deplete our available capital resources sooner than we expect. See “—Liquidity and Capital Resources” and “—Capital Resources and Funding Requirements.”

Components of Our Results of Operations

Collaboration Revenue

To date, we have not generated any revenue from product sales and we do not expect to generate any revenue from product sales for the foreseeable future. Our revenue primarily consists of collaboration revenue under our arrangements with our collaboration partners, including amounts that are recognized related to upfront payments, milestone payments and option exercise payments, and amounts due to us for research and development services. In the future, revenue may include additional milestone payments and option exercise payments, and royalties on any net product sales under our collaborations. We expect that any revenue we generate will fluctuate from period to period as a result of the timing and amount of license, research and development services, milestone and other payments, as well as the exercise or expiration of options.

Expenses

Research and Development Expenses

Research and development expenses consist primarily of costs incurred for our research and development activities, including our discovery efforts, and the development of our product candidates, which include:

●

employee-related expenses including salaries, benefits, and share-based compensation expense;

●

expenses incurred under agreements with third parties that conduct research and development, preclinical activities, clinical activities and manufacturing on our behalf;

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the cost of consultants;

●

the cost of lab supplies and acquiring, developing and manufacturing preclinical study materials and clinical trial materials;

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costs related to compliance with regulatory requirements; and

●

facilities, depreciation, and other expenses, which include direct and allocated expenses for rent and maintenance of facilities, and other operating costs.

Research and development costs are expensed as incurred. Costs for certain activities are recognized based on an evaluation of the progress to completion of specific tasks. Payments for these activities are based on the terms of the individual agreements, which may differ from the pattern of costs incurred, and are reflected in our condensed consolidated financial statements as a prepaid expense or accrued research and development expenses. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are capitalized. The capitalized amounts are expensed as the related goods are delivered or the services are performed.

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Our direct external research and development expenses are tracked on a program-by-program basis and consist of costs, such as fees paid to consultants, CROs and contract manufacturing organizations, or CMOs, in connection with our preclinical and clinical development activities. Costs incurred after a product candidate has been designated and that are directly related to the product candidate are included in direct research and development expenses for that program. Costs incurred prior to designating a product candidate are included in discovery, platform and other expenses. We do not allocate employee costs, costs associated with our discovery efforts, laboratory supplies, and facilities, including depreciation or other indirect costs, to specific product development programs because these costs are deployed across multiple product development programs and, as such, are not separately classified.

Through our subsidiaries in the U.K., we receive reimbursements of certain research and development expenditures as part of a U.K. government research and development tax reliefs program. For 2024, we benefitted from the Small and Medium-sized Enterprises, or SME, R&D Tax Relief program, under which we were able to surrender trading losses that arose from qualifying research and development expenses incurred by our subsidiaries in the U.K. for a cash rebate of up to 26.97% of qualifying expenditure incurred as long as we 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 the Finance Act 2024 in February 2024. For accounting periods beginning on or after April 1, 2024, the 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, or RDEC, and an enhanced research and development intensive support scheme, or ERIS. Therefore, for 2025 we qualify for the ERIS scheme, and are therefore eligible for a cash rebate up to 26.97% of qualifying expenditures, as we remain 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 we no longer qualify as an R&D intensive SME during an accounting period, we will be subject to a single 20% gross rebate rate applying to all claims under the RDEC scheme.

For 2025 and beyond, the Finance Act 2024 also introduces restrictions (unless limited exceptions apply) on the tax relief that can be claimed for expenditures incurred on sub-contracted R&D activities or externally provided workers, where such sub-contracted activities are not carried out in the U.K. or such workers are not subject to U.K. payroll taxes. These restrictions may limit our ability to claim R&D tax credits for sub-contracted R&D in the future.

The U.K. research and development tax credit is fully refundable to us after surrendering tax losses and is not dependent on current or future taxable income. As a result, we have recorded the entire benefit from the U.K. research and development tax credit as a reduction to research and development expenses and is not reflected as part of the income tax provision.

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We expect that our research and development expenses will continue to increase for the foreseeable future as a result of our expanded portfolio of product candidates and as we: (i) continue the clinical development and seek to obtain marketing approval for our product candidates; (ii) initiate clinical trials for our product candidates; and (iii) build our in-house process development and analytical capabilities and continue to discover and develop additional product candidates.

The successful development of our product candidates is highly uncertain. As such, at this time, we cannot reasonably estimate or know the nature, timing and estimated costs of the efforts that will be necessary to complete the remainder of the development of these product candidates. We are also unable to predict when, if ever, material net cash inflows will commence from our product candidates. This is due to the numerous risks and uncertainties associated with developing products, including the uncertainty of:

●

identifying new product candidates to add to our development pipeline, including expanding our pipeline of BRC and next-generation BDC molecules;

●

completing research and preclinical development of our product candidates;

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establishing an appropriate safety profile with IND-enabling studies to advance our preclinical programs into clinical development;

●

successful enrollment in, and the initiation and completion of clinical trials, including conducting future clinical trials of zelenectide pevedotin and BT5528;

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the timing, receipt and terms of any marketing approvals from applicable regulatory authorities;

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commercializing the product candidates, if and when approved, whether alone or in collaboration with others;

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establishing commercial manufacturing capabilities or making arrangements with third-party manufacturers;

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the development and timely delivery of commercial-grade drug formulations that can be used in our clinical trials;

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addressing any competing technological and market developments, as well as any changes in governmental regulations;

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negotiating favorable terms in any collaboration, licensing or other arrangements into which we may enter and performing our obligations under such arrangements;

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maintaining, protecting and expanding our portfolio of intellectual property rights, including patents, trade secrets and know-how, as well as obtaining and maintaining regulatory exclusivity for our product candidates;

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continued acceptable safety profile of the drugs following approval; and

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attracting, hiring and retaining qualified personnel.

A change in the outcome of any of these variables with respect to the development of a product candidate could mean a significant change in the costs and timing associated with the development of that product candidate. For example, the FDA, the European Medicines Agency, or EMA, or another regulatory authority may require us to conduct clinical trials beyond those that we anticipate will be required for the completion of clinical development of a product candidate, or we may experience significant trial delays due to patient enrollment or other reasons in which case we would be required to expend significant additional financial resources and time on the completion of clinical development. In addition, we may obtain unexpected results from our clinical trials and we may elect to discontinue, delay or modify clinical trials of some product candidates or focus on others. Identifying potential product candidates and conducting preclinical testing and clinical trials is a time-consuming, expensive and uncertain process that takes years to complete, and we may never generate the necessary data or results required to obtain marketing approval and achieve product sales. In addition, our product candidates, if approved, may not achieve commercial success. In addition, on April 26, 2023, the European Commission adopted a proposal for a new Directive and Regulation to revise the current EU pharmaceutical legislation. The proposed revisions remain to be agreed and adopted by the European Council. Moreover, on December 1, 2024, a new European Commission took office. The proposal could, therefore, still be subject to revisions. If adopted in the form proposed, the European Commission proposals may result in a decrease in data and market exclusivity opportunities for our product candidates in the EU and make them open to generic or biosimilar competition earlier than is currently the case with a related reduction in reimbursement status.

General and Administrative Expenses

General and administrative expenses consist primarily of salaries and other related costs, including share-based compensation, for personnel in our executive, finance, corporate and business development, commercial and

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administrative functions. General and administrative expenses also include professional fees for legal, patent, accounting, auditing, tax and consulting services, insurance, travel expenses and facility-related expenses, which include direct depreciation costs and allocated expenses for rent and maintenance of facilities and other operating costs.

Foreign currency transactions in currencies different from the applicable functional currency are translated into the functional currency using the exchange rates prevailing at the dates of the transactions. Foreign exchange differences resulting from the settlement of such transactions and from the remeasurement at period-end exchange rates in foreign currencies are recorded in general and administrative expenses in the condensed consolidated statements of operations and comprehensive loss. As such, our operating expenses may be impacted by future changes in exchange rates. See “Quantitative and Qualitative Disclosure About Market Risks” for further discussion.

We expect that our general and administrative expenses will increase in the future as we increase our general and administrative headcount to support our continued research and development and potential commercialization of our portfolio of product candidates. We also expect to continue to incur increased expenses associated with being a public company including costs of accounting, audit, information systems, legal, intellectual property, regulatory and tax compliance services, director and officer insurance and investor and public relations.

Other Income (Expense)

Interest and Other Income

Interest and other income consists primarily of interest earned on our cash held in operating accounts and our cash equivalents.

Interest Expense

Interest expense consists primarily of interest expense for financing arrangements.

Loss on Extinguishment of Debt

Loss on extinguishment of debt is related to the loss recognized from the repayment and voluntary termination of the Loan Agreement on July 9, 2024.

Provision for (Benefit from) Income Taxes

We are subject to corporate taxation in the United States and the U.K. We have generated losses since inception and have therefore not paid U.K. corporation tax. The provision for (benefit from) income taxes included in the condensed consolidated statements of operations and comprehensive loss represents the tax impact from operating activities in the United States, which has generated taxable income based on intercompany service arrangements.

After consideration of our history of cumulative net losses in the U.K., we have concluded that it is more likely than not that we will not realize the benefits of our U.K. deferred tax assets and accordingly we have provided a valuation allowance for the full amount of the net deferred tax assets in the U.K. We intend to continue to maintain a full valuation allowance on our 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 we are able to actually achieve.

Unsurrendered U.K. losses may be carried forward indefinitely to be offset against future taxable profits, subject to numerous utilization criteria and restrictions. The amount that can be offset each year is limited to £5.0 million plus an incremental 50% of U.K. taxable profits.

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Results of Operations

Comparison of the Three Months Ended September 30, 2025 and 2024

The following table summarizes our results of operations for the periods presented:


	Three Months Ended
	September 30,
	2025		2024		Change

	(in thousands)
Collaboration revenue	$	11,734	$	2,676	$	9,058
Operating expenses:
Research and development		58,426		48,265		10,161
General and administrative		18,859		18,257		602
Total operating expenses		77,285		66,522		10,763
Loss from operations		(65,551)		(63,846)		(1,705)
Other income (expense):
Interest and other income		6,700		10,583		(3,883)
Interest expense		(44)		(33)		(11)
Loss on extinguishment of debt		—		(954)		954
Total other income, net		6,656		9,596		(2,940)
Net loss before income tax provision		(58,895)		(54,250)		(4,645)
Provision for (benefit from) income taxes		205		(3,448)		3,653
Net loss	$	(59,100)	$	(50,802)	$	(8,298)

Collaboration Revenue

Collaboration revenue increased by $9.1 million in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, due to increases of $6.0 million from our collaboration with Genentech primarily due to the recognition of remaining deferred revenue under the arrangement of $6.5 million upon the termination of our Discovery Collaboration and License Agreement with Genentech during the third quarter of 2025, $2.0 million for a milestone achieved from our collaboration with Ionis, and $0.9 million from our collaboration with Novartis.

Research and Development Expenses

The table below summarizes our research and development expenses for the periods presented:


	Three Months Ended September 30,
	2025		2024		Change

	(in thousands)
Zelenectide pevedotin (Nectin‑4)	$	27,461	$	22,006	$	5,455
BT5528 (EphA2)		2,295		2,794		(499)
Bicycle tumor-targeted immune cell agonists		484		1,510		(1,026)
Discovery, platform and other expense		11,969		8,033		3,936
Employee and contractor related expenses		18,375		15,403		2,972
Share-based compensation		3,645		4,444		(799)
Facility expenses		1,814		2,617		(803)
Research and development incentives and government grants		(7,617)		(8,542)		925
Total research and development expenses	$	58,426	$	48,265	$	10,161

Research and development expenses increased by $10.2 million in the three months ended September 30, 2025 compared to the three months ended September 30, 2024, due to increases of $5.5 million in clinical program expenses for zelenectide pevedotin primarily due to the ongoing Phase II/III Duravelo-2 registrational trial as well as the ongoing

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Phase I/II clinical trials assessing 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; $3.9 million in discovery, platform and other expense due to continued development of our pipeline programs, including advancing our BRC molecule pipeline; $3.0 million in employee and contractor related expenses primarily attributable to increased headcount as well as incremental severance-related costs of $1.4 million period over period; and $0.9 million resulting from lower research and development incentives primarily due to restrictions, effective in 2025, on the tax relief that can be claimed on expenditures for certain activities that are not carried out in the U.K. These increases were primarily offset by decreases of $1.0 million in Bicycle TICA program development expenses due to the timing of clinical program activities and $0.8 million in share-based compensation expense due to the Company’s workforce reduction in August 2025.

We begin to separately track program expenses at candidate nomination, at which point we accumulate all direct external program costs to support that program to date. Through September 30, 2025, we have incurred approximately $260.8 million and $55.4 million of direct external expenses for the development of zelenectide pevedotin and BT5528, respectively, since their candidate nominations, and an aggregate of $50.9 million of direct external expenses for the development of two named Bicycle TICA candidates since their nominations.

General and Administrative Expenses

The table below summarizes our general and administrative expenses for the periods presented:


	Three Months Ended September 30,
	2025		2024		Change

	(in thousands)
Personnel-related costs	$	7,305	$	5,837	$	1,468
Professional and consulting fees		4,113		4,812		(699)
Other general and administration costs		2,473		2,531		(58)
Share-based compensation		5,126		4,758		368
Effect of foreign exchange rates		(158)		319		(477)
Total general and administrative expenses	$	18,859	$	18,257	$	602

General and administrative expenses increased by $0.6 million in the three months ended September 30, 2025 compared to the three months ended September 30, 2024. This increase is primarily due to an increase of $1.5 million in personnel-related costs as a result of increased headcount as well as incremental severance-related costs of $0.8 million period over period, offset by a decrease of $0.7 million in professional and consulting fees due to ongoing cost reduction initiatives.

Other Income, net

Other income, net decreased by $2.9 million in the three months ended September 30, 2025 compared to the three months ended September 30, 2024, which was primarily due to a decrease in interest income of $3.9 million related to lower interest rates as well as lower average interest-bearing cash and cash equivalents balances period over period offset by the loss on extinguishment of debt of $1.0 million recognized in the third quarter of 2024.

Provision For (Benefit From) Income Taxes

The provision for income taxes of $0.2 million for the three months ended September 30, 2025 was primarily due to the impact of the August 2025 workforce reduction on our estimated effective tax rate. The benefit of income taxes of $3.4 million for the three months ended September 30, 2024 was mainly the result of incremental income tax benefits of approximately $3.5 million recognized during the third quarter of 2024 related to the completion of a U.S. research and development tax credit study.

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Comparison of the Nine Months Ended September 30, 2025 and 2024

The following table summarizes our results of operations for the periods presented:


	Nine Months Ended
	September 30,
	2025		2024		Change

	(in thousands)
Collaboration revenue	$	24,631	$	31,567	$	(6,936)
Operating expenses:
Research and development		188,513		123,188		65,325
General and administrative		58,475		50,588		7,887
Total operating expenses		246,988		173,776		73,212
Loss from operations		(222,357)		(142,209)		(80,148)
Other income (expense):
Interest and other income		22,587		23,981		(1,394)
Interest expense		(149)		(1,678)		1,529
Loss on extinguishment of debt		—		(954)		954
Total other income, net		22,438		21,349		1,089
Net loss before income tax provision		(199,919)		(120,860)		(79,059)
Benefit from income taxes		(1,113)		(3,683)		2,570
Net loss	$	(198,806)	$	(117,177)	$	(81,629)

Collaboration Revenue

Collaboration revenue decreased by $6.9 million in the nine months ended September 30, 2025, compared to the nine months ended September 30, 2024, due to decreases of $6.9 million from our collaboration with Ionis primarily due to the completion of the combined licenses and research and discovery performance obligation in the second quarter of 2024, and $1.2 million from our collaboration with Novartis due to the recognition of revenue related to the expiration of Novartis’ material rights for limited substitution rights for the first and second targets in the second quarter of 2024. These decreases were offset by an increase of $0.8 million from our collaboration with Genentech.

Research and Development Expenses

The table below summarizes our research and development expenses for the periods presented:


	Nine Months Ended September 30,
	2025		2024		Change

	(in thousands)
Zelenectide pevedotin (Nectin‑4)	$	104,204	$	55,326	$	48,878
BT5528 (EphA2)		6,641		7,011		(370)
Bicycle tumor-targeted immune cell agonists		1,596		6,184		(4,588)
Discovery, platform and other expense		33,113		22,994		10,119
Employee and contractor related expenses		53,919		43,001		10,918
Share-based compensation		12,150		13,574		(1,424)
Facility expenses		5,345		6,294		(949)
Research and development incentives and government grants		(28,455)		(31,196)		2,741
Total research and development expenses	$	188,513	$	123,188	$	65,325

Research and development expenses increased by $65.3 million in the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024, due to increases of $48.9 million in clinical program expenses for zelenectide pevedotin primarily related to the ongoing Phase II/III Duravelo-2 registrational trial as well as the ongoing Phase I/II clinical trials assessing zelenectide pevedotin in patients with NECTIN4 amplified advanced breast cancer and NECTIN4 amplified advanced or metastatic non-small cell lung cancer, which commenced recruiting

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patients in the first and third quarters of 2025; $10.9 million in employee and contractor related expenses primarily attributable to increased headcount; $10.1 million in discovery, platform and other expense due to continued development of our pipeline programs, including advancing our BRC molecule pipeline; and $2.7 million resulting from a decrease in research and development incentives due to the retroactive impact of U.K. R&D tax credit reimbursement rate changes that were enacted and effective in the first quarter of 2024, retroactively applied to April 1, 2023. These increases were primarily offset by decreases of $4.6 million in Bicycle TICA program development expenses due to the timing of clinical program activities, and $1.4 million in share-based compensation expense due to our workforce reduction in August 2025.

General and Administrative Expenses

The table below summarizes our general and administrative expenses for the periods presented:


	Nine Months Ended September 30,
	2025		2024		Change

	(in thousands)
Personnel-related costs	$	21,411	$	17,078	$	4,333
Professional and consulting fees		15,114		12,726		2,388
Other general and administration costs		6,993		6,463		530
Share-based compensation		15,661		14,174		1,487
Effect of foreign exchange rates		(704)		147		(851)
Total general and administrative expenses	$	58,475	$	50,588	$	7,887

General and administrative expenses increased by $7.9 million in the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024. This increase is primarily due to increases of $4.3 million in personnel-related costs as a result of increased headcount, $2.4 million in professional and consulting fees primarily associated with increased legal and consulting fees to support our growth, and $1.5 million of incremental share-based compensation expense primarily associated with equity grants issued since the same period in the prior year.

Other Income, net

Other income, net increased by $1.1 million in the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024, which was primarily due to a decrease in interest expense of $1.5 million due to the repayment and termination of the Loan Agreement in July 2024 as well as the loss on extinguishment of debt of $1.0 million recognized in the third quarter of 2024, offset by a decrease in interest income of $1.4 million primarily related to lower average interest rates period over period as well as higher cash and cash equivalents balances during the second half of 2024.

Benefit from Income Taxes

The benefit from income taxes of $1.1 million and $3.7 million for the nine months ended September 30, 2025 and 2024, respectively, is mainly the result of deferred tax assets in the United States that do not have a valuation allowance against them because of profits that will be generated by an intercompany service agreement. The benefit from income taxes for the nine months ended September 30, 2024 includes incremental income tax benefits of approximately $3.5 million recognized during the third quarter of 2024 related to the completion of a U.S. research and development tax credit study.

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Liquidity and Capital Resources

Liquidity

From our inception through September 30, 2025, we have not generated any revenue from product sales and have incurred significant operating losses and negative cash flows from our operations. We do not expect to generate significant revenue from sales of any products for several years, if at all.

To date, we have financed our operations primarily with proceeds from the sale of our equity securities; proceeds received from upfront payments, payments for research and development services, and development milestone payments pursuant to collaboration agreements; and borrowings pursuant to our Loan Agreement with Hercules.

On May 23, 2024, we entered into a securities purchase agreement, or the Purchase Agreement, with purchasers named therein. Pursuant to the Purchase Agreement, we 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, each at a purchase price equal to $21.42 per share, or the Private Placement. We completed the Private Placement on May 28, 2024. The transaction resulted in gross proceeds to us of $555.5 million, and after deducting commissions and offering expenses of $11.4 million, net proceeds to us of $544.1 million.

Cash Flows

The following table summarizes our cash flows for each of the periods presented:


	Nine Months Ended September 30,
	2025		2024

	(in thousands)
Net cash used in operating activities	$	(230,329)	$	(155,328)
Net cash used in investing activities		(1,776)		(867)
Net cash (used in) provided by financing activities		(116)		519,547
Effect of exchange rate changes on cash		1,026		1,087
Net (decrease) increase in cash, cash equivalents and restricted cash	$	(231,195)	$	364,439

Operating Activities

Net cash used in operating activities for the nine months ended September 30, 2025 was $230.3 million as compared to $155.3 million for the nine months ended September 30, 2024. The increase in cash used in operations of $75.0 million is primarily due to an increase in cash payments for clinical program activities, primarily related to the multiple ongoing clinical trials for zelenectide pevedotin, including for the ongoing Phase II/III registrational trial for zelenectide pevedotin in patients with untreated and previously treated metastatic urothelial cancer and the initiation of the Phase I/II clinical trials for zelenectide pevedotin in patients with NECTIN4 amplified advanced breast cancer and NECTIN4 amplified advanced or metastatic non-small cell lung cancer.

Investing Activities

During the nine months ended September 30, 2025 and 2024, we used $1.8 million and $0.9 million, respectively, of cash in investing activities for purchases of property and equipment, consisting primarily of laboratory equipment.

Financing Activities

During the nine months ended September 30, 2025, net cash used in financing activities was $0.1 million, primarily consisting of payments of finance lease obligations.

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During the nine months ended September 30, 2024, net cash provided by financing activities was $519.5 million, primarily consisting of net proceeds of $544.1 million from the Private Placement and $7.3 million from the exercise of share options, offset by payments on debt of $31.9 million associated with the repayment and voluntary termination of the Loan Agreement.

Loan Agreement with Hercules

On July 9, 2024, we repaid all amounts outstanding, including $30.0 million in outstanding borrowings, $0.1 million in accrued and unpaid interest, 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 the termination of the Loan Agreement, all security interests granted to the secured parties thereunder were terminated and released. For additional information on the Loan Agreement, see Note 6. “Debt” of our condensed consolidated financial statements included elsewhere in this Quarterly Report.

Capital Resources and Funding Requirements

Our material cash requirements include expenses associated with our ongoing activities, particularly as we advance the preclinical activities and clinical trials of our product candidates and as we:

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continue our development of our product candidates, including continuing current trials and conducting future clinical trials of zelenectide pevedotin, and BT5528;

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seek to identify and develop additional product candidates, including expanding our pipeline of BRC and next-generation BDC molecules;

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develop the necessary processes, controls and manufacturing data to seek to obtain marketing approval for our product candidates and to support manufacturing of product to commercial scale;

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develop, maintain, expand and protect our intellectual property portfolio;

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seek marketing approvals for any of our product candidates that successfully complete clinical trials, if any;

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acquire or in-license other products and technologies;

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expand our infrastructure and facilities to accommodate our growing employee base, including adding equipment and infrastructure to support our research and development; and

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add operational, financial and management information systems and personnel, including personnel to support our research and development programs, any future commercialization efforts.

If we obtain marketing approval for any product candidate that we identify and develop, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing, and distribution to the extent that such sales, marketing, and distribution are not the responsibility of our collaboration partners.

The following table summarizes our contractual obligations as of September 30, 2025, and the effects that such obligations are expected to have on our liquidity and cash flows in future periods. For additional information, see Note 11 to our condensed consolidated financial statements included in this Quarterly Report.

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	Payments due by period
			Less than
	Total		1 year		1 to 3 years		3 years to 5 years

	(in thousands)
Operating lease commitments⁽¹⁾	$	5,790	$	4,770	$	1,020	$	—
Finance lease commitments		1,119		274		548		297
Total	$	6,909	$	5,044	$	1,568	$	297

(1)

Amounts reflect minimum payments due for our office and laboratory space leases. We have one office and laboratory lease in Cambridge, U.K. under an operating lease with a lease term through December 2026. We have two office and laboratory leases in Massachusetts, U.S. under operating leases with lease terms through March 2026 and December 2027.

In the ordinary course of business, we enter into various agreements with contract research organizations to provide clinical trial services, with contract manufacturing organizations to provide clinical trial materials, and with vendors for preclinical research studies, synthetic chemistry and other services for operating purposes. These payments are not included in the table above since the contracts are generally cancelable with advanced written notice, generally with a notice period of 90 days or less. From the time of notice until termination, we are contractually obligated to make certain minimum payments to the vendors, based on the timing of the notification and the exact terms of the agreement.

We have 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 $105.8 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 September 30, 2025. As of September 30, 2025, we were unable to estimate the timing or likelihood of achieving these milestones.

We have based our estimates on assumptions that may prove to be wrong, and we may use our available capital resources sooner than we currently expect. Because of the numerous risks and uncertainties associated with the development of product candidates and programs, and because the extent to which we may enter into collaborations with third parties for development of our product candidates is unknown, we are unable to estimate the timing and amounts of increased capital outlays and operating expenses associated with completing the research and development of our product candidates. Our future capital requirements will depend on many factors, including:

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our ability to raise capital in light of the impacts of the unfavorable global economic and political conditions;

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the scope, progress, results, and costs of drug discovery, preclinical development, laboratory testing, and clinical trials for the product candidates we may develop;

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our ability to enroll clinical trials in a timely manner and to quickly resolve any delays or clinical holds that may be imposed on our development programs;

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the costs associated with our manufacturing process development and evaluation of third-party manufacturers and suppliers;

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the costs, timing and outcome of regulatory review of our product candidates;

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the costs of preparing and submitting marketing approvals for any of our product candidates that successfully complete clinical trials, and the costs of maintaining marketing authorization and related regulatory compliance for any products for which we obtain marketing approval;

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the costs of preparing, filing, and prosecuting patent applications, maintaining and enforcing our intellectual property and proprietary rights, and defending intellectual property-related claims;

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the costs of future activities, including product sales, medical affairs, marketing, manufacturing, and distribution, for any product candidates for which we receive marketing approval;

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the terms of our current and any future license agreements and collaborations; and the extent to which we acquire or in-license other product candidates, technologies and intellectual property.

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the success of our ongoing or future collaborations;

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our ability to establish and maintain additional collaborations on favorable terms, if at all; and

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the costs of operating as a public company.

Until such time, if ever, that we can generate product revenue sufficient to achieve profitability, we expect to finance our cash needs through a combination of equity offerings, debt financings, collaborations, monetization transactions, government contracts or other strategic transactions. To the extent that we raise additional capital through the sale of equity, ownership interests of existing holders of our ADSs and ordinary shares will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of holders of our ADSs or ordinary shares. If we raise additional funds through collaboration agreements, strategic alliances, licensing arrangements, monetization transactions, or marketing and distribution arrangements, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates or grant licenses on terms that may not be favorable to us or grant rights to develop and market products or product candidates that we would otherwise prefer to develop and market ourselves. Future debt financing, if available, may involve covenants restricting our operations or our ability to incur additional debt. Any debt or equity financing that we raise may contain terms that are not favorable to us or our shareholders.

Recent global trade disruption, volatility in the capital markets and continued uncertainty may contribute to a general global economic slowdown or recession. The resulting high inflation rates may materially affect our business and corresponding financial position and cash flows. Inflationary factors, such as increases in the cost of our clinical trial materials and supplies, interest rates and overhead costs may adversely affect our operating results. High interest rates also present a recent challenge impacting the U.S. economy and could make it more difficult for us to obtain traditional financing on acceptable terms, if at all, in the future. Additionally, the general consensus among economists suggests that we should expect a higher recession risk to continue over the next year, which, together with the foregoing, could result in further economic uncertainty and volatility in the capital markets in the near term, and could negatively affect our operations. Furthermore, such economic conditions have produced downward pressure on share prices. Although we do not believe that inflation has had a material impact on our financial position or results of operations to date, we may experience increases in the near future (especially if inflation rates remain high or begin to rise again) on our operating costs, including our labor costs and research and development costs, due to supply chain constraints, consequences associated with geopolitical conflicts such as those involving Ukraine and Israel, worsening global macroeconomic conditions, including those resulting from changes in global trade policies, which may result in additional stress on our working capital resources. If we are unable to raise capital when needed or on attractive terms, we would be forced to delay, reduce, or eliminate our research and development programs or future commercialization efforts.

Critical Accounting Estimates

Our management’s discussion and analysis of financial condition and results of operations is based on our condensed consolidated financial statements, which have been prepared in accordance with U.S. GAAP. The preparation

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of our condensed consolidated financial statements and related disclosures requires us to make estimates, assumptions and judgments that affect the reported amount of assets, liabilities, revenue, costs and expenses, and related disclosures. We base our estimates on historical experience, known trends and events and various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. We evaluate our estimates and assumptions on an ongoing basis. Our actual results may differ from these estimates under different assumptions or conditions.

Our critical accounting policies are described under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations—Critical Accounting Estimates” in our 2024 Annual Report, which was filed with the SEC on February 25, 2025. If actual results or events differ materially from the estimates, judgments and assumptions used by us in applying these policies, our reported financial condition and results of operations could be materially affected. Other than as disclosed in Note 2 to the condensed consolidated financial statements included in this Quarterly Report, there have been no significant changes to our critical accounting estimates from those described in our 2024 Annual Report.

Item 3. Quantitative and Qualitative Disclosure About Market Risk

Interest Rate Sensitivity

As of September 30, 2025, we had cash and cash equivalents of $648.3 million. Our exposure to interest rate sensitivity is impacted by changes in the underlying U.K. and U.S. bank interest and treasury rates. Our surplus cash has been invested in money market funds that invest primarily in U.S. Treasury obligations and fully collateralized repurchase obligations and that maintain a constant net asset value. We have not entered into investments for trading or speculative purposes. Due to the conservative nature of our investment portfolio, which is predicated on capital preservation of investments with short-term maturities, we do not believe an immediate one percentage point change in interest rates would have a material effect on the fair market value of our portfolio. Our earnings would be affected by changes in interest rates due to the impact those changes have on interest income generated from our cash and cash equivalents. We believe we have minimal interest rate risk as a one percentage point change in the average interest rate on our portfolio would not have a material effect on our condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2025.

Foreign Currency Exchange Risk

The functional currency is the currency of the primary economic environment in which an entity’s operations are conducted. The functional currency of Bicycle Therapeutics plc and Bicycle Therapeutics Inc. is the United States Dollar, or USD. The functional currency of Bicycle Therapeutics plc’s wholly owned non-U.S. subsidiaries, BicycleTx Limited and BicycleRD Limited, is the British Pound Sterling, and the condensed consolidated financial statements are presented in USD. The functional currency of our subsidiaries is the same as the local currency.

Monetary assets and liabilities denominated in currencies other than the functional currency are remeasured into the functional currency at rates of exchange prevailing at the balance sheet dates. Non-monetary assets and liabilities denominated in foreign currencies are remeasured into the functional currency at the exchange rates prevailing at the date of the transaction. Exchange gains or losses arising from foreign currency transactions are included in the determination of net loss for the respective periods. Adjustments that arise from exchange rate changes on transactions denominated in a currency other than the local currency are included in general and administrative expenses in the condensed consolidated statements of operations and comprehensive loss as incurred. We recorded foreign exchange gains of $0.2 million and $0.7 million for the three and nine months ended September 30, 2025, respectively. We recorded foreign exchange losses of $0.3 million and $0.1 million for the three and nine months ended September 30, 2024, respectively.

For financial reporting purposes, our condensed consolidated financial statements have been translated into USD. We translate the assets and liabilities of BicycleTx Limited and BicycleRD Limited into USD at the exchange rate in effect on the balance sheet date. Revenues and expenses are translated at the average exchange rate in effect during the period and shareholders’ equity amounts are translated based on historical exchange rates as of the date of each

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transaction. Translation adjustments are not included in determining net loss but are included in our foreign exchange adjustment included in the condensed consolidated statements of shareholders’ equity as a component of accumulated other comprehensive income (loss).

We do not currently engage in currency hedging activities in order to reduce our currency exposure, but we may begin to do so in the future.

Item 4. Controls and Procedures

Evaluation of Disclosure Controls and Procedures

As required by Rule 13a-15(d) of the Exchange Act, our management, including our principal executive officer and our principal financial officer, conducted an evaluation of the internal control over financial reporting to determine whether any changes occurred during the period covered by this Quarterly Report that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. Based on the evaluation of our disclosure controls and procedures at September 30, 2025, our Chief Executive Officer and Chief Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

Changes in Internal Control over Financial Reporting.

There were no changes in our internal control over financial reporting identified in connection with the evaluation required by Rule 13a-15(d) and 15d-15(d) of the Exchange Act that occurred during the quarter ended September 30, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II - OTHER INFORMATION

Item 1. Legal Proceedings.

From time to time, we may become involved in various legal proceedings and claims, either asserted or unasserted, which arise in the ordinary course of business. We are not currently subject to any material legal proceedings.

Item 1A. Risk Factors.

Our operations and financial results are subject to various risks and uncertainties, including those described below. The following information about these risks and uncertainties, together with the other information appearing elsewhere in this Quarterly Report, and our 2024 Annual Report on Form 10-K, filed with the Securities and Exchange Commission, or SEC, on February 25, 2025, including our consolidated financial statements and related notes thereto, should be carefully considered before a decision to invest in our American Depositary Shares, or ADSs. The occurrence of any of the following risks could have a material adverse effect on our business, financial condition, results of operations and future growth prospects or cause our actual results to differ materially from those contained in forward-looking statements we have made in this report and those we may make from time to time. Additional risks that are currently unknown to us or that we currently believe to be immaterial may also impair our business. In these circumstances, the market price of our ADSs could decline and holders of our ADSs may lose all or part of their investment. We cannot provide assurance that any of the events discussed below will not occur.

Summary of Selected Risk Factors

Our business is subject to numerous risks and uncertainties, of which you should be aware before making

BICYCLE THERAPEUTICS PLC 10-Q