Karyopharm Therapeutics Inc. Debt Disclosure

10. Long-Term Obligations

2025 Notes

In October 2018, we issued $172.5 million aggregate principal amount of the 2025 Notes in a private offering to qualified institutional buyers in reliance on Rule 144A under the Securities Act. The 2025 Notes were senior unsecured obligations, bore interest at a rate of 3.00% per year, and matured on October 15, 2025. Holders were able to convert the 2025 Notes at an initial

conversion rate of 4.2049 shares of common stock per $1,000 principal amount (equivalent to an initial conversion price of approximately $237.82 per share of common stock) following July 15, 2025. No holders elected to convert their 2025 Notes. In connection with the issuance of the 2025 Notes, we incurred $5.6 million of debt issuance costs, which were amortized to interest expense using an effective interest rate of 3.53% over seven years.

In May 2024, we exchanged $148.0 million aggregate principal amount of the 2025 Notes for: (i) $111.0 million aggregate principal amount of the 2029 Notes and (ii) 2024 Warrants to purchase up to 3,051,750 shares of our common stock. In October 2025, we exchanged $24.3 million aggregate principal amount of 2025 Notes for: (i) 2,435,146 shares of common stock, (ii) pre-funded warrants to purchase an aggregate of 1,404,087 shares of common stock, and (iii) common stock warrants to purchase an aggregate of 2,502,151 shares of common stock with an exercise price of $6.64 per share and an expiration date of October 10, 2030. We repaid $0.3 million principal amount of 2025 Notes at maturity on October 15, 2025. There were no 2025 Notes outstanding as of December 31, 2025.

Senior Secured Term Loan

In May 2024, we entered into a credit and guaranty agreement (the “Credit Agreement”) with certain holders of the 2025 Notes and certain entities managed by HealthCare Royalty Management, LLC (“HCRx”), which was subsequently assigned by HCRx to an affiliate of KKR & Co. Inc. (“KKR”) in connection with its acquisition of a majority ownership stake in HCRx in July 2025. The Credit Agreement provides for a senior secured term loan facility of $100.0 million which bore interest at a variable rate equal to the applicable secured overnight financing rate plus 9.25%, subject to a floor of 3.00% through June 30, 2025.

In October 2025, we entered into the First Amendment and Waiver to Credit and Guaranty Agreement (the “Amended Credit Agreement”), under which we borrowed an additional $12.5 million, resulting in a senior secured term loan facility with aggregate borrowings of $112.5 million (the “Amended Term Loan”) which matures in May 2028 and bears interest at a variable rate equal to the applicable secured overnight financing rate plus 10.25% for all interest incurred after June 30, 2025, subject to a floor of 3.00%. Interest incurred on borrowings under the Amended Term Loan from July 1, 2025 to March 31, 2026 is payable in-kind. Interest incurred on borrowings under the Amended Term Loan after March 31, 2026 is payable in cash quarterly in arrears on March 31, June 30, September 30, and December 31 of each year.

We are required to make quarterly principal payments under the Amended Term Loan on March 10, June 10, September 10, and December 10 of each year beginning on June 10, 2026 in the amount of 6.25% of the aggregate principal amount of the Amended Term Loan, with the remaining principal due when the Amended Term Loan matures in May 8, 2028. We are permitted to prepay the Amended Term Loan at any time, subject to a prepayment premium ranging from 3.00% to 8.00% of the principal prepaid. In addition, we are required to repay the Amended Term Loan with proceeds from certain asset sales and condemnation events, subject, in some cases, to reinvestment rights.

All obligations under the Amended Credit Agreement are secured on a first priority basis, subject to certain exceptions, by substantially all of our assets. The Amended Credit Agreement contains customary covenants, including a requirement to maintain a certain amount of cash, cash equivalents and investments at all times (the “Minimum Liquidity Covenant Amount”). From October 10, 2025 to October 10, 2026, the Minimum Liquidity Covenant Amount will be the lesser of: (x) the sum of $10.0 million plus 50% of the net cash proceeds of any issuance of indebtedness for borrowed money or capital stock of the Company, and (y) $25.0 million.

After October 10, 2026, the Minimum Liquidity Covenant Amount will be $25.0 million. As of December 31, 2025, we were in compliance with the Minimum Liquidity Covenant Amount.

The Amended Credit Agreement contains restrictions on indebtedness, liens, investments, fundamental changes, asset sales, licensing transactions, dividends, modifications to material agreements, payment of subordinated indebtedness, and other matters customarily restricted in such agreements. Specifically, we are prohibited from exclusively licensing, selling or otherwise disposing of U.S. rights to oncology indications of selinexor. As of December 31, 2025, we were in compliance with these covenants. If certain events of default occur, the Amended Term Loan may be due and payable immediately. These events include the withdrawal of approval of certain indications of selinexor, payment defaults, covenant defaults, bankruptcy, cross-defaults to certain other agreements, change in control and lien priority. Additionally, we have an obligation under the Amended Credit Agreement to appoint a candidate selected by the lenders under the Amended Term Loan to serve as a non-voting observer to our board of directors.

We determined the expected life of the Amended Term Loan was equal to its term. The principal value of the Amended Term Loan approximates its fair value due to the variable interest rate. In connection with the issuance of the Term Loan in May 2024, we incurred $6.8 million of debt issuance costs, which were being amortized to interest expense through May 2028 using an effective interest rate of 17%. Total unamortized debt issuance costs immediately following the creation of the Amended Term Loan was $5.2 million, which are being amortized to interest expense through May 2028 using an effective interest rate of 17%.

2029 Notes, New 2029 Notes, and 2028 Notes

On May 13, 2024, pursuant to privately negotiated agreements with certain holders of the 2025 Notes, we exchanged $148.0 million aggregate principal amount of the 2025 Notes for: (i) $111.0 million aggregate principal amount of 2029 Notes maturing on May 13, 2029 and (ii) 2024 Warrants to purchase up to 3,051,750 shares of our common stock. We also issued $5.0 million aggregate principal amount of 2029 Notes to HCRx in exchange for a $5.0 million reduction in our deferred royalty obligation. The 2029 Notes bore interest at a rate of 6.00% per year and were convertible into shares of our common stock at an initial conversion rate of 29.6296 shares per $1,000 principal amount, which is equivalent to a conversion price of $33.75 per share of common stock.

In October 2025, we entered into privately negotiated agreements with the holders of the 2029 Notes to exchange $101.0 million aggregate principal amount of the 2029 Notes for $103.5 million aggregate principal amount of newly issued New 2029 Notes

maturing on May 13, 2029. We also exchanged $15.0 million aggregate principal amount of the 2029 Notes for: (i) 2,024,344 shares of common stock and (ii) pre-funded warrants to purchase an aggregate of 552,164 shares of common stock. All 2029 Notes were fully cancelled after these exchange transactions. There were no 2029 Notes outstanding as of December 31, 2025.

The New 2029 Notes are second-lien secured obligations of the Company and are convertible by the holders into shares of our common stock at an initial conversion rate of 44.444 shares per $1,000 principal amount (the “New 2029 Notes Conversion Option”) which is equivalent to an initial conversion price of $22.50 per share and subject to customary anti-dilution adjustments. Holders of the New 2029 Notes may convert their New 2029 Notes at any time prior to the close of business on May 11, 2029. Upon conversion of the New 2029 Notes, we will deliver shares of our common stock plus cash in lieu of any fractional shares to the holders.

In October 2025, we issued $15.0 million aggregate principal amount of new 9.00% senior secured convertible notes maturing on October 15, 2028 (the “2028 Notes”) for cash proceeds of $15.0 million. The 2028 Notes are senior secured second-lien obligations and are convertible by the holders into shares of our common stock at an initial conversion rate of 150.6024 shares per $1,000 principal amount of 2028 Notes (the “2028 Notes Conversion Option”) which is equivalent to an initial conversion price of $6.64 per share of common stock and subject to customary anti-dilution adjustments. Holders of the 2028 Notes may convert at any time prior to the close of business on October 13, 2028. Upon conversion of the 2028 Notes, we will deliver shares of our common stock plus cash in lieu of any fractional shares to the holders.

Both the New 2029 Notes and 2028 Notes bear interest at a rate of 9.00% per year. Interest on the New 2029 Notes and 2028 Notes incurred from October 10, 2025 to March 31, 2026 will be payable in-kind. Interest incurred after March 31, 2026 will be payable in cash quarterly in arrears on March 31, June 30, September 30, and December 31 of each year.

On or after May 13, 2026 (for the New 2029 Notes) or October 15, 2026 (for the 2028 Notes), we may redeem all or a portion of the New 2029 Notes or all of the 2028 Notes if the last reported sale price of our common stock equals or exceeds 130% (for the New 2029 Notes) or 165% (for the 2028 Notes) of the applicable conversion price then in effect for at least 20 trading days during any 30 consecutive trading day period (the “New 2029 Notes and 2028 Notes Redemption Options”). Upon redemption, we will pay the redemption price in a cash payment, which will be equal to the principal amount of the notes to be redeemed and any accrued and unpaid interest, if any, up to but excluding the redemption date. The number of shares of common stock deliverable as make-whole consideration is subject to a cap of 85.1374 shares per $1,000 principal amount for the New 2029 Notes or 173.3102 shares per $1,000 principal amount for the 2028 Notes. In some cases, we will be required to make an offer to repurchase the New 2029 Notes or 2028 Notes at a 101% premium with proceeds from certain asset sales, subject, in some cases, to reinvestment rights.

If certain corporate events occur prior to the maturity date of the New 2029 Notes or the 2028 Notes, a holder that elects to convert their New 2029 Notes or 2028 Notes, as applicable, may be entitled to receive additional shares of common stock based on a fundamental change make-whole adjustment in the conversion rate in connection with such corporate event. However, in no event can the conversion rate exceed 85.1374 shares per $1,000 principal amount for the New 2029 Notes or 173.3102 shares per $1,000 principal amount for the 2028 Notes. In addition, if we undergo certain fundamental changes, holders may require us to repurchase for cash all or any portion of their New 2029 Notes or 2028 Notes at a price equal to the principal amount to be repurchased, plus any accrued and unpaid interest, up to but excluding the fundamental change repurchase date.

No holder will be entitled to receive shares of our common stock in connection with the New 2029 Notes or 2028 Notes if such receipt would cause the holder (together with its affiliates) to own more than 4.99% (subject to increase or decrease at the election of the holder, but in no event to exceed 19.99%) of the number of shares of the common stock outstanding immediately after giving effect to such event. In addition, a holder may elect to receive pre-funded warrants with respect to any shares of common stock that would otherwise be issuable in connection with the New 2029 Notes or 2028 Notes but for the foregoing ownership limitations. These pre-funded warrants will have an exercise price of $0.0001 per share and will not expire. As of December 31, 2025, no New 2029 Notes or 2028 Notes have been converted into shares of common stock or pre-funded warrants.

All obligations under the New 2029 Notes and 2028 Notes are secured on a second priority basis by the same collateral that secures the obligations under the Amended Term Loan. The 2028 Notes rank pari passu with the New 2029 Notes, ahead of indebtedness under the Amended Revenue Interest Agreement (as defined below) and behind indebtedness under the Amended Credit Agreement with respect to distributions of proceeds of the enforcement of certain collateral. The New 2029 Notes and 2028 Notes contain covenants and events of default that are generally consistent with the Amended Term Loan, including the Minimum Liquidity Amount. As of December 31, 2025, we were in compliance with these covenants.

We have determined that the New 2029 Notes Conversion Option, the 2028 Notes Conversion Option, and the New 2029 Notes and 2028 Notes Redemption Options are embedded derivatives that require bifurcation from the debt instrument and fair value

recognition. These derivatives are referred to as the Convertible Notes Derivatives in Note 6, “Fair Value Measurements” to our consolidated financial statements.

We determined the expected life of the New 2029 Notes and 2028 Notes is equal to their contractual terms. As of December 31, 2025, the “if-converted value” did not exceed the remaining principal amount for both the New 2029 Notes and 2028 Notes. The fair value of the New 2029 Notes and 2028 Notes are influenced by market interest rates, our stock price and stock price volatility, and have been classified as Level 3 within the fair value hierarchy as they use unobservable inputs. The estimated fair value of the New 2029 Notes and 2028 Notes as of December 31, 2025 was approximately $92.7 million and $22.8 million, respectively.

Debt issuance costs and discounts related to the New 2029 Notes of $33.3 million are being amortized to interest expense over the term of the New 2029 Notes at an effective interest rate of 22%. The following table sets forth total interest expense recognized related to the New 2029 Notes and 2029 Notes (in thousands):

Debt issuance costs and discounts related to the 2028 Notes of $5.6 million are being amortized to interest expense over the term of the 2028 Notes at an effective interest rate of 25%. We recognized interest expense of $0.6 million related to the 2028 Notes for the year ended December 31, 2025, which included $0.3 million of contractual interest expense and $0.3 million of amortization.

Deferred Royalty Obligation

In September 2019, we entered into a Revenue Interest Financing Agreement (the “Revenue Interest Agreement”) with HCRx which was subsequently amended in June 2021, August 2023, May 2024, August 2025, and October 2025, and which was subsequently assigned by HCRx to KKR in connection with its acquisition of a majority ownership stake in HCRx in July 2025 (as amended, the “Amended Revenue Interest Agreement”) under which we have received a total of $135.0 million, less certain transaction expenses. In exchange for this amount, KKR (as successor in interest to HCRx) receives payments from us at a percentage (the “Royalty Rate”) of net revenues of selinexor and any of our other future products, including worldwide net product sales and upfront payments, milestones, and royalties. Total aggregate payments to HCRx and KKR under the Amended Revenue Interest Agreement are capped at $263.3 million (the “Payment Cap”).

In May 2024, we entered into an amendment (the “HCRx Amendment”) to the Amended Revenue Interest Agreement with HCRx, pursuant to which we:

As the repayment of the funded amount is contingent upon worldwide net product sales and upfront payments, milestones, and royalties, the repayment term may be shortened or extended depending on actual worldwide net product sales and upfront payments, milestones, and royalties. The repayment period expires on the earlier of (i) the date on which HCRx and KKR have received cash payments in the aggregate totaling $263.3 million or (ii) the legal maturity date of September 26, 2035. If HCRx and KKR have not received total payments in the aggregate equal to $263.3 million by September 26, 2035, we will be required to pay an amount equal to $135.0 million plus a specific annual rate of return less aggregate payments previously paid to HCRx and KKR.

In the event of a change of control, an event of default, including, among others, our failure to pay any amounts due to KKR, insolvency, our failure to pay indebtedness when due, the revocation of regulatory approval of XPOVIO in the U.S. or our breach of any covenant contained in the Amended Revenue Interest Agreement and our failure to cure the breach within the prescribed time frame, we are obligated to pay KKR an amount equal to $263.3 million less aggregate payments previously paid to HCRx and KKR.

After giving effect to the above, as of May 2024, we had made aggregate payments under the Amended Revenue Interest Agreement totaling $135.0 million and the maximum remaining amount we owed to KKR, as successor in interest to HCRx, was $128.3 million. After May 2024, we are obligated to make quarterly payments in the amount of a fixed percentage of our net product revenues, upfront payments, milestones, and royalties earned in the applicable quarter, except that in connection with the October 2025 amendment, KKR waived our obligation to pay royalties on revenue recognized between April 1, 2025 and March 31, 2026.

The HCRx Amendment also subordinates the indebtedness and liens under the Amended Revenue Interest Agreement to the indebtedness and liens under the Amended Term Loan, and, subject to certain exceptions, makes the indebtedness and liens under the Amended Revenue Interest Agreement pari passu with the indebtedness and liens under the New 2029 Notes.

We have evaluated the terms of the Amended Revenue Interest Agreement and concluded that its features are similar to those of a debt instrument. Accordingly, we have accounted for the transaction as long-term debt and presented it as a deferred royalty obligation on our consolidated balance sheets.

As of December 31, 2025, we have made $147.1 million in payments to HCRx. The effective interest rate as of December 31, 2025 was approximately 16%. We have incurred debt issuance costs totaling $2.8 million which have been netted against the debt and are being amortized over the estimated term of the debt using the effective interest method, adjusted on a prospective basis for changes in the underlying assumptions and inputs.

The carrying value of the deferred royalty obligation as of December 31, 2025 and December 31, 2024 was $72.3 million and $73.5 million, respectively, which includes the carrying amount of the debt and unamortized debt issuance costs. The carrying value of the deferred royalty obligation approximated fair value as of December 31, 2025 and 2024 and was based on our estimates of future payments over the life of the arrangement, which are considered Level 3 inputs.