SEC Form SCHEDULE 13D filed by Sionna Therapeutics Inc.

The address of the principal business office of each of the Reporting Persons is 200 Berkeley Street, 18th Floor, Boston, MA 02116.

Each of the Fund and the Nexus Fund III is a private investment vehicle. RA Capital provides investment management services to the Fund, the Nexus Fund, the Nexus Fund III and the Account. The principal occupation of each of Dr. Kolchinsky and Mr. Shah is investment management.

During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree of final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

See Item 6 of the cover pages.

Prior to the Issuer's initial public offering (the "IPO"), (i) the Fund purchased an aggregate of 1,284,000 shares of Common Stock, 819,153 shares of Series Seed Preferred Stock, 1,229,830 shares of Series A Preferred Stock, 923,773 shares of Series B Preferred Stock and 4,364,874 shares of Series C Preferred Stock; (ii) the Nexus Fund purchased an aggregate of 500,000 shares of Common Stock, 319,069 shares of Series Seed Preferred Stock, and 451,580 shares of Series A Preferred Stock; (iii) the Nexus Fund III purchased an aggregate of 2,155,469 shares of Series B Preferred Stock and 1,091,219 shares of Series C Preferred Stock; and (iv) the Account purchased an aggregate of 216,000 shares of Common Stock, 138,054 Shares of Series Seed Preferred Stock and 124,908 shares of Series A Preferred Stock. The aggregate purchase price of the foregoing was $95,573,941. On January 31, 2025, the Issuer effected a 1-for-1.4611 reverse stock split of its common stock (the "Reverse Stock Split"). In connection with the closing of the IPO, on February 10, 2025, the Preferred Stock discussed above automatically converted into shares of Common Stock on a 1-for-1.4611 basis. The Fund and the Nexus Fund III also purchased 1,022,586 and 102,414 shares of Common Stock, respectively, from the underwriters of the IPO at the IPO price of $18.00 per share, for an aggregate purchase price of $20,250,000. All purchases of the securities described herein were for cash and were funded by working capital of the Fund, the Nexus Fund, the Nexus Fund III and the Account, as applicable.

The Reporting Persons acquired the Common Stock reported herein for investment purposes and not with an intent, purpose or effect of changing control of the Issuer. Although the Reporting Persons currently have no plan or proposal to acquire any additional Issuer securities or to dispose of any of the Issuer securities reported herein, the Reporting Persons may, from time to time, acquire additional equity securities or debt securities of the Issuer, which debt securities may be convertible or non-convertible, secured or unsecured, and could involve the monetization of potential revenue streams deriving from development-stage or commercial programs of the Issuer, or dispose of Issuer securities they beneficially own, on the open market or in private transactions or otherwise (including by means of 10b5-1 programs), consistent with their investment purposes and in amounts, on such terms and at such times as to be determined by the Reporting Persons based upon a number of factors, including, without limitation, their ongoing assessment of the Issuer's business prospects, the availability of Issuer securities at prices that would make the purchase or sale of such securities desirable, prevailing market conditions, the availability of other investment opportunities, and/or other considerations. In addition, consistent with their investment purpose, the Reporting Persons may engage in communications with persons associated with the Issuer, including stockholders of the Issuer, officers of the Issuer, members of the board of directors of the Issuer, and/or or other third parties, to discuss matters regarding the Issuer, including but not limited to its operations, strategic direction, governance or capitalization, and potential business combinations or dispositions involving the Issuer or certain of its businesses. Joshua Resnick, a Partner at RA Capital, currently serves as a director of the Issuer and therefore will engage in regular discussions with the Issuer's board of directors and management as part of his duties as a director. Neither Dr. Resnick (other than in his capacity as a director) nor the Reporting Persons have any present plans or proposals that relate to, or could result in, any of the matters referred to in paragraphs (a) through (j), inclusive, of the instructions to Item 4 of Schedule 13D. Depending on various factors including, without limitation, the Issuer's financial position, results and strategic direction, actions taken by the Issuer's management and Board, other investment opportunities available to RA Capital, the price levels of the Issuer securities, conditions in the securities markets and general economic and industry conditions, the Reporting Persons may change their purpose and formulate and implement plans or proposals with respect to the Issuer at any time and from time to time. Any such action may be made by the Reporting Persons alone or in conjunction with other stockholders, potential acquirers, financing sources and/or other third parties and could include one or more purposes, plans or proposals that relate to or would result in actions required to be reported herein in accordance with Item 4 of Schedule 13D.

Rows 11 and 13 of each Reporting Person's cover page to this Schedule 13D set forth the aggregate number of shares of Common Stock and percentages of the shares of Common Stock beneficially owned by such Reporting Person and are incorporated by reference. The percentage set forth in each row 13 is based upon 44,108,934 shares of Common Stock outstanding as of February 10, 2025 upon the closing of the Issuer's IPO, as reported in the prospectus, dated February 6, 2025, filed with the Securities and Exchange Commission (the "SEC") on February 4, 2025.

Rows 7 through 10 of each Reporting Person's cover page to this Schedule 13D set forth the number of shares of Common Stock as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated by reference.

Except as set forth herein, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer during the past sixty days.

No person (other than the Reporting Persons) is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the shares of Common Stock subject to this 13D.

Not applicable.

Lock-up Agreements The holders of substantially all of the Issuer's pre-IPO capital stock, including the Fund, the Nexus Fund, the Nexus Fund III and the Account, and each of the Issuer's directors, entered into lock-up agreements (the "Lock-Up Agreements") with the representatives of the underwriters of the Issuer's IPO. Pursuant to the Lock-Up Agreements, none of the Fund, the Nexus Fund, the Nexus Fund III and the Account is permitted, with limited exceptions, for a period of 180 days from February 6, 2025, to dispose of or hedge any of the Issuer's securities, except with the prior written consent of Goldman Sachs & Co. LLC and TD Securities (USA) LLC. The description of the Lock-Up Agreements contained in this Item 6 is qualified in its entirety by reference to the full text of the form of Lock-up Agreement filed as Exhibit 99.2 to this Schedule 13D and incorporated by reference herein. Investors' Rights Agreement On March 4, 2024, the Issuer, the Fund, the Nexus Fund, the Nexus Fund III and the Account and certain other parties entered into an amended and restated investors' rights agreement (the "Investors' Rights Agreement"). The Investors' Rights Agreement provides the Fund, the Nexus Fund, the Nexus Fund III and the Account and other parties thereto with certain demand registration rights, including shelf registration rights, in respect of the shares of Common Stock issued to it upon conversion of the convertible preferred stock, subject to certain conditions. In addition, in the event that the Issuer registers additional shares of Common Stock for its own account or for the account of other holders of its securities, the Fund, the Nexus Fund, the Nexus Fund III and the Account and certain other parties are entitled to include their shares in the registration, subject to certain limitations. The registration rights will terminate on the earlier to occur of (a) the closing of certain liquidation events, or (b) the fifth anniversary of the completion of the IPO. The Investors' Rights Agreement contains customary cross-indemnification provisions, pursuant to which the Issuer is obligated to indemnify the Fund, the Nexus Fund, the Nexus Fund III and the Account and other parties in the event of material misstatements or omissions in the registration statement attributable to the Issuer or any violation or alleged violation whether by action or inaction by the Issuer under certain securities laws and each of the Fund, the Nexus Fund, the Nexus Fund III and the Account is obligated to indemnify the Issuer for material misstatements or omissions in the registration statement attributable to it, subject to certain limitations. The description of the Investors' Rights Agreement contained in this Item 6 is qualified in its entirety by reference to the full text of the Investors' Rights Agreement filed as Exhibit 99.3 to this Schedule 13D and incorporated by reference herein. Equity Awards Joshua Resnick, a Partner at RA Capital, is a member of the Board of Directors of the Issuer. From time to time, Dr. Resnick may receive stock options or other awards of equity-based compensation pursuant to the Issuer's compensation arrangements for non-employee directors. Pursuant to an agreement with RA Capital, Dr. Resnick is obligated to transfer any securities issued under any such stock options or other awards, or the economic benefit thereof, to RA Capital.

Exhibit 99.1 Joint Filing Agreement Exhibit 99.2 Form of Lock-up Agreement (incorporated by reference to Annex II to the Form of Underwriting Agreement filed as Exhibit 1.1 to the Issuer's Registration Statement on Form S-1, as amended (Registration No. 333-284352), filed with the SEC on February 3, 2025). Exhibit 99.3 Amended and Restated Investors' Rights Agreement, by and among the Issuer and certain of its stockholders (incorporated by reference to Exhibit 4.2 to the Issuer's Registration Statement on Form S-1, as amended (Registration No. 333-284352), filed with the SEC on February 3, 2025).