X0407 4 2023-05-22 0 0001678660 Prelude Therapeutics Inc PRLD 0001263508 BAKER BROS. ADVISORS LP 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001551139 667, L.P. 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001087939 BAKER JULIAN 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001087940 BAKER FELIX 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001580575 Baker Bros. Advisors (GP) LLC 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001363364 Baker Brothers Life Sciences LP 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0 Prelude Non-Voting Common Stock 2023-05-22 4 A 0 121178 5.75 A Common Stock 121178 630658 I See Footnotes Prelude Non-Voting Common Stock 2023-05-22 4 A 0 1327044 5.75 A Common Stock 1327044 6539415 I See Footnotes Warrants to purchase Common Stock 0.0001 2023-05-22 4 A 0 970220 5.7499 A Common Stock 970220 970220 I See Footnotes Warrants to purchase Common Stock 0.0001 2023-05-22 4 A 0 10625036 5.7499 A Common Stock 10625036 10625036 I See Footnotes 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences" and together with 667, the "Funds") purchased 121,178 and 1,327,044 shares of non-voting common stock ("Non-Voting Common Stock") of Prelude Therapeutics Incorporated (the "Issuer"), respectively, for $5.75 per share pursuant to an underwritten offering that closed on May 22, 2023. The Non-Voting Common Stock have no expiration date and are convertible immediately at any time at the option of the holder on a 1-for-1 basis without consideration into common stock of the Issuer ("Common Stock") to the extent that after giving effect to such conversion the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Act of 1934, as amended, no more than 9.99% of the outstanding shares of Common Stock (the "Beneficial Ownership Limitation") immediately prior to and following such conversion. By written notice to the Issuer, the Funds may from time to time increase or decrease the Beneficial Ownership Limitation applicable to that Fund to any other percentage not in excess of 19.99%. Any such change will not be effective until the 61st day after such notice is delivered to the Issuer. After giving effect to the transaction reported herein and as a result of their ownership interest in (i) Baker Biotech Capital, L.P. and (ii) 667, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 7 of Table II directly held by 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to their interest in 667 and Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667. Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held by the Funds. Baker Bros. Advisors (GP) LLC (the "Adviser GP") is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held by the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held by the Funds. Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose. After giving effect to the transaction reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital L.P. and (ii) Life Sciences, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the securities reported in column 7 of Table II beneficially owned by Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences. 667 and Life Sciences purchased 970,220 and 10,625,036 warrants to purchase common stock of the Issuer ("Prefunded Warrants"), respectively, for $5.7499 per share pursuant to an underwritten offering that closed on May 22, 2023. The Prefunded Warrants have no expiration date and are exercisable at an exercise price of $0.0001 per share immediately at any time at the option of the holder on a 1-for-1 basis without consideration into Common Stock to the extent that after giving effect to such conversion the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Act of 1934, as amended, no more than 4.99% of the outstanding shares of Common Stock (the "Maximum Percentage") immediately prior to and following such exercise. By written notice to the Issuer, the Funds may from time to time increase or decrease the Maximum Percentage applicable to that Fund to any other percentage not in excess of 19.99%. Any such increase will not be effective until the 61st day after such notice is delivered to the Issuer. Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC, the sole general partner of Baker Bros. Advisors LP, is a director of Prelude Therapeutics Incorporated (the "Issuer"). By virtue of their representation on the Board of Directors of the Issuer, for purposes of Section 16 of the Securities Exchange Act of 1934, as amended, the reporting persons other than Julian C. Baker are deemed directors by deputization of the Issuer. By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2023-05-24 Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to 667, L.P., pursuant to authority granted by Baker Biotech Capital, L.P., GP to 667, L.P. Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2023-05-24 /s/ Julian C. Baker 2023-05-24 /s/ Felix J. Baker 2023-05-24 By: Baker Bros. Advisors (GP) LLC, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2023-05-24 Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to BAKER BROTHERS LIFE SCIENCES, L.P., pursuant to authority granted by Baker Brothers Life Sciences Capital, L.P., GP to Baker Brothers Life Sciences, L.P., Name: Scott L. Lessing, Title: President /s/ 2023-05-24