PRLD / Prelude Therapeutics Incorporated - Pengajuan SECLaporan Tahunan, Pernyataan Proksi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 June 30, 2025 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Amended and Restated Certificate of Incorporation

Exhibit 3.1 CERTIFICATE OF AMENDMENT TO AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF PRELUDE THERAPEUTICS INCORPORATED Prelude Therapeutics Incorporated, a corporation organized and existing under and by the virtue of the Delaware General Corporation Law (the “Corporation”), hereby certifies as follows: 1. The name of the Corporation is Prelude Therapeutics Incorporated. The date of the fi

Prelude Therapeutics Reports Second Quarter 2025 Financial Results and Provides Corporate Update PRT7732, once daily oral SMARCA2 degrader, currently enrolling at the seventh dosing cohort (125 mg); Company to provide an update with preliminary clini

Exhibit 99.1 Prelude Therapeutics Reports Second Quarter 2025 Financial Results and Provides Corporate Update PRT7732, once daily oral SMARCA2 degrader, currently enrolling at the seventh dosing cohort (125 mg); Company to provide an update with preliminary clinical data, including PK/PD, safety and initial clinical activity by year end 2025 Phase 1 study of PRT3789, a once weekly IV SMARCA2 degra

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 14, 2025 Prelude Therapeut

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 14, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation August 2025 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety, eff

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 11, 2025 Prelude Therapeutic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 11, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or o

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 6, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or org

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 March 31, 2025 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation May 2025 Update Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety,

Prelude Therapeutics Reports First Quarter 2025 Financial Results and Provides Corporate Update PRT3789 monotherapy and combination with docetaxel escalation enrollment is complete and the Company plans to present updated results in the second half o

Exhibit 99.1 Prelude Therapeutics Reports First Quarter 2025 Financial Results and Provides Corporate Update PRT3789 monotherapy and combination with docetaxel escalation enrollment is complete and the Company plans to present updated results in the second half of 2025 Enrollment of the Phase 1 study of Prelude’s once daily, oral SMARCA2 degrader, PRT7732 is advancing rapidly, and an initial data

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defin

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

Prelude Announces Presentations at 2025 AACR Annual Meeting Preclinical data elucidating the mechanism of action of PRT3789, Prelude’s first-in-class, highly selective SMARCA2 degrader currently in early clinical development Highlights from Prelude’s

Exhibit 99.1 Prelude Announces Presentations at 2025 AACR Annual Meeting Preclinical data elucidating the mechanism of action of PRT3789, Prelude’s first-in-class, highly selective SMARCA2 degrader currently in early clinical development Highlights from Prelude’s efforts to discover and develop selective KAT6A degraders, including preclinical data, demonstrating potential for a differentiated effi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 25, 2025 Prelude Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 25, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☒ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Defin

Notice of Delisting or Failure to Satisfy a Continued Listing Rule or Standard; Transfer of Listing

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 27, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Amended Executive Employment Agreement, dated February 4, 2025, by and between Prelude Therapeutics Incorporated and Bryant Lim.

Exhibit 10.7 AMENDED EXECUTIVE EMPLOYMENT AGREEMENT This Amended Executive Employment Agreement (the “Agreement”), made between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and Bryant Lim (“Executive” and, collectively with the Company, the “Parties”), is entered into as of February 4, 2025. Whereas, the Company desires to employ Executive as the Company’s Chief Legal

As filed with the Securities and Exchange Commission on March 10, 2025

As filed with the Securities and Exchange Commission on March 10, 2025 Registration No.

Prelude Therapeutics Reports Full Year 2024 Financial Results and Provides Program Outlook for 2025 PRT3789 has demonstrated clinical proof-of-concept that selectively degrading SMARCA2 is generally safe and has monotherapy anti-tumor activity in pat

Exhibit 99.1 Prelude Therapeutics Reports Full Year 2024 Financial Results and Provides Program Outlook for 2025 PRT3789 has demonstrated clinical proof-of-concept that selectively degrading SMARCA2 is generally safe and has monotherapy anti-tumor activity in patients with SMARCA4-deficient, non-small cell lung (NSCLC), gastric and esophageal cancer PRT3789 monotherapy dose escalation enrollment i

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 10, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Filing Fee Table

EXHIBIT 107 Calculation Of Filing Fee Tables Form S-8 Prelude Therapeutics Incorporated (Exact Name of Registrant as specified in its Charter) Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common stock, par value $0.

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation March 2025 Update Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safet

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2024 or ☐ 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 001-39527 PRELUDE THERAPE

Insider Trading Policy

Exhibit 19 INSIDER TRADING POLICY Purpose The Board of Directors (the “Board”) of Prelude Therapeutics Incorporated (“Prelude”) has adopted this Insider Trading Policy (this “Policy”) to promote compliance with U.

Exhibit B

Exhibit B Due to the relationships between them, the reporting persons hereunder may be deemed to constitute a “group” with one another for purposes of Section 13(d)(3) of the Securities Exchange Act of 1934.

Joint Filing Agreement

EX-99.A 2 e664193ex99-a.htm Exhibit A Joint Filing Agreement The undersigned agree that this Schedule 13G, and all amendments thereto, relating to the Common Stock of Prelude Therapeutics Incorporated shall be filed on behalf of the undersigned. DEERFIELD MGMT, L.P. By: J.E. Flynn Capital, LLC, General Partner By: /s/ Jonathan Isler Jonathan Isler, Attorney-In-Fact DEERFIELD MANAGEMENT COMPANY, L.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 3, 2025 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation o

Prelude Therapeutics Presents Preliminary Results of Phase 1 Dose-escalation Study of PRT2527 as Monotherapy and in Combination with Zanubrutinib in Patients with Relapsed/Refractory Lymphoid Malignancies - PRT2527 demonstrated activity across a rang

Exhibit 99.1 Prelude Therapeutics Presents Preliminary Results of Phase 1 Dose-escalation Study of PRT2527 as Monotherapy and in Combination with Zanubrutinib in Patients with Relapsed/Refractory Lymphoid Malignancies - PRT2527 demonstrated activity across a range of relapsed/refractory lymphoid malignancies, including patients who received prior CAR-T therapy - Prelude plans to seek a partner for

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 11, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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, 2024 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Prelude Therapeutics Reports Third Quarter 2024 Financial Results and Provides Corporate Update Presented interim data from the ongoing Phase 1 dose escalation study of PRT3789, its first-in-class IV SMARCA2 degrader, demonstrating clinical proof of

Exhibit 99.1 Prelude Therapeutics Reports Third Quarter 2024 Financial Results and Provides Corporate Update Presented interim data from the ongoing Phase 1 dose escalation study of PRT3789, its first-in-class IV SMARCA2 degrader, demonstrating clinical proof of concept Initiated a Phase 1 trial for PRT7732, its first-in-class oral SMARCA2 degrader in patients with SMARCA4-mutated cancers Presente

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation November 2024 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety, e

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 6, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation o

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation October 2024 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety, ef

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 24, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation o

Prelude Therapeutics Presents New Data from SMARCA Degrader Portfolio at the 36th EORTC-NCI-AACR Symposium - Interim data from ongoing trial of PRT3789 showed additional clinical activity at higher doses in patients with non-small cell lung cancer (N

Exhibit 99.1 Prelude Therapeutics Presents New Data from SMARCA Degrader Portfolio at the 36th EORTC-NCI-AACR Symposium - Interim data from ongoing trial of PRT3789 showed additional clinical activity at higher doses in patients with non-small cell lung cancer (NSCLC) - First safety data presented from combination study of PRT3789 and docetaxel demonstrated an acceptable safety profile - First pre

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation September 2024 Exhibit 99.3 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety,

Prelude Therapeutics’ SMARCA2 Degrader PRT3789 Demonstrated Promising Initial Clinical Activity and Safety Profile in Phase 1 Trial - Encouraging signs of anti-tumor activity including objective responses observed in patients with SMARCA4-mutated non

Exhibit 99.1 Prelude Therapeutics’ SMARCA2 Degrader PRT3789 Demonstrated Promising Initial Clinical Activity and Safety Profile in Phase 1 Trial - Encouraging signs of anti-tumor activity including objective responses observed in patients with SMARCA4-mutated non-small cell lung cancer (NSCLC) and esophageal cancer in early PRT3789 monotherapy dose escalation - At doses studied to date, PRT3789 wa

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 13, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

PRT3789 Phase 1 Interim Clinical Data Update from 2024 ESMO Congress 13 September 2024 Investor Presentation Exhibit 99.

Prelude Therapeutics Announces Publication of Abstract for Presentation at the European Society of Medical Oncology (ESMO) Congress 2024 PRT3789, a novel, highly-selective SMARCA2 degrader in patients with advanced solid tumors with a SMARCA4 mutatio

Exhibit 99.1 Prelude Therapeutics Announces Publication of Abstract for Presentation at the European Society of Medical Oncology (ESMO) Congress 2024 PRT3789, a novel, highly-selective SMARCA2 degrader in patients with advanced solid tumors with a SMARCA4 mutation oral session presentation: September 13, 2024, 4:00 PM CEST (10:00 AM EST) Prelude will host an investor webcast on September 13, 2024,

Regulation FD Disclosure, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 9, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 12, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, precl

Corporate Presentation August 2024 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety, eff

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 June 30, 2024 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Prelude Therapeutics Reports Second Quarter 2024 Financial Results and Provides Corporate Update Interim Phase 1 data for its first-in-class, highly selective IV SMARCA2 degrader, PRT3789, selected for an oral presentation at the European Society for

Exhibit 99.1 Prelude Therapeutics Reports Second Quarter 2024 Financial Results and Provides Corporate Update Interim Phase 1 data for its first-in-class, highly selective IV SMARCA2 degrader, PRT3789, selected for an oral presentation at the European Society for Medical Oncology (ESMO) Congress 2024 in September Received investigational new drug (IND) authorization for PRT7732, its first-in-class

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 14, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or o

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 12, 2024 Prelude Therapeutic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 12, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or o

Corporate Presentation June 2024

Corporate Presentation June 2024 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety, efficacy, benefits and addressable market for Prelude’s product candidates, the expected timeline for proof-of-concept data and clinical trial results for Prelude’s product candidates including its SMARCA2 degrader molecules.

Highly Selective SMARCA2 Degraders

Highly Selective SMARCA2 Degraders Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, anticipated discovery, preclinical and clinical development activities for Prelude’s product candidates, the potential safety, efficacy, benefits and addressable market for Prelude’s product candidates, the expected timeline for proof-of-concept data and clinical trial results for Prelude’s product candidates including its SMARCA2 degrader molecules.

June 6, 2024

June 6, 2024 VIA EDGAR Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

As filed with the Securities and Exchange Commission on May 30, 2024

Table of Contents As filed with the Securities and Exchange Commission on May 30, 2024 Registration No.

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables FORM S-3 (Form Type) Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities and Carry Forward Securities Security Type Security Class Title Fee Calculation or Carry Forward Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Carry Forward Form Type Carry Forward File Number Carry Forward Initial Effective date Filing Fee Previously Paid In Connection with Unsold Securities to be Carried Forward Newly Registered Securities Fees to Be Paid Equity Common Stock, par value $0.

Form of Debt Security

Exhibit 4.4 FORM OF DEBT SECURITY [Face of Security] PRELUDE THERAPEUTICS INCORPORATED [If applicable, insert—FOR PURPOSES OF THE ORIGINAL ISSUE DISCOUNT PROVISIONS OF THE INTERNAL REVENUE CODE OF 1986, THE ISSUE PRICE OF THIS SECURITY IS % OF ITS PRINCIPAL AMOUNT AT STATED MATURITY SET FORTH BELOW (ITS “PRINCIPAL AMOUNT”), THE AMOUNT OF ORIGINAL ISSUE DISCOUNT IS % OF ITS PRINCIPAL AMOUNT, THE YI

Form of Indenture

Exhibit 4.5 PRELUDE THERAPEUTICS INCORPORATED And , as Trustee INDENTURE Dated as of , TABLE OF CONTENTS ARTICLE 1 – DEFINITIONS AND INCORPORATION BY REFERENCE 1 1.1 DEFINITIONS 1 1.2. OTHER DEFINITIONS 4 1.3. INCORPORATION BY REFERENCE OF TRUST INDENTURE ACT 4 1.4. RULES OF CONSTRUCTION 5 ARTICLE 2 – THE SECURITIES 5 2.1. ISSUABLE IN SERIES 5 2.2. ESTABLISHMENT OF TERMS OF SERIES OF SECURITIES 5

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A (Amendment No. 1) CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 8, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction o

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 March 31, 2024 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 7, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or org

Prelude Therapeutics Reports First Quarter 2024 Financial Results and Provides Corporate Update First-in-class IV SMARCA2 degrader, PRT3789 and potentially best-in-class CDK9 inhibitor, PRT2527 remain on track to generate initial proof-of-concept dat

Exhibit 99.1 Prelude Therapeutics Reports First Quarter 2024 Financial Results and Provides Corporate Update First-in-class IV SMARCA2 degrader, PRT3789 and potentially best-in-class CDK9 inhibitor, PRT2527 remain on track to generate initial proof-of-concept data in 2024 New preclinical data presented at AACR 2024 included first characterization of PRT7732, a highly-selective, orally bioavailable

As filed with the Securities and Exchange Commission on May 6, 2024

S-3/A As filed with the Securities and Exchange Commission on May 6, 2024 Registration No.

PRELUDE THERAPEUTICS INCORPORATED 175 Innovation Boulevard Wilmington, Delaware 19805

PRELUDE THERAPEUTICS INCORPORATED 175 Innovation Boulevard Wilmington, Delaware 19805 May 6, 2024 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

PRELUDE THERAPEUTICS INCORPORATED 175 Innovation Boulevard Wilmington, Delaware 19805

PRELUDE THERAPEUTICS INCORPORATED 175 Innovation Boulevard Wilmington, Delaware 19805 May 3, 2024 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

PRELUDE THERAPEUTICS INCORPORATED 175 Innovation Boulevard Wilmington, Delaware 19805

PRELUDE THERAPEUTICS INCORPORATED 175 Innovation Boulevard Wilmington, Delaware 19805 May 1, 2024 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defin

Separation Agreement and General Release, dated April 10, 2024, by and between Prelude Therapeutics Incorporated and Laurent Chardonnet.

Exhibit 10.2 SEPARATION AGREEMENT AND GENERAL RELEASE This Separation Agreement and General Release (“Agreement”) is between Prelude Therapeutics Incorporated (“Company”) and Laurent Chardonnet (“Employee”). WHEREAS, the Company and Employee agreed that Employee will not serve as an employee as of April 8, 2024 (“Termination Date”); WHEREAS, the Company is willing to pay Employee certain severance

Consulting Agreement, dated April 10, 2024, by and between Prelude Therapeutics Incorporated and Laurent Chardonnet.

Exhibit 10.1 PRELUDE THERAPEUTICS INCORPORATED CONSULTING AGREEMENT This Consulting Agreement (this “Agreement”) is entered into April 8th, 2024 (the “Effective Date”) between Prelude Therapeutics Incorporated, a Delaware corporation with its principal place of business at 175 Innovation Boulevard, Wilmington, Delaware 19805 USA (“Company”) and Laurent Chardonnet (“Consultant”). Company desires to

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 8, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or o

As filed with the Securities and Exchange Commission on February 15, 2024

As filed with the Securities and Exchange Commission on February 15, 2024 Registration No.

Filing Fee Table

EX-FILING FEES Exhibit 107 Calculation of Fee Filing Tables Form S-3 (Form Type) Prelude Therapeutics Incorporated (Exact name of Registrant as Specified in its Charter) Table 1 – Newly Registered Securities Security Type  Security Class Title Fee Calculation or Carry Forward Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common stock, par value $0.

Filing Fee Table

EXHIBIT 107 Calculation Of Filing Fee Tables Form S-8 Prelude Therapeutics Incorporated (Exact Name of Registrant as specified in its Charter) Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common stock, par value $0.

As filed with the Securities and Exchange Commission on February 15, 2024

S-3 Table of Contents As filed with the Securities and Exchange Commission on February 15, 2024 Registration No.

Subsidiaries of Prelude Therapeutics Incorporated.

Exhibit 21.1 LIST OF SUBSIDIARIES As of the date of this Annual Report on Form 10-K, Prelude Therapeutics Incorporated has no subsidiaries.

Form of Securities Purchase Agreement by and among Prelude Therapeutics Incorporated and certain Investors.

Exhibit 10.13 SECURITIES PURCHASE AGREEMENT This SECURITIES PURCHASE AGREEMENT (this “Agreement”) is made and entered into as of December 11, 2023, by and among Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and the Investors identified on Exhibit A attached hereto (each an “Investor” and collectively the “Investors”). Recitals A. The Company and the Investors are execu

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2023 OR ☐ 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 001-39527 PRELUDE THERAPE

Exhibit 4.5

Exhibit 4.5 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of December 31, 2023, Prelude Therapeutics Incorporated (the “Company,” “we” or “our”) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934 (the “Exchange Act”): our common stock, $0.0001 par value per share. Our non-voting com

Executive Employment Agreement, dated January 30, 2023, by and between the Registrant and Bryant Lim.

Exhibit 10.7 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the “Agreement”), made between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and Bryant Lim (“Executive” and, collectively with the Company, the “Parties”), is entered into as of January 30, 2023. Whereas, the Company desires to employ Executive as the Company’s Chief Legal Counsel and Cor

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 15, 2024 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

Compensation Recovery Policy of Prelude Therapeutics Incorporated

Exhibit 97.1 prelude therapeutics incorporated Compensation Recovery Policy (Adopted September 2023) The Board has determined that it is in the best interests of the Company and its stockholders to adopt this Policy enabling the Company to recover from specified current and former Company executives certain incentive-based compensation in the event of an accounting restatement resulting from mater

Form of Amended and Restated Registration Rights Agreement by and among Prelude Therapeutics Incorporated and certain Investors.

Exhibit 4.4 AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT This Amended and Restated Registration Rights Agreement (this “Agreement”) is made as of December 11, 2023, by and between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and the persons listed on the attached Schedule A who are signatories to this Agreement (collectively, the “Investors”). Unless otherwise d

Prelude Therapeutics Reports Full Year 2023 Financial Results and Outlines Key Objectives for 2024 First-in-class IV SMARCA2 degrader and potentially best-in-class CDK9 inhibitor on track to generate potential proof-of-concept data in 2024 Highly sel

Exhibit 99.1 Prelude Therapeutics Reports Full Year 2023 Financial Results and Outlines Key Objectives for 2024 First-in-class IV SMARCA2 degrader and potentially best-in-class CDK9 inhibitor on track to generate potential proof-of-concept data in 2024 Highly selective oral SMARCA2 degrader PRT7732 IND expected to be filed in first half and enter Phase 1 clinical trial in second half of 2024 Recen

PRLD / Prelude Therapeutics Incorporated / Flynn James E Passive Investment

SC 13G/A 1 e619249sc13ga-prelude.htm SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b)(c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendment No. 1) * Prelude Therapeutics Incorporated (Name of Issuer) Common Stock (Title of Class of Securities) 74065P101 (CUSIP Number

PRLD / Prelude Therapeutics Incorporated / Vaddi Krishna - SC 13G/A Passive Investment

SC 13G/A 1 d749523dsc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 3)* Prelude Therapeutics Incorporated (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 74065P101 (CUSIP Number) December 31, 2023 (Date of Event Which Requires Filing of this S

Amended and Restated Registration Rights Agreement by and between 667, L.P., Baker Brothers Life Sciences, L.P., and Prelude Therapeutics Incorporated, dated as of December 11, 2023.

EX-99.2 3 tm2332807d1ex99-2.htm EXHIBIT 99.2 Exhibit 99.2 EXECUTION VERSION AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT This Amended and Restated Registration Rights Agreement (this “Agreement”) is made as of December 11, 2023, by and between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and the persons listed on the attached Schedule A who are signatories to th

PRLD / Prelude Therapeutics Inc / BAKER BROS. ADVISORS LP - SC 13D/A Activist Investment

SC 13D/A 1 tm2332807d1sc13da.htm SC 13D/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13D (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (Amendment No. 3)* Prelude Therapeutics Incorporated (Name of Issuer) Common stock, par value $0.0001 per share (Title of Class of S

Securities Purchase Agreement by and between 667, L.P., Baker Brothers Life Sciences, L.P., and Prelude Therapeutics Incorporated, dated as of December 11, 2023.

EX-99.1 2 tm2332807d1ex99-1.htm EXHIBIT 99.1 Exhibit 99.1 EXECUTION VERSION SECURITIES PURCHASE AGREEMENT This SECURITIES PURCHASE AGREEMENT (this “Agreement”) is made and entered into as of December 11, 2023, by and among Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and the Investors identified on Exhibit A attached hereto (each an “Investor” and collectively the “In

Prelude Therapeutics Announces $25 Million Private Placement

Exhibit 99.1 Prelude Therapeutics Announces $25 Million Private Placement WILMINGTON, DE, Dec. 11, 2023 – Prelude Therapeutics Incorporated (Nasdaq: PRLD) (“Prelude” or the “Company”), a clinical-stage precision oncology company, today announced a private placement that the Company estimates will result in gross proceeds of approximately $25 million before deducting estimated offering expenses pay

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 11, 2023 Prelude Therape

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 11, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

Form of Pre-Funded Warrant

Exhibit 4.1 NEITHER THE ISSUANCE AND SALE OF THE SECURITIES REPRESENTED BY THIS CERTIFICATE NOR THE SECURITIES INTO WHICH THESE SECURITIES ARE EXERCISABLE HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR APPLICABLE STATE SECURITIES LAWS. THE SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD, TRANSFERRED OR ASSIGNED (I) IN THE ABSENCE OF (A) AN EFFECTIVE REGISTRATION STATEMENT FOR T

PRLD / Prelude Therapeutics Inc / Flynn James E - SCHEDULE 13G Passive Investment

SC 13G 1 e619055sc13g-prelude.htm SCHEDULE 13G SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b)(c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendment No. ) * Prelude Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 74065P101 (CUSIP Numb

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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, 2023 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Prelude Announces Strategic Pipeline Progress and Updates, including its Partnership with AbCellera, and Reports Third Quarter Financial Results Prioritization of its first-in-class SMARCA2 degrader and potentially best-in-class CDK9 inhibitor progra

Exhibit 99.1 Prelude Announces Strategic Pipeline Progress and Updates, including its Partnership with AbCellera, and Reports Third Quarter Financial Results Prioritization of its first-in-class SMARCA2 degrader and potentially best-in-class CDK9 inhibitor programs for continued clinical development Enters partnership with AbCellera to develop a portfolio of precision ADCs with first program being

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 1, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation o

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

EX-99.2 Corporate Presentation July 2023 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enro

Amended and Restated Certificate of Incorporation

Exhibit 3.1 PRELUDE THERAPEUTICS INCORPORATED AMENDED AND RESTATED CERTIFICATE OF INCORPORATION Prelude Therapeutics Incorporated (the “Corporation”), a corporation organized and existing under and by virtue of the Delaware General Corporation Law, hereby certifies as follows: 1. The name of the Corporation is “Prelude Therapeutics Incorporated.” The date of the filing of its original Certificate

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 3, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 June 30, 2023 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Prelude Therapeutics Announces Second Quarter 2023 Financial Results and Provides Corporate Update Four lead programs on track to deliver clinical data and to inform future development plans. Recent equity financing extends cash runway into 2026, ena

EX-99.1 Exhibit 99.1 Prelude Therapeutics Announces Second Quarter 2023 Financial Results and Provides Corporate Update Four lead programs on track to deliver clinical data and to inform future development plans. Recent equity financing extends cash runway into 2026, enabling advancement of Prelude’s pipeline through critical milestones WILMINGTON, Del. – (Globe Newswire) August 3, 2023 – Prelude

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 16, 2023 Prelude Therapeutic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 16, 2023 Prelude Therapeutics Incorporated (Exact name of Registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (Co

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 1, 2023 Prelude Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 1, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or or

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

Corporate Presentation May 2023 Exhibit 99.1 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enroll or com

PRLD / Prelude Therapeutics Inc / BAKER BROS. ADVISORS LP - SC 13D/A Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13D (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (Amendment No.

PRLD / Prelude Therapeutics Inc / ORBIMED ADVISORS LLC - AMENDMENT NO. 2 Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. 2)* Prelude Therapeutics Incorporated (Name of Issuer) COMMON STOCK (Title of Class of Securities) 74065P101 (CUSIP Number) OrbiMed Advisors LLC OrbiMed Capital GP VI LLC OrbiMed Capital LLC 601 Lexington Avenue, 54th Floor New York, NY 10022 Telephone: (212

JOINT FILING AGREEMENT

Exhibit 1 JOINT FILING AGREEMENT The undersigned hereby agree that Amendment No. 2 to the Statement on Schedule 13D, dated May 22, 2023, with respect to the common stock of Prelude Therapeutics Incorporated is filed on behalf of each of us pursuant to and in accordance with the provisions of Rule 13d-1(k) under the Securities Exchange Act of 1934, as amended. Each of the undersigned agrees to be r

Prelude Therapeutics Announces Launch of Proposed Public Offering

EX-99.1 Exhibit 99.1 Prelude Therapeutics Announces Launch of Proposed Public Offering WILMINGTON, Del. – (Globe Newswire) May 17, 2023 – Prelude Therapeutics Incorporated (“Prelude” or the “Company”) (Nasdaq: PRLD), a clinical-stage precision oncology company, today announced that it has commenced an underwritten public offering of $100.0 million of shares of common stock and, in lieu of common s

4,496,744 Shares of Common Stock Pre-Funded Warrants to Purchase 12,895,256 Shares of Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-261019 PROSPECTUS SUPPLEMENT (To Prospectus Dated November 24, 2021) 4,496,744 Shares of Common Stock Pre-Funded Warrants to Purchase 12,895,256 Shares of Common Stock We are offering 4,496,744 shares of our common stock and, in lieu of common stock to certain investors that so choose, pre-funded warrants to purchase 12,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 18, 2023 Prelude Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 18, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or or

Prelude Therapeutics Announces Pricing of Public Offering

EX-99.2 Exhibit 99.2 Prelude Therapeutics Announces Pricing of Public Offering WILMINGTON, Del. – (Globe Newswire) May 18, 2023 – Prelude Therapeutics Incorporated (“Prelude” or the “Company”) (Nasdaq: PRLD), a clinical-stage precision oncology company, today announced the pricing of its underwritten public offering of 3,048,522 shares of its voting common stock and 1,448,222 shares of its non-vot

Underwriting Agreement dated May 18, 2023

EX-1.1 Exhibit 1.1 4,496,744 SHARES OF COMMON STOCK (PAR VALUE $0.0001 PER SHARE) PRE-FUNDED WARRANTS TO PURCHASE 12,895,256 SHARES OF COMMON STOCK PRELUDE THERAPEUTICS INCORPORATED UNDERWRITING AGREEMENT May 18, 2023 May 18, 2023 Morgan Stanley & Co. LLC As Representative of the several Underwriters named in Schedule I hereto c/o Morgan Stanley & Co. LLC 1585 Broadway New York, New York 10036 Lad

Form of Pre-Funded Warrant

EX-4.1 Exhibit 4.1 PRELUDE THERAPEUTICS INCORPORATED FORM OF PRE-FUNDED WARRANT TO PURCHASE COMMON STOCK Number of Shares: [ ] (subject to adjustment) Warrant No. Original Issue Date: [ ], 2023 Prelude Therapeutics incorporated, a Delaware corporation (the “Company”), hereby certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, [ ] or it

Prelude Therapeutics Incorporated

FWP Free Writing Prospectus Filed Pursuant to Rule 433 To Prospectus dated November 24, 2021 Preliminary Prospectus Supplement dated May 17, 2023 Registration Statement File No.

$100,000,000 Shares of Common Stock Pre-Funded Warrants to Purchase Shares of Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-261019 This preliminary prospectus supplement and the accompanying prospectus relate to an effective registration statement under the Securities Act of 1933, as amended, but the information in this prospectus supplement is not complete and may be changed. This preliminary prospectus supplement and the accompanying prospe

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 17, 2023 Prelude Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 17, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or or

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

EX-99.1 Corporate Presentation May 2023 Exhibit 99.1 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enrol

Prelude Therapeutics Announces First Quarter 2023 Financial Results and Operations Update Eight abstracts presented at AACR 2023 demonstrate progress of the pipeline Cash runway unchanged, supporting operations into the fourth quarter of 2024

Exhibit 99.1 Prelude Therapeutics Announces First Quarter 2023 Financial Results and Operations Update Eight abstracts presented at AACR 2023 demonstrate progress of the pipeline Cash runway unchanged, supporting operations into the fourth quarter of 2024 WILMINGTON, Del. – May 8, 2023 – Prelude Therapeutics Incorporated (Nasdaq: PRLD), a clinical-stage precision oncology company, today reported f

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

Corporate Presentation May 2023 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enroll or com

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 8, 2023 Prelude Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 8, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or org

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 March 31, 2023 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defin

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☒ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Defin

Filing Fee Table

EXHIBIT 107.1 Calculation Of Filing Fee Tables Form S-8 Prelude Therapeutics Incorporated (Exact Name of Registrant as specified in its Charter) Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common stock, par value $0.0001 p

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

Corporate Presentation March 2023 Exhibit 99.2 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enroll or c

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 15, 2023 Prelude Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 15, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Prelude Therapeutics Reports Full Year 2022 Financial Results and Provides Corporate Update Four differentiated clinical compounds progressing through Phase 1 towards key data milestones Eight abstracts accepted for presentation at the 2023 American

Exhibit 99.1 Prelude Therapeutics Reports Full Year 2022 Financial Results and Provides Corporate Update Four differentiated clinical compounds progressing through Phase 1 towards key data milestones Eight abstracts accepted for presentation at the 2023 American Association for Cancer Research (AACR) Annual Meeting Cash balance of $201.7 million as of December 31, 2022; runway remains unchanged th

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2022 OR ☐ 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 001-39527 PRELUDE THERAPE

Exhibit 4.4

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of December 31, 2022, Prelude Therapeutics Incorporated (the “Company,” “we” or “our”) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934 (the “Exchange Act”): our common stock, $0.0001 par value per share. Our non-voting com

Open Market Sale Agreement SM, dated March 15, 2023, by and between Prelude Therapeutics Incorporated and Jefferies LLC.

EX-1.1 Exhibit 1.1 OPEN MARKET SALE AGREEMENTSM March 15, 2023 JEFFERIES LLC 520 Madison Avenue New York, New York 10022 Ladies and Gentlemen: Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), proposes, subject to the terms and conditions stated herein, to issue and sell from time to time through Jefferies LLC, as sales agent and/or principal (the “Agent”), shares of the C

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 15, 2023 Prelude Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 15, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

As filed with the Securities and Exchange Commission on March 15, 2023

As filed with the Securities and Exchange Commission on March 15, 2023 Registration No.

Up to $75,000,000 Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-261019 PROSPECTUS SUPPLEMENT (to Prospectus dated November 24, 2021) Up to $75,000,000 Common Stock We have entered into an Open Market Sale AgreementSM,, or Sales Agreement, with Jefferies LLC, or Jefferies, relating to shares of our common stock, par value $0.0001 per share, offered by this prospectus supplement. In ac

Prelude Therapeutics Announces Clinical Trial Collaboration with BeiGene to Evaluate PRT2527 in Combination with Zanubrutinib in Hematologic Cancers

Exhibit 99.3 Prelude Therapeutics Announces Clinical Trial Collaboration with BeiGene to Evaluate PRT2527 in Combination with Zanubrutinib in Hematologic Cancers WILMINGTON, Del. – March 15, 2023 – Prelude Therapeutics Incorporated (Prelude) (Nasdaq: PRLD), a clinical-stage precision oncology company, today announced a clinical trial collaboration with BeiGene, for future evaluation of its investi

Regulation FD Disclosure, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 14, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

SVB Global Biopharma Conference Presentation February 2023 Exhibit 99.1 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability

PRLD / Prelude Therapeutics Inc / Vaddi Krishna - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 2)* Prelude Therapeutics Incorporated (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 74065P101 (CUSIP Number) December 31, 2022 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 19, 2023 Prelude Therapeu

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 19, 2023 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation o

Amended and Restated Bylaws

Exhibit 3.1 PRELUDE THERAPEUTICS INCORPORATED (a Delaware corporation) AMENDED AND RESTATED BYLAWS As Amended and Restated on January 19, 2023 PRELUDE THERAPEUTICS INCORPORATED (a Delaware corporation) AMENDED AND RESTATED BYLAWS TABLE OF CONTENTS Page Article I: STOCKHOLDERS 1 Section 1.1: Annual Meetings 1 Section 1.2: Special Meetings 1 Section 1.3: Notice of Meetings 1 Section 1.4: Adjournment

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

EX-99.1 2 prld-ex991.htm EX-99.1 Corporate Presentation January 2023 Exhibit 99.1 Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing a

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 9, 2023 Prelude Therapeut

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 9, 2023 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Second Amendment to Single-Tenant Triple Net Lease, dated August 8, 2022, by and between Prelude Therapeutics Incorporated and CRISP Partners LLC

Exhibit 10.1 CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS NOT MATERIAL AND WOULD LIKELY CAUSE COMPETITIVE HARM TO THE COMPANY IF PUBLICY DISCLOSED. SECOND AMENDMENT TO SINGLE-TENANT TRIPLE NET LEASE This SECOND AMENDMENT TO SINGLE-TENANT TRIPLE NET LEASE (this ?Second Amendment?), is made on this 8th day of August, 2022, by and betwee

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 14, 2022 Prelude Therape

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 14, 2022 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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, 2022 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Prelude Therapeutics Announces Third Quarter 2022 Financial Results and Provides Business Update FDA clearance of two new INDs: PRT3789 (First-in-class Selective SMARCA2 degrader) and PRT3645 (next generation CDK4/6 inhibitor) Company to reprioritize

Exhibit 99.1 Prelude Therapeutics Announces Third Quarter 2022 Financial Results and Provides Business Update FDA clearance of two new INDs: PRT3789 (First-in-class Selective SMARCA2 degrader) and PRT3645 (next generation CDK4/6 inhibitor) Company to reprioritize clinical pipeline and discontinue PRMT5 program for internal development Strong cash, cash equivalents and marketable securities of $224

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

PRELUDE Corporate Presentation NOVEMBER 2022 Exhibit 99.2 Forward Looking Statements This presentation contains ?forward-looking? statements within the meaning of the ?safe harbor? provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 June 30, 2022 OR ? 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Separation Agreement, dated April 6, 2022, between the Registrant and Deborah Morosini, M.D.

Exhibit 10.1 PRELUDE THERAPEUTICS INCORPORATED CONSULTING AGREEMENT THIS CONSULTING AGREEMENT (this ?Agreement?) is entered into as of May 6, 2022 (the ?Effective Date?) between Prelude Therapeutics Incorporated, a Delaware corporation with its principal place of business at 200 Powder Mill Road, Experimental Station E400/3213, Wilmington, Delaware 19803 USA (?Company?) and Deborah Morosini (?Cons

Prelude Therapeutics Announces Second Quarter 2022 Financial Results and Business Update Prelude Announces Acceptance of IND For a Differentiated and Brain Penetrant CDK4/6 inhibitor PRT3645 by the US Food and Drug Administration (FDA) Clinical data

Exhibit 99.1 Prelude Therapeutics Announces Second Quarter 2022 Financial Results and Business Update Prelude Announces Acceptance of IND For a Differentiated and Brain Penetrant CDK4/6 inhibitor PRT3645 by the US Food and Drug Administration (FDA) Clinical data readouts and next steps for the PRMT5 program, MCL1 inhibitor PRT1419, and CDK9 inhibitor PRT2527 are on track for the second half of 202

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 9, 2022 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 17, 2022 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (Co

Prelude Therapeutics Announces First Quarter 2022 Financial Results and Operations Update Prelude remains on track for clinical data readouts and next steps for the PRMT5 program, MCL1 inhibitor PRT1419, and CDK9 inhibitor PRT2527 in 2H2022 Strong ca

Exhibit 99.1 Prelude Therapeutics Announces First Quarter 2022 Financial Results and Operations Update Prelude remains on track for clinical data readouts and next steps for the PRMT5 program, MCL1 inhibitor PRT1419, and CDK9 inhibitor PRT2527 in 2H2022 Strong cash and cash equivalents of $266.2 million as of March 31, 2022, expected to fund operations into 2H2024 Wilmington, DE ? May 10, 2022 ? P

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 10, 2022 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or or

Executive Employment Agreement, dated January 21, 2022, by and between Registrant and Jane Huang.

Exhibit 10.1 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the ?Agreement?), made between Prelude Therapeutics Incorporated, a Delaware corporation (the ?Company?), and Jane Huang (?Executive? and, collectively with the Company, the ?Parties?), is entered into as of January 21, 2022 (the ?Effective Date?). Whereas, the Company desires to employ Executive as the Company?s Pres

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 March 31, 2022 OR ? 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ? Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ? Definitive Proxy State

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ? Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ? Definitive Proxy State

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 6, 2022 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or o

Description of Voting Common Stock Registered Under Section 12 of the Securities Exchange Act of 1943, as amended.

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of December 31, 2021, Prelude Therapeutics Incorporated (the ?Company,? ?we? or ?our?) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934 (the ?Exchange Act?): our common stock, $0.0001 par value per share. Our non-voting com

Executive Employment Agreement, dated December 19, 2020, by and between the Registrant and Brian Piper.

Exhibit 10.10 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the ?Agreement?), made between Prelude Therapeutics Incorporated, a Delaware corporation (the ?Company?), and Brian Piper (?Executive? and, collectively with the Company, the ?Parties?), is entered into as of December 19, 2020 (the ?Effective Date?). Whereas, the Company desires to continue to employ Executive as the

Executive Employment Agreement, dated December 19, 2020, by and between the Registrant and Peggy Scherle.

Exhibit 10.7 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the ?Agreement?), made between Prelude Therapeutics Incorporated, a Delaware corporation (the ?Company?), and Peggy Scherle (?Executive? and, collectively with the Company, the ?Parties?), is entered into as of December 19, 2020 (the ?Effective Date?). Whereas, the Company desires to continue to employ Executive as th

First Amendment to Single-Tenant Triple Net Lease, dated November 30, 2021, by and between the Registrant and Crisp Partners, LLC.

Exhibit 10.12 FIRST AMENDMENT TO SINGLE-TENANT TRIPLE NET LEASE This FIRST AMENDMENT TO SINGLE-TENANT TRIPLE NET LEASE (the ?First Amendment?) is made as of 11/15/2021, by and between CRISP PARTNERS LLC, a Delaware limited liability company (?Landlord?) and PRELUDE THERAPEUTICS INCORPORATED, a Delaware corporation (?Tenant?). WHEREAS, Landlord and Tenant entered into that certain Single-Tenant Tri

Filing Fee Table

EXHIBIT 107.1 Calculation Of Filing Fee Tables Form S-8 Prelude Therapeutics Incorporated (Exact Name of Registrant as specified in its Charter) Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common stock, par value $0.0001 p

Single-Tenant Triple Net Lease, dated November 30, 2021, by and between the Registrant and Crisp Partners, LLC.

Exhibit 10.11 CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS NOT MATERIAL AND WOULD LIKELY CAUSE COMPETITIVE HARM TO THE COMPANY IF PUBLICY DISCLOSED. SINGLE-TENANT TRIPLE NET LEASE This Single-Tenant Triple Net Lease (this ?Lease?) is made and entered into as of September 13, 2021 (the ?Effective Date?), by and between CRISP PARTNERS L

Executive Employment Agreement, dated November 5, 2021, by and between Registrant and Laurent Chardonnet.

Exhibit 10.9 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the ?Agreement?), made between Prelude Therapeutics Incorporated, a Delaware corporation (the ?Company?), and Laurent Chardonnet (?Executive? and, collectively with the Company, the ?Parties?), is entered into as of 11/5/2021 | 5:16 PM EDT. Whereas, the Company desires to employ Executive as the Company?s Chief Financ

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2021 OR ? 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 001-39527 PRELUDE THERAPE

Executive Employment Agreement, dated December 19, 2020, by and between the Registrant and Andrew Combs.

Exhibit 10.8 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the ?Agreement?), made between Prelude Therapeutics Incorporated, a Delaware corporation (the ?Company?), and Andrew Combs (?Executive? and, collectively with the Company, the ?Parties?), is entered into as of December 19, 2020 (the ?Effective Date?). Whereas, the Company desires to continue to employ Executive as the

As filed with the Securities and Exchange Commission on March 17, 2022

As filed with the Securities and Exchange Commission on March 17, 2022 Registration No.

Prelude Therapeutics Reports Full Year 2021 Financial Results Significant progress achieved in 2021: Pipeline now includes six internally discovered small molecule compounds targeting clinically validated pathways in cancers with underserved patients

Exhibit 99.1 Prelude Therapeutics Reports Full Year 2021 Financial Results Significant progress achieved in 2021: Pipeline now includes six internally discovered small molecule compounds targeting clinically validated pathways in cancers with underserved patients Objectives for 2022: Focused on demonstrating proof-of-concept clinical data for lead pipeline compounds and continued advancement of Pr

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 16, 2022 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Regulation FD Disclosure, Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 9, 2022 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (Co

Jane Huang, M.D., Joins Prelude Therapeutics as President and Chief Medical Officer

Exhibit 99.1 Jane Huang, M.D., Joins Prelude Therapeutics as President and Chief Medical Officer Wilmington, DE ? March 9, 2022 ? Prelude Therapeutics Incorporated (Nasdaq: PRLD) a clinical-stage precision oncology company, today announced that Jane Huang, M.D., has been appointed to the newly created position of President and Chief Medical Officer, effective on April 4, 2022. Dr. Huang is current

Prelude Therapeutics Provides Clinical Update and Announces Presentation of New Preclinical Data at the Upcoming 2022 AACR Annual Meeting Announces strategic prioritization within lead programs targeting PRMT5 and MCL1 Describes new pipeline candidat

Exhibit 99.2 Prelude Therapeutics Provides Clinical Update and Announces Presentation of New Preclinical Data at the Upcoming 2022 AACR Annual Meeting Announces strategic prioritization within lead programs targeting PRMT5 and MCL1 Describes new pipeline candidate, PRT3645, a highly brain penetrant CDK4/6 inhibitor; IND submission planned mid-2022 Advances PRT2527, a highly selective CDK9 inhibito

Regulation FD Disclosure, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 16, 2022 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation)

Forward-Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

Exhibit 99.1 Precision Oncology Redefined February 2022 Forward-Looking Statements This presentation contains ?forward-looking? statements within the meaning of the ?safe harbor? provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, en

PRLD / Prelude Therapeutics Inc / Vaddi Krishna - SC 13G/A Passive Investment

SC 13G/A 1 d221199dsc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 1)* Prelude Therapeutics Incorporated (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 74065P101 (CUSIP Number) December 31, 2021 (Date of Event Which Requires Filing of this S

Forward Looking Statements This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and com

Precision Oncology Redefined Corporate Presentation January 2022 Exhibit 99.1 Forward Looking Statements This presentation contains ?forward-looking? statements within the meaning of the ?safe harbor? provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and a

Regulation FD Disclosure, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 10, 2022 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation)

Entry into a Material Definitive Agreement

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 30, 2021 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation)

PRELUDE THERAPEUTICS INCORPORATED 200 Powder Mill Road Wilmington, Delaware 19803

PRELUDE THERAPEUTICS INCORPORATED 200 Powder Mill Road Wilmington, Delaware 19803 November 22, 2021 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

Form of Debt Security

Exhibit 4.4 FORM OF DEBT SECURITY [Face of Security] PRELUDE THERAPEUTICS INCORPORATED [If applicable, insert?FOR PURPOSES OF THE ORIGINAL ISSUE DISCOUNT PROVISIONS OF THE INTERNAL REVENUE CODE OF 1986, THE ISSUE PRICE OF THIS SECURITY IS % OF ITS PRINCIPAL AMOUNT AT STATED MATURITY SET FORTH BELOW (ITS ?PRINCIPAL AMOUNT?), THE AMOUNT OF ORIGINAL ISSUE DISCOUNT IS % OF ITS PRINCIPAL AMOUNT, THE YI

Form of Indenture

Exhibit 4.5 PRELUDE THERAPEUTICS INCORPORATED And , as Trustee INDENTURE Dated as of , TABLE OF CONTENTS ARTICLE 1 ? DEFINITIONS AND INCORPORATION BY REFERENCE 1 1.1 DEFINITIONS 1 1.2. OTHER DEFINITIONS 4 1.3. INCORPORATION BY REFERENCE OF TRUST INDENTURE ACT 4 1.4. RULES OF CONSTRUCTION 5 ARTICLE 2 ? THE SECURITIES 5 2.1. ISSUABLE IN SERIES 5 2.2. ESTABLISHMENT OF TERMS OF SERIES OF SECURITIES 5

Prelude Therapeutics Announces Third Quarter 2021 Financial Results and Operations Update PRT543 and PRT811 Demonstrate Favorable Safety Profile, Tolerability and Evidence of Preliminary Clinical Activity in Phase 1 Dose Escalation in Unselected Pati

Exhibit 99.1 Prelude Therapeutics Announces Third Quarter 2021 Financial Results and Operations Update PRT543 and PRT811 Demonstrate Favorable Safety Profile, Tolerability and Evidence of Preliminary Clinical Activity in Phase 1 Dose Escalation in Unselected Patients Phase 1 Dose Expansion Ongoing in Biomarker-Selected Solid Tumor and Hematologic Malignancy Expansion Cohorts for PRT543; Dose Expan

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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, 2021 OR ? 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

As filed with the Securities and Exchange Commission on November 12, 2021

Table of Contents As filed with the Securities and Exchange Commission on November 12, 2021 Registration No.

2 Disclaimer This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize sma

Corporate Presentation November 2021 Exhibit 99.2 2 Disclaimer This presentation contains ?forward-looking? statements within the meaning of the ?safe harbor? provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enroll or complete cli

Regulation FD Disclosure, Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 5, 2021 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation o

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 16, 2021 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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 June 30, 2021 OR ? 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Prelude Therapeutics Announces Second Quarter 2021 Financial Results and Operations Update - Data from Dose Escalation Portion of Phase 1 Trials of Lead Oral PRMT5 Inhibitors PRT543 and PRT811 to be Presented in 4Q21 – - Enrollment Ongoing in Multipl

Exhibit 99.1 Prelude Therapeutics Announces Second Quarter 2021 Financial Results and Operations Update - Data from Dose Escalation Portion of Phase 1 Trials of Lead Oral PRMT5 Inhibitors PRT543 and PRT811 to be Presented in 4Q21 ? - Enrollment Ongoing in Multiple Expansion Cohorts in Phase 1 Trial of PRT543; Dose Expansion Portion of Phase 1 Trial of PRT811 Expected to Commence in 3Q21 ? - Dose E

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 12, 2021 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 15, 2021 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (Co

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 18, 2021 Prelude Therapeutics Incorporated (Exact name of Registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (Co

Disclaimer This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small

Corporate Presentation May 2021 Exhibit 99.1 Disclaimer This presentation contains ?forward-looking? statements within the meaning of the ?safe harbor? provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enroll or complete clinical s

Regulation FD Disclosure, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 12, 2021 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (Com

Quarterly Report - 10-Q

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 March 31, 2021 OR ? 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 11, 2021 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or or

Prelude Therapeutics Announces First Quarter 2021 Financial Results and Operations Update - Enrollment Now Underway in Multiple Solid Tumor and Hematologic Malignancy Expansion Cohorts in Phase 1 Trial of Oral PRMT5 Inhibitor PRT543 - - Initial Clini

Exhibit 99.1 Prelude Therapeutics Announces First Quarter 2021 Financial Results and Operations Update - Enrollment Now Underway in Multiple Solid Tumor and Hematologic Malignancy Expansion Cohorts in Phase 1 Trial of Oral PRMT5 Inhibitor PRT543 - - Initial Clinical Data Readouts for Lead Oral PRMT5 Inhibitors PRT543 and PRT811 Expected in 2H21 - - Dose Escalation Ongoing in Phase 1 Trial of Oral

Schedule 14A

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A (Rule 14a-101) SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ? Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (

- DEFA14A

SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

Regulation FD Disclosure, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 17, 2021 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation) (C

Disclaimer This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small

Corporate Presentation March 2021 Exhibit 99.1 Disclaimer This presentation contains ?forward-looking? statements within the meaning of the ?safe harbor? provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about timing and ability to commence, enroll or complete clinical

Description of Voting Common Stock Registered Under Section 12 of the Securities Exchange Act of 1943, as amended

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of December 31, 2020, Prelude Therapeutics Incorporated (the ?Company,? ?we? or ?our?) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934 (the ?Exchange Act?): our common stock, $0.0001 par value per share. Our non-voting com

Prelude Therapeutics Announces Fourth Quarter and Full Year 2020 Financial Results and Provides Operational Update – Dose Escalation Portion of Phase 1 Trial of PRT543 Complete; Additional Expansion Cohorts Set to Initiate Early in the Second Quarter

Exhibit 99.1 Prelude Therapeutics Announces Fourth Quarter and Full Year 2020 Financial Results and Provides Operational Update ? Dose Escalation Portion of Phase 1 Trial of PRT543 Complete; Additional Expansion Cohorts Set to Initiate Early in the Second Quarter ? ?Clinical Data Readouts Expected in 2H21 for Lead PRMT5 Inhibitors PRT543 and PRT811 ? ? Phase 1 Dose-Escalation Study of Oral PRT1419

Annual Report - 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2020 OR ? 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 001-39527 PRELUDE THERAPE

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 16, 2021 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation or

- S-8

As filed with the Securities and Exchange Commission on March 16, 2021 Registration No.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 2, 2021 Prelude Therapeutics Incorporated (Exact name of registrant as specified in its charter) Delaware (State or other jurisdiction of incorporation) Delaware 001-39527 81-13

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Prelude Therapeutics Incorporated (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Cl

SC 13G UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Prelude Therapeutics Incorporated (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 74065P101 (CUSIP Number) December 31, 2020 (Date of Event Which Requires Filing of this Statement) Check the appropriate box

Lock-Up Agreement by and among Morgan Stanley & Co. LLC, Goldman Sachs & Co. LLC, BofA Securities, Inc. and the Funds dated July 23, 2020.

Exhibit 99.2 FORM OF LOCK-UP AGREEMENT July 23, 2020 Morgan Stanley & Co. LLC Goldman Sachs & Co. LLC BofA Securities, Inc. c/o Morgan Stanley & Co. LLC 1585 Broadway New York, NY 10036 c/o Goldman Sachs & Co. LLC 200 West Street New York, NY 10282 c/o BofA Securities, Inc. One Bryant Park New York, NY 10036 Ladies and Gentlemen: The undersigned understands that Morgan Stanley & Co. LLC, Goldman S

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13D (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (Amendment No. 1)* Prelu

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13D (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (Amendment No.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers - 8-K

8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 22, 2021 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporati

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D (Amendment No. 1)* Under the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D (Amendment No. 1)* Under the Securities Exchange Act of 1934 Prelude Therapeutics Incorporated (Name of Issuer) COMMON STOCK (Title of Class of Securities) 74065P101 (CUSIP Number) OrbiMed Advisors LLC OrbiMed Capital GP VI LLC OrbiMed Capital LLC 601 Lexington Avenue, 54th Floor New York, NY 10022 Telephone: (212

LOCK-UP AGREEMENT

LOCK-UP AGREEMENT , 20 Morgan Stanley & Co. LLC Goldman Sachs & Co. LLC BofA Securities, Inc. c/o Morgan Stanley & Co. LLC 1585 Broadway New York, NY 10036 c/o Goldman Sachs & Co. LLC 200 West Street New York, NY 10282 c/o BofA Securities, Inc. One Bryant Park New York, NY 10036 Ladies and Gentlemen: The undersigned understands that Morgan Stanley & Co. LLC, Goldman Sachs & Co. LLC and BofA Securi

JOINT FILING AGREEMENT

Exhibit 1 JOINT FILING AGREEMENT The undersigned hereby agree that the Statement on Schedule 13D, dated January 12, 2021, with respect to the ordinary shares of Prelude Therapeutics Incorporated is filed on behalf of each of us pursuant to and in accordance with the provisions of Rule 13d-1(k) under the Securities Exchange Act of 1934, as amended.

2,500,000 Shares Common Stock

424B4 Table of Contents Filed Pursuant to Rule 424(b)(4) Registration No. 333-251874 Registration No.333-251929 PROSPECTUS 2,500,000 Shares Common Stock We are offering 2,500,000 shares of our common stock. Our common stock is listed on The Nasdaq Global Select Market under the symbol “PRLD”. The closing price of our common stock on January 6, 2021, as reported by The Nasdaq Global Select Market,

- S-1MEF

S-1MEF As filed with the U.S. Securities and Exchange Commission on January 6, 2021. Registration No. 333- UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 PRELUDE THERAPEUTICS INCORPORATED (Exact name of Registrant as specified in its charter) Delaware 2834 81-1384762 (State of incorporation or organization) (

Regulation FD Disclosure, Results of Operations and Financial Condition

8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 4, 2021 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporatio

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CORRESP January 4, 2021 U.S. Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Deanna Virginio Re: Prelude Therapeutics Incorporated Registration Statement on Form S-1 (File No. 333-251874) Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 460 of the General Rules and Regulations under the Securities Act of 1933, a

Form of Registration Rights Agreement, by and among Prelude Therapeutics Incorporated and certain of its stockholders

EX-4.3 Exhibit 4.3 REGISTRATION RIGHTS AGREEMENT This Registration Rights Agreement (this “Agreement”) is made as of [ ], 2020 by and between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and the persons listed on the attached Schedule A who are signatories to this Agreement (collectively, the “Investors”). Unless otherwise defined herein, capitalized terms used in thi

Executive Employment Agreement, dated December 19, 2020, by and between the Registrant and Christopher Pierce.

EX-10.8 Exhibit 10.8 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the “Agreement”), made between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and Christopher Pierce (“Executive” and, collectively with the Company, the “Parties”), is entered into as of December 19, 2020 (the “Effective Date”). WHEREAS, the Company desires to continue to employ Ex

Executive Employment Agreement, dated December 30, 2020, by and between the Prelude Therapeutics Incorporated and Krishna Vaddi.

EX-10.6 5 d85697dex106.htm EX-10.6 EXHIBIT 10.6 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the “Agreement”), made between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and Krishna Vaddi (“Executive” and, collectively with the Company, the “Parties”), is entered into as of December 30, 2020 (the “Effective Date”). WHEREAS, the Company desires to

Form of Underwriting Agreement

EX-1.1 Exhibit 1.1 [•] Shares PRELUDE THERAPEUTICS INCORPORATED COMMON STOCK (PAR VALUE $0.0001 PER SHARE) UNDERWRITING AGREEMENT January [•], 2021 January [•], 2021 Morgan Stanley & Co. LLC Goldman Sachs & Co. LLC BofA Securities, Inc. As Representatives of the several Underwriters named in Schedule I hereto c/o Morgan Stanley & Co. LLC 1585 Broadway New York, New York 10036 c/o Goldman Sachs & C

Power of Attorney (incorporated by reference to Exhibit 24.1 to the Registration Statement on Form S-1 (Registration No. 333-251874))

S-1 Table of Contents As filed with the Securities and Exchange Commission on January 4, 2021.

Executive Employment Agreement, dated December 19, 2020, by and between the Registrant and Deborah Morosini.

EX-10.7 Exhibit 10.7 EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the “Agreement”), made between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and Deborah Morosini (“Executive” and, collectively with the Company, the “Parties”), is entered into as of December 19, 2020 (the “Effective Date”). WHEREAS, the Company desires to continue to employ Exec

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CORRESP Prelude Therapeutics Incorporated 200 Powder Mill Road Wilmington, Delaware 19803 January 4, 2021 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, NE Washington, DC 20549 Attention: Deanna Virginio Re: Prelude Therapeutics Incorporated Registration Statement on Form S-1 (File No.

Disclaimer This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small

EX-99.1 Exhibit 99.1 Corporate January 2021 PresentationExhibit 99.1 Corporate January 2021 Presentation Disclaimer This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to: our plans to develop and commercialize small molecule therapies, our expectations about t

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DRS Table of Contents Confidential Treatment Requested by Prelude Therapeutics Incorporated Pursuant To 17 C.

Confidential Treatment Requested by Prelude Therapeutics Incorporated Pursuant To 17 C.F.R. Section 200.83

EX-4.3 Confidential Treatment Requested by Prelude Therapeutics Incorporated Pursuant To 17 C.F.R. Section 200.83 Exhibit 4.3 REGISTRATION RIGHTS AGREEMENT This Registration Rights Agreement (this “Agreement”) is made as of [ ], 2020 by and between Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), and the persons listed on the attached Schedule A who are signatories to thi

Prelude Therapeutics Announces Third Quarter 2020 Financial Results - Completed Initial Public Offering of Common Stock, Raising Gross Proceeds of ~$181.9M million - - Partial Response Confirmed in Glioblastoma Multiforme Patient in Phase 1 Trial of

Exhibit 99.1 Prelude Therapeutics Announces Third Quarter 2020 Financial Results - Completed Initial Public Offering of Common Stock, Raising Gross Proceeds of ~$181.9M million - - Partial Response Confirmed in Glioblastoma Multiforme Patient in Phase 1 Trial of PRT811 - - Durable Complete Response Ongoing in HRD+ High Grade Serous Ovarian Cancer Patient in Phase 1 Trial of PRT543 - Wilmington, DE

Financial Statements and Exhibits, Results of Operations and Financial Condition - 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 10, 2020 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporation

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

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, 2020 OR ☐ 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: 001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact Name of Registrant as Specified in its Charter) Delaware 81-1384762 (State or other jurisdiction of incorporation or organization) (I.

Restated Bylaws of Prelude Therapeutics Incorporated

Exhibit 3.2 PRELUDE THERAPEUTICS INCORPORATED (a Delaware corporation) RESTATED BYLAWS As Adopted September 14, 2020 and As Effective September 29, 2020 PRELUDE THERAPEUTICS INCORPORATED (a Delaware corporation) RESTATED BYLAWS TABLE OF CONTENTS Page Article I: STOCKHOLDERS 1 Section 1.1: Annual Meetings 1 Section 1.2: Special Meetings 1 Section 1.3: Notice of Meetings 1 Section 1.4: Adjournments

Restated Certificate of Incorporation of Prelude Therapeutics Incorporated

Exhibit 3.1 PRELUDE THERAPEUTICS INCORPORATED RESTATED CERTIFICATE OF INCORPORATION Prelude Therapeutics Incorporated, a Delaware corporation, hereby certifies as follows: 1.The name of this corporation is “Prelude Therapeutics Incorporated.” The date of the filing of its original Certificate of Incorporation with the Secretary of State of the State of Delaware was February 5, 2016. 2.The Restated

Entry into a Material Definitive Agreement, Financial Statements and Exhibits - 8-K

8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 1, 2020 Prelude Therapeutics Incorporated (Exact Name of Registrant as Specified in its Charter) Delaware 001-39527 81-1384762 (State or other jurisdiction of incorporati

Second Amended and Restated Entrepreneur Client License Agreement, dated November 1, 2020, by and between Prelude Therapeutics Incorporated and Delaware Innovation Space, Inc.

EX-10.1 Exhibit 10.1 SECOND AMENDED AND RESTATED ENTREPRENEUR CLIENT LICENSE AGREEMENT THIS SECOND AMENDED AND RESTATED ENTREPRENEUR CLIENT LICENSE AGREEMENT (“License Agreement”), made as of the Effective Date between Licensee, and Delaware Innovation Space, Inc., a Delaware charitable non-profit nonstock corporation (“DISI”). WHEREAS, DISI and Licensee are parties to that certain Amended and Res

JOINT FILING AGREEMENT

Exhibit 1 JOINT FILING AGREEMENT The undersigned hereby agree that the Statement on Schedule 13D, dated October 5, 2020, with respect to the ordinary shares of Prelude Therapeutics Incorporated is filed on behalf of each of us pursuant to and in accordance with the provisions of Rule 13d-1(k) under the Securities Exchange Act of 1934, as amended.

PRLD / Prelude Therapeutics Incorporated / ORBIMED ADVISORS LLC - SCHEDULE 13D Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 Prelude Therapeutics Incorporated (Name of Issuer) COMMON STOCK (Title of Class of Securities) 74065P101 (CUSIP Number) OrbiMed Advisors LLC OrbiMed Capital GP VI LLC OrbiMed Capital LLC 601 Lexington Avenue, 54th Floor New York, NY 10022 Telephone: (212) 739-6400 (Name, A

JOINT FILING AGREEMENT

Exhibit 99.1 JOINT FILING AGREEMENT Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, as amended, the undersigned hereby agree that only one statement containing the information required by Schedule 13D need be filed with respect to the beneficial ownership by each of the undersigned of securities of Prelude Therapeutics Incorporated. This Agreement may be executed in any num

PRLD / Prelude Therapeutics Incorporated / BAKER BROS. ADVISORS LP - SC 13D Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13D (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (Amendment No.

8,325,000 Shares Common Stock

424B4 Table of Contents Filed Pursuant to Rule 424(b)(4) Registration No. 333-248628 PROSPECTUS 8,325,000 Shares Common Stock We are offering 8,325,000 shares of our common stock. This is our initial public offering and no public market currently exists for our common stock. The initial public offering price is $19.00 per share. We have been approved to list our common stock on The Nasdaq Global S

- S-8

S-8 As filed with the Securities and Exchange Commission on September 24, 2020 Registration No.

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CORRESP September 22, 2020 U.S. Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Jeffrey Gabor Laura Crotty Rolf Sundwall Jeanne Baker Re: Prelude Therapeutics Incorporated Registration Statement on Form S-1 (File No. 333-248628) Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 460 of the General Rules and Regula

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CORRESP Prelude Therapeutics Incorporated 200 Powder Mill Road Wilmington, Delaware 19803 September 22, 2020 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, NE Washington, DC 20549 Attention: Jeffrey Gabor Laura Crotty Rolf Sundwall Jeanne Baker Re: Prelude Therapeutics Incorporated Registration Statement on Form S-1 (File No.

Certificate of Incorporation, as amended, as currently in effect.

EX-3.1 Exhibit 3.1 FIFTH AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF PRELUDE THERAPEUTICS INCORPORATED (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) Prelude Therapeutics Incorporated, a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the “General Corporation Law”)

2020 Employee Stock Purchase Plan and forms of award agreements.

EX-10.4 Exhibit 10.4 PRELUDE THERAPEUTICS INCORPORATED 2020 EMPLOYEE STOCK PURCHASE PLAN 1. Establishment of Plan. Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”) proposes to grant options to purchase shares of Common Stock to eligible employees of the Company and its Participating Corporations pursuant to this Plan. The Company intends this Plan to qualify as an “employe

- S-1/A

S-1/A Table of Contents As Filed with the Securities and Exchange Commission on September 21, 2020.

2020 Equity Incentive Plan and forms of award agreements.

EX-10.3 4 d935180dex103.htm EX-10.3 Exhibit 10.3 PRELUDE THERAPEUTICS INCORPORATED 2020 EQUITY INCENTIVE PLAN 1. PURPOSE. The purpose of this Plan is to provide incentives to attract, retain, and motivate eligible persons whose present and potential contributions are important to the success of the Company, and any Parents, Subsidiaries, and Affiliates that exist now or in the future, by offering

Form of Common Stock Certificate

EX-4.1 Exhibit 4.1 ZQ|CERT#|COY|CLS|RGSTRY|ACCT#|TRANSTYPE|RUN#|TRANS# VOTING COMMON STOCK PAR VALUE $0.0001 VOTING COMMON STOCK Certificate Number ZQ00000000 PRELUDE THERAPEUTICS INCORPORATED INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE THIS CERTIFIES THAT is the owner of SEE REVERSE FOR CERTAIN DEFINITIONS CUSIP 74065P 10 1 THIS CERTIFICATE IS TRANSFERABLE IN CITIES DESIGNATED BY THE TRA

Form of Underwriting Agreement.

EX-1.1 Exhibit 1.1 [•] Shares PRELUDE THERAPEUTICS INCORPORATED COMMON STOCK (PAR VALUE $0.0001 PER SHARE) UNDERWRITING AGREEMENT [•], 2020 [•], 2020 Morgan Stanley & Co. LLC Goldman Sachs & Co. LLC BofA Securities, Inc. As Representatives of the several Underwriters named in Schedule I hereto c/o Morgan Stanley & Co. LLC 1585 Broadway New York, New York 10036 c/o Goldman Sachs & Co. LLC 200 West

Form of Restated Bylaws to be effective upon the completion of this offering.

EX-3.4 4 d935180dex34.htm EX-3.4 Exhibit 3.4 PRELUDE THERAPEUTICS INCORPORATED (a Delaware corporation) RESTATED BYLAWS As Adopted [•], 2020 and As Effective [•], 2020 PRELUDE THERAPEUTICS INCORPORATED (a Delaware corporation) RESTATED BYLAWS TABLE OF CONTENTS Page Article I: STOCKHOLDERS 1 Section 1.1: Annual Meetings 1 Section 1.2: Special Meetings 1 Section 1.3: Notice of Meetings 1 Section 1.4

- S-1/A

S-1/A Table of Contents As Filed with the Securities and Exchange Commission on September 16, 2020.