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

Corporate Presentation May 2023 Exhibit

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 complete clinical studies, present data and clinical results or updates, and to obtain regulatory approvals for PRT1419, PRT2527, PRT3645,

PRT3789, our oral SMARCA2 candidate and other candidates in development, the ability of our product candidates to treat various cancers, the ability to discover additional suitable candidates for regulatory approval and the sufficiency of our cash

and cash equivalents to fund our operations. Any statements contained herein or provided orally that are not statements of historical fact may be deemed to be forward-looking statements. In some cases, you can identify forward-looking statements by

such terminology as believe,'' may,'' will,'' potentially,'' estimate,'' continue,''

anticipate,'' intend,'' could,'' would,'' project,'' plan,''

expect'' and similar expressions that convey uncertainty of future events or outcomes, although not all forward-looking statements contain these words. Statements, including forward-looking statements, speak only to the

date they are provided (unless an earlier date is indicated). Certain data in this presentation are based on cross-study comparisons and are not based on any head-to-head clinical trials. Cross-study comparisons are inherently limited and may

suggest misleading similarities or differences. This presentation shall not constitute an offer to sell or the solicitation of an offer to buy, nor shall there be any sale of these securities in any state or other jurisdiction in which such

offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such state or other jurisdiction. These forward-looking statements are based on the beliefs of our management as well as

assumptions made by and information currently available to us. Although we believe the expectations reflected in such forward-looking statements are reasonable, we can give no assurance that such expectations will prove to be correct. If such

assumptions do not fully materialize or prove incorrect, the events or circumstances referred to in the forward-looking statements may not occur. We undertake no obligation to update publicly any forward-looking statements for any reason after the

date of this presentation to conform these statements to actual results or to changes in our expectations, except as required by law. Accordingly, readers are cautioned not to place undue reliance on these forward-looking statements.

Additional risks and uncertainties that could affect our business are included under the caption "Risk Factors" in our filings with the Securities and Exchange Commission, including our Annual Report on Form 10-K for the year ended

Prelude Therapeutics: Aiming to Deliver

Precision Medicines to Patients with Cancer Large Commercial Opportunities Diversified Pipeline Exceptional Team Well Capitalized Powerful R&D Engine

Prelude Discovery and Development

Engine R&D ENGINE DIFFERENTIATED PROGRAMS APPROACH CDK9 MCL1 SMARCA2 CDK4/6 Target Mechanisms that drive meaningful benefit in patients with cancer Discover Optimized molecules that overcome the limitations of current treatments

Translate Science into meaningful treatments for patients Internal Discovery Engine Clinical Development Expertise

Differentiated Programs with

Transformative Potential for Patients with Cancer Potentially Best-in-Class Selectivity Potential to avoid off-target toxicity and higher clinical activity Potent and Selective Degrader Potential to address major unmet need in

biomarker-selected patients Optimized PK Profile Potential for maximal target engagement and improved cardiac safety Highly Selective CDK4 Bias Potential for high tissue and brain penetration and better combinability CDK9 MCL1 SMARCA2 CDK4/6

Powerful Discovery Engine expected to generate new INDs every 12-18 months

PROGRAM CANCER INDICATIONS

DISCOVERY PHASE 1 PHASE 2/3

AREAS OF CLINICAL FOCUS CDK9 PRT2527 Selected solid and hematologic

malignancies CLL, Lymphoma MCL1 PRT1419 Selected hematologic malignancies and solid tumors AML, CLL, Lymphoma CDK4/6 PRT3645 Selected solid tumors Breast Cancer, Gliomas, HNSCC, Lung, and Endometrial cancers SMARCA2 PRT3789 (IV)

Multiple genomically- selected cancers SMARCA4 mutated NSCLC and Other cancers SMARCA2 (Oral) Multiple genomically- selected cancers SMARCA4 mutated NSCLC and Other cancers New Programs (Multiple targets) Selected solid and

hematologic malignancies Solid Tumors Heme Malignancies Prelude Precision Oncology Pipeline: Diversified and Differentiated

Driving The Programs to Key Milestones

and Value Creation PRT2527 PRT1419 PRT3645 SMARCA2 CDK9 MCL1 Next Generation CDK4/6 Present solid tumor data at AACR 2023 RP2D in solid tumors in early-2023 RP2D in hematological malignancies in 2H Present initial clinical data for hematological

malignancies in 2H Present solid tumor data at AACR 2023 RP2D in hematological malignancies in 2H Present initial clinical data for hematological malignancies in 2H Expected to provide initial clinical data in 2H PROGRAM 2023 MILESTONES

Initiate Phase 1 in 1Q Expected to provide clinical update 2H PRT3789

PRT2527 CDK9 Inhibitor

CDK9 Inhibition: Targeting Cancer by

Regulating Oncogene Expression CDK9 regulates expression of several oncogenes that drive cancer cell growth and resistance (i.e. MYC, MYB, MCL1) Non-selective CDK9 inhibitors have demonstrated clinical activity in multiple tumor types but poor

tolerability Improving the selectivity of CDK9 inhibitors may translate to better activity and safety profile SUPER ENHANCER RNA Pol II TSS MYC & MYB TARGET GENES mRNA CDK9

PRT2527: Potent and Highly Selective

CDK9 Inhibitor Compound AZD4573 KB0742 VIP152** PRT2527 Biochemical* IC50 (nM) CDK9 1.9 483 16 0.95 Proliferation* IC50 (nM) 11 915 84 18 Plasma* IC50 (nM) 192 1056 923 196 Fold Selectivity CDK9 vs Other Isoforms CDK1 23x >20x 371x 73x CDK2 35x

>20x 147x 340x CDK3 2x >20x 37x 35x CDK4 53x >20x 38x 250x CDK5 37x >20x >600x >1000x CDK6 79x >20x 296x >1000x CDK7 150x >20x >600x >1000x Highly Selective, ATP Competitive CDK9 Inhibitor >100x100-10x<10x

*Internal data; biochemical assay at 1 mM ATP, H929 CTG proliferation assay; **VIP151 was formerly BAY151 and licensed to Vincerx by Bayer

CDK9 inhibitor: PRT2527 Phase 1

Dose-Escalation Study in Advanced Solid Tumors Phase 1 dose escalation study of PRT2527 is ongoing and enrolling the following tumor types Selected sarcomas displaying a gene fusion Castrate resistant prostate cancer HR+ HER2- breast cancer

Non-small cell lung cancer Solid tumors with MYC amplification In the 18 patients treated in dose escalation, PRT2527 was generally well tolerated with manageable neutropenia and absence of significant gastrointestinal events or hepatotoxicity

The 15 m/mg2 QW dose of PRT2527 was selected for further evaluation in a dose-confirmation cohort Dose-dependent inhibition of CDK9 transcription targets observed in PBMCs HR+ Hormone receptor positive; HER2- Human epidermal growth factor negative

ClinicalTrials.gov Identifier: NCT05159518 Presented at AACR 2023; https://preludetx.com/wp-content/uploads/2023/04/Henry_2527-01_AACR-CT173-poster_23MAR23.pdf Timepoint Mean fold change SEM in MYC mRNA expression in PBMCs relative to

pre-dose Pre-dose 2 hours post dose 4 hours post dose 1 hour post dose 0.8 0.6 0.0 1.0 1.4 1.6 1.2 0.4 0.2 A 3 mg/m2 QW (n=3) 6 mg/m2 QW (n=3) 12 mg/m2 QW (n=3) 15 mg/m2 QW (n=4) 18 mg/m2 QW (n=4) Pre-dose 2 hours post dose 4 hours post dose 1 hour

post dose 0.8 0.6 0.0 1.0 1.4 1.6 1.2 0.4 0.2 Timepoint Mean fold change SEM in MCL-1 mRNA expression in PBMCs relative to pre-dose B 3 mg/m2 QW (n=3) 6 mg/m2 QW (n=3) 12 mg/m2 QW (n=3) 15 mg/m2 QW (n=4) 18 mg/m2 QW (n=4)

CDK9 Inhibitor: PRT2527 Phase 1

Studies in Solid Tumors and Hematologic Malignancies PRT2527 Solid Tumors N=18 PRT2527 MYC Amplified or Overexpressed Solid Tumors, Prostate Cancer N=15 Solid Tumors Dose dependent increases in drug concentrations and target engagement observed in

Phase 1 Clinical MYC and MCL1 depletion to levels consistent with tumor regression in preclinical models Generally well tolerated Dose Confirmation Dose Escalation PRT2527 Monotherapy Aggressive B cell lymphomas (multiple types), follicular

lymphoma, CLL/SLL/Richters, MCL PRT2527 N=30 Hematologic Malignancies ASH 2022 preclinical oral presentation CDK9 as a target externally validated in aggressive lymphoma and other heme malignancies Dose Confirmation Dose Escalation

ClinicalTrials.gov Identifier: NCT05159518 Solid Tumor data at AACR 2023 RP2D in hematological malignancies 2H 2023 Initial clinical data in 2H 2023 ClinicalTrials.gov Identifier: NCT05665530

CDK9 Inhibitor Differentiation and

Market Opportunity Potential for Improved Safety Based on Best-in-Class Kinome Selectivity PRT2527 is designed to be a highly potent CDK9 inhibitor with best-in-class kinome selectivity compared to competitor compounds Designed to have an optimized

PK profile to maximize therapeutic window Highly active in pre-clinical models at well-tolerated doses High levels of inhibition of CDK9 dependent genes in Phase 1 Market Opportunity CDK9 inhibitors in lymphomas, including CLL, Mantle cell and

DLBCL may address areas of high unmet need CDK9 MCL1 SMARCA2 CDK4/6

PRT2527: Broad Potential to Address

areas of High Unmet Need 1. SEER Cancer Stat Facts: https://seer.cancer.gov/statfacts/html/clyl.html; 2. Gena Kanas, et. al. Epidemiology of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) in the United States and Western

Europe 3. CancerMPact Treatment Architecture, Non-Hodgkin US, 4. CancerMPact Treatment Architecture, Chronic Lymphocytic Leukeimia, US, 5. CLL Patient Based Forecast, Datamonitor Healthcare Broad Opportunity: ~125K

patients treated annually(US): CLL, MCL and DLBCL1,2,3,4,5 Limited Treatment Options: >50% of High Risk CLL, MCL and DLBCL patients are refractory/relapsed within 1 year after 2L Treatment 2,3

MCL1 inhibition: Targeting Cancer

Cell Survival MCL1 is a member of the BCL2 family of inhibitors of apoptosis Emerged as a resistance mechanism to the BCL2 inhibitor Venetoclax Prolonged depletion of MCL1 is undesirable and may be associated with cardiac toxicity Optimizing

the PK profile of an MCL1 inhibitor may maximize the therapeutic window Mechanism

PRT1419 is Potent MCL1 Inhibitor

with Demonstrated Preclinical Activity as Monotherapy and in Combination Monotherapy Combination Robust monotherapy activity also seen in models of DLBCL & MM Proliferation IC50 (nM) Whole Blood IC50 (nM) AMG176 150 1800 AZD5991 31 320 MIK665

4.5 430 PRT1419 80 210 Prelude compounds are competitive inhibitors of BIM binding

PRT1419: Not Observed to Cause

Cardiac Injury in Preclinical Toxicology Studies Doses: 0.3, 1, 3 and 6 mg/m2; once weekly Linear increases in exposure No troponin elevations observed at any doses, even high dose which covered EC90 for 24h No histopathological evidence of cardiac

injury Pharmacokinetics Pharmacodynamics PRT1419 Module 2.6 IND: Tox Written Summary

MCL-1 inhibitor: PRT1419 Phase

1 Dose-Escalation Study in Advanced Solid Tumors PRT1419 demonstrated acceptable safety and tolerability in patients with advanced metastatic solid tumors, with the most common TRAEs of nausea, vomiting and diarrhea Neutropenia was deemed to be

dose related No cardiac toxicity was observed Induction of activated-BAX and cleaved caspase-3 was observed at 80 and 120 mg/m2: QW PRT1419, suggesting optimal MCL-1 inhibition Upregulation of MCL1 is a mechanism of resistance to BCL2

inhibition, particularly in CLL and AML; Strong preclinical hypothesis in heme Phase 1 Target Engagement Presented at AACR 2023; https://preludetx.com/wp-content/uploads/2023/04/Falchook_1419-02_AACR-CT172-poster-23MAR23.pdf

MCL1 inhibitor: PRT1419 Phase 1

Study in Hematologic Malignancies PRT1419 Monotherapy AML/MDS/CMML CLL/SLL FL/MZL/MCL N=24-30 PRT1419 Combination PRT1419+Aza: AML/MDS/CMML PRT1419+Ven: AML/MDS/CMML PRT1419+Ven: MCL N=24-30 Dose Confirmation Dose Escalation ClinicalTrials.gov

Identifier: NCT05107856 RP2D in heme monotherapy expected 2H 2023 Initial clinical data in 2H 2023

MCL1 Inhibitor Differentiation and

Market Opportunity Designed to have PK Profile to Achieve Desired Target Engagement MCL1 CDK9 SMARCA2 CDK4/6 PRT1419 is designed to be a highly potent and selective MCL1 inhibitor Designed to have a PK profile with high clearance to provide desired

target engagement with improved safety No cardiotoxicity or troponin changes in GLP preclinical studies at doses exceeding those required for efficacy No evidence of cardiotoxicity in the solid tumor Phase 1 at the recommended Phase 2 dose

Market Opportunity AML, CLL and MCL patients need additional treatment options PRT1419 Module 2.6 IND: Tox Written Summary

PRT1419: MCL1 Inhibitor

Offers Potential Benefit for Patients with Poor Outcomes 22 Broad Opportunity: ~95K patients treated annually(US): CLL, AML, MDS 1,2,3,4 Outcomes for relapsed / refractory patients are poor: >50% of CLL, High Risk MDS and Unfit AML

patients are refractory/relapsed within 1 year after second relapse2,3,4 1. SEER Cancer Stat Facts: Chronic Lymphocytic Leukemia. National Cancer Institute. Bethesda, MD, https://seer.cancer.gov/statfacts/html/clyl.html; 2. CancerMPact

Treatment Architecture, Non-Hodgkin US May 2022 3. CancerMPact Treatment Architecture, Chronic Lymphocytic Leukeimia, US May 2022 4. CancerMPact Treatment Architecture, MDS, US., August 2022 * MDS number represents annual incident

patients, treated patient number may be higher.

PRT3645 Next Generation CDK4/6

Next Generation CDK4/6 Inhibition:

Targeting Cancer Through Cell Cycle Regulation Mechanism Validated mechanism with approval of Next Generation CDK4/6 inhibitors in HR+ breast cancer Resistance mechanism to other inhibitors of the RAS and HER2 pathways, including KRAS G12C

Inability of current inhibitors to penetrate the blood-brain barrier (BBB) Next generation CDK4/6 inhibitor with improved tolerability and tissue penetrance could translate into activity in areas of unmet need beyond HR+ breast cancer Sequential use

of Next Generation CDK4/6 inhibitors in breast cancer may also improve outcomes ASCO 2022 reference: A randomized, phase II trial of fulvestrant or exemestane with or without ribociclib after progression on anti-estrogen therapy plus

cyclin-dependent kinase 4/6 inhibition (CDK 4/6i) in patients (pts) with unresectable or hormone receptor-positive (HR+), HER2-negative metastatic breast cancer (MBC): MAINTAIN trial. and See AACR 2023;

PRT3645 - Designed to be a

Highly Selective Next Generation CDK4/6 Inhibitor Bias towards CDK4 over CDK6 Compound Palbociclib Abemaciclib PRT3645 Biochemical* IC50 (nM) CDK4 25 5 3 Proliferation* IC50 (nM) 52 70 47 Phospho-Rb* IC50 (nM) 28 30 16 Fold Selectivity CDK4 vs Other

Isoforms CDK6 1x 6x 5x CDK1 >500x >500x >500x CDK2 >500x 173x >500x CDK3 >500x 212x >500x CDK5 >500x >500x >500x CDK7 >500x >500x >500x CDK9 209x 59x >500x >500x 500-50x 50-5x<2x *Internal data;

biochemical assay at 1 mM ATP, MCF7 CTG proliferation assay; MCF7 pRB Highly Selective, ATP Competitive

PRT3645: Next Generation CDK4/6