#18 COMPASS THERAPEUTICS 12214.153] Compass Therapeutics (Nasdaq: CMPX) Investor Call January 23, 2023 SRC#2DISCLAIMER This presentation has been prepared by Compass Therapeutics, Inc. ("we," "us," "our," or the "Company"). Statements contained herein are made as of the date of this presentation unless stated otherwise, and this presentation shall not under any circumstances create an implication that the information contained herein is correct as of any time after such date or that information will be updated or revised to reflect information that subsequently becomes available or changes occurring after the date hereof. This presentation includes forward-looking statements regarding our drug candidates, the timing of the start and conclusion of ongoing or planned clinical trials, including the potential impact of the ongoing COVID-19 pandemic on our business, the timing and outcome of regulatory decisions, future availability of clinical trial data, our collaborations for our product candidates and the maintenance of those collaborations, business and results from operations, and other matters. Actual results could differ materially from those contained in any forward-looking statements as a result of various factors, including without limitation: that our drug candidates do not advance in development or result in approved products on a timely or cost effective basis or at all; the cost, timing and results of clinical trials; our ability to manage and mitigate the impact of the ongoing COVID-19 pandemic; that many drug candidates that have completed early-stage trials do not become approved drugs on a timely or cost effective basis or at all; the ability to enroll patients in clinical trials; possible safety and efficacy concerns; regulatory developments; our ability to protect our intellectual property rights, and unexpected costs, charges or expenses that reduce cash runway. Our pipeline programs are in various stages of pre-clinical and clinical development, and the process by which such pre-clinical or clinical therapeutic candidates could potentially lead to an approved therapeutic is long and subject to significant risks and uncertainties. These and other risks and uncertainties that we face are described in our most recent Annual Report on Form 10-K, and in other filings that we make with the Securities and Exchange Commission from time to time. We undertake no obligation to update forward-looking statements as result of new information or otherwise. This presentation also contains estimates and other statistical data made by independent parties and by us relating to market size and growth and other data about our industry. This data involves a number of assumptions and limitations, and you are cautioned not to give undue weight to such estimates. In addition, projections, assumptions, and estimates of our future performance and the future performance of the markets in which we operate are necessarily subject to a high degree of uncertainty and risk. This presentation concerns drugs that are under clinical investigation, and which have not yet been approved for marketing by the U.S. Food and Drug Administration (FDA). It is currently limited by Federal law to investigational use, and no representation is made as to its safety or effectiveness for the purposes for which it is being investigated. COMPASS THERAPEUTICS 2#3Overview of CTX-009 Bispecific antibody blocking VEGF-A (soluble ligand) and DLL4 (Notch-1 ligand) ➤ Does not lead to ADCC, Fc inactive ➤ Binds to its targets with 2:2 valency At 10 mg/Kg, CTX-009 has approximately the same VEGF-A capturing ability as bevacizumab (Avastin) The only VEGF X DLL4 bispecific that demonstrated monotherapy activity in the clinic in colorectal and gastric cancer Durable responses in patients with cholangiocarcinoma seen in Phase 1b study of CTX-009 in combination with paclitaxel COMPASS THERAPEUTICS (A) (VEGF) DLL4 Anti-VEGF MoAb (Bevacizumab/Avastin) Dual blockade of VEGF and DLL4 overcomes VEGF resistance VEGF/VEGF-R signaling (VEGF) Decreased tumor vessel formation; Reduced tumor growth DLL4 (B) 8 ensin Anti-DLL4 MoAb DLL4-Notch Signaling Increased vessel formation with poor perfusion; Reduced tumor growth 3#4Phase 2 CTX-009 Combination Study (S. Korea) Patients with biliary tract cancers after one or two prior therapies Simon 2 Stage adaptive design COMPASS THERAPEUTICS Stage 1 CTX-009 at 10 mg/kg biweekly Paclitaxel 80 mg/m² weekly 3 of 4 weeks N = 21 3 or more PRs Stage 2 CTX-009 at 10 mg/kg biweekly Paclitaxel 80 mg/m² weekly 3 of 4 weeks N = 45 additional patients 4#5Phase 2 CTX-009 Combination Study - Patient Demographics Age Median (years) Gender, n(%) Male Female ECOG performance status, n(%) 0 1 COMPASS THERAPEUTICS 24 Total Patients 61.5 14 (58%) 10 (42%) 13 (54%) 11 (46%) Prior systemic therapies, n(%) 1 2 Prior Gem/Cis regimen BTC subtype, n (%) Intrahepatic cholangiocarcinoma Extrahepatic cholangiocarcinoma Gallbladder cancer Ampullary cancer 24 Total Patients 11 (46%) 13 (54%) 23 (96%) 9 (38%) 3 (13%) 7 (29%) 5 (21%) 5#6Percent tumor decline Phase 2 CTX-009 Data Responses achieved across multiple BTC subclasses. Data as of November 9, 2022 Patient Number 0 -10 -20 -30 -40 -50 -60 1 -1 2 -7 3 -7 4 5 6 7 8 9 10 11 -12 COMPASS THERAPEUTICS -9 Intrahepatic cholangiocarcinoma Extrahepatic cholangiocarcinoma Gallbladder cancer Ampullary cancer -12 -12 -17 -17 -19 11 -20 12 -25 13 -33 2 patients were not evaluable (one missing post baseline scan; one had a scan outside of protocol window) 14 -33 15 -37 16 CONFIRMED PARTIAL RESPONSE -38 17 -41 18 -44 19 ORR = 37.5% CBR = 91.5% -44 20 -48 21 -52 22 -57 6#7Swimmer Plot (November 9, 2022 data cut off) 0 COMPASS THERAPEUTICS 58 Q O 49 78 100 CO AL 93 92 119 119 159 175 168 183 O 182 173 200 C1D1 to EOT (Days) 300 O 277 287 297 310 303 324 316 343 O O 400 500 511 600 580 PR SD PD O Death On-going 700 7#8CTX-009 Phase 2 Results (Median follow-up of 12.1 months) 24 patients enrolled and dosed 1 patient remains on study Endpoint Overall Response Rate (ORR) Stable Disease (SD) Progression Free Survival (PFS) Overall Survival (OS) Duration of Response COMPASS THERAPEUTICS Value (95% CI) 37.5% 54.2% 9.4 m (5.4-11.1) 12.5 m (10.9 - NA) 6.9 m (3.5-NA) Number of previous systemic therapies Pts treated in the 2L [n=11] Pts treated in the 3L [n=13] ORR 7/11 (63.6%) 2/13 (15.4%) 8#9Secondary Endpoints: PFS and OS (as of Nov 9, 2022) Median OS: NA (12.5-NA) ● Median PFS: 9.40 m (5.4-11.1) A 1.0 Survival Probability 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0 0 All T 1 2 2nd line COMPASS THERAPEUTICS 3 4 5 3rd line 6 7 8 9 10 11 12 13 14 Progression Free Survival (months) Number at risk All 24 23 21 20 17 17 10 10 10 10 7 5 2 2 2 2nd line 11 11 10 9 9 9 1 1 3rd line 13 12 11 11 8 8 1 155 155 055 055 122 Group All 2nd line 3rd line 21 2 5 3 1 1 15 16 2 1 1 2 1 1 Median (95% CI) 9.4(5.4-11.1) T 17 1 + Censored 1 0 10.0(5.1-NA) 5.5(3.6-11.1) 18 1 1 T 19 20 0 0 B Survival Probability 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0 ● — All 0 1 - 2nd line T 2 3 T 4 5 - T 6 Number at risk All 24 24 23 21 21 21 20 2nd line 11 11 11 11 11 11 11 3rd line 13 13 12 10 10 10 3rd line 7 8 9 10 11 12 13 14 15 16 Overall Survival (months) 19 19 19 17 16 12 10 10 10 9 8 5 8 8 7 Group All 2nd line 3rd line 9 9 9 9 835 633 532 + Censored Median(95% CI) 12.5(10.9-NA) 11.7(9.1-NA) 12.9(5.3-NA) 17 18 2 1 1 1 1 0 1 1 19 20 0 0 % 9#10Treatment-Emergent ≥ Grade 3 Adverse Events (>10% of patients) Phase 2 BTC study of CTX-009 plus paclitaxel Event Neutropenia Anemia Hypertension Thrombocytopenia 24 total Patients N (%) 20 (83.3%) COMPASS THERAPEUTICS 5 (20.8%) 4 (16.7%) 3 (12.5%) TEAE leading to discontinuation: confusion, embolism, pneumonia (grade 5), biliary fistula, large intestine perforation, blood creatinine increased, and blood urea nitrogen increased Bevacizumab and paclitaxel label information Event Neutropenia Hypertension Anemia Thrombocytopenia Bevacizumab (label) 5-18% Additional events: Gl perforation, wound healing complications, Proteinuria, hemorrhage Paclitaxel (label) 52% 16% 7% Additional events: Hypersensitivity reactions, infections, bleeding, neuropathy 10#11CTX-009 Interim Phase 2 Study Summary 24 patients with BTC have been enrolled and dosed 10 partial responses (PRs) for a 37.5% ORR in patients treated in the second- and third-line settings (64% ORR of patients treated in the 2nd line setting) Median PFS 9.4 months Median OS 12.5 months Adverse event profile similar to Phase 1 studies COMPASS THERAPEUTICS Other regimens in BTC FOLFOX (NCCN guidelines): 5% ORR in the second-line setting 4.0 month median PFS 6.2 month median OS TOPAZ-1 (Phase 3 study): 26.7% ORR for Gem/Cis/Durvalumab (anti PD-L1) in the first-line setting 11#12Phase 2/3 U.S. BTC Study Design Patients who have received one prior line of therapy 2:1 Randomization COMPASS THERAPEUTICS CTX-009 + Paclitaxel n=100 Paclitaxel n=50 Study Treatment 28 Day Cycles CTX-009 10mg/kg Day 1 and 15 Paclitaxel 80 mg/m² Day 1, Day 8, and Day 15 of every 28 day cycle. Disease Progression per RECIST 1.1, as confirmed by Independent Central Radiology Follow Up Death, Lost to Follow Up, Withdrawal of Consent 12#13CTX-009: BTC Patient Demographics and Current Treatments Incident Cases 1L Treatment Doublet chemo of gemcitabine + cisplatin (ABC-02 study) Or Gemcitabine/cisplatin + durvalumab (recently approved for 1L) US 18,400¹ FOLFOX 5% ORR 0.9 Mos OS A EU5 21,800² 1. NCI Surveillance, Epidemiology, and End Results (SEER) program 2. Delveinsight/company estimates COMPASS THERAPEUTICS 3. International Agency for Research on Cancer/GLOBOCAN Japan Worldwide 14,329² >200,000³ 2L Treatment FGFR2 mutation Pemigatinib (10-15% of CCA) IDH1 mutation Ivosidenib (1-3% of BTC) MSI-H tumors PD-1 Inhibitor (<1% of BTC) Clinical trial 13#14Phase 1a CTX-009 Monotherapy Data Clinical activity at RP2D dosages (10 and 12.5 mg/kg) All patients (n=16) Colorectal Cancer (n=6) Gastric Cancer (n=8) COMPASS THERAPEUTICS Prior VEGF Targeted Therapy 75% 100% 63% Partial Response (PR) 19% 33% 13% Stable Disease (SD) 50% 33% 63% Clinical Benefit Rate (PR + SD) 69% 67% 75% Median Time to Progression (TTP) (Months) 3.9 6.7 3.9 14#15Phase 2 U.S. CRC Study Design COMPASS THERAPEUTICS Simon 2 Stage Adaptive Design Stage 1 Stop Recruitment Stage 2 No n = 37 subjects ORR > 3/37 Yes n = 47 subjects 15#16CTX-009: CRC Patient Demographics and Current Treatments Japan Chemotherapy FOLFOX/FOLFIRI Incident Cases ~50% Metastatic³ 50-70% reach 3L4 1L Treatment Bevacizumab or EGFR inhibitor + chemotherapy US 153,020¹ 38,000-53,000 patients Anti-PD-1 with MSI-H/dMMR mutation ~5% of CRC EU5 1. NCI Surveillance, Epidemiology, and End Results (SEER) program 2. International Agency for Research on Cancer/GLOBOCAN COMPASS 3. L Biller, D Schrag, JAMA 2021 Feb 16 THERAPEUTICS 4. Bekaii-Saab, Clin advances in Hem and Onc, Supp Jan 2021 246,734² 2L Treatment Bevacizumab or EGFR + chemo 148,505² BRAF/EGFR with V600E mutation 5-8% of CRC Worldwide 1,931,590² 3L Treatment Regorafenib ORR 1%, Median PFS 2.0 months Trifluridine/ tipiracil ORR 1-2% Median PFS ~2 months 16#17CTX-009 Development Plans Initiated Q4 2022 Phase 2 study in third- and fourth- line colorectal cancer in the US COMPASS THERAPEUTICS Initiated Q1 2023 Phase 2/3 Randomized BTC study in the US O Initiate H2 2023 Phase 2 study in advanced ovarian or other cancer in the US Evaluating additional indications for CTX-009 both as a monotherapy and in combination with chemotherapy 17#18Dr. Richard M. Goldberg Professor and Director Emeritus The West Virginia University Cancer Institute#19How Does CTX-009 Data Compared to Other BTC Studies? FOLFOX (ABC-06) 1 Gem/Cis 2 1L Only 2L Parameter ORR OS PFS Any AE Gr 3/4 AEs Deaths (as Gr 5) AEs leading to discontinuation COMPASS THERAPEUTICS CTX-009 Mixed 2L and 3L N=24 37.5% [64% 2L; 15% 3L] 12.5 m 9.4 m 100% 92% 1 (4%) 25% N=81 5% 6.2 m 4.0 m 99% 60% 10 (12%) ~ 12% 1. Lamarca D, Lancet Oncol 2021; March 30 2. Valle, J. et al., N ENGL J MED, 362; 14 Apr 8, 2010, p. 1273 Oh, D. et al., ESMO Poster 56P 2022 3. N=204 26% 11.7 m 8.0 m 55% 71% 17 (8%) 10% Gem/Cis + Durv ³ Only 1L N=341 26.7% 12.9 m 7.2 m 99.4% 74% 13 (4%) 13% 19#20Q & A