This Management's Discussion and Analysis of Financial Condition and Results of Operations should be read in conjunction with the unaudited financial information and the notes thereto included in this Quarterly Report on Form 10-Q and the audited financial information and the notes thereto included in the Annual Report on Form 10-K for the year ended December 31, 2020 filed with the SEC on March 19, 2021.

Certain matters discussed in this Quarterly Report on Form 10-Q may be deemed to be forward-looking statements that involve risks and uncertainties. We make such forward-looking statements pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. In this Quarterly Report on Form 10-Q, words such as "may," "will," "anticipate," "estimate," "expects," "projects," "intends," "plans," "believes" and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) are intended to identify forward-looking statements.

Our actual results and the timing of certain events may differ materially from the results discussed, projected, anticipated, or indicated in any forward-looking statements. We caution you that forward-looking statements are not guarantees of future performance and that our actual results of operations, financial condition and liquidity, and the development of the industry in which we operate may differ materially from the forward-looking statements contained in this Quarterly Report. In addition, even if our results of operations, financial condition and liquidity, and the development of the industry in which we operate are consistent with the forward-looking statements contained in this Quarterly Report, they may not be predictive of results or developments in future periods.

The following information and any forward-looking statements should be considered in light of factors discussed elsewhere in this Quarterly Report on Form 10-Q and under "Risk Factors" in Part I, Item 1A of our Annual Report on Form 10-K for the year ended December 31, 2020.

We caution readers not to place undue reliance on any forward-looking statements made by us, which speak only as of the date they are made. We disclaim any obligation, except as specifically required by law and the rules of the SEC, to publicly update or revise any such statements to reflect any change in our expectations or in events, conditions or circumstances on which any such statements may be based, or that may affect the likelihood that actual results will differ from those set forth in the forward-looking statements.

You should read the following discussion and analysis of financial condition and results of operations together with Part I, Item 1, "Financial Statements," which includes our financial statements and related notes, elsewhere in this Quarterly Report on Form 10-Q. In preparing this Management's Discussion and Analysis of Financial Condition and Results of Operations, we presume that readers have access to and have read the Management's Discussion and Analysis of Financial Condition and Results of Operations in our Annual Report on Form 10-K, pursuant to Instruction 2 to paragraph (b) of Item 303 of Regulation S-K.

Overview

Molecular Templates is a clinical-stage biopharmaceutical company focused on the discovery and development of targeted biologic therapeutics. Our proprietary drug platform technology, known as engineered toxin bodies, or ETBs, leverages the resident biology of a genetically engineered form of Shiga-like Toxin A subunit, or SLTA to create novel therapies with potent and differentiated mechanisms of action for cancer and other serious diseases.

Business

ETBs use a genetically engineered version of the SLTA. In its wild-type form, Shiga-like Toxin or "SLT" is thought to induce its own entry into a cell when proximal to the cell surface membrane, self-route to the cytosol, and enzymatically and irreversibly shut down protein synthesis via ribosome inactivation. SLTA is normally coupled to its cognate Shiga-like Toxin B subunit, or SLTB, to target the CD77 cell surface marker, a non-internalizing glycosphingolipid. In our scaffold, a genetically engineered SLTA with no cognate SLTB component is genetically fused to antibody domains or fragments specific to a target, resulting in a biologic therapeutic that can identify the particular target and specifically kill the cell. The antibody domains may be substituted with other antibody domains having different specificities to allow for the rapid development of new drugs to selected targets in cancer and other serious diseases.

ETBs combine the specificity of an antibody with SLTA's potent mechanism of cell destruction. Based on the disease setting, we have created ETBs that have reduced immunogenicity and are capable of delivering additional payloads into a target cell. Immunogenicity is the ability of a foreign substance to provoke an immune response in a host. ETBs have relatively predictable pharmacokinetic, or PK, and absorption, distribution, metabolism and excretion, or ADME, profiles and can be rapidly screened for desired activity in robust cell-based and animal-model assays. Because SLTA can induce internalization against non- and poorly-internalizing receptors, the universe of targets for ETBs should be substantially larger than that seen with antibody drug conjugates, or ADCs, which are not likely to be effective if the target does not readily internalize the ADC payload.



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ETBs have a differentiated mechanism of cell kill in cancer therapeutics (the inhibition of protein synthesis via ribosome destruction), and we have preclinical and clinical data demonstrating the utility of these molecules in chemotherapy-refractory cancers. ETBs have shown good tolerability in multiple animal models as well as a generally favorable tolerability profile in our clinical studies to date. We believe the target specificity of ETBs, their ability to self-internalize, their potent and differentiated mechanism of cell kill and their tolerability profile provide opportunities for the clinical development of these agents to address multiple cancer types.

Our initial approach to drug development in oncology involves the selection of lead compounds to validated targets in cancer. We have developed ETBs for various targets, including CD38, HER2, and PD-L1. HER2 is clinically validated as a target for the treatment of solid tumors including breast and gastric cancer. CD38 has been validated as a meaningful clinical target in the treatment of multiple myeloma. PD-L1 is central to immune checkpoint pathways and is a target expressed in a variety of solid tumor cancers.

We filed an IND for MT-5111, our ETB targeting HER2, in March 2019 and the IND was accepted in April 2019. We began dosing study subjects in a Phase I study of MT-5111 for the treatment of HER2-positive cancers in the fourth quarter of 2019. The ongoing Phase I study has two parts: Part 1 is dose escalation and Part 2 is dose expansion, which will begin when a maximum tolerated dose (MTD) or Recommended Phase II Dose (RP2D) is established in Part 1. We provided an update on this study in December 2020. All of the following information on the Phase I study for MT-5111 was as of that update. 16 subjects, with a median of 4 prior lines of therapy and a median of 2 prior HER2-targeting regimens, have been treated with MT-5111; subjects with breast cancer received a median of 6 prior lines of therapy, 4 of which contained HER2- targeting agents (metastatic breast cancer n=6, metastatic biliary tract carcinoma n=6, metastatic pancreatic cancer n=2, and one each of metastatic colon adenocarcinoma and metastatic gastroesophageal junction adenocarcinoma). Five cohorts (0.5, 1.0, 2.0, 3.0, and 4.5 ?g/kg/week) have been successfully completed and the sixth cohort (6.75 ?g/kg) has been initiated. Pharmacokinetic (PK) data confirm the predicted human PK based on non-human primate studies. PK modeling has suggested that doses equal to or greater than 5.0 ?g/kg are likely needed for efficacy. Thus far, no life-threatening toxicities have been observed in any cohort and MT-5111 appears to be well tolerated. To date, we have observed no cases of capillary leak syndrome (CLS) (any grade) in human subjects who have been dosed with MT-5111.

As of our December 2020 update, no cardiac AEs or abnormalities in cardiac biomarkers have been noted thus far. The most commonly reported AEs that may be causally related among the 4 dosing cohorts to date and for which source-verified data were available include the following: fatigue (n=3), AST increased (n=2) at 0.5 ?g/kg and 1 ?g/kg, and chills (n=2). These most commonly reported AEs were all of grade 1 or 2 severity. No cases of CLS (any grade) were observed. One subject with metastatic breast cancer in cohort 2 (1.0 µg/kg) remained on treatment for 10 cycles with stable disease; although she had unmeasurable disease by RECIST criteria, she had three sub-centimeter hepatic lesions that disappeared at the end of cycle 8 before she discontinued at cycle 10. This subject had received three prior HER-2 targeting regimens which initially included pertuzumab plus trastuzumab followed by trastuzumab and TDM1 as monotherapies. As of our December 2020 update, 15 subjects have discontinued for disease progression and one subject is too early to evaluate. The HER2-positive breast cancer expansion cohort initiated as of November 2021 at a dose of 10.0 ?g/kg (anticipated to be a therapeutic dose level). Dose escalation will continue to determine the recommended Phase II dose while the breast cancer expansion cohort collects efficacy and safety data.

We are encouraged by the safety profile to date in these heavily pretreated subjects and believe the study has reached clinically active dose levels.

Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited ("Takeda") filed an IND for TAK-169, now known as MT-0169, our jointly discovered ETB targeting CD38, in May 2019 and the IND was accepted in June 2019.

In April 2021, we received notice from Takeda that Takeda had decided to terminate the Development Collaboration and Exclusive License Agreement by and between the Company and Takeda, dated September 18, 2018, as amended (the "Collaboration Agreement") to co-develop one or more products incorporating or comprised of one or more SLT-A fusion proteins targeting CD38 for the treatment of patients with diseases such as multiple myeloma. Following receipt of the termination notice from Takeda, we notified Takeda of our intent to assume full rights to MT-0169, by entering into an agreement for such rights pursuant to the termination provisions of the Collaboration Agreement. In August 2021, we assumed full rights to MT-0169, including full control of MT-0169 clinical development, per the terms of the terminated Collaboration Agreement. Following the transfer of the full MT-0169 rights to us, we will owe low-single digit royalties on future net sales of MT-0169 to Takeda as well as to certain third-party licensors. We will also owe certain third-party licensors potential aggregate clinical and regulatory milestone payments of up to $22.25 million.

MT-0169 is in an ongoing Phase 1 study in relapsed/refractory multiple myeloma and non-Hodgkins lymphoma with dose escalation planned through six dose cohorts, in which the first subject was dosed in February 2020. Patient enrollment in the 50 ?g/kg cohort in relapsed/refractory multiple myeloma has resumed following the transfer of the IND to us in August 2021. We continue to see pharmacodynamic activity with MT-0169.





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We filed an IND for MT-6402, our ETB targeting PD-L1, in December 2020 and the IND was accepted in January 2021. A Phase 1 study of MT-6402 in PD-1/PD-L1 antibody relapsed/refractory patients was initiated in July 2021. The Phase 1 study for MT-6402 is a multi-center, open-label, dose escalation and dose expansion trial in the United States. Patients with confirmed PD-L1 expressing tumors or confirmed PD-L1 expression in the tumor microenvironment are eligible for enrollment. The starting dose is 16.0 mcg/kg with patient enrollment in this cohort currently ongoing. Following determination of the maximum tolerated dose (MTD) or recommended Phase 2 dose, expansion cohorts are planned to evaluate MT-6402 as a monotherapy in tumor-specific and tumor-agnostic cohorts.

We expect to provide an update on MT-5111, MT-0169 and MT-6402 by the end of this year and expect to provide periodic updates throughout 2022. We continue to advance our pipeline of next-generation ETBs targeting CTLA-4, TIGIT, TROP2, SLAMF-7, CD20, and CD45.

Our trials and plans for our ETB product candidates, including MT-5111, MT-0169, and MT-6402, which utilize next-generation ETB technology, are not affected by the discontinuation of our first-generation ETB, MT-3724, which occurred in April 2021. Next-generation ETB scaffolds have been designed to reduce or eliminate the propensity for innate immunity, including CLS. To date, we have observed no cases of CLS (any grade) in human subjects who have been dosed with MT-5111, MT-0169 or MT-6402.

We have built up multiple core competencies around the creation and development of ETBs. We developed the ETB technology in-house and continue to make iterative improvements in the scaffold and identify new uses of the technology. We also developed the proprietary process for manufacturing ETBs under Current Good Manufacturing Process, or cGMP regulatory standards and continue to make improvements to its manufacturing processes.

We have conducted multiple cGMP manufacturing runs with our compounds and believe this process is robust and could support commercial production with gross margins that are similar to those seen with antibodies.

Impact of COVID-19

In March 2020, the outbreak of COVID-19 caused by a novel strain of the coronavirus was recognized as a pandemic by the World Health Organization. It has impacted, and is continuing to impact, all aspects of society, including the operation of the healthcare system and other business and economic activity worldwide. The COVID-19 pandemic, and other similar outbreaks of contagious diseases, may adversely impact our business, financial condition, and results of operations. For example, we and the third-party clinical trial sites or investigators involved in our current and future clinical trials may experience significant interruptions or delays as a result of this pandemic, and these could impact the conduct of our clinical trials and our ability to complete them in a timely manner or at all, which in turn could delay and/or negatively impact the regulatory review and approval of our drug or biologic candidates.

We are carefully and continually evaluating the potential individual patient risk associated with continuing to enroll in our existing clinical studies during the ongoing COVID-19 pandemic, in accordance with FDA and foreign regulatory authorities' recommendations for clinical trials. Our Phase 1 studies for MT-5111, MT-0169 and MT-6402 are open and able to treat enrolled subjects and screen new subjects.

The decision to continue our ongoing studies throughout the COVID-19 pandemic was predicated on the treating investigator determining that the potential benefit to the patient of investigational therapy outweighs the potential risk of contracting COVID-19 as the subjects enrolled in our trials had relapsed or refractory incurable malignancies with few or no standard-of-care therapeutic options and limited life expectancy.

Overall, COVID-19 led to a significant slowdown in the pace of site initiations and patient enrollment into our clinical trials. The degree of disruption was, and continues to be, variable by geography and individual clinical site, with some sites screening and enrolling only subjects with an urgent need for treatment, and some attempting to operate as usual. The COVID-19 pandemic resulted in a significant slowdown in the pace of site initiations and patient enrollment across the MT-0169 program, which had a temporary pause in the activation of new study sites and new patient enrollment (along with most of Takeda's other early-stage studies) due to COVID-19 and was reinitiated in the fourth quarter of 2020. To date, screening and enrollment for the MT-5111 Phase I study, which remained open throughout the pandemic, has been less adversely affected than the MT-0169 studies were during 2020. Our Phase 1 study of MT-6402 was recently initiated in July 2021. To date, we have been able to continue to work at our cGMP manufacturing facility and laboratories without significant interruption from COVID-19. As a result, manufacturing of product supply for clinical trials and research activities to support advancement of our preclinical pipeline (including partnered programs) have not been adversely affected by COVID-19 to date.

The extent to which the COVID-19 pandemic may impact our business, financial condition and results of operations will depend on the manner in which this pandemic continues to evolve and future developments in response thereto, which are highly uncertain and cannot be predicted with confidence and which may include, among other things, the ultimate severity, intensity and duration of this pandemic (including any resurgences); impact of the new COVID-19 variants, the rollout of COVID-19 vaccines? governmental, business or other actions that have been, or will be, taken in response to this pandemic, including restrictions on travel and mobility,



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business closures and imposition of social distancing measures? impacts of the pandemic on the vendors or distribution channels in our or our partners' supply chain and ability to continue to manufacture our investigational products? impacts of the pandemic on the conduct of our clinical trials, including with respect to enrollment rates, availability of investigators and clinical trial sites or monitoring of data? and impacts of the pandemic on the regulatory agencies with which we interact in the development, review, approval and commercialization of our therapeutic products.

Collaboration Agreements

Takeda Pharmaceuticals

Takeda Development and License Agreement

On September 18, 2018, we entered into a development collaboration and exclusive license agreement (the "Takeda Development and License Agreement") with Takeda for the development and commercialization of products incorporating or comprised of one or more CD38 SLT-A fusion proteins ("Licensed Products") for the treatment of patients with diseases such as multiple myeloma.

Pursuant to the Takeda Development and License Agreement, we initially co-developed with Takeda one or more of the Licensed Products up to and including Phase Ia clinical trials, with us having an option to continue to co-develop the Licensed Products following Phase Ia clinical trials. Pursuant to the terms of the Takeda Development and License Agreement, Takeda was to be responsible for all regulatory activities and commercialization of the Licensed Products. We granted Takeda specified intellectual property licenses to enable Takeda to perform its obligations and exercise its rights under the Takeda Development and License Agreement, including exclusive license grants to enable Takeda to conduct development, manufacturing, and commercialization activities pursuant to the terms of the Takeda Development and License Agreement.

The Takeda Development and License Agreement had a total transaction price of $29.8 million, which consisted of (1) the $30.0 million upfront payment, (2) a $10.0 million development milestone payment which was achieved in the first quarter of 2020, (3) minus $10.2 million which was the expected co-share payments payable to Takeda during Early-Stage Development.

In July 2019, we exercised our co-development option and the agreed upon collaboration budget was increased to cover additional research and development activities.

In April 2021, we received notice from Takeda that Takeda decided to terminate the Takeda Development and License Agreement. Following receipt of the termination notice from Takeda, we notified Takeda of our intent to assume full rights to MT-0169, a second-generation ETB targeting CD38, by entering into an agreement for such rights pursuant to the termination provisions of the Takeda Development and License Agreement. The termination of the Takeda Development and License Agreement was effective August 4, 2021. As of the same date, we assumed full rights to MT-0169, including full control of MT-0169 clinical development, per the terms of the terminated Takeda Development and License Agreement. Following the transfer of the full MT-0169 rights to us, we will owe low-single digit royalties on future net sales of MT-0169 to Takeda as well as to certain third-party licensors. We will also owe certain third-party licensors potential aggregate clinical and regulatory milestone payments of up to $22.25 million.

Takeda Multi-Target Agreement

In June 2017, we entered into a Multi-Target Collaboration and License Agreement with Takeda ("Takeda Multi-Target Agreement") in which we agreed to collaborate with Takeda to identify and generate ETBs, against two targets designated by Takeda. Takeda designated certain targets of interest as the focus of the research. Each party granted to the other nonexclusive rights in its intellectual property for purposes of the conduct of the research, and we agreed to work exclusively with Takeda with respect to the designated targets.

Under the Takeda Multi-Target Agreement, Takeda has an option during an option period to obtain an exclusive license under our intellectual property to develop, manufacture, commercialize and otherwise exploit ETBs against the designated targets. The option period for each target ends three months after the completion of the evaluation of such designated target.

We received an upfront fee of $1.0 million and an additional $2.0 million following the designation of each of the two targets in December 2017. As of September 30, 2021, we have received $5.0 million from Takeda pursuant to the Takeda Multi-Target Agreement.

The Takeda Multi-Target Agreement also provides for potential additional future payments based upon the exercise by Takeda of certain options and our achievement of various development, regulatory and sales milestone events, and potential royalty payments and contingency fees as further described in Note 3 "Research and Development Agreements", of our previously filed Annual Report on Form 10-K for the year ended December 31, 2020, filed with the SEC on March 19, 2021.

The Takeda Multi-Target Agreement will expire on the expiration of the option period (within three months after the completion of the evaluation of each designated target) for the designated targets if Takeda does not exercise its options, or, following exercise of



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the option, on the later of the expiration of patent rights claiming the licensed ETB or ten years from first commercial sale of a licensed ETB. The Takeda Multi-Target Agreement might be sooner terminated by Takeda for convenience or upon a change of control in our ownership, or by either party for an uncured material breach of the agreement.

Vertex Pharmaceuticals

On November 18, 2019, we entered into a Master Collaboration Agreement ("Vertex Collaboration Agreement") with Vertex Pharmaceuticals Incorporated ("Vertex"), in which we and Vertex agreed to enter into a strategic research collaboration to leverage our ETB technology platform to discover and develop novel targeted biologic therapies for applications outside of oncology.

Pursuant to the terms of and upon the Company's entry into the Vertex Collaboration Agreement, Vertex paid us an upfront payment of $38.0 million, which included proceeds from a concurrent equity investment pursuant to a Share Purchase Agreement (the "SPA"), described further below. In addition to the upfront payments, we had the opportunity to receive an additional $22.5 million through the exercise of the options to license ETB products or to add an additional target. We would have provided, and Vertex would have reimbursed us for, certain mutually agreed manufacturing technology transfer activities.

We also had the opportunity, for each target under the Vertex Collaboration Agreement, to receive up to an additional $180.0 million in milestone payments upon the achievement of certain development and regulatory milestone events and up to an additional $70.0 million in milestone payments upon the achievement of certain sales milestone events. We also would have been entitled to receive, subject to certain reductions, tiered mid-single digit royalties as percentages of calendar year net sales, if any, on any licensed product.

We would have been responsible for conducting the research activities through the designation of one or more development candidates. If Vertex had exercised its option for a development candidate, Vertex would have been responsible for all development, manufacturing, regulatory and commercialization activities with respect to that development candidate. In connection with the Company's entry into the Vertex Collaboration Agreement, we and Vertex entered into the SPA pursuant to which Vertex purchased 1,666,666 shares of our common stock, par value $0.001 per share, at a price per share of $9.00. The issuance of these shares was pursuant to a private placement exemption from registration afforded by Section 4(a)(2) of the Securities Act of 1933, as amended, and Rule 506 of Regulation D thereunder.

In October 2021, the Company received notice from Vertex that Vertex had decided to terminate the Vertex Collaboration Agreement. The termination of the Vertex Collaboration Agreement was effective October 29, 2021.

For more information concerning our collaboration agreements, refer to Note 3, "Research and Development Agreements" to our unaudited consolidated financial statements for the three and nine months ended September 30, 2021, included in this Quarterly Report on Form 10-Q.

Bristol Myers Squibb Company

On February 10, 2021, we entered into a Collaboration Agreement ("BMS Collaboration Agreement") with Bristol Myers Squibb Company ("Bristol Myers Squibb"), in which we and Bristol Myers Squibb agreed to enter into a strategic research collaboration to leverage our ETB technology platform to discover and develop novel products containing ETBs directed to multiple targets.

Pursuant to the BMS Collaboration Agreement, Bristol Myers Squibb paid us an upfront payment of $70.0 million. We may receive near term and development and regulatory milestone payments of up to an additional $874.5 million and will be eligible to receive up to an additional $450.0 million in milestone payments upon the achievement of certain sales milestone events. We will also be entitled to receive, subject to certain reductions, tiered royalties ranging from mid-single digits up to mid-teens as percentages of calendar year net sales, if any, on any licensed product.

We will be responsible for conducting the research activities through the designation, if any, of one or more development candidates. Upon the exercise of its option for a development candidate, Bristol Myers Squibb will be responsible for all development, manufacturing, regulatory and commercialization activities with respect to that development candidate, subject to the terms and conditions of the BMS Collaboration Agreement.

For more information concerning this collaboration agreement, refer to Note 3, "Research and Development Agreements" to our unaudited consolidated financial statements for the three and nine months ended September 30, 2021, included in this Quarterly Report on Form 10-Q.



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Grant Agreements

CPRIT Grant Contract

In September 2018, we entered into a Cancer Research Grant Contract (the "CD38 CPRIT Agreement") with the Cancer Prevention and Research Institute of Texas ("CPRIT"), which was extended in May 2021, in connection with a grant of approximately $15.2 million awarded by CPRIT to us in November 2016 to fund research of a cancer therapy involving an ETB that is targeting CD38 (the "Award"). Pursuant to the CD38 CPRIT Agreement, we might also use such funds to develop a replacement CD38 targeting ETB, with or without a partner. The Award is contingent upon funds being available during the term of the CD38 CPRIT Agreement and subject to CPRIT's ability to perform its obligations under the CD38 CPRIT Agreement as well as our progress towards achievement of specified milestones, among other contractual requirements.

In 2011, we were awarded a $10.6 million product development grant from CPRIT for its CD20 targeting ETB MT-3724. This product development grant ended in November 2019.

Subject to the terms of the CD38 CPRIT Agreement, full ownership of any CPRIT funded technology and CPRIT funded intellectual property rights developed pursuant to the CD38 CPRIT Agreement will be retained by us, our Collaborators (as defined in the CD38 CPRIT Agreement) and, to the extent applicable, any participating third party (the "Project Results"). With respect to any Project Results, we agreed to grant to CPRIT a nonexclusive, irrevocable, royalty-free, perpetual, worldwide license, solely for academic, research and other non-commercial purposes, under the Project Results and to exploit any necessary additional intellectual property rights, subject to certain exclusions.

We will pay to CPRIT, during the term of the CD38 CPRIT Agreement, certain payments equal to a percentage of revenue ranging from the low- to mid-single digits. These payments will continue up to and until CPRIT receives an aggregate amount of 400% of the sum of all monies paid to us by CPRIT under the CD38 CPRIT Agreement. If we are required to obtain a license from a third party to sell any such product, the revenue sharing percentages might be reduced. In addition, once we pay CPRIT 400% of the monies the Company has received under the CD38 CPRIT Agreement, we will continue to pay CPRIT a revenue-sharing percentage of 0.5%.

The CD38 CPRIT Agreement will terminate, with certain obligations extending beyond termination, on the earlier of (a) November 30, 2021 or (b) the occurrence of any of the following events: (i) by mutual written consent of the parties, (ii) by CPRIT for an Event of Default (as defined in the CD38 CPRIT Agreement) by us, (iii) by CPRIT if allocated funds should become legally unavailable during the term of the CD38 CPRIT Agreement and CPRIT is unable to obtain additional funds or (iv) by us for convenience. CPRIT might approve a no cost extension for the CD38 CPRIT Agreement for a period not to exceed six months after the termination date if additional time is required to ensure adequate completion of the approved project, subject to the terms and conditions of the CD38 CPRIT Agreement.

For more information about our grant agreements, please see Note 3, "Research and Development Agreements" to our unaudited consolidated financial statements for the three and nine months ended September 30, 2021, included in this Quarterly Report on Form 10-Q.

Financial Operations Overview

Revenue

To date, we have not generated any revenue from product sales to customers. We do not expect to receive any revenue from any ETB candidates that we or our collaboration partners develop, including MT-5111, MT-0169, MT-6402 and other pre-clinical ETB candidates, until we obtain regulatory approval and commercialize such biologics. Our revenue consists principally of collaboration revenue and grant revenue.

Research and Development revenue primarily relates to our collaboration agreements with Takeda, Vertex and Bristol Myers Squibb which are accounted for using the percentage-of-completion cost-to-cost method.

Grant revenue relates to our CPRIT grant for a CD38 ETB (MT-0169). CPRIT grant funds for MT-0169 are provided to us in arrears as cost reimbursement where revenue is recognized as allowable costs are incurred. Revenue recognized in excess of amounts collected are recorded as unbilled revenue.

For more information about our revenue recognition policy, please see Note 1, "Organization and Summary of Significant Accounting Policies" to our audited consolidated financial statements for the year ended December 31, 2020, included in our Annual Report on Form 10-K for the year ended December 31, 2020 filed with the SEC March 19, 2021.



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Research and Development Expenses

Research and development expenses consist principally of:



    •   salaries for research and development staff and related expenses,
        including stock-based compensation expenses;


    •   costs for current good manufacturing practices, or cGMP, manufacturing of
        drug substances and drug products by contract manufacturers;


    •   fees and other costs paid to clinical trials sites and clinical research
        organizations, ("CROs"), in connection with the performance of clinical
        trials and preclinical testing;


  • costs for consultants and contract research;


  • costs of laboratory supplies and small equipment, including maintenance; and


  • depreciation of long-lived assets.

Our research and development expenses may vary substantially from period to period based on the timing of our research and development activities, including the initiation and enrollment of subjects in clinical trials and manufacture of drug or biologic materials for clinical trials. We expect research and development expenses to increase as we advance the clinical development of MT-5111, MT-0169 and/or MT-6402 and further advance the research and development of our pre-clinical ETB candidates, and other earlier stage drugs or biologics. The successful development of our ETB candidates is highly uncertain. At this time, we cannot reasonably estimate the nature, timing and estimated costs of the efforts that will be necessary to complete the development of, or the period, if any, in which material net cash inflows may commence from any of our ETB candidates. This is due to numerous risks and uncertainties associated with developing drugs, including the uncertainty of:



    •   the scope, rate of progress and expense of our research and development
        activities;


  • clinical trials and early-stage results;


  • the terms and timing of regulatory approvals; and


    •   the ability to market, commercialize and achieve market acceptance for
        MT-5111, MT-0169, MT-6402 or any other ETB candidate that we or our
        collaboration partners may develop in the future.

Any of these variables with respect to the development of MT-5111, MT-0169, or any other ETB candidate that we may develop could result in a significant change in the costs and timing associated with the development of such candidates. For example, if the FDA the European Medicines Agency ("EMA") or other regulatory authority were to require us to conduct pre-clinical and clinical studies beyond those which we currently anticipate will be required for the completion of clinical development or if we experience significant delays in enrollment in any clinical trials, we could be required to expend significant additional financial resources and time on the completion of our clinical development programs.

General and Administrative Expenses

Our general and administrative expenses consist principally of:



    •   salaries for employees other than research and development staff,
        including stock-based compensation expenses;


    •   professional fees for auditors and other consulting expenses related to
        general and administrative activities;


    •   professional fees for legal services related to the protection and
        maintenance of our intellectual property and regulatory compliance;


  • cost of facilities, communication and office expenses;


  • information technology services; and


  • depreciation of long-lived assets.

We expect that our general and administrative costs will increase in the future as our business expands and we increase our headcount to support the expected growth in our operating activities. Additionally, we expect these expenses will also increase in the future as we incur additional costs associated with operating as a public company. These increases will likely include additional legal fees, accounting and audit fees, management board and supervisory board liability insurance premiums and costs related to investor relations. In addition, we expect to grant stock-based compensation awards to key management personnel and other employees.



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Other Income (Expense)

Other income (expense) mainly includes interest income earned on our cash and marketable securities balances held, and interest expense on our outstanding borrowings.





Results of Operations

Revenues

The table below summarizes our revenues as follows (in thousands):





                                         Three Months Ended              Nine Months Ended
                                            September 30,                  September 30,
                                        2021             2020           2021            2020
Research and development revenue,
related party                        $         -      $    1,566     $    13,136     $    4,962
Research and development revenue,
other                                      2,379           2,732           7,597          7,176
Grant revenue                                  -               -               -          3,210
Total revenue                        $     2,379      $    4,298     $    20,733     $   15,348

Research and Development Revenue - from related party

The decrease in research and development revenue - from related parties for the three months ended September 30, 2021 and increase for the nine months ended September 30, 2021 was due to timing of research and development revenues related to the Takeda Development and License Agreement (MT-0169).

For more information about our collaboration agreements, please see Note 3 "Research and Development Agreements" to our unaudited consolidated financial statements for the three and nine months ended September 30, 2021, included in this Quarterly Report on Form 10-Q.

Research and Development Revenue - other

The decrease for the three months ended September 30, 2021 and increase for the nine months ended September 30, 2021 in research and development revenue - other is a result of revenue associated with our Vertex Collaboration Agreement and BMS Collaboration Agreement.

For more information about our collaboration agreements, please see Note 3 "Research and Development Agreements" to our unaudited consolidated financial statements for the three and nine months ended September 30, 2021, included in this Quarterly Report on Form 10-Q.

Grant Revenue

The decrease in grant revenue for the nine months ended September 30, 2021 was primarily due to the Company not incurring additional expenses for the CD38 CPRIT Agreement grant during the nine months ended September 30, 2021.

Operating Expenses

The table below summarizes our operating expenses as follows (in thousands):



                                        Three Months Ended          Nine Months Ended
                                           September 30,              September 30,
                                         2021          2020         2021          2020

Research and development expenses $ 22,881 $ 19,622 $ 65,328 $ 70,667 General and administrative expenses 9,027 7,547 26,178 19,606 Total operating expenses

$   31,908     $ 27,169     $  91,506     $ 90,273


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Research and Development Expenses



The table below summarizes our research and development expenses as follows (in
thousands):

                                            Three Months Ended          Nine Months Ended
                                               September 30,              September 30,
                                             2021          2020         2021          2020
Program costs                             $    8,192     $  7,554     $  22,783     $ 35,938
Employee compensation                         10,774        9,304        31,956       24,529
Laboratory costs                               1,545          937         4,102        2,932
Other research and development costs           2,370        1,827         6,487        7,268

Total research and development expenses $ 22,881 $ 19,622 $ 65,328 $ 70,667

Research and development ("R&D") expenses increased $3.3 million during the three months ended September 30, 2021 compared to the three months ended September 30, 2020 primarily due to an increase in employee compensation and decreased $5.3 million during the nine months ended September 30, 2021 compared to the nine months ended September 30, 2020 due to a decrease in program costs related to the discovery and development of ETBs, partially offset by an increase in employee compensation.

Program costs increased $0.6 million during the three months ended September 30, 2021 compared to the three months ended September 30, 2020 and decreased $13.2 million for the nine months ended September 30, 2021 compared to the nine months ended September 30, 2020. The program costs primarily driving the increase for the three months ended September 30, 2021 were $1.8 million for MT-0169, $1.6 million for MT-6402, $1.3 million for CTLA-4 and $0.1 million for BMS partially offset by decreases of $2.2 million for MT-3724, $0.7 million for next generation CD-20, $0.5 million for MT-5111, $0.5 million for Vertex, $0.3 million for SLAMF-7 and $0.1 million for other programs. The program costs primarily driving the decrease for the nine months ended September 30, 2021 were $8.4 million for MT-3724, $6.2 million for MT-0169, $1.6 million for MT-6402, $1.0 million for MT-5111, $0.5 million for SLAMF-7, partially offset by increases of $3.5 for CTLA-4 and $1.1 for next generation CD-20.

Headcount increased in R&D 8% from September 30, 2020 to September 30, 2021 in support of collaboration research and additional support staff. This staffing increase resulted in an increase in employee compensation costs of $7.4 million for the nine months ended September 30, 2021 compared to the nine months ended September 30, 2020, respectively.

Other R&D costs decreased $0.8 million during the nine months ended September 30, 2021 compared to the nine months ended September 30, 2020, respectively. This decrease was driven by lower consulting and recruiting fees.

General and Administrative Expenses

General and administrative expenses increased $1.5 million during the three months ended September 30, 2021 compared to the three months ended September 30, 2020 and $6.6 million during the nine months ended September 30, 2021 compared to the nine months ended September 30, 2020. The main driver of this increase being payroll and related costs.

Nonoperating activities



The table below summarizes our nonoperating activities as follows (in
thousands):

                                   Three Months Ended          Nine Months Ended
                                      September 30,              September 30,
                                    2021           2020        2021          2020

Interest and other income, net $ 175 $ 167 $ 308 $ 925 Interest expense

                      (1,033 )      (521 )      (2,301 )     (1,229 )
Loss on extinguishment of debt             -           -             -       (1,237 )

Total nonoperating activities $ (858 ) $ (354 ) $ (1,993 ) $ (1,541 )






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Interest and Other Income and Interest Expense

The increase in interest and other income for the three months ended September 30, 2021, compared to the three months ended September 30, 2020, was primarily due to higher interest related to our marketable securities. The decrease in interest and other income for the nine months ended September 30, 2021 compared to the nine months ended September 30, 2020, was primarily due to lower interest related to our marketable securities.

The increase in interest expense for the three and nine months ended September 30, 2021, compared to the three and nine months ended September 30, 2020, was primarily due to the increase in our debt holdings.

The decrease in loss on extinguishment of debt for the nine months ended September 30, 2021, is in connection with the repayment of the Perceptive Credit Facility during the nine months ended September 30, 2020.

Liquidity and Capital Resources

Sources of Funds

We have devoted substantially all of our resources to developing our ETB candidates and platform technology, building our intellectual property portfolio, developing our supply chain, conducting business planning, raising capital and providing for general and administrative support for these operations. We plan to increase our research and development expenses for the foreseeable future as we continue to advance MT-5111, MT-0169, MT-6402 and our earlier-stage pre-clinical programs. At this time, due to the inherently unpredictable nature of preclinical and clinical development and given the early stage of our programs and drug or biologic candidates, we cannot reasonably estimate the costs we will incur and the timelines that will be required to complete development, obtain marketing approval and commercialize our drugs or biologics, if and when approved. For the same reasons, we are also unable to predict when, if ever, we will generate revenue from product sales or whether, or when, if ever, we may achieve profitability. Clinical and preclinical development timelines, the probability of success, and development costs can differ materially from expectations.

In addition, we cannot forecast which drugs or biologics, if and when approved, may be subject to future collaborations, when such arrangements will be secured, if at all, and to what degree such arrangements would affect our development plans and capital requirements.

We expect to incur substantial additional losses in the future as we expand our research and development cost-sharing activities with our collaboration partners, we believe such investment is strategically aligned with increasing the value of our technology. For the nine months ended September 30, 2021 and 2020, we incurred net losses of $72.8 million and $76.5 million, respectively. At September 30, 2021, we had an accumulated deficit of $341.8 million.

To date, we have financed our operations through public offerings of common and preferred stock, private placements of equity securities, a reverse merger, and upfront and milestone payments received from our collaboration agreements, as well as funding from governmental bodies and bank and bridge loans.

In May 2020, we entered into a debt financing facility for up to $45.0 million with K2 HealthVentures, a healthcare-focused specialty finance company (the "K2 Loan and Security Agreement"). The K2 Loan and Security Agreement is drawable in three tranches subject to the satisfaction of the terms and conditions therein. The first tranche of $15.0 million was drawn at the initial closing. The second tranche of $20.0 million was drawn in May 2021, at our option and was subject to the achievement of certain clinical milestones, which we had achieved. The third tranche of $10.0 million may become available subject to lender consent and certain additional conditions prior to December 31, 2021. Pursuant to the terms of the K2 Loan and Security Agreement, the principal accrues interest at an annual rate equal to the greater of 8.45% or the sum of the Prime Rate plus 5.2%. Monthly payments commenced on July 1, 2020 and payments will be interest only until July 1, 2023. Thereafter, the loan shall amortize monthly such that the principal amount of the loan and interest accrued thereon shall be fully amortized by the loan's maturity date of June 1, 2024.

In July 2020, we raised gross proceeds of approximately $50.0 million through at-the-market sales ("ATM") of our common stock pursuant to our ATM facility. We sold approximately 3.6 million shares of our common stock at a purchase price of $12.00 per share and 0.5 million shares at a purchase price of $12.70, in each case the market price at the time of sale. These sales constituted the full available dollar amount under our then-current ATM facility, and with such completion, this ATM facility has been terminated.

In August 2020, we filed a universal shelf registration statement on Form S-3 (Registration No. 333-242078) with the SEC, which was declared effective on August 17, 2020. In August 2020, we entered into a sales agreement (the "Sales Agreement') with Cowen and Company, LLC ("Cowen"), pursuant to which we may offer and sell to or through Cowen acting as agent and/or principal shares of our common stock having an aggregate offering price of up to $100,000,000. Under the Sales Agreement, Cowen may sell the shares by any method permitted by law and deemed to be an "at the market" offering as defined in Rule 415 of the Securities Act. To date, we have not sold any shares under the Sales Agreement.



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In February 2021, we completed a public offering of 6,000,000 shares of common stock at an offering price of $12.65 per share. We received net proceeds of approximately $71.1 million, after deducting underwriting discounts, commissions and estimated offering expenses payable by us.

We expect to incur significant expenses and operating losses for the foreseeable future as we advance our lead ETB candidates through clinical trials, progress our pipeline ETB candidates from discovery through pre-clinical development, and seek regulatory approval and pursue commercialization of our ETB candidates. In addition, if we obtain regulatory approval for any of our ETB candidates, we expect to incur significant commercialization expenses related to product manufacturing, marketing, sales and distribution. In addition, we may incur expenses in connection with the in-license or acquisition of additional technology to augment or enable development of future ETB candidates. Furthermore, we expect to incur additional costs associated with operating as a public company, including significant legal, accounting, investor relations and other expenses that we did not incur as a private company.

As a result, we will need additional financing to support our continuing operations. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through a combination of public or private equity and debt financings or other sources, which may include collaborations with third parties. Adequate additional financing may not be available to us on acceptable terms, or at all. Our inability to raise capital as and when needed would have a negative impact on our financial condition and our ability to pursue our business strategy. We will need to generate significant revenue to achieve profitability, and we may never do so.

At September 30, 2021 and December 31, 2020, we had cash, cash equivalents and marketable securities of $175.4 million and $93.9 million, respectively. We expect that our existing cash and cash equivalents will enable us to fund our operating expenses and capital expenditure requirements into the second half of 2023. We have based this estimate on assumptions that may prove to be wrong, and we may use our available capital resources sooner than we currently expect.

Cash Flows

Comparison of Nine Months Ended September 30, 2021 and 2020

The table below summarizes our cash flows for the nine months ended September 30, 2021 and 2020 (in thousands):



                                                             Nine Months Ended
                                                               September 30,
                                                          2021              2020

Net cash provided by/(used in) operating activities $ (7,926 ) $ (62,291 ) Net cash used in investing activities

                       (82,253 )         (47,869 )
Net cash provided by financing activities                    92,554            58,787
Net increase (decrease) in cash, cash equivalents
and restricted cash                                   $       2,375     $     (51,373 )

The decrease in net cash used in operating activities for the nine months ended September 30, 2021 was primarily due to an decrease in deferred revenue primarily from the BMS Collaboration Agreement.

The increase in net cash used in investing activities for the nine months ended September 30, 2021 was primarily due to increased investment activity in marketable securities.

The increase in net cash provided by financing activities was primarily due to proceeds from issuance of common stock and debt.

Operating and Capital Expenditure Requirements

We have not achieved profitability since our inception and had an accumulated deficit of $341.8 million at September 30, 2021. We expect to continue to incur significant operating losses for the foreseeable future as we continue our research and development efforts and seek to obtain regulatory approval and commercialization of our ETB candidates.

We expect our expenses to increase substantially in connection with our ongoing development activities related to MT-5111, MT-0169 and MT-6402, our collaboration with BMS, our pre-clinical programs, and expanding our operating capabilities. In addition, we expect to incur additional costs associated with operating as a public company. We anticipate that our expenses will increase substantially if and as we:



  • support the ongoing Phase I study of MT-5111;


    •   continue clinical development of MT-0169, an ETB biologic candidate to
        which we have full rights, and support the ongoing Phase I study;


  • support the PD-L1 program and the ongoing Phase I study for MT-6402;


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    •   continue the research and development of our other ETB candidates, such as
        other CD20 targeted molecules, including completing pre-clinical studies
        and commencing clinical trials;


    •   research activities through the designation of the development
        candidate(s) with Bristol Myers Squibb;


    •   seek to enhance our technology platform using our antigen-seeding
        technology approach to immuno-oncology;


    •   seek regulatory approvals for any ETB candidates that successfully
        complete clinical trials;


    •   potentially establish a sales, marketing and distribution infrastructure
        and scale up manufacturing capabilities to commercialize any drugs for
        which we may obtain regulatory approval;


    •   add clinical, scientific, operational, financial and management
        information systems and personnel, including personnel to support our
        product development and potential future commercialization efforts and to
        support our increased operations;


    •   experience any delays or encounter any issues resulting from any of the
        above, including but not limited to failed studies, complex results,
        safety issues or other regulatory challenges;


  • service long-term debt; and


  • complete the expansion of the Company's research and development spaces.



Because of the numerous risks and uncertainties associated with the development of MT-5111, MT-0169 and MT-6402, our collaboration with Bristol Myers Squibb and our other pre-clinical programs, and because the extent to which we may enter into collaborations with third parties for development of these ETB candidates is unknown, we are unable to estimate the amount of increased capital outlays and operating expenses associated with completing the research and development of our ETB candidates. Our future capital requirements for MT-5111, MT-0169, MT-6402 or our other pre-clinical programs will depend on many factors, including:



    •   the progress, timing and completion of pre-clinical testing and clinical
        trials for our current or any future ETB candidates;


  • the number of potential new ETB candidates we identify and decide to develop;


    •   the costs involved in growing our organization to the size needed to allow
        for the research, development and potential commercialization of our
        current or any future ETB candidates;


    •   the costs involved in filing patent applications and maintaining and
        enforcing patents or defending against claims or infringements raised by
        third parties;


    •   the time and costs involved in obtaining regulatory approval for our ETB
        candidates and any delays we may encounter as a result of evolving
        regulatory requirements or adverse results with respect to any of these
        ETB candidates;


    •   any licensing or milestone fees we might have to pay during future
        development of our current or any future ETB candidates;


    •   selling and marketing activities undertaken in connection with the
        anticipated commercialization of our current or any future ETB candidates
        and costs involved in the creation of an effective sales and marketing
        organization; and


    •   the amount of revenues, if any, we may derive either directly or in the
        form of royalty payments from future sales of our ETB candidates, if
        approved.

Identifying potential ETB candidates and conducting pre-clinical testing and clinical trials is a time-consuming, expensive and uncertain process that takes years to complete, and we may never generate the necessary data or results required to obtain marketing approval and achieve product sales. In addition, our ETB candidates, if approved, may not achieve commercial success. Our commercial revenues, if any, will be derived from sales of drugs or biologics that we do not expect to be commercially available for many years, if ever. Accordingly, we will need to obtain substantial additional funds to achieve our business objectives.

Adequate additional funds may not be available to us on acceptable terms, or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, stockholders' ownership interest will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect their rights as stockholders. Additional debt financing and equity financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends and may require the issuance of warrants, which could potentially dilute stockholders' ownership interest.

If we raise additional funds through collaborations, governmental grants, strategic alliances or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or ETB candidates or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings



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when needed, we may be required to delay, limit, reduce or terminate our product development programs or any future commercialization efforts or grant rights to develop and market ETB candidates that we would otherwise prefer to develop and market ourselves.

Critical Accounting Policies and Use of Estimates

Our discussion and analysis of our financial condition and results of operations are based on our unaudited condensed consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States of America for interim financial information. The preparation of these unaudited condensed consolidated financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities and expenses based on historical experience and on various assumptions that we believe to be reasonable under the circumstances. Actual results may differ from these estimates under different assumptions or conditions. For further information on our critical accounting policies, see the discussion of critical accounting policies in our Annual Report on Form 10-K for the year ended December 31, 2020, which we filed with the SEC on March 19, 2021.

Recently Adopted Accounting Pronouncements

For a discussion of recently adopted accounting pronouncements see the discussion in our Annual Report on Form 10-K for the year ended December 31, 2020, which we filed with the SEC on March 19, 2021.

Recent Accounting Pronouncements Not Yet Adopted

For a discussion of recently issued accounting pronouncements and interpretations not yet adopted by us, see Note 1, "Organization and Summary of Significant Accounting Policies", to our unaudited condensed financial statements for the September 30, 2021, included in this Quarterly Report on Form 10-Q.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any off-balance sheet arrangements, as defined in the rules and regulations of the SEC.

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