The following discussion and analysis should be read in conjunction with the unaudited condensed consolidated financial statements and related notes included elsewhere in this Quarterly Report. This discussion and analysis and other parts of this Quarterly Report contain forward-looking statements based upon current beliefs, plans and expectations that involve risks, uncertainties and assumptions, such as statements regarding our plans, objectives, expectations, intentions and projections. Our actual results and the timing of selected events could differ materially from those anticipated in these forward-looking statements as a result of several factors, including those set forth in "Part I, Item 1A, Risk Factors" in our 2021 Annual Report and under Part II, Item 1A, "Risk Factors" and elsewhere in this Quarterly Report. You should carefully read the "Risk Factors" section of this Quarterly Report to gain an understanding of the important factors that could cause actual results to differ materially from our forward-looking statements. Please also see the section entitled "Special note regarding forward-looking statements."

Overview

We are a biotechnology company developing a portfolio of novel small molecule precision medicines that employ the body's natural mechanisms to selectively degrade therapeutically-relevant proteins. We have developed a proprietary protein degradation platform, called QuEENTM, that enables us to rapidly identify protein targets and molecular glue degrader, or MGD, product candidates that are designed to eliminate therapeutically-relevant proteins in a highly selective manner. We believe our small molecule MGDs may give us significant advantages over existing therapeutic modalities, including other protein degradation approaches, by allowing us to target proteins that have been considered undruggable or inadequately drugged. We focus on therapeutic targets backed by strong biological and genetic rationale with the goal of discovering and developing novel precision medicines.

Monte Rosa Therapeutics AG, a Swiss operating company, was incorporated under the laws of Switzerland in April 2018. Monte Rosa Therapeutics, Inc was incorporated in Delaware in November 2019. In 2020, Monte Rosa Therapeutics, Inc. and Monte Rosa Therapeutics AG, entities under common control since the incorporation of Monte Rosa Therapeutics, Inc., consummated a contribution and exchange agreement, or the Contribution and Exchange, whereby Monte Rosa Therapeutics, Inc. acquired the net assets and shareholdings of Monte Rosa Therapeutics AG via a one-for-one exchange of equity between Monte Rosa Therapeutics, Inc. and the shareholders of Monte Rosa Therapeutics AG in a common control reorganization. We are headquartered in Boston, Massachusetts with research operations in both Boston and Basel, Switzerland. To date, we have been financed primarily through the issuance of convertible promissory notes, convertible preferred stock and, common stock in our initial public offering, or IPO.

Liquidity

Since inception, we have had significant operating losses. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures and, to a lesser extent, general and administrative expenditures. To date, we have financed our operations primarily through the issuance and sale of convertible promissory notes and our convertible preferred stock to outside investors in private equity financings, as well as our initial public offering. From our inception through the date hereof, we raised an aggregate of $493 million of gross proceeds from such transactions. Since inception, we have had significant operating losses. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures and, to a lesser extent, general and administrative expenditures. Our net loss was $74 million and $35.9 million for the years ended December 31, 2021 and 2020, respectively, and our net loss was $77.7 million for the nine months ended September 30, 2022. As of September 30, 2022, we had an accumulated deficit of $199.8 million and $277.4 million in cash, cash equivalents, restricted cash and marketable securities.

Business effects of COVID-19

The ongoing COVID-19 pandemic has presented a substantial public health and economic challenge around the world with continuing impact on our employees our employees, potential patients, communities and business operations, as well as the U.S. economy and financial markets. To date, our financial conditions and operations have not been significantly impacted by the ongoing COVID-19 pandemic; however, the full extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations, liquidity and financial condition will depend on future developments, which are highly uncertain and cannot be accurately predicted, including new information that may emerge concerning COVID-19, the emergence of variants, the actions taken to contain it or treat its impact, including vaccination efforts, and the economic impact on local, regional, national and international markets.



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To date, our vendors have been able to continue to provide services and supply reagents, materials, and products and currently do not anticipate any material disruption in services or interruptions in supply. However, we are continuously assess the potential impact of the COVID-19 pandemic on our business and operations, including our expenses, and our ability to hire and retain employees.

The COVID-19 pandemic has caused us to modify our business practices (including but not limited to curtailing or modifying employee travel, moving to partial remote work, and cancelling physical participation in meetings, events and conferences), and we may take further actions as may be required by government authorities or that we determine are in the best interests of our employees, patients and business partners.

We continue to monitor COVID-19 levels local to our research operations and adapt our employee working practices to ensure essential staffing levels in our operations remain in place, including maintaining key personnel in our laboratories.

For additional information on the various risks posed by the COVID-19 pandemic, please read the section entitled "Risk factors" in this Quarterly Report and Part I, Item 1A; Risk Factors" included in our 2021 Annual Report.

Components of operating results

Research and development expenses

Our research and development expenses include:

expenses incurred under agreements with consultants, third-party service providers that conduct research and development activities on our behalf;

personnel costs, which include salaries, benefits, pension and stock-based compensation;

laboratory and vendor expenses related to the execution of preclinical studies;

laboratory supplies and materials used for internal research and development activities; and

facilities and equipment costs.

Most of our research and development expenses have been related to the development of our QuEENTM platform and advancement of our GSPT1 program, advancement of our disclosed and undisclosed programs including for CDK2, NEK7, VAV1, and multiple sickle cell disease (SCD) targets. We have not reported program costs since our inception because we have not historically tracked or recorded our research and development expenses on a program-by-program basis. We use our personnel and infrastructure resources across the breadth of our research and development activities, which are directed toward identifying and developing product candidates.

We expense all research and development costs in the periods in which they are incurred. Costs for certain research and development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors and third-party service providers.

We expect our research and development expenses to increase substantially for the foreseeable future as we continue to invest in research and development activities related to developing our product candidates, including investments in manufacturing, as we advance our programs and conduct clinical trials. The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our product candidates is highly uncertain. As a result, we are unable to determine the duration and completion costs of our research and development projects, the costs of related clinical development costs or when and to what extent we will generate revenue from the commercialization and sale of any of our product candidates.

General and administrative expenses

Our general and administrative expenses consist primarily of personnel costs and other expenses for outside professional services, including legal fees relating to patent and corporate matters, professional fees for accounting, auditing, tax and administrative consulting services, insurance costs and other operating costs. We expect our general and administrative expenses to increase over the next several years to support our continued research and development activities, manufacturing activities, and the potential commercialization of our product candidates and development of commercial infrastructure. We also anticipate our general and administrative costs will increase and with respect to the hiring of additional personnel, fees to outside consultants, lawyers and accountants, and increased costs associated with being a public company such as expenses related to services associated with maintaining compliance with Nasdaq listing rules and SEC reporting requirements, insurance and investor relations costs.



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Non-operating income and (expense)

Our non-operating income and (expense) includes (i) interest earned on our investments, including marketable securities and U.S. government-backed money-market funds and marketable securities; (ii) gains and losses on transactions of our Swiss subsidiary denominated in currencies other than the U.S. Dollar; and (iii) proceeds from the sale of lab equipment.

Results of operations for the three months ended September 30, 2022 and 2021

The following sets forth our results of operations:



                               Three months ended
                                  September 30,
(in thousands)                 2022          2021         Dollar change
Operating expenses:
Research and development     $  21,342     $  15,115     $         6,227
General and administrative       7,020         4,753               2,267
Total operating expenses        28,362        19,868               8,494
Loss from operations           (28,362 )     (19,868 )            (8,494 )
Other expense                    1,044            31               1,013
Net loss                     $ (27,318 )   $ (19,837 )   $        (7,481 )

Research and development expenses

Research and development expenses were comprised of:



                                               Three months ended
                                                  September 30,
(in thousands)                                  2022          2021        Dollar change

External research and development services $ 8,557 $ 6,449 $ 2,108 Personnel costs

                                   6,868        5,392               1,476
Laboratory and related expenses                   1,778        1,586                 192
Facility costs and other expenses                 4,139        1,688               2,451
Research and development expenses            $   21,342     $ 15,115     $         6,227


As of September 30, 2022, we had 97 employees engaged in research and development activities in our facilities in the United States and Switzerland. As of September 30, 2021, we had 73 research and development employees in our facilities in the United States and Switzerland.

Most of our research and development expenses have been related to the development of our QuEENTM platform, advancement of our GSPT1 program including IND-enabling work for MRT-2359, and the advancement of our disclosed and undisclosed programs including for CDK2, NEK7, VAV1, multiple SCD targets, and other discovery efforts. The increase for the three months ended September 30, 2022 as compared to 2021 was primarily due to the expansion of research and development activities in the United States and Switzerland including increased headcount and facilities, as well as corresponding increases in laboratory related expenses. Research and development expenses for the three months ended September 30, 2022 and 2021 included non-cash stock-based compensation expense of $1.7 million and $1.1 million, respectively.

General and administrative expenses



General and administrative expenses to support our business activities were
comprised of:

                                        Three months ended
                                           September 30,
(in thousands)                           2022          2021        Dollar change
Personnel costs                       $    3,770      $ 2,750     $         1,020
Professional services                      1,246          772                 474
Facility costs and other expenses          2,004        1,231                 773

General and administrative expenses $ 7,020 $ 4,753 $ 2,267

As of September 30, 2022 and September 30, 2021 we had 21 and 19 employees engaged in general and administrative activities, respectively, principally in our U.S. facility. Personnel and professional service costs increased in the three months ended September 30, 2022 as compared to 2021 due to an increase in stock compensation driven by the increase in our stock price. The increase in other expenses in the three months ended September 30, 2022 as compared to 2021 to support our growth and operations as a public company. General and administrative expenses for the three



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months ended September 30, 2022 and 2021 included non-cash stock-based compensation expense of $1.5 million and $1.0 million, respectively.

Other income (expense)

Other income (expense), net was comprised of:



                                                Three months ended
                                                  September 30,
(in thousands)                                   2022           2021
Interest income, net                         $        997       $  13
Foreign currency exchange gain (loss), net             63          18
Loss on disposal of fixed assets                      (16 )         -
Other income                                 $      1,044       $  31

The increase in interest and other income for the three months ended September 30, 2022 is principally attributable to interest income on marketable securities purchased in 2022.

Foreign exchange gains on transactions of our Swiss subsidiary denominated in currencies other than the U.S. dollar increased in the three months ended September 30, 2022 as to compared to the three months ended September 30, 2021 principally due to the strengthening of the U.S. Dollar with respect to, principally, the Swiss franc.

Results of operations for the nine months ended September 30, 2022 and 2021

The following sets forth our results of operations:



                                Nine months ended
                                  September 30,
(in thousands)                 2022          2021         Dollar change
Operating expenses:
Research and development     $  60,193     $  39,025     $        21,168
General and administrative      19,702        10,470               9,232
Total operating expenses        79,895        49,495              30,400
Loss from operations           (79,895 )     (49,495 )           (30,400 )
Other expense                    2,176        (1,023 )             3,199
Net loss                     $ (77,719 )   $ (50,518 )   $       (27,201 )

Research and development expenses

Research and development expenses were comprised of:



                                               Nine months ended
                                                 September 30,
(in thousands)                                 2022          2021        Dollar change

External research and development services $ 24,778 $ 18,436 $ 6,342 Personnel costs

                                 19,364       11,935               7,429
Laboratory and related expenses                  5,507        4,144               1,363
Facility costs and other expenses               10,544        4,510               6,034
Research and development expenses            $  60,193     $ 39,025     $        21,168

As of September 30, 2022, we had 97 employees engaged in research and development activities in our facilities in the United States and Switzerland. As of September 30, 2021, we had 73 employees engaged in research and development activities in our facilities in the United States and Switzerland.

Most of our research and development expenses have been related to the development of our QuEENTM platform, advancement of our GSPT1 program including IND-enabling work for MRT-2359, and the advancement of our disclosed and undisclosed programs including for CDK2, NEK7, VAV1, multiple SCD targets, and other discovery efforts. The increase for the nine months ended September 30, 2022 as compared to 2021 was primarily due to the expansion of research and development activities in the United States and Switzerland including increased headcount and facilities, as well as corresponding increases in laboratory related expenses. Research and development expenses for the nine months ended September 30, 2022 and 2021 included non-cash stock-based compensation expense of $4.3 million and $1.6 million, respectively.



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General and administrative expenses



General and administrative expenses to support our business activities were
comprised of:


                                        Nine months ended
                                          September 30,
(in thousands)                          2022          2021        Dollar change
Personnel costs                       $  10,819     $  6,414     $         4,405
Professional services                     3,616        1,960               1,656
Facility costs and other expenses         5,267        2,096               3,171

General and administrative expenses $ 19,702 $ 10,470 $ 9,232

As of September 30, 2022 and September 30, 2021 we had 21 and 19 employees engaged in general and administrative activities, respectively, principally in our U.S. facility. Personnel and professional service costs increased in the nine months ended September 30, 2022 as compared to 2021 due to an increase in stock compensation driven by the increase in our stock price. The increase in other expense in the nine months ended September 30, 2022 as compared to 2021 to support our growth and operations as a public company. General and administrative expenses for the nine months ended September 30, 2022 and 2021 included non-cash stock-based compensation expense of $4.0 million and $1.8 million, respectively.

Other income (expense)

Other income (expense), net was comprised of:



                                                              Nine months ended
                                                                September 30,
(in thousands)                                              2022              2021
Interest income, net                                    $       1,774     $         33
Foreign currency exchange gain (loss), net                        293              (96 )
Gain on disposal of fixed assets                                  109                -
Changes in fair value of preferred stock tranche
obligations, net                                                    -             (960 )
Other income (expense)                                  $       2,176     $     (1,023 )

The increase in interest and other income for the nine months ended September 30, 2022 is principally attributable to interest income on marketable securities purchased in 2022.

Foreign exchange gains on transactions of our Swiss subsidiary denominated in currencies other than the U.S. dollar increased in the nine months ended September 30, 2022 as to compared to the nine months ended September 30, 2021 principally due to the strengthening of the U.S. Dollar with respect to, principally, the Swiss franc.

Liquidity and capital resources

Overview

We were incorporated in November 2019 in Delaware and our operations to date have been financed primarily through the issuance of convertible promissory notes, convertible preferred stock and, most recently, common stock in our IPO. As of September 30, 2022, we had $277.4 million in cash, cash equivalents, restricted cash and marketable securities. We have incurred losses since our inception and, as of September 30, 2022, we had an accumulated deficit of $199.8 million. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures, and to a lesser extent, general and administrative expenditures. Cash used to fund operating expenses is impacted by the timing of when we pay these expenses, as reflected in the change in our outstanding accounts payable and accrued expenses.



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Cash flows

The following table summarizes our cash flows for the periods indicated:



                                                              Nine months ended
                                                                September 30,
(in thousands)                                              2022             2021
Net cash (used in) provided by:
Operating activities                                    $    (68,505 )   $    (45,191 )
Investing activities                                        (165,280 )         (6,606 )
Financing activities                                              32          377,697
Net (decrease) increase in cash, cash equivalents and
restricted cash                                         $   (233,753 )   $    325,900



Operating activities

Net cash used in operating activities of $68.5 million during the nine months ended September 30, 2022, was attributable to our net loss of $77.7 million and a net decrease in our working capital of $4.2 million, offset by non-cash charges of $13.4 million principally with respect to noncash lease expense, depreciation expense and stock-based compensation.

Net cash used in operating activities of $45.2 million during the nine months ended September 30, 2021, was attributable to our net loss of $50.5 million and a net decrease in our working capital of $0.3 million, offset by non-cash charges of $5.6 million principally with respect to changes in fair value of our preferred stock tranche obligation, depreciation expense and stock-based compensation.

Investing activities

Cash used in investing activities of $165.3 million during the nine months ended September 30, 2022, was primarily attributable to purchases of marketable securities of $290 million and purchases of property and equipment of $5.6 million, offset by proceeds from the maturity of marketable securities of $130.3 million.

For the six months ended September 30, 2021, our investing activities consisted of purchases of property and equipment of $6.6 million, as we expanded our operations.

Financing activities

On September 30, 2022, the Company sold 1,638,226 shares of common stock in an at-the-market (ATM) offering for aggregate gross proceeds of $13.9 million, or aggregate net proceeds of $13.2 million after deducting underwriting discounts and commissions and other offering costs. The proceeds from the ATM offering were receivable as of September 30, 2022. On October 5, 2022, the transaction was settled and the cash proceeds net of underwriting costs were received.

Net cash provided by financing activities for the nine months ended September 30, 2021, amounted to $377.7 million comprised principally of aggregate net proceeds upon the issuance of our Series B and Series C convertible preferred stock in February and March 2021 and the issuance of common stock in our IPO in June 2021.

Funding requirements

Any product candidates we may develop may never achieve commercialization and we anticipate that we will continue to incur losses for the foreseeable future. We expect that our research and development expenses, general and administrative expenses, and capital expenditures will continue to increase. As a result, until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs through a combination of equity offerings, debt financings or other capital sources, including potentially collaborations, licenses and other similar arrangements. Our primary uses of capital are, and we expect will continue to be, compensation and related expenses, third-party clinical research, manufacturing and development services, costs relating to the build-out of our headquarters, laboratories and manufacturing facility, license payments or milestone obligations that may arise, laboratory and related supplies, clinical costs, manufacturing costs, legal and other regulatory expenses and general overhead costs.

Based upon our current operating plan, we believe that our existing cash, cash equivalents, and marketable securities will enable us to fund our operating expenses and capital expenditure requirements for at least the next twelve months. We base this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect.

We will continue to require additional financing to advance our current product candidates through clinical development, to develop, acquire or in-license other potential product candidates and to fund operations for the foreseeable future. We will continue to seek funds through equity offerings, debt financings or other capital sources, including potentially collaborations, licenses and other similar arrangements. However, we may be unable to raise additional funds or enter



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into such other arrangements when needed on favorable terms or at all. If we do raise additional capital through public or private equity offerings, the ownership interest of our existing stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect our stockholders' rights. If we raise additional capital through debt financing, we may be subject to covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. Any failure to raise capital as and when needed could have a negative impact on our financial condition and on our ability to pursue our business plans and strategies. If we are unable to raise capital, we will need to delay, reduce or terminate planned activities to reduce costs.

Because of the numerous risks and uncertainties associated with research, development and commercialization of pharmaceutical products, we are unable to estimate the exact amount of our operating capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

the scope, progress, results and costs of researching, developing and manufacturing our current product candidates or any future product candidates, and conducting preclinical studies and clinical trials;

the timing of, and the costs involved in, obtaining regulatory approvals or clearances for our lead product candidates or any future product candidates;

the number and characteristics of any additional product candidates we develop or acquire;

the cost of manufacturing our lead product candidate or any future product candidates and any products we successfully commercialize, including costs associated with building-out our manufacturing capabilities;

our ability to establish and maintain strategic collaborations, licensing or other arrangements and the financial terms of any such agreements that we may enter into;

the expenses needed to attract and retain skilled personnel;

the costs associated with being a public company;

the timing, receipt and amount of sales of any future approved or cleared products, if any; and

the impact of the COVID-19 pandemic and the corresponding responses of businesses and governments.

Further, our operating plans may change, and we may need additional funds to meet operational needs and capital requirements for clinical trials and other research and development activities. We currently have no credit facility or committed sources of capital. Because of the numerous risks and uncertainties associated with the development and commercialization of our product candidates, we are unable to estimate the amounts of increased capital outlays and operating expenditures associated with our current and anticipated product development programs.

Critical accounting policies and significant judgments and estimates

Our unaudited interim condensed consolidated financial statements are prepared in accordance with generally accepted accounting principles in the United States. The preparation of our unaudited interim condensed consolidated financial statements and related disclosures requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, costs and expenses, and the disclosure of contingent assets and liabilities in our condensed financial statements. We base our estimates on historical experience, known trends and events and various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. We evaluate our estimates and assumptions on an ongoing basis. However, even though we believe we have used reasonable estimates and assumptions in preparing our interim condensed consolidated financial statements, the future effects of the COVID-19 pandemic on our results of operations, cash flows, and financial position are unclear. Our actual results may differ from these estimates under different assumptions or conditions.

There have been no significant changes to our critical accounting policies from those described in "Part II, Item 7, Management's Discussion and Analysis of Financial Condition and Results of Operations" included in our 2021 Annual Report.

For a complete discussion of our significant accounting policies and recent accounting pronouncements, see Note 2 to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report and Note 2 to our 2021 Annual Report.





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Recently issued and adopted accounting pronouncements

Refer to Note 2, "Summary of Significant Accounting Policies," in the accompanying notes to our and consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q for a discussion of recent accounting pronouncements.

Contractual obligations and commitments

During the nine months ended September 30, 2022, there have been no material changes to our contractual obligations and commitments from those described under "Part II, Item 7, Management's Discussion and Analysis of Financial Condition and Results of Operations" included in our Annual Report on Form 10-K for the year ended December 31, 2021, filed with the Securities and Exchange Commission on March 29, 2022.

Off-balance sheet arrangements

During the periods presented, we did not have, nor do we currently have, any off-balance sheet arrangements as defined under SEC rules.

Emerging growth company status

In April 2012, the Jumpstart Our Business Startups Act of 2012, or the JOBS Act was enacted. Section 107 of the JOBS Act provides that an "emerging growth company" may take advantage of the extended transition period provided in Section 7(a)(2)(B) of the Securities Act for complying with new or revised accounting standards. Therefore, an emerging growth company can delay the adoption of certain accounting standards until those standards would otherwise apply to private companies. We have elected to avail ourselves of this extended transition period and, as a result, we may adopt new or revised accounting standards on the relevant dates on which adoption of such standards is required for non-public companies instead of the dates required for other public companies. However, we may early adopt these standards.

We will cease to be an emerging growth company on the date that is the earliest of (i) the last day of the fiscal year in which we have total annual gross revenues of $1.07 billion or more, (ii) the last day of our fiscal year following the fifth anniversary of the date of the closing of our IPO, (iii) the date on which we have issued more than $1.0 billion in nonconvertible debt during the previous three years or (iv) the date on which we are deemed to be a large, accelerated filer under the rules of the SEC.

We are also a "smaller reporting company," meaning that the market value of our stock held by non-affiliates plus the aggregate amount of gross proceeds to us as a result of our IPO is less than $700 million and our annual revenue was less than $100 million during the most recently completed fiscal year. We may continue to be a smaller reporting company after our IPO if either (i) the market value of our stock held by non-affiliates is less than $250 million or (ii) our annual revenue was less than $100 million during the most recently completed fiscal year and the market value of our stock held by non-affiliates is less than $700 million. If we are a smaller reporting company at the time we cease to be an emerging growth company, we may continue to rely on exemptions from certain disclosure requirements that are available to smaller reporting companies. Specifically, as a smaller reporting company we may choose to present only the two most recent fiscal years of audited financial statements in our Annual Report on Form 10-K and, similar to emerging growth companies, smaller reporting companies have reduced disclosure obligations regarding executive compensation.



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