Codexis : Q1 2024 Results

Q1 2024 Results

May 2, 2024

We engineer enzymes

Forward Looking Statements

These slides contain forward-looking statements that involve risks and uncertainties. These statements relate to future events or our future financial or operational performance and involve known and unknown risks, uncertainties and other factors that could cause our actual results or levels of activity, performance or achievement to differ materially from those expressed or implied by these forward-looking statements. In some cases, you can identify forward-looking statements by terms such as "may," "will," "should," "could," "would," "expects," "plans," "anticipates," "believes," "estimates," "projects," "predicts," "potential" or the negative of these terms, and similar expressions and comparable terminology intended to identify forward-looking statements. In addition, forward-looking statements include all statements that are not historical facts including, but not limited to, anticipated milestones, including product launches, technical milestones and public announcements related thereto; the potential revenues of Codexis' Pharmaceutical Manufacturing business and expected drivers of such revenues; whether Codexis will be able to, and the timing of it entering pre-commercial testing of the ECO Synthesis platform with select customers in 2024, entering into initial commercial licensing opportunities in 2025 and the subsequent expected commercial launch in 2026; potential benefits of the ECO Synthesis platform, such as it being scalable and able to reduce waste, as well as having higher purity and better unit economics than existing methods, and whether it can obviate the need for massive early stage investment required for phosphoramidite chemistry; expectations regarding Codexis' planned ECO Synthesis Innovation Lab; and Codexis' expectations regarding 2024 total revenues, R&D revenues and gross margin on product revenue, as well as its ability to achieve positive cash flow around the end of 2026. These forward- looking statements represent our estimates and assumptions only as of the date hereof, and, except as required by law, Codexis undertakes no obligation to update or revise publicly any forward-looking statements, whether as a result of new information, future events or otherwise.

Actual results could differ materially from Codexis' current expectations for a variety of reasons, including due to the factors set forth in Codexis' most recently filed periodic report, including under the caption "Risk Factors," and Codexis' other current and periodic reports filed with the SEC. If any of these risks or uncertainties materialize, or if Codexis' underlying assumptions prove to be incorrect, actual results or levels of activity, performance or achievement, or any of the foregoing forward-looking statements, may vary significantly from what Codexis projected.

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1

Strong Fundamentals Enable Consistent Execution

01 Strong Q1 2024 Financial Results

02 Historic Technical Milestone Expected

03 Commercial Traction in Ligation Market

04	ECO Synthesis Innovation Lab
Build-Out Remains on Track

Remain on track for 10%+ YoY growth in product revenue

On track to achieve enzymatic synthesis of full-length oligonucleotides by TIDES USA

Secured first order of engineered double-stranded RNA ligase with a large pharma company

Venue to define and optimize manufacturing process for each customer before scale-up

05

Expanding Impact of Enzymes Across Full Manufacturing Lifecycle

Continued progress toward enzymatic synthesis of input materials and seamless incorporation of targeting moieties

2

ECO Synthesis Manufacturing Platform: Planned Presentation at Upcoming TIDES USA

Major milestone: very close to enzymatically synthesizing full-length oligonucleotide; expect to complete by TIDES USA

Share performance improvements across the ECO Synthesis manufacturing platform

Demonstrate successful incorporation of all modified RNA building blocks targeted for initial version of ECO Synthesis technology

Validates viability of the ECO Synthesis manufacturing platform

Shows customers we are well within range of synthesizing their siRNA therapeutics

3

ECO Synthesis

Technology: Modularity to Maximize Versatility

Core Technology

Sequential Enzymatic

Synthesis of Oligos

Composed of Modified

Building Blocks

Enzymatic

Attachment of

Targeting Moieties

Enzymatic

Synthesis of NQPs

& Starter Oligo

Ligation Approach

(dsRNA Ligase Program)

4

dsRNA Ligase Program: Multi-Pronged Commercial Strategy

Variety of Approaches to Meet Customers Where They Are

Ongoing

Customized dsRNA ligase programs

1. Current programs in partnership with large pharma evaluating as a platform for all assets

1. First commercial order from large pharma customer in Q1 2024

1. Partners assessing ligation in parallel with PAC1 for late-stage assets

Launching at 2024 TIDES USA

dsRNA ligase screening service

1. Leverages deep catalog of existing ligase variants

1. Drives additional customized dsRNA ligase programs

1. Enables scaling of promising assets already in clinical development

Expected to Launch in

2H 2024

ecoRNA ligase kit

1. Puts ligase variants in customer hands for testing

In-house ligation capabilities

1. First step toward becoming full- service provider of RNA oligonucleotides

Offerings Designed to Encourage Rapid, Seamless Customer Uptake

5

1Phosphoramidite chemistry

ECO Synthesis Innovation Lab: First Step to Becoming a Full-Service Provider

Establishing a Center of Excellence for Enzymatic RNA Synthesis

Offers Customers	Enables Process	Supports GMP
Path to GLP-	Development &
Scale Up
Grade Material	Optimization

- "Show and tell" bridges gap between	- Informs different process	- Enables creation of full CMC
concept and implementation to	conditions required for each	roadmap from pre-clinical
encourage adoption	customer's molecule	development through approval
- Enables production of GLP-grade	- Assists with development of tech	- Facilitates transition to scale-up
material via ligation and semi-	transfer protocol	with GMP capable CDMO partners
enzymatic methods, leading to a		or our own facility
complete enzymatic process

Continued Strong Engagement with Customers and Inbound Interest from Potential Partners

6

Strong Q1; On Track for FY Double Digit Product Revenue Growth

Fill pipeline with new programs

Early Development-Stage

R&D - Preclinical, Phase 1

R&D Revenue

Later Development-Stage

Phase 2/3 Clinical Trials

Product Revenue

Commercial

-Stage

Product Revenue

Continued progress filling		Encouraging engagement
pipeline with programs to		with new, mid-sized pharma
sustain future growth		and large biotech customers

Ongoing discussions for 2024 R&D services expected to translate into R&D revenues in 2H24

7

Q1 2024 Financial Results

$M, Except Per Share Amounts	Q1 2023	Q1 2024
Product Revenue	$8.4		$9.6
R&D Revenue	$4.6		$7.5
Total Revenue	$13.0		$17.1
Cost of Product Revenue	$4.5	$4.9
Product Gross Margin	46%		49%
R&D Expenses	$16.7		$11.2
SG&A Expenses	$15.4		$12.9
One-Time Restructuring Charge		$0.07	--
Total Costs and Operating Expenses		$36.6	$29.0
Loss from Operations	($23.7)	($11.9)
Interest Income	$1.1	$0.9
Other Income (Expense), Net		($.03)	($0.5)
Loss Before Income Taxes		($22.6)	($11.5)
Net Loss	($22.6)	($11.5)
Net Loss Per Share, Basic and Diluted	($0.34)	($0.16)

8

YoY Expense Trends ($M)

25

				Down
20			32%								Down
										16%
		16.7
15							15.4
													12.9
								12.2

11.2 11.2

10

5

0

R&DSG&A

Q1 2023		Q4 2023		Q1 2024

$10

$9

$8

$7

$6

$5

$4

$3

$2

$1

$0

9

Q1 2024 Product Revenue

YoY Product Revenue ($M)

	$9.6M
	5%
$8.4M	1%
			Life Sciences & other portfolio
11%
34%			programs
7%
9%				Enzymes supplying clinical trials
	19%			Enzymes supplying generic products
	5%
72%				Enzymes supplying other
				commercially approved products
	37%
				Big 3 commercial pharma
				manufacturing products
Q1 2023	Q1 2024

Reiterating 2024 Product Revenue Guidance

• Q1 2024 product revenue up 14% YoY
• Q2 2024 expected to be lowest product revenue quarter of the year and down vs. Q2 2023
• Expect Q2 2024 to be roughly 60-70% of Q1 2024 product revenue
• Expect to recognize large, customized dsRNA ligase pharma order by EOY