Codexis Corporate Presentation to GEF · 2012 Target 8w+ 3-4w 2w 3-6m 2½-3m 1½-2m 1-3 yrs 3-12m 2-6m 2008 2012 Target 2008 2012 Target SCREEN FOR SUCCESS Blurs the line between

Codexis Corporate Presentation to GEF

March 19 2013

© 2011 SAP AG. All rights reserved. 2

Forward-Looking Statements

These slides and the accompanying oral presentation 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, levels of activity, performance or achievement to differ materially from those expressed or implied by these forward-looking statements. Forward-looking statements include all statements that are not historical facts. 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. These forward-looking statements represent our estimates and assumptions only as of the date hereof, and, except as required by law, we undertake no obligation to update or revise publicly any forward-looking statements, whether as a result of new information, future events or otherwise. Other factors that could materially affect actual results, levels of activity, performance or achievements can be found in Codexis’ Quarterly Report on Form 10-Q filed with the SEC on November 7, 2012, including under the caption “Risk Factors.” If any of these risks or uncertainties materialize, or if our underlying assumptions prove to be incorrect, actual results, levels of activity, performance or achievement may vary significantly from what we projected. Our logo, “Codexis,” “CodeXyme™ Cellulase,” “CodeXol™ Detergent Alochol” and other trademarks or service marks of Codexis, Inc. appearing in this presentation are the property of Codexis, Inc. This presentation contains additional trade names, trademarks and service marks of other companies. We do not intend our use or display of other companies’ trade names, trademarks or service marks to imply relationships with, or endorsement or sponsorship of us by, these other companies.


About Codexis

Biocatalytic solutions to meet customer needs

Proven technologies for scale-up and implementation

Rapid, cost-effective and green process development, integrated from research to manufacturing

154 employees worldwide; 91 in research and development

Codexis develops engineered enzymes for pharmaceutical, biofuel and chemical production

Core Assets, Key Partners & Customers

R&

D

Established, Growing Pharma Business

Pharma

Enzymes to Enable 2nd Gen Fuels and Chemicals

Bio-Based Chemicals For Consumer Products

®


Investment Highlights

Leading enzyme developer and innovative partner of choice for complex chemistry markets

Industry leading customers and partnerships

Driving a financial model that is predictable and intrinsically high margin

Long-term opportunities in fuels and chemicals to be unlocked through a strategic partnership

Experienced management team focused on execution

© 2011 SAP AG. All rights reserved. 5 5

Core Value Proposition


Enzymes Can Be Improved for Targeted Biological and Process Traits

LEADING EDGE DESIGN OF NEW ENZYMES

• IDENTIFY DRIVERS OF ENZYME IMPROVEMENT

• MAKE ENZYMES WORK IN HARSH ENVIRONMENTS

• INVESTING TO STAY AT THE LEADING EDGE OF SCREENING AND EVOLUTION TECHNIQUES

Beginning Biocatalyst

Proprietary Optimization

Optimized Biocatalyst

+ =

BENEFITS OF ENZYMATIC PROCESS

• HIGH CHEMICAL YIELDS & PURITIES

• POTENTIAL FOR REDUCED # OF STEPS

• OPERATE AT AMBIENT CONDITIONS

• MINIMAL WASTE & IMPROVED SAFETY

Design The Biocatalyst Enhance The Process

Codexis delivers effective enzymes in concert with improved processes


The Evolution of Our Enzyme Evolution Platform

Staying at the leading edge through innovation

Classical mutagenesis

Open source

1970s

Codexis 1.0

Maxygen “DNA Shuffling”

IP portfolio, acquired 200+ patents in 2010

1998

Codexis 2.0

Bioinformatics guided enzyme

evolution

ProSARTM

2007

Codexis 3.0

Advanced Bioinformatics and

Next Generation sequencing

FURTHER,

FASTER & MORE EFFICIENT THAN

EVER

MOSAICTM

2013


MOSAIC™: A New Integrated Next-Gen Evolution Platform

MOSAICTM

Next-Gen Technologies

Model Predictions

deleterious beneficial

beneficial in combination neutral

Advantages:

In-house technology enables access to broader fields

Reduce project costs by reducing R&D costs

Increase R&D productivity

Improve enzymes even faster than before

IP: Filed patent application and MOSAIC trademark registration application

“Best”


Improving Enzyme Characteristics for Process Conditions

STABILITY

• Temperature and acidic pH

Cellulases

Cellulosic Sugars

e.g., US8088608 US8143050

• Temperature (>100oC) and

alkaline pH

Carbonic anhydrase

CO2 capture

e.g., WO201203277 WO201203299

• Solvent Stability

Transaminase

Sitagliptin

Science 2010

Codexis’ success is making enzymes work where they never could before

NOVEL ACTIVITY

• Improved substrate binding (from zero)

Transaminase

Sitagliptin

e.g., US8293507

wt 1 2 3 4 5 6 7

acti

vity

[ECAA] (mM)

Evolved KRED

wt KRED Rat

e

INHIBITOR RESISTANCE

• Removed product inhibition intrinsic to natural enzymes

KRED

Atorvastatin

ECHB Green Chem. 2010, 12:81

US8088610


The Codexis Advantage

“The genetic diversity uncovered during the screening suggests that the enzyme can be readily evolved to meet much more aggressive performance targets, enabling an economic process at scale.”

Codexis screening report

Codexis offers innovative and economically feasible biocatalysis, which competitors do not match

Parameter CRO

Screening Results

Codexis Screening

Results

Codexis Advantage

Enzymes tested

20 800

Substrate load

5 g/L 10 g/L

Enzyme Load

40 g/L 10 g/L

Reaction time

72 h 24 h

Conversion 65% >95%

Selectivity 90% e.e. >98% e.e.

“…the probability that this approach will ever be translated into an economically viable process is estimated to be small. Hence, it is recommended not to proceed with this approach.”

Competitor recommendation

Codexis’ rapid screening cycles uncover biocatalytic routes that competitors do not


We make it easy and profitable for customers to access the benefits of enzymes

Codexis is the Biocatalysis Partner of Choice for Pharma

R&D CYCLE: CONTINUOUS IMPROVEMENT

Faster and less costly than the competition

Screen

Proof of Concept

Optimize

2008 2012 Target

8w+ 3-4w 2w

3-6m 2½-3m 1½-2m

1-3 yrs 3-12m 2-6m

2008 2012 Target

2008 2012 Target

SCREEN FOR SUCCESS

Blurs the line between Codexis R&D and customers’ R&D

Interest in biocatalysis

Inexpensive test project

Economically advantaged

process


Pharmaceuticals – Core Business


Be the partner of choice for biocatalysis

Replace chemical processes with new biocatalysis processes to grow the market

Quick screening and rapid & significant improvement of enzyme performance

Deliver enzymes and in selected cases intermediates

Established enzyme optimization, tech transfer and manufacturing track record

Proven track record for improving enzymes for commercial processes

Existing capacity and strong capability from rapid 1-10s kg through MTs commercial production and further rapid scale up to 100+ kg batches (~3-6 months) including regulatory support

Deliver enzymes and in selected cases intermediates

Use research enzyme business and services to feed the pipeline

Broaden pipeline through AMRI and Strem agreements

Broadened into adjacent spaces such as food, agrochem, and others

High margin enzyme supply business with lean structure and external manufacturing

Flexibility in deal structure possible

Able to accommodate some cost/risk sharing in the development phase, in order to provide mutual benefit to Codexis and customer

Market Opportunity

Technology Advantage

Commercial Plan

Financial Return

Pharma: Opportunity for Significant Growth


The Merck Relationship is a Model for Future Development

Started in 2007, extended 2012 for 3 years

Hundreds of products screened, enzyme supply for >10 clinical projects, optimization programs for phase III programs and for second generation processes

Joint development and commercial enzyme supply for production of sitagliptin

2008 2009 2010 2012 2011 2013

FDA

approval

CDXS

process

Commercial

variant

identified

Research

Agreement

executed

First

Commercial

scale enzyme

manufacture

Commercial

supply

Presidential

Green

Chemistry

Award

2014


Broadly Applicable Technology

Example Products

Feature Metrics

Achieved

Benefit Beyond

Cost Savings

Telaprevir (Vertex)

Route re-design 3 steps vs. 6

steps Green

Sitagliptin (Januvia - Merck)

Increased volumetric

productivity

Reduction in plant

occupation Green

No specialty equipment

High pressure hydrogenation

replaced Increased safety

Simvastatin (Merck)

Increased yield 95% yield (no

PGs) Green

Atorvastatin (Lipitor – Pfizer)

(Generics)

Reduced energy consumption

Cryo-step eliminated

Green

Ezetimibe (Merck)

Replacement of toxic reagents

Use of THF/BH3 replaced

Increased safety

Critical Success Factors

• Well-selected and qualified opportunities

• Seek/develop customer support & steerage as early as possible

• Solidify product plans pre- and post- technical PoC

• Look for “off-the-shelf” opportunities as well as development projects


Pharma Capabilities Provide Significant Value for Customers

Intermediates for the world’s biggest

blockbuster

Used in the API process for new

blockbuster NDAs

Three customers used our

enzymes in their approvals

Awards

2006: Atorvastatin (Lipitor®) 2010: Sitagliptin (Januvia®) 2012: Simvastatin (Zocor®)

More efficient (fewer reaction steps, resources required)

Faster development timelines (months vs. years)

Environmentally friendlier (lower-impact solvents, less hazardous waste)

Collaborative approach to full life-cycle drug development

Success supporting “Big Pharma” on blockbuster drugs


CodeXyme® Cellulase Enzymes


CodeXyme®: Leading, Cost-Competitive Enzyme Business

Financial Impact

CodeXyme is expected to capture market share and margins by 2020

Industry is poised for significant expansion, resulting in strong top-line growth

Seeking partner to further development and commercialization

CodeXyme® cellulase serves the high-growth biofuel and bio-based chemical end markets

Attractive Market

Cellulosic (2G) biofuels and bio-based chemicals poised for stepout growth

Codexis expects the global biofuel market to increase to greater than 5 billion gallons and greater than 10 million tons of cellulosic sugar for chemicals in 2020

Technology Advantage

CodeXyme® cellulase performance is among the best in the sector

Higher biomass conversion rates at lower enzyme loads than peers

Enzyme effectiveness improvements have yet to plateau in our R&D

Global Opportunity

CodeXyme will be able to access the global market with license from Shell

Brazil license expected from Raízen in the near-term

Plan to build onsite facilities to capture regional economies of scale while limiting capital outlays


CodeXyme® Cellulase Overview

Flexibility Performance Manufacturing Cost

CodeXyme® cellulase allows for feedstock and pretreatment flexibility

Best-in-class performance will enable cost savings

Robust enzymes work well under a range of solid loads, inhibitor profile, pH and temperature

Performance is among the best enzyme packages

Higher biomass sugar conversion rates at lower enzyme loads than peers

Enzyme effectiveness improvements have yet to plateau in our R&D

Faster hydrolysis rates resulting in lower capital and opex costs

Expected to be the cost competitive by 2014-15

Lower manufacturing cost with onsite plant model

Minimal downstream processing and no transportation

®


Progress in CodeXyme® Cellulase

Base Strain

CodeXyme 1

CodeXyme 2

CodeXyme 3

CodeXyme 4

1.0x

3.0x

5.0x

7.0x

9.0x

11.0x

13.0x

Jan-09 Feb-13

Improvement in Enzyme Performance

Base Strain

CodeXyme 1

CodeXyme 2 & 3

CodeXyme 4

CodeXyme 4X

1.0x

1.5x

2.0x

2.5x

3.0x

3.5x

Jan-09 Feb-13

Reduction in Enzyme Manufacturing Cost

Increased enzyme activity (left): Better hydrolysis process performance at commercial loads Decreased enzyme cost (right): Better strains and improved manufacturing process

Codexis has delivered significant improvements in enzyme performance and manufacturing cost

Fold

-im

pro

vem

ent

in C

6 s

uga

rs p

rod

uce

d

Fold

-re

du

ctio

n in

re

lati

ve u

nit

s

CodeXyme 4X (incl. C5)


NREL Study: Enzymes Performance Comparison

CodeXyme® Performance is Industry-Leading

0

10

20

30

40

50

60

70

80

90

Enzyme A Enzyme B Enzyme C Enzyme D CodeXyme 3

C6 S

ug

ar

Co

nv

ers

ion

%

C6 Conversion @ 30 mg/g Load

0

10

20

30

40

50

60

70

80

Enzyme A Enzyme B Enzyme C Enzyme D CodeXyme 3

Lo

ad

ing

(m

g p

rote

in/g

su

ga

r)

Load to Achieve 75% C6 Conversion

• NREL study compared CodeXyme 3 versus DuPont, DSM, NZ, and Verenium (A-D, unassigned)

• Enzymes tested on dilute-acid pretreated corn stover at each product's optimal pH and temperature

• Compared 2009-10 enzyme packages provided by the four key competitors

• The latest version, CodeXyme® 4 ( ) added for comparison


CodeXyme® Commercial Scale-Up Timeline

Manufacturing enzymes via CMOs in the near-term, continuing to drive improved enzyme performance

Initiated sampling & applications program

Off-take agreements

Launch CodeXyme®4X

15,000 L scale up at CMO

Launched CodeXyme®4

Launch CodeXyme®5


CodeXol ® Detergent Alcohol


High growth market

Use of personal care products increasing in developing markets

End-use customers are demanding green, sustainable ingredients

Consumer product companies want reduced carbon footprint products from 2nd generation (non-food) feedstocks locally produced with decreased price volatility

CodeXol® - a mid-cut C12/C14 product

Product will not require additional processing or equipment – drop-in to current manufacturing

Exclusive relationship with Chemtex

Demonstration scale-up at Rivalta – operational 1H 2013

JDA for basic engineering package developed

In negotiations with potential funding partners

Market Opportunity

Drop-In Product

Pilot and Scale-up

Path Forward

CodeXol: Lower-Cost Drop-In Detergent Alcohol


CodeXol® Technical Development

0 1 2 3 4 5 6 7 8 9

Months

% Chain Length Achieved

65% C12 Target

Technical focus on mid-cut (C12/C14) detergent alcohol to meet Palm Kernel Oil spec

Chain length target distribution achieved in short time frame

Codexis has developed strain producing C12/C14 detergent alcohol to meet commercial target


CodeXol® Detergent Alcohol Process

Feedstock Concentrated End Market

Fermentation Pretreatment Refining Enzyme

Application

Proprietary Jointly Developed

Proprietary In-licensed

CodeXol®

Detergent Alcohol

10 L Lab 650 L Pilot 1,500 L Demo Commercial

Build-Out

Strategic Partnerships

Redwood City, CA

2011 2012 mid-2013

Rivalta Geography

Based

We have a unique process for a truly “green” detergent alcohol product …

… and are currently running pilot-scale production.

Tech & Process

Licensing Package


Financials


Projecting strong pharma sales and profitability growth for 2013

Pharma revenue expected to be $35 - $40 million

Product revenue expected to approach $30 million

Product gross margin of 30 – 35%

Total gross margin approaching 50%

Head count reduction and restructuring completed in Q4 2012

Reduction in headcount effective November 1st. Full effect of cost reductions will be seen in first quarter 2013

Aggressively monitor third party spend

Goal is to have fuels/chemicals funding partner or JV in place by July 1, 2013

Cash balance at 12/31/2012 was $49.2M

• $4M more than projected; committed to minimizing cash burn

• Projected cash burn for 2013 of $12 - $16 million

Pharma Financials

Cost Reductions

Cash Position

Financial Highlights


Conclusion


Our Core Value Proposition Addresses More than Pharma

Superior enzymes for cost-advantaged process solutions

Improved process performance

Efficiency & simplicity

Faster development

Sustainability

Robust Supply Chain

Agricultural Chemicals Animal Health

Flavors and Fragrances

Pharmaceuticals and Intermediates

Personal Care

Food and Nutrition


Codexis Summary

A problem solver that’s best-in-class at helping partners achieve dramatic total cost reduction and/or performance improvement

+ Flexible services and product offerings for big and small customers

+ Customers get products to market more quickly

+ More control of supply chain and a truly green process

Leader in deploying and continuously upgrading a fast- evolving biotechnology suite that is scarce and in growing long term demand

Driving a financial model that is predictable, accelerating to mid-term revenue growth and expanding margins

We Make It Easy & Profitable For Customers To Access The Benefits Of Enzymes


Management Team

Name & Title Background Joined

David Anton, Ph. D.

SVP, Bioindustrials 2008

Douglas Sheehy

SVP, General Counsel & Secretary 2007

Peter Seufer-Wasserthal, Ph. D.

SVP, Pharmaceuticals 2006

John Nicols

President & CEO 2012 (June)

David O’Toole

SVP & CFO 2012

(September)

Matt Tobin, Ph. D.

SVP, Research & Development 1997

Management team brings industry-leading commercial & technical experience

Documents

Codexis Corporate Presentation to GEF · 2012 Target 8w+ 3-4w 2w 3-6m 2½-3m 1½-2m 1-3 yrs 3-12m 2-6m 2008 2012 Target 2008 2012 Target SCREEN FOR SUCCESS Blurs the line between