Forward Looking Statements

Corporate Overview p John Nicols, President and CEO February  2014 Forward‐Looking Statements These slides and the accompanying oral presentation co...
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Corporate Overview p John Nicols, President and CEO February  2014

Forward‐Looking Statements These slides and the accompanying oral presentation contain forward‐looking statements that involve risks and  p y g p g 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  p , , , p j , p , p , g , 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  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 for the period ended September 30, 2013 filed with the SEC on  November 12, 2013, 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,  Our logo “Codexis Codexis,” “We We are Biocatalysis™ are Biocatalysis™” and other trademarks or service marks of Codexis, Inc. appearing in this  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.

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Who We Are • Codexis is the global leader in  is the global leader in •



• • • 3

biocatalysis Delivers most advanced and  customized solutions for  t i d l ti f pharmaceutical and complex  chemistry industries Proven technology enables rapid,  cost‐effective and sustainable process  development – from research to  manufacturing f i 90 employees; 45 in R&D NASDAQ‐listed: CDXS NASDAQ‐listed: CDXS Headquartered in Redwood City, CA

Investment Highlights • A leading edge biotechnology toolkit A leading edge biotechnology toolkit − Disruptive value creation built on unrivaled technological prowess

• A profitable, growing platform business p ,g gp − Growing portfolio of products serving an expanding customer list − Robust development pipeline set to feed future sales growth

• Accelerating penetration in large, underserved markets A l ti t ti i l d d k t − Process development in pharma and other complex chemistry markets − Long‐term opportunities in development of new improved drugs

• Focused on future profit growth and cash flow generation − Gross profit CAGR of 50% over last 5 years − Expect year‐on‐year gross profit growth of 15‐20% in 2014 Expect year‐on‐year gross profit growth of 15‐20% in 2014 − 2014 cash burn expected to be less than $8M 4

Biocatalysis iocatalysis Technology Technology Platform Platform

Technology Platform to Engineer Biocatalysts Beginning Biocatalyst

• Enable novel manufacturing processes Enable novel manufacturing processes • Deliver better economics than 

traditional chemistries • Work in wide industrial conditions • Timelines that fit drug development 

cycle demands cycle demands • Unrivaled capability as the industry 

Proprietary Engineering

pioneer − 210 worldwide patents granted − Reduced proof‐of‐concept screen time from 8 

to 2 weeks over the past 3 years − Investing (sophisticated marriage of biology &  computation) to stay ahead 

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Optimized p Biocatalyst

Codexis is the Biocatalysis Partner of Choice

New Biocatalyst Evolution

objective performance

Codexis

Competitors

time

Best Performing  Biocatalysts

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Full  C Commercialization  i li ti Capability

Delivering  Value for Pharma Customers Upgrade the Chemical Process U d h Ch i l Conventional Process

The conventional  process produces  process produces toxic waste and  requires purification Waste

Benefits of  Benefits of Biocatalysis fi f Biocatalysis i l i • Higher quality and yield • Minimized waste generation • Less energy intensive • Improved operator safety • Run in multi‐purpose assets

Hazardous Chemicals

• Shrink # of unit operations

Codexis’ Green Process Evolved  Biocatalyst

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Minimal Waste

• Lower capex p ambient 

operating design

Product Portfolio Product Portfolio

Early Adoption in Pharma Development Pipeline  KITS: KITS:  

BENCH  CHEMIST AWARENESS/  ACCESS 

• Sets of readily available  biocatalysts for given  chemistry • Off the shelf or from a  catalog

$10‐$50k Orders (Proof of Concept):

FOLLOW‐ONS  FOLLOW‐ TO VALIDATE 

LOCKED‐ LOCKED‐ IN BY IN BY  PHASE III 10

• • • •

2010‐2012 kit sales:

+151% Up to $100k Orders (RFP Optimization):

2010‐2012 sales:

2010‐2012 sales:

+100%

+100%

Customer buy‐in Inclusion in DMF/NDA Patents filed Supply chain

Drug Patent  Filings  Referencing Referencing  Biocatalysis:

2010‐2012:

+100% 100%

Growing Portfolio of Profitable Products PRECLINICAL

PHASE 1 PHASE 1

PHASE 2 PHASE 2

PHASE 3 PHASE 3

AstraZeneca BMS BMS Glycom/Nestle y / Krka Merck Merck Merck Merck Merck Merck Merck Merck Novartis Novartis Lilly Pfizer Roche Teva Teva Teva

2010 11

2013

LAUNCHED

Commercial Products & Customers • Expanding portfolio of commercial revenue  Expanding portfolio of commercial revenue

with leading biopharma companies • Over 50 pharma companies use CDXS  products or technology d t t h l

Top revenue sources in 2013  (>$1mm each) (>$1mm each) Atorvastatin (Arch Pharma) Boceprevir (Merck) Sitagliptin (Merck) Service Rev. (Merck)

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Top revenue sources in 2010  (>$1mm each)

Simvastatin (Undisclosed)

Atorvastatin (Arch Pharma) (A h Ph )

Argatroban (E l ) (Exela)

Boceprevir (Merck)

Rivastigmine (Novartis)

Patented Drug ( (Pfizer) )

Crizotinib ( (Pfizer) )

Service Rev. (Teva)

Patented Drug (Undisclosed)

Transforming Blockbuster  Drug Manufacturing Drug Manufacturing • Developed new commercial production  new commercial production •

• • • • 13

route for Januvia  Merck announced process saved  potentially $100M in manufacturing  t ti ll $100M i f t i capacity expansion Improved productivity by 56%, increased  yield by 7‐10% and reduced waste by 19% Merck received FDA approval for new  CDXS 1 CDXS 1‐step step process process CDXS received EPA Presidential Green  Chemistry Award in 2010 Merck and CDXS signed 3‐year extension  of collaboration 

PRIOR CHEMICAL PROCESS PRIOR CHEMICAL PROCESS

BIOCATALYTIC PROCESS

Growth Strategy Growth Strategy

Growth Strategy Overview • Replicate deep partnering success with  Replicate deep partnering success with • • • •

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Merck at other major pharma Building out our commercial team and  g sales force Increase early adoption and access to  biocatalysis technology Expand late stage project flow through  CMO partnerships p p Continue expanding reach of our leading  technology platform in pharma and  complex chemistry markets l h it k t

Substantial, Underserved Market Opportunity Significant untapped global market for biocatalyst platform

Small Molecule Pharma Small Molecule  Pharma

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Value  of API: 

Addressable with  Biocatalysis: 

Biocatalyst  Cost in Use: 

Biocatalysis Market Potential: 

$60bn

30%

5‐10%

$1‐2bn

Replicating Merck Partnership • Pursuing Pursuing development  development

agreements with large biotech  and pharma companies • From development services, to 

customized biocatlayst engineering and technology  g g gy license to CDXS platform • CDXS receives future commercial 

royalties, milestone payments,  technology fees and FTE funding

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Target Markets Big pharma Major biotech Major biotech Small biotech, CMOs,  industrial biotech 

Beyond Pharma: Expanding Biocatalysis in  Complex Chemistry Markets Complex Chemistry Markets Superior enzymes for cost‐advantaged process solutions Improved process performance Efficiency & simplicity Pharmaceuticals  and Intermediates

Faster development Sustainability  Robust supply chain Robust supply chain

Flavors and  Fragrances F

Food and  Nutrition N t iti Agricultural  Chemicals 18

Personal  Care

Animal  Health

Corporate Summary Corporate Summary

Financial Summary • Driving top‐line revenue  − Expect $8M to 9M in Q4 2013 $ − 2013 year end revenue guidance of $30‐$32M − Projecting 5‐10% in total revenue growth in 2014

• Accelerating Biocatalysis profit growth in 2014 − Maintain greater than  50% gross margin; 10‐15% gross margin increase 

year over year

• Operating discipline − Implementing needed cost efficiencies

• Preserve solid balance sheet P lid b l h − $31M cash (9/30/13), 2013 cash burn of approximately $23M.  End of 

year cash projected to be at approximately $26M − 2014 cash burn guidance of less than $8M 2014 cash burn guidance of less than $8M − No debt 20

Accelerating Long‐Term Profit Growth Total Biocatalysis Gross  Total Biocatalysis Total  Gross Profit Gross Profit

Revenue make up Revenue make‐up • Product revenues:  sales of 

($ in millions, USD)

biocatalysts or chemical  intermediates (using biocatalysts) intermediates (using biocatalysts)

$20

• Collaborative R&D:  FTE service 

$15

revenues, royalties, milestone  payments, & licensing fees

$10

Profit growth results $5

• 51% profit CAGR from 2009 ‐ 2013F • 2013  total gross margins: ~ 50%

$0 2009

2010

2011

2012

Product  Gross Profit Collaborative R&D Gross Profit 21

((Est.) 2013 )

− Up from 18% in 2009 Up from 18% in 2009 − 2013 product gross margins of 30+% 

Investment Highlights • A leading edge biotechnology toolkit A leading edge biotechnology toolkit − Disruptive value creation built on unrivaled technological prowess

• A profitable, growing platform business p ,g gp − Growing portfolio of products serving an expanding customer list − Robust development pipeline set to feed future sales growth

• Accelerating penetration in large, underserved markets A l ti t ti i l d d k t − Process development in pharma and other complex chemistry markets − Long‐term opportunities in development of new improved drugs

• Focused on future profit growth and cash flow generation − Gross profit CAGR of 50% over last 5 years − Expect year‐on‐year gross profit growth of 15‐20% in 2014 Expect year‐on‐year gross profit growth of 15‐20% in 2014 − 2014 cash burn expected to be less than $8M 22

C Corporate Overview t O i February  2014