A D V E R T I S E R R E TA I N S S O L E R E S P O N S I B I L I T Y F O R C O N T E N T

A D V E R T I S E M E N T F E A T U R E

Codexis, Inc.www.codexis.com

Better than natural: next-generation therapeuticsthrough advanced protein engineeringWith cutting-edge protein-engineering tools, Codexis designs transformative therapeutics tailored to patient needs.

Darwin’s great achievement was to show how nat-ural selection could fashion unimaginable biologi-cal complexity and adaptive functionality, withoutthe need for a creative designer. Today, Codexisharnesses the power of evolutionary processes inthe lab to create highly desired molecules neverseen in nature. With scientists in the driving seat,these selective approaches are enhanced withartificial intelligence (AI) that guides the creationof new biological molecules for a wide range oftherapeutic indications. Codexis is at the forefrontof directed, evolutionary protein engineering and isapplying this expertise to develop optimal proteinand gene therapies.

Codexis therapeutic discoveryWith the exception of antibodies created by theadaptive immune system, proteins in nature donot evolve to explicitly treat disease. Thus, mostnatural proteins administered as therapeutics topatients have suboptimal properties for treatingthe target disease. Natural proteins are not onlyless efficacious and less safe than desired, but theirmanufacture also often creates additional risksand complications. Codexis uses its CodeEvolvertechnology platform to overcome the suboptimalproperties and limitations of natural proteins bygenerating novel biological variants with safetyand efficacy profiles specifically tailored to tar-get diseases (Fig. 1). As CodeEvolver acts onthe DNA level, the resulting variants can also bedeveloped for mRNA and gene therapy applica-tions. Codexis’s belief is that by applying advancedprotein-engineering principles, every biologic canbe improved for the benefit of patients.

Non-invasive protein therapiesThe power to precisely engineer proteins withdesired properties opens new possibilities intheir application to treat disease. For instance,proteins can be engineered to function in previ-ously unexplored harsh conditions and environ-ments. Codexis has pursued this path with thedevelopment of CDX-6114, an orally administeredenzyme for the potential treatment of the orphanmetabolic disorder phenylketonuria (PKU).

PKU is an inborn error of metabolism caused bya mutation in the gene encoding the phenylalaninehydroxylase enzyme that converts the essentialamino acid phenylalanine (Phe) into tyrosine.Without a functional version of this enzyme,Phe builds up to toxic levels, causing neurologi-cal damage in the brain that leads to intellectualdisability, seizures, and cognitive and behavioraldisabilities. As Phe is present in almost all dietary

protein, the estimated 50,000 PKU patients in thedeveloped world must adhere to a strict, lifelong,low-Phe diet consisting of designated medicalfoods and nutritional supplements. However,as their caloric requirements increase with age,many patients are unable to continue adheringto PKU diets.

To address this critical need, Codexis has devel-oped CDX-6114, an orally delivered, gastrointestinal(GI)-active enzyme that degrades Phe in the upperintestines before it can be taken up systemically.CDX-6114 compensates for the defective liverenzyme as a GI-specific enzyme, working in tan-dem with natural proteases in the duodenum andjejunum. From proprietary libraries of a natural Phe-degrading enzyme, Codexis scientists screenedapproximately 27,000 variants before identifyingCDX-6114 as an effective variant that, as a result of22 introduced mutations, is tolerant of the low pHconditions of the stomach, resistant to intestinalproteases, and can be readily manufactured.

Codexis reported top-line data from a phase 1asingle ascending-dose study evaluating the safetyand tolerability of CDX-6114 in healthy volunteersin November 2018. This study found that CDX-6114was well tolerated at all doses, with no reportedserious adverse events, GI symptoms, or evidenceof systemic exposure. In February 2019, NestléHealth Sciences—which entered a development,option and licensing agreement for CDX-6114 in2017—exercised its option to acquire an exclusivelicense for its global development and triggered a$3 million milestone payment.

The success of CDX-6114 and the recognitionthat Codexis-designed proteins could function inthe harsh environment of the GI-tract, subjectedto low pH, proteases, and detergents, provided theimpetus for Codexis to further bolster its pipelineof non-invasive proteins. Expanding on its devel-opment of GI-active enzymes for inborn errorsof metabolism, Codexis is also advancing similarcandidates for more widespread diet-relatedindications, as well as other GI-stable proteins tolocally address disorders such as inflammatorybowel disease.

Gene therapySince the first approval in the 1990s, enzyme-replacement therapies (ERTs) for genetic disorderssuch as Gaucher, Fabry, and Pompe disease initi-ated rapid industry growth to develop therapiesfor rare diseases. These ERTs were based on thenatural sequences of the active human enzymesdeficient in patients. Yet, because the naturalsequences were not innately designed to be usedas disease treatments, their pharmacological prop-erties are suboptimal. For example, the naturalmaturation of α-galactosidase A (GLA; for Fabrydisease) takes place within the cells in which it isactive. However, the ERT manufactured throughbiotechnology is administered intravenously andmust be taken up from the bloodstream and intoaffected tissue cells deficient in the enzyme, allwhile maintaining functional stability.

Realizing these considerable challenges withERTs, Codexis sought to engineer GLA variants

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Non-invasive proteintherapeutics

Systemically-deliveredproteins(Genetic disorders,metabolic disease,oncology, etc.)

Gene therapies(Lysosomal storagedisorders, hemato-logical disorders, etc.)

GI-stable protein therapies(Inborn errors in metabo-lism, food intolerances,inflammatory boweldisease, etc.)

E�cient and safeprotein variants as:

Systemic proteintherapeutics

Referenceprotein

Fig. 1 | Engineering next-generation therapeutics with the CodeEvolver technology. Suboptimalproperties of natural proteins are resolved to generate novel variants with safety and efficacy profilesspecifically tailored to target diseases. GI, gastrointestinal.

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A D V E R T I S E R R E TA I N S S O L E R E S P O N S I B I L I T Y F O R C O N T E N T

A D V E R T I S E M E N T F E A T U R E

that are highly stable at neutral pH (to increaseplasma half-life and simplify CMC characteristics)as well as within the lysosome, more effectivelytaken up by impacted tissue, and with a greatlyreduced ‘predicted’ immunogenicity profile. One ofits lead GLA variants, CDX-6311, has 19 mutationsand was identified after screening ~20,000 vari-ants. CDX-6311 has a 7-fold longer serum half-lifeand demonstrated greater efficacy in removingthe disease-causing Gb3 substrate in the cardiactissue of Fabry mice.

CDX-6311 formed the basis of a strategic col-laboration and license agreement with TakedaPharmaceuticals announced in March 2020.Under this agreement, Takeda combines theseoptimized transgenes with its gene-therapyresearch capabilities and manufacturing infra-structure, to generate highly efficacious, next-generation gene therapies, which has expandedthe use of CodeEvolver into the gene therapy field.

Not only is Codexis using CodeEvolver to engi-neer novel human protein variants that are morestable, better taken up by target cells, and moreefficacious; CodeEvolver is also being applied tofurther improve other components of gene thera-pies, including the viral vectors (Fig. 2). In the past,better vectors have generally been identified viaselection procedures that are limited by their gen-eral lack of actionable information output. WithCodeEvolver technology it is possible to parse outvarious aspects of gene therapy, such as tropism,efficacy, and manufacturability to improve thesecharacteristics in tandem. As a result, Codexis’spipeline has further expanded to include both noveltransgenes and vector development programs.

The technologyWith a long history and deep experience in design-ing and developing nearly 100 enzyme productsused in various clinical and commercial applica-tions, Codexis can develop a desired protein variantgenerally containing tens of mutations. While thatnumber may seem small, there are more than 1075

ways of making 20 amino acid changes in a proteinthat has 400 amino acid residues. Exploring suchan enormously diverse sequence space is possiblewith the CodeEvolver platform technology via theuse of disease-relevant high-throughput screens,intention-inspired protein libraries, proprietarynext-generation sequencing technologies, and AI.

Where some protein-engineering approachesattempt to construct proteins from scratch,CodeEvolver begins exploring the vast sequencespace by identifying ‘beneficial diversity’ via thegeneration and screening of focused sets of vari-ants containing amino-acid changes that are likelyto lead to improvements for the desired attributes(for instance, by targeting the protein surface,active site, predicted epitopes, hydrophobicpatches and so on). Such beneficial amino aciddiversity is then iteratively recombined, while the

introduction of new diversity continues in parallel,eventually arriving at the optimal combinationof mutations that bestows the protein with thepharmacological, efficacy, safety, and CMC char-acteristics that make for an ideal therapy. This pro-cess is executed at high pace through proprietaryworkflows, information management systems, andAI tools that Codexis has continuously practicedand improved over more than 20 years, duringwhich it evolved these systems for a variety ofother industrial applications.

Built on deep experienceCodexis’s therapeutic discovery business andCodeEvolver are built on a directed protein evo-lution platform that has delivered major contribu-tions to industrial chemical processes.

Using chemoenzymatic processes (enzymes forthe synthesis of organic compounds) has becomewidespread for the sustainable manufacture ofpharmaceutical products. Codexis, in partnershipwith Merck, continues to be a pioneer in this field.A breakthrough came with a collaboration betweenthe two companies 10 years ago that developed anovel chemoenzymatic route that is now imple-mented at commercial scale for the synthesis ofMerck’s type 2 diabetes drug Januvia (sitagliptin).

Since then, Codexis has continued to pushadvances in industrial biocatalysis. In December2019, the company reported another landmarkcollaboration with Merck for the synthesis of theinvestigational HIV drug islatravir (MK8591). Inthis case, the goal was not to simply replace onecatalytic step, but to engineer an entire biocata-lytic cascade of nine enzymatic steps, in which theproduct of one reaction becomes the substratefor the next.

Codexis has also applied its expertise to cre-ate a portfolio of high-performance enzymes forlife sciences. In 2019, Codexis engineered a DNAligase that was licensed exclusively to Roche, Inc.In June 2020, Codexis entered a collaboration withAlphazyme LLC to produce and co-market threeenzymes for life science applications: a high-fidel-ity DNA polymerase that delivers uniformity ofcoverage and provides an accurate and representa-tive DNA diagnostic result; a T7 RNA polymerasefor the efficient manufacture and capping of mRNAvaccines; and a reverse transcriptase for RNA-directed, point-of-care viral diagnostics.

In addition, Codexis is working with MolecularAssemblies, Inc. to improve enzymatic DNA syn-thesis that can potentially overcome limitationsof phosphoramidite chemistry, which date back tothe 1980s and have been a bottleneck in expandingthe applications of synthetic DNA. The two com-panies announced their partnership in June 2020to further this goal by using the CodeEvolver plat-form to create new, more cost-effective enzymesfor enzymatic DNA synthesis.

Discovering biologicsRelying on natural, Darwinian evolution—the algo-rithmic process of random variation and selectiveretention— is too slow to support the discovery ofbiologic therapeutics that patients urgently needtoday. Codexis has addressed this through appli-cation of its technology platform and laboratorycapabilities to exponentially accelerate Darwinianevolution, and continues to advance a pipeline ofintentionally engineered protein therapeutics forsystemic and oral administration, either as protein,mRNA, or gene therapies.

The opportunities of the CodeEvolver technol-ogy in discovering highly effective therapies arelimitless. As Codexis pursues new protein thera-peutics for non-invasive administration as wellas building novel, differentiated gene therapies,alone, and in collaboration with its partners atNestlé Health Science and Takeda, the companycontinues searching for new partners to add fuelto its discovery engine. With the high likelihoodthat any protein of interest can be improved forpharmaceutical properties and therapeutic use,Codexis welcomes discussions with potential part-ners who want to advance novel biologic therapiesand contribute to a better future for patients.

Gjalt HuismanSVP, Strategic Development &GM, BiotherapeuticsCodexis, Inc.Redwood City, CA, USTel: +1-650-421-8206Email: gjalt.huisman@codexis.com

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Identified leadcandidate

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Biasedtowardsselectionsurvival, notspecifictherapeuticattributes

Intentionallydesignedtowardsmultipletherapeuticperformanceattributes

HTP screeningSequence spacecovered: ~1050

SelectionSequence space

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• Limited potency• Immunogenic• Poor half-life• CMC challenges• Poor tissue

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CodeEvolverprotein

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Natural protein,often with

deficiencies fortherapeutic use

Fig. 2 | Efficiently searching sequence space for intentionally designed protein therapeutics. Theiterative nature of the CodeEvolver technology that includes high-throughput (HTP) experimentationand artificial intelligence elements, enables efficient searching of sequence space. CMC, chemistry,manufacturing and controls.

“The opportunities of theCodeEvolver technology

in discovering highly effectivetherapies are limitless

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