Revolutionizing Pharmaceutical Manufacturing: A Leap Forward in Biocatalysis

When a leading pharmaceutical partner hit a roadblock in developing enzymatic solutions for their production process, Ginkgo Bioworks leveraged protein discovery and engineering to develop bio-based manufacturing.

Ginkgo’s engineers developed an end-to-end work package starting from high-throughput assay development through advanced protein engineering, identifying and improving on a new class of enzymes to catalyze an unprecedented activity. Our protein engineering work helped our partner reshape their production process, offering sustainable, cost-effective alternatives to traditional synthetic methods.

Executive Summary

Ginkgo Bioworks partnered with a pharmaceutical company to replace traditional synthetic chemistry for a hydroxylation reaction with biocatalysis in drug production, aiming for a lower-cost and more sustainable process. Ginkgo developed an end-to-end solution to develop a novel enzyme for this process.

  • The work began with custom high-throughput Assay Development, which facilitated precise characterization of multiple phenotypes in large  enzyme libraries.
  • We then identified a strong starting sequence capable of performing the desired reaction. This leveraged Ginkgo’s Ginkgo’s metagenomic sequence database and computational modeling and machine learning tools to select variants for high-throughput screening.
  • Finally, we optimized the starting sequence towards commercial performance. Zero-shot ML-guided design tools combining sequence- and structure-based modeling enable the design of initial libraries exploring a wide parameter space. Subsequent libraries continue to use these techniques, now augmented by the data from all previous rounds, to recombine observed mutations and identify new ones. This led to order-of-magnitude improvements in each of two difficult phenotypes in only three rounds of engineering. 

Ginkgo Bioworks’ Cell Engineering Platform leveraged its proprietary database and AI-enabled tool to discover and engineer biocatalysts for activities that were previously unattainable. Ginkgo’s Enzyme Intelligence suite of tools, paired with a highly-automated Foundry offers our partners the tools they need to identify and leverage the tools they need to have a competitive advantage in the market.


The Challenge:

Traditionally reliant on synthetic chemistry for a hydroxylation reaction necessary to produce their small molecule drug, our partner in the pharmaceutical space recognized the potential for a more sustainable and precise approach through biocatalysis. Biocatalysis had the potential to perform this reaction, resulting in enhanced efficiency, reduced environmental impact, and lower cost of production of their target molecule. 

However there were no known enzymes that could catalyze the reaction they were achieving through synthetic chemistry. Developing a bio-based solution for this reaction would require them to source, produce, test, and engineer large libraries of enzymes–a research and development project that their team did not have the resources or expertise to execute.

They turned to Ginkgo’s cell engineering platform to help them navigate a large protein discovery and engineering space and develop an enzyme with an activity that had never been described in the literature.


Our Work:

The Assay Development team initiated this collaboration, finding ways to onboard their assay methods for high-throughput screening.

  • De-novo Assay Design: Ginkgo’s engineers developed a two-pronged assay testing for products of our partner’s reaction by combining EchoMS for rapid, high-throughput primary screening and Chiral HPLC for detailed, precise secondary analysis. This approach ensured comprehensive detection and quantification of reaction products at a scale that allowed screening of large enzyme libraries.
  • Unexpected Product Discovery: Our assay development uncovered an additional regioisomer that our partner hadn’t anticipated. 
  • Assay Optimization: We optimized the assay to differentiate between our target product and newly discovered byproducts; we adjusted our methods to achieve clear separation and accurate quantification of all relevant chemical species.

After developing a high-throughput assay for the products of interest, we initiated a Metagenomic Enzyme Discovery workflow.

  • Sequence sourcing: An initial scan of Ginkgo’s metagenomic sequence database using three different seed sequences identified over 183,000 enzyme sequences that had high potential for performing the activity our customer was searching for. 
  • Computational modeling: To narrow down this collection of sequences, we applied molecular dynamics to model substrate docking to identify residue positions associated with substrate binding, catalysis, and dynamical regions implicated in specificity.
  • Machine learning in metagenomics: Multiple-sequence alignment (MSA) and Language Learning Models were leveraged to score candidate sequences. Statistical sampling and clustering algorithms tuned the diversity of sequences that Ginkgo would test.
  • High throughput screening: The initial metagenomic library identified 1,000 enzymes that were capable of performing the reaction. Ginkgo’s Foundry expressed these candidates in bacteria and, using the tools developed in the Assay Development phase of this work, identified two sequences with high function. For the first time, we demonstrated that our partner’s reaction could be catalyzed by enzymes; our search found enzymes that resulted in the 0.4mM target product–a key starting point for protein engineering.

Although Protein Engineering improved these enzymes further, optimizing both productivity and selectivity to produce the products of interest, while also minimizing the off-target regioisomers. Each round of protein engineering iterated through well-trod workflows at Ginkgo that led to ultrafast data acquisition: entire cycles of protein design, synthesis, strain construction, testing and data analysis were completed in 7 weeks, allowing our team to make fast, effective decisions in protein engineering.

  • Generation 1: Our first round of protein engineering utilized both sequence (MSA- and LLM-based methods) and structural methods (Molecular dynamics and AlphaFold, among others) to identify improved variants. Result: These results identified variants with >4x improvements in productivity and >10x improvement in selectivity, although typically not together in a single variant. Collectively, all the variants in the generation 1 library were used to train models that were applied to develop the generation 2 library, optimizing for both activity and selectivity.
  • Generation 2:  With our learnings from Generation 1 and our metagenomic campaigns, we leveraged our proprietary OWL technology to engineer enzymes with improved activities.. Our previous campaigns developed a rich data set informing how enzyme sequence affected productivity and selectivity. OWL leveraged this data set to predict which enzymes would have better function. Result: We engineered enzyme sequences with a ~20x improvement in productivity and a 2.5x improvement in selectivity over the starting point.
  • Generation 3: A final round of enzyme improvement using our machine learning tools resulted in an 80-fold improvement in productivity, and an enzyme that was 17-fold more selective in the reaction products. Result: Ginkgo’s Enzyme Intelligence suite of tools identified  an enzyme with an activity never before reported in the literature and optimized it to produce 33mM product, enabling our partner to move from costly and toxic chemical reactions to greener bio-based drug solutions.


  • Validated Novel Solution: Ginkgo’s work developing a novel biocatalyst to replace the synthetic chemistry in their production process is a first-of-a-kind technology that fundamentally changes their drug production. Superior Performance Over Traditional Chemistry: Our discovery of an enzyme that performed the reaction in our partner’s process eliminated a step in their original process using synthetic chemistry. Our ability to find this novel enzymatic activity surprised our customer and unlocked a new production process with significant cost savings.
  • Expanded Project Scope: Our initial success in providing our partner data about the feasibility of a bio-based reaction has led them to extend their collaboration with Ginkgo, aiming to optimize the enzyme’s performance towards commercial viability and to develop a robust manufacturing strain and process.
  • Broader Application and Strategic Development: Encouraged by these results, our partner is now engaged in identifying and developing new biocatalysts to address other small molecule production challenges in the pharmaceutical field, leveraging the full potential of Ginkgo’s Cell Engineering Platform.

 Our Capabilities

  • High-throughput assay development: We develop custom assays, targeted to the exact analytes of interest, eliminating the need to rely on proxy or indirect assays. This allows us to collect high-quality characterization data for our enzyme panels and engineer the enzyme for the exact activity needed for commercial success. 
  • Metagenomic Discovery: Ginkgo’s proprietary database is a rich source of diversity for screening new enzymes and protein sequences. Our metagenomic sequence database, coupled with ML tools to search it, can uncover activities never-before described in biology or chemistry.
  • Fast closed-loop engineering fed by lab data: Our suite of machine learning-enabled protein engineering tools can provide data in 7 weeks. This rapid iterative cycle of design-build-test-learn on Ginkgo’s Cell Engineering Platform can achieve massive improvements, fast.


Work With Us

Ginkgo Bioworks’ Enzyme Intelligence suite of tools enables our partners to achieve their production goals through biology. turns significant technical challenges into opportunities. We work with our partners to optimize pathways to produce their target small molecules production processes. We encourage potential partners to discover how our tools and expertise can elevate your projects, lower costs, and enhance sustainability. Shape the future of biotechnology and drug development with us—contact us to begin exploring revolutionary solutions.

Work with Us


Discovering and Manufacturing Next-Generation Vaccine Adjuvants Using Generative Molecular Design


We’re thrilled to have been awarded a 5-year contract alongside SaponiQx, Inc., totaling up to $31 million including program options, to discover and develop next-generation vaccine adjuvants.

This award comes to us from the Defense Threat Reduction Agency’s (DTRA) Joint Science and Technology Office (JSTO) for the Chemical and Biological Defense (CBD) Program, through the Medical CBRN [Chemical, Biological, Radiological, and Nuclear] Defense Consortium (MCDC) requirement 22-05, “Adjuvant Activity to Vaccines Prototype.”

We’ve been partners with SaponiQx in adjuvant discovery and development since 2021, and we’re honored to work with them on this project. Together, we will use a combination of high-throughput empirical and artificial intelligence/machine learning approaches, including Generative Molecular Design (GMD), to develop superior novel saponin-based adjuvants.

Adjuvants are components of vaccines that help to enhance the magnitude, breadth, and duration of the immune response to vaccination. Currently, only a handful of adjuvants are available for human use in licensed vaccines. SaponiQx’s STIMULON™ QS-21 is a key adjuvant component in market-leading vaccines for shingles, malaria, and respiratory syncytial virus. Novel adjuvants with enhanced properties, including tailored humoral and cellular immune responses, could pave the way for a new wave of innovative vaccines against existing and emerging pathogens.

The COVID-19 pandemic revealed the critical need for safe, effective, and accessible vaccines against emerging biothreat agents.

Imagine a future where vaccines are not only more affordable but also provide consistent protection in fewer doses, without causing discomfort or requiring refrigeration. We’re very excited by this opportunity to strengthen and expand the SaponiQx–Ginkgo partnership and to work with DTRA to make that future a reality.

Building on our achievements with STIMULON QS-21, SaponiQx is excited to realize our company’s founding vision of harnessing the potential of Generative Molecular Design to dramatically increase access to lifesaving vaccines around the world.

Rebecca Kurnat, Head of Operations at SaponiQx

We aim to demonstrate in the laboratory and in animal studies the ability of these novel adjuvants to protect against challenges from biothreat agents, such as the plague, and to provide lower cost, sustainable and scalable manufacturing processes by leveraging Ginkgo’s leading platform for cell programming. Together, we intend to design candidate adjuvants using SaponiQx’s leading platform for adjuvant generation, and to identify additional candidates by screening natural extracts for previously uncharacterized saponins and creating non-natural saponins with enzyme-based techniques. Harnessing a first-of-its-kind “data lake” for adjuvants, we plan to use iterative GMD to propose and optimize adjuvant structures against eight functional parameters. Adjuvant candidates will be put through in-depth testing, first in the laboratory for immune and toxicity responses, and then in studies of their effectiveness in protecting vaccinated animals from pathogens; QS-21 and the related QS-7 will serve as benchmarks.

By leveraging our leading platform for cell programming, we also intend to develop more affordable, sustainable, and scalable adjuvant manufacturing processes.

Ginkgo will develop a first-generation Adjuvant Development Candidate (ADC) production method, using a heterologous production strain such as brewers’ yeast, Saccharomyces cerevisiae. Our platform powers iterative Design–Build–Test–Learn-driven cell engineering to enable the rapid prototyping, optimization, and development of proteins, enzymes, metabolic pathways, and whole organisms under commercial-scale manufacturing conditions. Development of a first-generation ADC production method could facilitate further development of a sustainable mass-production manufacturing process for these complex adjuvants.

Ginkgo Bioworks Provides Business Updates at J.P. Morgan Healthcare Conference

Today we’re thrilled to provide updates on our business at the J.P. Morgan Healthcare Conference in San Francisco, live and on webcast at 9:45am PT/12:45pm ET.

In short, we:

  • Expect to meet our 2023 new program and revenue guidance ranges
  • Ended 2023 with nearly $950 million in cash and cash equivalents, a strong balance sheet providing multi-year runway as we see operational efficiencies in our business
  • See strong growth among blue chip pharma and biotech (“biopharma”) customers including Pfizer, Novo Nordisk, Merck and Boehringer Ingelheim
  • Will highlight more updates today at the 42nd Annual J.P. Morgan Healthcare Conference at 9:45 a.m. PT (12:45 p.m. ET) here.

I’m very pleased with the robust revenue and program growth we have seen in 2023, particularly in the biopharma sector – growing the portion of our cell engineering revenue that is attributable to biopharma customers by more than 50% over the past year.

Our strong balance sheet, with nearly $950 million of cash and cash equivalents, positions us well to take advantage of strategic opportunities while the market faces continued pressure. This, combined with the meaningful improvements we have seen in operational efficiency, gives us a long runway as we plan to increase new programs while reducing operating expenses. I’m proud of our team’s accomplishments in 2023 and am excited to drive continued strong growth in our biopharma vertical in 2024.

Preliminary 2023 Key Performance Highlights

  • Ginkgo continues to expect Total revenue of $250 – $260 million in 2023
    • Preliminary unaudited Cell Engineering revenue is expected to be within the previously disclosed guidance range of $145 – $150 million in 2023
    • Preliminary unaudited Biosecurity revenue is expected to be in line with the previously disclosed guidance of up to $110 million in 2023
  • New Cell Programs are expected to be within the previously disclosed guidance range of 80-85 new Cell Programs added to the platform in 2023
  • Ginkgo signed or advanced several major new biopharma programs in 2023, including with Pfizer, Merck, Novo Nordisk, and Boehringer Ingelheim in which Ginkgo is eligible to receive, in aggregate, over $1.2 billion in upfront research payments, research fees and development and commercial milestones. Ginkgo also successfully completed the pilot phase of a program with Novo Nordisk, as well as completed a gene therapy collaboration with Biogen.
  • In connection with its strategic partnership with Google Cloud, Ginkgo is training a series of foundation and application-specific models incorporating Ginkgo’s proprietary metagenomics and assay-labeled training data as well as data from public repositories. Ginkgo’s ability to bring together automated data generation at scale with AI models targeted towards customer program areas is expected to be the foundation for additional pharmaceutical partnerships in 2024.
  • Ginkgo ended 2023 with nearly $950 million of cash and cash equivalents, putting Ginkgo in a strong financial position to pursue its strategic objectives while driving towards profitability

We plan to report fourth quarter and full year 2023 financial results in February 2024, at which time we intend to provide our outlook for full year 2024.

To learn more about Ginkgo’s biopharmaceutical services offerings, visit

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Ginkgo Bioworks Announces Inaugural Members of New Biopharma Advisory Board

Today we’re thrilled to announce the formation of our new Biopharma Advisory Board!

This council of experts from across the biopharmaceutical industry will provide critical insight into the development of Ginkgo’s core platform service offerings across target discovery, drug discovery, optimization, and manufacturing. The group, which will conduct regular meetings at Ginkgo and with its partners, includes (in alphabetical order) —

  • Norbert Bischofberger, PhD, is the President and Chief Executive Officer of Kronos Bio, a clinical-stage biopharmaceutical company developing medicines that target the deregulated transcription that is the hallmark of cancer and other serious diseases. Prior to Kronos, Dr. Bischofberger spent 28 years at Gilead, where he presided over the development and approval of more than 25 medicines for a range of serious conditions, including the transformation in the treatment of diseases such as HIV and viral hepatitis. Notably, he is one of the inventors of Tamiflu, an oral medication on the market for both the prevention and treatment of influenza A and B. Norbert was part of the core management team that grew Gilead from less than 50 employees with no revenues to 10,000 employees with $25B in revenue.
  • Jeff Legos, PhD, MBA, is currently an Executive Vice President and Global Head of Oncology and Hematology at Novartis, where he leads development, registration, approval, and life cycle management for a clinical pipeline of 35+ assets across a broad range of cancers and blood disorders. Dr. Legos has a proven track record of successfully leading large multinational teams across all functions and stages of R&D in both his current and previous role as Vice President and Global Medicine Development Leader at GlaxoSmithKline, which has resulted in more than 30 global regulatory drug and companion diagnostic approvals.
  • John Maraganore, PhD, served as the founding Chief Executive Officer and a Director of Alnylam from 2002 to 2021. Under his leadership, Alnylam helped lead the interventional RNA revolution by launching the first RNAi therapeutic medicine, ONPATTRO®, in 2018, followed by four more RNAi therapeutics through mid-2022. Dr. Maraganore was the chair of the Biotechnology Innovation Organization (BIO) from 2017 to 2019 and is an active mentor to leaders across the biotechnology industry. John is the principal of JMM Innovation, and also serves as a Venture Partner for Arch Ventures and Atlas Ventures, an executive partner for RTW Investments, a senior advisor for Blackstone Life Sciences, and as an advisor for M28.
  • Paolo Martini, PhD, is the Chief Scientific Officer of International Therapeutic Research Centers and the Founder of Rare Diseases at Moderna, where he previously worked on messenger RNA therapy for rare and orphan diseases. He has more than 20 years of experience in drug discovery working on molecular mechanisms underlying monogenic and multigenic metabolic and fibrotic disorders as well as hematologic malignancies.
  • Mark McCamish, MD, PhD, is the President & Chief Executive Officer of IconOVir Bio, a preclinical-stage biotechnology company pioneering the next generation of oncolytic virus therapy to improve the treatment of patients with cancer. He was previously the President & Chief Executive Officer of Forty Seven, which he led from a valuation of $169M to an acquisition by Gilead for $4.9B. Previously he has had extensive experience at multiple companies including Abbott, Amgen, and Novartis/Sandoz and is a renowned expert in biologic and biosimilars development and manufacturing.
  • Christi Shaw is an Independent Director on the Boards of Beam Therapeutics, ReAlta Life Sciences, and Avantor. She previously served as Chief Executive Officer of Kite Pharma and as Senior Vice President at Eli Lilly & Company, where she was President of Lilly Bio-Medicines. Ms. Shaw has also held prominent leadership roles at Johnson & Johnson and Novartis where she served as US Country Head and President. Christi co-founded the More Moments More Memories Foundation which provides financial assistance to help cancer patients access potentially life saving clinical trials.

Together, this council represents a wide breadth of technical experience and deep business expertise that will contribute to the development of Ginkgo’s service offerings in Gene Therapy, Cell Therapy, RNA, Biologics, Process R&D and more.

Over the past year, we announced new R&D services collaborations with Boehringer Ingelheim, DARPA, Esperovax, Merck, Pfizer, Prokarium, Sensible, Synplogen, WARF, as well as advancements in its work with Novo Nordisk, Persephone Biosciences, and Synlogic. Ginkgo acquires and integrates new technologies to expand its horizontal platform, with past acquisitions serving to develop our capabilities in AAV and circular RNA.

The discovery and development of new medicines is critically important and incredibly challenging. Advanced technologies in high throughput automation, synthetic biology, and more recently AI, have opened up possibilities for the development of novel modalities and exploration of more design space for the discovery and optimization of new targets and candidate therapies.

It’s an incredibly exciting time for the industry as these technologies come together at scale, and we’re thrilled to have this group of luminaries as part of our inaugural cohort of advisors.

“I’m excited to welcome this incredible deep bench of wisdom and creativity to the Ginkgo family,” said Jennifer Wipf, SVP & Head of Commercial at Ginkgo Bioworks. “These leaders have shaped the modern vaccines and therapeutics landscapes by spearheading the discovery, testing, manufacturing, and deployment of entirely new modalities, and reinventing how researchers and drugmakers work with more familiar areas of medicine. I can’t wait to see how their mentorship, insights, and provocations help our growing team reach new heights.”

“We live in a global, interconnected society, and therefore, we are all susceptible to the spread of novel infectious diseases. Now more than ever, the speed of drug discovery and development is important,” said Norbert Bischofberger, Ginkgo Biopharma Advisory Board member. “Ginkgo’s experience in accelerating biological R&D across modalities and their extensive work in biosecurity and epidemiology positions the company to make a meaningful impact. I look forward to supporting the growth of their team and offerings.”

“Ginkgo represents a huge opportunity for businesses who want to take new pharmaceuticals to market. By outsourcing risky R&D to a partner with unprecedented scale, companies can optimize their approach to new modalities and targets wherever they are in the pipeline,” said John Maraganore, Ginkgo Biopharma Advisory Board member. “Our industry is at a pivotal moment. More and more of biopharma can leverage scale and AI to turn scientific uncertainty into predictable engineering, so I’m thrilled to be able to contribute to the energy and movement I saw firsthand when I spoke onstage with Jen at Ferment.”

To learn more about Ginkgo’s biopharmaceutical services offerings, visit

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Completed Program with Biogen to Boost Productivity of Gene Therapy Manufacturing Platform

Today we’re thrilled to announce the successful completion of our gene therapy collaboration previously announced with Biogen in May 2021!

Together, we aimed to redefine the industry standard for manufacturing recombinant adeno-associated virus (AAV)-based vectors. The collaboration achieved our goals of enhancing the AAV production titers of Biogen’s gene therapy manufacturing processes.

We’re proud to work with industry-defining partners like Biogen to help global leaders in the biopharmaceutical industry redefine what’s possible in therapeutics discovery and manufacturing.

Significant improvements like these are the result of a platform-based approach to biological R&D. They are possible because our program leads work closely with our collaboration partners to take full advantage of the broad scale and deep sophistication of our highly-automated foundry and growing codebase.

Learn more about Ginkgo’s Gene Therapy Services here.

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Ginkgo Receives Grant to Develop Innovative Live Cell Delivery Platform of Antibody Therapeutics for Treating HIV and Malaria

We’re thrilled to receive a grant from the Bill & Melinda Gates Foundation!

Under this grant, we will work to develop a live cell therapeutic that can produce antibodies to fight human immunodeficiency virus (HIV) and/or malaria directly in the body.

Protein therapeutics have transformed the standard of care for many diseases — the best known example being insulin for diabetes — and have helped to extend lives across the world, thanks to revolutionizing treatments of diseases such as anemia, cancers, and certain genetic disorders. Yet access to these therapeutics remains a challenge, especially in low- and middle-income countries (LMICs), because of complex manufacturing processes and degradation during storage and delivery of such therapeutics. Developing a new therapeutic delivery modality for patients could increase accessibility and lower cost of treatment.

We will focus on creating a prototype engineered cell line that can express antibodies for the treatment of HIV and/or malaria via an implantable device.

Globally, approximately 39 million people live with HIV, which attacks the body’s immune system and weakens its ability to fight infection. The World Health Organization (WHO) reports that nearly half the world’s population is at risk of malaria transmission, with 96% of malaria-caused deaths in 2020 taking place in the WHO Africa Region. The engineered cell line would be designed to act as a “cell factory” capable of delivering protein therapeutics to the patient for up to a year, or longer. This prototype cell line could potentially lead to protein therapeutic delivery systems that function as long-term and cost-effective treatments for these diseases.

Ginkgo, with support from the foundation, plans to use its expertise in mammalian cell engineering to engineer highly synthetic cell lines that have both high productivity and extended longevity.

We will use our expertise in genomics and systems biology to predict the genomic components underlying these complex cellular phenotypes. We will then utilize our expertise in genome engineering, including a fully automated clonal cell line generation workflow, to combine these features in a mammalian chassis. This engineered cell line will be combined with an implant device for continuous delivery of the therapeutic antibodies. If successful, the eventual product could create a novel delivery platform for antibody-based therapies in communities where access to such drugs is challenging.

Protein-based drugs were some of the earliest applications of cell programming for medicine half a century ago. We’re honored to be receiving support from the Gates Foundation to reimagine how these medicines are made and delivered so that we can open up access to these critical therapies. We look forward to leveraging our learnings from this project to ensure the success of future programs with our partners.

Learn more about Ginkgo’s biopharmaceutical services at

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Advancing Discovery and Development of Precision Gene Editors with Arbor Biotechnologies

We’re so excited to announce our new collaboration with Arbor Biotechnologies!

Arbor utilizes its computational metagenomic discovery engine and protein engineering expertise to identify and optimize genetic editors with the potential to treat a broad range of genetic diseases. The company’s portfolio of novel gene editors has significant therapeutic potential due to, among other things, their unique protospacer adjacent motifs (PAMs), which may enable access to nearly all sites in the genome, their varied cut types, which can potentially correct a wider range of diseases, their smaller editing technology, which allows the use of additional delivery technologies, and their high specificity, which can enable improved safety profiles.

Ginkgo’s expertise in high throughput exploration of genetic design spaces complements Arbor’s in-house capabilities, and the collaboration is expected to accelerate Arbor’s precision editor optimization campaign through massively parallel library design, automated mammalian cell experimentation and iterative AI-guided protein engineering.

“Patients are at the center of everything we do at Arbor, and we are thrilled to partner with Ginkgo to hasten the advancement of our precision editing technologies into therapeutic applications that have the potential to address diseases with high unmet medical need. Ginkgo’s expertise aligns well with our goals, and their technology will synergize with our in-house capabilities, potentially fueling a faster, more efficient expansion of our toolbox of gene editing technologies.”

Devyn Smith, Ph.D., CEO of Arbor

As we can see from the recent landmark regulatory approval of the world’s first CRISPR-based treatment, the gene editing landscape is rapidly advancing, with continuous innovation and optimization of novel technologies that are revolutionizing the way we consider and address disease. This collaboration with Arbor is an exciting project for us, as it gives us an opportunity to leverage our platform-driven approach to contribute to the gene editing sector’s fast-moving evolution.

We look forward to expanding our capabilities in this field by working with such an innovative pioneer as Arbor to power technologies with the potential for transformative impact.

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Reusable Bacteroides Anaerobic Engineering Toolkit Completed with Persephone Biosciences

Today we are pleased to announce the completion of our first collaboration together with Persephone Biosciences — a Bacteroides engineering toolkit!

Under the collaboration, both Persephone and Ginkgo have access to this reusable toolkit. Persephone will utilize the technology to develop a pipeline of microbiome therapeutics, and Ginkgo can use the technology as part of our broader platform offering for future customers.

The technology comprises a set of generalizable genetic tools which can facilitate rapid Bacteroides engineering, including in the high-throughput anaerobic engineering context. Over the course of this collaboration, Ginkgo incorporated our flagship hardware and software workflows under an anaerobic blanket, meaningfully extending its cell engineering platform capabilities to perform productively in an anaerobic environment.

Ginkgo and Persephone announced in April 2022 that we would collaborate to develop novel microbiome products based on the bacterial genus Bacteroides, a promising vehicle for stable and long-term delivery of microbial products. Through this collaboration, a high-throughput anaerobic cell engineering platform has been developed. With it, Ginkgo designed and screened hundreds of promoters, shuttle vectors, ribosome binding sites, and terminators to characterize their efficiency and expression levels and selected parts across the expression range for the final toolkit.

While Persephone plans to utilize the Bacteroides technology for the rapid generation of therapeutics from its planned and ongoing oncology biomarker studies, Ginkgo may leverage the toolkit to address a wide range of customer needs and applications, including for customers developing microbiome based therapeutics.

At Ginkgo, we are growing our network of partners and striving to provide a platform to all the innovators that have a vision of using biology to solve the world’s most pressing problems.

Continuous improvement to our platform is key, and together with Persephone’s expertise in the microbiome and with bacterial strains, we’ve improved yet another valuable offering in a therapeutic area of interest to many of our partners.

“We’re delighted with the results of our collaboration with Ginkgo Bioworks. The resulting technology offers us previously unimaginable inhouse scale, that promises to save us valuable time as we seek to rapidly generate therapeutics from our oncology biomarker studies, including our ongoing ARGONAUT trial. This in turn could enable us to bring much-needed better health outcomes – across a range of cancer types – much sooner than would otherwise be possible.”

Stephanie Culler, co-founder and CEO of Persephone Biosciences

Find the full press release here along with all of the latest news from the Ginkgo team.

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Multi-Target RNA Discovery Collaboration with Pfizer

Today we’re thrilled to announce a collaboration with Pfizer focused on the discovery of RNA-based drug candidates.

Pfizer will leverage Ginkgo’s proprietary RNA technology to advance the discovery and development of novel RNA molecules across priority research areas. Ginkgo will receive an upfront payment and is eligible to receive research fees and development and commercial milestone payments, up to an aggregate total of $331 million across three programs. Ginkgo is entitled to potential further downstream value in the form of royalties on sales.

RNA therapeutics that encode proteins with the potential to treat or cure diseases represent an exciting new approach in medicine with the possibility of far-reaching application.

Our RNA technology combines high-throughput screening of the behavior of RNA constructs with a multi-parameter design framework to identify novel natural and synthetic elements optimal for a particular application. We will deploy these capabilities with the goal of achieving efficient production, circularization, improved stability, and enhanced translation of each RNA construct.

“RNA therapeutics are proving to be an important platform to advance the world of scientific innovation, and with progress in synthetic biology we have the potential to create new RNA treatments that may benefit patients worldwide. Access to Ginkgo’s proprietary platform will help enable Pfizer to search for novel and exciting RNA constructs with improved stability and expression that could lead to more effective treatments.”

Will Somers, PH.D., Head, Biomedicine Design, Pfizer

Billions of patients around the world have already benefited from advances in RNA-based technologies.

We’re thrilled to be able to help enable the discovery and development of novel drugs using this powerful modality by applying our platform technologies which are designed to program RNA for maximum therapeutic effect. Ginkgo’s approach enables and accelerates discovery across different disease areas and modalities for our partners, who bring deep expertise in drug development. We can’t wait to leverage our broad and deep RNA Codebase and deploy our Foundry to enable the era of programmable medicines with the Pfizer team.

To learn more about Ginkgo’s RNA Therapeutics offering, visit our webpage.

Ready to talk to our team about your RNA project? Get in touch here.

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Ginkgo Awarded DARPA Contract to Reimagine the Manufacturing of Complex Therapeutic Proteins

We’re pleased to share that the Defense Advanced Research Projects Agency (DARPA) announced that we have been awarded a 4-year contract worth up to $18 million to reimagine how to manufacture complex therapeutic proteins.

As a performer on DARPA’s Reimagining Protein Manufacturing (RPM) project, we aim to deliver revolutionary advances in on-demand protein manufacturing by leveraging Cell-Free Protein Synthesis (CFPS) to enable rapid, high-yield, distributed production of human therapeutic proteins that support national security objectives. We will lead a team comprising representatives from Imperial College London, led by Prof. Paul Freemont, Nature’s Toolbox, Inc., led by Alex Koglin, and consultant Michael Feldhaus (former Executive VP of Antibody Discovery at Adimab).

There is growing recognition that pharmaceutical supply chains are at risk. One way to meet this challenge is distributed manufacturing at the point of care. Imagine a future where drugs, including complex biologics, are produced locally or in a widely distributed manner on-demand. We’re very excited to be working with DARPA to make that future a reality.

Replacing cell-based methods with cell-free methods

Therapeutic proteins bearing so-called “post-translational modifications,” such as antibodies, cytokines, and clotting factors are particularly important in the marketplace and to DARPA, as are subunit and conjugate vaccines. Half of the top-selling drugs used to treat cancer and autoimmune diseases are such therapeutic proteins; many are also used as medical countermeasures to treat or prevent disease, injury, or death related to chemical, biological, radiological, or nuclear threats. Through this program, we hope to transform how therapeutic proteins are made, replacing cell-based methods with cell-free methods. Traditional centralized, large-scale manufacturing methods have usually sufficed, but increasingly there are use cases where rapid distributed or on-demand manufacturing is needed, such as supplying of therapeutic proteins to geographically isolated locales, providing hospitals and clinics with point-of-need rapid production of medicines from common precursors, and improving our ability to mount rapid and targeted responses to natural or man-made biological threats and emergencies.

Traditional production methods rely on weeks- to months-long construction of bespoke cellular organisms that have been engineered to produce the desired therapeutic protein during days-long fermentation processes. Even with standardized methods, it typically takes months to achieve the first useful production of a biological drug. Post-expression isolation and purification are equally challenging: each unique process is costly and time-consuming to develop.

Enabling the rapid prototyping of enzymes for diverse therapeutic and nontherapeutic projects

Cell-Free Protein Synthesis (CFPS), by contrast, brings the key advantages of greater speed and flexibility than cell- and fermentation-based production. Significant improvements are needed to make CFPS competitive with traditional therapeutic protein production, however, primarily with respect to efficiency and the identity and homogeneity of post-translational modifications. In this program, we seek to address these challenges and hope to enable the rapid prototyping of enzymes and other proteins for diverse therapeutic and nontherapeutic projects. One aim of the project is to create production methods that are compatible with Good Manufacturing Practices, thereby facilitating adoption by the pharmaceutical industry.

We will leverage innovative technologies enabled by our high-throughput, automated Foundry and our proprietary genetic data Codebase, a portfolio of reusable biological assets which includes more than one billion proprietary gene sequences. Our synthetic biology platform, coupled with our extensive expertise in iterative Design–Build–Test–Learn-driven biological engineering, enables the rapid prototyping, optimization, and development of proteins, enzymes, metabolic pathways, and whole organisms under commercial-scale manufacturing conditions processes.

Find the full press release here along with all of the latest news from the Ginkgo team.

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