Neochromosome, Inc., a biotechnology company focused on genome-scale cell engineering and a wholly owned subsidiary of Opentrons Labworks, Inc., today announced a collaboration with Dr. Giovanni Stracquadanio of the University of Edinburgh utilizing artificial intelligence and machine learning to accelerate the development of new and more stable enzymes. Creating improved engineering processes for designer enzymes could lead to safer and more effective therapeutics, such as enzyme replacement therapy, for a broad range of genetic diseases.
While enzymes are highly abundant in nature, many are not powerful enough to be used in industrial or clinical applications, including the development of highly effective and safe therapeutics. To overcome this challenge, scientists use computational and experimental techniques to create libraries of thousands of ‘designer’ synthetically created enzymes. However, this process is time-consuming and often these new designer enzymes ultimately don’t perform as expected. Compared to conventional protein design approaches, AI and machine learning could better predict exact enzyme structures, encoded by specific DNA sequences not previously found in nature.
“Current methods of engineering enzymes are expensive and low throughput, and most designer enzymes lack efficacy. Therefore, there is an urgent need to establish new methods of reliably creating designer enzymes on demand,” said Dr. Leslie Mitchell, Co-founder and CEO of Neochromosome. “This project has enabled Neochromosome to explore a new approach to enzyme engineering, demonstrating the power of our DNA foundry to enable machine learning-directed protein engineering.”
Under the collaboration, which was supported by the Industrial Biotechnology Innovation Centre (IBioIC), the partners developed a workflow for improved enzyme engineering using a combination of automation, AI and biophysics to predict ideal enzyme candidates for experimental screening. Neochromosome utilized the Company’s DNA foundry to build a defined variant library, while scientists from Dr. Stracquadanio’s lab evaluated enzyme production and testing on Opentrons’ automated liquid handling robots.
The teams created thousands of different kinase mutations in silico, predicting the free energy of each mutant using a biophysical model. With the goal of creating new and more stable enzymes, the data was then fed into an AI tool to generate new sequences with predicted low free energy, ultimately leading to the creation of 40 novel, designer-engineered enzymes..
“The ability to create designer enzymes by leveraging AI is a significant milestone for the field of synthetic biology, especially for the development of safe and effective treatments for genetic disorders,” said Dr. Giovanni Stracquadanio, Senior Lecturer in Synthetic Biology and Co-director of the Edinburgh Genome Foundry at the University of Edinburgh and Co-founder of ZYTHERA. “We’re excited to continue our partnership with the world-class scientists and bioengineers at Neochromosome and use their impressive platform to generate novel engineered enzymes.”
Through customized flexible workflows, scientists can leverage Neochromosome’s expertise and DNA foundry to scale and streamline upstream biological engineering experiments, enabling researchers to focus on downstream cell-based experiments. From defined variant libraries and variant mining to clonal selection and DNA repository, Neochromosome works with its partners through an iterative, customized process to ensure high-quality deliverables with fast turnaround times.
About Neochromosome, Inc.
Neochromosome is a cell engineering company with a vision to power the future of biotechnology product development using whole-genome writing. The company utilizes proprietary DNA design, build, delivery and test technologies coupled with expertise in a variety of cell types including E. coli, yeast, and mammalian cells. Our partners leverage Neochromosome’s automated screening and engineering approaches, relying on our systematic approach to scientific development. Neochromosome was founded on technology developed to write the world’s first designer eukaryotic genome, The Synthetic Yeast Genome Project, Sc2.0. The company is headquartered in New York City and is a wholly owned subsidiary of Opentrons Labworks. For more information, please visit https://neochromosome.com and follow us on LinkedIn.
About the Industrial Biotechnology Innovation Centre
The Industrial Biotechnology Innovation Centre (IBioIC) was established in 2014 to stimulate growth of the Industrial Biotechnology (IB) in Scotland. IBioIC is recognized as a European center of excellence and connects world-leading industry with outstanding academic expertise and government to bring new IB processes and products to the global market.
IBioIC is a key driver of Scotland’s National Plan for Industrial Biotechnology, which recently set a new target of £1.2 billion in associated turnover and 4,000 direct employees by 2025 for the industry in Scotland.
IBioIC facilitates collaboration, provides scale-up capabilities, creates networks and develops skills and training provisions. IBioIC has more than 180 industry members, over 85% of which are SME or micro companies. To date, IBioIC has provided support for more than 200 companies, across a range of collaborative innovation projects, fostering academic-business partnership and co-funded by business.
A total investment of £6.4 million to date has leveraged an additional £28.5 million from businesses, follow-on funding from other sources or partnering with other funding initiatives. As a direct outcome from the collaborative projects funded alone, 327 high value green jobs have been protected or created by the businesses involved, leading to a further 3,000 jobs.
IBioIC has supported 369 students through its skills and training partnerships across 18 Universities and research institutes and four Further Education Colleges in Scotland. For more information, please visit www.IBioIC.com and follow on X, formerly known as Twitter.
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