Flagship Pioneering’s Scientists Invent Machine Learning–Powered Platform to Generate Novel Biomedicines

Generate Biomedicines emerges from three years of stealth operations to pioneer Generative Biology™ and reimagine drug discovery and development across multiple therapeutic modalities and numerous diseases.

Generate has employed its Generative Biology platform to invent novel antibodies, peptides, enzymes, receptors, and other therapeutic proteins, including the generation of novel therapeutic proteins against SARS-CoV-2 in less than 3 weeks.

CAMBRIDGE, Mass., September 10, 2020 – Flagship Pioneering today announced the unveiling of Generate Biomedicines, a new company whose machine learning–powered Generative Biology platform can rapidly invent new drugs across a wide range of modalities—from antibodies, peptides, enzymes, and cytokines to heretofore undiscoverable protein therapeutics.

The proprietary Generative Biology platform learns from all known proteins in order to encode and apply the fundamental principles of how genetic sequences lead to protein structure and function. The platform creates novel protein sequences with optimized therapeutic potential. The company has demonstrated that Generative Biology can be applied to all protein modalities and generate both novel proteins with desired functions and those that interact potently and specifically with therapeutic targets. The platform’s generalizability enables broad applications in the creation of enzymes, peptides, and antibodies, and it opens the possibility of entirely new classes of protein drugs.

“Breakthroughs in machine learning algorithms, the exponential growth in computing power, and the acceleration and democratization of DNA sequencing and DNA synthesis are allowing us to learn from biology at unprecedented scale,” says Noubar Afeyan, Ph.D., founder and CEO of Flagship Pioneering. “Protein design is not a new idea, but it has been frustrated by the limitations of previous technologies. Generate Biomedicines was formed to move biomedicine past its dependence on existing discovery methods and develop a new machine learning technology that can generate biologic drugs for potentially any target, in order to treat previously intractable diseases.”

Generating Novel Biomedicines

Generate is the product of multiple explorations inside Flagship Pioneering’s innovation foundry, Flagship Labs, and was co-founded in 2018 by Flagship Pioneering scientist-entrepreneurs Avak Kahvejian, Ph.D.; Geoffrey von Maltzahn, Ph.D.; Molly Gibson, Ph.D.; and Professor Gevorg Grigoryan, Ph.D. They proposed to create a multimodality, multiproduct platform company that could conceive, generate, and launch potent and diverse biomedicines with unprecedented speed and success. The co-founders have co-founded numerous biotechnology companies in the past, including Sana Biotechnology, Rubius Therapeutics, Indigo Agriculture, Cellarity, Codiak Biosciences, Kaleido Biosciences, and Seres Therapeutics.

“Generate began with the question, ‘What if we could generate novel protein therapeutics using new computational tools, without having to discover them through trial and error?’” says von Maltzahn. “In much the same way that the patterns found in large libraries of songs, texts, or photographs have been used to create AI-generated music, language, and faces, we have shown that patterns in protein sequences and structures can be broadly applied to generate novel biomedicines. The rules of biotechnology are about to fundamentally change. With our combination of talent, experience, and technology, we are working to build a therapeutic company of remarkable breadth and impact.”

The company’s Generative Biology platform holds the potential to overcome a variety of limitations of protein drug discovery. The platform makes possible:

• Generation of antibodies or binders to pre-specified epitopes on a target
• Generation of antibodies to membrane targets or multiprotein complexes that are traditionally difficult to express in vitro or immunize against in vivo
• Generation of therapeutics that agonize their targets or control specific receptor signaling
• Generation of highly selective molecules capable of distinguishing desired targets from undesired ones
• Generation of synthetic gene editing proteins with novel functions

Generate has applied its platform to build an expansive portfolio of therapeutic candidates for both internal development and potential partnerships. In response to the COVID-19 pandemic, the company has built a portfolio of therapeutic candidates for SARS-CoV-2 neutralization, including antibodies and peptides that target multiple epitopes on the spike protein peptide. The effort took less than 17 days in all, and its success rate is orders of magnitude higher than that of a typical discovery campaign. These candidates are being developed in partnership with the Coronavirus Immunotherapy Consortium (CoVIC)–an initiative led by La Jolla Institute for Immunology with support from the COVID-19 Therapeutics Accelerator. The Therapeutics Accelerator was launched by the Bill & Melinda Gates Foundation, Wellcome Trust, and Mastercard in March 2020 to identify, assess, develop and scale up treatments for COVID-19.

“In the history of modern medicine, nearly every drug has been discovered or identified from a lengthy, cumbersome, and costly process of trial and error,” says Generate co-founder Kahvejian. “Machine learning has evolved to a point where it can unlock the underlying principles of biology. With our proprietary computational platform, we believe we can move from chance drug discovery to intentional drug generation, not only accelerating the development of existing therapeutic modalities but also creating previously impossible ones.”

Generate is led by von Maltzahn and Kahvejian as co-CEOs, and Lovisa Afzelius, an origination partner at Flagship and the former SVP of Strategy & Operations at Repertoire Immune Medicines, serves as President. Gibson is Chief Innovation Officer, and Grigoryan is Chief Technology Officer. Members of Generate’s Board of Directors include Chairman Noubar Afeyan, founder and CEO of Flagship Pioneering; Frances Arnold, Nobel Laureate and Professor of Chemical Engineering, Bioengineering and Biochemistry at the California Institute of Technology; Stéphane Bancel, founding CEO of Moderna, Inc.; and Gary Pisano, the Harry E. Figgie, Jr. Professor of Business Administration at Harvard Business School.

About Generate Biomedicines

Generate Biomedicines is an early-stage life sciences company pioneering a machine learning– powered biomedicines platform with the potential to generate new drugs on demand across a wide range of biologic modalities—from short peptides to complex antibodies, enzymes, cytokines, and yet to be described protein compositions. Generate Biomedicine’s multimodality generation platform represents a potentially fundamental shift in what’s possible in the field of therapeutic development, addressing key challenges of drug discovery and drastically expanding the available search space for novel biomedicines. Generate Biomedicines was founded by Flagship Pioneering.

About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, the firm has applied a unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, resulting in over $34 billion in aggregate value. To date, Flagship is backed by more than $4.4 billion of aggregate capital commitments, of which over $1.9 billion has been deployed toward the founding and growth of its pioneering companies alongside more than $10 billion of follow-on investments from other institutions. The current Flagship ecosystem comprises 41 transformative companies, including Axcella Health (NASDAQ: AXLA), Denali Therapeutics (NASDAQ: DNLI), Evelo Biosciences (NASDAQ: EVLO), Foghorn Therapeutics, Indigo Ag, Kaleido Biosciences (NASDAQ: KLDO), Moderna (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), Sana Biotechnology, Seres Therapeutics (NASDAQ: MCRB), and Syros Pharmaceuticals (NASDAQ: SYRS).