A versatile biocatalytic platform for scalable therapeutic oligonucleotide manufacturing

Lead Research Organisation: University of Manchester
Department Name: Chemistry

Abstract

Proteins control almost all biochemical processes in the human body. These biological macromolecules are encoded in our DNA, which is first transcribed to mRNA and subsequently translated to proteins. Traditional, small molecule pharmaceuticals are designed to selectively bind to a target protein in order to modulate its function. While this approach has proven very powerful, there are numerous diseases which are difficult or not possible to treat in this manner. In recent years, a new class of drug molecules called therapeutic oligonucleotides have emerged, which offer a potentially versatile approach for the treatment of a wide range of genetic disorders and diseases. These molecules are short modified DNA sequences, which are designed to bind to mRNA and directly modulate the production of disease related proteins. Despite the fact that there are currently more than 160 different oligonucleotide therapies in clinical trials, to date the only treatments approved by the Food and Drug Administration (FDA) have been for rare diseases and are extremely expensive. To establish therapeutic oligonucleotides as viable and cost-effective treatments for more common diseases, it is now essential that we develop sustainable, scalable and versatile manufacturing strategies for their production.
Existing methods of producing oligonucleotides rely on chemical synthesis, which requires large excesses of expensive reagents, huge volumes of organic solvent (1 ton of acetonitrile per Kg of product) and deliver the final products with low yield and modest (~90%) purity. Reactions are performed on solid supports or columns, which limits the process scalability meaning that these methods are only suitable for producing oligonucleotides in <10 Kg batches. In short, current chemical methods are not suitable for the synthesis of high volume oligonucleotide products required for the treatment of common diseases.
In this application, I will develop a green, cost-efficient and truly versatile biocatalytic approach to manufacture therapeutic oligonucleotides on a large scale. Biocatalysis is an exciting technology which is widely used across the chemical industry, whereby enzymes are used to convert starting materials into high-value products. In nature, DNA is copied or 'amplified' by enzymes called polymerases. I will exploit these polymerases as biocatalysts to amplify a reusable catalytic DNA template to produce large quantities of therapeutic oligonucleotides in high yield and purity under environmentally friendly conditions. Compared to natural DNA, therapeutic oligonucleotides contain chemical modifications which are designed to improve their efficacy, selectivity and metabolic stability. These chemical modifications are not well tolerated by natural polymerases, however using a technology called directed evolution we are able to quickly engineer enzymes to modify their functions and optimize their properties to make them suitable for practical applications. I will use directed evolution to engineer polymerases to operate under process conditions to efficiently produce oligonucleotides containing the chemical modifications needed for therapeutic applications. This approach will be developed and optimized using the billion dollar therapeutic oligonucleotide Spinraza as an initial synthetic target, which will be prepared on a multi gram scale to showcase the power of this biocatalytic platform and to attract further investment for multi-kilo scale processes.

Planned Impact

Therapeutic oligonucleotides are a new drug modality, which have the potential to treat a wide range of genetic diseases and viral infections. Recent FDA approvals of therapeutic oligonucleotides for the treatment of rare diseases, has resulted in significant interest and investment from all of the top 12 pharmaceutical companies. However, current approaches to therapeutic oligonucleotide synthesis are restricted to 10Kg batches and to date all approved therapies are for the treatment of rare diseases. This proposal aims to deliver a scalable (>100 Kg) and sustainable biocatalytic approach to therapeutic oligonucleotide manufacture which will open up the market to allow the development of population based therapies.

This fellowship programme will have the following impacts:

1. Society: Therapeutic oligonucleotides have the potential to treat a wide range of diseases including those previously deemed undruggable. The development of a cost-effective and scalable manufacturing route will make treatments available to the global population significantly improving patient's quality of life. The new strategy is also expected to deliver therapeutics with higher purity than those made using existing chemical methods which will result in improved patient safety. Furthermore the approach is sustainable, allowing manufacturing industries to meet the needs of the current population without compromising the ability of future generations to meet their own manufacturing needs.

2. Pharmaceutical Industry and Economy: Current chemical approaches of oligonucleotide manufacture require huge volumes of acetonitrile solvent. Recent years have seen world shortages of acetonitrile, which is made as a by-product in the manufacture of acrylonitrile. The proposed strategy is environmentally sustainable and does not require organic solvents, thus ensuring the security of the materials supply chain. The biocatalytic process is atom efficient, performed in a single reaction and generates minimal waste products, ensuring it is both economically viable and environmentally sustainable. The platform will deliver a transformative bio-based manufacturing solution which will support the UK Industrial Strategy for sustainable growth and the development of a low-carbon, low waste, circular economy with significant societal benefits.

3. University of Manchester: The University of Manchester will benefit from increased engagement with industrial partners and from collaborations with world leading academics (Prof Lye UCL). The institute will further benefit from IP and licencing agreements generated throughout this programme.

4. Fellow: The award on a UKRI Future Leader Fellowship will provide the ideal platform for the fellow to establish her independent research programs aimed at developing sustainable biocatalytic solutions to therapeutic oligonucleotide production, a topic which is of great interest to both academic and industrial communities. The research within this proposal is expected to deliver a number of high impact publications which will allow the fellow to build an international reputation as a world leading researcher. The program will allow the fellow to strengthen existing academic and industrial collaborations, and to build new ones, creating ample opportunities for future collaborative funding applications.

5. Researchers and Students: PDRAs, PhD and MChem students trained by the PI will not only receive training in the theoretical and practical aspects of the project but will benefit from the PI's industrial experience and contacts. They will each develop an understanding of manufacturing and scale up processes, which will equip them with the knowledge for a future career in pharmaceutical, biotechnological and related industries.

Publications

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Description In recent years, a new class of drug molecules called therapeutic oligonucleotides have emerged which offer a potentially versatile approach for the treatment of a wide range of genetic disorders and diseases. These molecules are short modified DNA sequences which are designed to bind to mRNA and directly modulate the production of disease related proteins. Existing methods of producing oligonucleotides rely on chemical synthesis, which requires large excesses of expensive reagents, huge volumes of organic solvent (1 ton of acetonitrile per Kg of product) and deliver the final products with low yield and modest (~90%) purity. Reactions are performed on solid supports or columns, which limits the process scalability meaning that these methods are only suitable for producing oligonucleotides in <10 Kg batches. In short, current chemical methods are not suitable for the synthesis of high volume oligonucleotide products required for the treatment of common diseases. To establish therapeutic oligonucleotides as viable and cost-effective treatments for a wide range of diseases, it is now essential that we develop sustainable, scalable and versatile manufacturing strategies for their production.
My laboratory have developed a bio-based solution to oligonucleotide synthesis. Our approach uses renewable biocatalysts (enzymes), operates under aqueous conditions avoiding the use of solvents, and does not rely on solid supports making it scalable. Using our approach, we have produced a range of pharmaceutically relevant products in high purity without the need for costly purification steps.
Exploitation Route We are currently working in partnership with the Medicines Manufacturing Centre, AstraZeneca and Novartis to optimize and intensify our approach making it suitable for industrial scale manufacturing.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Executive Management Board, Future Biomanufacturing Research Hub, a National Centre (£10M UKRI investment and £5M Industrial Investment) for Biomanufacturing
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Biocatalytic Manufacturing of Nucleic Acid Therapeutics
Amount £6,292,440 (GBP)
Funding ID MR/W029324/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 08/2022 
End 08/2026
 
Description Biocatalytic Oligonucleotide Conjugation 
Organisation Amgen Inc
Country United States 
Sector Private 
PI Contribution We will be developing biocatalytic approaches to oligonucleotide conjugation
Collaborator Contribution Amgen will offer guidance in process optimization, analytics and purification techniques
Impact This partnership funds a PhD student in my lab for four years It is a multidiscipinary project involving biocatalysis, protein engineering, process chemistry and analytical chemistry
Start Year 2023
 
Description 19th RSC Chemical Biology and Bioorganic Group (CBBG) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Presentation on research conducted during fellowship to other early career researchers from UK institutes.
Year(s) Of Engagement Activity 2022
 
Description 55th ESBOC: The Chemical Biology of Molecules and Materials, hybrid event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation on research conducted during fellowship to a large international audience.
Year(s) Of Engagement Activity 2022
 
Description 9th Annual Peptides and Oligonucleotides Congress 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Dissemination of published and ongoing research activities in my group to a broad audience of industrialists and academics involved in diverse branches of therapeutic oligonucleotides research. I also chaired a session at conference, introducing speakers and mediating questions following the talks.
Year(s) Of Engagement Activity 2022
 
Description Chemical Development Symposium at Novo Nordisk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Dissemination of published and ongoing research activities in my group to a broad audience of industrialists
Year(s) Of Engagement Activity 2022
 
Description ECI Enzyme Engineering XXVI 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Dissemination of ongoing research activities in my group.
Year(s) Of Engagement Activity 2022
 
Description Protein Engineering Biocatalysis Congress 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation on research conducted during fellowship to a large international audience. I also chaired a session, introducing speakers and facilitating the questions after each talk.
Year(s) Of Engagement Activity 2022
 
Description RSC New Frontiers in Synthetic Chemistry 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Dissemination of ongoing research activities in my group to a synthetic chemistry audience
Year(s) Of Engagement Activity 2022