By: Masha Kononov, Director of Business Development (North America), and Reuben Carr, Head of Chemical Biology, Ingenza Ltd

INTRODUCTION

Biocatalysis has emerged as a versatile tool for streamlining purification processes to replace lengthy, multi-step chemical pathways. The past decade has seen a notable rise in the use of biocatalysis for producing small-molecule drug substances, fueled by growing academic and industrial interest in harnessing enzymes to transform chemical pathways. As the biocatalytic toolbox expands, chemists have gained access to a wider range of catalytic options, enabling improved stereo- and regioselectivity, simplified chemical synthesis routes, improved process mass intensity (PMI), reduced environmental impact and stronger process economics.

However, the adoption of this methodology is not without its hurdles. While biocatalysis is starting to make impressive inroads into manufacturing routes, its uptake in early discovery chemistry has been slower. Technical and operational barriers, including enzyme durability, the management of aqueous waste streams and a lack of change mindset, are challenging to more widespread implementation. Nonetheless, increased collaboration and greater access to enzyme resources are beginning to open opportunities for early discovery R&D. This article examines both the promise and the practical constraints of biocatalysis in modern drug substance development, as well as the role of contract research, development and manufacturing organizations (CRDMOs) in meeting the evolving demands of modern small molecule synthesis.

BENEFITS OF BIOCATALYSIS

Enzymes, the catalysts evolved by nature, are capable of guiding chemical reactions with a level of precision that is difficult to match using conventional methods.¹ Their highly specific active sites confer exceptional control over regio-, chemo- and enantioselectivity, enabling reactions that might otherwise be challenging or inefficient.² Modern protein engineering has expanded this capability even further, producing enzymes customized for a growing variety of transformations. In drug substance synthesis, such precision can eliminate redundant purification steps, maintain strict stereochemical standards and condense what would normally be multiple stages into a single streamlined operation.² As a result, drug substance development becomes far more efficient and affordable than with traditional methods of small molecule synthesis.

Biocatalysis is also considered more environmentally friendly than chemical synthesis, helping drug developers to reach sustainability targets. This enzyme-driven chemistry is able to proceed under gentle, water-based conditions, avoiding the need for extreme temperatures and the hazards of harsh reagents.³ This gentler operating environment not only enhances worker safety and reduces energy requirements but also aligns with sustainable manufacturing practices by lowering solvent usage and removing the need for heavy metal catalysts.⁴ The resulting reduction in PMI represents both an environmental benefit and a tangible cost saving. For these reasons, biocatalysis is fast becoming a central strategy for efficient, economical and environmentally responsible drug substance development.

OVERCOMING STABILITY & PROCESS COMPATIBILITY CHALLENGES

The advantages of biocatalysis are clear, but its integration into drug substance manufacturing is far from straightforward without the right expertise. The ability of enzymes to function in aqueous environments feels like a benefit, however they also operate within very fine environmental margins, specifically evolved for nature – and not industrial processes.⁵ Industrial settings, however, often demand reaction conditions – such as organic solvents, high heat, or extreme acidity or alkalinity – that can diminish enzyme stability or halt activity altogether.⁵ In some cases, drug substances or their intermediates may also prove unstable or behave unpredictably under enzyme-friendly conditions, restricting the scope of possible transformations. These limitations become particularly problematic in complex, multi-step syntheses, where alternating between aqueous and non-aqueous stages can disrupt process flow. Without well-matched reaction conditions, manufacturers risk lower yields, inconsistent results or the need for intricate downstream purification. At larger scales, even slight deviations in pH, temperature or solubility can undermine process reliability and inflate production costs.

TAILORING BIOCATALYSTS FOR NON-NATURAL OR NOVEL REACTIONS

Another potential barrier to biocatalysis is that enzymes are not always suited for large-scale pharmaceutical production, particularly when dealing with synthetic substrates or entirely new reaction types. Engineering an enzyme to meet specific process needs – then fine-tuning traits like catalytic activity, thermal stability or binding specificity – typically involves repeated cycles of mutagenesis, screening and refinement, whether through directed evolution, rational design or integrated approaches.⁶ These optimization programs demand considerable technical infrastructure and capacity, which not all organizations possess. Without this investment, many developers revert to established synthetic chemistry routes, sacrificing the long-term process and sustainability benefits that biocatalysis could offer.

One of the most effective ways of avoiding this and accelerating the adoption of biocatalysis in drug development is to apply it where it has a clear edge over conventional chemistry. Natural products – and the small molecules derived from them – represent a prime example of where biocatalysis can be extremely beneficial. Many clinical candidates and approved drugs retain features of their natural counterparts. Their complexity can make chemical synthesis challenging and costly, but biocatalysis offers a way around these obstacles by streamlining synthetic routes, enhancing stereocontrol and enabling reactions to proceed under gentler, more environmentally friendly conditions – factors that together make large-scale manufacture far more practical.

Islatravir – a nucleoside analogue now in Phase 3 trials for HIV prevention and treatment – provides a compelling example of what biocatalysis can achieve. Instead of relying on lengthy chemical routes, its production uses a multi-enzyme cascade of engineered phosphorylases, kinases and oxidases to construct the chiral sugar and couple it to the nucleobase.⁷ This streamlined process not only cuts down the number of synthetic steps but also achieves high stereoselectivity while lowering the environmental burden. Similar innovations have opened the door to large-scale production of other natural product-derived substances, including artemisinin-based antimalarials generated in engineered yeast,⁸ paclitaxel analogues developed through targeted enzymatic modification of plant precursors,⁹ and erythromycin derivatives synthesized using glycosyltransferase-mediated sugar tailoring.¹⁰

MANAGING OFF-TARGET REACTIVITY

High selectivity is another celebrated advantage of biocatalysis, yet enzymes are not immune to unintended activity.¹¹ When a substrate contains multiple functional groups, there is a risk of catalyzing side reactions that reduce yield, complicate purification or introduce safety concerns. Even minor structural modifications to a substrate can alter reactivity or shift enzyme selectivity in unexpected ways. Identifying and mitigating these off-target effects early is essential to maintain process efficiency and product quality, particularly in complex or multi-step syntheses.

INCREASING ADOPTION OF BIOCATALYSIS

Cultural attitudes can also limit the adoption of the wider use of biocatalysis in drug substance development. Many process development teams – particularly in start-ups and small companies – are deeply rooted in well-established chemical synthesis methods. This reliance on a more familiar method that is widely accepted and works well enough reduces the drive to look for more efficient methods, particularly if establishing a new pathway requires time investment. For emerging companies, the pressure to move quickly with limited resources often reinforces chemical synthesis as the default, conservative approach. However, sticking with established chemistry can store up problems for later, such as processes with limited scalability, variable yields and increased development risks that might have been avoided with earlier adoption of biocatalytic strategies.

COMPREHENSIVE CRDMO CAPABILITIES

Many CRDMOs now offer biocatalysis as a platform service, combining enzyme discovery, optimization and process integration under one roof. Platform-based CRDMOs offer an invaluable blend of technical expertise and scalable infrastructure for companies seeking to integrate biocatalysis into drug substance development. These organizations bring together modular, end-to-end workflows designed to accelerate enzyme optimization and implementation. Their expertise spans the entire development cycle – from early feasibility studies that evaluate reaction performance and scale-up viability, through to host system engineering to maximize enzyme expression.¹² By combining computational protein design,¹³ high throughput screening¹⁴ and techniques such as directed evolution,¹⁵ CRDMOs can streamline the cycle from designs to tests, enabling tailored biocatalysts to be deployed earlier in the development process. This early adoption reduces project risk, improves process robustness and increases the likelihood of successful integration under real-world manufacturing pressures.

CRDMOs are also well-equipped to address common challenges such as enzyme instability, process incompatibilities and off-target reactivity. Predictive modelling tools, curated databases and advanced analytical platforms allow them to anticipate and identify unwanted side reactions before they compromise yields, safety or purification strategies. A broad screening approach means potential side products can be detected early, giving teams time to refine enzyme or process conditions proactively.

Importantly, these organizations are not only solving technical barriers but also helping companies overcome cultural reluctance to adopt new approaches. By delivering fully integrated solutions that embed biocatalysis directly into route design, CRDMOs make the transition less disruptive and more commercially viable. Validated workflows, enzyme expertise and early optimization strategies ensure drug substance developers gain greater confidence in adopting biocatalysis without jeopardizing timelines.

BIOCATALYSIS AS A CORNERSTONE OF FUTURE DRUG SUBSTANCE MANUFACTURING

Biocatalysis has become a powerful approach for complex small molecule synthesis, offering improved precision, sustainability and efficiency – particularly for stereochemically rich molecules, heterocyclic scaffolds and functionalized intermediates. Yet, its full potential will only be realized when the remaining scientific, operational and cultural challenges are addressed. Platform-based CRDMOs are driving this shift, bringing together advanced enzyme engineering, process integration and compliance expertise within a single framework. By bridging the gap between innovative science and industrial-scale implementation, they are helping to make biocatalysis not just a viable alternative, but a preferred strategy in modern drug substance manufacturing. As technology continues to advance and collaboration between stakeholders grows, biocatalysis is poised to become a cornerstone of greener, more efficient drug substance development.

REFERENCES

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ABOUT THE AUTHORS

Masha Kononov is Director of Business Development at Ingenza Ltd. She holds a Master’s degree in Biotechnology and has over 15 years of experience guiding strategic partnerships across the pharmaceutical and life sciences industries. Her work focuses on advancing platform technologies that support the efficient development of complex therapeutics.

Reuben Carr is Head of Chemical Biology at Ingenza Ltd. He has been instrumental in advancing the company’s proprietary bioprocess technologies since 2004, leading projects spanning biobased chemical production, small molecule API production, medical diagnostics and carbon capture. He is extremely passionate about chemical, life and biomedical sciences, and has a strong track record of delivering successful commercial partnerships and mentoring scientific teams.