4 bioprocess challenges we’ve helped our partners solve (with examples)

Over the years, our team has spent thousands of hours working alongside biomanufacturing R&D teams of all kinds.

That front-row seat has given us the opportunity to face the unexpected hurdles that can stall a pipeline: whether it's dealing with saturated patent landscapes, watching cofactor costs blow up a process model, or seeing low yields hit a wall right at the finish line. 

Having navigated these types of scenarios for over 8 years, we’ve learned what it takes to guide a project through every stage of development—from early enzyme discovery all the way to industrial execution. 

The challenges we’ve compiled below are a selection of some of those moments. We hope this peek into our experience gives you confidence that biocatalysis is a path well worth pursuing.

1. Finding novel enzymes unrestricted by large IP protection landscapes

A highly efficient process doesn't mean much if you can’t legally bring it to market.

Saturated market spaces often leave teams boxed in by third-party patents, forcing them to spend months searching for alternative biocatalysts that perform the exact same reaction without infringing on active claims.

This is a particularly common barrier in sectors like generics, where thin margins demand both low production costs and solid freedom to operate.

What we’re doubling down on

Overcoming intellectual property hurdles is easily one of the most frequent challenges we encounter. That’s why the use of structure-based enzyme discovery to map broad sequence spaces and identify patent-free enzyme alternatives has become an essential part of our process.

Candidate enzymes can be isolated with low sequence identity to protected proteins, but high catalytic efficiency for the target reaction. From there, these novel, cost-competitive variants can be engineered to fit directly into existing active production lines, keeping target metrics intact while securing complete freedom-to-operate.

Plus, custom-engineered enzymes do more than avoid active patents; they unlock distinct sequence-level differentiation. This enables teams to secure brand-new process claims (either through unique engineered variants or proven technical upgrades like boosted activity, selectivity, and stability), building a strong layer of proprietary IP around the manufacturing process. 

2. Upcycling waste into high-value industrial products via enzymatic cascades

Bridging the gap between discovering novel enzymes and deploying them at industrial scale is challenging, but essential for true waste revalorization.

Converting raw industrial side-streams into pure, commercial-grade chemicals requires navigating unpredictable feedstocks, enzyme instability, and incomplete conversions that stall scale-up.

Overcoming these hurdles has quickly become a top priority for forward-thinking companies aiming to minimize waste, hit circular economy targets, and build sustainable biomanufacturing processes.

What we’re doubling down on

Transforming complex industrial waste streams or bio-based feedstocks into high-value products is rarely a single-step job. Single conversions often yield partial breakdowns or unwanted side-products, making pure stream recovery economically unfeasible.

Tackling this challenge effectively often comes down to designing multi-enzyme cascades capable of running several chemical transformations simultaneously in a single pot.

The one-pot approach streamlines production by eliminating costly intermediate purification steps, lowering overall energy usage, and significantly boosting total product yield.

3. Reducing high cofactor costs

Oxidation and reduction reactions are incredible tools for biomanufacturing, but they come with a major catch: reliance on expensive nicotinamide cofactors (like NADH or NADPH). 

Using these costly cofactors in large amounts rapidly destroys process economics for bulk or high-volume products, rapidly turning the biocatalytic process unfeasible from an economic perspective.

What we’re doubling down on

Rather than trying to replace the primary biocatalyst, the key to scaling lies in engineering a dedicated, auxiliary cofactor regeneration system.

By designing and optimizing partner enzymes that continuously recycle the consumed cofactor in situ, raw cofactor consumption drops dramatically, turning an otherwise cost-prohibitive reaction into a commercially viable process.

4. Translating metagenomic dark matter into active enzymes

Millions of uncharacterized sequence fragments —often called metagenomic dark matter— remain completely untapped simply because standard tools cannot figure out what they do.

This leaves valuable, novel enzymes hidden right under our noses, buried inside massive datasets that traditional search methods simply can't identify without investing too many resources.

What we’re doubling down on

Over the years, our team has built advanced computational tools explicitly designed to navigate these vast metagenomic datasets. However, one of our biggest differentiators has been how we leverage sequence databases.

Public libraries offer a solid foundation (in fact, we often leverage them as the primary source in many of our campaigns), but when starting a project from scratch with zero baseline data, relying on them alone might lead to dead-ends or shared, non-exclusive IP.

For these circumstances, the sweet spot lies in using both public and private repositories to analyze structural models and identify active candidates directly from the metagenomic dataset.

This opens up entirely novel enzyme families while ensuring the resulting biocatalysts remain under full client exclusivity from day one.

Looking forward

These four challenges represent just a small window into the day-to-day problems we spend our time thinking about, solving, and constantly learning from. Every project leaves us with a deeper appreciation for just how complex natural systems really are—and how far computational tools have come in helping us understand them. 

We share these stories because we know biomanufacturing is rarely a smooth path.

But, as you can see, even the trickiest bottlenecks are solvable if you approach them with the right partner.

Talk with our team to get more clarity on how to effectively navigate the biomanufacturing space.