Volume 87 Issue 11 | pp. 14-16
Issue Date: March 16, 2009

Cover Stories: Pharma Outsourcing

Greatest Hits

Case Study #2: Merck advances process development by tuning up biocatalysts with Codexis
Department: Business
Optimum Enzymes
A Codexis researcher monitors a series of 1-kg capacity fermenters.
Credit: Codexis
Optimum Enzymes
A Codexis researcher monitors a series of 1-kg capacity fermenters.
Credit: Codexis

JUST AS AN ORCHESTRA needs instruments, Merck & Co.'s process development group needs synthesis tools. For several years, biocatalyst developer Codexis has focused on fine-tuning such tools. Together, Merck and Codexis believe they can make music through biocatalysis.

Although the companies each have expertise, like string and brass sections they see themselves as complementary, not overlapping. Codexis' strengths are in enzyme optimization and manufacturing, whereas Merck specializes in synthesis and process development. As partners they extend each other's reach.

Moreover, in coming months, when they present results of their process development work together, they expect to dispel any lingering doubts about the utility of biocatalysis for making pharmaceuticals.

Biocatalytic syntheses are appealing because they can be run in standard equipment under mild conditions with less solvent while giving high enantioselectivity and yield. But they have been plagued by what Merck and Codexis managers say are misconceptions about inconsistent catalyst quality, high cost, long development times, and an inability to adapt to different reaction conditions.

Customized enzymes can be extremely competitive with other catalytic approaches, contends Greg Hughes, an associate director in Merck's process research department. Typically, he notes, "a process that is more environmentally friendly also tends to be much more economically attractive." Codexis' enzymatic approach to catalysis meshes well with Merck's desire to develop environmentally benign syntheses, Hughes says. Merck's process research group strives to be "green by design" while implementing the best solutions across all stages of drug development and manufacturing, he explains.

"It's our philosophy that we should be able to do green chemistry well because we do chemistry well," Hughes says. "Our hope was that this collaboration would give rise to a number of biocatalysis-based approaches."

The partnership has its roots in 2006 discussions of Codexis' idea for putting its biocatalysts in process chemists' hands. Historically, says Gjalt Huisman, vice president for pharmaceuticals R&D at Codexis, the firm had kept its enzymes in-house and conducted the screening and optimization work for others. After Codexis launched its Codex biocatalyst panels in early 2007, Merck signed on as the first subscriber.

Each 96-well panel represents an enzyme class. Available chemistries include ene reductases, ketoreductases, transaminases, acylases, and halohydrin dehalogenases for making pharmaceutically relevant compounds such as chiral alcohols and chiral amines. "The ability to address different enantioselective transformations is very efficient," Hughes says.

To begin with, the enzymes in the panels have been engineered to be easy to manufacture at large scale, Huisman explains. They are also robust across a range of process conditions including solvent concentration, temperature, and pH.

Compatibility between a biocatalyst and a substrate molecule can be improved via directed evolution of the enzyme. After a substrate is screened against a panel for initial activity and selectivity, Codexis uses gene sequence and function information to transform hits into process-specific biocatalysts.

Following this approach, Merck began testing the panels and reporting results back to Codexis. Communication between the companies includes discussions of further optimization and scale-up. "In our experience over the past few years, the issues of turnaround and scale-up are really nonexistent," Hughes says. "We can turn around results very quickly and really be assured that 99 times out of 100 we are going to have success."

Success is tied in large part to the statistical protein sequence-activity relationship (ProSAR) technique that Codexis uses to optimize enzymes (Nat. Biotechnol. 2007, 25, 338). As a result, the speed at which enzymes can be developed and delivered in kilogram quantities has risen dramatically, Huisman says, often taking only two to three months from inquiry to commercial biocatalyst.

Work with Merck got off to an even faster start with the first panel, a ketoreductase collection. "Very quickly, the panel gave Merck an enzyme it could use to reduce a specific chloroketone and manufacture the desired alcohol," Huisman says. Compared with the biocatalytic process previously used to make this pharmaceutical intermediate, the enzyme operated at three times the substrate loading and at a 60-times-higher substrate-to-enzyme ratio, and it gave higher yield.

Through these and other results, the collaborators say, they have been learning a lot from each other. Weekly interactions help sustain what the companies call a highly collaborative and scientifically satisfying relationship. "Both sides really appreciate the efficiency with which this level of collaboration allows each of us to advance our programs," Hughes adds.

Although Merck's process chemists are no novices, the collaboration with Codexis is their first involving biocatalysts. "The use of biocatalyst-based process research at Merck has undergone a dramatic increase over the past few years that we have been involved in this partnership," Hughes says. "The barriers to using this technology have been significantly lowered."

Ketone Reduction
A Codexis biocatalyst improved a synthetic step for Merck.
Ketone Reduction
A Codexis biocatalyst improved a synthetic step for Merck.

ACCESS TO A VARIETY of readily available catalysts for screening is a key factor, Hughes says. Being able to then rapidly move from screening hits into larger scale execution with minimal development has helped increase the efficiency with which Merck can employ this chemistry.

"For large-scale ketone reductions, the use of ketoreductases has become the methodology of first choice within Merck," Hughes adds. Merck has reported that these enzymes can be screened and scaled up as rapidly as their chemocatalytic counterparts, and their environmental impact and cost of use at large scale is lower (Acc. Chem. Res. 2007, 40, 1412).

"Biocatalysis can exceed other chemical capabilities in terms of its flexibility and adaptability," Hughes says. "In addition to being able to solve any one particular problem effectively, you can also solve problems across a broad scope of substrates very easily.

"As a result of this collaboration and our history with biocatalysis, tremendous progress has been made in addressing some of the issues with earlier forms of this technology," Hughes adds. "We've come a really long way in unlocking the tremendous potential that enzymes offer in the development and production of pharmaceuticals."

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