UCLA chemists join with pharma to understand industrially important enzyme catalysts

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The UCLA groups of Houk and Tang have combined with the Codexis company, a biotech firm, to develop methods to understand the origins of enzyme selectivity.

How do these enzymes achieve their remarkable selectivity? Where other catalysts fail, these green biocatalysts can often deliver pharmaceuticals in high yield and purity.

The research was published this week in the Proceedings of the National Academy of Sciences of the USA (PNAS). 

Codexis, located in Redwood City, CA, specializes in enzyme catalysts. VP of Pharma Technology and Innovation at Codexis, Gjalt Huisman, said, “the UCLA chemists have done a fantastic job of figuring out the intricate details of how these enzymes produce a molecule or its mirror image.”  Codexis is a world leading company for directed evolution, which is the random alteration of protein sequence followed by screening to create catalysts that produce a desired product more effectively. 

Computational studies including quantum mechanics and molecular dynamics in Houk’s group, performed by Elizabeth Noey, Jiyong Park, Gonzalo Jimenez, and Silvia Osuna, explained the origins of enantioselectivity (production of one of two possible mirror images) observed in the reduction of highly similar and nearly symmetrical substrates by artificial ketoreductases (KREDs). A KREDs converts a ketones to an alcohols selectively, and are the most prominent enzymes in industrial pharmaceutical synthesis. The catalysts were generated by directed evolution by the efforts of Jack Liang, Xiyun Zhang (UCLA PhD), and Gjalt Huisman at Codexis. The enzymes’ effectiveness was evaluated and X-ray crystal structures were obtained by Yi Tang’s group, namely, by biochemists Carly Bond and Nidhi Tibrewal along with UCLA crystallographer, Duilio Cascio.

Mutants of a common yeast enzyme were used as KREDs to reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Novel methods based on quantum mechanical calculations and molecular dynamics (MD) simulations were developed to investigate the mechanism of reduction by the enzyme and origins of selectivity changes upon mutation. 

PNAS Houk Image

On overlay of results from MD simulations (A), showing open (green) and closed (blue) loop positions, and a plot of the selectivity vs. a protein structural change observed are shown above.

To learn more about Professor Houk’s research visit his group’s website.