Enzyme Design

Arzeda’s groundbreaking technology enables engineering enzymes for virtually any reaction or application, far exceeding the limited supply and variety of enzymes found in nature. Our process harnesses the elegance and speed of computational power to rapidly design and evaluate new enzymes via computer simulation (in silico). We can generate a library of potential enzymes exceeding 1037 variations.

This vast library of virtual enzyme candidates greatly increases the chance of finding an ideal biocatalyst and eliminates the necessity of using traditional enzyme engineering approaches, which are limited in scale, cumbersome and laboratory-intensive. Arzeda’s approach represents a new paradigm in enzyme technology and opens up previously inaccessible product development opportunities. Arzeda’s enzyme design technology vertically integrates Archytas™, our proprietary computational platform, along with ensuing enzyme validation, resulting in a two-step process to obtain active enzymes ready for industry applications.

By using in silico assays for the majority of the computational protein design and screening process, we are able to efficiently search a limitless algorithm of synthetic variations for the enzyme design needed to address a specific solution. Only the best candidates are chosen for wet lab chemical synthesis and follow-up biological assays, which removes the need for wasting unnecessary laboratory resources, trial-and-error validation screens and high throughput assays that other technologies depend upon.

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Arzeda’s core team capitalized on several converging technological advances to develop our pioneering technology platform and approach. First, the continually decreasing cost of gene synthesis has greatly expanded the breadth of rational and computational enzyme engineering. Second, increased computer processing speeds and storage capacities have facilitated faster computation and more complex algorithms to be applied. Third, a DARPA grant funding Protein Design Processes was awarded to David Baker’s academic research group, allowing our founding team to begin their development of future Arzeda technology while at the University of Washington.

The technology has moved beyond the theoretical stage. Arzeda has successfully applied de novo enzyme design methodology to four important industrial reactions for which naturally occurring enzymes do not currently exist: the aldol reaction to form new carbon-carbon bonds, the Diels-Alder reaction to form cyclohexene rings, the Kemp elimination ring-opening reaction, and a recent array of enzymes for our partner DuPont Pioneer Hi-Bred. The designed enzymes behave like natural enzymes and can be improved by design and synthetic iterations to perform at industrial levels.

Arzeda has continued to expand its core technologies by continuously identifying the best natural enzyme scaffolds through our Arzeda Identification technology. Arzeda’s computational enzyme design technology is able to successfully deliver enzymes for virtually any industrial need or application.