SBIR-STTR Award

This Small Business Innovation Research Phase I project will develop an enabling technology for computer-directed high throughput screening of proteins for improved properties. By combining a fast computer screen with experimental methods, the capabilities of random library screening can be greatly extended. This technology will be tested on Bacillus circulans xylanase with the goal of improving its activity at high temperature and pH. Starting from the enzyme crystal structure, Xencor's proprietary protein design automation (PDA) technology will be used to computationally prescreen the possible sequences resulting from varying selected residue positions, thereby eliminating unfavorable sequences and thus enormously reducing the number to be screened experimentally. The result of the computer screen is an amino acid probability distribution for the selected residue positions. A method will be developed to transform these probabilities into a DNA library that will be synthesized and experimentally screened for improved enzymatic activity. The computational prescreening will allow screening of ~10^80 sequences compared to 10^10 to 10^15 with conventional in vitro evolution techniques. The proposed research will result in a generally applicable procedure that allows optimization of far more residue positions and results in the more efficient development of improved proteins by coupling rational and random methods.

This Small Business Innovation Research (SBIR) Phase II project focuses on the development of an enabling technology for computer- directed high-throughput screening of proteins with improved properties. Xencor's Protein Design Automation (PDA) predicts all the possible amino acid sequences that will fold into the three-dimensional structure of a protein. There should be molecules among those sequences that have the structure and function of the "parent "protein, together with additional novel properties such as increased thermo-stability or alkaline pH optima. In Phase I the company addressed this possibility using xylanase as a model protein. After targeting the active site of the enzyme for PDA re-design, the company found sequences that were more active than the wild-type protein and one that had a different pH profile. These results were achieved by testing only 260 of a possible 110,592 sequences. In Phase II the company will develop a high-throughput assay system that will allow testing the majority of the predicted sequences. The research will also improve electrostatic functions of the PDA algorithm, and then use this version of the program to re-design the entire xylanase molecule instead of just the active site, thereby finding mutations located away from the active site that effect the protein's characteristics. The PDA technology improves enzyme efficiency and expands the reactions and process conditions where they can be applied. Major markets include polymer manufacturers, value extraction from waste streams and food processing.