Universal fibronectin type III binding-domain libraries

Abstract

Walk-through mutagenesis and natural-variant combinatorial fibronectin Type III (FN3) polypeptide libraries are described, along with their method of construction and use. Also disclosed are a number of high binding affinity polypeptides selected by screening the libraries against a variety of selected antigens.

Description

[0001]This patent application claims priority to U.S. Provisional Patent Application No. 60 / 955,334 filed Aug. 10, 2007 and U.S. Provisional Patent Application No. 61 / 075,107 filed Jun. 24, 2008, both of which are incorporated herein by reference in their entirety.BACKGROUND OF THE INVENTION[0002]Scaffold based binding proteins are becoming legitimate alternatives to antibodies in their ability to bind specific ligand targets. These scaffold binding proteins share the quality of having a stable framework core that can tolerate multiple substitutions in the ligand binding regions. Some scaffold frameworks have immunoglobulin like protein domain architecture with loops extending from a beta sandwich core. A scaffold framework core can then be synthetically engineered from which a library of different sequence variants can be built upon. The sequence diversity is typically concentrated in the exterior surfaces of the proteins such as loop structures or other exterior surfaces that can ...

AI Technical Summary

Benefits of technology

[0236]WTM for FG / 11 using the nine pre-chosen WTM™ amino acids produces a library diversity of approximately 2×95 or 59049 (which includes WTM co-products). For comparative purposes, saturation mutagenesis of five FG / 11 “variable” positions with all twenty amino acids would be 205 or 3.2×106. Accordingly, performing saturation mutagenesis at all of the FG / 11 loop positions would create a library diversity of 209 or 5×1011 which is just at the limit of current library display and screening technology. However, it is important to note that is for an FN3 loop library with just one mutated loop, and if the other FN3 loops (e.g. BC / 11 and DE / 6) were diversified by saturation mutagenesis, the minimum FN3 library would then be 2026 or 6.7×1033. In contrast, the minimum and maximum FN3 library based on identifying the “variable” BC, DE and FG loop positions are 6.7×1033. This illustrates an advantage of the invention which, by contrast, allows for a smaller but more representative library to be constructed. Indeed, the methods of the invention provide for a manageable library for some loop positions in order to identify the first generation of binding molecules. Subsequent affinity maturation mutagenesis in the other CDR positions then optimizes those identified binding molecules.

Problems solved by technology

One potential problem in creating these synthetic libraries is the high frequency of unproductive variants leading therefore, to inefficient candidate screens.

These strategies are inherently stochastic and often require the construction of exceedingly large libraries to comprehensively explore sufficient sequence diversity.

Additionally, there is no way to enumerate the number, what type and where in the protein the mutations have occurred.

Furthermore, these random strategies create indiscriminate substitutions that cause protein architecture destabilization.

It has been shown that improvement in one characteristic, such as affinity optimization, usually leads to decreased thermal stability when compared to the original protein scaffold framework.

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