Fibronectin based scaffold proteins

Abstract

Fibronectin type III (10Fn3) binding domains having novel designs that are associated with reduced immunogenicity are provided. The application describes alternative 10Fn3 binding domains in which certain immunogenic regions are not modified when producing a binder in order to maintain recognition as a self antigen by the host organism. The application also describes 10Fn3 binding domains in which HLA anchor regions have been destroyed thereby reducing the immunogenic contribution of the adjoining region. Also provided are 10Fn3 domains having novel combinations of modified regions that can bind to a desired target with high affinity.

1 .- 512 . (canceled) 
     
     
         513 . A polypeptide comprising comprising a tenth fibronectin type 3 ( 10 Fn3) domain, wherein the  10 Fn3 domain comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 73-131, and wherein at least 50% of amino acids x are not the amino acid at the corresponding position in SEQ ID NO: 1 or 6. 
     
     
         514 . The polypeptide of  claim 513 , wherein the  10 Fn3 domain comprises an amino acid sequence selected from the group consisting of SEQ ID NOS: 76-87, 118-121 and 128-131. 
     
     
         515 . The polypeptide of  claim 513 , wherein each x amino acid is any amino acid except the amino acid at the corresponding position of SEQ ID NO: 1 or 6. 
     
     
         516 . The polypeptide of  claim 514 , wherein each x amino acid is any amino acid except the amino acid at the corresponding position of SEQ ID NO: 1 or 6. 
     
     
         517 . The polypeptide of  claim 513 , wherein the amino acid sequence of the  10 Fn3 domain that is located outside of the variable regions is at least 90% identical to the corresponding regions in SEQ ID NO: 1 or 6. 
     
     
         518 . The polypeptide of  claim 514 , wherein the amino acid sequence of the  10 Fn3 domain that is located outside of the variable regions is at least 90% identical to the corresponding regions in SEQ ID NO: 1 or 6. 
     
     
         519 . A library consisting of a plurality of polypeptides, wherein each of the polypeptides in the library comprises a  10 Fn3 domain comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 73-131, wherein at least 50% of amino acids x are not the amino acid at the corresponding position in SEQ ID NO: 1 or 6. 
     
     
         520 . The library of  claim 519 , wherein each x amino acid residue is any amino acid residue except the amino acid at the corresponding position in SEQ ID NO: 1 or 6. 
     
     
         521 . The library of  claim 519 , wherein the plurality of polypeptides in the library comprises at least 10 5  polypeptides each comprising a different  10 Fn3 amino acid sequence. 
     
     
         522 . The library of  claim 519 , wherein the  10 Fn3 domain of each polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 or 6. 
     
     
         523 . A method for identifying a polypeptide that binds to a target comprising screening the library of  claim 519  to identify a polypeptide that binds to the target. 
     
     
         524 . An isolated polypeptide identified by the method of  claim 523 . 
     
     
         525 . A nucleic acid encoding the polypeptide of  claim 513 . 
     
     
         526 . A nucleic acid encoding the polypeptide of  claim 524 . 
     
     
         527 . A vector comprising the nucleic acid of  claim 525 . 
     
     
         528 . A vector comprising the nucleic acid of  claim 526   
     
     
         529 . A host cell expressing the nucleic acid of  claim 513 . 
     
     
         530 . A host cell expressing the nucleic acid of  claim 527 .