Modular peptide-based reagent
AssigneeKimberly-Clark Worldwide, Inc.
InventorStephen Quirk
Life of this patent
Estimating the term…
Abstract
The invention provides stable peptide backbones into which one or interactive domains may be incorporated. Such interactive domains may be specific binding domains, inhibitor domains, linkers, labels, solid supports, reactive sites, catalytic sites, useful chemical entities, and reagents. Attachment or incorporation of an interactive domain into the peptide backbone generates a peptide-based reagent. The invention also provides methods for generating libraries of peptides that can be used as interactive domains
Claims41
A stable isolated peptide comprising an amino acid sequence with at least 90% identity to any one of SEQ ID NO:
- 2-6, 8-11 or 14.
A stable isolated peptide comprising any one of SEQ ID NO:
- 2-6, 8-11 or 14.
A stable isolated peptide comprising SEQ ID NO:
- 11 or 14.
An isolated nucleic acid encoding a stable peptide comprising an amino acid sequence with at least 90% identity to any one of SEQ ID NO:
- 2-6, 8-11 or 14.
An isolated nucleic acid encoding a stable peptide comprising amino acid sequence SEQ ID NO:
- 11 or 14.
A peptide-based reagent comprising a peptide backbone and an interactive domain, where the peptide backbone comprises an amino acid sequence with at least 90% identity to any one of SEQ ID NO:
- 2-6, 8-11 or 14.
A peptide-based reagent comprising a peptide backbone and an interactive domain, where the peptide backbone comprises any one of SEQ ID NO:
- 2-6, 8-11 or 14.
A peptide-based reagent comprising a peptide backbone and an interactive domain, where the peptide backbone comprises SEQ ID NO:
- 11 or 14.
A method comprising:
- (a) defining a search zone comprising a site of interaction on a target protein to which a peptide can interact;
- (b) defining a size for the peptide;
- (c) defining a class of amino acids for each position in the amino acid sequence of the peptide;
- (d) substituting each member of a defined class of amino acids into each position of the amino acid sequence of the peptide sequence to generate an output library file comprising a plurality of output peptide sequences;
- (e) communicating the output library file to a molecular docking program to fit each of the plurality of output peptide sequences to the search zone and to create a target protein-peptide sequence fit score;
- (f) ranking the plurality of output peptides sequences by target protein-peptide sequence fit score;
- and
- (g) displaying each of the plurality of output peptide sequences and its associated target protein-peptide sequence fit score;
- wherein a portion of the plurality of output peptide sequences can stably interact with the target protein.
A system for creating peptide sequences, comprising:
- (a) a processor;
- (b) a memory coupled to the processor;
- (c) a display couple to the processor;
- (d) a make peptide sequence component capable of executing on the processor to generate peptide sequences;
- (e) an output class component capable of executing on the processor to display each class of amino acid residues used by the make peptide sequence component;
- and
- (f) an output peptide sequence component capable of executing on the processor to display peptide sequences.
A machine-accessible medium having associated content capable of directing the machine to perform a method, the method comprising:
- (a) receiving a search zone comprising a plurality of coordinates for atoms in an target site to which a plurality of peptides can bind with varying affinities;
- (b) receiving a peptide length parameter comprising a number of amino acids;
- (c) receiving a defined class of amino acid structures to be analyzed for fitness at each position along the peptide length;
- (d) generating an output library file comprising a plurality of output peptide sequences containing each amino acid from each defined class of amino acid structures at each position along the peptide length;
- (e) sequentially translating and rotating each member of the class of amino acid structures at each position within a peptide relative to the search zone to sequentially create a peptide sequence with a target site-peptide sequence fit score;
- (f) ranking peptide sequences by target site-peptide sequence fit scores;
- and
- (g) displaying a selected percentage of the target site-peptide sequence fit scores with the associated peptide sequences.
Dependencies are inferred from the claim text.