NASA Technical Reports Server (NTRS) 20080005129: Streptavidin-binding peptides and uses thereof

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US006841359B2
United States Patent
(12) (io) Patent No.: US 6,841,359 B2
Szostak et al. (45) Date of Patent: Jan. 11,2005
(54) STREPTAVIDIN-BINDING PEPTIDES AND Katz et al., “Topochemical catalysis achieved by structure-
USES THEREOF based ligand design,” J. Biol. Chem. 270:31210-31218
(19 95).
(75) Inventors: Jack W. Szostak, Boston, MA (US); Katz et al., “In crystals of complexes of streptavidin with
David S. Wilson, Hayward, CA (US);
peptide ligands containing the HPQ sequence the pK, of the
Anthony D. Keefe, Cambridge, MA
peptide histidine is less that 3.0,” J. Biol. Chem.
(US) 272:13220-13228 (1997).
Assignee: The General Hospital Corporation, Katz et al., “Structural and mechanistic determinants of
Boston, MA (US) affinity and specificity of ligands discovered or engineered
by phage display,” Annu. Rev. Biophys. Biomol. Struct.
Notice: Subject to any disclaimer, the term of this 26: 27-45 (19 97).
patent is extended or adjusted under 35
Kay et al., “An M13 phage library displaying random
U.S.C. 154(b) by 67 days.
38-amino-acid peptides as a source of novel sequences with
affinity to selected targets,” Gene. 128:59-65 (1993).
Appl. No.: 10/004,381
Lam et al., “A new type of synthetic peptide library for
Filed: Oct. 31, 2001 identifying ligand-binding activity,” Nature 354:82-84
(19 9 1).
Prior Publication Data
Liu et al., “Optimized synthesis of RNA-protein fusions
US 200210155578 A1 Oct. 24, 2002
for in vitro protein selection,” Methods Enzymol.,
318:268-293 (2000).
Related U.S. Application Data
Provisional application No. 601244,541, filed on Oct. 31, McLafferty et al., “M13 bacteriophage displaying disulfide-
2000. constrained microproteins,” Gene 128:29-36 (1993).
McCafferty et al., “Phage antibodies: filamentous phage
Int. C1.7 ................................................. C12P 21/06
displaying antibody variable domains,” Nature 348:552-554
(19 90).
U.S. C1. ...................................................... 435/69.1
Ostergaard et al., “Novel avidin and streptavidin binding
Field of Search ......................... 435169.1; 5301300,
sequences found in synthetic peptide libraries,” Febs Letters
5301350; 51212
362:306-308 (1995).
(56) References Cited Roberts et al., “RNA-peptide fusions for the in vitro
selection of peptides and proteins,” Proc. Natl. Acad. Sci.
U.S. PATENT DOCUMENTS
94:12297-12302 (1997).
5,506,121 A 411996 Skerra et al.
Roberts, “Totally in vitro protein selection using mRNA-
5,821,047 A 1011998 Garrard et al.
protein fusions and ribosome display,” Cur% Opin. Chem.
6,103,493 A 812000 Skerra et al.
6,326,157 B1 * 1212001 Nolan et al. ................. 43517.1 Bioi. 3:268-273 (1999).
Schmidt et al., “The random peptide library-assisted engi-
FOREIGN PATENT DOCUMENTS
neering of a C-terminal affinity peptide, useful for the
wo WO 98131700 711998 detection and purification of a functional Ig Fv fragment,”
Protein Eng 6:109-122 (1993).
OTHER PUBLICATIONS
Schmidt et al., “Molecular interaction between thestrep-tag
Katz BA. Binding to protein targets of peptidic leads dis-
affinity peptide and its cognate target,” J. Mol. Biol.
covered by phage display: crystal structures of streptavid-
255:753-766 (1995).
in-bound linea and cyclic peptide ligands containing the
HPQ sequence. Biochemistry. 1995 Nov. Scott et al., “Searching for peptide ligands with an epitope
28;34(47):15421-9.* library,” Science 249:386-390 (1990).
Bayer et al., “Postsecretory modifications of streptavidin,”
Biochem. J. 259:369-376 (1989). (List continued on next page.)
Cho et al., “Constructing high complexity synthetic libraries
of long ORFs using in vitro selection,” J. Mol. Biol.
Primary Examinerxaren Cochrane Carlson
297:309-319 (2000).
Assistant ExaminerSheridan K Snedden
Clackson et al., “In vitro selection from protein and peptide
(74) Attorney, Agent, or Firmxlark & Elbing LLP
libraries,” TZBTECH. 12:1 73-184 (1994).
Devlin et al., “Random peptide libraries: Asource of specific (57) ABSTRACT
protein binding molecules,” Science 249:404-406 (1991).
Giebel et al., “Screening of cyclic peptide phage libraries The invention provides peptides with high affinity for
identifies ligands that bind streptavidin with high affinities,” streptavidin. These peptides may be expressed as part of
Biochemistry 34: 1543CL15435 (1995). fusion proteins to facilitate the detection, quantitation, and
Haeuptle et al., “Binding sites for lactogenic and somato- purification of proteins of interest.
genic hormones from rabbit mammary gland and liver,” J.
Biol. Chem. 258:305-314 (1983). 21 Claims, 22 Drawing Sheets
US 6,841,359 B2
Page 2
OTHER PUBLICATIONS Caparon et al., “Analysis of Novel Streptavidin-Binding
Peptides, Identified Using a Phage Display Library, Shows
Weber et al., “Crystal structure and ligand-binding studies
that Amino Acids External to a Perfectly Conserved Con-
of a screened peptide complexed with streptavidin,” Bio-
sensus Sequence and to the Presented Peptides Contribute to
chemistry, 31:9350-9354 (1992).
Binding,” Molecular Diversity 1:241-246 (1995).
Zang et al., “Tight-binding streptavidin ligands from a
Katz, “Streptavidin-Binding and -Dimerizing Ligands Dis-
peptide library,” Bioorg. Med. Chern. Lett. 8:2327-2332
covered by Phage Display, Topochemistry, and Structure-
(1998).
Based Design,” Biornolecular Engineering 16:57-65
Jack W. Szostak, “Evolution of Novel Proteins from Ran-
(19 99).
domSequence Libraries” 2000 (Abstract).
Wilson et al., “The Use of mRNA Display to Select
Szostak and Keefe, “ATP-Binding Proteins Selected from a
High-Affinity Protein-Binding Peptides,” PNAS
Random-Sequence Polypeptide Library,” The Protein Soci-
98:3750-3755 (2001).
ety, Fourteenth Symposium, Program and Abstracts, vol.
9:Suppl. 1, San Diego, CA, pp. 19 and 84, 2000. * cited by examiner
US. Patent
Jan. 11,2005 Sheet 1 of 22
US 6,841,359 B2
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US. Patent
Jan. 11,2005 Sheet 2 of 22 US 6,841,359 B2
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US. Patent
Jan. 11,2005 Sheet 3 of 22 US 6,841,359 B2
SELECTION ROUND
Fig. 2A
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US. Patent Jan. 11,2005 Sheet 4 of 22 US 6,841,359 B2
US. Patent
Jan. 11,2005 Sheet 5 of 22 US 6,841,359 B2
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US. Patent Jan. 11,2005 Sheet 6 of 22 US 6,841,359 B2
US. Patent
Jan. 11,2005 Sheet 7 of 22 US 6,841,359 B2
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