IP Library › Patent Application 12456516

Patent Application

App. No. 12/456,516

Protein scaffolds and uses thereof

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Patent No.: US None
App. No.: 12/456,516

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Abstract

The present invention provides thrombospondin, thyroglobulin and trfoil/PD monomer domains and multimers comprising the monomer domains are provided. Methods, compositions, libraries and cells that express one or more library member, along with kits and integrated systems, are also included in the present invention.

Claims (112)

1 . A method for identifying a monomer domain that binds to a target molecule, the method comprising,

a) providing a library of non-naturally-occurring monomer domains, wherein the monomer domain is selected from the group consisting of: a thrombospondin monomer domain, a trefoil monomer domain, and a thyroglobulin monomer domain,

wherein the thrombospondin monomer domain comprises the following sequence:

(SEQ ID NO: 2)

(wxxWxx)C 1 sxtC 2 xxGxx(x)xRxrxC 3 xxxx(Pxx)xxxxxC 4 xxxx

xx(x)xxxC 5 (x)xxxxC 6 ;

the trefoil monomer domain comprises the following sequence: C 1 (xx)xxxpxxRxnC 2 gx(x)pxitxxxC 3 xxxgC 4 C 5 fdxxx(x)xxxpwC 6 f (SEQ ID NO:8); and

the thyroglobulin monomer domain comprises the following sequence:

(SEQ ID NO: 3)

C 1 xxxxxxxxxxxxxxx(xxxxxxxxxx)xxxxxxxyxPxC 2 xxxGxyxx

xQC 3 x(x)s(xxx)xxgxC 4 WC 5 Vdxx(x)GxxxxGxxxxxgxx(xx)x

C 6 ;

wherein “x” is any amino acid;

b) screening the library of monomer domains for affinity to a first target molecule; and

c) identifying at least one monomer domain that binds to at least one target molecule.

2 . The method of claim 1 , wherein the at least one monomer domain specifically binds to a target molecule not bound by a naturally-occurring monomer domain at least 90% identical to the non-naturally occurring monomer domain.

3 . The method of claim 1 , wherein

C 1 -C 5 , C 2 -C 6 and C 3 -C 4 of the thrombospondin monomer domain form disulfide bonds; and

C 1 -C 2 , C 3 -C 4 and C 5 -C 6 of the thyroglobulin monomer domain form disulfide bonds.

4 . The method of claim 1 , wherein

the thrombospondin monomer domain comprises the following sequence:

(WxxWxx)C 1 [Stnd][Vkaq][Tspl]C 2 xx[Gq]xx(x)x[Re]x[Rktvm]xC 3 [vldr]xxxx ([Pq]xx)xxxxxC 4 [ldae]xxxxxx(x)xxxC 5 (x)xxxxC 6 (SEQ ID NO:4), wherein C 1 -C 5 , C 2 -C 6 and C 3 -C 4 form disulfide bonds;

the trefoil monomer domain comprises the following sequence:

(SEQ ID NO: 9)

C 1 (xx)xxx[Pvac]xxRx[ndpm]C 2 [Gaiy][ypfst]([de]x)

[pskq]x[lvap][Tsa]xx[keqd]C 3 xx[krln][Gnk]C 4 C 5 [α]

[Dnrs][sdpnte]xx(x)xxx[pki][Weash]C 6 [Fy];

the thyroglobulin monomer domain comprises the following sequence: C 1 [qerl]xxxxxxxxxxxxxx(xxxxxxxxxx)xxxxxxx[αhp]xPxC 2 xxxGx[α]xx[vkrl]QC 3 x(x[sa]xxx)xx [gas]xC 4 [α]C 5 V[Dnα]xx(x)Gxxxx[φg]xxxxxgxx(xx)xC 6 (SEQ ID NO:5), wherein C 1 -C 2 , C 3 -C 4 and C 5 -C 6 form disulfide bonds; and

wherein α is selected from the group consisting of: w, y, f, and l; φ is selected from the group consisting of: d, e, and n; and “x” is selected from any amino acid.

5 . The method of claim 1 , wherein

the thrombospondin monomer domain comprises the following sequence:

(SEQ ID NO: 6)

C 1 [nst][acgiklqrstv][adenpqrst]C 2 [adetgs]xgx

[ikqrstv]x[aqrst]x[almrtv]xC 3 xxxxxxxxx(xxxxxxx)

C 4 xxxxxxxxx(xx)C 5 xxxxC 6 [[:]];

the trefoil monomer domain comprises the following sequence: C 1 ([dnps])[adiklnprstv][dfilmv][adenprst][adelprv][ehklnqrs][adegknsv][kqr][fiklqrtv][dnpqs]C 2 [agiy][flpsvy][dknpqs][adfghlp][aipv][st][aegkpqrs][adegkpqs][deiknqt]C 3 [adefknqrt][adegknqs][gn]C 4 C 5 [wyfh][deinrs][adgnpst][aefgqlrstw][giknsvmq]([afmprstv][degklns][afiqstv][iknpv]w) C 6 (SEQ ID NO:10); and

the thyroglobulin monomer domain comprises the following sequence:

(SEQ ID NO: 7)

C 1 [qerl]xxxxxxxxxxxxxx(xxxxxxxxxx)xxxxxxx[Yfhp]

xPxC 2 xxxGx[Yf]xx[vkrl]QC 3 x(x[sa]xxx)xx[Gsa]xC 4

[Wyf]C 5 V[Dnyfl]xx(x)Gxxxx[Gdne]xxxxxgxx(xx)xC 6 .

6 . The method of claim 1 , further comprising linking the identified monomer domains to a second monomer domain to form a library of multimers, each multimer comprising at least two monomer domains;

screening the library of multimers for the ability to bind to the first target molecule; and

identifying a multimer that binds to the first target molecule.

7 . The method of claim 6 , wherein each monomer domain of the selected multimer binds to the same target molecule.

8 . The method of claim 6 , wherein the selected multimer comprises three monomer domains.

9 .- 11 . (canceled)

12 . The method of claim 1 , further comprising,

screening the library of monomer domains for affinity to a second target molecule;

identifying a monomer domain that binds to a second target molecule;

linking at least one monomer domain with affinity for the first target molecule with at least one monomer domain with affinity for the second target molecule, thereby forming a multimer with affinity for the first and the second target molecule.

13 . The method of claim 1 , wherein the library of monomer domains is expressed as a phage display, ribosome display or cell surface display.

14 . The method of claim 1 , wherein the library of monomer domains is presented on a microarray.

15 . A protein, comprising a non-naturally occurring monomer domain that specifically binds to a target molecule

wherein the target molecule is not bound by a naturally-occurring monomer domain at least 90% identical to the non-naturally occurring monomer domain,

wherein the non-naturally occurring monomer domain is selected from the group consisting of a thrombospondin monomer domain, a trefoil monomer domain, and a thyroglobulin monomer domain.

16 .- 17 . (canceled)

18 . The protein of claim 15 , wherein the monomer domain is 30-100 amino acids in length.

19 . The protein of claim 15 ,

wherein the thrombospondin monomer domain comprises the following sequence:

(SEQ ID NO: 2)

(wxxWxx)C 1 sxtC 2 xxGxx(x)xRxrxC 3 xxxx(Pxx)xxxxxC 4 xxxx

xx(x)xxxC 5 (x)xxxxC 6 ;

the trefoil monomer domain comprises the following sequence: C 1 (xx)xxxpxxRxnC 2 gx(x)pxitxxxC 3 xxxgC 4 C 5 fdxxx(x)xxxpwC 6 f (SEQ ID NO:8); and

the thyroglobulin monomer domain comprises the following sequence:

(SEQ ID NO: 3)

C 1 xxxxxxxxxxxxxxx(xxxxxxxxxx)xxxxxxxyxPxC 2 xxxGxyxx

xQC 3 x(x)s(xxx)xxgxC 4 WC 5 Vdxx(x)GxxxxGxxxxxgxx(xx)x

C 6 ;

wherein “x” is any amino acid.

20 . The protein of claim 19 , wherein

C 1 -C 5 , C 2 -C 6 and C 3 -C 4 of the thrombospondin monomer domain form disulfide bonds; and

C 1 -C 2 , C 3 -C 4 and C 5 -C 6 of the thyroglobulin monomer domain form disulfide bonds.

21 . The protein of claim 15 ,

wherein the thrombospondin monomer domain comprises the following sequence:

(WxxWxx)C 1 [Stnd][Vkaq][Tspl]C 2 xx[Gq]xx(x)x[Re]x[Rktvm]xC 3 [vldr]xxxx ([Pq]xx)xxxxxC 4 [ldae]xxxxxx(x)xxxC 5 (x)xxxxC 6 (SEC) ID NO:4), wherein C 1 -C 5 , C 2 -C 6 and C 3 -C 4 form disulfide bonds;

the trefoil monomer domain comprises the following sequence:

(SEC ID NO: 9)

C 1 (xx)xxx[Pvae]xxRx[ndpm]C 2 [Gaiy][ypfst]([de]x)

[pskq]x[Ivap][Tsa]xx[kcqd]C 3 xx[krln][Gnk]C 4 C 5 [α]

[Dnrs][sdpnte]xx(x)xxx[pki][Wcash]C 6 [Fy];

wherein α is selected from the group consisting of: w, y, f, and l; φ is selected from the group consisting of: d, e, and n; and “x” is selected from any amino acid.

22 . The protein of claim 15 ,

wherein the thrombospondin monomer domain comprises the following sequence:

(SEQ ID NO: 6)

C 1 [nst][acgiklqrstv][adenpqrst]C 2 [adetgs]xgx

[ikqrstv]x[aqrst]x[almrtv]xC 3 xxxxxxxxx(xxxxxxx)

C 4 xxxxxxxxx(xx)C 5 xxxxC 6 [[:]];

the thyroglobulin monomer domain comprises the following sequence:

(SEQ ID NO: 7)

C 1 [qerl]xxxxxxxxxxxxxx(xxxxxxxxxx)xxxxxx[Yfhp]xP

xC 2 xxxGx[Yf]xx[vkrl]QC 3 x(x[sa]xxx)xx[Gsa]xC 4 [Wyf]

C 5 V[Dnyfl]xx(x)Gxxxx[Gdne]xxxxxgxx(xx)xC 6 .

23 . An isolated polynucleotide encoding the protein of claim 15 .

24 . A library of proteins comprising non-naturally-occurring monomer domains, wherein the monomer domain is selected from the group consisting of: a thrombospondin monomer domain, a trefoil monomer domain, and a thyroglobulin monomer domain,

wherein the thrombospondin monomer domain comprises the following sequence:

(SEQ ID NO: 2)

(wxxWxx)C 1 sxtC 2 xxGxx(x)xRxrxC 3 xxxx(Pxx)xxxxxC 4 xxxx

xx(x)xxxC 5 (x)xxxxC 6 ;

the trefoil monomer domain comprises the following sequence: C 1 (xx)xxxpxxRxnC 2 gx(x)pxitxxxC 3 xxxgC 4 C 5 fdxxx(x)xxxpwC 6 f (SEQ ID NO:8); and

the thyroglobulin monomer domain comprises the following sequence:

(SEQ ID NO: 3)

C 1 xxxxxxxxxxxxxxx(xxxxxxxxxx)xxxxxxxyxPxC 2 xxxGxyxx

xQC 3 x(x)s(xxx)xxgxC 4 WC 5 Vdxx(x)GxxxxGxxxxxgxx(xx)x

C 6 ;

wherein “x” is any amino acid.

25 . The library of claim 24 , wherein each monomer domain of the multimers is a non-naturally occurring monomer domain.

26 . The library of claim 24 , wherein the library comprises a plurality of multimers, wherein the multimers comprise at least two monomer domains linked by a linker.

27 . The library of claim 24 , wherein the library comprises at least 100 different proteins comprising different monomer domains.

28 . A library of polynucleotides encoding the library of proteins of claim 24 .