# Patent

## Title
Polynucleotides encoding extracellular-signal-regulated kinase (ERK) heteropolyligand polypeptides

## Abstract

The invention relates to kinase inhibitor ligands and polyligands. In particular, the invention relates to ligands and polyligands that modulate ERK activity. The ligands and polyligands are utilized as research tools or as therapeutics. The invention includes linkage of the ligands and polyligands to a cellular localization signal, epitope tag and/or a reporter. The invention also includes polynucleotides encoding the ligands and polyligands.

## Background
This application claims benefit of priority to provisional application 60/865,589 filed 13 Nov. 2006.


REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY VIA EFS-WEB
This application includes a “SequenceListing—ascii.txt,”141,754 bytes, created on Sep. 12, 2013, and submitted electronically via EFS-Web, which is hereby incorporated by reference in its entirety.
FIELD OF INVENTION
The invention relates to mammalian kinase ligands, substrates and modulators. In particular, the invention relates to polypeptides, polypeptide compositions and polynucleotides that encode polypeptides that are ligands, substrates, and/or modulators of ERK. The invention also relates to polyligands that are homopolyligands or heteropolyligands that modulate ERK activity. The invention also relates to ligands and polyligands tethered to a subcellular location.
This application has subject matter related to application Ser. No. 10/724,532 (now U.S. Pat. No. 7,071,295), 10/682,764 (US2004/0185556, PCT/US2004/013517, WO2005/040336), Ser. No. 11/233,246, and US20040572011P (WO2005116231). Each of these patents and applications is hereby incorporated by reference.
BACKGROUND OF THE INVENTION
The ability to modulate protein activities has long been the hallmark of small molecule drug discovery and development, and the success of this traditional therapeutic approach is unquestioned. However, the number and nature of small molecule drug targets are more limiting than would be ideal and have less target specificity and more off-target side effects that will likely make for significant commercial and regulatory challenges in the years ahead. A newer technology for inhibiting protein activity that has received acceptance is siRNA-mediated gene silencing. The mechanism for siRNA inhibition is post-transcriptional and pre-translational. It has the advantage of being relatively selective for target RNA sequences but, like small molecules, suffers from off-target side effects.
Kinases are enzymes that catalyze the addition of phosphate to a molecule. The addition of phosphate by a kinase is called phosphorylation. When the kinase substrate is a protein molecule, the amino acids commonly phosphorylated are serine, threonine and tyrosine. Phosphatases are enzymes that remove phosphate from a molecule. The removal of phosphate is called dephosphorylation. Kinases and phosphatases often represent competing forces within a cell to transmit, attenuate, or otherwise modulate cellular signals and cellular control mechanisms. Kinases and phosphatases have both overlapping and unique natural substrates. Cellular signals and control mechanisms, as regulated by kinases, phosphatases, and their natural substrates are a target of research tool design and drug design.
Mammalian mitogen-activated protein kinase (MAPK) and extracellular-signal-regulated kinase (ERK) are the same enzyme, herein referred to as ERK. ERK has two isoforms, both of which can phosphorylate serine and threonine residues in protein or peptide substrates. Use of the term ERK herein encompasses both ERK isoforms. Many cellular substrates of ERK have been identified. Furthermore, polypeptides have been used to examine ERK substrate specificity. While polypeptides and variants thereof have been studied as individual substrates or ligands, mixed ligands linked together as polyligands that modulate ERK activity have not been demonstrated before this invention. An aspect of the invention is to provide novel, modular, inhibitors of ERK activity by modifying one or more natural substrates by truncation and/or by amino acid substitution. A further aspect of the invention is the subcellular localization of an ERK inhibitor, ligand, or polyligand by linking to a subcellular localization signal. Examples of ERK substrates and/or regulators include those described in the following references: Adams, et al. 2000 J Neurochem 75:2277-87, Arnaud, et al. 2004 J Immunol 173:3962-71, Chung, et al. 1997 Mol Cell Biol 17:6508-16, Clark-Lewis, et al. 1991 J Biol Chem 266:15180-4, Eymin, et al. 2006 Cell Cycle 5:759-65, Fantz, et al. 2001 J Biol Chem 276:27256-65, Garcia, et al. 2002 Embo J 21:5151-63, Gille, et al. 1995 Embo J 14:951-62, Haycock, et al. 1992 Proc Natl Acad Sci USA 89:2365-9, Hedges, et al. 2000 Am J Physiol Cell Physiol 278:C718-26, Hindley, et al. 2002 J Cell Sci 115:1575-81, Howell, et al. 1991 Mol Cell Biol 11:568-72, Ishibe, et al. 2004 Mol Cell 16:257-67, Jacobs, et al. 1999 Genes Dev 13:163-75, Jacque, et al. 1998 Embo J 17:2607-18, Kelemen, et al. 2002 J Biol Chem 277:8741-8, Kolch 2000 Biochem J 351 Pt 2:289-305, Lefebvre, et al. 2002 J Cell Biol 157:603-13, Lin, et al. 1999 J Biol Chem 274:15971-4, Matallanas, et al. 2006 Mol Cell Biol 26:100-16, Matsuura, et al. 2005 Biochemistry 44:12546-53, Matter, et al. 2002 Nature 420:691-5, Missero, et al. 2000 Mol Cell Biol 20:2783-93, Morton, et al. 2004 FEBS Lett 572:177-83, Pandey, et al. 2005 Mol Cell Biol 25:10695-710, Sanghera, et al. 1990 FEBS Lett 273:223-6, Schaeffer, et al. 1999 Mol Cell Biol 19:2435-44, Songyang, et al. 1996 Mol Cell Biol 16:6486-93, Soond, et al. 2005 J Cell Sci 118:2371-80, Tenet, et al. 2003 Development 130:5169-77, Veeranna, et al. 1998 J Neurosci 18:4008-21, Xu, et al. 2001 Mol Cell Biol 21:2981-90, Zhang, et al. 2001 J Biol Chem 276:14572-80, and MAP Kinase Substrate Peptide Catalog #2-125 Lot #23369 (Upstate, Lake Placid, N.Y.).
Design and synthesis of polypeptide ligands that modulate calcium/calmodulin-dependent protein kinase and that localize to the cardiac sarco(endo)plasmic reticulum was performed by Ji et al. (J Biol Chem (2003) 278:25063-71). Ji et al. accomplished this by generating expression constructs that localized calcium/calmodulin-dependent protein kinase inhibitory polypeptide ligands to the sarcoplasmic reticulum by fusing a sarcoplasmic reticulum localization signal derived from phospholamban to a polypeptide ligand. See also U.S. Pat. No. 7,071,295.
DETAILED DESCRIPTION OF POLYPEPTIDE AND POLYNUCLEOTIDE SEQUENCES
SEQ ID NOS:1-8 are example polyligands and polynucleotides encoding them.
Specifically, the ERK polyligand of SEQ ID NO:1 is encoded by SEQ ID NO:2, SEQ ID NO:3, and by SEQ ID NO:4, wherein the codons have been optimized for mammalian expression. SEQ ID NO:3 and SEQ ID NO:4 include different alternatives of predetermined flanking restriction sites. Furthermore, SEQ ID NO:4 utilizes alternative codons for mammalian expression. A vector map of a vector containing SEQ ID NO:4 is shown in FIG. 12 (labeled ERK decoy). SEQ ID NO:1 is an embodiment of a polyligand of the structure A-S1-B-S2-C- S3-D-S4-E-S5-F, wherein A is SEQ ID NO:91, B is SEQ ID NO:97, C is SEQ ID NO:28, D is SEQ ID NO:29, E is SEQ ID NO:30, and F is SEQ ID NO:31, wherein Xaa is alanine, and wherein S1 is a spacer of the amino acid sequence AA, and S2 is a spacer of amino acid sequence AAAA (SEQ ID NO: 109), S3 is a spacer of the amino acid sequence GAGA (SEQ ID NO: 110), S4 is a spacer of the amino acid sequence GGGG (SEQ ID NO: 111), and S5 is a spacer of the amino acid sequence AGAG (SEQ ID NO: 112). A polyligand of structure A-S1-B-S2-C-S3-D-S4-E -S5-F is also called herein a heteropolyligand, shown generically in FIG. 4D.
SEQ ID NO:5 is an embodiment of a polyligand of the structure X-Y-S2-Z-S3-A-S4-B -S6-C-S5-D-S7-E-S8-F, wherein X is SEQ ID NO:32, Y is SEQ ID NO:98, Z is SEQ ID NO:33, A is SEQ ID NO:34, B is SEQ ID NO:35, C is SEQ ID NO:100, D is SEQ ID NO:36, E is SEQ ID NO:37, and F is SEQ ID NO:107, wherein Xaa is alanine, and wherein S2 is a spacer of amino acid sequence AAAA (SEQ ID NO: 109), S3 is a spacer of the amino acid sequence GAGA ( SEQ ID NO: 110), S4 is a spacer of the amino acid sequence GGGG (SEQ ID NO: 111, S6 is a spacer of the amino acid sequence AGPGAEF (SEQ ID NO: 113), S5 is a spacer of the amino acid sequence AGAG (SEQ ID NO: 112), S7 is a spacer of the amino acid sequence AAGG (SEQ ID NO: 114), and S8 is a spacer of the amino acid sequence GGAA (SEQ ID NO: 115). The ERK polyligand of SEQ ID NO:5 is encoded by SEQ ID NO:6, SEQ ID NO:7 and by SEQ ID NO:8, wherein the codons have been optimized for mammalian expression. SEQ ID NO:7 and SEQ ID NO:8 include different alternatives of predetermined flanking restriction sites. Furthermore, SEQ ID NO:8 utilizes alternative codons for mammalian expression. A polyligand of structure X-Y-S2-Z-S3-A-S4-B-S6-C-S5-D-S7-E-S8-F is also called herein a heteropolyligand, shown generically in FIG. 4E.
SEQ ID NOS:9-27 are full length ERK protein substrates. These sequences have the following public database accession numbers: NP004032, NP001871, NP149129, NP001781, 075956, NP005220, NP536739, CAI17445, AAF65618, NP001006666, NP035353, NP062651, Q07666, AAL68976, NP644805, NP003174, Q15648, NP033411, and AAA42258. Each of the sequences represented by these accession numbers is incorporated by reference herein. In SEQ ID NOS:9-27, the positions of the amino acid(s) phosphorylatable by ERK are represented by Xaa. In wild-type proteins, Xaa is serine or threonine. In the ligands of the invention, Xaa is any amino acid.
SEQ ID NOS:28-90 are peptide sequences including subsequences of SEQ ID NOS:9-27, which represent examples of kinase active site blocker peptide ligand sequences where the location of the ERK phosphorylatable serine or threonine in the natural polypeptide is designated as Xaa.
SEQ ID NOS:91-108 are polypeptide inhibitors of ERK (see FIG. 15). Specifically, SEQ ID NOS:91-96 are ERK activation site blockers, and SEQ ID NOS:97-108 are ERK docking site blockers.
SEQ ID NOS:28-108 represent examples of monomeric polypeptide ligand sequences.
Amino acid sequences containing Xaa encompass polypeptides where Xaa is any amino acid.
DETAILED DESCRIPTION OF DRAWINGS
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
FIGS. 1A-1C show examples of homopolymeric ligands without spacers.
FIGS. 2A-2C show examples of homopolymeric ligands with spacers.
FIGS. 3A-3E show examples of heteropolymeric ligands without spacers.
FIGS. 4A-4F show examples of heteropolymeric ligands with spacers. In FIG. 4E, the abbreviation, S, stands for SPACER.
FIGS. 5A-5G show examples of ligands and polymeric ligands linked to an optional epitope tag.
FIGS. 6A-6G show examples of ligands and polymeric ligands linked to an optional reporter.
FIGS. 7A-7G show examples of ligands and polymeric ligands linked to an optional localization signal.
FIGS. 8A-8G show examples of ligands and polymeric ligands linked to an optional localization signal and an optional epitope tag.
FIGS. 9A-9G show examples of gene constructs where ligands and polyligands are linked to an optional localization signal, an optional epitope tag, and an optional reporter.
FIGS. 10A-10D show examples of vectors containing ligand gene constructs.
FIG. 11 shows an example of a sequential cloning process useful for combinatorial synthesis of polyligands.
FIG. 12 shows a diagram of a vector for cell transformation.
FIG. 13 shows Cos7 cells transformed with the vector depicted in FIG. 12, wherein the vector includes SEQ ID NO:4 which encodes the ERK polyligand of SEQ ID NO:1. This figure demonstrates endoplasmic reticulum (ER) localization of an ERK polyligand: Cos7 cells were transfected with vector containing an ER localization signal, a c-Myc epitope tag, and the ERK polyligand of SEQ ID NO:1 (ERK decoy). Panels A and B depict Cos7 cells transfected with the ERK decoy while Panel C depicts a Cos7 cell transfected with a localization signal control vector lacking an ERK polyligand. The cells in each panel were treated with a stain for the ER-resident protein calreticulin (red) as well as anti-c-Myc antibody staining specific to the c-Myc epitope tag (green). Panels A, B and C show concentrated protein expression to the endoplasmic reticulum as evidenced by the co-localization between both the ERK decoy and localization control with the ER-resident protein calreticulin (yellow).
FIG. 14 shows localized inhibition of ERK-mediated myelin basic protein phosphorylation by the ERK polyligand of SEQ ID NO:1 (decoy). A constitutively-active form of the RasV 12 protein, a known activator of MAPK signaling pathways, was used to activate ERK kinase in defined regions of Cos7 cells. Several fusion proteins as described by Matallanas et al. Mol Cell Biol. 2006 January; 26(1):100-116 (hereby incorporated by reference), were used to activate ERK kinase in specific subcellular compartments. The constitutively-active RasV12 protein promoted cell-wide activation of ERK. The Lck-RasV 12 fusion protein activated ERK-protein associated with lipid rafts in or near the plasma membrane. The M1-RasV12 fusion protein activated ERK in the endoplasmic reticulum. Lane 1: control. Lane 2: ERK activity in cells expressing active Lck-RasV12 fusion protein. Lane 3: ERK activity in cells co-expressing active Lck-RasV12 fusion protein, and ERK decoy protein (ER localization signal, a c-Myc epitope tag, and the ERK polyligand of SEQ ID NO:1). Lane 4: ERK activity in cells co-expressing active Lck-RasV 12 fusion protein, and CAT fragment-containing ER localization control protein. Lane 5: ERK activity in cells expressing active M1-RasV12 fusion protein. Lane 6: ERK activity in cells co-expressing active M1-RasV12 fusion protein, and ERK decoy protein. Lane 7: ERK activity in cells co-expressing active M1-RasV12 fusion protein, and CAT fragment-containing ER localization control protein. Lane 8: ERK activity cells expressing active RasV12 protein. Lane 9: ERK activity in cells co-expressing active RasV12 fusion protein, and ERK decoy protein. Lane 10: ERK activity in cells co-expressing active RasV12 protein, and CAT fragment-containing ER localization control protein. This figure represents compartmentalized ERK activity in the plasma membrane (Lanes 2-4), in the endoplasmic reticulum (Lanes 5-7), and cell wide (Lanes 8-10) in Cos-7 cells. The bands on the gel represent varying phosphorylation states of ERK substrate, myelin basic protein (MBP); darker bands represent higher levels of ERK activity. When SEQ ID NO:1 was added to cells with ER-active ERK, ERK activity in the endoplasmic reticulum was reduced by approximately 60%. Again, Lane 1 is the control. Lanes 2-4 show activated ERK at the plasma membrane. Lanes 5-7 show activated ERK in the ER. Lanes 8-10 show activated ERK in the entire cell. Lanes 2, 5, & 8 show normal ERK activity. Lanes 3, 6, & 9 show ERK activity with co-expressed SEQ ID NO:1 fusion protein. Lanes 4, 7, & 10 show ERK activity with co-expressed control.
FIG. 15 shows a diagram of the ERK interaction sites of the different categories of ERK monomeric ligands including active site blockers, docking site blockers, and activation site blockers.
FIG. 16 shows nuclear localization of SEQ ID NO:1 fused to a nuclear localization signal and c-Myc epitope tag. Location was detected by immunostaining for c-Myc (green).
FIG. 17 shows cytoplasmic localization of SEQ ID NO:1 fused to a nuclear-exclusion localization signal and c-Myc epitope tag. Location was detected by immunostaining for c-Myc (green).
FIG. 18 shows inhibition of cell proliferation using ERK polyligands of SEQ ID NO:1 and SEQ ID NO:5 as compared to siRNA and a small molecule inhibitor. G418-resistant colony formation was assayed in NIH3T3 cells using siRNA specific for ERK1 or ERK2 isoforms; a small molecule inhibitor; and pancellular (no localization signal) polyligands of SEQ ID NO:1 and SEQ ID NO:5. G418-resistant colony formation was assayed in NIH3T3 cells transfected with vector (C) (1 μg) plus: siRNA oligonucleotides for ERK isoform 1 (Si1) or ERK isoform 2 (Si2) (25 ng); or vectors encoding for SEQ ID NO:1 (Dy1) or SEQ ID NO:5 (Dy2) (1 μg); or treated with the MEK inhibitor UO126 (1 μM). Colonies were stained and counted after 15 days in culture.
FIG. 19 shows inhibition of cell proliferation using localized ERK polyligand SEQ ID NO:1 fused to different localization signals. G418-resistant colony formation was assayed in NIH3T3 cells using pancellular SEQ ID NO:1 and SEQ ID NO:5, or SEQ ID NO:1 targeted to either the cytoplasm (NXP, nuclear exclusion), nucleus (NLS), plasma membrane (PLA), or endoplasmic reticulum (ER). G418-resistant colony formation was assayed in NIH3T3 cells transfected with vector (C) (1 μg) plus constructs (1 μg each) encoding for SEQ ID NO:1 (Dy1), SEQ ID NO:5, (Dy2) or SEQ ID NO:1 targeted to: cytoplasm (NXP), nucleus (NLS), plasma membrane (PLA), and endoplasmic reticulum (ER). Colonies were stained and counted after 15 days in culture.
FIG. 20 shows inhibition of cell transformation with pancellular SEQ ID NO:1 (Dy1), pancellular SEQ ID NO:5 (Dy2), and ER-localized SEQ ID NO:1 (ER1), and plasma membrane-localized SEQ ID NO:1 (PLA1) as compared to siRNA against ERK isoform 2 (Si2). Transformed foci formation was assayed in NIH3T3 cells transfected with H-ras V12 or v-Src (0.25 ng) plus constructs (1 μg each).
BRIEF DESCRIPTION OF THE INVENTION
The invention relates to polypeptide ligands and polyligands for ERK. Various embodiments of the ERK ligands and polyligands are represented in SEQ ID NOS:1-108. More specifically, the invention relates to ligands, homopolyligands, and heteropolyligands that comprise any one or more of SEQ ID NOS:28-108. Additionally, the invention relates to ligands and polyligands comprising one or more subsequences of SEQ ID NOS:9-27 or any portion thereof. Furthermore, the invention relates to polyligands with at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% sequence identity to a polyligand comprising one or more of SEQ ID NOS:28-108 or any portion thereof. Furthermore, the invention relates to polyligands with at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% sequence identity to a polyligand comprising one or more subsequences of SEQ ID NOS:9-27.
Polyligands, which can be homopolyligands or heteropolyligands, are chimeric ligands composed of two or more monomeric polypeptide ligands. An example of a monomeric ligand is the polypeptide represented by SEQ ID NO:38, wherein Xaa is any amino acid. SEQ ID NO:38 is a selected subsequence of wild-type full length SEQ ID NO:9, wherein the amino acid corresponding to Xaa in the wild-type sequence is a serine or threonine phosphorylatable by ERK. An example of a homopolyligand is a polypeptide comprising a dimer or multimer of SEQ ID NO:38, wherein Xaa is any amino acid. An example of a heteropolyligand is a polypeptide comprising SEQ ID NO:28 and one or more of SEQ ID NOS:29-108, wherein Xaa is any amino acid. There are numerous ways to combine SEQ ID NOS:28-108 into homopolymeric or heteropolymeric ligands. Furthermore, there are numerous ways to combine additional subsequences of SEQ ID NOS:9-27 with each other and with SEQ ID NOS:28-108 to make polymeric ligands.
The polyligands of the invention optionally comprise spacer amino acids before, after, or between monomers. SEQ ID NO:1 is an embodiment of a polyligand of the structure A-S1-B-S2-C-S3-D-S4-E-S5-F, wherein A is SEQ ID NO:91, B is SEQ ID NO:97, C is SEQ ID NO:28, D is SEQ ID NO:29, E is SEQ ID NO:30, and F is SEQ ID NO:31, wherein Xaa is alanine, and wherein S1, S2, S3, S4 and S5 are spacers. This invention intends to capture all combinations of homopolyligands and heteropolyligands without limitation to the examples given above or below. In this description, use of the term “ligand(s)” encompasses monomeric ligands, polymeric ligands, homopolymeric ligands and/or heteropolymeric ligands.
Monomeric ligands can be categorized into types (FIG. 15). One type of monomeric ligand is a polypeptide where at least a portion of the polypeptide is capable of being recognized by ERK as a substrate or pseudosubstrate (active site blocker). The portion of the polypeptide capable of recognition is termed the recognition motif. In the present invention, recognition motifs can be natural or synthetic. Examples of recognition motifs are well known in the art and include, but are not limited to, naturally occurring ERK substrates and pseudosubstrate motifs (SEQ ID NOS:28-90 and subsequences of SEQ ID NOS:9-27 containing a recognition motif). Another type of monomeric ligand is a polypeptide where at least a portion of the polypeptide is capable of associating with ERK at a substrate or pseudosubstrate docking site (docking site blocker). A docking site type of monomeric ligand prevents ERK substrate phosphorylation by interfering with substrate association and alignment (SEQ ID NOS:97-108). Yet another type of monomeric ligand is a polypeptide where at least a portion of the polypeptide is capable of associating with ERK at ERK's activation site (SEQ ID NOS: 91-96), thereby blocking ERK activation (activation site blocker), thereby preventing ERK from phosphorylating a substrate.
A polymeric ligand comprises two or more monomeric ligands linked together.
A homopolymeric ligand is a polymeric ligand where each of the monomeric ligands is identical in amino acid sequence, except that a phosphorylatable residue may be substituted or modified in one or more of the monomeric ligands.
A heteropolymeric ligand is a polymeric ligand where some of the monomeric ligands do not have an identical amino acid sequence.
The ligands of the invention are optionally linked to additional molecules or amino acids that provide an epitope tag, a reporter, and/or a cellular localization signal. The cellular localization signal targets the ligands to a region of a cell. The epitope tag and/or reporter and/or localization signal may be the same molecule. The epitope tag and/or reporter and/or localization signal may also be different molecules.
The invention also encompasses polynucleotides comprising a nucleotide sequence encoding ligands, homopolyligands, and heteropolyligands. The nucleic acids of the invention are optionally linked to additional nucleotide sequences encoding polypeptides with additional features, such as an epitope tag, a reporter, and/or a cellular localization signal. The polynucleotides are optionally flanked by nucleotide sequences comprising restriction endonuclease sites and other nucleotides needed for restriction endonuclese activity. The flanking sequences optionally provide unique cloning sites within a vector and optionally provide directionality of subsequence cloning. Further, the nucleic acids of the invention are optionally incorporated into vector polynucleotides. The ligands, polyligands, and polynucleotides of this invention have utility as research tools and/or therapeutics.
Terms used in the specification and claims are intended to have meanings consistent with that known in the art. For example, as used herein, G418 is an aminoglycoside antibiotic also known as Geneticin. Resistance to G418 is conferred by the neo gene. HEK293 cells are human embryonic kidney 293 cell line. H-RasV12 is a constitutively active mutant form of Ras. NIH3T3 is a mouse fibroblast cell line. Raf stand for Ras-activated factor. Ras is a small GTPase or G protein. RNA stands for ribonucleic acid. SiRNA stands for small interfering RNA. Transfection is the introduction of foreign material (such as DNA) into eukaryotic cells. Transformation is a process of tumorigenesis whereby normal cells become cancerous and possess phenotypes including but not limited to excessive growth, plasticity, chromosome abnormalities, foci formation, cell cycle abnormalities, among others. V-Src is a tyrosine kinase encoded by the viral oncogene isolated from Rous sarcoma virus.


DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to ligands and polyligands that are ERK modulators. Various embodiments of ligands and polyligands are represented in SEQ ID NOS:1-108. Polyligands are chimeric ligands comprising two or more monomeric polypeptide ligands. An example of a monomeric ligand is the polypeptide represented by SEQ ID NO:43, wherein Xaa is any amino acid. SEQ ID NO:43 is a selected subsequence of wild-type full length SEQ ID NO:11, wherein the amino acid corresponding to Xaa in the wild-type sequence is a serine or threonine phosphorylatable by ERK. Another example of a monomeric ligand is the polypeptide represented by SEQ ID NO:99. Another example of a monomeric ligand is the polypeptide represented by SEQ ID NO:94. Each of SEQ ID NOS:28-108 represents an individual polypeptide ligand in monomeric form, wherein Xaa is any amino acid. SEQ ID NOS:28-90 are selected examples of subsequences of SEQ ID NOS:9-27, however, other subsequences of SEQ ID NOS:9-27 containing a recognition motif may also be utilized as monomeric ligands. Monomeric ligand subsequences of SEQ ID NOS:9-27 may be wild-type subsequences. Additionally, monomeric ligand subsequences of SEQ ID NOS:9-27 may have the ERK phosphorylatable amino acids replaced by other amino acids. Furthermore, monomeric ligands and polyligands may have at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to a ligand comprising an amino acid sequence in one or more of SEQ ID NOS:28-108. Furthermore, monomeric ligands and polyligands may have at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% sequence identity to a subsequence of SEQ ID NOS:9-27.
An example of a homopolyligand is a polypeptide comprising a dimer or multimer of SEQ ID NO:86, wherein Xaa is any amino acid. Another example of a homopolyligand is a polypeptide comprising a dimer or multimer of SEQ ID NO:95. Another example of a homopolyligand is a polypeptide comprising a dimer or multimer of SEQ ID NO:106.
An example of a heteropolyligand is a polypeptide comprising SEQ ID NO:108 and one or more of SEQ ID NOS:28-107, wherein Xaa is any amino acid. There are numerous ways to combine SEQ ID NOS:28-108 into homopolymeric or heteropolymeric ligands. Furthermore, there are numerous ways to combine additional subsequences of SEQ ID NOS:9-27 with each other and with SEQ ID NOS:28-108 to make polymeric ligands.
Polyligands may comprise any two or more of SEQ ID NOS:28-108, wherein Xaa is any amino acid. A dimer or multimer of SEQ ID NO:91 is an example of a homopolyligand. An example of a heteropolyligand is a polypeptide comprising SEQ ID NO:28 and one or more of SEQ ID NOS:29-108. There are numerous ways to combine SEQ ID NOS:28-108 into homopolymeric or heteropolymeric ligands. SEQ ID NOS:28-90 are selected examples of subsequences of SEQ ID NOS:9-27, however, additional subsequences, wild-type or mutated, may be utilized to form polyligands. The instant invention is directed to all possible combinations of homopolyligands and heteropolyligands without limitation.
SEQ ID NOS:9-27 show proteins that contain at least one serine or threonine residue phosphorylatable by ERK, the positions of which are represented by Xaa. SEQ ID NOS:28-90 are subsequences of SEQ ID NOS:9-27 where, again, the locations of the ERK phosphorylatable residues are represented by Xaa. In nature, Xaa is, generally speaking, serine or threonine. In one embodiment of the instant invention, Xaa can be any amino acid. Ligands where Xaa is serine or threonine can be used as part of a polyligand, however in one embodiment, at least one phosphorylatable serine or threonine is replaced with another amino acid, such as one of the naturally occurring amino acids including, alanine, aspartate, asparagine, cysteine, glutamate, glutamine, phenylalanine, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, arginine, valine, tryptophan, or tyrosine. The Xaa may also be a non-naturally occurring amino acid. In another embodiment, the ERK phosphorylatable serine(s) or threonine(s) are replaced by alanine. The ligands and polyligands of the invention are designed to modulate the endogenous effects of one or more isoforms of ERK.
In general, ligand monomers based on natural ERK substrates are built by isolating a putative ERK phosphorylation recognition motif in a ERK substrate. Sometimes it is desirable to modify the phosphorylatable residue to an amino acid other than serine or threonine. Additional monomers include the ERK recognition motif as well as amino acids adjacent and contiguous on either side of the ERK recognition motif. Monomeric ligands may therefore be any length provided the monomer includes the ERK recognition motif. For example, the monomer may comprise an ERK recognition motif and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30-100 or more amino acids adjacent to the recognition motif.
For example, in one embodiment, the invention comprises an inhibitor of ERK comprising at least one copy of a peptide selected from the group consisting of:
a) a peptide at least 80% identical to a peptide comprising amino acid residues corresponding to amino acid residues 407-415 of SEQ ID NO:9, wherein the amino acid residue corresponding to amino acid residue 412 of SEQ ID NO:9 is an amino acid residue other than serine or threonine;

    b) a peptide at least 80% identical to a peptide comprising amino acid residues corresponding to amino acid residues 403-416 of SEQ ID NO:9, wherein the amino acid residue corresponding to amino acid residue 412 of SEQ ID NO:9 is an amino acid residue other than serine or threonine;
    c) a peptide at least 80% identical to a peptide comprising amino acid residues corresponding to amino acid residues 400-417 of SEQ ID NO:9, wherein the amino acid residue corresponding to amino acid residue 412 of SEQ ID NO:9 is an amino acid residue other than serine or threonine; and
    d) a peptide at least 80% identical to a peptide comprising amino acid residues corresponding to amino acid residues 399-418 of SEQ ID NO:9, wherein the amino acid residue corresponding to amino acid residue 412 of SEQ ID NO:9 is an amino acid residue other than serine or threonine.


As used herein, the terms “correspond(s) to” and “corresponding to,” as they relate to sequence alignment, are intended to mean enumerated positions within a reference protein, e.g., CDC25c (SEQ ID NO:12), and those positions that align with the positions on the reference protein. Thus, when the amino acid sequence of a subject peptide is aligned with the amino acid sequence of a reference peptide, e.g., SEQ ID NO:12, the amino acids in the subject peptide sequence that “correspond to” certain enumerated positions of the reference peptide sequence are those that align with these positions of the reference peptide sequence, but are not necessarily in these exact numerical positions of the reference sequence. Methods for aligning sequences for determining corresponding amino acids between sequences are described below.
Additional embodiments of the invention include monomers (as described above) based on any putative or real substrate for ERK, such as substrates identified by SEQ ID NOS:9-27. Furthermore, if the substrate has more than one recognition motif, then more than one monomer may be identified therein.
Further embodiments of the invention include monomers based on ERK inhibitors, regulators, or binding partners, such as those identified by SEQ ID NOS:91-108 (ERK activation site blockers and ERK substrate docking site blockers) and subsequences thereof.
Another embodiment of the invention is a nucleic acid molecule comprising a polynucleotide sequence encoding at least one copy of a ligand peptide.
Another embodiment of the invention is a nucleic acid molecule wherein the polynucleotide sequence encodes one or more copies of one or more peptide ligands.
Another embodiment of the invention is a nucleic acid molecule wherein the polynucleotide sequence encodes at least a number of copies of the peptide selected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9 or 10.
Another embodiment of the invention is a vector comprising a nucleic acid molecule encoding at least one copy of a ligand or polyligand.
Another embodiment of the invention is a recombinant host cell comprising a vector comprising a nucleic acid molecule encoding at least one copy of a ligand or polyligand.
Another embodiment of the invention is a method of inhibiting ERK in a cell comprising transfecting a vector comprising a nucleic acid molecule encoding at least one copy of a ligand or polyligand into a host cell and culturing the transfected host cell under conditions suitable to produce at least one copy of the ligand or polyligand.
The invention also relates to modified inhibitors that are at least about 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a reference inhibitor. A “modified inhibitor” is used to mean a peptide that can be created by addition, deletion or substitution of one or more amino acids in the primary structure (amino acid sequence) of a inhibitor protein or polypeptide. A “modified recognition motif” is a naturally occurring ERK recognition motif that has been modified by addition, deletion, or substitution of one or more amino acids in the primary structure (amino acid sequence) of the motif. For example, a modified ERK recognition motif may be a motif where the phosphorylatable amino acid has been modified to a non-phosphorylatable amino acid. The terms “protein” and “polypeptide” are used interchangeably herein. The reference inhibitor is not necessarily a wild-type protein or a portion thereof. Thus, the reference inhibitor may be a protein or peptide whose sequence was previously modified over a wild-type protein. The reference inhibitor may or may not be the wild-type protein from a particular organism.
A polypeptide having an amino acid sequence at least, for example, about 95% “identical” to a reference an amino acid sequence is understood to mean that the amino acid sequence of the polypeptide is identical to the reference sequence except that the amino acid sequence may include up to about five modifications per each 100 amino acids of the reference amino acid sequence encoding the reference peptide. In other words, to obtain a peptide having an amino acid sequence at least about 95% identical to a reference amino acid sequence, up to about 5% of the amino acid residues of the reference sequence may be deleted or substituted with another amino acid or a number of amino acids up to about 5% of the total amino acids in the reference sequence may be inserted into the reference sequence. These modifications of the reference sequence may occur at the N-terminus or C-terminus positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among amino acids in the reference sequence or in one or more contiguous groups within the reference sequence.
As used herein, “identity” is a measure of the identity of nucleotide sequences or amino acid sequences compared to a reference nucleotide or amino acid sequence. In general, the sequences are aligned so that the highest order match is obtained. “Identity” per se has an art-recognized meaning and can be calculated using published techniques. (See, e.g., Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York (1988); Biocomputing: Informatics And Genome Projects, Smith, D. W., ed., Academic Press, New York (1993); Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey (1994); von Heinje, G., Sequence Analysis In Molecular Biology, Academic Press (1987); and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York (1991)). While there exist several methods to measure identity between two polynucleotide or polypeptide sequences, the term “identity” is well known to skilled artisans (Carillo, H. & Lipton, D., Siam J Applied Math 48:1073 (1988)). Methods commonly employed to determine identity or similarity between two sequences include, but are not limited to, those disclosed in Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego (1994) and Carillo, H. & Lipton, D., Siam J Applied Math 48:1073 (1988). Computer programs may also contain methods and algorithms that calculate identity and similarity. Examples of computer program methods to determine identity and similarity between two sequences include, but are not limited to, GCG program package (Devereux, J., et al., Nucleic Acids Research 12(i):387 (1984)), BLASTP, ExPASy, BLASTN, FASTA (Atschul, S. F., et al., J Molec Biol 215:403 (1990)) and FASTDB. Examples of methods to determine identity and similarity are discussed in Michaels, G. and Garian, R., Current Protocols in Protein Science, Vol 1, John Wiley & Sons, Inc. (2000), which is incorporated by reference. In one embodiment of the present invention, the algorithm used to determine identity between two or more polypeptides is BLASTP.
In another embodiment of the present invention, the algorithm used to determine identity between two or more polypeptides is FASTDB, which is based upon the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990), incorporated by reference). In a FASTDB sequence alignment, the query and subject sequences are amino sequences. The result of sequence alignment is in percent identity. Parameters that may be used in a FASTDB alignment of amino acid sequences to calculate percent identity include, but are not limited to: Matrix=PAM, k-tuple=2, Mismatch Penalty=1, Joining Penalty=20, Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5, Gap Size Penalty 0.05, Window Size=500 or the length of the subject amino sequence, whichever is shorter.
If the subject sequence is shorter or longer than the query sequence because of N-terminus or C-terminus additions or deletions, not because of internal additions or deletions, a manual correction can be made, because the FASTDB program does not account for N-terminus and C-terminus truncations or additions of the subject sequence when calculating percent identity. For subject sequences truncated at both ends, relative to the query sequence, the percent identity is corrected by calculating the number of amino acids of the query sequence that are N- and C-terminus to the reference sequence that are not matched/aligned, as a percent of the total amino acids of the query sequence. The results of the FASTDB sequence alignment determine matching/alignment. The alignment percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This corrected score can be used for the purposes of determining how alignments “correspond” to each other, as well as percentage identity. Residues of the query (subject) sequences or the reference sequence that extend past the N- or C-termini of the reference or subject sequence, respectively, may be considered for the purposes of manually adjusting the percent identity score. That is, residues that are not matched/aligned with the N- or C-termini of the comparison sequence may be counted when manually adjusting the percent identity score or alignment numbering.
For example, a 90 amino acid residue subject sequence is aligned with a 100 residue reference sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence and therefore, the FASTDB alignment does not show a match/alignment of the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched the final percent identity would be 90%. In another example, a 90 residue subject sequence is compared with a 100 reference sequence. This time the deletions are internal deletions so there are no residues at the N- or C-termini of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by FASTDB is not manually corrected.
The polyligands of the invention optionally comprise spacer amino acids before, after, or between monomers. The length and composition of the spacer may vary. An example of a spacer is glycine, alanine, polyglycine, or polyalanine. Specific examples of spacers used between monomers in SEQ ID NO:5 are the four amino acid spacers AAAA (SEQ ID NO:109), GAGA (SEQ Id NO:110), GGGG (SEQ ID NO:111), AGAG (SEQ ID NO:112), AAGG (SEQ ID NO:114),GGAA (SEQ ID NO:115), and the six amino acid spacer AGPGAEF (SEQ ID NO:113). In the instance of SEQ ID NO:5, the proline-containing spacer is intended to break an alpha helical secondary structure. Spacer amino acids may be any amino acid and are not limited to alanine, glycine and proline. The instant invention is directed to all combinations of homopolyligands and heteropolyligands, with or without spacers, and without limitation to the examples given above or below.
The ligands and polyligands of the invention are optionally linked to additional molecules or amino acids that provide an epitope tag, a reporter, and/or localize the ligand to a region of a cell (See FIGS. 5A-5G, FIGS. 6A-6G, FIGS. 7A-7G, and FIGS. 8A-8G). Non-limiting examples of epitope tags are FLAGTM (Kodak; Rochester, N.Y.), HA (hemagluttinin), c-Myc and His6. Non-limiting examples of reporters are alkaline phosphatase, galactosidase, peroxidase, luciferase and green fluorescent protein (GFP). Non-limiting examples of cellular localizations are sarcoplamic reticulum, endoplasmic reticulum, mitochondria, golgi apparatus, nucleus, plasma membrane, apical membrane, and basolateral membrane. The epitopes, reporters and localization signals are given by way of example and without limitation. The epitope tag, reporter and/or localization signal may be the same molecule. The epitope tag, reporter and/or localization signal may also be different molecules.
Ligands and polyligands and optional amino acids linked thereto can be synthesized chemically or recombinantly using techniques known in the art. Chemical synthesis techniques include but are not limited to peptide synthesis which is often performed using an automated peptide synthesizer. Pepetides can also be synthesized utilizing non-automated peptide synthesis methods known in the art. Recombinant techniques include insertion of ligand-encoding nucleic acids into expression vectors, wherein nucleic acid expression products are synthesized using cellular factors and processes.
Linkage of a cellular localization signal, epitope tag, or reporter to a ligand or polyligand can include covalent or enzymatic linkage to the ligand. When the localization signal comprises material other than a polypeptide, such as a lipid or carbohydrate, a chemical reaction to link molecules may be utilized. Additionally, non-standard amino acids and amino acids modified with lipids, carbohydrates, phosphate or other molecules may be used as precursors to peptide synthesis. The ligands of the invention have therapeutic utility with or without localization signals. However, ligands linked to localization signals have utility as subcellular tools or therapeutics. For example, ligands depicted generically in FIGS. 7A-7G represent ligands with utility as subcellular tools or therapeutics. ERK ligand-containing gene constructs are also delivered via gene therapy. FIGS. 10B and 10C depict embodiments of gene therapy vectors for delivering and controlling polypeptide expression in vivo. Polynucleotide sequences linked to the gene construct in FIGS. 10B and 10C include genome integration domains to facilitate integration of the transgene into a viral genome and/or host genome.
FIG. 10A shows a vector containing an ERK ligand gene construct, wherein the ligand gene construct is releasable from the vector as a unit useful for generating transgenic animals. For example, the ligand gene construct, or transgene, is released from the vector backbone by restriction endonuclease digestion. The released transgene is then injected into pronuclei of fertilized mouse eggs; or the transgene is used to transform embryonic stem cells. The vector containing a ligand gene construct of FIG. 10A is also useful for transient transfection of the trangene, wherein the promoter and codons of the transgene are optimized for the host organism. The vector containing a ligand gene construct of FIG. 10A is also useful for recombinant expression of polypeptides in fermentable organisms adaptable for small or large scale production, wherein the promoter and codons of the transgene are optimized for the fermentation host organism.
FIG. 10D shows a vector containing an ERK ligand gene construct useful for generating stable cell lines.
The invention also encompasses polynucleotides comprising nucleotide sequences encoding ligands, homopolyligands, and heteropolyligands. The polynucleotides of the invention are optionally linked to additional nucleotide sequences encoding epitopes, reporters and/or localization signals. Further, the nucleic acids of the invention are optionally incorporated into vector polynucleotides. The polynucleotides are optionally flanked by nucleotide sequences comprising restriction endonuclease sites and other nucleotides needed for restriction endonuclese activity. The flanking sequences optionally provide cloning sites within a vector. The restriction sites can include, but are not limited to, any of the commonly used sites in most commercially available cloning vectors. Examples of such sites are those recognized by BamHI, ClaI, EcoRI, EcoRV, SpeI, Anil, NdeI, NheI, XbaI, XhoI, SphI, NaeI, SexAI, HindIII, HpaI, and PstI restriction endonucleases. Sites for cleavage by other restriction enzymes, including homing endonucleases, are also used for this purpose. The polynucleotide flanking sequences also optionally provide directionality of subsequence cloning. It is preferred that 5′ and 3′ restriction endonuclease sites differ from each other so that double-stranded DNA can be directionally cloned into corresponding complementary sites of a cloning vector.
Ligands and polyligands with or without localization signals, epitopes or reporters are alternatively synthesized by recombinant techniques. Polynucleotide expression constructs are made containing desired components and inserted into an expression vector. The expression vector is then transfected into cells and the polypeptide products are expressed and isolated. Ligands made according to recombinant DNA techniques have utility as research tools and/or therapeutics.
The following is an example of how polynucleotides encoding ligands and polyligands are produced. Complimentary oligonucleotides encoding the ligands and flanking sequences are synthesized and annealed. The resulting double-stranded DNA molecule is inserted into a cloning vector using techniques known in the art. When the ligands and polyligands are placed in-frame adjacent to sequences within a transgenic gene construct that is translated into a protein product, they form part of a fusion protein when expressed in cells or transgenic animals.
Another embodiment of the invention relates to selective control of transgene expression in a desired cell or organism. The promotor portion of the recombinant gene can be a constitutive promotor, a non-constitutive promotor, a tissue-specific promotor (constitutive or non-constitutive) or a selectively controlled promotor. Different selectively controlled promotors are controlled by different mechanisms. For example, RHEOSWITCH is an inducible promotor system available from New England Biolabs (Ipswich, Mass.). Temperature sensitive promotors can also be used to increase or decrease gene expression. An embodiment of the invention comprises a ligand or polyligand gene construct whose expression is controlled by an inducible promotor. In one embodiment, the inducible promotor is tetracycline controllable.
Polyligands are modular in nature. An aspect of the instant invention is the combinatorial modularity of the disclosed polyligands. Another aspect of the invention are methods of making these modular polyligands easily and conveniently. In this regard, an embodiment of the invention comprises methods of modular subsequence cloning of genetic expression components. When the ligands, homopolyligands, heteropolyligands and optional amino acid expression components are synthesized recombinantly, one can consider each clonable element as a module. For speed and convenience of cloning, it is desirable to make modular elements that are compatible at cohesive ends and are easy to insert and clone sequentially. This is accomplished by exploiting the natural properties of restriction endonuclease site recognition and cleavage. One aspect of the invention encompasses module flanking sequences that, at one end of the module, are utilized for restriction enzyme digestion once, and at the other end, utilized for restriction enzyme digestion as many times as desired. In other words, a restriction site at one end of the module is utilized and destroyed in order to effect sequential cloning of modular elements. An example of restriction sites flanking a coding region module are sequences recognized by the restriction enzymes NgoM IV and Cla I; or Xma I and Cla I. Cutting a first circular DNA with NgoM IV and Cla I to yield linear DNA with a 5′ NgoM IV overhang and a 3′ Cla I overhang; and cutting a second circular DNA with Xma I and Cla I to yield linear DNA with a 5′ Cla I overhang and a 3′ Xma I overhang generates first and second DNA fragments with compatible cohesive ends. When these first and second DNA fragments are mixed together, annealed, and ligated to form a third circular DNA fragment, the NgoM IV site that was in the first DNA and the Xma I site that was in the second DNA are destroyed in the third circular DNA. Now this vestigial region of DNA is protected from further Xma I or NgoM IV digestion, but flanking sequences remaining in the third circular DNA still contain intact 5′ NgoM IV and 3′ Cla I sites. This process can be repeated numerous times to achieve directional, sequential, modular cloning events. Restriction sites recognized by NgoM IV, Xma I, and Cla I endonucleases represent a group of sites that permit sequential cloning when used as flanking sequences.
Another way to assemble coding region modules directionally and sequentially employs linear DNA in addition to circular DNA. For example, like the sequential cloning process described above, restriction sites flanking a coding region module are sequences recognized by the restriction enzymes NgoM IV and Cla I; or Xma I and Cla I. A first circular DNA is cut with NgoM IV and Cla I to yield linear DNA with a 5′ NgoM IV overhang and a 3′ Cla I overhang. A second linear double-stranded DNA is generated by PCR amplification or by synthesizing and annealing complimentary oligonucleotides. The second linear DNA has 5′ Cla I overhang and a 3′ Xma I overhang, which are compatible cohesive ends with the first DNA linearized. When these first and second DNA fragments are mixed together, annealed, and ligated to form a third circular DNA fragment, the NgoM IV site that was in the first DNA and the Xma I site that was in the second DNA are destroyed in the third circular DNA. Flanking sequences remaining in the third circular DNA still contain intact 5′ NgoM IV and 3′ Cla I sites. This process can be repeated numerous times to achieve directional, sequential, modular cloning events. Restriction sites recognized by NgoM IV, Xma I, and Cla I endonucleases represent a group of sites that permit sequential cloning when used as flanking sequences. This process is depicted in FIG. 11.
One of ordinary skill in the art recognizes that other restriction site groups can accomplish sequential, directional cloning as described herein. Preferred criteria for restriction endonuclease selection are selecting a pair of endonucleases that generate compatible cohesive ends but whose sites are destroyed upon ligation with each other. Another criteria is to select a third endonuclease site that does not generate sticky ends compatible with either of the first two. When such criteria are utilized as a system for sequential, directional cloning, ligands, polyligands and other coding regions or expression components can be combinatorially assembled as desired. The same sequential process can be utilized for epitope, reporter, and/or localization signals.
Polyligands and methods of making polyligands that modulate ERK activity are disclosed. Therapeutics include delivery of purified ligand or polyligand with or without a localization signal to a cell. Alternatively, ligands and polyligands with or without a localization signals are delivered via adenovirus, lentivirus, adeno-associated virus, or other viral constructs that express protein product in a cell.
Methods
Assays. Ligands of the invention are assayed for kinase modulating activity using one or more of the following methods.
Method 1. A biochemical assay is performed employing commercially-obtained kinase, commercially-obtained substrate, commercially-obtained kinase inhibitor (control), and semi-purified inhibitor ligand of the invention (decoy ligand). Decoy ligands are linked to an epitope tag at one end of the polypeptide for purification and/or immobilization, for example, on a microtiter plate. The tagged decoy ligand is made using an in vitro transcription/translation system such as a reticulocyte lysate system well known in the art. A vector polynucleotide comprising a promotor, such as T7 and/or T3 and/or SP6 promotor, a decoy ligand coding sequence, and an epitope tag coding sequence is employed to synthesize the tagged decoy ligand in an in vitro transcription/translation system. In vitro transcription/translation protocols are disclosed in reference manuals such as: Current Protocols in Molecular Biology (eds. Ausubel et al., Wiley, 2004 edition.) and Molecular Cloning: A Laboratory Manual (Sambrook and Russell (Cold Spring Harbor Laboratory Press, 2001, third edition). Immunoreagent-containing methods such as western blots, elisas, and immunoprecipitations are performed as described in: Using Antibodies: A Laboratory Manual (Harlow and Lane Cold Spring Harbor Laboratory Press, 1999).
Specifically, tagged decoy ligand synthesized using an in vitro transcription/translation system is semi-purified and added to a microtiter plate containing kinase enzyme and substrate immobilized by an anti-substrate specific antibody. Microtiter plates are rinsed to substantially remove non-immobilized components. Kinase activity is a direct measure of the phosphorylation of substrate by kinase employing a phospho-substrate specific secondary antibody conjugated to horseradish peroxidase (HRP) followed by the addition of 3,3′,5,5′-tetramethylbenzidine (TMB) substrate solution. The catalysis of TMB by HRP results in a blue color that changes to yellow upon addition of phosphoric or sulfuric acid with a maximum absorbance at 450 nm. The Control experiments include absence of kinase enzyme, and/or absence of decoy ligand, and/or presence/absence of known kinase inhibitors. A known kinase inhibitor useful in the assay is staurosporine.
Method 2. A similar assay is performed employing the same reagents as above but the substrate is biotinylated and immobilized by binding to a streptavidin-coated plate.
Method 3. A biochemical assay is performed employing commercially-obtained kinase, commercially-obtained substrate, commercially-obtained kinase inhibitor (control), and semi-purified inhibitor ligand of the invention (decoy ligand) in a microtiter plate. A luminescent-based detection system, such as Promega's Kinase-Glo, is then added to inversely measure kinase activity.
Specifically, tagged decoy ligand synthesized using an in vitro transcription/translation system is semi-purified and added to a microtiter plate containing kinase enzyme and substrate. After the kinase assay is performed, luciferase and luciferin are added to the reaction. Luciferase utilizes any remaining ATP not used by the kinase to catalyze luciferin. The luciferase reaction results in the production of light which is inversely related to kinase activity. Control experiments include absence of kinase enzyme, and/or absence of decoy ligand, and/or presence/absence of known kinase inhibitors. A known kinase inhibitor useful in the assay is staurosporine.
Method 4. A similar cell-based assay is performed employing same reagents as above, but synthesizing the decoy ligand in a mammalian cell system instead of an in vitro transcription/translation system. Decoy ligands are linked to an epitope tag at one end of the polypeptide for immobilzation and/or for purification and/or for identification in a western blot. Optionally, tagged decoy ligands are also linked to a cellular localization signal for phenotypic comparison of pan-cellular and localized kinase modulation. A vector polynucleotide comprising a constitutive promotor, such as the CMV promotor, a decoy ligand coding sequence, an epitope tag coding sequence, and optionally a localization signal coding sequence is employed to express the decoy ligand in cells. Transfection and expression protocols are disclosed in reference manuals such as: Current Protocols in Molecular Biology (eds. Ausubel et al., Wiley, 2004 edition.) and Molecular Cloning: A Laboratory Manual (Sambrook and Russell (Cold Spring Harbor Laboratory Press, 2001, third edition). Western Blots and immunoreagent-containing methods are performed as described in: Using Antibodies: A Laboratory Manual (Harlow and Lane Cold Spring Harbor Laboratory Press, 1999).
EXAMPLES
Example 1
A polypeptide comprising a heteropolyligand, an endoplasmic reticulum cellular localization signal, and a His6 epitope is synthesized. Examples of such polypeptides are generically represented by FIGS. 8A, 8B, 8D, 8E and 8F. The polypeptide is synthesized on an automated peptide synthesizer or is recombinantly expressed and purified. Purified polypeptide is solubilized in media and added to cells. The polypeptide is endocytosed by the cells, and transported to the endoplasmic reticulum. Verification is performed by immunohistochemical staining using an anti-His6 antibody.
Example 2
A transgene is constructed using a human cytomegalovirus (CMV) promoter to direct expression of a fusion protein comprising SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:89, wherein Xaa is alanine (POLYLIGAND), green fluorescent protein (REPORTER), and a plasma membrane localization signal (LOCALIZATION SIGNAL). Such a transgene is generically represented by FIG. 9C. The transgene is transfected into cells for transient expression. Verification of expression and location is performed by visualization of green fluorescent protein (GFP) by confocal microscopy.
Example 3
A transgene construct is built to produce a protein product with expression driven by a tissue-specific promoter. The transgene comprises a synthetic gene expression unit engineered to encode three domains. Each of these three domains is synthesized as a pair of complimentary polynucleotides that are annealed in solution, ligated and inserted into a vector. Starting at the amino-terminus, the three domains in the expression unit are nucleotide sequences that encode an ERK ligand, a FLAGTM epitope, and a nuclear localization signal. The ERK ligand is a monomeric ligand, homopolymeric ligand or heteropolymeric ligand as described herein. Nucleotide sequences encoding a FLAGTM epitope are placed downstream of nucleotide sequences encoding the ERK ligand. Finally, nucleotide sequences encoding the localization signal are placed downstream of those encoding the FLAGTM epitope. The assembled gene expression unit is subsequently subcloned into an expression vector, such as that shown in FIG. 10A, and used to transiently transfect cells. Verification is performed by immunohistochemical staining using an anti-FLAGTM antibody.
Example 4
Modulation of ERK cellular function by subcellularly localized ERK polyligand is illustrated. A transgene construct containing nucleic acids that encode a polyligand fusion protein, epitope, and endoplasmic reticulum localization signal is made. The expression unit contains nucleotides that encode SEQ ID NO:1 (POLYLIGAND), a c-Myc epitope (EPITOPE), and an endoplasmic reticulum localization signal (LOCALIZATION SIGNAL). This expression unit is subsequently subcloned into a vector between a EF1alpha promoter and an SV40 polyadenylation signal (depicted in FIG. 12). The completed transgene-containing expression vector is then used to transfect cells. Inhibition of ERK activity is demonstrated by measuring phosphorylation of endogenous substrates against controls (see FIG. 14).
Example 5
Ligand function and localization is demonstrated in vivo by making a transgene construct used to generate mice expressing a ligand fusion protein targeted to the endoplasmic reticulum. The transgene construct is shown generically in FIG. 10B. The expression unit contains nucleotides that encode a tetramer of SEQ ID NO:65, a hemagluttinin epitope, and a nuclear localization signal. This expression unit is subsequently subcloned into a vector between nucleotide sequences including an inducible promoter and an SV40 polyadenylation signal. The completed transgene is then injected into pronuclei of fertilized mouse oocytes. The resultant pups are screened for the presence of the transgene by PCR. Transgenic founder mice are bred with wild-type mice. Heterozygous transgenic animals from at least the third generation are used for the following tests, with their non-transgenic littermates serving as controls.
Test 1: Southern blotting analysis is performed to determine the copy number. Southern blots are hybridized with a radio-labeled probe generated from a fragment of the transgene. The probe detects bands containing DNA from transgenic mice, but does not detect bands containing DNA from non-transgenic mice. Intensities of the transgenic mice bands are measured and compared with the transgene plasmid control bands to estimate copy number. This demonstrates that mice in Example 5 harbor the transgene in their genomes.
Test 2: Tissue homogenates are prepared for Western blot analysis. This experiment demonstrates the transgene is expressed in tissues of transgenic mice because hemagluttinin epitope is detected in transgenic homogenates but not in non-transgenic homogenates.
Test 3: Function is assessed by phenotypic observation or analysis against controls.
These examples demonstrate delivery of ligands to a localized region of a cell for therapeutic or experimental purposes. The purified polypeptide ligands can be formulated for oral or parenteral administration, topical administration, or in tablet, capsule, or liquid form, intranasal or inhaled aerosol, subcutaneous, intramuscular, intraperitoneal, or other injection; intravenous instillation; or any other routes of administration. Furthermore, the nucleotide sequences encoding the ligands permit incorporation into a vector designed to deliver and express a gene product in a cell. Such vectors include plasmids, cosmids, artificial chromosomes, and modified viruses. Delivery to eukaryotic cells can be accomplished in vivo or ex vivo. Ex vivo delivery methods include isolation of the intended recipient's cells or donor cells and delivery of the vector to those cells, followed by treatment of the recipient with the cells.
Results
Results show that the ERK polyligands of the invention (decoys) localized to the appropriate subcellular compartments and inhibited ERK activity at those locations. Localized inhibition caused distinct functional changes in the treated cells, including inhibition of oncogene-induced cell proliferation and transformation. Furthermore, depending on the source of the activation signal for the ERK pathway, the specific subcellular site of inhibition (endoplasmic reticulum or plasma membrane) had a differentiating effect on transformation phenotype of the cells. In contrast, inhibition of ERK by siRNA or a small molecule inhibitor did not reveal this functional difference.
Fluorescence microscopy of the ligand of SEQ ID NO:1 is shown localized to the nucleus (FIG. 16), cytoplasm (FIG. 17), and endoplasmic reticulum (FIG. 13A). The localized ERK ligands were detected by immunostaining for the c-myc epitope tag. FIG. 14 shows ERK activity localized to specific compartments with localized Ras overexpression and SEQ ID NO:1 expressed pancellularly (lanes 8-9) or targeted to the endoplasmic reticulum (lanes 5-7) or plasma membrane (lanes 2-4). The result was location-selective inhibition of ERK activity at the endoplasmic reticulum as measured by phosphorylation of the ERK substrate myelin basic protein (MBP).
Additionally, experiments where inhibition of ERK signaling using ERK ligands of the invention was compared to siRNAs and a small molecule inhibitor. The commercial siRNAs were designed for target specificity to either the ERK1 (sc-29307) or ERK2 (sc-35335) isoforms (Santa Cruz Biotechnology, Inc.). The small molecule inhibitor, UO126 (1,4-diamino-2,3-dicyano-1,4-bis(2-aminophenylthio) butadiene), inhibits ERK signaling through its upstream effector, MEK, and ERK is the only known substrate for MEK. Assays performed were phenotypic assays. The effects of inhibiting ERK activity were measured by looking at functional properties of the cells associated with the MAPK signaling pathway, such as, cell proliferation and transformation. The MAPK signaling cascade in these experiments is initiated by transfection of the cells with a vector containing a constitutively active proto-oncogene, either H-RasV12 or v-Src, which eventually causes the cells to acquire enhanced growth rate (colony formation) and cell transformation rate (foci formation). Inhibition of ERK activity in this cascade will result in reduced rates of proliferation or transformation as measured by numbers of G418-resistant colonies or foci.
Data for colony formation inhibition with the various treatments is presented in FIG. 18. UO126 is very effective at inhibiting the pathway due to its high potency for MEK ( ̃70 nM) and its stability. Furthermore, the siRNAs targeted against ERK1 or ERK2 show isoform specificity as to the effects on proliferation. This is consistent with a recent report that showed interplay between ERK1 and ERK2 in regulating Ras-mediated signaling, wherein ERK2 has a positive role in controlling cell proliferation and ERK1 can affect signal output by counteracting ERK2 activity (Vantaggiato et al. 2006 J. of Biol. 5:14). The two ERK ligands (SEQ ID NO:1 and SEQ ID NO:5, both fused to c-Myc and FLAG tags) used in this experiment are not targeted to a specific subcellular location but are expressed throughout the cell under the control of a constitutive promoter. The ERK ligands, as described herein, are designed with multiple domains (usually mutated substrates) believed capable of competing with the normal endogenous ERK substrates. Thus, unlike siRNAs, which can have RNA sequence specificity for each of the two isoforms of ERK, the ERK decoy ligands may bind to both ERK1 and ERK2 proteins, which may result in only partial inhibition of cell proliferation. Possible reasons for partial inhibition may include a titration effect whereby some of the decoy ligand is “trapped” by ERK1 and unavailable to inhibit ERK2. Partial inhibition may also be due to the inhibition of the ERK1, possibly antagonizing or mitigating the inhibitory effects on ERK2.
Based on the similar effectiveness of SEQ ID NO:1 and SEQ ID NO:5 in inhibiting Ras-mediated cell proliferation, a similar experiment was conducted with SEQ ID NO:1 localized to the nucleus (NLS), the cytoplasm (NXP, nuclear exclusion), the endoplasmic reticulum (ER), and the plasma membrane (PLA). In all cases, location-specific SEQ ID NO:1 causes some inhibition of cell proliferation, with the greatest degree of inhibition arising when the decoy is localized to the plasma membrane (FIG. 19). ER-localized inhibition was also significant, consistent with the results previously reported using dominant negative location-targeted Ras inhibitors (Matallanas et al. (2006) Mol. Cell. Biol. 26: 100-116). SEQ ID NO:1 targeted to the nucleus and cytoplasm gives slight inhibition of proliferation.
Next, the effect of ERK inhibition on cell transformation was investigated using two means of initiating signaling cascades that lead to this biological property (FIG. 20). The first method is the constitutively active Ras mutant used herein above. The second is a constitutively active nonreceptor tyrosine kinase v-Src mutant (pp60v-src) that also leads to cell transformation, potentially by multiple signaling pathways including the Ras-Raf-MEK-ERK pathway. As shown in FIG. 20, the pancellular decoys (SEQ ID NO:1 and SEQ ID NO:5), ERK2 siRNA, and localized decoy (SEQ ID NO:1 fused to localization signals indicated) all inhibited cell transformation. Treatment of H-RasV 12 transformed cells with ER-localized and PLA-localized SEQ ID NO:1 inhibited cell transformation rates by  ̃50%, similar to results obtained with the pancellularly expressed SEQ ID NO:1 and SEQ ID NO:5. However, when transformation was initiated with v-Src, there was a difference in the inhibition specificity arising from use of SEQ ID NO:1 localized to the ER and PLA. The ER-localized SEQ ID NO:1 caused little to no inhibition relative to the untreated control, while the PLA-localized SEQ ID NO:1 caused  ̃60% decrease in transformation. That is, ER-localized SEQ ID NO:1 has a significant effect on transformation induced by H-RasV12 but little to no effect when transformation is induced by v-Src. In contrast, inhibition of ERK by siRNA was identical for both the H-Ras and v-Src pathways. Thus, siRNA does not differentiate the effects on transformation induced by distinct oncogenes H-Ras and v-Src.
Disclosed are ligands and polyligands that modulate ERK activity and methods of making and using these ligands. The ligands and polyligands are synthesized chemically or recombinantly and are utilized as research tools or as therapeutics. The invention includes linking the ligands and polyligands to cellular localization signals for subcellular therapeutics.

## Claims

1. An isolated polynucleotide comprising a nucleotide sequence encoding a polypeptide polyligand comprising a first amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, and 49 and one or more additional amino acid sequences that are at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102,
wherein Xaa of SEQ ID NOS: 28, 32, 36, 48, and 49 is any naturally occurring amino acid other than serine or threonine, and
wherein the polypeptide polyligand inhibits the kinase activity of extracellular-signal-regulated kinase (ERK).

2. The isolated polynucleotide of claim 1, wherein said polypeptide polyligand is a heteropolyligand.

3. The isolated polynucleotide of claim 1, wherein said polypeptide polyligand is linked to one or more of a localization signal, an epitope tag, or a reporter.

4. A vector comprising the isolated polynucleotide of claim 1.

5. An isolated host cell comprising the vector of claim 4.

6. The isolated polynucleotide of claim 1, operably linked to a promoter.

7. The isolated polynucleotide of claim 6, wherein said promoter is an inducible promoter.

8. The isolated polynucleotide of claim 1, wherein said one or more additional amino acid sequences are at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102.

9. The isolated polynucleotide of claim 1, wherein said one or more additional amino acid sequences are at least 96% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102.

10. The isolated polynucleotide of claim 1, wherein said one or more additional amino acid sequences are at least 97% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102.

11. The isolated polynucleotide of claim 1, wherein said one or more additional amino acid sequences are at least 98% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102.

12. The isolated polynucleotide of claim 1 wherein said one or more additional amino acid sequences are at least 99% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102.

13. The isolated polynucleotide of claim 1, wherein said one or more additional amino acid sequences are selected from the group consisting of SEQ ID NOS: 28, 32, 36, 48, 49, 91, 93-96 and 102.

14. A method of inhibiting ERK in a cell, said method comprising
(a) transfecting the vector of claim 4 into an isolated host cell that expresses ERK, and
(b) culturing the transfected host cell under conditions suitable to produce at least one copy of the polypeptide polyligand, thereby inhibiting ERK in the host cell.