# Patent

## Title
Inhibitors of guanine exchange factors and their use as anticancer drugs

## Abstract

A peptide including the amino acids sequence X9CGYX13X14AX16X17X18MX20X21X22X23X24X25X26X27CPLCX32X33, a nucleic acid coding for the peptide, and/or a recombinant vector including the nucleic acid for the preparation of a drug intended for the treatment of cancer.

## Background
FIELD OF THE INVENTION
The present invention relates to inhibitors of guanine exchange factor, and their use as anticancer drugs.
BACKGROUND OF THE INVENTION
By remodeling the actin cytoskeleton, Rho GTPases regulate various cellular processes, such as proliferation, migration, cell adhesion and cell shape (Etienne-Manneville and Hall, 2002). They are activated by the Dbl family of Rho Guanine Nucleotide Exchange Factors (RhoGEFs), which accelerates their GDP/GTP exchange rate (Rossman et al., 2005). RhoGEFs represent a large family (over seventy members in mammals) of complex proteins with numerous signaling domains, but they almost invariably contain a functional tandem, including a Dbl Homology (DH) domain responsible for guanine nucleotide exchange, followed by a Pleckstrin Homology (PH) domain, which targets the GEF to the plasma membrane and/or regulates nucleotide exchange (Chhatriwala et al., 2007; Lutz et al., 2007; Rojas et al., 2007; Rossman et al., 2003; Rossman et al., 2005). Deregulation of Rho GTPase function has been associated with various human disorders, including cancer and metastasis, (Sahai and Marshall, 2002; Toksoz and Merdek, 2002). Indeed, an increase in RhoGTPase activation due to overexpression of Rac1 or RhoA and C has been associated with tumor proliferation and metastasis. In addition, many Dbl family RhoGEFs have been isolated based on their oncogenic potency, which often results from a truncation of the protein, leading to uncontrolled GEF activity and subsequent aberrant Rho GTPase activation (Eva and Aaronson, 1985; Katzav et al., 1989; Miki et al., 1993; Whitehead et al., 1995; Whitehead et al., 1996).
Trio belongs to the RhoGEF family and is a complex protein harboring two GEF domains (GEFD1 and GEFD2), activating the GTPases Rac1/RhoG and RhoA, respectively, and thus potentially linking several Rho-GTPase signaling pathways in vivo (Blangy et al., 2000; Debant et al., 1996; Bellanger et al., 1998). Studies on invertebrate Trio orthologs have established a central role for Trio in cell migration and axon guidance, mainly through the activation of Rac1 by the GEFD1 domain (Steven et al., 1998; Newsome et al., 2000). Trio knock-out mice are embryonic lethal (E15 to birth) and show defects in brain organization and secondary myogenesis, suggesting a major role for mammalian Trio in these developmental processes (O'Brien et al., 2000). Consistently, we have shown that Trio is required for RhoG-mediated neurite outgrowth in PC12 cells in response to NGF (Estrach et al., 2002) and that Trio is the GEF responsible for Rac1 activation during netrin/DCC-induced axon outgrowth and guidance (Briançon-Marjollet et al., 2008). Recently, an oncogenic isoform of Trio, called Tgat, has been identified from Adult T-Cell Leukemia patient cells and encodes only the RhoA-specific GEF domain. Tgat induces cell transformation and tumor formation in nude mice, mainly via activation of RhoA (Yoshizuka et al., 2004).
Rho GTPases and their GEFs thus represent attractive targets for inhibition, not only to understand their function but also in pathology, to develop anti-cancer drugs.
When trying to inhibit signalling pathways controlled by small G proteins and their activating GEFs, the challenge is that these are not mere enzymes with a well-defined active site that can be blocked. Rather, protein-protein interactions have to be targeted and the lack of reactive pockets to which inhibitors could bind is a challenging issue. This might in part explain why, although oncogenic Ras has been discovered more than 20 years ago, no inhibitor with clinical validation has been identified. Therefore, research has focused on trying to inhibit the guanine nucleotide exchange factors instead, and recent studies report the successful identification of such inhibitors.
For instance, the international application WO/2003/099778 discloses a peptide inhibitor that specifically inhibits the Trio GEFD2 domain, and its use for modulating axon retraction.
However, to date, only one specific inhibitor of GEFD2 domain of Trio has been described, but said inhibitor has never been used for treating other pathologies than neural retraction.
Thus, there is a need to provide new inhibitors that can be used in cancer therapy that selectively inhibit specific GEF domains.
SUMMARY OF THE INVENTION
One aim of the invention is to provide new peptides for treating cancer, or alternatively nucleic acid sequences coding said peptides.
Another aim of the invention is to provide peptides inhibiting Rho-GEF protein with a high efficiency.
Another aim of the invention is to provide specific in vivo inhibitors of a Rho-GEF family member, and their oncogenic forms.
Another aim of the invention is to provide specific in vivo inhibitors of a Rho-GEF family member, blocking specifically the RhoA pathway.
Still another aim of the invention is to provide pharmaceutical compositions for treating cancer.
DETAILED DESCRIPTION OF THE INVENTION
The invention relates to the use of a peptide, possibly at least one peptide, comprising or consisting of the following amino acid sequence SEQ ID NO: 2,









Nter-X9CGYX13X14AX16X17X18MX20X21X22X23X24X25X26



 



X27CPLCX32X33-Cter






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X9, X13, X14, X16, X17, X18, X20, X21, X22, X23, X24, X25, X26, X27, X32 and X33 represent any amino acids,
with the proviso that said peptide does not comprise or consist of the amino acid sequence SEQ ID NO: 1,
for the preparation of a drug intended for the treatment of cancer.
The peptides according to the invention are able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat. Tgat retains only the RhoA-specific DH2 domain of Trio and, instead of the associated PH2 domain, carries a unique C-terminal sequence of 15 amino acids, not found in Trio. Said peptides have inhibiting properties at least 2 fold, preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα (SEQ ID NO: 197).
The peptide TRIPα consisting of the amino acid sequence SEQ ID NO: 197 comprises the peptide consisting of the amino acid sequence SEQ ID NO: 1, excluded from the object of the invention. SEQ ID NO 1 corresponds to the peptidic sequence delimited by the amino acids from the position 9 to the position 33 of TRIPα.
The invention also relates to a method for treating cancer, comprising the administration to a person in a need thereof of a pharmaceutically effective amount of a peptide comprising or consisting of the following amino acids sequence SEQ ID NO: 2,









X9CGYX13X14AX16X17X18MX20X21X22X23X24X25X26X27CPLC



 



X32X33






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X9, X13, X14, X16, X17, X18, X20, X21, X22, X23, X24, X25, X26, X27, X32 and X33 represent any amino acids,
said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
said peptide having inhibiting properties at least 2 fold, preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα.
with the proviso that said peptide does not comprise or consist of the amino acid sequence SEQ ID NO: 1.
The present invention is based on the unexpected observation made by the Inventors that the peptides according to the invention are able to inhibit Tgat, an oncogenic isoform of Trio, and have an inhibitory effect similar to or higher than the inhibitory effect of TRIPα represented by the amino acid sequence SEQ ID NO:1.
According to the invention, the amino acid residues represented by X9, X13, X14, X16, X17, X18, X20, X21, X22, X23, X24, X25, X26, X27, X32 and X33 represent “any amino acid”. This means that X9, X13, X14, X16, X17, X18, X20, X21, X22, X23, X24, X25, X26, X27, X32 and X33 can be any of the twenty natural amino acids, or any non-natural amino acid commonly used by a skilled person.
All the peptides according to the invention are able to specifically inhibit Trio GEFD2 domain which means that said peptides inhibit only the TrioGEFD2 domain of Trio and have neither effect on the activity of Trio GEFD1 domain, nor effect on the activity of other GEF domains contained in GEF proteins such as p63RhoGEF, p115RhoGEF, Lbc, Vav, or Dbl. In other words, the peptides according to the invention inhibit only the RhoA GEF domain (GEFD2) contained in Trio and Tgat.
Moreover, the GEFD2 domain of Trio contained in Tgat oncoprotein is also a target of the peptides according to the invention, and said Tgat GEF domain is inhibited by said peptides.
Also, the peptides according to the invention have an increased inhibitory efficiency of the GEF activity of both Trio GEFD2 and Tgat, compared to TRIPα (SEQ ID NO: 197), or its active fragments (for instance fragment 9-33 of TRIPα as set forth by SEQ ID NO: 1). The following properties of the peptides according to the invention have been demonstrated:

    
    
        first, the underlined bold residues are essential for the inhibitory activity of said peptides, as determined by ALA-Scan (see example section)
        second, some variation in other amino acids can enhance significantly the inhibitory efficiency of said peptides.
    
    


The determination of the inhibitory efficiency of the peptides according to the invention on the exchange activity of the GEFD2 domain of Trio and of Tgat, as well as their in vitro and in vivo activities, are illustrated in the Example section hereafter.
The peptides according to the invention are artificial, isolated, purified, and have never been described in the art, prior to the characterization by the Inventors.
Another advantageous embodiment of the invention relates to the above-mentioned method or use, wherein said peptide comprises or consists of the amino acid sequence SEQ ID NO: 3,









ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids,
said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
said peptide having inhibiting properties at least 2 fold, preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα.
with the proviso that said amino acids sequence does not comprises or consist of the amino acids sequence SEQ ID NO: 1.
The invention relates, in one other advantageous embodiment, to the above-mentioned method or use, wherein said peptide comprises or consists of the amino acid sequence SEQ ID NO: 3 having at least one of the following features:

    
    
        X13 is D,
        X16 is M or A,
        X17 is S,
        X18 is D, G or A,
        X23 is G,
        X24 is A,
        X27 is L, and
        X32 is G.
    
    


According to the invention, the peptide comprising or consisting of the amino acid sequence SEQ ID NO: 3 can be for instance
the peptide SEQ ID NO: 3 wherein X13 is D, and X16, X17, X18, X23, X24, X27 and X32 represent any amino acid, or
the peptide SEQ ID NO: 3 wherein X13 is D, X17 is S, and X16, X18, X23, X24, X27 and X32 represent any amino acid, . . . .
The skilled person would easily reproduce all the peptides according to the invention, taking into account the above mentioned conditions regarding the definitions of amino acid residues X13, X16, X17, X18, X23, X24, X27 and X32.
The invention relates, in one other advantageous embodiment, to the above-mentioned method or use, wherein said peptide comprises or consists of the amino acid sequences chosen among the group comprising SEQ ID NO: 4 to SEQ ID NO: 51.
For instance, the peptides consisting of the amino acid sequences SEQ ID NO: 4 to SEQ ID NO: 15 are specifically defined hereafter.
The peptide consisting in the amino acid sequence SEQ ID NO: 4 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is T, X17 is L, X18 is V, X23 is 5, X24 is E, X27 is F, and X32 is G.
The peptide consisting in the amino acid sequence SEQ ID NO: 5 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is M, X17 is 5, X18 is V, X23 is 5, X24 is E, X27 is F, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 6 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is M, X17 is L, X18 is V, X23 is 5, X24 is E, X27 is F, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 7 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is T, X17 is S, X18 is V, X23 is S, X24 is E, X27 is F, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 8 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is M, X17 is L, X18 is V, X23 is G, X24 is E, X27 is F, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 9 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is T, X17 is L, X18 is D, X23 is 5, X24 is E, X27 is L, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 10 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is T, X17 is L, X18 is V, X23 is 5, X24 is E, X27 is F, and X32 is G.
The peptide consisting in the amino acid sequence SEQ ID NO: 11 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is A X17 is L, X18 is G, X23 is 5, X24 is E, X27 is F, and X32 is G.
The peptide consisting in the amino acid sequence SEQ ID NO: 12 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is T, X17 is L, X18 is A, X23 is 5, X24 is A, X27 is F, and X32 is G.
The peptide consisting in the amino acid sequence SEQ ID NO: 13 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is D, X16 is M, X17 is L, X18 is V, X23 is 5, X24 is E, X27 is F, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 14 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is A, X17 is 5, X18 is V, X23 is 5, X24 is E, X27 is F, and X32 is E.
The peptide consisting in the amino acid sequence SEQ ID NO: 15 corresponds to the amino acid sequence SEQ ID NO: 3, wherein X13 is N, X16 is T, X17 is L, X18 is D, X23 is S, X24 is E, X27 is F, and X32 is E.
In one other advantageous embodiment, the invention relates to the use or the method mentioned-above, wherein said peptide comprises or consists of the amino acid sequences chosen among the group comprising SEQ ID NO: 4 to SEQ ID NO: 10, SEQ ID NO: 16 to SEQ ID NO: 21, SEQ ID NO: 28 to SEQ ID NO: 34 and SEQ ID NO: 40 to SEQ ID NO: 46.
In one other advantageous embodiment, the invention relates to the use or the method mentioned-above, wherein said peptide comprises or consists of the amino acid sequences chosen among the group comprising SEQ ID NO: 4 to SEQ ID NO: 6, SEQ ID NO: 16 to SEQ ID NO: 18, SEQ ID NO: 28 to SEQ ID NO: 30 and SEQ ID NO: 40 to SEQ ID NO: 42.
Peptides defined above, and consisting of the amino acid sequences SEQ ID NO: 4 to SEQ ID NO: 6, SEQ ID NO: 16 to SEQ ID NO: 18, SEQ ID NO: 28 to SEQ ID NO: 30 and SEQ ID NO: 40 to SEQ ID NO: 42 are such that:

    
    
        the peptide consisting of the amino acid sequence SEQ ID NO: 40 corresponds to the peptide consisting in the amino acid sequence SEQ ID NO: 197 in which the Glutamate (E) in position 32 is substituted by a Glycine (G),
        the peptide consisting of the amino acid sequence SEQ ID NO: 41 corresponds to the peptide consisting in the amino acid sequence SEQ ID NO: 197 in which the Threonine (T) in position 16 is substituted by a Methionine (M), and the Leucine (L) in position 17 is substituted by a Serine (S),
        the peptide consisting of the amino acid sequence SEQ ID NO: 42 corresponds to the peptide consisting in the amino acid sequence SEQ ID NO: 197 in which the Leucine (L) in position 17 is substituted by a Serine (S),
        the peptide consisting of the amino acid sequence SEQ ID NO: 4 corresponds to a fragment delimited by the amino acids from the position 9 to the position 33 of the amino acid sequence SEQ ID NO: 40,
        the peptide consisting of the amino acid sequence SEQ ID NO: 5 corresponds to a fragment delimited by the amino acids from the position 9 to the position 33 of the amino acid sequence SEQ ID NO: 41,
        the peptide consisting of the amino acid sequence SEQ ID NO: 6 corresponds to a fragment delimited by the amino acids from the position 9 to the position 33 of the amino acid sequence SEQ ID NO: 42,
        the peptide consisting of the amino acid sequence SEQ ID NO: 16 corresponds to a fragment delimited by the amino acids from the position 1 to the position 33 of the amino acid sequence SEQ ID NO: 40,
        the peptide consisting of the amino acid sequence SEQ ID NO: 17 corresponds to a fragment delimited by the amino acids from the position 1 to the position 33 of the amino acid sequence SEQ ID NO: 41,
        the peptide consisting of the amino acid sequence SEQ ID NO: 18 corresponds to a fragment delimited by the amino acids from the position 1 to the position 33 of the amino acid sequence SEQ ID NO: 42,
        the peptide consisting of the amino acid sequence SEQ ID NO: 28 corresponds to a fragment delimited by the amino acids from the position 9 to the position 42 of the amino acid sequence SEQ ID NO: 40,
        the peptide consisting of the amino acid sequence SEQ ID NO: 29 corresponds to a fragment delimited by the amino acids from the position 9 to the position 42 of the amino acid sequence SEQ ID NO: 41,
        the peptide consisting of the amino acid sequence SEQ ID NO: 30 corresponds to a fragment delimited by the amino acids from the position 9 to the position 42 of the amino acid sequence SEQ ID NO: 42.
    
    


In one another preferred embodiment, the invention relates to the above-defined use or method, wherein said peptide contains flanking parts consisting of fragments of thioredoxin A.
The peptides according to the invention can be inserted into the active site (residue 35) of the E. coli thioredoxin A, as disclosed in Colas et al. [Colas et al. 1996, Nature 380, 548-50] and the international application n° WO 96/02561.
E. coli thioredoxin A is a small, very stable protein which can be produced at high levels. Thioredoxin contains a Cys-Cys active loop where peptides can be inserted and subjected to conformational constraint, since both cysteines can form a disulphide bond under appropriate conditions.
The expression “flanking parts consisting of fragments of the thioredoxin” can mean either that the N-terminal and C-terminal flanking parts when considered together correspond to the complete sequence of thioredoxin (in such a case the above-mentioned amino sequences are inserted in thioredoxin), or that the N-terminal and C-terminal flanking parts are themselves fragments of thioredoxin, the size of said fragment advantageously being from about 20 to about 60 amino acids.
In still another advantageous embodiment, the invention relates to the above-mentioned use or method, wherein said peptide comprises or consists in the amino acid sequences selected from SEQ ID NO: 52 to SEQ ID NO: 99.
The peptides consisting of SEQ ID NO: 52 to SEQ ID NO: 99 correspond respectively to the peptides consisting of SEQ ID NO: 4 to SEQ ID NO: 51 inserted between the amino acid at the position 35 and 36 of the E. coli Thioredoxin A.
In another advantageous embodiment, the invention relates to the use or the method previously defined wherein said cancer comprises leukemia, including T-cell acute Leukemia, sarcoma, lung cancer and breast cancer.
All the above cancers concern abnormal proliferation, differentiation, migration of cells that abnormally express Trio protein, for instance by gene amplification, translocation or transcriptional deregulation, or express an abnormal Trio protein form, for instance an “activated” mutant of Trio, due to a point mutation, or due to aberrant alternative splicing, generating an oncogenic isoform such as Tgat.
The invention also relates to an isolated peptide comprising or consisting of the amino acid sequence SEQ ID NO: 3,









ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids,
said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
said peptide having inhibiting properties at least 2 fold preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα
with the proviso that said amino acid sequence does not comprise or consist of the amino acid sequence SEQ ID NO: 1.
The above peptides are novel, and have never been referenced in any protein data bases known by the skilled person.
These peptides can be prepared by adapting common protocols known by a skilled person, such as described in the examples section, preferentially by site directed mutagenesis, or by random PCR-based mutagenesis.
In one advantageous embodiment, the invention relates to the isolated peptide previously defined, wherein said peptide comprises or consists of the amino acid sequence SEQ ID NO: 3 having at least one of the following features: X13 is D, X16 is M or A, X17 is 5, X18 is D, G or A, X23 is G, X24 is A, X27 is L, and X32 is G.
In one advantageous embodiment, the invention relates to the isolated peptide previously defined, wherein said peptide comprises or consists of the amino acid sequences chosen among the group comprising SEQ ID NO: 4 to SEQ ID NO: 51.
In one advantageous embodiment, the invention relates to the isolated peptide previously defined, wherein said peptide contains flanking parts consisting of fragments of the thioredoxin A.
In one advantageous embodiment, the invention relates to the isolated peptide previously defined, wherein said peptide comprises or consists in the amino acid sequences selected from SEQ ID NO: 52 to SEQ ID NO: 99.
The following table 1 recapitulates the correspondence between the peptides according to the invention:







TABLE 1







correspondence between peptides according to the invention.










SEQ ID NO: 197 (TRIP α)
SEQ ID NO: 1 (TRIPα 9-33)




Peptide derived from
Corresponding
Corresponding
Corresponding


TRIPα 1-42
fragments 9-33
fragments 1-33
fragments 9-42





SEQ ID NO: 40
SEQ ID NO: 4
SEQ ID NO: 16
SEQ ID NO: 28


SEQ ID NO: 41
SEQ ID NO: 5
SEQ ID NO: 17
SEQ ID NO: 29


SEQ ID NO: 42
SEQ ID NO: 6
SEQ ID NO: 18
SEQ ID NO: 30


SEQ ID NO: 43
SEQ ID NO: 7
SEQ ID NO: 19
SEQ ID NO: 31


SEQ ID NO: 44
SEQ ID NO: 8
SEQ ID NO: 20
SEQ ID NO: 32


SEQ ID NO: 45
SEQ ID NO: 9
SEQ ID NO: 21
SEQ ID NO: 33


SEQ ID NO: 46
SEQ ID NO: 10
SEQ ID NO: 22
SEQ ID NO: 34


SEQ ID NO: 47
SEQ ID NO: 11
SEQ ID NO: 23
SEQ ID NO: 35


SEQ ID NO: 48
SEQ ID NO: 12
SEQ ID NO: 24
SEQ ID NO: 36


SEQ ID NO: 49
SEQ ID NO: 13
SEQ ID NO: 25
SEQ ID NO: 37


SEQ ID NO: 50
SEQ ID NO: 14
SEQ ID NO: 26
SEQ ID NO: 38


SEQ ID NO: 51
SEQ ID NO: 15
SEQ ID NO: 27
SEQ ID NO: 39









The Invention also relates to an isolated nucleic acid comprising or consisting of a nucleic acid sequence coding for a peptide as previously defined.
The Invention also relates to an isolated nucleic acid comprising or consisting of a nucleic acid sequence coding for a peptide, an isolated peptide, comprising or consisting of the amino acid sequence SEQ ID NO: 3,









ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids,
said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
said peptide having inhibiting properties at least 2 fold, preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα (SEQ ID NO:197)
with the proviso that said amino acid sequence does not comprise or consist of the amino acid sequence SEQ ID NO: 1.
In one advantageous embodiment, the invention relates to an isolated nucleic acid as defined above, comprising or consisting of a nucleic acid sequence selected from SEQ ID NO: 100 to SEQ ID NO: 196.
The following table 2 recapitulates the correspondence between the nucleic acid molecules according to the invention and their corresponding peptides which are encoded by them:







TABLE 2







Correspondences between nucleic acid


sequences and amino acid sequences.










peptide
is coded by the nucleic



consisting of:
acid consisting of:







SEQ ID NO: 3
SEQ ID NO: 100



SEQ ID NO: 4
SEQ ID NO: 101



SEQ ID NO: 5
SEQ ID NO: 102



SEQ ID NO: 6
SEQ ID NO: 103



SEQ ID NO: 7
SEQ ID NO: 104



SEQ ID NO: 8
SEQ ID NO: 105



SEQ ID NO: 9
SEQ ID NO: 106



SEQ ID NO: 10
SEQ ID NO: 107



SEQ ID NO: 11
SEQ ID NO: 108



SEQ ID NO: 12
SEQ ID NO: 109



SEQ ID NO: 13
SEQ ID NO: 110



SEQ ID NO: 14
SEQ ID NO: 111



SEQ ID NO: 15
SEQ ID NO: 112



SEQ ID NO: 16
SEQ ID NO: 113



SEQ ID NO: 17
SEQ ID NO: 114



SEQ ID NO: 18
SEQ ID NO: 115



SEQ ID NO: 19
SEQ ID NO: 116



SEQ ID NO: 20
SEQ ID NO: 117



SEQ ID NO: 21
SEQ ID NO: 118



SEQ ID NO: 22
SEQ ID NO: 119



SEQ ID NO: 23
SEQ ID NO: 120



SEQ ID NO: 24
SEQ ID NO: 121



SEQ ID NO: 25
SEQ ID NO: 122



SEQ ID NO: 26
SEQ ID NO: 123



SEQ ID NO: 27
SEQ ID NO: 124



SEQ ID NO: 28
SEQ ID NO: 125



SEQ ID NO: 29
SEQ ID NO: 126



SEQ ID NO: 30
SEQ ID NO: 127



SEQ ID NO: 31
SEQ ID NO: 128



SEQ ID NO: 32
SEQ ID NO: 129



SEQ ID NO: 33
SEQ ID NO: 130



SEQ ID NO: 34
SEQ ID NO: 131



SEQ ID NO: 35
SEQ ID NO: 132



SEQ ID NO: 36
SEQ ID NO: 133



SEQ ID NO: 37
SEQ ID NO: 134



SEQ ID NO: 38
SEQ ID NO: 135



SEQ ID NO: 39
SEQ ID NO: 136



SEQ ID NO: 40
SEQ ID NO: 137



SEQ ID NO: 41
SEQ ID NO: 138



SEQ ID NO: 42
SEQ ID NO: 139



SEQ ID NO: 43
SEQ ID NO: 140



SEQ ID NO: 44
SEQ ID NO: 141



SEQ ID NO: 45
SEQ ID NO: 142



SEQ ID NO: 46
SEQ ID NO: 143



SEQ ID NO: 47
SEQ ID NO: 144



SEQ ID NO: 48
SEQ ID NO: 145



SEQ ID NO: 49
SEQ ID NO: 146



SEQ ID NO: 50
SEQ ID NO: 147



SEQ ID NO: 51
SEQ ID NO: 148



SEQ ID NO: 52
SEQ ID NO: 149



SEQ ID NO: 53
SEQ ID NO: 150



SEQ ID NO: 54
SEQ ID NO: 151



SEQ ID NO: 55
SEQ ID NO: 152



SEQ ID NO: 56
SEQ ID NO: 153



SEQ ID NO: 57
SEQ ID NO: 154



SEQ ID NO: 58
SEQ ID NO: 155



SEQ ID NO: 59
SEQ ID NO: 156



SEQ ID NO: 60
SEQ ID NO: 157



SEQ ID NO: 61
SEQ ID NO: 158



SEQ ID NO: 62
SEQ ID NO: 159



SEQ ID NO: 63
SEQ ID NO: 160



SEQ ID NO: 64
SEQ ID NO: 161



SEQ ID NO: 65
SEQ ID NO: 162



SEQ ID NO: 66
SEQ ID NO: 163



SEQ ID NO: 67
SEQ ID NO: 164



SEQ ID NO: 68
SEQ ID NO: 165



SEQ ID NO: 69
SEQ ID NO: 166



SEQ ID NO: 70
SEQ ID NO: 167



SEQ ID NO: 71
SEQ ID NO: 168



SEQ ID NO: 72
SEQ ID NO: 169



SEQ ID NO: 73
SEQ ID NO: 170



SEQ ID NO: 74
SEQ ID NO: 171



SEQ ID NO: 75
SEQ ID NO: 172



SEQ ID NO: 76
SEQ ID NO: 173



SEQ ID NO: 77
SEQ ID NO: 174



SEQ ID NO: 78
SEQ ID NO: 175



SEQ ID NO: 79
SEQ ID NO: 176



SEQ ID NO: 80
SEQ ID NO: 177



SEQ ID NO: 81
SEQ ID NO: 178



SEQ ID NO: 82
SEQ ID NO: 179



SEQ ID NO: 83
SEQ ID NO: 180



SEQ ID NO: 84
SEQ ID NO: 181



SEQ ID NO: 85
SEQ ID NO: 182



SEQ ID NO: 86
SEQ ID NO: 183



SEQ ID NO: 87
SEQ ID NO: 184



SEQ ID NO: 88
SEQ ID NO: 185



SEQ ID NO: 89
SEQ ID NO: 186



SEQ ID NO: 90
SEQ ID NO: 187



SEQ ID NO: 91
SEQ ID NO: 188



SEQ ID NO: 92
SEQ ID NO: 189



SEQ ID NO: 93
SEQ ID NO: 190



SEQ ID NO: 94
SEQ ID NO: 191



SEQ ID NO: 95
SEQ ID NO: 192



SEQ ID NO: 96
SEQ ID NO: 193



SEQ ID NO: 97
SEQ ID NO: 194



SEQ ID NO: 98
SEQ ID NO: 195



SEQ ID NO: 99
SEQ ID NO: 196










The Invention also relates to a recombinant vector, especially a plasmid, a cosmid, a phage or a DNA virus, containing a nucleotide sequence as defined above, more preferably containing a nucleotide sequence coding for a peptide, especially an isolated peptide, comprising or consisting of the amino acid sequence SEQ ID NO: 3,









ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids,
said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
said peptide having inhibiting properties at least 2 fold, preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα (SEQ ID NO:197)
with the proviso that said amino acid sequence does not comprise or consist of the amino acid sequence SEQ ID NO: 1.
In one advantageous embodiment, the invention relates to the recombinant vector previously defined, containing the elements necessary for the expression in a host cell of the polypeptides, or peptide, coded by the nucleic acids above defined, inserted in said vector.
In one advantageous embodiment, the invention relates to the recombinant vector previously defined, containing the elements necessary for the expression in a host cell of the polypeptides, or peptide, coded by the nucleic acid sequence coding for a peptide, an isolated peptide, comprising or consisting of the amino acid sequence SEQ ID NO: 3,









ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P






wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids,
said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
said peptide having inhibiting properties at least 2 fold, preferably 3 fold higher, more preferably 5 fold higher compared to the inhibiting activity of TRIPα (SEQ ID NO:197)
with the proviso that said amino acid sequence does not comprise or consist of the amino acid sequence SEQ ID NO: 1,
said nucleic acid sequence being inserted in said vector.
The invention also relates to a host cell, in particular chosen from bacteria, viruses, yeasts, fungi, plants or mammalian cells, the said host cell being transformed, especially by means of a vector defined above, in such a way that its genome contains a nucleotide sequence defined above.
The invention also relates to a pharmaceutical composition comprising at least one of the following active ingredients, at least one of the following ones:

    
    
        at least a peptide as defined above, preferably a peptide comprising or consisting of the amino acid sequence SEQ ID NO: 3,
    
    











ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P






    
    
        wherein bold underlined amino acids represent essential amino acids for the activity of said peptide, and wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids,
        said peptide being able to specifically inhibit the RhoA GEF activity of Trio and the RhoA GEF activity of the oncogenic form of Trio, i.e. Tgat,
        said peptide having inhibiting properties at least 2 fold, preferably 3 fold, more preferably 5 fold higher compared to the inhibiting activity of TRIPα (SEQ ID NO:1),
        with the proviso that said amino acid sequence does not comprise or consist of the amino acid sequence SEQ ID NO: 1,
        at least a nucleic acid as defined above, preferably a nucleic acid coding for the above peptide, and
        at least a recombinant vector as defined above, preferably a recombinant vector comprising the above mentioned nucleic acid molecule coding for the above mentioned peptide,
        or their pharmaceutically acceptable salts thereof,
    
    


in association with a pharmaceutically acceptable vehicle.
Dosage of the active substance depends on the administration route, and can be easily determined by a skilled person. The pharmaceutical composition according to the invention can be administered by intravenous route, sub-cutaneous route, systemic route, or can be administered locally by infiltration, or per os.
The invention relates, in one advantageous embodiment, to the pharmaceutical composition as defined above, characterized in that it contains from about 1 μg to about 10 mg, preferably from about 700 μg to about 80 mg, more preferably from about 7 to about 40 mg, as a unit dose, of the above mentioned peptide and/or nucleic acid and/or recombinant vector.
The invention relates, in one advantageous embodiment, to the pharmaceutical composition previously defined, in association with at least a chemotherapy agent,

    
    
        said chemotherapy agent being in particular
        
            a. chosen from the group comprising or consisting of: doxorubicin, methotrexate, vinblastine, vincristine, cladribine, fluorouracil, cytarabine, anthracyclines, cisplatin, cyclophosphamide, fludarabine, gemcitabine, aromatase inhibitors, irinotecan, navelbine, oxaliplatin, taxol, and docetaxel, or
            b. chosen from the group comprising or consisting of: bevacizumab, pegaptanib, and ranibizumab, which are anti angiogenic agents.
        
        
    
    


In one another embodiment, the invention relates to the pharmaceutical composition previously defined, for a simultaneous, separated or sequential use for the treatment of cancer.
In the invention, “cancer” designates benign tumors or malignant tumors.
Malignant tumors are a class of diseases in which a group of cells display uncontrolled growth (division beyond the normal limits), invasion (intrusion on and destruction of adjacent tissues), and sometimes metastasis (spread to other locations in the body via lymph or blood). These three malignant properties of cancer differentiate them from benign tumors, which are self-limited, and do not invade or metastasize.
Cancer according to the invention includes solid tumors, leukemia and lymphomas.
The invention also relates to the use of the recombinant vector as defined above, for the preparation of a drug intended for the treatment of cancer.
The invention also relates to the use of the isolated nucleic acid as defined above, for the preparation of a drug intended for the treatment of cancer.
The invention will be better understood with the following figures and examples, but in any case have to be limited to them.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a schematic representation of Trio and its splice variant Tgat, and the Tgat mutants
FIGS. 2A and 2B show that the transforming activity of Tgat requires its GEF activity towards RhoA.
FIG. 2A represents a RhoA activation assay. Lysates of NIH3T3 cells stably expressing GFP, GFP-Tgat, or GFP-TgatL190E were subjected to GST-pulldown using recombinant RBD (RhoA binding domain of Rhotekin). The levels of GTP-bound RhoA (top panel) and total RhoA protein (middle panel) were assessed by Western Blot with a monoclonal anti-RhoA antibody. All GEF constructs were expressed at a similar level as shown by Western blotting using an anti-GFP antibody (lower panel).
FIG. 2B represents the quantification of the RhoA activation assay from at least three independent experiments. Y-axis represents Fold RhoA activation. “Fold RhoA activation” means the amount of RhoA-GTP in the sample, as compared to the amount in the GFP control, which was set to 1.
FIGS. 3A and 3B show the ex vivo transforming properties of Tgat.
FIG. 3A represents a focus formation assay of NIH3T3 cells stably expressing GFP, GFP-Tgat, GFP-TgatL190E or GFPTrio.
FIG. 3B represents Quantification of three independent focus formation assays. The Y-axis represents the foci formation expressed in %. The number of foci induced by Tgat was set to 100%. Error bars represent standard deviation.
FIG. 4 represents the inhibition of Tgat GEF activity by TRIPT16M/L17S (SEQ ID NO: 41) and TRIPE32G (SEQ ID NO: 40) in vitro. FRET fluorescence exchange assays were performed using constant concentrations of RhoA (1 μM), equal amounts (0.5 μM) of Tgat (left panel) or Trio DH2 (right panel), and increasing concentrations of GST-TRIP peptides, up to 100 μM. Results were expressed as kobs values plotted as a function of the indicated TRIP inhibitor concentration.
FIG. 5 represents a histogram showing the apparent inhibition constants (Ki app) of the TRIP peptides for Tgat and Trio DH2, as indicated. The values and error bars are calculated from at least three independent experiments. Error bars represent standard deviation
FIGS. 6A-6F represent the specificity of the optimized inhibitory peptides according to the invention TRIPT16M/L17S (SEQ ID NO: 41) and TRIPE32G (SEQ ID NO: 40).
Figures represent the comparison of TRIPE32G and TRIPT16M/L17S inhibition efficiency on different GTPase/RhoGEF systems, using 1 μM GTPase and 0.5 μM GEF as follows:
FIG. 6A. RhoA/Tgat;
FIG. 6B. RhoA/p63RhoGEF;
FIG. 6C. RhoA/p115RhoGEF;
FIG. 6D. RhoA/Lbc;
FIG. 6E. RhoA/Dbl;
FIG. 6F. RhoG/Trio DH1PH1.
In each assay, the peptides were used at a concentration of 20 μM, corresponding to a 40 fold molar excess of inhibitor versus GEF. All fluorescence kinetics assays were performed using 1 μM mant-GTP. Results are expressed as Relative Fluorescence Units (RFU) versus time. The reaction performed in the absence of GEF reflects the spontaneous exchange activity of the GTPase.
Curves with squares (▪) represents experiments with GEF+GST, curves with triangles (▴) represent experiments with GEF+GST-TRIPE32G, curves with reverse triangles (▾) represent experiments with GEF+GST-TRIPT16M/L17S, and curves with reverse lozenges (♦) represent experiments with no GEF+GST.
FIGS. 7A and 7B represent the Tgat GEF inhibition by TRIPE32G in cells.
The RhoA activation in NIH3T3-Tgat cells stably transfected with GFP, GFP-TRIPE32G or GFPTRIP T16M/L17S was assayed by the GST-RBD-pulldown assay as described in FIG. 2A.
FIG. 7A represents the levels of GTP-bound and total RhoA protein, shown in the upper two panels. Expression levels of all GFP-tagged proteins are shown in the lower panel.
FIG. 7B represents a quantification of the RhoA activity assay from at least three independent experiments. Error bars represent standard deviation.
FIG. 8 represents the effect of GFP-TRIPE32G on RhoA activation induced by Dbl (left panel) or Tgat (right panel) in NIH3T3 cells, assayed by GST-RBD pulldown. The levels of GTP-bound and total RhoA protein are shown in the upper two panels. Expression levels of Myc-Dbl and of all GFP-tagged proteins are shown in the lower two panels.
FIGS. 9A and 9B represent TRIPE32G mediated inhibition of the transforming activity of Tgat ex vivo.
FIG. 9A represents the focus formation assay of NIH3T3 cells, stably expressing GFP or GFP-Tgat, together with GST or GST-TRIPE32G.
FIG. 9B represents the quantification of three independent focus formation assays. The number of foci formed by Tgat/GST expressing cells was set to 100%.
FIGS. 10A and 10B represent the TRIPE32G inhibition of the transforming activity of Tgat in vivo.
FIG. 10A represents tumor formation in Balb/c nude mice. NIH3T3 cells stably expressing GFP-Tgat/GST or GFP-Tgat/GSTTRIP E32G were injected subcutaneously into the flanks of Balb/c nude mice and tumor volume was measured every week. The graph is representative of the three independent assays that were performed.
FIG. 10B represents the tumor weights (in grams) after the experiments. Ten weeks post graft, mice were euthanised, tumors were excised and weighed, and the mean tumor weight was plotted on the graph. (*) A paired Student's t-test was performed, matching the samples for each mouse, and the P value was 0.019. Error bars represent standard deviation in all graphs.



EXAMPLES
Example 1
TRIPα Derived Peptides Target an Oncogenic RhoGEF
Rho GTPases and their GEFs represent challenging targets for inhibition, not only to understand their function but also in pathology, and strategies to inhibit their function are actively being sought (Bos et al., 2007). The main issue when trying to inhibit RhoGEFs is to achieve a high degree of specificity within such a complex and large family of related proteins, and to target protein-protein interactions which are not yet well characterized. To date only few strategies have been devised successfully, allowing the discovery of chemical and peptidic RhoGEF inhibitors, that block the activation of Rho GTPases by their cognate GEFs (Blangy et al., 2006; Gao et al., 2004; Schmidt et al., 2002). The inventors described previously peptide aptamer screening as such a strategy, which enabled them to discover the first RhoGEF inhibitor (Schmidt et al., 2002). Peptide aptamers are short peptides constrained by a bacterial Thioredoxin (TrxA) scaffold, which bind to their protein targets with high affinity (Baines and Colas, 2006; Hoppe-Seyler et al., 2004). This technology has been applied initially to the discovery of inhibitors against various intracellular targets, involved mainly in cell-cycle control or cell survival (Butz et al., 2000; Colas et al., 1996; Crnkovic-Mertens et al., 2003; Fabbrizio et al., 1999; Martel et al., 2006; Nouvion et al., 2007). Peptide aptamers present interesting advantages over other classes of inhibitory molecules, mainly because of their simple design and their high degree of binding specificity, which enables them to discriminate between closely related proteins within a functional family. But most remarkably, these highly combinatorial proteins are screened and designed to function inside living cells and allow the study of protein function within complex regulatory networks (Bickle et al., 2006). The RhoGEF inhibitor the inventors have isolated using this aptamer screening strategy, called TRIPα (Trio Inhibitory Peptide α), targets specifically the DH2-PH2 tandem of the RhoGEF Trio and inhibits its activation of RhoA both in vitro and in intact cells, reverting the neurite retraction phenotype induced by Trio DH2-PH2 in PC12 cells (Schmidt et al., 2002). Most interestingly, although TRIPα was initially selected with the TrxA scaffold, it remained equally active as a linear peptide (Schmidt et al., 2002). The recently identified oncogenic RhoGEF Tgat is an interesting novel candidate target for such peptidic inhibitors. Indeed, Tgat has been identified from Adult T-Cell Leukemia (ATL) patient cells as a gene with oncogenic potency and originates from an alternate splicing of the trio gene (hence the name Tgat, for Trio-related transforming Gene in ATL Tumor cells) (Yoshizuka et al., 2004). Tgat retains only the RhoA-specific DH2 domain of Trio and, instead of the associated PH2 domain, carries a unique C-terminal sequence of 15 amino acids. It induces cell transformation and tumor formation in nude mice (Yoshizuka et al., 2004) and has been proposed to enhance tumor invasion by stimulating Matrix MetalloProteinases (MMPs) via the RECK protein (Mori et al., 2007) and by activating the transcription factor NF-κB, which plays a crucial role in tumorigenesis, including ATL (Yamada et al., 2007).
In this context, designing peptide inhibitors against the RhoGEF Tgat is very challenging from a pathological point of view. In this study the inventors devised a screen to identify optimized peptides based on the TRIPα peptide. This screen allowed them to identify a novel peptide that is active as a Tgat inhibitor, targeting its GEF activity in vitro in a highly specific manner. Moreover, it strongly reduces its oncogenic properties in vivo, most remarkably by decreasing foci formation and tumor development in nude mice. The peptide optimization strategy identifies the first inhibitor of the Tgat oncogene, and demonstrates that aptamers can be used to interfere with RhoGEF functions in vivo with exquisite specificity.
Results
The GEF Activity of the DH Domain is Required for Tgat-Induced Transformation.
In order to design inhibitors that would target Tgat oncogenic activity, the inventors first established whether the GEF activity of Tgat is involved in transformation. To do so, the inventors designed a Tgat mutant, called TgatL190E, which harbors a point mutation in its DH domain, the equivalent mutation in Trio DH2-PH2 being known to abolish its exchange activity on RhoA (FIG. 1) (Bellanger et al., 2003). The inventors established NIH3T3 cell lines stably expressing similar levels of GFP or GFP-tagged Tgat or TgatL190E (FIG. 2A, lower panel), and analyzed the ability of these constructs to activate RhoA and to induce transformation. The inventors measured RhoA activation in intact cells by pull-down of RhoA-GTP, using the RhoA-binding domain (RBD) of its effector Rhotekin fused to GST (FIG. 2A-B). Tgat strongly stimulated RhoA activation (8-fold over control), while the GEF-impairing mutation completely abolished the formation RhoA-GTP in cells. The inventors then tested the oncogenic properties of the different Tgat constructs, by scoring the formation of foci in the different cell lines (FIG. 3A-B). While Tgat-expressing cells formed numerous foci, TgatL190E-expressing cells presented no foci after 3 weeks in culture, showing that the GEF activity of the DH domain is required for the transforming potential of Tgat. In addition, NIH3T3 cells stably expressing full length Trio did not exhibit any foci, showing that the transforming potential is not inherent to Trio but only to its oncogenic isoform Tgat (FIG. 3A-B).
Strategy to Identify a Tgat Inhibitor.
Since the GEF activity of Tgat is necessary for transformation, molecules that block this biochemical activity could also inhibit its transforming potential. The inventors previously identified a peptide aptamer, TRIPα, which targets the RhoA-specific DH2-PH2 tandem of Trio (Schmidt et al., 2002). As Tgat harbors the DH2 domain of Trio, the inventors tested whether Tgat activity was also inhibited by TRIPα. However, and very surprisingly, when tested in a [3H]-GDP dissociation inhibition assay in vitro, TRIPα was only a weak inhibitor of Tgat (Kiapp=89±33 μM; see below).
The inventors thus sought to optimize TRIPα inhibition efficiency, by first determining which amino acids are essential for its inhibition, using an Ala-Scan analysis.
Each residue of the active core of TRIPα (amino acids 9-36; Schmidt et al., 2002) was mutated to alanine, except cysteines which were changed into serines. All TRIPα mutants were then tested for their inhibitory activity on Trio DH2-PH2 in [3H]-GDP dissociation assays. This analysis mapped two essential regions of TRIPα, amino acids 9-20 and 28-33, where single mutations were sufficient to impair inhibition (see table 3).







TABLE 3





Alanine-scanning of the active core of TRIPα.

















(SEQ ID NO: 197)














Inhibition efficiency of the mutated peptides was measured by [3H]-GDP dissociation assays using Trio DH2-PH2, and compared to the original TRIPα peptide.



Black bold letters 


correspond to residues strictly required for inhibition;



Grey bold underlined letters 


correspond to residues retaining a weak inhibitory potential.



All the other residues are non essential.



Shaded residues (grey boxes 


correspond to regions (aa 9-20 and 28-33) that emerge as being essential for TRIPα activity.






However, none of the mutants exhibited stronger inhibition towards Trio DH2-PH2 and were not further investigated on Tgat.
The inventors next reasoned that peptides that would bind stronger to the GEF domain may also be better at inhibiting its activity. The inventors thus generated a library of peptide aptamers derived from TRIPα by random mutagenesis, which the inventors screened for GEF binding in a yeast two-hybrid assay. The inventors chose a system in which the threshold of interaction detection can be modulated by the concentration of the 3-aminotriazole (3-AT) drug (Sardet et al., 1995). Since Tgat is toxic in yeast, the inventors used Trio DH2-PH2 to screen this TRIP-like peptide library. Thirty-five independent clones bound to Trio DH2-PH2 at concentrations of 3-AT at which no interaction with TRIPα was detected anymore (80-120 mM). These clones were then produced as GST fusions and analyzed for their inhibition of Trio DH2-PH2, using the [3H]-GDP dissociation assay.
Table 4 represents the 11 peptides being stronger inhibitors than TRIPα. In particular, the peptides according to the invention have an increase of activity from about 3 fold to about 6 fold compared to TRIPα. Inhibition efficiency was measured on Trio DH2-PH2 and compared to TRIPα, as described in Table 3.
Analysis of their sequence revealed that they contained one to four mutations per peptide, and that, consistently, most of them resided within the two regions identified as crucial for the inhibitory properties of TRIPα.







TABLE 4







represents the amino acid sequence of the optimized TRIP-


like peptides according to


the invention, obtained by random


 mutagenesis of the original TRIPα peptide.









Name
SEQ ID NO:
SEQUENCE





TRIPα
197






E32G
40






T16M/L17S
41






T16M
42






T16M/S32G
44






A1T/V18D/F27L
45






E32G/S36T
46






T16A/V18G/E32G/I38N
47






V18A/E24A/E32G
48






N13D/T16M/C34R
49






T16A/L17S/C34R/S36P
50






V18D/I38S
51













The inventors then analyzed the inhibitory activity towards Tgat of TRIPE32G and TRIPT16M/L17S, the two TRIP-like peptides that displayed the highest inhibition on Trio DH2-PH2 (Table 4). Both peptides inhibited Tgat GEF activity in a dose-dependent manner in a kinetics fluorescence assay, while GST alone (not shown) or GST-TRIPα, at the same concentrations, had no effect (FIG. 4). Accordingly, the apparent inhibition constant (Kiapp) of TRIPα towards Tgat was 89±33 μM, and decreased to 7.4±5 μM for TRIPE32G and 5.1±4 μM for TRIPT16M/L17S (FIG. 5). These data show that TRIPE32G and TRIPT16M/L17S are both about 15 times more efficient than TRIPα at inhibiting the exchange activity of Tgat. Interestingly, the optimized peptides were equally efficient on Tgat and on Trio DH2, as shown by their similar Kiapp values (FIGS. 4 and 5). This suggests that the unique Cterminal extension of Tgat is not involved in the inhibitory mechanism of the optimized peptides, and is consistent with the fact that this sequence does not interfere with the GEF activity in vitro (data not shown).
Similar results were obtained with the mutant TRIPT16M.
Inhibition by TRIP Peptides is Specific for Tgat.
The inventors then analyzed the specificity of the optimized TRIP peptides, by testing their inhibitory properties on other related RhoGEFs. The inventors had shown previously that TRIPα is not active on the RhoA-specific GEFs p115RhoGEF, Lbc, p63RhoGEF, nor on Dbl (Schmidt et al., 2002 and unpublished results). Similarly, when tested in mant-GTP fluorescence kinetics at a concentration at which Tgat is fully inhibited, TRIPE32G and TRIPT16M/L17S had no effect on the exchange activities of these closely related RhoGEF/Rho-GTPase tandems, p115RhoGEF/RhoA, Lbc/RhoA, Dbl/RhoA, and even the very closely Trio-related p63RhoGEF/RhoA (70% identity within the DH-PH module), or Trio DH1-PH1/RhoG (40% identity with Tgat) (FIG. 6). Taken together, these data show that the optimized TRIP peptides are highly specific for Tgat and Trio DH2.
TRIPE32G Inhibits the Transforming Activity of Tgat In Vivo.
The inventors next analyzed whether their TRIP-like peptides inhibited Tgat-mediated RhoA activation in intact cells. For that purpose, NIH3T3 cells stably expressing Tgat were transfected with the GFP-tagged TRIP-like peptides or GFP alone, and RhoA activation levels were assessed by the GST-RBD pull-down assay. Although TRIPE32G and TRIPT16M/L17S inhibited the in vitro GEF activity of Tgat to a similar extent, TRIPE32G was more efficient than TRIPT16M/L17S at inhibiting Tgat-mediated activation of RhoA in cells (FIG. 7A-B). These data show that, in addition to its effect on in vitro guanine nucleotide exchange, TRIPE32G inhibits Tgat GEF activity also in intact cells. In order to verify the exquisite specificity of the peptide towards Tgat/DH2 in vivo, the inventors analyzed by GST-RBD pull-down assay whether TRIPE32G could inhibit oncogenic Dbl mediated RhoA activation in intact cells. FIG. 8 shows that, in contrast to its effect on Tgat activity, TRIPE32G was not able to inhibit RhoA activation by Dbl, confirming the in vitro specificity of TRIPE32G towards Tgat. The inventors then investigated whether TRIPE32G was able to inhibit Tgat-induced transformation. To do so, the inventors stably expressed GST or GST-TRIPE32G in Tgat-expressing NIH3T3 cells and characterized their transforming potential. After 3 weeks of culture, the foci present in Tgat expressing cells were severely reduced when co-expressing TRIPE32G (FIG. 9A-B). This reduction is not due to a non-specific effect of TRIPE32G on cell proliferation or apoptosis (data not shown). These data show therefore that targeting Tgat GEF activity with TRIPE32G is sufficient to impair Tgat transforming activity. To further establish the inhibitory effect of TRIPE32G on Tgat transforming activity in vivo, the inventors subcutaneously inoculated Balb/c nude mice with NIH3T3 cells expressing either Tgat, or Tgat and TRIPE32G, and analyzed their effect on tumor formation. Tgat-transformed cells produced tumors in ten out of twelve mice. Remarkably, when TRIPE32G was co-expressed with Tgat, only seven mice had tumors and the inventors observed a delay of about three weeks in the formation of tumors (FIG. 10A). In addition, even though tumor formation was not abolished, the weight of the tumors was significantly reduced when TRIPE32G was expressed (FIG. 10B). Altogether, these data show that expression of TRIPE32G strongly reduces Tgat transformation activity in cells and affects tumor formation in nude mice, most likely by inhibiting Tgat-mediated GTP loading of RhoA.
Interpretation
Peptide Aptamers as New Inhibitors of RhoGEFs.
Because of their deregulation in many human disorders including cancer, Rho GTPases and their activating GEFs represent challenging targets for inhibition. In humans there are only 20 Rho GTPases but more than 70 RhoGEFs, and it appears that signaling specificity is mostly determined by the GEFs, which activate the GTPases at defined timing and location. RhoGEF inhibitors therefore represent an emerging field of investigation. Here the inventors developed a peptide aptamer screening strategy to inhibit the RhoGEF Tgat, a potential target in the ATL disease. Since Tgat is an isoform of the RhoGEF Trio, which includes the RhoA-specific DH2 domain plus a unique C-terminal sequence, the inventors based their screen on their previously identified Trio inhibitor TRIPα, the first peptidic RhoGEF inhibitor described, which targets the DH2-PH2 domain of Trio (Schmidt et al., 2002). Intriguingly, despite the fact that Tgat harbors the Trio DH2 domain, their original TRIPα inhibitor was rather ineffective at inhibiting Tgat. This suggests that the PH2 domain of Trio is involved in the mechanism of action of TRIPα, and that its replacement by the C-terminal extension decreases TRIPα's ability to inhibit the GEF activity of Tgat.
The inventors show here that GEF inhibitors selected with the peptide aptamer screening approach are readily amenable to structure-activity relationship analysis and optimization. Of the 28 residues located in the active core of TRIPα, alanine scanning mapped 9 residues in two regions (residues 9-20 and 28-33) that were critical for the catalytic activity, while 6 had a moderate effect and the others had no effect. The inventors also show that peptide aptamer optimization can be achieved by random mutagenesis combined with a selection screen based on interaction strength. At least one third of the isolated clones yielded stronger inhibition, thus validating the rationale of the screen. The two selected peptides, TRIPE32G and TRIPT16M/L17S, were 15-fold more efficient than TRIPα and inhibited Tgat GEF activity at concentrations lying in the low micromolar range. Interestingly, mutations found in these clones also fell within the two important regions identified by the Ala-scan. Furthermore, this approach allowed us to turn TRIPα into a Tgat inhibitor, which could be achieved with as few as one mutation, E32G. It remains to be determined whether these different amino acids are important for binding to the GEF and/or for inhibition of the exchange reaction. It should be emphasized that the screening and optimization method of the inventors is effective, irrespective of the inhibitory mechanism, which is of big advantage for the discovery of inhibitors of protein-protein interactions. The way the original screen was performed, i.e. two-hybrid screening with the GEF as bait in the absence of GTPase, strongly suggests that the target of the peptides is the GEF itself, rather than the GTPase. This is reinforced by the fact that the peptides do not inhibit spontaneous GDP release from RhoA using [3H]-GDP-loaded RhoA (data not shown), and by their specificity data in vitro and in intact cells, which show that other GEF activities towards RhoA are not inhibited (FIGS. 6 to 8).
Peptide Aptamers are Functional In Vivo
The screening method of the inventors demonstrates that TRIPE32G is not only effective and specific at inhibiting Tgat GEF activity in vitro, but that it also blocks Tgat-induced cell transformation and tumor formation in vivo. This is the first example of a peptidic RhoGEF inhibitor that is functional in vivo, and demonstrates that aptamers can be used as active peptides to perturb the function of GEFs in vivo. In this context, efficient in vivo delivery is a critical issue when working with peptides. To circumvent this problem, the use of recently developed cell penetrating peptides represents a good means of delivery for TRIPE32G, and could be an attractive strategy to investigate the contribution of Tgat in leukemogenesis. Indeed, to date, the incidence of Tgat in ATL leukemogenesis is unknown, but given the strong effect of Tgat on RhoA activation and transformation, the inventors can hypothesize that Tgat is involved in the progression of ATL by contributing to RhoA-mediated proliferation and/or metastasis. The inventor's series of TRIP peptides should now prove useful tools to decipher the cellular role of Tgat.
Peptide Aptamers Versus Other GEF Inhibitor Screening Strategies.
Besides the peptide aptamer screening approach of the inventors, other strategies have recently been devised to discover chemical inhibitors of Rho GTPase/GEF tandems, and also other classes of small G proteins, such as the Arf family and their activating GEFs (Blangy et al., 2006; Desire et al., 2005; Gao et al., 2004; Mayer et al., 2001; Shutes et al., 2007; Viaud et al., 2007). Computer-assisted virtual screening, for example, identified the NSC23766 compound, based on structure-function information of the Rac1/Tiam1 complex. This powerful molecule inhibits specifically Rac1-induced events in vitro and in vivo, however the targeted associated RhoGEFs include at least Tiam1 and Trio DH1-PH1 (Gao et al., 2004). In silico screening also yielded the LM11 compound, which inhibits specifically the ARNO/Arf1 interface in vitro and is active in cells (Viaud et al., 2007). Given their membrane permeability, both NSC23766 and LM11 have the advantage of being easily applied in vivo. The Yeast Exchange Assay is another screening method that allowed the identification of the TrioDH1-PH1 specific NPPD compound and its analogues (Blangy et al., 2006). Like peptide aptamer screening, this strategy has the advantage over virtual screening of identifying inhibitors directly in cells, and without any bias as to the targeted interaction site. Finally, in vitro RNA-aptamer screening selected the RNA aptamer M69 as an inhibitor of the Cytohesin/Arf1 tandem (Mayer et al., 2001). Like peptide-aptamers, these RNA aptamers are highly combinatorial and easily screened, but their application as potential drugs remains limited, due to difficult in vivo delivery. To circumvent this problem, RNA-aptamer displacement represents an elegant method, in which a small-molecule library is screened for compounds that displace the RNA-aptamer from its target and reproduce its inhibitory activity (Hafner et al., 2006).
The inventors' study shows that peptide aptamer screening represents a valid strategy for inhibitor identification that can be applied to a variety of different proteins, because of the in vivo screening method and the highly combinatorial libraries available, yielding strong affinity inhibitors. This is illustrated here by the identification of a highly specific peptidic RhoGEF inhibitor targeting the Tgat oncogene in vitro and in vivo.
Experimental Procedures
DNA Constructs—
Tgat (aa 1-255) was designed by ligating dimerized oligonucleotides coding for the specific C-terminus of Tgat (15 aa) to the Trio DH2 domain (residues 1862-2101, corresponding to aa 1-240). The oligonucleotide sequences are available upon request. The TgatL190E mutant was obtained using the Quick Change Site Directed Mutagenesis Kit (Stratagene Inc.), according to the manufacturer's instructions. To create stable NIH3T3 cell lines, GFP-tagged Tgat, TgatL190E and full length Trio were cloned into the puromycin-resistant retroviral vector pBabePuro. GST-tagged TRIP peptides were cloned into the G418-resistant retroviral vector pLXSN. For transient transfections, both Tgat and TRIP peptides were cloned into the pEGFP vector (Clontech Inc.). Myc-Dbl was a kind gift of Michael Olson (Beatson Institute for Cancer Research, Glasgow). For in vitro GEF assays, Tgat (aa 1-255) was fused to maltose-binding protein (MBP) by cloning into a modified pMAL C2X vector (New England Biolabs Inc.). The TRIP peptides were fused to GST by cloning into the pGEX-5X2 vector (GE Healthcare Inc.). All constructs were checked by sequencing.
Expression and Purification of Recombinant Proteins—Tgat.
MBP-Tgat and MBP-DH2 expression in E. coli was induced for 24 h at 16° C. with 0.1 mM isopropylthiogalactopyranoside (IPTG). After cell lysis (in 50 mM Tris pH 7.5, 1 mM EDTA, 2 mM MgCl2, 1 mM DTT), the suspension was centrifuged at 10,000 g for 20 min, then at 400,000 g for 1 h30. The supernatant was applied to a Q-Sepharose column fast flow (GE Healthcare) equilibrated with lysis buffer. The protein was eluted with a linear gradient of 0-250 mM NaCl in 50 mM Tris pH 7.5. Fractions containing the protein were adjusted to a concentration of 2 M NaCl and loaded on a Phenyl sepharose Fast flow High Sub (GE Healthcare Inc.). The protein was eluted with a linear gradient of 2-0 M NaCl in 50 mM Tris pH 7.5. The purified proteins were concentrated on a Vivaspin concentrator (Vivascience AG Inc.) at 18 mg/mL. Other proteins. Recombinant GST-Trio DH2-PH2, GST-Trio DH1-PH1, GST-Dbl (DH-PH domain), GST-Lbc (DH-PH), GST-p63RhoGEF (DH domain) and GST-RhoG were purified as described previously (Schmidt et al., 2002; Souchet et al., 2002). Expression and purification of GST-p115RhoGEF using the baculo virus system will be described elsewhere. GST-Peptides. GST-TRIP peptides were purified as described (Schmidt et al., 2002), except that the cell lysate was centrifuged as above, before loading on a GSTrap Fast Flow column (GE Healthcare Inc.) equilibrated with lysis buffer. Peptides were eluted with reduced glutathione (10 mM) in Tris 50 mM pH 7.5 and concentrated on Vivaspin concentrator at about 5-10 mg/mL.
Optimization of TRIPα—Alanine-Scanning of TRIPα.
Every amino acid of the active core of TRIPα (amino acids 9-36) was mutated to alanine (or serine for cysteine residues) by site directed mutagenesis of GST-TRIPα. Each TRIPα mutant was tested for its inhibitory activity on DH2-PH2 in [3H]-GDP dissociation assays.
Two-Hybrid Screening of TRIPα-Like Peptides.
An aptamer library derived from TRIPα was created by PCR-based random mutagenesis of TRIPα inserted into the yeast two-hybrid vector pPC86. Sequencing of a statistically representative number of clones yielded a mutation rate of  ̃3 mutations/clone. 6×105 independent clones were screened for interactors, using Trio DH2-PH2 (in the pPC97 vector) as a bait, in the MAV 103 yeast strain, on high concentrations of 3-AT (3-amino-triazol, Sigma) (80-120 mM). Selected peptides were then produced as GST-fusions and analyzed for their inhibition of Trio DH2-PH2 using the [3H]-GDP dissociation assay.
Nucleotide Exchange Kinetics Assay—
Specific exchange rates of Tgat were measured with a fluorescence-based kinetics assay, using a 6His-RhoA construct (gift of Dr Derewenda, Charlottesville University, Virginia) purified as described (Oleksy et al., 2004). Exchange activities were followed by fluorescence resonance energy transfer (FRET) between the GTPase tryptophanes (λex=292 nm) and the methylanthranyloil group of mant-GTP (λem=440 nm) as described (Zeeh et al., 2006). All fluorescence measurements were performed with a CARY Eclipse fluorimeter (Varian). For each kobs determination, RhoA (1 μM) and Tgat (or Trio DH2) were preincubated 3 min at 25° C. in 700 μL reaction buffer (50 mM Tris pH 7.5, 50 mM NaCl, 2 mM MgCl2, 1 mM DTT). The exchange reaction was initiated by 10 μM mant-GTP and measured for 10 min until the plateau was reached. kobs were calculated by fitting the FRET fluorescence changes to a single exponential, using the Kaleidagraph software. Specific exchange activities were calculated by linear regression of kobs values determined for a range of GEF concentrations (0, 0.2, 0.3, 0.4, 0.5 and 1 μM).
Nucleotide Exchange Inhibition Assays—
Radioactive [3H]-GDP dissociation assays were performed as described (Schmidt et al., 2002). Briefly, 0.15 μM GST-Trio DH2-PH2 was preincubated for 15 min with 3 μM of GST-TRIP inhibitors. The reaction was started by addition of 0.4 μM [3H]-GDP-loaded RhoA and 1 mM GTP, and the reaction mix was filtered after 0 min and 15 min incubation at 25° C. Inhibition efficiency is expressed as the ratio between [3H]-GDP-bound RhoA at 15 and 0 min. Apparent inhibition constants (Kiapp) of TRIP-like peptides were determined from kobs values obtained at increasing peptide concentrations using the above fluorescence nucleotide exchange assay. Kiapp was calculated from the hyperbolic fit of kobs values as a function of the inhibitor concentration as described (Zeeh et al., 2006). TRIP-like peptide specificity was assayed using mant-GTP fluorescence kinetics (λex=360 nm, λem=460 nm) in a FLX800 Microplate Fluorescence Reader (BioTek Instruments). 0.5 μM Tgat, p63RhoGEF, Lbc, and p115RhoGEF, or 0.1 μM Dbl and Trio DH1-PH1 were preincubated 5 min at 25° C. in the presence of 20 μM GST, GST-TRIPE32G or TRIPT16M/L17S and 1 μM mant-GTP. The exchange reaction was initiated by addition of 1 μM RhoA or RhoG and monitored for 10 min.
Cell Lines, Transfection and Focus Formation Assay—
NIH3T3 cells were maintained as described previously (Sirvent et al., 2007). Transient transfection experiments were performed using the Jet PEI reagent, according to the manufacturer's protocol (QBiogene Inc.). NIH3T3 cell lines stably expressing GFP-Tgat, GFP-TgatL190E, or GFP-Trio, with or without the GST-TRIP peptides, were generated as follows: the indicated retroviral constructs were transfected into BOSC packaging cells, using the Lipofectamine reagent (Invitrogen Inc.). Forty-eight hours after transfection, virus containing supernatants were collected and used to infect NIH3T3 cells. Infected cells were selected with 6 μg/mL puromycin and/or 1 mg/mL G418 and stable transfectants were pooled after selection. Tgat or TRIP mRNA levels in the different cell lines were monitored by RTPCR, and protein expression levels by Western blot analysis using a polyclonal anti-GFP antibody (Toney Pines Laboratories). Focus formation assays were performed using stable NIH3T3 cell lines as indicated, seeded at 5×104 cells in 6-well plates and maintained for 15 to 21 days in 10% FBS. Medium was renewed every two days. After staining with Crystal Violet (1%), plates were photographed and foci were scored using the Metamorph software. All experiments were done in triplicate.
RhoA Activation Assay in Cells—
The level of GTP-bound RhoA was measured by a GST pulldown assay as described (Schmidt et al., 2002). Briefly, cell lysates were incubated with glutathione beads coated with the recombinant Rho-binding domain (RBD) of the RhoA specific effector Rhotekin (Cytoskeleton Inc.). Total or GTP-bound RhoA in the samples was revealed by Western blot analysis, using a monoclonal anti-RhoA antibody (Santa-Cruz Biotechnology Inc.).
Mice and Xenografting—
Female Balb/c nu/nu mice were purchased from Charles River France and used at 6-8 weeks of age. 12 Balb/c nu/nu mice were subcutaneously grafted with 2×106 cells of each cell line on both sides (Tgat on the left and Tgat+TRIPE32G on the right flank of the leg). The appearance of tumors was scored visually every week. 10 weeks post graft, mice were euthanized and tumors excised and weighed. mRNA and protein levels in the tumors were verified by RT-PCR and Western blot (data not shown).
Example 2
Targeting Trio Amplification in Human Cancer
The Trio gene has been found amplified in a variety of human cancers, including glioblastoma, breast cancer, soft tissue sarcoma, urinary bladder cancer, cervical carcinoma, oral squamous cell carcinoma and lung cancer (Adamowicz et al., 2006; Baldwin et al., 2005; Calaf and Roy, 2007a, b; Coe et al., 2005; Garnis et al., 2005; Kloth et al., 2007; Lane et al., 2008; Mhawech-Fauceglia et al., 2006; Ng et al., 2007; Salhia et al., 2008; Zheng et al., 2004). CGH array studies, aimed at characterizing the genetics of these various cancer types, revealed amplification of chromosome 5p and of the trio gene in particular, which, in many cases, was correlated to an increase in its transcript. In addition, in urinary bladder cancer for example, Trio amplification was strongly associated with invasive tumor phenotype, high tumor grade and rapid tumor cell proliferation. In other cases, like glioblastoma or breast cancer, Trio overexpression was associated with poor prognosis and poor patient survival. This suggests a potential implication of Trio in the aggressive phenotype of these cancers, most probably by activating Rho GTPase signaling. In addition, an oncogenic Trio isoform, Tgat (harboring only the RhoA-activating GEF2 domain of Trio), has been identified in patients with Acute T-cell leukemia (ATL).
Trio thus appears as an attractive target for drug design and the TRIP peptides according to the invention, which manipulate its cellular activity with high specificity, are therefore of enormous therapeutic potential.
In this context, the inventors have analyzed the contribution of Trio and/or its oncogenic isoform Tgat in the proliferative/motile/invasive properties of tumor-derived cell lines, and have evaluated the inhibitory potential of the TRIP peptides to inhibit these phenotypes.

    
    
        A. Using available tumor-derived cell lines originating from various cancer types where Trio is overexpressed, the inventors have first analysed if high levels of Trio protein correlate with an over-activation of its target GTPases, Rac1 and RhoA. To do so, the inventors have performed Rho-activation pulldown assays as described earlier (Bouquier et al., 2009), on the following cell lines (but not limited to):
        
            Bladder tumor cell lines that show Trio amplification: 5-HTB, RT11-D21, RT112 and CRL-7930, compared to other bladder cell lines without Trio amplification (3-HTB, 4-HTB),
            Cervical squamous cell carcinoma with Trio upregulation: CasKi, SiHa, HeLa, compared to cell lines without Trio amplification (CSCCI, CSCC7, CCB, CC10A, CC10B, CCII− and CCII+),
            Small cell lung carcinoma SCLC cell lines: NCI-H187, NCI-H378, NCI-H889, NCI-H1184, NCI-H1607, NCI-H1672, NCI-H1963, NCI-H2141, NCI-H2171, NCI-H2195, NCI-H2227, HCC33, NCI-H82, NCI-H289 and NCI-H526.
            Breast cancer cell lines: MCF7, MDA-435 and SKBR3.
        
        
        B. In those cell lines where RhoA activation is enhanced, the inventors have assessed proliferation, motility and invasive properties, compared to cell lines with basal level RhoA activation. Theses experiments have been done by cell growth and focus formation assays, anchorage-independent growth assays and wound-healing assays, as well as cell invasion assays in Boyden Chambers (see Example 5).
        C. In the cell lines which show Trio amplification, RhoA activation and one or more of the phenotypes analyzed in (B), the inventors have targeted Trio directly, using the TRIPE32G peptide. Cell lines have been transfected with a GFP-tagged-TRIPE32G plasmid or infected using retroviral vectors (see (Bouquier et al., 2009). The inventors have evaluated the effect of Trio inhibition on RhoA activation, proliferation, motility and invasiveness using the assays mentioned above. When successful, in vivo assays have been achieved, using mouse models for the various cancer types. For example, to assess invasion, the inventors have used a lung colonization mouse model, where breast cancer cell lines (Forozan et al., 2000), stably expressing TRIPE32G (or a control plasmid), have been injected into the mouse tail and the number/size of lung metastases have been measured three weeks later (see example 5).
    
    


Example 3
Targeting Trio Mutations in Human Cancer
A large number (210) of diverse human cancers (including breast, lung, colorectal, gastric, testis, ovarian, renal, melanoma, glioma, ALL cancers) have been screened by systematic sequencing for the presence of mutations in the 518 kinases of the entire genome (Greenman et al., 2007). Thus, 7 recurrent mutations have been found in the Trio gene, among which are 5 point mutations (1 in GEF1, 1 in GEF2, 2 in the kinase, 1 just after ATG), 1 insertion and 1 deletion mutant: TrioG53E, Trio A97(InsP), Trio T1258M, TrioV1920M, TrioG2795D, TrioR2817C, TrioA2983V.
In order to further investigate the potential relevance of these Trio mutations in tumorigenesis, the inventors have introduced each one of these mutations (by site directed mutagenesis) in the Trio gene and have created stable NIH3T3 cell lines expressing these mutants. The inventors have measured the proliferative, migratory and invasive properties of the cell lines (see above and Materials and Methods). The inventors are particularly focusing on the V1920M mutation, which lies in the GEF2 domain of Trio.
The inventors have infected the NIH3T3 cell lines stably expressing the Trio mutants with a retroviral vector expressing the TRIPE32G peptide, and have analyzed its inhibitory effect, using the above assays as readouts.
In parallel the inventors have tested if Trio GEF activity was modified due to the mutations, especially in the GEF2 domain mutant (V1920M), which could lead to deregulated RhoA activity. To do so, the inventors have inserted the mutation V1920M (by site directed mutagenesis) in the GEF2 domain of Trio or in Tgat, and have produced recombinant GST-fusion proteins. In vitro nucleotide exchange assays have been performed as described (Bouquier et al., 2009) in order to assess the GEF activity of the mutant.
Example 4
Delivery of the Peptides into the Cells
Therapeutic peptides have great potential as anticancer agents, owing to their ease of rational design and target specificity. However, the main hurdle to their in vivo application for cancer therapy is their low stability and poor tumor penetration. Therefore, successful development of various strategies for efficient peptide delivery could make possible the use of this new and very promising class of anticancer agents.
In this context the inventors have developed different approaches in order to increase the stability and deliverability of the TRIP peptides. The inventors will take advantage of the advances in peptide chemistry and delivery that have been made recently (Borghouts et al., 2005b).

    
    
        A. Increasing peptide stability
        Stability of the peptide is an important issue to be addressed. There are technologies available to increase the half-life of peptides, like for example the use of fused-recombinant proteins or the use of non-natural amino acids (for more details see Borghouts et al., 2005a).
        The inventors have then produced such construction comprising non-natural amino acids, without affecting the essential residues defined in example 1 (Black bold residues)
        B. Delivery of the peptides across the cell membrane.
        To date there are mainly two ways of getting peptides efficiently into cells: fusing the peptide to a second, cell-permeable, peptide or using a lentiviral vector that carries a gene encoding the peptide.
        A variety of cell-penetrating peptides have been described in the past few years, including PenetratinTM (the third helix of the Drosophila Antennapedia homeodomain) and TAT-derived sequences (the protein transduction domain of the HIV virus), which are able to transduce fused proteins across the plasma membrane, without cytotoxicity or immunogenicity. In this context, the inventors will fuse the TAT-derived peptide to TRIPE32G peptide (for instance SEQ ID NO: 4), and apply it directly to cells in the culture medium. The above mentioned readouts will be used to assess the efficient delivery and effect of the peptide in the cell.
        Lentiviral vectors are also a promising alternative for the in vivo use of peptides aptamers. The inventors have used retroviral vectors (Bouquier et al., 2009), and have also improved the use of such vectors with new generation lentiviral vectors.
        C. Aptamer-displacement screen
        An alternative, elegant, method to circumvent the problem of in vivo delivery is the use of an aptamer-displacement screen, in which a small-molecule library is screened for compounds that displace the aptamer from its target and reproduce its inhibitory activity, thus converting an aptamer into a small compound inhibitor (Baines and Colas, 2006). The advantage is that the corresponding compound targets the same site and shares the same properties as the already characterized peptide, and shows cell-permeable features. To perform such an aptamer-displacement screen, the inventors have used the high-throughput screening assay as described (Bardou et al., 2009). AptaScreen is a duplex yeast two-hybrid assay featuring two luciferase reporter genes. It can be performed in 96- or 384-well plates and can be fully automated. For details of the experimental procedure, see (Bardou et al., 2009). The library of compounds used is purchased from ChemBridge (San Diego, Calif., USA).
    
    


Example 5
Materials and Methods of Example 2
DNA Constructs—
The Trio mutants were obtained using the Quick Change Site Directed Mutagenesis Kit (Stratagene Inc.), according to the manufacturer's instructions. To create stable NIH3T3 cell lines, GFP-tagged Tgat and full length Trio were cloned into the puromycin-resistant retroviral vector pBabePuro.
Recombinant Proteins—
Recombinant GST-Trio DH2-PH2, GST-Tgat were purified as described previously (Bouquier et al., 2009; Schmidt et al., 2002).
RhoA Activation Assay in Cells—
The level of GTP-bound RhoA was measured by a GST pull-down assay as described (Bouquier et al., 2009). Briefly, cell lysates were incubated with glutathione beads coated with the recombinant Rho-binding domain (RBD) of the RhoA-specific effector Rhotekin (Cytoskeleton Inc.). Total or GTP-bound RhoA in the samples was revealed by Western blot analysis, using a monoclonal anti-RhoA antibody (Santa-Cruz Biotechnology Inc.).
Nucleotide Exchange Inhibition Assays—
Mant-GTP fluorescence nucleotide exchange assays are performed as described (Bouquier et al., 2009), in a FLX800 Microplate Fluorescence Reader (BioTek Instruments). Briefly, 0.5 μM Tgat or Trio DH2-PH2 (wild type or mutated) are preincubated 5 min at 25° C. in the presence of 20 μM GST, GST-TRIPE32G and 1 μM mant-GTP. The exchange reaction is initiated by addition of 1 μM RhoA and monitored for 10 min.
Cell Lines, Transfection—
NIH3T3 cells were maintained as described previously (Sirvent et al., 2007). NIH3T3 cell lines stably expressing the different Trio mutants with or without the GST-TRIP peptides, were generated as follows: the indicated retroviral constructs were transfected into BOSC packaging cells, using the Jet PEI reagent, according to the manufacturer's protocol (QBiogene Inc.). Forty-eight hours after transfection, virus-containing supernatants were collected and used to infect NIH3T3 cells. Infected cells were selected with 6 μg/mL puromycin and/or 1 mg/mL G418 and stable transfectants were pooled after selection. mRNA levels in the different cell lines were monitored by RT-PCR, and protein expression levels by Western blot analysis using a polyclonal anti-GFP antibody (Torrey Pines Laboratories).
Cell Growth Assay:
the growth rate of the NIH3T3 cells stably expressing the different Trio mutants is measured by the CellTiter 96 Aqueous assay (Promega), according to the manufacturer's instructions. 1500 cells per well in 200 μl of 5% FBS medium were plated in 96-well plates and were grown under normal conditions.
Focus Formation Assays—
Focus formation assays are performed using stable NIH3T3 cell lines as indicated, seeded at 5×104 cells in 6-well plates and maintained for 15 to 21 days in 10% FBS. Medium is renewed every two days. After staining with Crystal Violet (1%), plates are photographed and foci are scored using the Metamorph software. All experiments are done in triplicate.
Anchorage-Independent Growth Assay—
NIH3T3 cells stably expressing the different Trio mutants (1.25×103 per well) are grown in 0.3% agarose, in a six-well plate. Duplicate wells are tested for each condition. The cells are fed with 1 ml of top agar once every week. Colonies are scored after 3 to 5 weeks.
Wound-Healing Assay—
Confluent cells stably expressing the TRIP peptides in a 24-multiwell plate were wounded with a sterile pipette tip and exposed to 10% FBS-DMEM. Plates were kept at 37° C. in a 5% CO2 of a Zeiss inverted microscope equipped with a motorized stage. One field that includes the scratched path from each dish was selected and scanned sequentially every 15 min for 20 h.
Cell Invasion Assay—
Cell invasion assays are performed using the 6.4-mm Biocoat Matrigel invasion chambers equipped with the 8 μm pore sized PET membrane filters (BD Biosciences) according to the manufacturer's instructions. Briefly, 2.5×104 cells are suspended in 0.5 ml of culture medium and were added to the upper chamber. 10% FBS in the culture medium is plated in the lower chamber as chemoattractant. Cells in the invasion chambers are incubated in a humidified incubator. The cells that traversed the Matrigel matrix and the 8 μm membrane pores and spread to the lower surface of the filters are stained with 5% Giemsa solution for visualization. Each data point of the invasion test is derived from triplicate chambers, and error bars represent the mean standard error.
Lung Colonization Model—
Twenty 6- to 8-wk-old female nude mice are injected with a breast cancer cell line expressing, or not, TRIPE32G (Bouquier et al., 2009) (2.5×106 cells in 100 μL of sterile PBS, 97% viability) in the tail vein. After 22 d, mice are weighted and sacrificed by cervical dislocation. Lungs are removed, sectioned, and fixed in buffered 4% formaldehyde and examined blindly. The number of lung metastases is assessed in three H&E-stained sections per mouse and expressed as mean metastases number/mm2. The extent of normal and tumor lung parenchyma is measured in three fields per sample on H&E-stained sections. Area of lung metastasis is assessed using the Axiovision 4.4 software. Right lower lobe from each lung is lysed, and 50 μg proteins/sample were analyzed by Western blot using 1 μg/mL anti-GFP antibody or 1 μg/mL anti-α-tubulin mAb (Sigma-Aldrich). Densitometry was done by AIDA software. Statistical analysis was done using the Student's t test. Differences were considered statistically significant if P<0.05.

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## Claims

1. A method for treating cancer, comprising administering to a subject in need thereof a therapeutically effective amount of an isolated peptide comprising the amino acid sequence SEQ ID NO: 3









ICGYX13LAX16X17X18MLGPX23X24RVX27CPLCX32P





wherein X13, X16, X17, X18, X23, X24, X27 and X32 represent any amino acids, and having at least one of the following features:
X13 is D;
X16 is M or A;
X17 is S;
X18 is D, G or A;
X23 is G;
X24 is A;
X27 is L; and
X32 is G.

2. The method according to claim 1, wherein said peptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 4 to SEQ ID NO: 51.

3. The method according to claim 1, wherein said peptide further comprises fragments of thioredoxin A, said fragments flanking the N-terminal and C-terminal of said peptide of SEQ ID NO: 3.

4. The method according to claim 3, wherein said peptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 99.

5. The method according to claim 1, wherein the cancer is leukemia, T-cell acute Leukemia, sarcoma, lung cancer or breast cancer.