# Patent

## Title
Diphtheria toxin variant

## Abstract

The present invention relates to methods and compositions of modified variants of diphtheria toxin (DT) that reduce binding to vascular endothelium or vascular endothelial cells, and therefore, reduce the incidence of Vascular Leak Syndrome. One aspect of the present invention relates to a polypeptide toxophore from a modified DT, wherein the mutation is the substitution or deletion at least one amino acid residue at the amino acid residues 6-8, 28-30 or 289-291 of native DT. Another aspect of the present invention relates to a fusion protein which comprises a modified DT and a non-DT fragment. Another aspect of the present invention relates to the use of modified DT for the treatment of cancer.

## Background
This application claims priority from U.S. Provisional Application Ser. No. 60/524,615, filed Nov. 25, 2003. The entirety of that provisional application is incorporated herein by reference.


FIELD OF THE INVENTION
The present invention is directed to methods and compositions of modified variants of diphtheria toxin (hereinafter “DT) that reduce binding to vascular endothelium or vascular endothelial cells, therefore, reduce the incidence of Vascular Leak Syndrome (hereinafter “VLS”).
BACKGROUND OF THE INVENTION
Vascular Leak Syndrome is primarily observed in patients receiving protein fusion toxin or recombinant cytokine therapy. VLS can manifest as hypoalbuminemia, weight gain, pulmonary edema and hypotension. In some patients receiving immunotoxins and fusion toxins, myalgia and rhabdomyolysis result from VLS as a function of fluid accumulation in the muscle tissue or the cerebral microvasculature [Smallshaw et al., Nat Biotechnol. 21(4):387-91 (2003)]. VLS has occurred in patients treated with immunotoxins containing ricin A chain, saporin, pseudomonas exotoxin A and DT. All of the clinical testing on the utility of targeted toxins, immunotoxins and recombinant cytokines reported that VLS and VLS-like effects were observed in the treatment population. VLS occurred in approximately 30% of patients treated with DAB389IL-2 [(Foss et al., Clin Lymphoma 1(4):298-302 (2001), Figgitt et al., Am J Clin Dermatol., 1(1):67-72 (2000)]. DAB389IL-2, is interchangeable referred to in this application as DT387-IL2, is a protein fusion toxin comprised of the catalytic (C) and transmembrane (T) domains of DT (the DT toxophore), genetically fused to interleukin 2 (IL-2) as a targeting ligand. [Williams et al., Protein Eng., 1:493-498 (1987); Williams et al., J. Biol. Chem., 265:11885-11889 (1990); Williams et al., J. Biol. Chem., 265 (33):20673-20677, Waters et al., Ann. New York Acad. Sci., 30(636):403-405, (1991); Kiyokawa et al., Protein Engineering, 4(4):463-468 (1991); Murphy et al., In Handbook of Experimental Pharmacology, 145:91-104 (2000)]. VLS has also been observed following the administration of IL-2, growth factors, monoclonal antibodies and traditional chemotherapy. Severe VLS can cause fluid and protein extravasation, edema, decreased tissue perfusion, cessation of therapy and organ failure. [Vitetta et al., Immunology Today, 14:252-259 (1993); Siegall et al., Proc. Natl. Acad. Sci., 91(20):9514-9518 (1994); Baluna et al., Int. J. Immunopharmacology, 18(6-7):355-361 (1996); Baluna et al., Immunopharmacology, 37(2-3):117-132 (1997); Bascon, Immunopharmacology, 39(3):255 (1998)].
Reduction or elimination of VLS as a side effect would represent a significant advancement as it would improve the “risk benefit ratio” of protein therapeutics, and in particular, the immunotoxin and fusion toxin subclasses of protein therapeutics. (Baluna et al., Int. J. Immunopharmacology, 18(6-7):355-361 (1996); Baluna et al., Immunopharmacology, 37(No. 2-3):117-132 (1997); Bascon, Immunopharmacology, 39(3): 255 (1998). The ability to develop fusion proteins, single chain molecules comprised of a cytotoxin and unique targeting domain (scfv antibodies in the case of immunotoxins) could facilitate the development of the therapeutic agents for autoimmune diseases, such as rheumatoid arthritis and psoriasis transplant rejection and other non-malignant medical indications. (Chaudhary et al., Proc. Natl. Acad. Sci. USA, 87(23):9491-9494 (1990); Frankel et al., In Clinical Applications of Immunotoxins Scientific Publishing Services, Charleston S.C., (1997), Knechtle et al., Transplantation, 15(63):1-6 (1997); Knechtle et al., Surgery, 124(2): 438-446 (1998); LeMaistre, Clin. Lymphoma, 1:S37-40 (2000); Martin et al., J. Am. Acad. Dermatol., 45(6):871-881, 2001)). DAB389IL-2 (ONTAK) is currently the only FDA approved protein fusion toxin and employs a DT toxophore and the cytokine interleukin 2 (IL-2) to target IL-2 receptor bearing cells and is approved for the treatment of cutaneous T-cell lymphoma (CTCL). (Figgitt et al., Am. J. Clin. Dermatol., 1(1):67-72 (2000); Foss, Clin. Lymphoma, 1(4):298-302 (2001); Murphy et al., In Bacterial Toxins: Methods and Protocols, Holst O, ed, Humana Press, Totowa, N.J., pp. 89-100 (2000)). A number of other toxophores, most notably ricin toxin and pseudomonas exotoxin A, have been employed in developing both immuntoxins and fusion toxins; however, these molecules have not successfully completed clinical trials and all exhibit VLS as a pronounced side effect (Kreitman, Adv. Pharmacol., 28:193-219 (1994); Puri et al., Cancer Research, 61:5660-5662 (1996); Pastan, Biochim Biophys Acta., 24:1333(2):C1-6 (1997); Frankel et al., Supra (1997); Kreitman et al., Current Opin. Inves. Drugs, 2(9):1282-1293 (2001)).
VLS arises from protein-mediated damage to the vascular endothelium. In the case of recombinant proteins, immunotoxins and fusion toxins, the damage is initiated by the interaction between therapeutic proteins and vascular endothelial cells. Lindstrom et al. provided evidence that ricin toxin A had direct cytotoxic effects on human umbilical vein vascular epithelial cells but that these effects were not mediated by fibronectin (Lindstrom et al., Blood, 90(6):2323-34 (1997); Lindstrom et al., Methods Mol. Biol., 166:125-35 (2001)). Baluna et al. postulated that the interaction disrupts fibronectin mediated cell-to-cell interactions resulting in the breakdown of vascular integrity, and Baluna further suggested that in the toxin ricin, the interaction is mediated by a conserved three amino acid motif, (x)D(y), where x is L, I, G or V and y is V, L or S (Baluna et al., Int. J. Immunopharmacology, 18(6-7):355-361 (1996); Baluna et al., Proc. Natl. Acad. Sci. USA, 30:96(7):3957-3962, (1999); Baluna et al., Exp Cell Res., 58(2):417-24 (2000)). It was reported that one of the VLS motifs found in ricin toxin, the ‘LDV’ motif, essentially mimics the activity of a subdomain of fibronectin which is required for binding to the integrin receptor. Integrins mediate cell-to-cell and cell-to-extracellular matrix interactions (ECM). Integrins function as receptors for a variety of cell surface and extracellular matrix proteins including fibronectin, laminin, vitronectin, collagen, osteospondin, thrombospondin and von Willebrand factor. Integrins play a significant role in the development and maintenance of vasculature and influence endothelial cell adhesiveness during angiogenesis. Further, it is reported that the ricin ‘LDV’ motif can be found in a rotavirus coat protein, and this motif is important for cell binding and entry by the virus. (Coulson, et al., Proc. Natl. Acad. Sci. USA, 94(10):5389-5494 (1997)). Thus, it appears to be a direct link between endothelial cell adhesion, vascular stability and the VLS motifs which mediate ricin binding to human vascular endothelial cells (HUVECs) and vascular leak.
Mutant dgRTAs were constructed in which this motif was removed by conservative amino acid substitution, and these mutants illustrated fewer VLS effects in a mouse model (Smallshaw et al. Nat Biotechnol., 21(4):387-91 (2003)). However, the majority of these constructs yielded dgRTA mutants that were not as cytotoxic as wild type ricin toxin, suggesting that significant and functionally critical structural changes in the ricin toxophore resulted from the mutations. It should also be noted that no evidence was provided to suggest that the motifs in dgRTA mediated HUVEC interactions and VLS in any other protein. Studies revealed that the majority of the mutant dgRTAs were much less effective toxophores and no evidence was provided to suggest that fusion toxins could be assembled using these variant toxophores.
DT is composed of three domains: the catalytic domain; transmembrane domain; and the receptor binding domain (Choe et al. Nature, 357:216-222 (1992)). Native DT is targeted to cells that express heparin binding epidermal growth factor-like receptors (Naglish et al., Cell, 69:1051-1061 (1992)). The first generation targeted toxins were initially developed by chemically cross-linking novel targeting ligands to toxins such as DT or mutants of DT deficient in cell binding (e.g. CRM45). (Cawley, Cell 22:563-570 (1980); Bacha et al., Proc. Soc. Exp. Biol. Med., 181(1):131-138 (1986); Bacha et al., Endocrinology, 113(3):1072-1076 (1983); Bacha et al., J. Biol. Chem., 258(3):1565-1570 (1983)). The native cell binding domain or a cross-linked ligand that directs the DT toxophore to receptors on a specific class of receptor-bearing cells must possess intact catalytic and translocation domains. (Cawley et al., Cell, 22:563-570 (1980); vanderSpek et al., J. Biol. Chem., 5:268(16):12077-12082 (1993); vanderSpek et al., J. Biol. Chem., 7(8):985-989 (1994); vanderSpek et al., J. Biol. Chem., 7(8)985-989 (1994); Rosconi, J. Biol. Chem., 10;277(19):16517-161278 (2002)). These domains are critical for delivery and intoxification of the targeted cell following receptor internalization (Greenfield et al., Science, 238(4826)536-539 (1987)). Once the toxin, toxin conjugate or fusion toxin has bound to the cell surface receptor the cell internalizes the toxin bound receptor via endocytic vesicles. As the vesicles are processed they become acidified and the translocation domain of the DT toxophore undergoes a structural reorganization which inserts the 9 transmembrane segments of the toxin into the membrane of the endocytic vesicle. This event triggers the formation of a productive pore through which the catalytic domain of the toxin is threaded. Once translocated the catalytic domain which possess the ADP-ribosyltransferase activity is released into the cytosol of the targeted cell where it is free to poison translation thus effecting the death of the cell (reviewed in vanderSpek et al., Methods in Molecular Biology, Bacterial Toxins: methods and Protocols, 145:89-99, Humana press, Totowa, N.J., (2000)).
Chemical cross-linking or conjugation results in a variety of molecular species representing the reaction products, and typically only a small fraction of these products are catalytically and biologically active. In order to be biologically active, the reaction products must be conjugated in manner that does not interfere with the innate structure and activity of the catalytic and translocation domains in the toxophore. Resolution of the active or highly active species from the inactive species is not always feasible as the reaction products often possess similar biophysical characteristics, including for example size, charge density and relative hydrophobicity. It is noteworthy that isolation of large amounts of pure clinical grade active product from chemically crosslinked toxins is not typically economically feasible for the production of pharmaceutical grade product for clinical trials and subsequent introduction to clinical marketplace. To circumvent this issue, a genetic DT-based protein fusion toxin in which the native DT receptor-binding domain was genetically replaced with melanocyte-stimulating hormone as a surrogate receptor-targeting domain was created (Murphy et al., PNAS, 83:8258-8262 (1986)). This approach was used with human IL-2 as a surrogate targeting ligand to create DAB486IL-2 that was specifically cytotoxic only to those cells that expressed the high-affinity form of the IL-2 receptor (Williams et al., Protein Eng., 1:493-498 (1987)). Subsequent studies of DAB486IL-2 indicated that truncation of 97 amino acids from the DT portion of the molecule resulted in a more stable, more cytotoxic version of the IL-2 receptor targeted toxin, DAB389IL-2 (Williams et al., J. Biol Chem., 265:11885-889 (1990)). The original constructs (the 486 forms) still possessed a portion of the native DT cell binding domain. The DAB389 amino acid residue version contains the C and T domains of DT with the DT portion of the fusion protein ending in a random coil between the T domain and the relative receptor binding domain. A number of other targeting ligands have since been genetically fused to this DT toxophore, DAB389. (vanderSpek et al., Methods in Molecular Biology, Bacterial Toxins:Methods and Protoclos., 145:89-99, Humana Press, Totowa, N.J. (2000)). Similar approaches have now been employed with other bacterial proteins and genetic fusion toxins are often easier to produce and purify.
SUMMARY OF THE INVENTION
The present invention provides compositions of modified variants of DT that reduce binding to vascular endothelium or vascular endothelial cells, and therefore, reduce the incidence of Vascular Leak Syndrome.
One aspect of the present invention relates to a composition comprising a polypeptide toxophore from a DT, said polypeptide toxophore comprising amino acid residues 7-9, 29-31 and 290-292 of SEQ ID NO:6, wherein at least one amino acid in said amino acid residues 7-9, 29-31 or 290-292 of SEQ ID NO:6, has been substituted or deleted.
Another aspect of the present invention relates to a fusion protein comprising a modified DT mutant or fragment and a non-DT fragment.
Another aspect of the present invention relates to the use of a modified DT or a fusion protein carrying such modified DT for the treatment of diseases, such as cancer.
Yet another aspect of the present invention relates to a method of making a modified DT fragment having a reduced binding activity to human vascular endothelial cells (HUVEC) and having a reduced induction of Vascular Leak Syndrome (VLS).



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a schematic diagram of DT387. The positions of the (x)D(y) motifs of the toxophore which are implicated in VLS are indicated by triangles and listed below in the table of proposed DT387 and corresponding DAB389IL2 (hereinafter “DT387IL2”) mutants. The flexible linker sterically enhances disulfide bond formation between the C-terminal cysteine residue and a Sulfo-LC SPDP modified targeting ligand.
FIG. 2 is a ribbon diagram and space filling model of native DT showing the presence of (x)D(y) motifs implicated in VLS.
FIG. 3 shows the nucleic acid and amino acid sequence SEQ ID NOs: 109-120 changes in various DT variants.
FIG. 4A shows analysis of DT387 toxophore yield by Coomassie.
FIG. 4B shows analysis of DT387 toxophore yield by Western Blot.
FIGS. 5A and 5B show representative photomicrographs illustrating the levels of fluorescence between wild type DT toxophore mediated HUVEC staining (FIG. 5A) and VLS modified HUVEC staining (FIG. 5B).
FIG. 6 illustrates HUVEC binding to DT387 and VLS modified DT387 toxophores.
FIG. 7 is a diagram showing the ADP ribosyltransferase activity of certain DT mutants. ADP ribosyltransferase assay in which the activity of alanine substitute VLS modified DT toxphores or DT387IL2 fusion proteins were compared to fragment A of native DT.
FIG. 8 depicts an example of Coomassie stained SDS-PAGE analysis of crude and purified refolded samples of DT387EGF fusion protein (DT387(D8EV29A)EGF). Tubes 1-9 not depicted.
FIG. 9 is a diagram showing the cytotoxicity of 8×10−9 M DT387(D8EV29A)linker EGF in EGF receptor positive U87MG glioblastoma cells under refolding buffer conditions 1-9.
FIG. 10 is a diagram showing the cytotoxicity of 4×10−8 M DT387(D8EV29A)linkerEGF in U87MG cells under refolding buffer conditions 10-18.
FIG. 11 is a diagram showing the cytotoxicity of DT389EGF and VLS modified DT387linkerEGF fusion proteins, DT387linkerEGF, DT387(D8E,V29A)linker EGF, DEF, DT387(D8S,V29A)linkerEGF, DT387(D8E,V29A,D291E)linkerEGF, DT387(V7A,V29A)linkerEGF, DT387(V29A)linkerEGF, DT387(V7S,V29A)linkerEGF, DT387(D291E)linker IL2 in U87MG cell.
FIG. 12 is a Coomassie stained SDS-PAGE gel showing the level of purity for the VLS-modified DT387EGF fusion protein tested in FIG. 11.
FIG. 13 is a diagram showing the cytotoxicity of DT387IL2, DT387(D8S,V29A)linkerIL2, DT387(V7A,V29A,D291E)linkerIL2, DT387(V7A)linkerIL2, DT387(V7S,V29A)linkerIL2, DT387(D8E,V29A)linkerIL2 in IL-2 receptor positive HUT102/6TG cells.
FIGS. 14 (A) and (B) are a Coomassie stained SDS-PAGE gel (FIG. 14A) and Western blot (FIG. 14B) showing the level of purity for the VLS-modified DT387linkerIL2 fusion proteins tested in FIG. 13.



DETAILED DESCRIPTION OF THE INVENTION
The primary objective of the present invention is to provide compositions comprising modified variants of DT that reduce binding to vascular endothelium or vascular endothelial cells, and therefore, reduce the incidence of Vascular Leak Syndrome (hereinafter “VLS”). The second objective of the present invention is to provide methods of making such modified variants of DT that reduce binding to vascular endothelium or vascular endothelial cells. The third objective of the present invention is to provide methods of treating various diseases, such as cancer, by using modified variants of DT or by using a fusion protein comprising modified variants of DT and non-DT protein.
One aspect of the present invention relates to genetically modified molecules of diphtheria toxin (DT) having reduced binding to human vascular endothelial cells(HUVECs). These modified DT molecules are hereinafter referred to as “DT variants.” The invention specifically relates to DT variants having one or more conservative changes within the (x)D(y) motifs of the DT molecule, i. e., at residues 6-8 (VDS), residues 28-30 (VDS), and residues 289-291 (IDS) of the native DT sequence (SEQ ID NO: 1), or at residues 7-9 (VDS), residues 29-31 (VDS), and residues 290-292 (IDS) of the SEQ ID NO:6. Since the (x)D(y) motifs are referred to as “VLS motifs,” the DT variants with modified (x)D(y) motif are sometimes referred to as “VLS-modified DT molecules.”
Conservative changes are defined as those amino acid substitutions which permit the alteration of the native sequence within these regions but do not impair the cytotoxicity of the toxophore. These conservative changes would not include those that regenerate the VDS/IDS sequences responsible for mediating the interaction with endothelial cells. Such non-native recombinant sequences therefore comprise a novel series of mutants that maintain the native function of the unique domains of diphtheria toxin while significantly decreasing their ability to interact with vascular endothelial cells.
In one embodiment, the DT variants of the present invention contain at least one conservative change within one of the (x)D(y) motifs of the DT molecule, i. e., within residues 6-8 (VDS), residues 28-30 (VDS), and residues 289-291 (IDS) of SEQ ID NO:1 to eliminate motifs that are associated with VLS and thereby reduce the clinical adverse effects commonly associated with this syndrome. The DT variants of the present invention, however, are as effective and efficient as DT387 in their ability to facilitate the delivery of its catalytic domain to the cytosol of targeted eukaryotic cells when incorporated into protein fusion toxins. DT387 (SEQ ID NO:6) is a truncated DT protein comprising amino acid residues 1-386 (SEQ ID NO: 2) of the native DT protein including the catalytic domain and the translocation domain.
In another embodiment, in addition to the modification in the (x)D(y) motifs, the DT variants may further comprise a deletion or substitution of 1 to 30 amino acids of SEQ ID NO:6, preferably 1 to 10 amino acids, most preferably 1-3 amino acids.
To produce DT variants with a modified (x)D(y) sequence, one could delete or substitute another amino acid for the aspartic acid (D), or insert one or more amino acids at or adjacent to its position. Any amino acid that may replace the (D) residue in the sequence as a consequence of a deletion or mutation event must retain the ability to effectively deliver the catalytic domain of DT to a targeted cell within the context of a fusion protein, and not reconstitute an intact VLS motif.
Alternatively the (x) residue could be deleted, substituted, or moved by the insertion of one or more amino acids, to remove the (x)D(y) sequence. Any amino acid that may replace the (x) residue in the sequence as a consequence of the deletion or mutation event should preferably not be leucine (L), isoleucine (I), glycine (G) or valine (V). The (y) residue could be deleted, substituted, or moved by the insertion of one or more amino acids, to remove the (x)D(y) sequence. Any amino acid that may replace the (y) residue in the sequence as a consequence of the deletion or mutation event should preferably not be valine (V), leucine (L) or serine (S).
In a preferred embodiment, the DT variants of the present invention contain at least one of the mutations selected from the group of V7A, V7S, D8S, D8E, V29A, I290A, D291S, and D291E. It should be noted that the first amino acid residue of mature processed native DT protein corresponds to the second amino acid residue of the DT variants (recombinant expression requires insertion of met residue). Accordingly, residues 6-8 (VDS), 28-30 (VDS) and 289-291 (IDS) of the native DT correspond to residues 7-9, 29-31, and 290-292 of the DT variants.
In another preferred embodiment, the DT variants of the present invention contain a double mutation selected from the group of V7AV29A, V7SV29A, D8SV29A, D8SD291S, D8EV29A, and V29AD291E.
In another preferred embodiment, the DT variants of the present invention contain a triple mutation selected from the group of V7AV29AD291E and V7AV29AI290A.
In yet another preferred embodiment, the DT variants comprise an amino acid sequence recited in one of SEQ ID NOs:52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74 and 76. It is conceivable that other residues that are positioned in the physical region, three-dimensional space, or vicinity of the HUVEC binding site and/or the (x)D(y) motif may be mutated or altered to abrogate, reduce, or eliminate VLS. The amino acids targeted for mutation in the flanking regions include amino acids on or near the surface of a native DT protein. The alteration may remove or substitute a charged residue in the region of a (x)D(y) motif, which may negate or reverse the charge in a particular area on the surface of the protein. The alteration may also change size and/or hydrophilic nature of an amino acid in the physical region, space or vicinity of the (x)D(y) sequence or active site of a protein.
In certain aspects, mutagenesis of nucleic acids encoding peptides, polypeptides or proteins may be used to produce the desired mutations in the (x)D(y) and flanking sequences of the DT variants. Mutagenesis may be conducted by any means disclosed herein or known to one of ordinary skill in the art.
One particularly useful mutagenesis technique is alanine scanning mutagenesis in which a number of residues are substituted individually with the amino acid alanine so that the effects of losing side-chain interactions can be determined, while minimizing the risk of large-scale perturbations in protein conformation [(Cunningham et al., Science, 2:244(4908):1081-5 (1989)].
As specific amino acids may be targeted, site-specific mutagenesis is a technique useful in the preparation of individual peptides, or biologically functional equivalent proteins or peptides, through specific mutagenesis of the underlying DNA. The technique further provides a ready ability to prepare and test sequence variants, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the DNA. Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the mutation site being traversed. Typically, a primer of about 17 to 25 nucleotides in length is preferred, with about 5 to 10 residues on both sides of the junction of the sequence being altered.
In general, the technique of site-specific mutagenesis is well known in the art. Briefly, a bacteriophage vector that will produce a single stranded template for oligonucleotide directed PCR mutagenesis is employed. These phage vectors, typically M13, are commercially available and their use is generally well known to those skilled in the art. Similarly, double stranded plasmids are also routinely employed in site directed mutagenesis, which eliminates the step of transferring the gene of interest from a phage to a plasmid. Synthetic oligonucleotide primers bearing the desired mutated sequence are used to direct the in vitro synthesis of modified (desired mutant) DNA from this template and the heteroduplex DNA used to transform competent E. Coli for the growth selection and identification of desired clones. Alternatively, a pair of primers may be annealed to two separate strands of a double stranded vector to simultaneously synthesize both corresponding complementary strands with the desired mutation(s) in a PCR reaction.
In one embodiment, the Quick Change site-directed mutagenesis method using plasmid DNA templates as described by Sugimoto et al. is employed (Sugimoto et al., Annal. Biochem., 179(2):309-311 (1989)). PCR amplification of the plasmid template containing the insert target gene of insert is achieved using two synthetic oligonucleotide primers containing the desired mutation. The oligonucleotide primers, each complementary to opposite strands of the vector, are extended during temperature cycling by mutagenesis-grade PfuTurbo DNA polymerase. On incorporation of the oligonucleotide primers, a mutated plasmid containing staggered nicks is generated. Amplified un-methylated products are treated with Dpn I to digest methylated parental DNA template and select for the newly synthesized DNA containing mutations. Since DNA isolated from most E. Coli strains is dam methylated, it is susceptible to DpnI digestion, which is specific for methylated and hemimethylated DNA. The reaction products are transformed into high efficiency strains of E. coli to obtain plasmids containing the desired mutants.
The preparation of sequence variants of the selected gene using site-directed mutagenesis is provided as a means of producing potentially useful species and is not meant to be limiting, as there are other ways in which sequence variants of genes may be obtained. For example, recombinant vectors encoding the desired gene may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants. These basic techniques, the protocols for sequence determination, protein expression and analysis are incorporated by reference to citations in this specification and are generally accessible to those reasonably skilled in the art within Current Protocols in Molecular Biology (Fred M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J.G. Seidman, John A. Smith, Kevin Struhl, Editors John Wiley and Sons Publishers (1989)).
The present invention also provides DT fusion proteins. A DT fusion protein contains a DT-related polypeptide (e. g., a DT variant of the present invention) and a non-DT polypeptide fused in-frame to each other. The DT-related polypeptide corresponds to all or a portion of DT variant having reduced binding to human vascular endothelial cells. In one embodiment, a DT fusion protein comprises at least one portion of a DT variant sequence recited in one of SEQ ID NOs:19-50.
Preferably, a DT-fusion protein of the present invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example, by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence.
A peptide linker sequence may be employed to separate the DT-related polypeptide from non-DT polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion protein using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the DT-related polypeptide and non-DT polypeptide; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain gly, asn and ser residues. Other near neutral amino acids, such as thr and ala, may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene, 40: 39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA, 83: 8258-8262, 1986 ; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the DT-related polypeptide and non-DT polypeptide have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference. For example, DT389/DT387-linker has a sequence of SEQ ID NOs:7-8, DT380-linker has sequence of SEQ ID NOs:9-10. The non-DT polypeptides can be any polypeptide.
In one embodiment, the non-DT polypeptide is a cell-specific binding ligand. The specific-binding ligands used in the invention can contain an entire ligand, or a portion of a ligand which includes the entire binding domain of the ligand, or an effective portion of the binding domain. It is most desirable to include all or most of the binding domain of the ligand molecule.
Specific-binding ligands include but not limited to: polypeptide hormones, chimeric toxins, e.g., those made using the binding domain of α-MSH, can selectively bind to melanocytes, allowing the construction of improved DT-MSH chimeric toxins useful in the treatment of melanoma. (Murphy, J. R., Bishai, W., Miyanohara, A., Boyd, J., Nagle, S., Proc. Natl. Acad. Sci. U.S.A., 83(21):8258-8262 (1986)). Other specific-binding ligands which can be used include insulin, somatostatin, interleukins I and III, and granulocyte colony stimulating factor. Other useful polypeptide ligands having cell-specific binding domains are follicle stimulating hormone (specific for ovarian cells), luteinizing hormone (specific for ovarian cells), thyroid stimulating hormone (specific for thyroid cells), vasopressin (specific for uterine cells, as well as bladder and intestinal cells), prolactin (specific for breast cells), and growth hormone (specific for certain bone cells). Specific-binding ligands which can be used include cytokines. Examples of cytokines include, but are not limited to, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, β-interferon, α-interferon (INF α), INFγ, angiostatin, thrombospondin, endostatin, METH-1, METH-2, GM-CSF, G-CSF, M-CSF, tumor necrosis factor (TNF), SVEGF, TGFβ, Flt3 and B-cell growth factor. IL-2 is of particular importance because of its role in allergic reactions and autoimmune diseases such as systemic lupus erythmatosis (SLE), involving activated T cells. DT fusion protein made using B-cell growth factor can be used as immunosuppressant reagents which kill proliferating B-cells, which bear B-cell growth factor receptors, and which are involved in hypersensitivity reactions and organ rejection. Other preferred cytokines include Substance P (Benoliel et al., Pain, 79(2-3):243-53 (1999)), VEGF (Hotz et al., J Gastrointest Surg., 6(2):159-66 (2002)), IL3 (Jo et al., Protein Exp Purif. 33(l):123-33 (2004)) and GMCSF (Frankel et al., Clin Cancer Res, 8(5):1004-13 (2002)). VLS modified DT fusion toxins using these ligands are useful in treating cancers or other diseases of the cell type to which there is specific binding.
For a number of cell-specific ligands, the region within each such ligand in which the binding domain is located is now known. Furthermore, recent advances in solid phase polypeptide synthesis enable those skilled in this technology to determine the binding domain of practically any such ligand, by synthesizing various fragments of the ligand and testing them for the ability to bind to the class of cells to be labeled. Thus, the chimeric genetic fusion toxins of the invention need not include an entire ligand, but rather may include only a fragment of a ligand which exhibits the desired cell-binding capacity. Likewise, analogs of the ligand or its cell-binding region having minor sequence variations may be synthesized, tested for their ability to bind to cells, and incorporated into the hybrid molecules of the invention. Other potential ligands include antibodies (generally monoclonal) or antigen-binding, single-chain analogs of monoclonal antibodies, where the antigen is a receptor or other moiety expressed on the surface of the target cell membrane. The antibodies most useful are those against tumors; such antibodies are already well-known targeting agents used in conjunction with covalently bound cytotoxins. In the present invention, the anti-tumor antibodies (preferably not the whole antibody, but just the Fab portion) are those which recognize a surface determinant on the tumor cells and are internalized in those cells via receptor-mediated endocytosis; antibodies which are capped and shed will not be as effective.
Another aspect of the present invention pertains to vectors containing a polynucleotide encoding a DT variant or a DT fusion protein. One type of vector is a “plasmid,” which includes a circular double-stranded DNA loop into which additional DNA segments can be ligated. In the present specification, “plasmid” and “vector” can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of vectors, such as expression vectors, and gene delivery vectors.
The expression vectors of the invention comprise a polynucleotide encoding DT variant or a DT fusion protein in a form suitable for expression of the polynucleotide in a host cell. The expression vectors generally have one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the polynucleotide sequence to be expressed. It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to produce proteins or peptides, including fusion proteins or peptides, encoded by polynucleotides as described herein (e.g., a DT variant or a DT fusion protein, and the like).
The expression vectors of the present invention can be designed for expression of a DT variant or a DT fusion protein in prokaryotic or eukaryotic cells. It should be noted that the presence of a single DT molecule inside an eukaryotic cell would kill the cell. Specifically, the toxin binds to EF-tu which is required for translation and ribosylation. Accordingly, DT can only be expressed in cells with modified EF-tu that is no longer recognized by DT. (see, e.g., Liu et al., Protein Expr Purif., 30:262-274 (2003); Phan et al., J. Biol. Chem., 268(12):8665-8 (1993); Chen et al., Mol. Cell Biol., 5(12):3357-60 (1985); Kohne et al., Somat Cell Mol. Genet., 11(5):421-31 (1985); Moehring et al., Mol. Cell Biol., 4(4):642-50 (1984)). In addition, a DT variant or a DT fusion protein can be expressed in bacterial cells such as E. coli [Bishai et al., J Bacteriol 169(11):5140-51 (1987)]. Consideration must be given to the expression and activity of the types and levels of host protease expression, and this is dependent upon the cleavage site present in the engineered DT toxophore. The innate expression host protease expression profile could negatively impact the yields of DT fusion toxin produced [Bishai et al., Supra (1987)]. To the degree that this requisite cleavage site can be altered to modulate the cell selectivity of resultant fusion proteins, it is envisioned that such cleavage site mutants could be in VLS-modified toxophores (Gordon etal., Infect Immun, 63(1):82-7 (1995); Gordon etal., Infect Immun, 62(2):333-40 (1994); Vallera et al., J Natl. Cancer Inst., 94:597-606 (2002); Abi-Habib et al., Blood., 104(7):2143-8 (2004)]. Alternatively, the expression vector can be transcribed and translated in vitro.
The present invention further provides gene delivery vehicles for the delivery of polynucleotides to cells, tissue, or a mammal for expression. For example, a polynucleotide sequence of the present invention can be administered either locally or systemically in a gene delivery vehicle. These constructs can utilize viral or non-viral vector approaches in in vivo or ex vivo modality. Expression of such coding sequences can be induced using endogenous mammalian or heterologous promoters. Expression of the coding sequence in vivo can be either constitutive or regulated. The invention includes gene delivery vehicles capable of expressing the contemplated polynucleotides including viral vectors. For example, Qiao et al., developed a system employing PG13 packaging cells produce recombinant retroviruses carrying a DT fragment which kills cancer cell and provides a method for using DT as component a suicide vector. Qiao et al., J. Virol. 76(14):7343-8 (2002).
Expressed DT-mutants and DT-fusion proteins can be tested for their functional activity. Methods for testing DT activity are well-known in the art. For example, the VLS effect of DT-mutants and DT-fusion proteins can be tested in HUVECs as described in Example 2. The ribosyltransferase activity of DT variants or DT-fusion proteins can be tested by the ribosyltransferase assay described in Example 3. The cytotoxicity of DT variants or DT-fusion proteins can be tested as described in Examples 4-5.
DT-mutants and DT-fusion proteins having reduced binding to HUVECs while maintaining the cytotoxicity can be used for the treatment of various cancers, including, but not limited to breast cancer, colon-rectal cancer, lung cancer, prostate cancer, skin cancer, osteocarcinoma, or liver cancer and others.
In an exemplary embodiment, the VLS modified DT fusion toxins of the invention are administered to a mammal, e.g., a human, suffering from a medical disorder, e.g., cancer, or non-malignant conditions characterized by the presence of a class of unwanted cells to which a targeting ligand can selectively bind.
The pharmaceutical composition can be administered orally or by intravenouslly. For example, intravenous now possible by cannula or direct injection or via ultrasound guided fine needle. Mishra (Mishra et al., Expert Opin. Biol., 3(7):1173-1180 (2003)) provides for intratumoral injection.
The term “therapeutically effective amount” as used herein, is that amount achieves at least partially a desired therapeutic or prophylactic effect in an organ or tissue. The amount of a modified DT necessary to bring about prevention and/or therapeutic treatment of the disease is not fixed per se. The amount of VLS modified DT fusion toxin administered will vary with the type of disease, extensiveness of the disease, and size of species of the mammal suffering from the disease. Generally, amounts will be in the range of those used for other cytotoxic agents used in the treatment of cancer, although in certain instances lower amounts will be needed because of the specificity and increased toxicity of the VLS-modified DT fusion toxins. In certain circumstances and as can be achieved by, currently available techniques for example (cannulae or convection enhanced delivery, selective release) attempts to deliver enhanced locally elevated fusion toxin amounts to specific sites may also be desired. (Laske et al., J Neurosurg., 87:586-5941(997); Laske et al., Nature Medicine, 3:1362-1368 (1997), Rand et al., Clin. Cancer Res., 6:2157-2165 (2000); Engebraaten et al., J. Cancer, 97:846-852 (2002), Prados et al., Proc. ASCO, 21:69b (2002), Pickering et al., J CLin Invest, 91(2):724-9 (1993)).
The invention is further directed to pharmaceutical compositions comprising a DT variant or DT-fusion protein described hereinabove and a pharmaceutically acceptable carrier.
As used herein the language “pharmaceutically acceptable carrier” is intended to include any and all solvents, solubilizers, stabilizers, absorbents, bases, buffering agents, lubricants, controlled release vehicles, diluents, emulsifying agents, humectants, lubricants, dispersion media, coatings, antibacterial or antifungal agents, isotonic and absorption delaying agents, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well-known in the art. See e.g., A. H. Kibbe Handbook of Pharmaceutical Excipients, 3rd ed. Pharmaceutical Press London, UK (2000). Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary agents can also be incorporated into the compositions.
A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, or glycerine; propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfate; chelating agents such as ethylene-diaminetetracetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose pH which can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
Mainly if not exclusively this pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the injectable composition should be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption (e.g. aluminum monostearate or gelatin), however, any stabilizer or additive posited by this disclosure envisioned for use in protein fusion toxin delivery will be compatible with protein based therapeutics.
Sterile injectable solutions can be prepared by incorporating the active ingredient (e.g., a viral or non viral vector) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active ingredient into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Toxicity and therapeutic efficacy of such ingredient can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to noncancerous and otherwise healthy cells and, thereby, reduce side effects.
The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration arrange that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture and as presented below examples 4-5. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography. The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
The present invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patents and published patent applications cited throughout this application, as well as the Figures and Tables, are incorporated herein by reference.
EXAMPLE 1
Construction Expression and Purification of DT Variant and DT-fusion Proteins
1 (a) Construction of DT Variant and DT-fusion Proteins
A truncated DT-based toxophore comprising a methionine residue at the N-terminus, amino acid residues 1 through 386 (SEQ ID NO: 2) of the native DT (now residues 2-387 in the truncated toxophore), and two additional amino acids residues His and Ala at the C-terminal was constructed. The inclusion of the His and Ala residues was resulted from additional nucleotide sequences introduced during the cloning process. This construct is designated as DT387 SEQ ID NOs:5-6). A schematic diagram of DT387 is shown in FIG. 1 which is equivalent to the DAB389 construct described by Williams et al. with the exception that codon was altered and optimized for E. Coli rather than C. diphtheria. A similar construct containing amino acid residues 1 through 379 of the native DT, with a methionine residue at the N-terminal, was also constructed, which was designated was DT380 SEQ ID NOs:3-4). A DT380 variant with a linker and caboxy terminal cysteine was used to determine the effects of VLS mutations on ribosyltransferase activities and to determine propensity to induce VLS as a function of HUVEC binding.
As shown in FIG. 2, native DT contains three (x)D(y) motifs at residues 6-8 (VDS), residues 28-30 (VDS), and residues 289-291 (IDS). (The number of the residues in the genetic constructs is +1 with respect to native DT). Briefly, site directed mutagenesis was employed to alter the (x)D(y) motif in DT387. A Stratagene Quickchange mutagenesis kit was used to construct the mutations. Oligonucleotide primers were designed to alter encoding residues within the (x)D(y) motif implicated in VLS.
Table 1 provides a list of all the DT mutants that were created, expressed in E. coli, partially purified (not to absolute homogeneity) and tested for cytotoxicity. The corresponding nucleic acid and amino acid sequence changes are shown in FIG. 3. The mutants were tested in the context of protein fusion toxin genetically fused to sequences encoding either human interleukin 2 or human epidermal growth factor.







TABLE 1







Mutant DT toxophores









SEQ ID NOs














SINGLE MUTANT




DT387 (V7A)
51-52



DT387 (D8S)
53-54



DT387 (AD8)
83-84



DT387 (V7S)
55-56



DT387 (D8E)
57-58



DT387 (V29A)
59-60



DT387 (V290A)
61-62



DT387 (D291E)
63-64



DOUBLE MUTANT



DT387 (V7A, V29A)
65-66



DT387 (V7S, V29A)
67-68



DT387 (D8E, V29A)
69-70



DT387 (D8S, V29A)
71-72



DT387 (V29A, D291E)
73-74



TRIPLE MUTANT



DT387 (V7A, V29A, I290A)
75-76



DT387 (V7A, V29A, D291E)
77-78










A number of DT-fusion proteins were also expressed and purified. These proteins and their corresponding DT counterparts are listed in Table 2.







TABLE 2







DT-fusion proteins and control proteins.









SEQ ID NOs














Fusion proteins




DT387EGF/DAB389 EGF
11-12



DT387 linker EGF/DAB389 linker EGF
13-14



DT387IL2/DAB389IL-2
15-16



DT387 linker IL2/DAB389 linker IL2
17-18



DT387 (V7A) linker IL2
19-20



DT387 (D8S) linker IL2
21-22



DT387 (D8E) linker IL2
23-24



DT387 (V29A) linker IL2
25-26



DT387 (I290A) linker IL2
27



DT387 (D291E) linker IL2
28-29



DT387 (V7AV29A) linker IL2
30-31



DT387 (V7AV29AD291E) linker IL2
32



DT387 (D8SV29A) linker IL2
33-34



DT387 (V7SV29A) linker IL2
79-80



DT387 (D8EV29A) linker IL2
81-82



DAB389 (V7AV29AI290A) linker IL2
35-36



DT387 (V29A) linker EGF
37-38



DT387 (D291E) linker EGF
39-40



DT387 (D8EV29A)
41-42



DT387 (V7SV29A) linker EGF
43-44



DT387 (V7AV29A) linker EGF
45-46



DT387 (D8EV29AD291E) linker EGF
47-48



DT387 (D8SV29A) linker EGF
49-50



DT387 (V7A) IL2
87



DT387 (D8S) IL2
88



DT387 (D8E) IL2
89



DT387 (V29A) IL2
90



DT387 (I290A) IL2
91



DT387 (D291E) IL2
92



DT387 (V7AV29A) IL2
93



DT387 (V7AV29AD291E) IL2
94



DT387 (D8SV29A) IL2
95



DT387 (V7SV29A) IL2
96



DT387 (D8EV29A) IL2
97



DAB389 (V7AV29AI290A) IL2
98



DT387 (V29A) EGF
99



DT387 (D291E) EGF
100 



DT387 (D8EV29A) EGF
101 



DT387 (V7SV29A) EGF
102 



DT387 (V7AV29A) EGF
103 



DT387 (D8EV29AD291E) EGF
104 



DT387 (D8SV29A) EGF
105 



Corresponding DT counterparts



DT387/DAB389
5-6










1 (b) Expression and Purification of DT Variants and DT-Fusion Proteins
Plasmid constructs encoding truncated DT protein, DT mutants, and DT-fusion protein were transformed into E. coli HMS174 (DE3) cells. E. coli HMS174 is a protease-deficient strain in which over-expression of recombinant proteins can be achieved. Induction of the recombinant protein expression was obtained by addition of isopropylthiogalactosidase (ITPG) to E. coli HMS174. Following incubation, the bacterial cells were harvested by centrifugation and lysed, and the recombinant protein was further purified from inclusion body preparations as described by Murphs and vanderSpek, Methods in Molecular Biology, Bacterial Toxins:methods andprotocols, 145:89-99 Humana press, Totowa, N.J. (2000). The crude protein preparations were contaminated with endotoxin levels of between 2.5×104 and 2.5×105 EU/ml. It was necessary to remove endotoxins from the protein preparations to assure that effects on HUVECs are from VLS and not due to the presence of the endotoxins. Endotoxin was removed to <250 EU/ml by passage over an ion-exchange resin. As shown in FIG. 4, separation of breakdown products from full-length material also occurred during the ion-exchange chromatography. After another final purification over ion exchange resin endotoxin was reduced to <25 EU/ml and the toxophore was tested for VLS as a function of HUVEC cell binding in vitro. FIG. 4 is the analysis of DT387 toxophore yield by Coomassie and Western Blot. Samples from pilot production process described above resolved by SDS Polyacrylamide Gel Electrophoresis (PAGE). Samples 7 through 13 elute from column with less than 250 EU/ml [initial levels >25,000 EU/ml] and as essentially pure DT toxophore. Molecular weight standards are indicated (kDa). An anti-DT antibody was used for the Western blot.
Some of the constructs are more difficult to express and purify. Mutations that result in stable constructs with adequate expression that do not affect ribosyltransferase activity of the DT387 toxophore were subsequently tested for targeted cytotoxicity in the corresponding VLS modified DT-EGF and VLS modified DT-IL-2 protein fusion toxins (Examples 4 and 5 respectively).
As described in more detail in Examples 2-4, DT387, VLS modified DT387EGF and DT387IL-2 have been used to distinguish between effects of the VLS mutations on catalytic activity, VLS activity and effective delivery of the targeted protein fusion toxins to the cytosol of target cells.
EXAMPLE 2
Binding of DT Toxophores to HUVEC In Vitro
Human vascular endothelial cells were maintained in EGM media (obtained from Cambrex, Walkersville, Md.). Sub-confluent early passage cells were seeded at equivalent cell counts onto plastic cover slips. Purified, endotoxin free wild type DT toxophore and mutants DT38(V7AV29A)gscys and DT380(D8SD291S)gscys were labeled with the fluorescent tag F-150 (Molecular Probes, Eugene, Oreg.) through chemical conjugation. HUVECs were incubated with equivalent amounts of the labeled toxophores. The media was then aspirated, the cells washed and then, fixed and prepared for analysis. Examination of the cells on cover slips from different treatment groups permitted the analysis of the number of cells labeled by the fluorescent toxophore. No targeting ligand was present on the toxophore, and consequently, the level of HUVEC interaction was proportional only to the toxophores affinity for HUVECs. Comparisons were carried out using a fluorescent microscope and comparing the number of cells labeled from at least ten independent fields, different coverslips or different slids. DAPI stain was used to localize cells, particularly in the case of the mutant constructs as cell labeling was not readily apparent. 4′-6-Diamidino-2-phenylindole (DAPI) is known to form fluorescent complexes with natural double-stranded DNA, as such DAPI is a useful tool in various cytochemical investigation. When DAPI binds to DNA, its fluorescence is strongly enhanced. Thus, DAPI serves as a method of labeling cell nuclei. In contrast, cells treated with F-150DT toxophore were easily observed. To facilitate that quantification of the mutant DT toxophore constructs the signal intensity and change in background signal were also increased.
FIGS. 5A and 5B show representative photomicrographs illustrating the levels of fluorescence between wild type DT toxophore mediated HUVEC staining and VLS modified HUVEC staining. There is a discemable difference in the number of cells labeled and the intensity of the labeled cells using the native DT toxophore molecule versus the VLS modified molecules. As shown in FIG. 6, this change in labeling accounts for the greater than ten fold decrease in average fluorescence observed when a VLS modified DT toxophore is employed to label HUVECs.
EXAMPLE 3
VLS Mutants Retain ADP-ribosyltransferase Activity
Ribosome inactivating protein toxins such as diphtheria toxin catalyze the covalent modification elongation factor tu (EF-tu). Ribosylation of a modified histidine residue in EF-tu halts protein systhesis at the ribosome and results in cell death. Ribosyltransferase assays to determine catalytic activity of the DT387 mutants are performed in 50 mM Tris-Cl, pH8.0, 25 mM EDTA, 20 mM Dithiothreitol, 0.4 mg/ml purified elongation factor tu, and 1.0 pM [32P]-NAD+ (10 mCi/ml, 1000 Ci.mmol, Amersham-Pharmacia). The purified mutant proteins are tested in a final reaction volume of 40 μl. The reactions are performed in 96 well, V-bottom microtiter plates (Linbro) and incubated at room temperature for an hour. Proteins are precipitated by addition of 200 μl 10% TCA and collected on glass fiber filters, and radioactivity dis etermined by standard protocols.
As shown in FIG. 7, DT mutants DT387(V7A), DT387(V7A)linkerIL-2, DT387(V7AV29A), and DT387(V7AV29A)linkerIL-2 exhibited ADP ribosyltransferase activity that was equivalent or higher than that exhibited by fragment A of native DT.
EXAMPLE 4
VLS Mutants Suitable for DT-fusion Proteins—VLS-Modified DTEGF
The ability to create, express and obtain selective receptor-specific fusion toxins using VLS modified DT-based toxophores is central to the disclosure. Proteins expressed from gene fusions between the modified toxophore and a specific targeting ligand allow the development of fusion toxins that can be used as research tools, as in vitro components of developing cell therapies and in vivo as therapeutics.
Cells integrate a variety of signals required for the maintenance of homeostasis and normal tissue function. These signals include soluble factors liberated by adjacent cells, regional tissue-specific factors an signals from remote sites with an organism. These signals can take the form of proteins, cytokines, hormones, peptides, enzymes, metabolites or small signaling molecules. The target cells express receptors specific to these signaling molecules and these receptors are critical for the appropriate reception and integration of these signals. Diseases such as cancer are often characterized by aberrant signaling and some signals have been shown to stimulate proliferation and differentiation of the malignant cells. The Epidermal Growth Factor, or EGF is a peptide cytokine that plays a variety of roles in the body including a role as a proliferation factor for cells bearing the EGF receptor or receptors capable of binding EGF. Inappropriate signaling through EGF receptors has been implicated in a number of tumors including breast cancer, squamous cell cancer of the head and neck, pancreatic cancer and glioblastoma. In the case of glioblastoma, patients often exhibit a rearrangement of the gene encoding the EGF receptor in tumor tissue. The rearrangement is typically associated with a dramatic over-expression of this growth factor receptor on the cancerous cells. This differential expression of EGF receptor on tumor cells makes it possible to direct an EGF diphtheria toxin protein fusion toxin to these cancerous cells and selectively ablate them from the patient. (Shaw, et al., Jour. Biol. Chem., 266:21118-21124 (1991)) EGF signaling has also been implicated in the establishment of new blood vessel formation are process known as angiogenesis. Angiogenesis is important in the development of a number of tumors and thus, DTEGF fusion toxin could be employed to prevent angiogeneisis in solid tumors and reduce its size or prevent its development. Thus a VLS-modified DTEGF would have clinical utility and could be used to treat a number of diseases characterized by aberrant EGF receptor expression.
In addition there are circumstances in which normally appropriate EGF signaling is undesirable and the use of a DTEGF fusion toxin under these circumstance could be clinically useful. For example, as described by Pickering et al “smooth muscle cell proliferation in arteries is a common event after balloon angioplasty and bypass surgery and it is associated with vascular narrowing”. DTEGF can be utilized to prevent smooth muscle cell proliferation and it can be locally applied to prevent vascular narrowing. (Pickering et al., J Clin Invest 91(2):724-9 (1993)).
To determine if the modified VLS DT-based toxophore described above could be employed to create viable, active fusion toxins, VLS-modified DT387linkerEGF fusion toxins were created and tested. Plasmids encoding VLS-modified toxophores were used as starting vectors and an in-frame insertion of the nucleotide sequence encoding EGF was inserted to create VLS-modified DTE387linkerEGF fusion proteins.
The fusion proteins were expressed essentially as described above. Induction of mutant DT387linker EGF fusion protein expression was obtained by addition of isopropylthiogalactosidase (ITPG) to E. coli HMS174 (DE3). E. coli HMS174 is a protease-deficient strain in which over-expression of recombinant proteins can be achieved. Following incubation, the bacterial cells were harvested by centrifugation, the DTEGF bacterial pellets were homogenized in 20 ml, ice cold, STET buffer (50 mM Tris-Cl, pH 8.0, 10 mM EDTA, 8% glucose, 5% Triton X-100). Lysozyme was added to 25 μg/ml and the bacteria were incubated on ice for 1 hour. The preparation was homogenized and then subjected to centrifugation at 6000×g for 30 minutes to 4° C. The resulting pellet was resuspended in 20 ml of STET and homogenized and the centrifugation step repeated. The final pellet was resuspended in 5 ml 7M GuHCl, 50 mM Tris-Cl, pH 8.0, homogenized and centrifuged, 6000×g, 30 minutes, 4° C. The supernatant was used in refolding assays.
The supernatant protein concentration was 5 mg/ml and refolding was performed at final concentrations of 0.4 mg/ml and 0.08 mg/ml. Refolding was assessed using a Pro-Matrix protein refolding kit from Pierce. (Pierce Biotechnology Inc., Rockford, Ill.) The refolding conditions are shown in Table 3.







TABLE 3







Folding conditions in Pierce Pro-Matric refolding kit used to determine


optimal refolding conditions for VLS-modified DT387linker


EGF fusion proteins produced in E. coli.












GuHC1
L-Arginine
GSG
GSSG


Tubes
(M)
(M)
(mM)
(mM)














1 + 10
0
0
2
0.2


2 + 11
0
0.4
2
0.4


3 + 12
0
0.8
1
1


4 + 13
0.5
0
2
0.4


5 + 14
0.5
0.4
1
1


6 + 15
0.5
0.8
2
0.2


7 + 16
1.0
0
1
1


8 + 17
1.0
0.4
2
0.2


9 + 18
1.0
0.8
2
0.4









Tubes 1-9 had a final concentration of 1.6×10−6 M and tubes 10-18 had a final concentration of 8×10−6 M DT387 (D8EV29A)linker EGF. The tubes were incubated overnight at 4° C. and 1 μl volumes were assayed the next day for cytotoxicity on U87MG glioblastoma cells (Glioblastoma cells have been shown to express EGF receptors ((Frankel et al., Clin Cancer Res., 8(5):1004-13 (2002)). The samples were also analyzed by gel electrophoresis to assure no degradation had occurred during refolding (FIG. 8).
Samples of VLS-modified fusion toxins (shown here VLS-modified DT387(D8EV29S)linker EGF and DT387EGF were purified through the inclusion body step, denatured and subjected to refolding under a variety of conditions. Samples were then dialysed to remove any residual contaminants from the refolding conditions and tested for activity in cytotoxicity assays against U87MG EGF-receptor-bearing cells. These preparations are still considered crude and were used only to compare conditions which resulted in enhanced activity relative to standard refolding conditions and fusion toxins created using the native DT toxophore [in the context of an EGF fusion toxin DTEGF]. FIG. 9 shows the results for cytotoxicity assays of samples 1-9, using protein concentration of DT387(D8EV29A)linker EGF of 8×10−9 M. FIG. 10 depicts the results for tubes 10-18 in which the protein concentration of DT387(D8EV29A)linker EGF employed were higher (4×10−8 M). Refolding to an actively cytotoxic form was more efficient when the lower concentrations of DT387(D8EV29A)linker EGF fusion toxin were employed. Buffer conditions 4, 6 and 8 were chosen for further refinement.
New preparations of DT387EGF and DT387(D8EV29A)linker EGF were prepared as described above. The final, denatured supernatants were refolded in buffers 4, 6 or 8, (see Table 3), at lower protein concentrations. After refolding, the samples were dialyzed against corresponding refolding buffers, without GuHCl, permitting higher concentrations of fusion toxin to be tested. The results indicate that the IC50S for DT387EGF ranged from 8×10−10 M to 1.5×10−9 M for the buffers tested. Buffer 8 appeared to yield the most productive protein. The same holds true for refolding of the DT387(D8EV29A)linker EGF mutant.
Other VLS-modified DT387EGF fusion proteins were also tested for their cytotoxicity in EGF-receptor-positive U87MG glioblastoma cells. As shown in FIG. 11, the EGF fusion toxins created with VLS modifications that exhibit the greatest selective toxicity against EGF-receptor-bearing cell are DT387(V7SV29A)linker EGF, DT387(D291E)linker EGF, DT387(V29A)linker EGF. These EGF fusion toxins display IC 50s comparable to cGMP prepared DT387linker EGF and DT 387linker EGF prepared under conditions identical to those used to express, refold and purify the VLS-modified DT387linker EGF fusion toxins. Thus, the VLS modified DT-based toxophores can be employed to create novel DT-based fusion toxins.
FIG. 12 is a Coomassie stained SDS-PAGE gel showing the level of purity for the VLS-modified DT387linker EGF fusion protein tested in FIG. 11. Several additional species are apparent on the gel and the variation of expression levels can be observed. Resolution of these species by both anion exchange chromatography and sizing yielded fusion preparations that were homogenous and exhibited higher specific toxicity. This presumably was a function of the relatively purity of the active species versus the total protein concentration used to determine IC50s.
EXAMPLE 5
VLS Mutants Suitable for DT-fusion Protein—VLS Modified DTIL-2
1 (a) Cytoxocity Assays on Crude Extracts of DT387linker IL-2 VLS Mutants.
The DT387 construct was initially used to demonstrate that VLS-modified toxophores could be chemically coupled to a number of targeting ligands and yield functional targeted toxins. The large-scale production of targeted toxins following chemical conjugation, however, was not a commercially viable enterprise and the advent of single chain fusions toxins as exemplified by DT387linker IL-2 circumvents the scale-up purification problems typically encountered in the development of conjugate toxins. Fusion toxins, however, do present challenges in that the single chain molecules must be purified into an active, appropriately folded form capable of effective delivery of the catalytic domain of the toxin to targeted cells. Thus, the site-directed changes in VLS modified DT387 and DT387linker IL-2 might not yield functional molecules or molecules that can be readily refolded into active fusion toxins. To confirm the effects of the engineered changes, a number of VLS modified DT387 IL-2 fusion toxins were produced and tested in cytotoxicity assays.
Conservative amino acid substitutions in the C and T domains of DT have been created. To determine that the changes do not yield inactive toxophores incapable of producing fusion toxins, cytotoxicity assays were performed. Readily apparent patterns have emerged which dictate the type of amino acid substitutions that can be accepted at each of the three VLS motifs within DT. Results indicate that mutations of the VLS sequences present at amino acid residues 7-9 or 290-292 of the DT toxophore resulted in less binding to human umbilical vein cell monolayers in culture. Some constructs demonstrated low levels of expression. Consequently additional VLS mutants were developed including: V7S, D8E, D8S and D291E.
The cytotoxicities of crude extracts of wild type DAB389IL-2, two of the VLS mutants and a control were assayed as indicated. The results are reported as a percentage of control incorporation (no toxin added to cells).
These mutants were incorporated alone or in combination (D8S, V29A and V7A, V29A, 1290A variants) into DT387linker IL-2 and have been tested as partially purified extracts in cytotoxicity assays and results indicate they are cytotoxic when compared to the negative control, DAB389linker EGF control, (which contains a targeting ligand to a receptor not expressed on HUT102/6TG cells) and DAB389linker IL-2. All VLS modified mutant toxophore fusion toxins were compared to DAB389linker IL-2 produced and tested at similar levels of purity and concentration. The triple mutant, DT387(V7A,V29A,D291E)linker IL-2 was expressed in full-length form, despite the valine to alanine change at position 7, and was also cytotoxic. FIG. 13 shows the representative results of a cytotoxicity assay using DT387linker IL-2, DT387(D8SV29A)linker IL-2, DT387, DT387(V7AV29A)linker IL2, DT387(V7AV29AI290A)linker IL2, DT387(V7SV29A)Iinker IL2, and DT387(D8EV29A)linker IL2.
Cytotoxicity assays are performed using HUT102/6TG cells, a human HTLV1 transformed T-cell line that expresses high affinity Interleukin-2 receptors. HUT102/6TG cells are maintained in RPMI 1640 (Gibco) media supplemented with 10% fetal bovine serum, 2 mM glutamine, 50 IU/ml penicillin and 50 μg/ml streptomycin. The cells are seeded at a density of 5×104/well into 96 well, V-microtiter plates. The fusion protein toxins are typically added to the wells in molarities ranging from 10−7 M down to 10−12 M. Final volume in the wells is 200 μl. The plates are incubated for 18 hours, at 37° C. in a 5% CO2 environment. The plates are subjected to centrifugation to pellet the cells, the media removed and replaced with 200 μl leucine-free, minimal essential medium containing 1.0 μCi/ml[14C] leucine (<280 mCi/mmol, Amersham-Pharmacia) and 21 mM glutamine, 50 IU/ml penicillin and 50 μg/ml streptomycin. The cells are pulsed for 90 minutes and then the plates subjected to centrifugation to pellet the cells. The supernatant is removed and the cells are lysed in 60 μl, 0.4 M KOH followed by a 10 minute incubation at room temperature. 140 μl of 10% TCA is then added to each well and another 10 minute, room temperature incubation is performed. The precipitated proteins are collected on glass fiber filters using a “PHD cell harvester” and the incorporated radioactivity is determined using standard methods. The results are reported as a percentage of control (no fusion protein added to inhibit protein synthesis) [14C]-leucine incorporation.
Pharmaceutical grade GMP purified DAB389IL-2 produced from E. Coli typically yields an IC50 of between 5×10−11 M to 1×10−12 M. Partially purified toxins exhibit activity between 10-100 fold lower in partially purified non-homogenous extracts. Pharmaceutical grade toxins are purified to homogeneity and the active fractions of refolded fusion toxins are used as biologically active drug. In the example above we utilize a moderate through put analysis to determine the receptor specific cytotoxicity of partially purified VLS modified DT-IL-2 fusion toxins and compared them to the activity of similarly purified DAB389IL-2. These assays demonstrate comparable activity of the VLS modified DT387linker IL-2 fusion to DAB389IL-2. It should be noted that the calculation of specific cytotoxicity was based upon the total amount of protein in the samples of partially fusion toxin. For assays equimolar concentrations of fusion toxins were tested. As shown below in panel FIG. 14 panels A and B each fusion toxins construct displayed patterns on 10% SDS PAGE and Western (anti diphtheria toxin) analysis. In FIG. 14, A is coomassie stained gel of partially purified inclusion body preparations. Lane 1, molecular weight markers; lane 2, DAB389IL-2; lane 3, DT387(V7AV29A)linker IL-2, lane 4, DT387(V7S,V29A)linker IL-2, lane 5, DT387(D8E,V29A)linker IL-2; lane 6, DT387(D8S,V29A) linker IL-2; lane 7, DT387(V7A,V29A,D291E) linker IL-2. B is corresponding Western blot with horse anti-DT first antibody and rabbit anti-horse secondary antibody. The relative amounts of non-fusion toxins protein in each sample could artificially alter the IC50 of any given construct. That is, the presence of non full length or non fusion toxin protein in the samples used in this analysis could potentially account for small differences in IC50.
The cytotoxicity data clearly demonstrate that the modifications that reduce HUVEC binding can be employed to create functional DTIL-2 fusion toxins.
Purified DAB389 IL-2 produced in E. coli typically yields an IC50 of between 5×10−11 M to 1×10−12 M. In the example above, a moderate through put cytotoxicity assay was used to analyze crude purifications of VLS modified DT-IL-2 fusion toxins and compared them to the activity of similarly purified DT387linkerIL-2. Insert figure for comparison of relative purity of IL2 fusion toxins in this assay.
It should be noted that there is one (x)D(y) motif in IL-2 located at residues 19-21 (LDL). The contribution of IL-2 to VLS can be determined by modifying the (x)D(y) motif in the IL-2 and test the modified protein using the cytotoxicity assay described above. [For example, using VLS-modified DT mutants derived from both DT387 and DT387linker IL-2, it is possible to distinguish between effects of the VLS mutations on catalytic activity, VLS activity and effective delivery of the targeted toxin to the cytosol of target cells]. The comparison between VLS-modified DT mutants of DT387 and DT387linker IL2 will also separate the effects of VLS sequences of the toxophore alone from the IL-2 targeting ligand present in DT387linker IL-2.
Table 4 summarizes the IC50S of VLS-modified DT mutants. Mutants not tested are indicated by “n.t.” Primary screening of mutants was performed following expression and crude primary inclusion body purification. Complete purification was not performed and the VLS modified toxophores have all been tested in the context of at least one fusion toxin (EGF receptor or IL-2 receptor targeted) and compared to DT387 based parental fusion toxin expressed and prepared to a similar level of purification.







TABLE 4







IC50S of VLS-modified DT mutants









SINGLE
DOUBLE
TRIPLE


MUTANT
MUTANT
MUTANT





DT387 (V7A) >10−7
DT387 (V7A, V29A) >10−7
DT387 (V7A,




V29A, D291E)




>10−7


DT387 (D8S) 2 × 10−8
DT387 (V7S, V29A) 2 × 10−8


DT387 (ΔD8) >10−7
DT387 (D8S, V29A)



2.5 × 10−10


DT387 (V29A)
DT387 (D8S, D291S) n.t.


2 × 10−10



DT387 (D8E, V29A) 5 × 10−9



DT387 (V29A, D291E) 2 × 10−9









The IC50S were determined in the cytotoxicity assay as described in Examples 4 and 5, IC50S for DT387linker EGF and DT387linker IL-2 were found to be in a similar range from 5×10−9 to 1×10−10 M. The cytotoxicity of both the parental DAB389-based fusion toxins and VLS-modified DT387 fusion toxins increased with increasing levels of purification. For example, pharmaceutical grade DAB389EGF exhibits an IC50 of 4.5×10−11 M in these assays whereas crude inclusion body preparations of DT387(V29A)linker EGF exhibit an IC50 of 2×10−10 M.
Among the VLS-modified DT387 toxophore constructs tested thus far, DT387(V29A) and DT387(D8S, V29A) appear to maintain cytotoxicity comparable to wild type. The DT387(D8S) single mutant was not as cytotoxic as the corresponding double mutant indicating the additional change to V29A helped stabilize the molecule.
The preferred embodiments of the compounds and methods of the present invention are intended to be illustrative and not limiting. Modifications and variations can be made by persons skilled in the art in light of the above teachings specifically those that may pertain to alterations in the DT toxophore surrounding the described VLS sequences that could result in reduced HUVEC binding while maintaining near native functionally with respect to the ability to use as a DT toxophore in protein fusion toxin constructions. It is also conceivable to one skilled in the art that the present invention can be used for other purposes, including, for example, the delivery of other novel molecules to a selected cell population. It is envisioned that the present invention would be employed under those circumstances in which amounts of DT toxophore would be used to deliver such agents in a clinical setting or in settings where it would be desirable to reduce as much as possible the potential for VLS. In this setting the catalytic domain or some portion thereof would be replaced, ro rendered inactive and fused with the desired agent or molecule. Acid sensitive or protease sensitive cleavage sites could be inserted between the remnant of the catalytic domain and the desired agent or molecule. Agents or molecules that might be coupled to VLS modified DT toxophore such as disclosed herein include but are not limited to; peptides or protein fragments, nucleic acids, ogligonucleotides, acid insensitive proteins, glycoproteins, proteins or novel chemical entities that required selective delivery. Therefore, it should be understood that changes may be made in the particular embodiments disclosed which are within the scope of what is described as defined by the appended claims.

## Claims

1. An isolated polypeptide comprising amino acid residues 1-380 of SEQ ID NO:4, wherein the polypeptide comprises amino acid substitution at position V7 of SEQ ID NO:4, and, optionally with at least one amino acid substitution or deletion made within the regions selected from the group consisting of residues 7-9, 29-31 and 290-292, and wherein said DT variant has cytotoxicity comparable to that of a DT molecule having a sequence of SEQ ID NO:4.

2. The polypeptide of claim 1, wherein the polypeptide has reduced binding activity to human vascular endothelial cells (HUVECs) compared to a polypeptide comprising an amino acid sequence as recited in SEQ ID NO:4 without substitutions.

3. The polypeptide of claim 1, wherein the polypeptide comprises a substitution at amino acid residue V7 selected from V7A or V7S.

4. The isolated polypeptide of claim 1, further comprising a protein selected from the group consisting of EGF, IL-1,IL-2,IL-3,IL-4,IL-5,IL-6,IL-7,IL-8,IL-9,IL-10,IL-11,IL-12,IL-13,IL-14,IL-15,INFa, INFy, GM-CSF, G-CSF, M-CSF, TNF, EGF, VEGF, Ephrin, BFGF, and TGF.

5. The isolated polypeptide of claim 4, selected from the group consisting of EGF, IL-1,IL-2,IL-3, and IL-7.

6. A composition comprising the isolated polypeptide of claim 1 in a pharmaceutically acceptable carrier.

7. The isolated polypeptide of claim 1, further comprising a linker peptide moiety at amino acid residue 380, 387 or 389 of SEQ ID NO:4.

8. The isolated polypeptide of claim 7, wherein the linker peptide moiety comprises non-charged amino acid residues.

9. The isolated polypeptide of claim 1, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 52.