Chlorotoxin variants, conjugates and methods for their use

FIELD OF THE INVENTION

The present invention generally relates to chlorotoxin, and more particularly to chlorotoxin variants, chlorotoxin variant conjugates, compositions that include the chlorotoxin variants or conjugates, and methods for using the chlorotoxin variants, conjugates, and compositions.

BACKGROUND OF THE INVENTION

Neurosurgeons have long sought methods to illuminate brain cancer cells to identify cancer foci and distinguish cancer from normal tissue in real time during tumor resection operations. A bioconjugate composed of chlorotoxin (CTX), a peptide discovered from the Leiurus quinquestriatus scorpion, and near infrared fluorescent (NIRF) molecules, such as Cy5.5, (tumor paint) clearly identifies tumor foci with high sensitivity (M. Veiseh, et al., Tumor Paint: A Chlorotoxin:Cy5.5 Bioconjugate for Intra-Operative Visualization of Cancer Foci, Cancer Research 67(14):6882-88, 2007). CTX was originally selected for these studies because it preferentially binds to glioma cells compared with normal brain tissue (L. Soroceanu, et al., Use of Chlorotoxin for Targeting of Primary Brain Tumors, Cancer Research 58:4871-4879, 1998). Because the CTX target appears to be shared by multiple other cancer types, CTX:Cy5.5 effectively illuminated prostate, colon, sarcoma, medulloblastoma, and other types of solid tumors (M. Veiseh 2007).

CTX is a 36 amino acid peptide with four disulfide bridges that confer a high degree of three dimensional structure to the polypeptide. CTX has three lysine residues at positions 15, 23, and 27 that have been utilized for conjugation to NHS-ester modified Cy5.5 and other fluorescent molecules. The resultant bioconjugate is a mixture of typically 75-85% mono-labeled peptide at position 27 and lesser amounts of di- and tri-labeled peptide conjugated to Lys 15 and Lys 23. Although it is possible to have mixtures approved by the Food and Drug Administration (FDA) and similar regulatory agencies elsewhere, commercialization is potentially hindered as it is expensive and difficult to match the ratio of mono-, di- and tri-labeled batches in the future.

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A need exists for a polypeptide having chlorotoxin’s advantageous properties and having a single lysine residue for conjugation with diagnostic or therapeutic agents to provide a single, homogenous new molecular entity. The present invention seeks to fulfill this need and provides further related advantages.

WO 2006/115633 chlorotoxin conjugate detectable by fluorescence imaging that allows for intra-operative visualization of cancerous tissues, compositions that include the chlorotoxin conjugate, and methods for using the chlorotoxin conjugate.

Veiseh M, et al., (Cancer Res; 2007 67 (14) 6882-6888) reported on chlorotoxin:Cy5.5 bioconjugate for intraoperative visualization of cancer foci.

Veiseh O, et al., (Nano Lett. 2005 Jun;5(6): 1003-8) reported on optical and MRI multifunctional nanoprobe for targeting gliomas.

Veiseh O, et al., (Cancer Res. 2009; 69(15):6200-7) reported on specific targeting of brain tumors with an optical/magnetic resonance imaging nanoprobe across the blood-brain barrier.

US 2009/004105 discloses methods for imaging MMP-2 positive tissue; methods of diagnosing the presence of one or more of MMP-2 positive precancerous cells, MMP-2 positive cancerous cells, MMP-2 positive tumor cells, and MMP-2 positive diseases in a tissue; method of monitoring the progress of one or more of MMP-2 positive precancerous cells, MMP-2 positive cancerous cells, MMP-2 positive tumor cells, and MMP-2 positive diseases in a tissue; pharmaceutical compositions for imaging one or more of MMP-2 positive precancerous cells, MMP-2 positive cancerous cells, MMP-2 positive tumor cells, and MMP-2 positive diseases; compositions; kits; and the like.

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SUMMARY OF THE INVENTION

The present invention provides chlorotoxin variants, conjugates made from the chlorotoxin variants, compositions that include the chlorotoxin variants or conjugates, and methods for using the chlorotoxin variants, conjugates, and compositions.

In one aspect, the invention provides a modified chlorotoxin peptide having a single lysine residue (Lys 27). In one embodiment, the modified chlorotoxin peptide has Lys 15 and Lys 23 of native chlorotoxin substituted by an amino acid other than lysine. In one embodiment, the modified chlorotoxin peptide having the amino acid sequence set forth in SEQ ID NO: 2. In one embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 3. In one embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 4. In one embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 5. In one embodiment, the modified chlorotoxin peptide having the amino acid sequence set forth in SEQ ID NO: 6.

Compositions comprising a modified chlorotoxin peptide of the invention are also provided. In one embodiment, the composition comprises a pharmaceutically acceptable carrier.

In another aspect, the invention provides a method for treating a disease or condition treatable by administering chlorotoxin, comprising administering an effective amount of a modified chlorotoxin peptide of the invention to a subject in need thereof.

In a further aspect of the invention, a chlorotoxin conjugate comprising a modified chlorotoxin peptide of the invention is provided. In one embodiment, the chlorotoxin conjugate comprises a modified chlorotoxin peptide covalently coupled to one or more of a therapeutic, diagnostic, imaging, or targeting agent, or a moiety that increases the circulatory half-life of the modified chlorotoxin peptide. In one embodiment, the therapeutic, diagnostic, imaging, or targeting agent, or a moiety that increases the circulatory half-life of the modified chlorotoxin peptide is covalently coupled to the modified chlorotoxin peptide through the lysine residue. Suitable diagnostic or imaging agents include fluorescent labels (e.g., quantum dot or polymeric dot), radiolabels, and magnetic resonance imaging labels (e.g., a boron nanoparticle, a boron and carbon nanoparticle, a boron carbide nanoparticle, boron-containing polymer, a boron and carbon

22293m containing polymer, a boron carbide polymer, and any of these nanoparticles or polymers further comprising gadolinium). Suitable targeting agents include antibodies, polypeptides, polysaccharides, and nucleic acids. Suitable therapeutic agents include chemotherapeutic agents (e.g., methotrexate, docetaxel, cisplatin, and etoposide) and biological therapeutic agents (e.g., cDNA, siRNA, shRNA, and RNAi). Suitable moieties that increase the circulatory half-life of the modified chlorotoxin peptide include peg moieties, glycosyl moieties, and glycosylpeg moieties.

In other aspects, methods for using the chlorotoxin conjugates are provided.

In one embodiment, the invention provides a method for imaging a tissue imagable by chlorotoxin, comprising contacting a tissue imagable by chlorotoxin with a chlorotoxin conjugate of the invention to image a tissue imagable by chlorotoxin.

In one embodiment, the invention provides a method for detecting cancer detectable by chlorotoxin, comprising contacting a tissue imagable by modified chlorotoxin with a modified chlorotoxin conjugate of the invention to detect cancer detectable by chlorotoxin.

In one embodiment, the invention provides a method for detecting and removing cancer detectable by chlorotoxin, comprising contacting a tissue with a modified chlorotoxin conjugate of the invention to detect cancerous tissue, and removing the cancerous tissue detected by the modified chlorotoxin conjugate.

In one embodiment, the invention provides a method for treating cancer targeted by a modified chlorotoxin conjugate, comprising contacting a tissue that binds to modified chlorotoxin with a modified chlorotoxin conjugate of the invention to treat the cancer.

DESCRIPTION OF THE DRAWINGS

The foregoing aspects and many of the attendant advantages of this invention will become more readily appreciated as the same become better understood by reference to the following detailed description, when taken in conjunction with the accompanying drawings.

FIGURE 1 compares the sequences of native chlorotoxin (Linear CTX) with representative modified chlorotoxin peptides of the invention (K15A_K23A CTX; K15R_K23R CTX). The sequences of native and substituted CTX with four disulfide bonds shown as yellow lines.

FIGURE 2 is a comparison of the secondary aH chemical shifts of representative modified chlorotoxin peptides of the invention and native chlorotoxin. The secondary aH shifts were calculated by subtracting the random coil shifts from the experimental aH shifts (D.S.

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Wishart, et al., II, ¹³C and ¹⁵N Chemical Shift Referencing in Biomolecular NMR, Journal of Biomolecular NMR 6, 135-140, 1995). A bar graph for native CTX (dark blue), linear CTX (blue), K15A_K23A CTX (red), and K15R_K23R CTX (orange). Two β-strands are shown as blue arrow, α-helix is shown in red. The substituted residues and residue DI8 are shown with a green asterisk.

FIGURES 3A and 3B illustrate functional imaging with representative modified CTX:Cy5.5 bioconjugates of the invention (FIGURE 3A, K15A_K23A CTX:Cy5.5; and FIGURE 3B, K15R_K23R CTX:Cy5.5). WT or ND2:SmoAl tumor-bearing mice were injected with 50 11 of 40 UM modified bioconjugate through the tail vein. Biophotonic images were taken three days after the injection using the Xenogen Spectrum. The brains were then frozen in OCT, cut in 12 Im sections, and stained with H&E to determine tumor burden.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides chlorotoxin variants, conjugates made from the chlorotoxin variants, compositions that include the chlorotoxin variants or conjugates, and methods for using the chlorotoxin variants, conjugates, and compositions.

In one aspect, the invention provides chlorotoxin variants. As used herein, the term chlorotoxin variant is used interchangeably with the term modified chlorotoxin peptide and refers to a non-native polypeptide possessing at least some of the useful activities of native chlorotoxin. Chlorotoxin is a naturally occurring polypeptide comprising 36 amino acids and having the amino acid sequence set forth in SEQ ID NO: 1.

The term modified chlorotoxin peptide refers to a polypeptide having an amino acid sequence in which one or more of the amino acid residues of native chlorotoxin are substituted (i.e., replaced) with an amino acid residue other than that of the native chlorotoxin at that position. For example, residues 15 and 23 of native chlorotoxin are lysine residues; in certain embodiments of the invention, modified chlorotoxin peptides are provided having alanine or arginine residues at positions 15 and 23.

In one embodiment, the invention provides a modified chlorotoxin peptide having a single lysine residue (Lys 27). In this embodiment, the modified chlorotoxin peptide has Lys 15 and Lys 23 of native chlorotoxin substituted by an amino acid other than lysine to provide a modified chlorotoxin having a single lysine residue (Lys 27). In this embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 2, where Lys 15 and

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Lys 23 are substituted by an amino acid independently selected from the group consisting of naturally occurring and non-natural amino acids, amino acid analogs and amino acid mimetics.

Naturally occurring amino acids are the twenty L-amino acids commonly found in naturally occurring proteins (Ala or A, Cys or C, Asp or D, Glu or E, Phe or F, Gly or G, His or H, lie or I, Lys or K, Leu or L, Met or M, Asn or N, Pro or P, Gin or Q, Arg or R, Ser or S, Thr or T, Vai or V, Trp or W, Tyr or Y). Non-natural amino acids include the D-amino acids. Amino acid analogs and amino acid mimetics function in a manner similar to the naturally occurring amino acids. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, by way of example only, an α-carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group. Such analogs may have modified R groups (by way of example, norleucine) or may have modified peptide backbones, while still retaining the same basic chemical structure as a naturally occurring amino acid. Nonlimiting examples of amino acid analogs include homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium.

In one embodiment, Lys 15 and/or Lys 23 are independently replaced with a basic amino acid (i.e., His, Arg), non-natural amino acid, amino acid analog, or amino acid mimetic.

In one embodiment, Lys 15 and/or Lys 23 are independently replaced with a nonpolar (hydrophobic) amino acid (i.e., Ala, Phe, lie, Leu, Met, Pro, Vai, Trp), related non-natural amino acid, amino acid analog, or amino acid mimetic.

In one embodiment, Lys 15 and/or Lys 23 are independently replaced with a polar (uncharged) amino acid (i.e., Cys, Gly, Asn, Gin, Ser, Thr, Tyr), non-natural amino acid, amino acid analog, or amino acid mimetic.

In one embodiment, Lys 15 and/or Lys 23 are independently replaced with an acidic amino acid (i.e., Glu, Asp), non-natural amino acid, amino acid analog, or amino acid mimetic.

In one embodiment, the modified chlorotoxin peptide has Lys 15 and Lys 23 substituted by alanine (K15A_K23A CTX). In this embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 3.

In one embodiment, the modified chlorotoxin peptide has Lys 15 and Lys 23 substituted by arginine (K15R_K23R CTX). In this embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 4.

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In one embodiment, the modified chlorotoxin peptide has Lys 15 substituted by alanine and Lys 23 substituted by arginine (K15A_K23R CTX). In this embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 5.

In another embodiment, the modified chlorotoxin peptide has Lys 15 substituted by arginine and Lys 23 substituted by alanine (K15R_K23A CTX). In this embodiment, the modified chlorotoxin peptide has the amino acid sequence set forth in SEQ ID NO: 6.

In another aspect of the invention, compositions that include the modified chlorotoxin peptides are provided. The composition can include a pharmaceutically acceptable carrier or diluent for delivery of the modified chlorotoxin peptide. Suitable pharmaceutically acceptable carriers or diluents include saline or dextrose for injection.

Treatment Methods. In a further aspect, the invention provides a method for treating a disease or condition treatable by administering chlorotoxin. In one embodiment, the method includes administering an effective amount of a modified chlorotoxin peptide of the invention to a subject in need thereof.

The term effective amount, as used herein, refers to a sufficient amount of an agent or a compound being administered which will relieve to some extent one or more of the symptoms of the disease or condition being treated. The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. Compositions containing such agents or compounds can be administered for prophylactic, enhancing, and/or therapeutic treatments. An appropriate effective amount in any individual case may be determined using techniques, such as a dose escalation study.

In one embodiment, the invention provides a method for treating a cancer that expresses chlorotoxin binding sites in a patient, comprising administering to a patient in need thereof an effective amount of a chlorotoxin variant of the invention.

In one embodiment, the invention provides a method for treating a cancer that expresses chlorotoxin binding sites, comprising administering to a patient in need thereof an effective amount of a pharmaceutical composition comprising a chlorotoxin variant of the invention and a pharmaceutically acceptable carrier.

In one embodiment, the invention provides a method for treating a tumor expressing chlorotoxin binding sites, comprising administering to a patient in need thereof an effective amount of a chlorotoxin variant of the invention.

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In one embodiment, the invention provides a method for inhibiting invasive activity of cells that express chlorotoxin binding sites, comprising administering an effective amount of a chlorotoxin variant to cells that express chlorotoxin binding sites.

The methods of treatment of the invention are applicable to human and animal subjects in need of such treatment.

Virtually every type of malignant cancer expressing chlorotoxin binding sites can be treated by the chlorotoxin variants and conjugates of the invention. These malignant cancers include gliomas, astrocytomas medulloblastomas, choroids plexus carcinomas, ependymomas, meningioma, glioblastoma, ganglioma, pheochromocytoma, and metastatic brain tumors, other brain tumors, neuroblastoma, head and neck cancer, small cell lung cancer, breast cancer, intestinal cancer, pancreatic cancer, colon cancer, liver cancer, kidney cancer, skin cancer, sarcomas (over 30 types), osteosarcoma, rhabdomyosarcoma, Ewing’s sarcoma, carcinomas, melanomas, ovarian cancer, cervical cancer, lymphoma, thyroid cancer, anal cancer, colo-rectal cancer, endometrial cancer, germ cell tumors, laryngeal cancer, multiple myeloma, prostate cancer, retinoblastoma, gastric cancer, testicular cancer, and Wilm’s tumor.

Chlorotoxin Conjugates. In another aspect, the invention provides conjugates of the modified chlorotoxin peptides of the invention. In one embodiment, the conjugates comprise a modified chlorotoxin peptide of the invention covalently coupled to a moiety that increases the circulatory half-life of the modified chlorotoxin peptide. In another embodiment, the conjugates comprise a modified chlorotoxin peptide of the invention covalently coupled to a therapeutic, diagnostic, imaging, or targeting agent. In certain embodiments, the therapeutic, diagnostic, imaging, or targeting agent, or moiety that increases the circulatory half-life of the modified chlorotoxin peptide is covalently coupled through the peptide’s lysine residue.

Suitable moieties that increase the circulatory half-life of the modified chlorotoxin peptide include those known in the art for increasing the circulatory half-life of polypeptides (e.g., pegylation, glycosylation, glycopegylation). Representative moieties for pegylation include polyalkylene oxides (polyethylene oxides, polypropylene oxides, and copolymers of polyethylene oxides and polypropylene oxides). Representative moieties for glycosylation include oligosaccharides (e.g., carbohydrates including polysialic acids). In one embodiment, the conjugate is a pegylated chlorotoxin and comprises a modified chlorotoxin peptide covalently coupled to one or more polyalkylene oxides (e.g., polyethylene oxide). In one embodiment, the

22293m conjugate is a glycosylated chlorotoxin and comprises a modified chlorotoxin peptide covalently coupled to one or more oligosaccharides. In one embodiment, the conjugate is a glycopegylated chlorotoxin and comprises a modified chlorotoxin peptide covalently coupled to one or more glycopolyalkylene oxides (e.g., glycopolyethylene oxide).

Suitable therapeutic agents include cytotoxic agents. Representative therapeutic agents include chemotherapeutic agents such as methotrexate, docetaxel, cisplatin, and etoposide, among others; biological therapeutic agents such as nucleic acid molecules (e.g., DNA such as cDNA, and RNA such as siRNA, shRNA, RNAi) including transcription and translocation inhibitors, and signal transduction modulators.

Suitable diagnostic agents include agents that provide for the detection by fluorescence methods as well as methods other than fluorescence imaging. Other suitable diagnostic agents include radiolabels (e.g., radio isotopically labeled compounds) such as ¹²⁵I, ¹⁴C, and ³¹P, among others; and magnetic resonance imaging agents.

Suitable targeting agents include antibodies, polypeptides, polysaccharides, and nucleic acids.

In another aspect of the invention, compositions that include the modified chlorotoxin peptide conjugates are provided. The composition can include a pharmaceutically acceptable carrier or diluent for delivery of the modified chlorotoxin peptide conjugate. Suitable pharmaceutically acceptable carriers or diluents include saline or dextrose for injection.

Imaging Methods. In a further aspect of the invention, methods of using the modified chlorotoxin peptide conjugates are provided. In one embodiment, the invention provides a method for imaging a tissue imagable by chlorotoxin. In the method, a tissue imagable by chlorotoxin is contacted with a chlorotoxin conjugate.

In one embodiment, the imaging method is a fluorescence imaging method. Representative methods for making and using fluorescent chlorotoxin conjugates are described in U.S. Patent Application Publication No. 20080279780 Al, Fluorescent Chlorotoxin Conjugate and Method for Intra-Operative Visualization of Cancer.

The present invention provides a chlorotoxin conjugate detectable by fluorescence imaging that allows for intra-operative visualization of cancerous tissues, compositions that include the chlorotoxin conjugate, and methods for using the chlorotoxin conjugate.

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In one aspect, the present invention provides a chlorotoxin conjugate detectable by fluorescence imaging that allows for intra-operative visualization of cancerous tissues.

The chlorotoxin is a targeting agent that directs the conjugate to a tissue of interest. In one embodiment, the chlorotoxin conjugate of the invention includes one or more fluorescent moieties (e.g., red or near infrared emitting fluorescent moieties) covalently coupled to the chlorotoxin.

As used herein, the term red or near infrared emitting fluorescent moiety refers to a fluorescent moiety having a fluorescence emission maximum greater than about 600 nm. Fluorescent chlorotoxin conjugates having shorter wavelength (e.g., from about 500 to about 600 nm) emitting fluorescent moieties are useful in histochemical imaging. These conjugates may be useful less for in vivo imaging in humans and animals where longer wavelength (e.g., greater than about 600 nm) emitting fluorescent moieties are preferred.

In certain embodiments of the chlorotoxin conjugate, the fluorescent moieties are derived from fluorescent compounds characterized by emission wavelength maxima greater than about 600 nm to avoid autofluorescence, emission that travels through millimeters to one centimeter of tissue/blood/fluids, emission that is not absorbed by hemoglobin, other blood components, or proteins in human or animal tissue.

The fluorescent moiety is covalently coupled to the chlorotoxin to allow for the visualization of the conjugate by fluorescence imaging. The fluorescent moiety is derived from a fluorescent compound. Suitable fluorescent compounds are those that can be covalently coupled to a chlorotoxin without substantially adversely affecting the targeting and binding function of the chlorotoxin conjugate. Similarly, suitable fluorescent compounds retain their fluorescent properties after conjugation to the chlorotoxin.

In one embodiment, the fluorescent moiety is a cyanine moiety. Cyanine compounds are characterized by their relative high extinction coefficients and favorable fluorescence quantum yields. The fluorescence emission wavelength maximum for a cyanine compound varies as a function of the cyanine structure. Depending on the particular cyanine compound, the fluorescence emission wavelength maxima can vary from the green (about 490 nm) to the near infrared (about 740 nm). In the practice of the methods of the invention, cyanine compounds having fluorescence emission maxima in the far red (about 650 nm) to the near infrared (about 750 nm) are preferred. At these emission wavelengths, background fluorescence from the local

22293m environment is minimal and tissues of interest are relatively transparent. Because of the relative transparency of the tissues of interest at these wavelengths, excitation and fluorescence emission visualization is maximized and relatively greater amounts of tissue targeted by the conjugate of the invention can be observed compared to other conjugates utilizing fluorescent compounds having emission at shorter wavelengths (less than 600 nm).

Suitable cyanines include the CYDYE fluors commercially available from GE Healthcare under the designation Cy2 (506 nm); Cy2 (506 nm); Cy3 (570 nm); Cy3B (572 nm); Cy3.5 (596 nm); Cy5 (670 nm); Cy5.5 (675 nm); and Cy7 (694 nm) (emission maxima in parentheses). In one embodiment, the cyanine compound is Cy5.5.

In one embodiment, the fluorescent moiety is a sulfonated xanthene moiety. Sulfonated xanthene compounds suitable for use in the practice of the invention are described in U.S. Patent No. 6,130,101, and commercially available under the designation ALEXA FLUOR from Molecular Probes, Inc., Eugene, OR. ALEXA FLUOR is the designation for a family of fluorophores that are characterized by their relative high extinction coefficients and favorable fluorescence quantum yields. The fluorescence emission wavelength maximum for a sulfonated xanthene compound varies as a function of the compound’s structure. Depending on the particular sulfonated xanthene compound, the fluorescence emission wavelength maxima can vary from the green (about 450 nm) to the near infrared (about 780 nm). In the practice of the methods of the invention, ALEXA FLUOR compounds having fluorescence emission maxima in the far red (about 650 nm) to the near infrared (about 750 nm) are preferred.

Suitable sulfonated xanthene compounds include ALEXA FLUORS, such as ALEXA FLUOR 350 (442 nm), ALEXA FLUOR 405 (421 nm), ALEXA FLUOR 488 (539 nm), ALEXA

FLUOR 500 (525 nm), ALEXA FLUOR 514 (540 nm), ALEXA FLUOR 532 (554 nm), ALEXA

FLUOR 546 (575 nm), ALEXA FLUOR 555 (565 nm), ALEXA FLUOR 568 (603 nm), ALEXA

FLUOR 594 (617 nm), ALEXA FLUOR 610 (628 nm), ALEXA FLUOR 633 (647 nm), ALEXA

FLUOR 635 (645 nm), ALEXA FLUOR 647 (668 nm), ALEXA FLUOR 660 (690 nm), ALEXA

FLUOR 680 (702 nm), ALEXA FLUOR 700 (719 nm), and ALEXA FLUOR 750 (779 nm) (emission maxima in parentheses). In one embodiment, the sulfonated xanthene is ALEXA FLUOR 680. Representative sulfonated xanthene-chlorotoxin conjugates can be prepared in manner analogous to that described in The Handbook - A Guide to Fluorescent Probes and

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Labeling Technologies, Richard P. Haugland (Molecular Probes, Inc., a subsidiary of Invitrogen Corp.).

Other suitable NIR fluorophores useful in the invention include DyLight-680, DyLight750, VivoTag-750, DyLight-800, IRDye-800, VivoTag-680, and indocyanine green.

The modified chlorotoxin peptides of the invention can also be coupled to quantum dots and polymer dots.

Suitable fluorescent compounds include a functional group that renders the compound chemically reactive toward the chlorotoxin. Suitable functional groups include the Nhydroxysuccinimide (NHS) group for covalent coupling to amine groups, the maleimide group for covalent coupling to thiol groups, and the hydrazide group for covalent coupling to aldehyde groups. Preferably, the fluorescent compound useful in preparing the conjugate of the invention includes a single reactive functional group (e.g., mono-NHS ester). It will be appreciated that other conjugating chemistries are suitable for making the chlorotoxin conjugate of the present invention.

Suitable conjugates of the invention include from about 1 to about 3 fluorescent moieties/chlorotoxin. In one embodiment, the conjugate includes about 1 fluorescent moiety.

In another aspect of the invention, compositions that include the chlorotoxin conjugate are provided. The composition is suitable for administration to a human and animal subjects and includes pharmaceutically acceptable carrier. The composition includes a pharmacologically effective amount of a modified chlorotoxin conjugate. An effective amount can be routinely determined by established procedures. An effective amount is an amount sufficient to occupy chlorotoxin binding sites in cancer cells, but low enough to minimize non-specific binding to nonneoplastic tissues. An effective amount optimizes signal-to-noise ratio for intra-operative imaging.

The invention provides methods for detecting a tissue using the chlorotoxin conjugates. The chlorotoxin conjugates of the invention target and are bound by chlorotoxin binding sites. It will be appreciated that chlorotoxin binding sites may take two forms: sites that bind chlorotoxin and sites that bind the chlorotoxin conjugates of the invention. It will be appreciated that chlorotoxin binding sites may be distinct from chlorotoxin conjugate binding sites.

In one embodiment, a method for differentiating foci of cancers that express chlorotoxin binding sites from non-neoplastic tissue is provided. The method includes the steps of:

22293m (a) contacting a tissue of interest with a chlorotoxin conjugate having affinity and specificity for cells that express chlorotoxin binding sites, wherein the chlorotoxin conjugate comprises one or more red or near infrared emitting fluorescent moieties covalently coupled to a chlorotoxin; and (b) measuring the level of binding of the chlorotoxin conjugate, wherein an elevated level of binding, relative to normal tissue, is indicative that the tissue is neoplastic.

In one embodiment, a method for detecting cancers that express chlorotoxin binding sites is provided. The method includes the steps of:

(a) contacting a tissue of interest with a chlorotoxin conjugate having affinity and specificity for cells that express chlorotoxin binding sites, wherein the chlorotoxin conjugate comprises one or more red or near infrared emitting fluorescent moieties covalently coupled to a chlorotoxin; and (b) measuring the level of binding of the chlorotoxin conjugate, wherein an elevated level of binding, relative to normal tissue, is indicative that the tissue is neoplastic.

In one embodiment, a method for determining the location of cancer cells that express chlorotoxin binding sites in a patient intra-operatively is provided. The method includes the steps of:

(a) administering a pharmaceutical composition to a patient, wherein the pharmaceutical composition comprises a pharmaceutically acceptable carrier and an amount of a chlorotoxin conjugate sufficient to image cancer cells that express chlorotoxin binding sites in vivo, wherein the chlorotoxin conjugate comprises one or more red or near infrared emitting fluorescent moieties covalently coupled to a chlorotoxin;

(b) measuring the level of binding of the chlorotoxin conjugate by fluorescence imaging to determine the location of cancer cells that express chlorotoxin binding sites, wherein an elevated level of binding, relative to normal tissue, is indicative of the presence of cancer cells that express chlorotoxin binding sites; and (c) surgically removing from the patient at least some cells that express chlorotoxin binding sites located by fluorescence imaging.

The imaging methods of the invention for detection of cancer foci is applicable to mouse and other animal models of cancer as well as to veterinary practice.

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The fluorescent chlorotoxin conjugate of the invention may include other useful agents. Other useful agents include diagnostic agents and therapeutic agents.

In another embodiment, the imaging method is a magnetic resonance imaging method. Representative methods for making and using chlorotoxin conjugates in magnetic resonance imaging are described in U.S. Patent Application Publication No. 200701254965 Al, Chlorotoxin-Labeled Nanoparticle Compositions and Methods for Targeting Primary Brain Tumors.

The present invention provides chlorotoxin-labeled nanoparticles capable of targeting primary brain tumors, compositions that include the nanoparticles, methods of imaging tissues using the nanoparticles, and methods for treating cells expressing chlorotoxin binding sites using the nanoparticles.

In one aspect, the invention provides a chlorotoxin-labeled particle comprising:

(a) a core having a surface, the core comprising a material having magnetic resonance imaging activity;

(b) a modified chlorotoxin peptide; and (c) a linker covalently coupling the modified chlorotoxin peptide to the surface.

The core includes a material having magnetic resonance imaging activity. Suitable materials having magnetic resonance imaging activity include metal oxides, such as ferrous oxide, ferric oxide, silicon oxide, polycrystalline silicon oxide, aluminum oxide, germanium oxide, zinc selenide, tin dioxide, titanium dioxide, indium tin oxide, and gadolinium oxide. Mixtures of one or more metal oxide can be used.

In addition to magnetic materials, the core can include non-magnetic materials, such as silicon nitride, stainless steel, titanium, boron, boron carbide, boron and carbon mixtures, and nickel titanium. Mixtures of one or more non-magnetic materials can also be used.

The particles of the invention include from about 1 to about 100 modified chlorotoxins/particle. In one embodiment, the particles include from about 10 to about 50 modified chlorotoxins/particle. In one embodiment, the particles include about 10 modified chlorotoxins/particle. In one embodiment, the particles include about 50 to about 100 modified chlorotoxins/particle.

As noted above, the magnetic nanoparticle of the invention includes a chlorotoxin that serves as a targeting moiety that is effective to direct the nanoparticle to cells expressing

22293m chlorotoxin binding sites where the nanoparticle is bound. Primary brain tumor cells (e.g., neuroectodermal-derived tumor cells and glioma cells) include chlorotoxin binding sites.

The chlorotoxin-labeled nanoparticles can further include other useful agents. Other useful agents include diagnostic agents.

Suitable diagnostic agents include agents that provide for the detection of the nanoparticle by methods other than magnetic resonance imaging. Suitable diagnostic agents include lightemitting compounds (e.g., fluorophores, phosphors, and luminophors). Suitable fluorophores include those noted above.

In one embodiment, the chlorotoxin-labeled particle further comprises a fluorescent moiety. The particles of the invention include from about 1 to about 10 fluorescent moieties/particle. In one embodiment, the particles include from about 1 to about 2 fluorescent moieties/particle.

In one embodiment, the fluorescent moiety is selected from red and near infrared emitting fluorescent moieties (i.e., fluorescent moieties having emission maxima greater than about 600 nm). In one embodiment, the fluorescent moiety is a cyanine moiety. In one embodiment, the fluorescent moiety is a Cy5.5 moiety.

Other suitable diagnostic agents include radiolabels (e.g., radio isotopically labeled compounds) such as ¹²⁵I, ¹⁴C, and ³¹P, among others.

In another aspect of the invention, compositions that include the particles of the invention are provided. In one embodiment, the composition includes a nanoparticle suitable for administration to a human or an animal subject. The composition can include an acceptable carrier. In one embodiment, the composition is a pharmaceutically acceptable composition and includes a pharmaceutically acceptable carrier. As used herein the term carrier refers to a diluent (e.g., saline) to facilitate the delivery of the particles.

In other aspects, the invention provides methods for using nanoparticles.

In one embodiment, the invention provides a method for differentiating neuroectodermalderived tumor cells from non-neoplastic brain tissue. In the method, neuroectodermal-derived tumor cells are differentiated from non-neoplastic brain tissue by:

(a) contacting a tissue of interest with a chlorotoxin-labeled nanoparticle having affinity and specificity for neuroectodermal-derived tumor cells; and

22293m (b) measuring the level of binding of the chlorotoxin-labeled nanoparticle, wherein an elevated level of binding, relative to normal tissue, is indicative that the tissue is neoplastic.

In one embodiment, the invention provides a method for detecting neuroectodermalderived tumor cells. In the method, neuroectodermal-derived tumor cells are detected by:

(a) contacting a tissue of interest with a chlorotoxin-labeled nanoparticle having affinity and specificity for neuroectodermal-derived tumor cells; and (b) measuring the level of binding of the chlorotoxin-labeled nanoparticle, wherein an elevated level of binding, relative to normal tissue, is indicative that the tissue is neoplastic.

The above methods are useful in differentiating and detecting glioma cells.

In the methods above, measuring the level of binding of the chlorotoxin-labeled nanoparticle comprises magnetic resonance imaging.

In certain embodiments of the methods above, the chlorotoxin-labeled nanoparticle further comprises a fluorescent moiety. In these embodiments, measuring the level of binding of the chlorotoxin-labeled nanoparticle can include fluorescence imaging.

In one embodiment, the invention provides a method for determining the location of glioma cells in a patient pre-operatively, intra-operatively, and post-operatively. The methods includes the steps of:

(a) administering a pharmaceutical composition to a patient, wherein the pharmaceutical composition comprises a pharmaceutically acceptable carrier and an amount of a fluorophore/chlorotoxin-labeled nanoparticle sufficient to image glioma cells in vivo;

(b) measuring the level of binding of the fluorophore/chlorotoxin-labeled nanoparticle by magnetic resonance imaging pre-operatively to determine the location of glioma cells, wherein an elevated level of binding, relative to normal tissue, is indicative of the presence of glioma cells;

(c) surgically removing from the patient at least some glioma cells located by magnetic resonance imaging;

(d) measuring the level of binding of the fluorophore/chlorotoxin-labeled nanoparticle by fluorescence imaging intra-operatively to determine the location of residual glioma cells, wherein an elevated level of binding, relative to normal tissue, is indicative of the presence of residual glioma cells;

22293m (e) surgically removing from the patient at least some residual glioma cells located by fluorescence imaging; and (f) measuring the level of binding of the fluorophore/chlorotoxin-labeled nanoparticle by magnetic resonance imaging post-operatively to determine the location of glioma cells, wherein an elevated level of binding, relative to normal tissue, is indicative of the presence of glioma cells.

In the method, an amount of a fluorophore/chlorotoxin-labeled nanoparticle sufficient to image glioma cells in vivo is an amount from about 1-20 mg Fe/kg body weight (Fe refers to iron present in particle core.

In the above method, steps (d) and (e) may be repeated.

The above method includes pre-operative, intra-operative, and post-operative imaging. It will be appreciated that variations of the above method are within the scope of the invention. Other variations of the method include, for example, (1) pre-operative imaging only; (2) intraoperative imaging only; (3) post-operative imaging only; (4) pre-operative and intra-operative imaging only; (5) pre-operative and post-operative imaging only; and (6) intra-operative and postoperative imaging only.

The invention provides methods for treating a tissue using the nanoparticles.

In one embodiment, the invention provides a method for treating a glioma in a patient, comprising administering to a patient in need thereof an effective amount of a pharmaceutical composition comprising a chlorotoxin-labeled nanoparticle and a pharmaceutically acceptable carrier.

In one embodiment, the invention provides a method for treating a neuroectodermal tumor, comprising administering to a patient in need thereof an effective amount of a pharmaceutical composition comprising a chlorotoxin-labeled nanoparticle and a pharmaceutically acceptable carrier.

In one embodiment, the invention provides a method for inhibiting invasive activity of neoplastic cells, comprising administering to neoplastic cells an effective amount of a pharmaceutical composition comprising a chlorotoxin-labeled nanoparticle and a pharmaceutically acceptable carrier.

22293m

The following describes three representative modified chlorotoxin peptides of the invention and their properties, conjugates of the peptides and their properties, and use of the conjugates in imaging.

Preparation of modified chlorotoxin peptides. Two representative modified chlorotoxin (CTX) peptides of the invention (alanine substituted chlorotoxin, K15A_K23A-CTX; arginine substituted chlorotoxin, K15R_K23R-CTX) sequences are shown in FIGURE 1. The peptides were synthesized using Boe (ieri-butoxycarbonyl)/HBTU [2-(lH-benzotriazol-l-yl)-l, 1,3,3tetramethyluronium hexafluorophosphate] in situ neutralization chemistry. A buffer solution of 0.1 M Tris-HCl, 0.2 M NaCl, 5 mM reduced glutathione / 0.5 mM oxidized glutathione with a pH 7.8 was used both to oxidize the substituted peptides and to cyclize and oxidize CTX at room temperature overnight. RP-HPLC was used to purify the peptides, and the purity and the molecular masses of the two CTX analogues K15A_K23A-CTX and K15R_K23R-CTX were confirmed by analytical RP-HPLC and ES-MS.

NMR assignment. The peptides were dissolved in 90% H2O and 10% D2O, and onedimensional and two-dimensional TOCSY and NOESY spectra were recorded at 600 MHz at 298°K. The NMR spectra were assigned using well established techniques (K. Wuthrich, NMR of Proteins and Nucleic Acids, Wiley-Inter science, New York, 1986). Chemical shifts in the amide region are well dispersed, confirming that the peptides are correctly folded, and the fingerprint region in the NOESY spectrum of each peptide shows a complete cycle of aH-NH sequential connectivities with the exception of the two proline residues (Pro4 and Pro31). However, as expected, NOEs were observed from the δ protons of the proline residues and their preceding residues. A comparison of secondary aH chemical shifts of native CTX and the synthesized analogues are shown in FIGURE 2.

Characterization of substituted CTX bioconjugates. The native and modified peptides were conjugated to Cy5.5 and purified as described below in the Examples. Resulting bioconjugates were analyzed by HPLC and mass spectrometry. As predicted, the Ala and Arg substitutions resulted solely in mono-labeled CTX:Cy5.5 bioconjugates.

Functional assessment of substituted CTX:Cy5.5. The potential benefits of substitution depend on whether the functional targeting activity of the peptides is comparable to native CTX bioconjugates. The capacity of each peptide to target Cy5.5 signal to medulloblastoma cells preferentially, over normal brain was assayed by biophotonic imaging. In each case, 50 pL of 40

22293m μΜ bioconjugate was injected into the tail vein of mice that showed clinical signs consistent with advanced brain tumors. After three days the mice were sacrificed and their brains were imaged using the Caliper/Xenogen Spectrum biophotonic imaging system. All of the modified peptide conjugates preferentially illuminated medulloblastoma cancer tissue compared with normal brain (FIGURES 3A and 3B). In all cases, signal in the tumor was compared with signal in cerebellum of injected control animals that did not have medulloblastoma. The signal in tumor compared with normal was 1.96 +/- 0.47 for native CTX:Cy5.5 (n =10); 3.3 +/- 1.8 for Ala substituted (n = 8) and 2.6 +/- 0.85 for Arg substituted (n = 5). Statistically, all of the modified peptide bioconjugates were indistinguishable from native CTX:Cy5.5 indicating that lysine substitutions did not interfere with CTX binding to its target.

Advantages of the Invention. When advancing a new therapeutic toward human clinical trials, consideration is given not only to efficacy, pharmacokinetics, pharmacodynamics and toxicity, but also practical issues that could compromise regulatory approval or increase manufacturing costs. Tumor Paint, a bioconjugate that safely and effectively illuminated solid tumors in mouse models, posed a manufacturing challenge related to the fact that the bioconjugate was actually a mixture of mono-, di- and tri-labeled CTX. The present invention provides three new representative chemical entities that are functionally equivalent to CTX for targeting NIRF molecules to cancer yet conjugate to only a single NIRF molecule.

CTX conjugation sites in CTX:Cy5.5 were mapped using arginase cleavage coupled with proteomic analyses and showed that typically >80% of product was mono-labeled at Lys 27 and lesser amounts were also conjugated at Lys 15 or Lys 23. In an analysis of CTX conjugated to four other NIRF dyes, similar patterns of predominantly mono-labeled peptide with smaller amounts of di- and tri-labeled peptide were observed, with the exception of Dylight 750, a NIRF dye that creates only mono-labeled species. The fact that Dylight 750 binds in a monomeric fashion to unmodified CTX suggests that access to the other two lysines is limited.

None of the lysine residues in CTX seem to be involved in the active binding of CTX to its target on cancer cells. This conclusion is based on the observations that target binding is preserved despite substitution of Lys 15 or Lys 23 with Ala or Arg and that addition of bulky Cy5.5 or other NIRF dyes to Lys 27 does not preclude binding to the active site.

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Experimental Procedures

Solid Phase Peptide Synthesis. Manual solid-phase peptide synthesis (SPPS) was used to synthesize the peptides with standard protecting groups (e.g. Asn(Xan), Asp(OcHex), Arg(TOS), Cys(MeBzl), Lys(ClZ), Ser(Bzl), Thr(Bzl) and Tyr(BrZ)). The Ala and Arg substituted linear CTX were assembled onto PAM-Arg resin without a thioester linker. Cleavage of the peptides from the resin was achieved by using hydrogen fluoride (HF) with p-cresol and p-lhiocresol as scavengers (9:0.8:0.2 (vol/vol) HF:p-cresol:p-thiocresol) at -5 to 0°C for 1.5 h. Reversed PhaseHigh Performance Liquid Chromatography (RP-HPLC) with a Cis column was used to purify the peptides using a gradient of 0-80% Solution B (Solution A: H20/0.05% trifluoroacetic acid; Solution B: 90% CH3CN/10%H20/0.045% trifluoroacetic acid) by monitoring the absorbance at 215 nm. Electro Spray Mass Spectroscopy (ES-MS) confirmed the purity and molecular mass of the synthesized peptides.

Folding. The Ala and Arg substituted analogues were oxidized in an aqueous buffer solution consisting of 0.1 M Tris-HCl, 0.2 M NaCl, 5 mM reduced glutathione/ 0.5 mM oxidized glutathione with a pH 7.8 at room temperature overnight. RP-HPLC was used to purify the peptides and the purity and the molecular weights were confirmed by analytical RP-HPLC and ES-MS.

NMR Spectroscopy. 600 MHz II NMR spectroscopy was used to monitor the threedimensional structures of the peptide analogues. The peptide samples were dissolved in 90% H2O and 10% D2O (v/v). D2O (99.99%) was obtained from Cambridge Isotope Laboratories, Woburn, MA. Two-dimensional NMR experiments included Total Correlation Spectroscopy (TOCSY) and Nuclear Overhauser Effect Spectroscopy (NOESY) spectra were recorded at 298°K.

Serum Stability Assay. Serum stability assay was carried out in 100% human male serum (Sigma) using a 20 /zM final peptide concentration. The serum was centrifuged at 14000 g for 10 min to remove the lipid component and the supernatant was incubated at 37°C for 15 min prior to the assay. Each peptide was incubated in serum at 37°C and 40 //L triplicate aliquots were taken out at 0, 1, 3, 6, 10, 16 and 24 h. Each serum aliquot was quenched with 40 //L of 6 M urea and incubated for 10 min at 4°C. Then, each serum aliquot was quenched with 40 //L of 20% trichloroacetic acid and incubated for another 10 min at 4°C to precipitate serum proteins. The samples were centrifuged at 14000 g for 10 min, and 100 //L of the supernatant was analyzed on RP-HPLC using a linear gradient of solvent B (0.3 mL/min flow rate). The control samples

22293m contained equivalent amount of peptides in phosphate-buffered saline subjected to the same treatment procedure. The percentage recovery of peptides was detected by integration at 215 nm.

Animal models. All animals were handled in strict accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. All animal studies were conducted in accordance with Fred Hutchinson Cancer Research Center’s Institute of Animal Care and Use Committee approved protocols. An autochthonous mouse model of medulloblastoma, ND2:SmoAl (A.R. Hallahan, et al., The SmoAl Mouse Model Reveals That Notch Signaling is Critical for the Growth and Survival of Sonic Hedgehog-Induced Medulloblastomas, Cancer Research 64:1194-1800, 2004. B.A. Hatton, et al. The Smo/Smo Model: Hedgehog-Induced Medulloblastoma With 90% Incidence and Leptomeningeal Spread, Cancer Research 68:17681776, 2008), on a C57bl/6 background was used to evaluate the specificity of cyclized CTX:Cy5.5, K15A_K23A CTX:Cy5.5, and K15R_K23R CTX:Cy5.5. Hemizygous or homozygous (referred as ND2:SmoAl) mice with symptomatic medulloblastoma were selected for enrollment in these studies. Symptoms were detected using an open field cage evaluation. Symptoms include head tilt, hunched posture, ataxia, protruding skull, and weight loss.

Ex vivo Imaging. ND2:SmoAl animals exhibiting symptoms of medulloblastoma were injected with 50 pL of 40 μΜ K15A K23A CTX:Cy5.5 or K15R K23R CTX:Cy5.5 through the tail vein. Mice were euthanized using CO2 inhalation three days after injection and ex vivo biophotonic images of their brain obtained using the Xenogen Spectrum Imaging System (Caliper). The brains were then frozen in Tissue-Tek Optimal Cutting Temperature (OCT) Compound (Sakura), sliced in 12 pm sections and Hemotoxylin and Eosin (H&E) stained according to standard procedures.

While the preferred embodiment of the invention has been illustrated and described, it will be appreciated that various changes can be made therein without departing from the spirit and scope of the invention.

22293m

ABSTRACT

Chlorotoxin variants, chlorotoxin variant conjugates, compositions that include the chlorotoxin variants or conjugates, and methods for using the chlorotoxin variants, conjugates, and compositions.

222930/3

Claims: