Protein Conjugates

Cross-Reference to Related Applications

This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 62/478,398, filed March 29, 2017, which is incorporated by reference in its entirety.

Statement Regarding Sequence Listing

The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is TDWG_007_01WO_ST25.txt. The text file is about 251 KB, was created on March 28, 2018 and is being submitted electronically via EFS-Web

Background

Technical Field

The present disclosure relates in part to conjugates of an arginine deiminase (ADI) and a Tumor Necrosis Factor (TNF) superfamily ligand, and related compositions and methods of use thereof. The present disclosure also relates to conjugates of a hexameric polypeptide and a trimeric polypeptide, conjugates of a first and second trimeric polypeptide, and related compositions and methods of use thereof.

Description of the Related Art

Arginine depletion therapy can be an effective treatment of certain forms of cancer, among other diseases. For instance, arginine deiminase can be used to deplete the bloodstream supply of arginine by converting it to citrulline and ammonia. ADI-PEG 20 is an exemplary ADI-PEG that is being investigated in the clinic for tumors deficient in the key enzyme argininosuccinate synthetase- 1 (ASS1), which is involved in the conversion of citrulline to arginine. ADI-PEG 20 has been well- tolerated and showed promise in clinical studies (see, e.g., Qiu et al., Cancer Lett. 2015 Aug l;364(l): l-7; Phillips et al., Cancer Res Treat. 2013 Dec;45(4):251-62; Feun et al., Curr Pharm Des. 2008;14(l l): 1049-57; Feun and Savaraj, Expert Opin Investig Drugs. 2006 Jul;15(7):815-22; Feun et al., Curr Opin Clin Nutr Metab Care. 2015 Jan;18(l):78-82).

Activation of cell surface death receptors of the tumor necrosis factor (TNF) receptor superfamily by the appropriate ligands represents an attractive therapeutic strategy to induce cell death by apoptosis in cancer cells (see, e.g., Palacios et al., Curr Pharm Des. 2014;20(17):2819-33). As one example, TNF-related apoptosis-inducing ligand (TRAIL, also known as Apo2L) possesses the ability to induce apoptosis selectively in cancer cells, and has demonstrated robust anticancer activity in a number of preclinical studies. However, there remains a need to optimize the pharmacokinetics and/or biological activities of these and other agents. The present disclosure provides these benefits and others.

Brief Summary

Embodiments of the present disclosure include conjugates, comprising an arginine deiminase (ADI) that is covalently linked to a Tumor Necrosis Factor (TNF) superfamily ligand.

In some embodiments, the ADI comprises, consists, or consists essentially of an amino acid sequence that is at least 90%, 95%, 96%, 97%, 98%, or 99% identical to a sequence selected from Table A1. In some embodiments, the ADI is a hexameric ADI polypeptide, for example, a homohexameric polypeptide. In some embodiments, the hexameric or homohexameric ADI comprises, consists, or consists essentially of an amino acid sequence that is at least 90%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 9, 37, 38, 50, or 57-68.

In some embodiments, the TNF superfamily ligand is selected from Table T1. In some embodiments, the superfamily ligand is selected from TNF-related apoptosis-inducing ligand (TRAIL), TNF-a, and FasL. In some embodiments, the TNF superfamily ligand comprises, consists, or consists essentially of an amino acid sequence that is at least 90%, 95%, 96%, 97%, 98%, or 99% identical to a sequence selected from Table T2. In some embodiments, the TNF superfamily ligand is a trimeric or homotrimeric polypeptide.

In some embodiments, the ADI and the TNF superfamily ligand are separated by a linker, optionally a physiologically-stable linker. In some embodiments, the linker is a peptide linker, optionally a flexible peptide linker or a rigid peptide linker. In some embodiments, the peptide linker is about 1-100 amino acids, about 1-90 amino acids, about 1-80 amino acids, about 1-70 amino acids, about 1-80 amino acids, about 1-50 amino acids, about 1-40 amino acids, about 1-30 amino acids, about 1-20 amino acids, about 1-10 amino acids, or about 1-5 amino acids in length, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, or 100 amino acids in length. In some embodiments, the peptide linker is selected from Table L1.

In some embodiments, the conjugate is a fusion polypeptide. In some embodiments, the ADI is fused to the N-terminus of the TNF superfamily ligand, optionally separated by a linker. In some embodiments, the ADI is fused to the C-terminus of the TNF superfamily ligand, optionally separated by a linker

In some embodiments, the linker is a non-peptide linker.

In some embodiments, the conjugate has improved pharmacokinetic, physical, and/or biological properties relative to the ADI alone and/or the TNF superfamily ligand alone, optionally selected from one or more of increased stability, increased serum half-life, increased bioavailability, increased biological activity, increased exposure, and decreased clearance. In some embodiments, the conjugate has increased stability and/or serum half-life relative to the ADI alone and/or the TNF superfamily ligand alone, optionally wherein the stability and/or serum half-life relative of the conjugate is increased by about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to the ADI alone and/or the TNF superfamily ligand alone.

In some embodiments, the conjugate has increased biological activity relative to the ADI alone and/or the TNF superfamily ligand alone, optionally wherein the biological activity of the conjugate is increased by about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to the ADI alone and/or the TNF superfamily ligand alone, or optionally wherein the biological activity is increased synergistically relative to the ADI alone and/or the TNF superfamily ligand alone. In some embodiments, the biological activity is induction of cell death or apoptosis in cancer cells, which is optionally increased synergistically relative to the ADI alone and/or the TNF superfamily ligand alone.

In some embodiments, the cancer cells are ADI-sensitive cells, which are optionally selected from one or more of breast cancer cells, hepatocellular carcinoma cells, Burkitt's Lymphoma cells, colon cancer cells, glioblastoma cancer cells, leukemic cells, melanoma cancer cells, non-small lung cell cancer (NSCLC) cells, ovarian cancer cells, pancreatic cancer cells, prostate cancer cells, and renal cancer cells.

In some embodiments, the cancer cells are ADI-non-sensitive cells, which are optionally selected from one or more of breast cancer cells, colon cancer cells, and NSCLC cells.

In some embodiments, the ADI increases the ability of the TNF superfamily ligand to induce cell death or apoptosis in cancer cells, optionally by about at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% relative to the TNF superfamily ligand alone.

In some embodiments, the ADI upregulates expression of Death Receptor 5 (DR5) on the cancer cells.

In some embodiments, the ADI polypeptide is covalently bonded via a linking group to at least one polyethylene glycol (PEG) molecule, optionally wherein the TNF superfamily ligand is not covalently bonded to a PEG molecule.

Also included are conjugates, comprising (a) a hexameric polypeptide that is covalently linked to a trimeric polypeptide, or (b) a first trimeric polypeptide that is covalently linked to a second trimeric polypeptide which differs from the first trimeric polypeptide.

In some embodiments, the hexameric polypeptide is a homohexameric polypeptide. In some embodiments, the hexameric polypeptide is selected from an arginine deiminase, optionally as described herein, and adiponectin or a collagen-like domain thereof.

In some embodiments, the trimeric polypeptide is a homotrimeric polypeptide. In some embodiments, the first trimeric polypeptide of (b) is selected from adiponectin or a collagen-like domain thereof, T4 fibritin or a trimerization domain thereof (foldon), C-propeptide of collagen, surfactant protein A (SP-A), and mannose-binding protein A (MBP-A).

In some embodiments, the trimeric polypeptide of (a) or the second trimeric polypeptide of (b) is selected from a Tumor Necrosis Factor (TNF) superfamily ligand, optionally as described herein. In some embodiments, for (a) the hexameric polypeptide of is covalently linked to the N- terminus of the trimeric polypeptide, or for (b) the first trimeric polypeptide is covalently linked to the N-terminus of the second trimeric polypeptide. In some embodiments, for (a) the hexameric polypeptide is covalently linked to the C-terminus of the trimeric polypeptide, or wherein for (b) the first trimeric polypeptide is covalently linked to the C-terminus of the second trimeric polypeptide. In some embodiments, for (a) the hexameric polypeptide and the trimeric polypeptide are separated by a linker, or for (b) the first and second trimeric polypeptide are separated by a linker, wherein the linker is optionally a physiologically-stable linker.

In some embodiments, the conjugate is a fusion polypeptide.

In some embodiments, the conjugate has increased physical, pharmacokinetic, and/or biological properties relative to the hexameric and/or trimeric polypeptide alone. In some embodiments, for (a) conjugation to the hexameric polypeptide increases the stability and/or serum half-life of the trimeric polypeptide, optionally by about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to the trimeric polypeptide alone, or for (b) conjugation to the first trimeric polypeptide increases the stability and/or serum half-life of the second trimeric polypeptide, optionally by about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to the second trimeric polypeptide alone.

Certain embodiments relate to isolated polynucleotides which encode a conjugate described herein, wherein the conjugate is a fusion protein. Also included are expression vectors that comprises the isolated polynucleotide, and host cells that comprise the isolated polynucleotide or the expression vector.

Also included are therapeutic compositions, comprising a conjugate described herein and a pharmaceutically -acceptable carrier or excipient. In particular embodiments, the conjugate forms a hexameric complex of six ADI-TRAIL and/or TRAIL-ADI conjugates, optionally as fusion proteins (see, for example, Figure 4). In some embodiments, the conjugate or composition is at least about 95% pure and less than about 5% aggregated, and is substantially endotoxin-free.

Also included are methods of treating, ameliorating the symptoms of, or reducing the progression of a cancer in a subject in need thereof, comprising administering to the subject a conjugate or therapeutic composition as described herein.

In some embodiments, the cancer is selected from one or more of hepatocellular carcinoma (HCC), melanoma, metastatic melanoma, pancreatic cancer, prostate cancer, small cell lung cancer, mesothelioma, lymphocytic leukemia, chronic myelogenous leukemia, lymphoma, hepatoma, sarcoma, leukemia, acute myeloid leukemia, relapsed acute myeloid leukemia, B-cell malignancy, breast cancer, ovarian cancer, colorectal cancer, gastric cancer, glioma (e.g., astrocytoma, oligodendroglioma, ependymoma, or a choroid plexus papilloma), glioblastoma multiforme (e.g., giant cell gliobastoma or a gliosarcoma), meningioma, pituitary adenoma, vestibular schwannoma, primary CNS lymphoma, primitive neuroectodermal tumor (medulloblastoma), non-small cell lung cancer (NSCLC), kidney cancer, bladder cancer, uterine cancer, esophageal cancer, brain cancer, head and neck cancers, cervical cancer, testicular cancer, and stomach cancer.

Brief Description of the Drawings

Figures 1A-1D illustrate the synergistic effects ADI-PEG 20 and rhTRAIL on the relative viability of various cancer cell lines, compared to each agent alone.

Figures 2A-2C demonstrate the synergistic effects ADI-PEG 20 and rhTRAIL on caspase 3/7 activation (Fig. 2A), induction of cell death (Fig. 2B), and reduction in the percentage of viable cells that are not committed to apoptosis (cells in which caspase 3/7 is not activated; Fig. 2C), compared to each agent alone in Raji Burkitt's lymphoma cell line.

Figures 3A-3D show up-regulated expression of TRAIL receptor DR5 in various cancer cell lines following treatment with ADI-PEG 20.

Figure 4 demonstrates reduction in survivin protein levels after treatment with ADI-PEG 20 of ADI-sensitive cell lines. Survivin has been shown to impede activity of TRAIL. Thus, lowering survivin levels (along with DR5 upregulation) may contribute to the ability of ADI to potentiate and/or increase apoptotic activity of TRAIL in cancer cell lines.

Figure 5 illustrates a hexameric complex composed of six ADI-TRAIL and/or TRAIL-ADI conjugates, for example, fusion proteins.

Figures 6A-6C show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptide with LI linker (see Table E3) on caspase 3/7 induction (Fig. 6A) and relative cell viability (Figs. 6B and 6C) in the ADI-resistant Colo 205 cancer cell line, relative to rhTRAIL alone, M. col. ADI alone and the combination of rhTRAIL and M.col.ADI as separate polypeptides.

Figures 7A-7C show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptide with LI linker (see Table E3) on caspase 3/7 induction (Fig. 7A) and relative cell viability (Figs. 7B and 7C) in the ADI-sensitive HCT116 tumor cell line, relative to rhTRAIL alone, M.col.ADI alone, and the combination of rhTRAIL and M.col.ADI as separate polypeptides.

Figures 8A-8B show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptide with LI linker (see Table E3) on caspase 3/7 induction (Fig. 8A) and relative cell viability (Fig. 8B) in the ADI-sensitive Jurkat tumor cell line, relative to rhTRAIL alone, M.col.ADI alone and the combination of rhTRAIL and M.col.ADI as separate polypeptides. Figures 9A-9D show the effects of the exemplary ADI-TRAIL fusion polypeptides from Table El on caspase 3/7 induction (Figs. 9A and 9B) and relative cell viability (Figs. 9C and 9D) in the ADI-resistant Colo 205 cancer cell line.

Figures lOA-lOC show the effects of exemplary ADI-TRAIL fusion polypeptides on caspase 3/7 induction (Fig. 10A) and relative cell viability (Figs. lOB-lOC) in the ADI-sensitive HCTl 16 cell line.

Figures 11A-11B show the effects of exemplary ADI-TRAIL fusion polypeptides on caspase 3/7 induction (Fig. 11A) and relative cell viability (Fig. 11B) in the ADI-sensitive Jurkat cell line.

Figures 12A-12C show the effects of exemplary M.col.ADI-TRAIL fusion polypeptides with point mutation in M.col.ADI (K192C or K287C), including non-PEGylated versus PEGylated with 2K or 20K PEG, on caspase 3/7 induction (Fig. 12A) and relative cell viability (Figs. 12B-12C) in the ADI-resistant Colo 205 cell line.

Figures 13A-13C show the effects of exemplary M.col.ADI-TRAIL fusion polypeptides with point mutation in M.col.ADI (K192C or K287C), including non-PEGylated versus PEGylated with 2K or 20K PEG, on caspase 3/7 induction (Fig. 13A) and relative cell viability (Figs. 13B-13C) in the ADI-sensitive HCTl 16 cell line.

Figures 14A-14C show the effects of exemplary TRAIL-M.col.ADI versus M.col.ADI - TRAIL fusion polypeptides on caspase 3/7 induction (Fig. 14A) and relative cell viability (Figs. 14B- 14C) in the ADI-resistant Colo 205 cell line.

Figures 15A-15C show the effects of exemplary TRAIL-M.col.ADI versus M.col.ADI - TRAIL fusion polypeptides on caspase 3/7 induction (Fig. 15A) and relative cell viability (Figs. 15B- 15C) in the ADI-sensitive HCTl 16 cell line.

Figures 16A-16B display pharmacokinetics (PK) of M.col.ADI-TRAIL over time in serum of CD-I mice after a single dose of 30 mg/kg administered intravenously. M.col.ADI-TRAIL protein level (Figs. 16A-16B), arginine and citrulline levels (Fig. 16A) as well as antibody titers against the fusion protein M.col.ADI-TRAIL, M.col.ADI and rhTRAIL (assessed by ELISA, Fig. 16B) were measured in serum of CD-I mice animals after a single injection of the fusion protein.

Figures 17A-17F demonstrate efficacy of the M.col.ADI-TRAIL in HCTl 16 xenograft model. The fusion protein did not cause any noticeable weight loss (Fig. 17A) and reduced tumor growth (Figs. 17B-17F). * p<0.05, ** pO.01, *** pO.001. The statistical significance of the tumor reduction in the fusion protein treated group as compared to the vehicle treated control group was assessed by the 2-way ANOVA.

Figures 18A-18D show that serum ADI-TRAIL inversely correlates with tumor volume (Figs. 18B-18C). Concentrations of fusion protein measured by ELISA (total protein) and in a biological assay (active protein) by were similar to one another. Serum was taken from tumor bearing mice on days 21 and 28 post tumor implantation. Treatment schedule and tumor growth are shown in Figs. 17A-17F. Arginine and citrulline levels in these serums samples are shown in Fig. 18D. Figure 19 demonstrates dose-dependent tumor growth reduction in HCT116 xenograft model after treatment with M.col. ADI-TRAIL.

Detailed Description

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art to which the disclosure belongs. Although any methods, materials, compositions, reagents, cells, similar or equivalent similar or equivalent to those described herein can be used in the practice or testing of the subject matter of the present disclosure, preferred methods and materials are described. All publications and references, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference in their entirety as if each individual publication or reference were specifically and individually indicated to be incorporated by reference herein as being fully set forth. Any patent application to which this application claims priority is also incorporated by reference herein in its entirety in the manner described above for publications and references.

The practice of the present disclosure will employ, unless indicated specifically to the contrary, conventional methods of virology, immunology, microbiology, molecular biology and recombinant DNA techniques within the skill of the art, many of which are described below for the purpose of illustration. Such techniques are explained fully in the literature. See, e.g., Current Protocols in Protein Science, Current Protocols in Molecular Biology or Current Protocols in Immunology, John Wiley & Sons, New York, N.Y. (2009); Ausubel et al, Short Protocols in Molecular Biology, 3 ^rd ed., Wiley & Sons, 1995; Sambrook and Russell, Molecular Cloning: A Laboratory Manual (3rd Edition, 2001); Maniatis et al. Molecular Cloning: A Laboratory Manual (1982); DNA Cloning: A Practical Approach, vol. I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., 1984); Nucleic Acid Hybridization (B. Hames & S. Higgins, eds., 1985); Transcription and Translation (B. Hames & S. Higgins, eds., 1984); Animal Cell Culture (R. Freshney, ed., 1986); Perbal, A Practical Guide to Molecular Cloning (1984) and other like references.

Standard techniques may be used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation {e.g., electroporation, lipofection). Enzymatic reactions and purification techniques may be performed according to manufacturer's specifications or as commonly

accomplished in the art or as described herein. These and related techniques and procedures may be generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. Unless specific definitions are provided, the nomenclature utilized in connection with, and the laboratory procedures and techniques of, molecular biology, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well- known and commonly used in the art. Standard techniques may be used for recombinant technology, molecular biological, microbiological, chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients.

For the purposes of the present disclosure, the following terms are defined below.

The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element.

By "about" is meant a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length that varies by as much as 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length.

An "antagonist" refers to biological structure or chemical agent that interferes with or otherwise reduces the physiological action of another agent or molecule. In some instances, the antagonist specifically binds to the other agent or molecule. Included are full and partial antagonists.

An "agonist" refers to biological structure or chemical agent that increases or enhances the physiological action of another agent or molecule. In some instances, the agonist specifically binds to the other agent or molecule. Included are full and partial agonists.

As used herein, the term "amino acid" is intended to mean both naturally occurring and non- naturally occurring amino acids as well as amino acid analogs and mimetics. Naturally occurring amino acids include the 20 (L)-amino acids utilized during protein biosynthesis as well as others such as 4-hydroxyproline, hydroxylysine, desmosine, isodesmosine, homocysteine, citrulline and ornithine, for example. Non-naturally occurring amino acids include, for example, (D)-amino acids, norleucine, norvaline, p-fluorophenylalanine, ethionine and the like, which are known to a person skilled in the art. Amino acid analogs include modified forms of naturally and non-naturally occurring amino acids. Such modifications can include, for example, substitution or replacement of chemical groups and moieties on the amino acid or by derivatization of the amino acid. Amino acid mimetics include, for example, organic structures which exhibit functionally similar properties such as charge and charge spacing characteristic of the reference amino acid. For example, an organic structure which mimics Arginine (Arg or R) would have a positive charge moiety located in similar molecular space and having the same degree of mobility as the e-amino group of the side chain of the naturally occurring Arg amino acid. Mimetics also include constrained structures so as to maintain optimal spacing and charge interactions of the amino acid or of the amino acid functional groups. Those skilled in the art know or can determine what structures constitute functionally equivalent amino acid analogs and amino acid mimetics.

"Biocompatible" refers to materials or compounds which are generally not injurious to biological functions and which will not result in any degree of unacceptable toxicity, including allergenic and disease states. By "coding sequence" is meant any nucleic acid sequence that contributes to the code for the polypeptide product of a gene. By contrast, the term "non-coding sequence" refers to any nucleic acid sequence that does not directly contribute to the code for the polypeptide product of a gene.

Throughout this disclosure, unless the context requires otherwise, the words "comprise," "comprises," and "comprising" will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.

By "consisting of is meant including, and limited to, whatever follows the phrase "consisting of." Thus, the phrase "consisting of indicates that the listed elements are required or mandatory, and that no other elements may be present. By "consisting essentially of is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase "consisting essentially of indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they materially affect the activity or action of the listed elements.

The term "conjugate" refers to an entity formed as a result of covalent or non-covalent attachment or linkage of at least two separate polypeptides (for example, a first polypeptide and a second polypeptide), as described herein. One example of a conjugate polypeptide is a "fusion protein" or "fusion polypeptide," that is, a polypeptide that is created through the joining of two or more coding sequences, which originally coded for separate polypeptides; translation of the joined coding sequences results in a single, fusion polypeptide, typically with functional properties derived from each of the separate polypeptides.

The term "endotoxin free" or "substantially endotoxin free" relates generally to compositions, solvents, and/or vessels that contain at most trace amounts (e.g., amounts having no clinically adverse physiological effects to a subject) of endotoxin, and preferably undetectable amounts of endotoxin. Endotoxins are toxins associated with certain micro-organisms, such as bacteria, typically gram- negative bacteria, although endotoxins may be found in gram-positive bacteria, such as Listeria monocytogenes. The most prevalent endotoxins are lipopolysaccharides (LPS) or lipo-oligo- saccharides (LOS) found in the outer membrane of various Gram-negative bacteria, and which represent a central pathogenic feature in the ability of these bacteria to cause disease. Small amounts of endotoxin in humans may produce fever, a lowering of the blood pressure, and activation of inflammation and coagulation, among other adverse physiological effects.

Therefore, in pharmaceutical production, it is often desirable to remove most or all traces of endotoxin from drug products and/or drug containers, because even small amounts may cause adverse effects in humans. A depyrogenation oven may be used for this purpose, as temperatures in excess of 300°C are typically required to break down most endotoxins. For instance, based on primary packaging material such as syringes or vials, the combination of a glass temperature of 250°C and a holding time of 30 minutes is often sufficient to achieve a 3 log reduction in endotoxin levels. Other methods of removing endotoxins are contemplated, including, for example, chromatography and filtration methods, as described herein and known in the art.

Endotoxins can be detected using routine techniques known in the art. For example, the Limulus Amoebocyte Lysate assay, which utilizes blood from the horseshoe crab, is a very sensitive assay for detecting presence of endotoxin. In this test, very low levels of LPS can cause detectable coagulation of the limulus lysate due a powerful enzymatic cascade that amplifies this reaction. Endotoxins can also be quantitated by enzyme-linked immunosorbent assay (ELISA). To be substantially endotoxin free, endotoxin levels may be less than about 0.001, 0.005, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.08, 0.09, 0.1, 0.5, 1.0, 1.5, 2, 2.5, 3, 4, 5, 6, 7, 8, 9, or 10 EU/mg of active compound. Typically, 1 ng lipopoly saccharide (LPS) corresponds to about 1-10 EU.

The "half-life" of a conjugate or polypeptide can refer to the time it takes for the conjugate or polypeptide to lose half of its pharmacologic, physiologic, or other activity, relative to such activity at the time of administration into the serum or tissue of an organism, or relative to any other defined time-point. "Half -life" can also refer to the time it takes for the amount or concentration of a conjugate or polypeptide to be reduced by half of a starting amount administered into the serum or tissue of an organism, relative to such amount or concentration at the time of administration into the serum or tissue of an organism, or relative to any other defined time-point. The half-life can be measured in serum and/or any one or more selected tissues.

The terms "modulating" and "altering" include "increasing," "enhancing" or "stimulating," as well as "decreasing" or "reducing," typically in a statistically significant or a physiologically significant amount or degree relative to a control. An "increased," "stimulated" or "enhanced" amount is typically a "statistically significant" amount, and may include an increase that is 1.1, 1.2, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 or more times (e.g., 500, 1000 times) (including all integers and ranges in between e.g., 1.5, 1.6, 1.7. 1.8, etc.) the amount produced by no composition (e.g., the absence of agent) or a control composition. A "decreased" or "reduced" amount is typically a "statistically significant" amount, and may include a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18% , 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% decrease (including all integers and ranges in between) in the amount produced by no composition (e.g., the absence of an agent) or a control composition. Examples of comparisons and "statistically significant" amounts are described herein.

The terms "polypeptide," "protein" and "peptide" are used interchangeably and mean a polymer of amino acids not limited to any particular length. The term "enzyme" includes polypeptide or protein catalysts, and with respect to ADI is used interchangeably with protein, polypeptide, or peptide. The terms include modifications such as myristoylation, sulfation, glycosylation, phosphorylation and addition or deletion of signal sequences. The terms "polypeptide" or "protein" means one or more chains of amino acids, wherein each chain comprises amino acids covalently linked by peptide bonds, and wherein said polypeptide or protein can comprise a plurality of chains non-covalently and/or covalently linked together by peptide bonds, having the sequence of native proteins, that is, proteins produced by naturally -occurring and specifically non-recombinant cells, or genetically -engineered or recombinant cells, and comprise molecules having the amino acid sequence of the native protein, or molecules having deletions from, additions to, and/or substitutions of one or more amino acids of the native sequence. The terms "polypeptide" and "protein" specifically encompass the ADI enzymes/proteins described herein, or sequences that have deletions from, additions to, and/or substitutions of one or more amino acid of the ADI proteins. In certain embodiments, the polypeptide is a "recombinant" polypeptide, produced by recombinant cell that comprises one or more recombinant DNA molecules, which are typically made of heterologous polynucleotide sequences or combinations of polynucleotide sequences that would not otherwise be found in the cell.

The term "isolated" polypeptide or protein referred to herein means that a subject protein (1) is free of at least some other proteins with which it would typically be found in nature, (2) is essentially free of other proteins from the same source, e.g., from the same species, (3) is expressed by a cell from a different species, (4) has been separated from at least about 50 percent of polynucleotides, lipids, carbohydrates, or other materials with which it is associated in nature, (5) is not associated (by covalent or non-covalent interaction) with portions of a protein with which the "isolated protein" is associated in nature, (6) is operably associated (by covalent or non-covalent interaction) with a polypeptide with which it is not associated in nature, or (7) does not occur in nature. Such an isolated protein can be encoded by genomic DNA, cDNA, mRNA or other RNA, or may be of synthetic origin, or any combination thereof. In certain embodiments, the isolated protein is substantially free from proteins or polypeptides or other contaminants that are found in its natural environment that would interfere with its use (therapeutic, diagnostic, prophylactic, research or otherwise).

In certain embodiments, the "purity" of any given agent (for example, a conjugate) in a composition may be specifically defined. For instance, certain compositions may comprise a conjugate that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% pure, including all decimals and ranges in between, as measured, for example and by no means limiting, by high performance liquid chromatography (HPLC), a well-known form of column chromatography used frequently in biochemistry and analytical chemistry to separate, identify, and quantify compounds. In some instances, the purity of a composition is characterized by the degree of aggregation. For instance, the degree of aggregation of a conjugate (for example, fusion protein) can be determined by Size-exclusion chromatography (SEC), which separates particles on the basis of size. It is a generally accepted method for determining the tertiary structure and quaternary structure of purified proteins. SEC is used primarily for the analysis of large molecules such as proteins or polymers. SEC works by trapping these smaller molecules in the pores of a particle. The larger molecules simply pass by the pores as they are too large to enter the pores. Larger molecules therefore flow through the column quicker than smaller molecules, that is, the smaller the molecule, the longer the retention time. Certain compositions are also substantially free of aggregates (greater than about 95% appearing as a single peak by SEC HPLC). Certain embodiments are free of aggregates with greater than about 96%, about 97%, about 98%, or about 99%, appearing as a single peak by SEC HPLC.

The term "reference sequence" refers generally to a nucleic acid coding sequence, or amino acid sequence, to which another sequence is being compared. All polypeptide and polynucleotide sequences described herein are included as references sequences, including those described by name and those described in the Tables and the Sequence Listing.

The terms "sequence identity" or, for example, comprising a "sequence 50% identical to," as used herein, refer to the extent that sequences are identical on a nucleotide-by -nucleotide basis or an amino acid-by -amino acid basis over a window of comparison. Thus, a "percentage of sequence identity" may be calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, He, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FAST A, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, Wis., USA) or by inspection and the best alignment (i.e., resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected. Reference also may be made to the BLAST family of programs as for example disclosed by Altschul et al., Nucl. Acids Res. 25:3389, 1997.

The term "solubility" refers to the property of an agent (for example, a conjugate) described herein to dissolve in a liquid solvent and form a homogeneous solution. Solubility is typically expressed as a concentration, either by mass of solute per unit volume of solvent (g of solute per kg of solvent, g per dL (100 mL), mg/mL, etc.), molarity, molality, mole fraction or other similar descriptions of concentration. The maximum equilibrium amount of solute that can dissolve per amount of solvent is the solubility of that solute in that solvent under the specified conditions, including temperature, pressure, pH, and the nature of the solvent. In certain embodiments, solubility is measured at physiological pH, or other pH, for example, at pH 5.0, pH 6.0, pH 7.0, pH 7.4, pH 7.6, pH 7.8, or pH 8.0 (e.g., about pH 5-8). In certain embodiments, solubility is measured in water or a physiological buffer such as PBS or NaCl (with or without NaP). In specific embodiments, solubility is measured at relatively lower pH (e.g., pH 6.0) and relatively higher salt (e.g., 500mM NaCl and lOmM NaP). In certain embodiments, solubility is measured in a biological fluid (solvent) such as blood or serum. In certain embodiments, the temperature can be about room temperature (e.g., about 20, 21, 22, 23, 24, 25°C) or about body temperature (37°C). In certain embodiments, an agent has a solubility of at least about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 60, 70, 80, 90 or 100 mg/mL at room temperature or at 37°C.

A "subject" or a "subject in need thereof or a "patient" or a "patient in need thereof includes a mammalian subject such as a human subject.

"Substantially" or "essentially" means nearly totally or completely, for instance, 95%, 96%, 97%, 98%, 99% or greater of some given quantity.

By "statistically significant," it is meant that the result was unlikely to have occurred by chance. Statistical significance can be determined by any method known in the art. Commonly used measures of significance include the p- value, which is the frequency or probability with which the observed event would occur, if the null hypothesis were true. If the obtained p- value is smaller than the significance level, then the null hypothesis is rejected. In simple cases, the significance level is defined at a p-value of 0.05 or less.

"Therapeutic response" refers to improvement of symptoms (whether or not sustained) based on administration of one or more therapeutic agents, for example, conjugates.

As used herein, "treatment" of a subject (e.g. a mammal, such as a human) or a cell is any type of intervention used in an attempt to alter the natural course of the individual or cell. Treatment includes, but is not limited to, administration of a pharmaceutical composition, and may be performed either prophylactically or subsequent to the initiation of a pathologic event or contact with an etiologic agent. Also included are "prophylactic" treatments, which can be directed to reducing the rate of progression of the disease or condition being treated, delaying the onset of that disease or condition, or reducing the severity of its onset. "Treatment" or "prophylaxis" does not necessarily indicate complete eradication, cure, or prevention of the disease or condition, or associated symptoms thereof.

The term "wild-type" refers to a gene or gene product (e.g., a polypeptide) that is most frequently observed in a population and is thus arbitrarily designed the "normal" or "wild-type" form of the gene.

Each embodiment in this specification is to be applied mutatis mutandis to every other embodiment unless expressly stated otherwise.

Conjugates

Embodiments of the present disclosure relate in part to the unexpected discovery that conjugation (for example, fusion) of an arginine deiminase (ADI) to a Tumor Necrosis Factor (TNF) superfamily ligand, for example, TRAIL, improves the pharmacokinetics and/or biological activity of the conjugate relative to one or both of the components alone, and in many instances does so synergistically. Also related is the discovery that conjugation of a hexameric or homohexameric polypeptide to a trimeric or homotrimeric polypeptide improves the pharmacokinetics and/or biological activity of the conjugate relative to one or both of the components alone. Also related is the discovery that conjugation of a first trimeric polypeptide to a second trimeric polypeptide (which differs from the first) improves the pharmacokinetics and/or biological activity of the conjugate relative to one or both of the components alone. In some instances, each component of the conjugate potentiates (for example, synergistically potentiates) the pharmacokinetics and/or biological activity of the other component.

Thus, certain embodiments relate to conjugates, comprising an arginine deiminase ADI that is covalently linked to a TNF superfamily ligand (for example, TRAIL), each of which is described in greater detail herein. In some embodiments, the ADI is conjugated to the N-terminus of the TNF superfamily ligand. In some embodiments, the ADI is conjugated to the C-terminus of the TNF superfamily ligand.

Also included are conjugates, comprising (a) a hexameric polypeptide that is covalently linked to a trimeric polypeptide, or (b) a first trimeric polypeptide that is covalently linked to a second trimeric polypeptide which differs from the first trimeric polypeptide. In some instances, the hexameric polypeptide is a homohexameric polypeptide. Examples of the hexameric or

homohexameric polypeptide of (a) include, for example, certain ADIs such as the native ADIs from Mycoplasma columbinum, M. iners, M. gallinarum, and meleagridis (e.g., SEQ ID NOs: 9, 37, 38, 50, respectively), the chimeric ADIs from Table Al (e.g., SEQ ID NOs: 57-68), and adiponectin or collagen-like domain thereof, which are described in greater detail herein. Adiponectin is a 244-amino acid protein composed of an amino-terminal signal peptide, a collagen-like domain at the N-terminus, and a globular domain at the C-terminus. Adiponectin self-associates into larger structures, for example, adiponectin molecules bind together via the collagen-like domain to form homotrimers, and in some instances the trimers continue to self-associate and form hexamers.

In some instances, the trimeric polypeptide is a homotrimeric polypeptide. Examples of the first trimeric or homotrimeric polypeptide of (b) include adiponectin or a collagen-like domain thereof, T4 fibritin or a trimerization domain thereof (foldon), C-propeptide of procollagen, surfactant protein A (SP-A), and mannose-binding protein A (MBP-A). As noted above, in some instances adiponectin or the collagen-liked domain thereof self-associates into trimers. Bacteriophage T4 fibritin is a triple-stranded, parallel, segmented alpha-helical coiled-coil protein. The C-terminal globular domain (foldon) of T4 fibritin is essential for correct trimerization and folding of the protein, however foldon is capable of trimerization in the absence of the coiled-coil part of fibritin (see Letarov et al., Biochemistry (Mosc). 64(7) :817-23, 1999). The C-propeptides of fibrillar procollagens play crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils, and are responsible for the selective formation of homotrimers and certain heterotrimers between various procollagens (see, e.g., Bourhis et al., Nat Struct Mol Biol. 19(10): 1031-1036, 2012). Surfactant protein A (SP-A), one of four proteins associated with pulmonary surfactant, binds with high affinity to alveolar phospholipid membranes, positioning the protein at the first line of defense against inhaled pathogens. SP-A exhibits both calcium -dependent carbohydrate binding, a characteristic of the collectin family, and specific interactions with lipid membrane components. The carbohydrate recognition domain (CRD) of SP-A forms trimeric structure with the neck domain (see, e.g., J. Biol Chem. 278(44):43254-60, 2003). Mannose-binding proteins (MBPs) are C-type (Ca(2+)-dependent) animal lectins found in serum. They recognize cell-surface oligosaccharide structures characteristic of pathogenic bacteria and fungi, and trigger the neutralization of these organisms. The carbohydrate-recognition domain (CRD) of MBP and the neck domain that links the carboxy -terminal CRD to the collagen-like portion of the intact molecule form trimeric structures (see, e.g., Weis and Drickamer, Structure. 2(12): 1227- 40, 1994). Thus, any of the foregoing trimeric polypeptides or trimeric fragments/domains thereof can be employed as the first trimeric polypeptide of (b).

In some embodiments, the trimeric or homotrimeric polypeptide of (a), or the second trimeric or homotrimeric polypeptide of (b), is a TNF superfamily ligand or receptor, which are described in greater detail herein.

In some embodiments, for (a) the hexameric polypeptide is covalently linked to the N- terminus of the trimeric polypeptide, or for (b) the first trimeric polypeptide is covalently linked to the N-terminus of the second trimeric polypeptide. In some embodiments, for (a) the hexameric polypeptide is covalently linked to the C-terminus of the trimeric polypeptide, or for (b) the first trimeric polypeptide is covalently linked to the C-terminus of the second trimeric polypeptide.

In some instances, the conjugate is a fusion protein, for example, where the covalent linkage between the two components of the conjugate is composed entirely of peptide bonds. In some instances, the conjugate is a non-fusion protein, for example, where the covalent linkage between the components of the conjugate comprises at least one non-peptide bond, or where the covalent linkage is chemically -reacted after each polypeptide of the conjugate has been separately produced (e.g., recombinantly produced) and optionally purified.

In some embodiments, the conjugate comprises a linker between each component of the conjugate, for example, a physiologically-stable linker. General examples of linkers include peptide linkers (for example, flexible and rigid peptide linkers) and non-peptide linkers. Exemplary linkers are described in greater detail herein.

In some instances, as noted above, at least one component of the conjugate improves one or more properties of the other component of the conjugate, and in some instances, the conjugate does so synergistically. In some instances, each component improves one or more properties of the other component of the conjugate. In some instances, the conjugate has one or more improved properties relative to one or both of the components alone. Exemplary properties include physical and/or pharmacokinetic properties such as protein stability, solubility, serum half-life, bioavailability, exposure, and clearance. Also included are biological properties or activities. In some instances, the conjugate has increased biological activity relative to one or both components alone. In some instances, the conjugate has an "additive" effect on a biological activity relative to each component alone. "Additivity" refers to increased conjugate activity that is about equal to the combined, additive activity of each component alone. In some instances, the conjugate has a "synergistic" effect on a biological activity relative to each component alone. "Synergy" or "synergism" refers to increased conjugate activity that is greater than the combined, additive activity of each component alone. In some instances, one component of the conjugate "potentiates" the biological activity of the other component (for example, in some instances, ADI potentiates the activity of TRAIL). "Potentiation" refers to increased conjugate activity in instances where only one component is active or significantly active alone. In some instances, there is "coalism" between the components of the conjugate, which refers to conjugate activity in instances where neither component is active by itself.

In specific embodiments, the conjugate comprises an ADI that is covalently linked to a TNF superfamily member ligand (for example, TRAIL, TNF-a, FasL) and the conjugate has improved pharmacokinetic, physical, and/or biological properties relative to the ADI alone and/or the TNF superfamily ligand alone. As noted above, exemplary pharmacokinetic and physical properties include increased stability, increased serum half-life, increased bioavailability, increased exposure, and decreased clearance. In some instances, the conjugate has increased stability and/or serum half-life relative to the ADI alone and/or the TNF superfamily ligand alone. In particular instances, the stability and/or serum half-life of the conjugate is increased by about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to the ADI alone and/or the TNF superfamily ligand alone.

In some instances, the conjugate has increased biological activity relative to the ADI alone and/or the TNF superfamily ligand alone. In particular instances, the biological activity of the conjugate is increased by about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to the ADI alone and/or the TNF superfamily ligand alone. In some instances, the increase in biological activity is a synergistic increase relative to the ADI alone and/or the TNF superfamily ligand alone. In some instances, the increase in biological activity is an additive increase relative to the ADI alone and/or the TNF superfamily ligand alone. In particular embodiments, the biological activity is induction of cell death or apoptosis in cancer cells and/or upregulation of TNF superfamily receptor expression, for example, Death Receptor 5 (DR5). In specific instances, the ADI component of the conjugate increases the ability of the TNF superfamily ligand to induce cell death or apoptosis in cancer cells, for example, by about at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% relative to the TNF superfamily ligand alone, for example, by upregulating expression of DR5 on the cancer cells. In specific instances, the conjugate has increased (for example, by about at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more) or synergistically -increased tumor cell-killing and/or apoptosis-inducing activity relative to the ADI alone and/or the TNF superfamily ligand alone. In some instances, the cancer cells are ADI-sensitive cancer cells, or cancer cells that express low or undetectable levels of argininosuccinate synthetase- 1 (ASS1). In particular instances, the cancer cells (for example, the ADI-sensitive cancer cells) are selected from one or more of breast cancer cells, hepatocellular carcinoma cells, Burkitt's Lymphoma cells, colon cancer cells, glioblastoma cancer cells, leukemic cells, melanoma cancer cells, non-small lung cell cancer (NSCLC) cells, ovarian cancer cells, pancreatic cancer cells, prostate cancer cells, and renal cancer cells. In some instances, the cancer cells are ADI-non-sensitive or ADI-resistant cancer cells, or cancer cells that express relatively high levels of ASS1. In particular instances, the cancer cells (for example, the ADI-non-sensitive cancer cells) are selected from one or more of breast cancer cells, colon cancer cells, and NSCLC cells.

In some embodiments, the conjugate comprises a hexameric (for example, homohexameric) polypeptide that is covalently linked to a trimeric (for example, homotrimeric) polypeptide, and in some instances conjugation to the hexameric polypeptide improves the physical, pharmacokinetic, and/or biological properties of the trimeric polypeptide relative to the latter alone, and/or vice versa. In some embodiments, the conjugate comprises a first trimeric (for example, homotrimeric) polypeptide that is covalently linked to a second trimeric (for example, homotrimeric) polypeptide, and in some instances conjugation to the first trimeric polypeptide improves the physical, pharmacokinetic, and/or biological properties of the second trimeric polypeptide relative to the latter alone, and/or vice versa. In some instances, the conjugate has increased physical, pharmacokinetic, and/or biological properties relative to one or both of the components alone. In specific instances, the conjugate has increased stability and/or serum half-life relative to one or both the components alone, for example, where the stability and/or serum half-life of the conjugate is increased by about at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to one or both the components alone. In some instances, the conjugate has increased biological activity relative to one or both the components alone, for example, where the biological activity of the conjugate is increased by about at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% or more relative to one or both the components alone.

The individual components of the conjugates are described in greater detail below.

Arginine Deiminases (APIs). Certain conjugates comprise one or more arginine deiminases (ADIs), also referred to as ADI polypeptides or ADI enzymes. In some embodiments, the ADI polypeptide is from M. hominis, M. arginini, M. arthritidis, M. phocicerebrale, M. gateae, M.

phocidae, M. columbinum, M. iowae, M. crocodyli, M. alligatoris, H. orenii, orM. bovis. In some embodiments, the ADI polypeptide is from Mycoplasma salivarium, Mycoplasma spumans, Mycoplasma canadense, Mycoplasma auris, Mycoplasma hyosynoviae, Mycoplasma cloacale, Mycoplasma anseris, Mycoplasma alkalescens, Mycoplasma orale, Mycoplasma iners, Mycoplasma meleagridis, Mycoplasma alvi, Mycoplasma penetrans, Mycoplasma gallinarum, Mycoplasma pirum, Mycoplasma primatum, Mycoplasma fermentans, Mycoplasma lipofaciens, Mycoplasma felifaucium, Mycoplasma imitans, Mycoplasma opalescens, Mycoplasma moatsii, Mycoplasma elephantis, Mycoplasma pneumoniae, Mycoplasma testudinis, Mycoplasma sp. CAG:877, or Mycoplasma sp. CAG:472.

The amino acid sequences of illustrative ADI polypeptides are provided in Table Al below.

Hence, in some embodiments, the ADI component of the conjugate comprises, consists, or consists essentially of an amino acid sequence selected from Table AI (SEQ ID NOs: l-68), or an active variant or fragment thereof. Particular examples of active variants and fragments comprise, consist, or consist essentially of an amino acid sequence that is at least 80%, 95%, 90%, 95%, 96%, 97%, 98%, or 99% identical to a sequence selected from Table AI. Additional examples of polypeptide "variants" and "fragments" are described elsewhere herein.

In certain embodiments, the ADI has an "ADI activity", or the ability to convert or metabolize arginine into citrulline and ammonia. ADI activity can be measured according to routine techniques in the art. For instance, the amount of L-citrulline can be detected by a colorimetric endpoint assay (see, for example, Knipp and Vasak, Analytical Biochem. 286:257-264, 2000) and compared to a standard curve of known amounts of L-citrulline in order to calculate the specific activity of ADI, which can be expressed as IU/mg of protein. In some embodiments, one IU of ADI enzyme activity is defined as the amount of enzyme that produces 1 μιηοΐ of citrulline per minute at the pH and temperature being tested.

In some embodiments, the ADI is a hexameric or homohexameric ADI, for example, an ADI is capable of forming a hexameric or homohexameric structure in its natural state and/or upon conjugation to the TNF Superfamily ligand component of the conjugate. Without being bound by any one theory, it is hypothesized that the hexameric or homohexameric structure of the ADI component of the conjugate can stabilize the TNF superfamily ligand component of the conjugate, especially where the latter forms a trimeric or homotrimeric structure in its natural state and/or upon conjugation to the ADI component of the conjugate. Particular examples of hexameric or homohexameric ADIs include the native ADIs derived from Mycoplasma columbinum, M. iners, M. gallinarum, and M. meleagridis (e.g., SEQ ID NOs: 9, 37, 38, 50, respectively), and the chimeric ADIs from Table Al (e.g., SEQ ID NOs: 57-68), including active variants and fragments thereof.

Any one or more of the ADI polypeptides described herein can be combined with any one or more of the TNF superfamily ligands or trimeric (for example, homotrimeric) polypeptides described herein, to form a conjugate, for example, a fusion protein.

TNF Superfamily Ligands. Certain conjugates comprise one or more Tumor Necrosis Factor (TNF) superfamily ligands, also referred to as TNF superfamily ligand polypeptides. The Tumor Necrosis Factor receptor superfamily (TNFRSF) is a protein superfamily of cytokine receptors characterized by the ability to bind tumor necrosis factors (TNFs) via an extracellular cysteine-rich domain. With the exception of nerve growth factor (NGF), all TNFs are homologous to the archetypal TNF-a. TNF receptors are primarily involved in apoptosis and inflammation, but also regulate other signal transduction pathways, such as cell proliferation, survival, and differentiation. The term death receptor refers to those members of the TNF receptor superfamily that contain a death domain, examples of which include TNFRl, the Fas receptor, Death Receptor 4 (DR4), and Death Receptor 5 (DR5).

An illustrative list of TNF superfamily receptors and their corresponding ligands is provided in Table Tl below.

Thus, in certain embodiments, the TNF superfamily ligand component of the conjugate is selected from a ligand polypeptide in Table Tl. In certain embodiments, the TNF superfamily ligand is a human polypeptide ligand selected from Table Tl.

In some embodiments, the TNF superfamily ligand is a trimeric or homotrimeric polypeptide. As noted above, according to one non-limiting theory the hexameric or homohexameric structure of the ADI component of the conjugate can stabilize the trimeric or homotrimeric TNF superfamily ligand component of the conjugate. In certain embodiments, the TNF superfamily ligand is a trimeric or homotrimeric polypeptide ligand selected from Table Tl.

In some embodiments, the TNF superfamily ligand induces apoptosis in cancer cells, for example, by binding to a death domain or death receptor of a TNF superfamily receptor. Thus, in some embodiments, TNF superfamily ligand (e.g., trimeric or homotrimeric ligand) binds to at least one TNF death receptor, or a TNF superfamily receptor that contains at least one death domain. Examples of TNF superfamily death receptors include TNFR1, Fas receptor, DR4, and DR5.

Particular examples of death receptor ligands include TRAIL, TNF-a, and FasL. Thus, in certain embodiments, the TNF superfamily ligand component of the conjugate is selected from one or more of TRAIL, TNF-a, and FasL, optionally a human TRAIL, human TNF-a, or human FasL.

The amino acid sequences of human TRAIL, human TNF-a, and human FasL are provided in

Table T2 below.

In some embodiments, the TNF superfamily ligand component of the conjugate comprises, consists, or consists essentially of an amino acid sequence selected from Table T2 (SEQ ID NOs: 69- 72), or an active variant or fragment thereof. Particular examples of variants and fragments comprise, consist, or consist essentially of an amino acid sequence that is at least 80%, 95%, 90%, 95%, 96%, 97%, 98%, or 99% identical to a sequence selected from Table T2. Additional examples of active polypeptide "variants" and "fragments" are described elsewhere herein.

In specific embodiments, the TNF superfamily ligand component of the conjugate is a human TNF-related apoptosis-inducing ligand (TRAIL) polypeptide, or a variant or fragment thereof. TRAIL is a cytokine that is produced and secreted by most normal tissue cells. It causes apoptosis in tumor cells, for example, by binding to certain death receptors. The predicted 281 amino acid TRAIL protein has the characteristic structure of a type II membrane protein, with a single internal hydrophobic domain and no signal sequence. The extracellular C-terminal domain of TRAIL shares 22 to 28% identity with the C-terminal domains of other TNF family members. Formation of a complex between TRAIL and its signaling receptors, DR4 and DR5, triggers apoptosis by inducing the oligomerization of intracellular death domains.

In certain embodiments, the TRAIL component of the conjugate comprises, consists, or consists essentially of a TRAIL sequence from Table T2 (SEQ ID NOs: 69 and 70), or a variant or fragment thereof. Specific examples of TRAIL variants include those having any one or more of the following substitutions; S96C, S101C, S111C, R170C, and K179C. In some embodiments, the TRAIL variant has a set of amino acid substitutions at the residue position selected from one or more of Y189Q, R191K, Q193R; H264R, I266L, D267Q; Y189Q, R191K, Q193R; and Y189Q, R191K, Q193R, I266L (see U.S. Application Nos. 2013/0165383; and 2012/0165267, incorporated by reference). Particular examples of TRAIL fragments include residues 114-281 (extracellular domain), residues 95-281, residues 92-281, residues 91-281, residues 41-281, residues 39-281, residues 15-281, residues 119-281, and residues 1-281 of the full-length sequence (SEQ ID NO:69). Additional examples of polypeptide "variants" and "fragments" are described elsewhere herein.

Any one or more of the TNF superfamily ligands described herein can be combined with any one or more of the ADI polypeptides or hexameric (e.g., homohexameric) polypeptides described herein, to form a conjugate, for example, a fusion protein.

Linkers. Certain conjugates comprise one or more linker groups. The term "linkage," "linker," "linker moiety," or "L" is used herein to refer to a linker that can be used to separate one polypeptide component of a conjugate from another polypeptide component, for example, an ADI polypeptide from a TNF superfamily ligand, or a hexameric polypeptide from a trimeric polypeptide. The linker may be physiologically stable or may include a releasable linker such as a labile linker or an enzymatically degradable linker (e.g., proteolytically cleavable linkers). In certain aspects, the linker is a peptide linker. In some aspects, the linker is a non-peptide linker or non-proteinaceous linker.

Certain embodiments comprise one or more peptide linkers. Such a peptide linker sequence can be incorporated into a conjugate, for example, a fusion polypeptide, using standard techniques in the art.

Certain peptide linker sequences may be chosen based on the following exemplary 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 first and second polypeptides; (3) their physiological stability; and (4) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes, or other features. See, e.g., George and Heringa, J Protein Eng. 15:871-879, 2002. In some embodiments, the peptide linker is a rigid linker. In some embodiments, the peptide linker is a flexible linker. In particular embodiments, flexible linkers can be rationally designed using a computer program capable of modeling the peptides themselves (Desjarlais & Berg, PNAS. 90:2256-2260, 1993; and PNAS. 91 : 11099-11103, 1994) or by phage display methods.

In some embodiments, the peptide linker sequence is from 1 to about 200 amino acids in length. Exemplary linkers can have an overall amino acid length of about 1-200 amino acids, 1-150 amino acids, 1-100 amino acids, 1-90 amino acids, 1-80 amino acids, 1-70 amino acids, 1-60 amino acids, 1-50 amino acids, 1-40 amino acids, 1-30 amino acids, 1-20 amino acids, 1-10 amino acids, 1-5 amino acids, 1-4 amino acids, 1-3 amino acids, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 or more amino acids.

A peptide linker may employ any one or more naturally -occurring amino acids, non-naturally occurring amino acid(s), amino acid analogs, and/or amino acid mimetics as described elsewhere herein and known in the art. Certain 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., PNAS USA. 83:8258- 8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. Particular peptide linker sequences contain Gly, Ser, and/or Asn residues. Other near neutral amino acids, such as Thr and Ala may also be employed in the peptide linker sequence, if desired.

Certain exemplary peptide linkers are provided in Table LI below.

Thus, in certain embodiments, a conjugate, for example, a fusion polypeptide, comprises one or more peptide linkers selected from Table PI.

In some embodiments, for example, in non-fusion or chemically -linked conjugates, the linker is a non-peptide linker. For example, in some embodiments the linker is an organic moiety constructed to contain an alkyl, or aryl backbone, and contains an amide, ether, ester, hydrazone, disulphide linkage or any combination thereof. Linkages containing amino acid, ether and amide bound components are stable under conditions of physiological pH, normally 7.4 in serum. Also included are linkages that contain esters or hydrazones and are stable at serum pH.

In some instances, a linker includes a spacer that increases the distance between the two joined atoms. A spacer may further add flexibility and/or length to the linker. Spacers may include, but are not be limited to, alkyl groups, alkenyl groups, alkynyl groups, aryl groups, aralkyl groups, aralkenyl groups, aralkynyl groups; each of which can contain one or more heteroatoms, heterocycles, amino acids, nucleotides, and saccharides.

In some embodiments, the linker is about 1 to about 30 atoms in length, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 atoms in length, including all ranges in between. In certain embodiments, the linker is about 1 to 30 atoms in length with carbon chain atoms which may be substituted by heteroatoms independently selected from the group consisting of O, N. or S. In some embodiments, from 1- 4 or from 5 to 15 of the C atoms are substituted with a heteroatom independently selected from O, N, S.

In certain embodiments, the linker comprises or consists of a structure selected from the following:— O— ,— NH— ,— S— ,—0(0)—, C(0)— NH, NH— C(0)— NH, O— C(0)— NH,— C(S)— ,— CH ₂ — ,— CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — CH ₂ — ,— O— CH ₂ — ,— CH ₂ — O— ,— O— CH ₂ — CH ₂ — ,— CH ₂ — O— CH ₂ — ,— CH ₂ — CH ₂ — O— ,— O— CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — O— CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — O— CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — O— ,— O— CH ₂ — CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — O— CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — O— CH ₂ — CH ₂ — , — CH ₂ — CH ₂ — CH ₂ — O— CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — CH ₂ — O— ,— C(O)— NH— CH ₂ — ,— C(O)— NH— CH ₂ — CH ₂ — ,— CH ₂ — C(O)— NH— CH ₂ — ,— CH ₂ — CH ₂ — C(O)— NH— ,— C(0)— NH— CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — C(O)— NH— CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — C(O)— NH— CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — C(O)— NH— ,— C(O)— NH— CH ₂ — CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — C(O)— NH— CH ₂ — CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — C(O)— NH— CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — C(O)— NH— CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — C(O)— NH— CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — CH ₂ — CH ₂ — C(O)— NH— ,— NH— C(O)— CH ₂ — ,— CH ₂ — NH— C(O)— CH ₂ — ,— CH ₂ — CH ₂ — NH— C(O)— CH ₂ — ,— NH— C(O)— CH ₂ — CH ₂ — ,— CH ₂ — NH— C(O)— CH ₂ — CH ₂ ,— CH ₂ — CH ₂ — NH— C(O)— CH ₂ — CH ₂ ,— C(O)— NH— CH ₂ — ,— C(O)— NH— CH ₂ — CH ₂ — ,— O— C(O)— NH— CH ₂ — ,— O— C(O)— NH— CH ₂ — CH ₂ — ,— NH— CH ₂ — ,— NH— CH ₂ — CH ₂ — ,— CH ₂ — NH— CH ₂ — ,— CH ₂ — CH ₂ — NH— CH ₂ — ,— C(0)— CH ₂ — ,— C(O)— CH ₂ — CH ₂ — ,— CH ₂ — C(O)— CH ₂ — ,— CH ₂ — CH ₂ — C(O)— CH ₂ — ,— CH ₂ — CH ₂ — C(0)— CH ₂ — CH ₂ — ,— CH ₂ — CH ₂ — C(O)— , — CH ₂ — CH ₂ — CH ₂ — C(O)— NH— CH ₂ — CH ₂ — NH— ,— CH ₂ — CH ₂ — CH ₂ — C(O)— NH— CH ₂ — CH ₂ — NH— C(O)— ,— CH ₂ — CH ₂ — CH ₂ — C(O)— NH— CH ₂ — CH ₂ — NH— C(O)— CH ₂ — , bivalent cycloalkyl group,— N(R ⁶ )— , R ⁶ is H or an organic radical selected from the group consisting of alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl and substituted aryl.

In some embodiments, the linker is a stable linker. In some embodiments, the stable linker is selected from the group consisting of: succinimide, propionic acid, carboxymethylate linkages, ethers, carbamates, amides, amines, carbamides, imides, aliphatic C-C bonds, and thio ethers. In some embodiments, the linker group is hydrophilic, for instance, to enhance the solubility of the conjugate in body fluids.

In some embodiments, the linker comprises or consists of polymer such as a polyethylene glycol or polypropylene glycol. The terms "PEG," "polyethylene glycol" and "poly(ethylene glycol)" as used herein, are interchangeable and meant to encompass any water-soluble poly(ethylene oxide) derivative. PEG is a well-known polymer with good solubility in many aqueous and organic solvents, which exhibits low toxicity, lack of immunogenicity, and is clear, colorless, odorless, and stable. Similar products may be obtained with other water-soluble polymers, as described herein, including without limitation; polyvinyl alcohol, other poly(alkylene oxides) such as poly (propylene glycol) and the like, poly(oxyethylated polyols) such as poly(oxyethylated glycerol) and the like,

carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl purrolidone, poly-l,3-dioxolane, poly- 1,3,6-trioxane, ethylene/maleic anhydride, and polyaminoacids. One skilled in the art will be able to select the desired polymer based on the desired dosage, circulation time, resistance to proteolysis, and other considerations.

Typically, PEGs for use in accordance with the conjugates described herein comprise the following structure "-(OCH2CH2)n-" where (n) is about 1 to 4000, about 20 to 1400, or about 20-800. In particular embodiments, PEG also includes "-0-(CH2CH20)n-CH2CH2-" and "-(OCH2CH2)n-0- " depending upon whether or not the terminal oxygens have been displaced. The term "PEG" includes structures having various terminal or "end capping" groups. The term "PEG" also includes a polymer that contains a majority, that is to say, greater than 50%, of -OCH2CH2- repeating submits. With respect to specific forms, the PEG can take any number of a variety of molecular weights, as well as structures or geometries such as "branched," "linear," "forked," "multifunctional" PEG molecules.

Representative polymeric reagents and methods for conjugating such polymers to an active moiety are described in Harris, J.M. and Zalipsky, S., Eds, Poly(ethylene glycol), Chemistry and Biological Applications, ACS, Washington, 1997; Veronese, F., and J.M. Harris, Eds., Peptide and Protein PEGylation, Advanced Drug Delivery Reviews, 54(4); 453-609 (2002); Zalipsky, S., et al., "Use of Functionalized Poly Ethylene Glycols) for Modification of Polypeptides" in Polyethylene Glycol Chemistry: Biotechnical and Biomedical Applications, J.M. Harris, ed., Plenus Press, New York (1992); Zalipsky (1995) Advanced Drug Reviews 16: 157-182; and in Roberts et al., Adv. Drug Delivery Reviews, 54, 459-476 (2002).

A wide variety of PEG derivatives are both commercially available and suitable for use in the preparation of the PEG-conjugates of the disclosure. For example, NOF Corp.'s SUNBRIGHT® Series provides numerous PEG derivatives, including methoxypolyethylene glycols and activated PEG derivatives such as succinimidyl ester, methoxy-PEG amines, maleimides, and carboxylic acids, for coupling by various methods to polypeptides and polynucleotides and Nektar Therapeutics' Advanced PEGylation also offers diverse PEG-coupling technologies to improve the safety and efficacy of therapeutics. Additional PEGs for use in forming conjugates include those available from Polypure (Norway), from QuantaBioDesign LTD (Ohio) JenKem Technology, Nanocs Corporation, and Sunbio, Inc (South Korea). Further PEG reagents suitable for use in forming a conjugate, and methods of conjugation are described, for example, in Pasut et al., Expert Opin. Ther. Patents. 14(6) 859-893, 2004.

The preparation of linear or branched PEG polymers and derivatives or conjugates thereof is described, for example, in U.S. Pat. Nos. 4,904,584; 5,428,128; 5,621,039; 5,622,986; 5,643,575; 5,728,560; 5,730,990; 5,738,846; 5,811,076; 5,824,701; 5,840,900; 5,880,131; 5,900,402; 5,902,588; 5,919,455; 5,951,974; 5,965,119; 5,965,566; 5,969,040; 5,981,709; 6,011,042; 6,042,822; 6,113,906; 6,127,355; 6,132,713; 6,177,087; 6,180,095; 6,448,369; 6,495,659; 6.602,498; 6,858,736; 6,828,401; 7,026,440; 7,608,678; 7,655,747; 7,786,221; 7,872,072; and 7,910,661, each of which is incorporated herein by reference in its entirety.

In certain embodiments, the foregoing linkers are optional.

Polypeptide Variants. Certain embodiments include "variants" and "fragments" of the reference sequences described herein, whether described by name or by reference to a Table or sequence identifier. Examples include any of the ADI polypeptides, TNF superfamily ligand polypeptides, and fusion polypeptides described herein. A "variant" sequence refers to a polypeptide or polynucleotide sequence that differs from a reference sequence by one or more substitutions, deletions (e.g., truncations), additions, and/or insertions. Variant polypeptides are biologically active, that is, they continue to possess the enzymatic or binding activity of a reference polypeptide. Such variants may result from, for example, genetic polymorphism and/or from human manipulation.

In many instances, a biologically active variant will contain one or more conservative substitutions. A "conservative substitution" is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. As described above, modifications may be made in the structure of the polynucleotides and polypeptides of the present disclosure and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable characteristics. When it is desired to alter the amino acid sequence of a polypeptide to create an equivalent, or even an improved, variant or portion of a polypeptide described herein, one skilled in the art will typically change one or more of the codons of the encoding DNA sequence.

For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid sequence substitutions can be made in a protein sequence, and, of course, its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated that various changes may be made in the peptide sequences of the disclosed compositions, or corresponding DNA sequences which encode said peptides without appreciable loss of their utility.

In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte & Doolittle, 1982, incorporated herein by reference). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics (Kyte & Doolittle, 1982). These values are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (- 4.5). It is known in the art that certain amino acids may be substituted by other amino acids having a similar hydropathic index or score and still result in a protein with similar biological activity, i.e., still obtain a biological functionally equivalent protein. In making such changes, the substitution of amino acids whose hydropathic indices are within +2 is preferred, those within ±1 are particularly preferred, and those within +0.5 are even more particularly preferred.

It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Patent 4,554,101 (specifically incorporated herein by reference in its entirety), states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein. As detailed in U. S. Patent 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 + 1); glutamate (+3.0 + 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 + 1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); tryptophan (-3.4). It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein. In such changes, the substitution of amino acids whose hydrophilicity values are within +2 is preferred, those within ±1 are particularly preferred, and those within +0.5 are even more particularly preferred.

As outlined above, amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine;

glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.

Amino acid substitutions may further be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his.

A variant may also, or alternatively, contain non-conservative changes. In a preferred embodiment, variant polypeptides differ from a native or reference sequence by substitution, deletion or addition of fewer than about 10, 9, 8, 7, 6, 5, 4, 3, 2 amino acids, or even 1 amino acid. Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure, enzymatic activity, and/or hydropathic nature of the polypeptide.

In certain embodiments, a polypeptide sequence is about, at least about, or up to about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000 or more contiguous amino acids in length, including all integers in between, and which may comprise all or a portion of a reference sequence (see, e.g., Tables or the Sequence Listing).

In some embodiments, a polypeptide sequence consists of about or no more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800. 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000 or more contiguous amino acids, including all integers in between, and which may comprise all or a portion of a reference sequence (see, e.g., Tables or the Sequence Listing).

In certain embodiments, a polypeptide sequence is about 10-1000, 10-900, 10-800, 10-700, 10-600, 10-500, 10-400, 10-300, 10-200, 10-100, 10-50, 10-40, 10-30, 10-20, 20-1000, 20-900, 20- 800, 20-700, 20-600, 20-500, 20-400, 20-300, 20-200, 20-100, 20-50, 20-40, 20-30, 50-1000, 50-900, 50-800, 50-700, 50-600, 50-500, 50-400, 50-300, 50-200, 50-100, 100-1000, 100-900, 100-800, 100- 700, 100-600, 100-500, 100-400, 100-300, 100-200, 200-1000, 200-900, 200-800, 200-700, 200-600, 200-500, 200-400, or 200-300 contiguous amino acids, including all ranges in between, and comprises all or a portion of a reference sequence. In certain embodiments, the C-terminal or N-terminal region of any reference polypeptide may be truncated by about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, or 800 or more amino acids, or by about 10-50, 20-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 500-550, 550-600, 600- 650, 650-700, 700-750, 750-800 or more amino acids, including all integers and ranges in between (e.g., 101, 102, 103, 104, 105), so long as the truncated polypeptide retains the binding properties and/or activity of the reference polypeptide. Typically, the biologically-active fragment has no less than about 1%, about 5%, about 10%, about 25%, or about 50% of an activity of the biologically- active reference polypeptide from which it is derived.

In certain instances, variants will display at least about 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% similarity or sequence identity or sequence homology to a reference polypeptide sequence. Moreover, sequences differing from the native or parent sequences by the addition (e.g., C-terminal addition, N-terminal addition, both), deletion, truncation, insertion, or substitution (e.g., conservative substitution) of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acids (including all integers and ranges in between) but which retain the properties or activities of a parent or reference polypeptide sequence are contemplated.

In some embodiments, variant polypeptides differ from reference sequence by at least one but by less than 50, 40, 30, 20, 15, 10, 8, 6, 5, 4, 3 or 2 amino acid residue(s). In certain embodiments, variant polypeptides differ from a reference sequence by at least 1% but less than 20%, 15%, 10% or 5% of the residues. (If this comparison requires alignment, the sequences should be aligned for maximum similarity. "Looped" out sequences from deletions or insertions, or mismatches, are considered differences.)

Calculations of sequence similarity or sequence identity between sequences (the terms are used interchangeably herein) are performed as follows. To determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In certain embodiments, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, 60%, and even more preferably at least 70%, 80%, 90%, 100% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.

The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.

The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch, (J. Mol. Biol. 48: 444-453, 1970) algorithm which has been incorporated into the GAP program in the GCG software package, using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package, using a NWSgapdn CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. A particularly preferred set of parameters (and the one that should be used unless otherwise specified) are a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

The percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller (Cabios. 4: 11-17, 1989) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.

The nucleic acid and protein sequences described herein can be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al., (1990, J. Mol. Biol, 215: 403-10). BLAST nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12 to obtain nucleotide sequences homologous to nucleic acid molecules described herein. BLAST protein searches can be performed with the XBLAST program, score = 50, wordlength = 3 to obtain amino acid sequences homologous to protein molecules described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (Nucleic Acids Res. 25: 3389-3402, 1997). When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used.

In some embodiments, as noted above, polynucleotides and/or polypeptides can be evaluated using a BLAST alignment tool. A local alignment consists simply of a pair of sequence segments, one from each of the sequences being compared. A modification of Smith-Waterman or Sellers algorithms will find all segment pairs whose scores cannot be improved by extension or trimming, called high- scoring segment pairs (HSPs). The results of the BLAST alignments include statistical measures to indicate the likelihood that the BLAST score can be expected from chance alone.

The raw score, S, is calculated from the number of gaps and substitutions associated with each aligned sequence wherein higher similarity scores indicate a more significant alignment.

Substitution scores are given by a look-up table (see PAM, BLOSUM).

Gap scores are typically calculated as the sum of G, the gap opening penalty and L, the gap extension penalty. For a gap of length n, the gap cost would be G+Ln. The choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15), e.g., 11, and a low value for L (1-2) e.g., 1.

The bit score, S', is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Bit scores are normalized with respect to the scoring system, therefore they can be used to compare alignment scores from different searches. The terms "bit score" and "similarity score" are used interchangeably. The bit score gives an indication of how good the alignment is; the higher the score, the better the alignment.

The E-Value, or expected value, describes the likelihood that a sequence with a similar score will occur in the database by chance. It is a prediction of the number of different alignments with scores equivalent to or better than S that are expected to occur in a database search by chance. The smaller the E-Value, the more significant the alignment. For example, an alignment having an E value of e ^"m means that a sequence with a similar score is very unlikely to occur simply by chance.

Additionally, the expected score for aligning a random pair of amino acids is required to be negative, otherwise long alignments would tend to have high score independently of whether the segments aligned were related. Additionally, the BLAST algorithm uses an appropriate substitution matrix, nucleotide or amino acid and for gapped alignments uses gap creation and extension penalties. For example, BLAST alignment and comparison of polypeptide sequences are typically done using the BLOSUM62 matrix, a gap existence penalty of 11 and a gap extension penalty of 1.

In some embodiments, sequence similarity scores are reported from BLAST analyses done using the BLOSUM62 matrix, a gap existence penalty of 11 and a gap extension penalty of 1.

In a particular embodiment, sequence identity /similarity scores provided herein refer to the value obtained using GAP Version 10 (GCG, Accelrys, San Diego, Calif.) using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix (Henikoff and Henikoff, PNAS USA. 89: 10915-10919, 1992). GAP uses the algorithm of Needleman and Wunsch (JMol Biol. 48:443-453, 1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps.

In particular embodiments, the variant polypeptide comprises an amino acid sequence that can be optimally aligned with a reference polypeptide sequence (see, e.g., Sequence Listing) to generate a BLAST bit scores or sequence similarity scores of at least about 50, 60, 70, 80, 90, 100, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, or more, including all integers and ranges in between, wherein the BLAST alignment used the BLOSUM62 matrix, a gap existence penalty of 11, and a gap extension penalty of 1.

As noted above, a reference polypeptide may be altered in various ways including amino acid substitutions, deletions, truncations, additions, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants of a reference polypeptide can be prepared by mutations in the DNA. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Kunkel (PNAS USA. 82: 488-492, 1985); Kunkel et al., (Methods in Enzymol. 154: 367-382, 1987), U.S. Pat. No. 4,873,192, Watson, J. D. et al., ("Molecular Biology of the Gene," Fourth Edition, Benjamin/Cummings, Menlo Park, Calif, 1987) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al., (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.).

Methods for screening gene products of combinatorial libraries made by such modifications, and for screening cDNA libraries for gene products having a selected property are known in the art. Such methods are adaptable for rapid screening of the gene libraries generated by combinatorial mutagenesis of reference polypeptides. As one example, recursive ensemble mutagenesis (REM), a technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify polypeptide variants (Arkin and Yourvan, PNAS USA 89: 7811-7815, 1992; Delgrave et al., Protein Engineering. 6: 327-331, 1993).

Polypeptide Modifications. Certain embodiments include conjugates that comprise at least one "modifying agent," examples of which included but are not limited to macromolecule polymers, proteins, peptides, polysaccharides, and other compounds. In some instances, the modifying agent is attached to the ADI component of a conjugate, the TNF superfamily ligand component of a conjugate, or both. In some embodiments, the modifying agent is attached only to the ADI component of a conjugate, that is, the modifying agent is not attached to the TNF superfamily ligand (for example, TRAIL) component of the conjugate. The conjugate and the modifying agent may be linked by either covalent bonds or non-covalent interaction to form a stable conjugate or a stable composition to achieve a desired effect. In certain embodiments, the modified conjugate retains the biological activity of a corresponding unmodified conjugate (e.g., of the same or similar sequence) and has a longer half- life in vivo, and lower antigenicity than the corresponding unmodified conjugate. In certain embodiments, the modified conjugate retains at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more of the biological activity of the corresponding unmodified conjugate. Generally, the modified conjugate retains biological activity sufficient for therapeutic use.

In some embodiments, the modifying agent is a polymer or a protein or a fragment thereof that is biocompatible and increases the half -life of the conjugate in blood. The modifying agent can be either chemically coupled to the conjugate or a component thereof or where applicable, linked to the conjugate or a component thereof via fusion protein expression.

Macromolecule polymers may include a non-peptide macromolecule polymer, which in certain embodiments, may have its own bioactivity. Suitable polymers include, but are not limited to, polyenol compounds, polyether compounds, polyvinylpyrrolidone, poly amino acids, copolymer of divinyl ether and maleic anhydride, N-(2-hydroxypropyl)-methacrylamide, polysaccharide, polyoxyethylated polyol, heparin or its fragment, poly-alkyl-ethylene glycol and its derivatives, copolymers of poly-alkyl-ethylene glycol and its derivatives, poly(vinyl ethyl ether), a,P-Poly[(2- hydroxyethyl)-DL-aspartamide], polycarboxylates, poly oxyethylene-oxymethylenes, poly aery loyl morpholines, copolymer of amino compounds and oxyolefin, poly hyaluronic acid, polyoxiranes, copolymer of ethanedioic acid and malonic acid, poly (1,3-dioxolane), ethylene and maleic hydrazide copolymer, poly sialic acid, cyclodextrin, etc. In certain embodiments, the polymer is polyethylene glycol.

The polyenol compounds as used herein include, but are not limited to, polyethylene glycol (including monomethoxy polyethylene glycol, monohydroxyl polyethylene glycol), polyvinyl alcohol, polyallyl alcohol, polybutenol and the like, and their derivatives, such as lipids.

The poly ether compounds include, but are not limited to poly alkylene glycol

(HO((CH2)xO) _n H), polypropylene glycol, polyoxyrehylene (HO((CH ₂ ) ₂ 0) _n H), polyvinyl alcohol ((CH ₂ CHOH) _n ).

Poly amino acids include, but are not limited to, polymers of one type of amino acid or copolymers of two or more types of amino acids, for example, polyalanine or poly lysine, or block copolymers thereof.

Polysaccharides include but are not limited to, glucosan and its derivatives, for example dextran sulfate, cellulose and its derivatives (including methyl cellulose and carboxymethyl cellulose), starch and its derivatives, polysucrose, etc.

In particular embodiments, the modifying agent is a PEG molecule. "Polyethylene glycol" or "PEG" refers to mixtures of condensation polymers of ethylene oxide and water, in a branched or straight chain, represented by the general formula H(OCH ₂ CH ₂ ) _n OH, wherein n is at least 4. In some instances, the PEG is attached to the ADI component of a conjugate, the TNF superfamily ligand component of a conjugate, or both. In some embodiments, the PEG is attached only to the ADI component of a conjugate, that is, the PEG is not attached to the TNF superfamily ligand (for example, TRAIL) component of the conjugate.

"Polyethylene glycol" or "PEG" is used in combination with a numeric suffix to indicate the approximate weight average molecular weight thereof. For example, PEG5,000 refers to PEG having a total weight average molecular weight of about 5,000; PEG12,000 refers to PEG having a total weight average molecular weight of about 12,000; and PEG20,000 refers to PEG having a total weight average molecular weight of about 20,000.

In some embodiments, the PEG has a total weight average molecular weight of about 1,000 to about 50,000; about 3,000 to about 40,000; about 5,000 to about 30,000; about 8,000 to about 30,000; about 11,000 to about 30,000; about 12,000 to about 28,000; about 16,000 to about 24,000; about 18,000 to about 22,000; or about 19,000 to about 21,000. In some embodiments, the PEG has a total weight average molecular weight of about 1,000 to about 50,000; about 3,000 to about 30,000; about 3,000 to about 20,000; about 4,000 to about 12,000; about 4,000 to about 10,000; about 4,000 to about 8,000; about 4,000 to about 6,000; or about 5,000. In specific embodiments, the PEG has a total weight average molecular weight of about 20,000. Generally, PEG with a molecular weight of 30,000 or more is difficult to dissolve, and yields of the formulated product may be reduced. The PEG may be a branched or straight chain. The PEG may be a branched or straight chain, and in certain embodiments is a straight chain. The PEG having a molecular weight described herein may be used in conjunction with the conjugate or a component thereof, and optionally, a biocompatible linker.

Certain embodiments employ thiol, sulfhydryl, or cysteine-reactive PEG(s). In some embodiments, the thiol, sulfhydryl, or cysteine-reactive PEG(s) are attached to one or more naturally- occurring cysteine residues, one or more introduced cysteine residues (e.g., substitution of one or more wild-type residues with cysteine residue(s)), insertion of one or more cysteine residues), or any combination thereof (see, e.g., Doherty et al., Bioconjug Chem. 16: 1291-98, 2005). In specific embodiments, the ADI component of the conjugate has one or both of K192C and/or K287C substitutions for attachment to cysteine-reactive PEG(s). In certain embodiments, one more of the wild-type cysteines residues of the conjugate are substituted with another amino acid to prevent attachment of the PEG polymer to wild-type cysteines, for example, to prevent the PEG(s) from disrupting an otherwise desirable biological activity. Some embodiments employ one or more non- natural cysteine derivatives (e.g., homocysteine) instead of cysteine.

Non-limiting examples of thiol, sulfhydryl, or cysteine-reactive PEGs include Methoxy PEG Maleimides (M-PEG-MAL) (e.g., MW 2000, MW 5000, MW 10000, MW 20000, MW 30000, MW 40000). M-PEG-MALs react with the thiol groups on cysteine side chains in proteins and peptides to generate a stable 3-thiosuccinimidyl ether linkage. This reaction is highly selective and can take place under mild conditions at about pH 5.0-6.5 in the presence of other functional groups. Thus, in certain embodiments, the conjugate or a component thereof is conjugated to any one or more of the thiol, sulfhydryl, or cysteine-reactive PEG molecules described herein.

The conjugate or a component thereof may be covalently bonded to a modifying agent, such as PEG, with or without a linker. In some instances, the conjugate or a component thereof may be coupled directly (i.e., without a linker) to a modifying agent such as PEG, for example, through an amino group, a sulfhydryl group, a hydroxyl group, a carboxyl group, or other group.

The linker used to covalently attach the conjugate or a component thereof to a modifying agent (e.g. PEG) can be any biocompatible linker. "Biocompatible" indicates that the compound or group is non-toxic and may be utilized in vitro or in vivo without causing injury, sickness, disease, or death. A modifying agent such as PEG can be bonded to the linker, for example, via an ether bond, a thiol bond, an amide bond, or other bond.

In some embodiments, suitable linkers can have an overall chain length of about 1-100 atoms, 1-80 atoms, 1-60 atoms, 1-40 atoms, 1-30 atoms, 1-20 atoms, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18, 19, or 20 atoms, for example, wherein the atoms in the chain comprise C, S, N, P, and/or O. In some instances, a linker group includes, for example, a succinyl group, an amide group, an imide group, a carbamate group, an ester group, an epoxy group, a carboxyl group, a hydroxyl group, a carbohydrate, a tyrosine group, a cysteine group, a histidine group, a methylene group, and combinations thereof. Particular examples of stable linkers includesuccinimide, propionic acid, carboxymethylate linkages, ethers, carbamates, amides, amines, carbamides, imides, aliphatic C-C bonds, and thio ethers. In certain embodiments, the biocompatible linker is a succinimidyl succinate (SS) group.

Other suitable linkers include an oxy carbonylimidazole group (including, for example, carbonylimidazole (CDI)), a nitro phenyl group (including, for example, nitrophenyl carbonate (NCP) or trichlorophenyl carbonate (TCP)), a trysylate group, an aldehyde group, an isocyanate group, a vinylsulfone group, or a primary amine. In certain embodiments, the linker is derived from SS, SPA, SCM, or NHS; in certain embodiments, SS, SPA, or NHS are used, and in some embodiments, SS or SPA are used. Thus, in certain embodiments, potential linkers can be formed from methoxy-PEG succinimidyl succinate(SS), methoxy-PEG succinimidyl glutarate(SG), methoxy-PEG succinimidyl carbonate (SC), methoxy-PEG succinimidyl carboxymethyl ester (SCM), methoxy-PEG2 N-hydroxy succinimide (NHS), methoxy-PEG succinimidyl butanoate (SBA), methoxy-PEG succinimidyl propionate (SPA), methoxy-PEG succinimidyl glutaramide, and/or methoxy-PEG succinimidyl succinimide.

Additional examples of linkers include, but are not limited to, one or more of the following: — O— ,— NH— ,— S— ,— C(O)— , C(O)— NH, NH— C(0)— NH, O— C(0)— NH,— C(S)— ,— CH2— ,— CH2— CH2— ,— CH2— CH2— CH2— ,— CH2— CH2— CH2— CH2— ,— O— CH2— ,— CH2— O— ,— O— CH2— CH2— ,— CH2— O— CH2— ,— CH2— CH2— O— ,— O— CH2— CH2— CH2— ,— CH2— O— CH2— CH2— ,— CH2— CH2— O— CH2— ,— CH2— CH2— CH2— O— ,— O— CH2— CH2— CH2— CH2— ,— CH2— O— CH2— CH2— CH2— ,— CH2— CH2— O— CH2— CH2— ,— CH2— CH2— CH2— O— CH2— ,— CH2— CH2— CH2— CH2— O— ,— C(O)— NH— CH2— ,— C(O)— NH— CH2— CH2— ,— CH2— C(O)— NH— CH2— ,— CH2— CH2— C(O)— NH— ,— C(O)— NH— CH2— CH2— CH2— ,— CH2— C(O)— NH— CH2— CH2— ,— CH2— CH2— C(O)— NH— CH2— ,— CH2— CH2— CH2— C(O)— NH— ,— C(O)— NH— CH2— CH2— CH2— CH2— ,— CH2— C(O)— NH— CH2— CH2— CH2— ,— CH2— CH2— C(O)— NH— CH2— CH2— ,— CH2— CH2— CH2— C(O)— NH— CH2— ,— CH2— CH2— CH2— C(O)— NH— CH2— CH2— ,— CH2— CH2— CH2— CH2— C(O)— NH— ,— NH— C(O)— CH2— ,— CH2— NH— C(O)— CH2— ,— CH2— CH2— NH— C(O)— CH2— ,— NH— C(O)— CH2— CH2— ,— CH2— NH— C(O)— CH2— CH2,— CH2— CH2— NH— C(O)— CH2— CH2,— C(O)— NH— CH2— ,— C(O)— NH— CH2— CH2— ,— O— C(O)— NH— CH2— ,— O— C(O)— NH— CH2— CH2— ,— NH— CH2— ,— NH— CH2— CH2— ,— CH2— NH— CH2— ,— CH2— CH2— NH— CH2— ,— C(O)— CH2— ,— C(O)— CH2— CH2— ,— CH2— C(O)— CH2— ,— CH2— CH2— C(O)— CH2— , — CH2— CH2— C(O)— CH2— CH2— ,— CH2— CH2— C(O)— ,— CH2— CH2— CH2— C(O)— NH— CH2— CH2— NH— ,— CH2— CH2— CH2— C(O)— NH— CH2— CH2— NH— C(O)— ,— CH2— CH2— CH2— C(O)— NH— CH2— CH2— NH— C(O)— CH2— , bivalent cycloalkyl group,— N(R6)— , R6 is H or an organic radical selected from the group consisting of alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl and substituted aryl. Additionally, any of the linker moieties described herein may further include an ethylene oxide oligomer chain comprising 1 to 20 ethylene oxide monomer units [i.e., -(CH ₂ CH ₂ 0)i-2o-].That is, the ethylene oxide oligomer chain can occur before or after the linker, and optionally in between any two atoms of a linker moiety comprised of two or more atoms. Also, the oligomer chain would not be considered part of the linker moiety if the oligomer is adjacent to a polymer segment and merely represent an extension of the polymer segment.

Specific exemplary PEG molecules and linkers are described in Table PI below.

In certain embodiments, the conjugate or a component thereof comprises one or more PEG molecules and/or linkers as described herein (e.g., in Table PI).

From 1 to about 30 PEG molecules may be covalently bonded to the conjugate or a component thereof. In certain embodiments, the conjugate or a component thereof is modified with (i.e., comprises) one PEG molecule. In some embodiments, the conjugate or a component thereof is modified with more than one PEG molecule. In particular embodiments, the conjugate or a component thereof is modified with about 1 to about 10, or from about 7 to about 15 PEG molecules, or from about 2 to about 8 or about 9 to about 12 PEG molecules. In some embodiments, the conjugate or a component thereof is modified with about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 PEG molecules. In specific embodiments, the conjugate or a component thereof is modified with 4.5 - 5.5 PEG molecules per conjugate. In some embodiment, the conjugate or a component thereof is modified with 5 ± 1.5 PEG molecules.

In certain embodiments, about 15% to about 70% of the primary amino groups in the conjugate or a component thereof are modified with PEG, in some embodiments about 20% to about 65%, about 25% to about 60%, or in certain embodiments about 30% to about 55%, or 45% to about 50%, or in some embodiments about 50% of the primary amino groups in arginine deiminase are modified with PEG.

PEG which is attached to the conjugate may be either a straight chain, as with SS-PEG, SPA- PEG and SC-PEG, or a branched chain of PEG may be used, as with PEG2-NHS.

In some embodiments, for example, as noted above, the amino acid substitutions employ non- natural amino acids for conjugation to PEG or other modifying agent (see, e.g., de Graaf et al., Bioconjug Chem. 20: 1281-95, 2009). Certain embodiments thus include a conjugate or a component thereof that is conjugated to one or more PEGs via one or more non-natural amino acids. In some embodiments the non-natural amino acid comprises a side chain having a functional group selected from the group consisting of: an alkyl, aryl, aryl halide, vinyl halide, alkyl halide, acetyl, ketone, aziridine, nitrile, nitro, halide, acyl, keto, azido, hydroxy 1, hydrazine, cyano, halo, hydrazide, alkenyl, alkynyl, ether, thio ether, epoxide, sulfone, boronic acid, boronate ester, borane, phenylboronic acid, thiol, seleno, sulfonyl, borate, boronate, phospho, phosphono, phosphine, heterocyclic-, pyridyl, naphthyl, benzophenone, a constrained ring such as a cyclooctyne, thioester, enone, imine, aldehyde, ester, thioacid, hydroxy lamine, amino, carboxylic acid, alpha-keto carboxylic acid, alpha or beta unsaturated acids and amides, glyoxyl amide, and an organosilane group. In some embodiments, the non-natural amino acid is selected from the group consisting of: p-acetyl-L-phenylalanine, O-methyl- L-tyrosine, L-3-(2-naphthyl)alanine, 3-methyl-phenylalanine, O-4-allyl-L-tyrosine, homocysteine, 4- propyl-L-tyrosine, tri-O-acetyl-GlcNAc -serine, β-0-GlcNAc-L-serine, tri-O-acetyl-GalNAc-a- threonine, α-GalNAc-L-threonine, L-Dopa, a fluorinated phenylalanine, isopropyl-L-phenylalanine, p-azido-L-phenylalanine, p-acyl-L-phenylalanine, p-benzoyl-L-phenylalanine, L-phosphoserine, phosphonoserine, phosphonotyrosine, p-iodo-phenylalanine, p-bromophenylalanine, p-amino-L- phenylalanine, and isopropyl-L-phenylalanine.

Polynucleotides. Expression Vectors, and Host Cells. Certain embodiments relate to polynucleotides that encode a conjugate, for example, a fusion polypeptide, as described herein. Also included are polynucleotides that encode any one or more of the individual ADI or hexameric polypeptides described herein, alone or in combination with polynucleotides that encode any one or more of the individual TNF superfamily ligand or trimeric polypeptides described herein. Thus, certain embodiments include a polynucleotide that encodes any one or more of the individual ADI polypeptides in Table Al, any one or more of the individual TNF superfamily ligands in Table Tl or Table T2, or a fusion polypeptide described herein, for example, a fusion polypeptide that comprise any one or more of the ADI polypeptides of Table Al fused to any one or more of the TNF superfamily ligands in Table Tl or Table T2.

Among other uses, these and related embodiments may be utilized to recombinantly produce a fusion polypeptide or an individual component thereof (ADI, TNF superfamily ligand, hexameric polypeptide, trimeric polypeptide) in a host cell. It will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that encode a polypeptide described herein. Some of these polynucleotides may bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated, for example, polynucleotides that are optimized for human, yeast or bacterial codon selection.

As will be recognized by the skilled artisan, polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present disclosure, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.

Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a fusion polypeptide or a component thereof) or may comprise a variant, or a biological functional equivalent of such a sequence. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions, as described herein, preferably such that the activity of the variant polypeptide is not substantially diminished relative to the unmodified polypeptide.

Additional coding or non-coding sequences may, but need not, be present within a polynucleotide, and a polynucleotide may, but need not, be linked to other molecules and/or support materials. Hence, the polynucleotides, regardless of the length of the coding sequence itself, may be combined with other DNA or RNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably.

The polynucleotide sequences may also be of mixed genomic, cDNA, RNA, and that of synthetic origin. For example, a genomic or cDNA sequence encoding a leader peptide may be joined to a genomic or cDNA sequence encoding the polypeptide, after which the DNA or RNA sequence may be modified at a site by inserting synthetic oligonucleotides encoding the desired amino acid sequence for homologous recombination in accordance with well-known procedures or preferably generating the desired sequence by PCR using suitable oligonucleotides. In some embodiments a signal sequence can be included before the coding sequence. This sequence encodes a signal peptide N-terminal to the coding sequence which communicates to the host cell to direct the polypeptide to the cell surface or secrete the polypeptide into the media. Typically the signal peptide is clipped off by the host cell before the protein leaves the cell. Signal peptides can be found in variety of proteins in prokaryotes and eukaryotes.

One or multiple polynucleotides can encode the ADI, TNF superfamily ligand, hexameric, trimeric, and/or fusion polypeptides described herein. Moreover, the polynucleotide sequence can be manipulated for various reasons. Examples include but are not limited to the incorporation of preferred codons to enhance the expression of the polynucleotide in various organisms (see generally Nakamura et al., Nuc. Acid. Res. 28:292, 2000). In addition, silent mutations can be incorporated in order to introduce, or eliminate restriction sites, decrease the density of CpG dinucleotide motifs (see for example, Kameda et al., Biochem. Biophys. Res. Commun. 349: 1269-1277, 2006) or reduce the ability of single stranded sequences to form stem-loop structures: (see, e.g., Zuker M., Nucl. Acid Res. 31 :3406-3415, 2003). In addition, mammalian expression can be further optimized by including a Kozak consensus sequence (i.e., (a/g)cc(a/g)ccATGg) (SEQ ID NO:95) at the start codon. Kozak consensus sequences useful for this purpose are known in the art (Mantyh et al., PNAS 92: 2662- 2666, 1995; Mantyh et al,. Prot. Exp. & Purif. 6:124, 1995).

Also included are expression vectors that comprise the polynucleotides, and host cells that comprise the polynucleotides and/or expression vectors. Polypeptides and conjugates, for example, fusion polypeptides, can be produced by expressing a DNA or RNA sequence encoding the polypeptide in a suitable host cell by well-known techniques. The term "host cell" is used to refer to a cell into which has been introduced, or which is capable of having introduced into it, a nucleic acid sequence encoding one or more of the polypeptides described herein, and which further expresses or is capable of expressing a polypeptide of interest, such as a polynucleotide encoding any herein described polypeptide. The term includes the progeny of the parent cell, whether or not the progeny are identical in morphology or in genetic make-up to the original parent, so long as the selected gene is present. Host cells may be chosen for certain characteristics, for instance, the expression of a formylglycine generating enzyme (FGE) to convert a cysteine or serine residue within a sulfatase motif into a formylglycine (FGly) residue, or the expression of aminoacyl tRNA synthetase(s) that can incorporate unnatural amino acids into the polypeptide, including unnatural amino acids with an azide side-chain, alkyne side-chain, or other desired side-chain, to facilitate chemical conjugation or modification.

In some instances, a polynucleotide or expression vector comprises additional non-coding sequences. For example, the "control elements" or "regulatory sequences" present in an expression vector are non-translated regions of the vector, including enhancers, promoters, 5' and 3' untranslated regions, which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.

A variety of expression vector/host systems are known and may be utilized to contain and express polynucleotide sequences. These include, but are not limited to, microorganisms such as bacteria transformed with an expression vector, for example, a recombinant bacteriophage, plasmid, or cosmid DNA expression vector; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems, including mammalian cell and more specifically human cell systems transformed with viral, plasmid, episomal, integrating, or other expression vectors. Certain embodiments therefore include an expression vector, comprising a polynucleotide sequence that encodes a polypeptide described herein, for example, a fusion polypeptide. Also included are host cells that comprise the polynucleotides and/or expression vectors.

Certain embodiments may employ E. coli-based expression systems (see, e.g., Structural Genomics Consortium et al., Nature Methods. 5: 135-146, 2008). These and related embodiments may rely partially or totally on ligation-independent cloning (LIC) to produce a suitable expression vector. In specific embodiments, protein expression may be controlled by a T7 RNA polymerase (e.g., pET vector series), or modified pET vectors with alternate promoters, including for example the TAC promoter. These and related embodiments may utilize the expression host strain BL21(DE3), a ΧΌΈ3 lysogen of BL21 that supports T7-mediated expression and is deficient in Ion and ompT proteases for improved target protein stability. Also included are expression host strains carrying plasmids encoding tRNAs rarely used in E. coli, such as ROSETTA™ (DE3) and Rosetta 2 (DE3) strains. In some embodiments other E. coli strains may be utilized, including other E. coli K-12 strains such as W3110 (F- lambda ^" IN(rrnD-rrnE)l rph-1), and UT5600 (F, araC14, leuB6(Am), secA206(aziR), lacYl, proC14, tsx67, A(ompTfepC)266, entA403, glnX44(AS), λ ^" , trpE38, rfbCl, rpsL109(strR), xylA5, mtl-1, thiEl), which can result in reduced levels of post-translational modifications during fermentation. Cell lysis and sample handling may also be improved using reagents sold under the trademarks BENZONASE® nuclease and BUGBUSTER® Protein Extraction Reagent. For cell culture, auto-inducing media can improve the efficiency of many expression systems, including high- throughput expression systems. Media of this type (e.g., OVERNIGHT EXPRESS™ Autoinduction System) gradually elicit protein expression through metabolic shift without the addition of artificial inducing agents such as IPTG.

Particular embodiments employ hexahistidine tags (such as those sold under the trademark HIS'TAG® fusions), followed by immobilized metal affinity chromatography (IMAC) purification, or related techniques. In certain aspects, however, clinical grade proteins can be isolated from E. coli inclusion bodies, without or without the use of affinity tags (see, e.g., Shimp et al., Protein Expr Purif. 50:58-67, 2006). As a further example, certain embodiments may employ a cold-shock induced E. coli high-yield production system, because over-expression of proteins in Escherichia coli at low temperature improves their solubility and stability (see, e.g., Qing et al., Nature Biotechnology. 22:877-882, 2004).

Also included are high-density bacterial fermentation systems. For example, high cell density cultivation of Ralstonia eutropha allows protein production at cell densities of over 150 g/L, and the expression of recombinant proteins at titers exceeding 10 g/L. In the yeast Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used. For reviews, see Ausubel et al. (supra) and Grant et al., Methods Enzymol. 153:516-544, 1987. Also included are Pichia pandoris expression systems (see, e.g., Li et al., Nature Biotechnology. 24, 210-215, 2006; and Hamilton et al., Science, 301: 1244, 2003). Certain embodiments include yeast systems that are engineered to selectively glycosylate proteins, including yeast that have humanized N-glycosylation pathways, among others (see, e.g., Hamilton et al., Science. 313: 1441-1443, 2006; Wildt et al., Nature Reviews Microbiol. 3: 119-28, 2005; and

Gerngross et al., Nature-Biotechnology. 22: 1409 -1414, 2004; U.S. Patent Nos. 7,629,163; 7,326,681; and 7,029,872). Merely by way of example, recombinant yeast cultures can be grown in Fernbach Flasks or 15L, 50L, 100L, and 200L fermentors, among others.

In cases where plant expression vectors are used, the expression of sequences encoding polypeptides may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 6:307-311,1987). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi et al., EMBO J.

3: 1671-1680, 1984; Broglie et al., Science. 224:838-843, 1984; and Winter et al., Results Probl. Cell Differ. 17:85-105, 1991). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (see, e.g., Hobbs in McGraw Hill, Yearbook of Science and Technology, pp. 191-196, 1992).

An insect system may also be used to express a polypeptide of interest. For example, in one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia cells. The sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia cells in which the polypeptide of interest may be expressed (Engelhard et al., PNAS USA. 91:3224- 3227, 1994). Also included are baculovirus expression systems, including those that utilize SF9, SF21, and T. ni cells (see, e.g., Murphy and Piwnica-Worms, Curr Protoc Protein Sci. Chapter 5:Unit5.4, 2001). Insect systems can provide post-translation modifications that are similar to mammalian systems.

In mammalian host cells, a number of expression systems are well known in the art and commercially available. Exemplary mammalian vector systems include for example, pCEP4, pREP4, and pREP7 from Invitrogen, the PerC6 system from Crucell, and Lentiviral based systems such as pLPl from Invitrogen, and others. For example, in cases where an adenovirus is used as an expression vector, sequences encoding a polypeptide of interest may be ligated into an adenovirus

transcription/translation complex consisting of the late promoter and tripartite leader sequence.

Insertion in a non-essential El or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan & Shenk, PNAS USA. 81:3655-3659, 1984). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.

Examples of useful mammalian host cell lines include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells sub-cloned for growth in suspension culture, Graham et al., J. Gen Virol. 36:59, 1977); baby hamster kidney cells (BHK, ATCC CCL 10); mouse Sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251, 1980); monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL- 1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TR1 cells (Mather et al., Annals N.Y. Acad. Sci. 383:44-68, 1982); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2). Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR-CHO cells (Urlaub et al., PNAS USA. 77:4216, 1980); and myeloma cell lines such as NSO and Sp2/0. For a review of certain mammalian host cell lines suitable for protein production, see, e.g., Yazaki and Wu, Methods in Molecular Biology, Vol. 248 (B. K.C Lo, ed., Humana Press, Totowa, N.J., 2003), pp.255-268. Certain preferred mammalian cell expression systems include CHO and HEK293-cell based expression systems. Mammalian expression systems can utilize attached cell lines, for example, in T-flasks, roller bottles, or cell factories, or suspension cultures, for example, in 1L and 5L spinners, 5L, 14L, 40L, 100L and 200L stir tank bioreactors, or 20/50L and 100/200L WAVE bioreactors, among others known in the art.

In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, post-translational modifications such as acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation, or the insertion of non- naturally occurring amino acids (see generally US Patent Nos. 7,939,496; 7,816,320; 7,947,473; 7,883,866; 7,838,265; 7,829,310; 7,820,766; 7,820,766; 7,7737,226, 7,736,872; 7,638,299; 7,632,924; and 7,230,068). Post-translational processing which cleaves a "prepro" form of the protein may also be used to facilitate correct insertion, folding and/or function. Different host cells such as yeast, CHO, HeLa, MDCK, HEK293, and W138, in addition to bacterial cells, which have or even lack specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.

Exemplary Methods for Conjugation. Conjugation or coupling of a first polypeptide (e.g., ADI, hexameric polypeptide) to a second polypeptide (e.g., TNF superfamily ligand, trimeric polypeptide) or more can be carried out using standard chemical, biochemical, and/or molecular techniques. It will be apparent how to make a conjugate in light of the present disclosure using available art-recognized methodologies. In some instances, it will generally be preferred when coupling the primary components of a conjugate that the techniques employed and the resulting linking chemistries do not substantially disturb the desired functionality or activity of the individual components of the conjugate.

In certain embodiments, the conjugate is a fusion polypeptide or fusion protein. In some instances, a fusion polypeptide is expressed as a recombinant polypeptide in an expression system, as described herein and known in the art. Fusion polypeptides can contain one or multiple copies of a polypeptide sequence and may contain one or multiple copies of a polypeptide-based agent of interest, present in any desired arrangement.

For fusion proteins, DNA sequences encoding the fusion polypeptide components and optionally the peptide linker components may be assembled separately, and then ligated into an appropriate expression vector. The 3' end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5 ' end of a DNA sequence encoding the other polypeptide component(s) so that the reading frames of the sequences are in phase. The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3 ' to the DNA sequence encoding the most C-terminal polypeptide. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.

Similar techniques, mainly the arrangement of regulatory elements such as promoters, stop codons, and transcription termination signals, can be applied to the recombinant production of non- fusion polypeptides, for instance, polypeptides for the production of non-fusion conjugates (e.g., chemically -coupled conjugates).

Polynucleotides and fusion polynucleotides of the disclosure can contain one or multiple copies of a nucleic acid encoding a polypeptide sequence, and/or may contain one or multiple copies of a nucleic acid encoding a polypeptide agent.

In some embodiments, a polynucleotide encoding a polypeptide and/or fusion polypeptide are introduced directly into a host cell, and the cell incubated under conditions sufficient to induce expression of the encoded polypeptide(s). The polypeptide sequences of this disclosure may be prepared using standard techniques well known to those of skill in the art in combination with the polypeptide and nucleic acid sequences provided herein.

Therefore, according to certain embodiments, there is provided a recombinant host cell that comprises a polynucleotide or a fusion polynucleotide which encodes a polypeptide or fusion polypeptide described herein. Expression of a polypeptide or a fusion polypeptide in the host cell may be achieved by culturing under appropriate conditions recombinant host cells containing the polynucleotide. Following production by expression, the polypeptide(s) may be isolated and/or purified using any suitable technique, and then used as desired. Exemplary polynucleotides, expression vectors, and host cells are described elsewhere herein.

The polypeptides, for example, fusion polypeptides, produced by a recombinant cell can be purified and characterized according to a variety of techniques known in the art. Exemplary systems for performing protein purification and analyzing protein purity include fast protein liquid chromatography (FPLC) (e.g., AKTA and Bio-Rad FPLC systems), high-performance liquid chromatography (HPLC) (e.g., Beckman and Waters HPLC). Exemplary chemistries for purification include ion exchange chromatography (e.g., Q, S), size exclusion chromatography, salt gradients, affinity purification (e.g., Ni, Co, FLAG, maltose, glutathione, protein A/G), gel filtration, reverse- phase, ceramic HYPERD® ion exchange chromatography, and hydrophobic interaction columns (HIC), among others known in the art.

In some embodiments, the conjugate is a non-fusion polypeptide, for example, a conjugate produced by chemically -linking or coupling a first polypeptide (e.g., ADI, hexameric polypeptide) to a second polypeptide (e.g., TNF superfamily ligand, trimeric polypeptide) or more. The particular coupling chemistry employed will depend upon the structure of the polypeptides, the potential presence of multiple functional groups within the biologically active agent, the need for protection/deprotection steps, chemical stability of the agent, and the like, and will be readily determined by one skilled in the art. Illustrative coupling chemistry useful for preparing the conjugates of the disclosure can be found, for example, in Wong (1991), "Chemistry of Protein Conjugation and Crosslinking", CRC Press, Boca Raton, Fla.; and Brinkley "A Brief Survey of Methods for Preparing Protein Conjugates with Dyes, Haptens, and Crosslinking Reagents," in Bioconjug. Chem., 3:2013, 1992. Preferably, the binding ability and/or activity of the conjugate is not substantially reduced as a result of the conjugation technique employed, for example, relative to the unconjugated polypeptides.

In certain embodiments, a first polypeptide (e.g., ADI, hexameric polypeptide) is coupled to a second polypeptide (e.g., TNF superfamily ligand, trimeric polypeptide) either directly or indirectly. A direct reaction between two polypeptides of interest is possible when each possesses a substituent capable of reacting with the other. For example, a nucleophilic group, such as an amino or sulfhydryl group, on one may be capable of reacting with a carbonyl-containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.

Alternatively, it may be desirable to indirectly couple a first polypeptide (e.g., ADI, hexameric polypeptide) and a second polypeptide (e.g., TNF superfamily ligand, trimeric polypeptide) of interest via a linker group, as described herein, including non-peptide linkers and peptide linkers, as described herein. A linker group can also function as a spacer to distance a first and second polypeptide in order to avoid interference with binding capabilities, targeting capabilities or other functionalities. A linker group can also serve to increase the chemical reactivity of a substituent on a polypeptide, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible. Examples of linking groups include, for example, disulfide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups and esterase labile groups. In other illustrative embodiments, the conjugates include linking groups such as those disclosed in U.S. Pat. No.

5,208,020 or EP Patent 0 425 235 Bl, and Chari et al., Cancer Research. 52: 127-131, 1992.

Additional exemplary linkers are described herein.

In certain exemplary embodiments, a reaction between a polypeptide comprising a succinimidyl ester functional group and a polypeptide comprising an amino group forms an amide linkage; a reaction between a polypeptide comprising a oxycarbonylimidizaole functional group and a polypeptide comprising an amino group forms an carbamate linkage; a reaction between a polypeptide comprising a p-nitrophenyl carbonate functional group and a polypeptide comprising an amino group forms an carbamate linkage; a reaction between a polypeptide comprising a trichlorophenyl carbonate functional group and a polypeptide comprising an amino group forms an carbamate linkage; a reaction between a polypeptide comprising a thio ester functional group and a polypeptide comprising an n-terminal amino group forms an amide linkage; a reaction between a polypeptide comprising a proprionaldehyde functional group and a polypeptide comprising an amino group forms a secondary amine linkage.

In some exemplary embodiments, a reaction between a polypeptide comprising a butyraldehyde functional group and a polypeptide comprising an amino group forms a secondary amine linkage; a reaction between a polypeptide comprising an acetal functional group and a polypeptide comprising an amino group forms a secondary amine linkage; a reaction between a polypeptide comprising a piperidone functional group and a polypeptide comprising an amino group forms a secondary amine linkage; a reaction between a polypeptide comprising a methylketone functional group and a polypeptide comprising an amino group forms a secondary amine linkage; a reaction between a polypeptide comprising a tresylate functional group and a polypeptide comprising an amino group forms a secondary amine linkage; a reaction between a polypeptide comprising a maleimide functional group and a polypeptide comprising an amino group forms a secondary amine linkage; a reaction between a polypeptide comprising a aldehyde functional group and a polypeptide comprising an amino group forms a secondary amine linkage; and a reaction between a polypeptide comprising a hydrazine functional group and a polypeptide comprising an carboxylic acid group forms a secondary amine linkage.

In particular exemplary embodiments, a reaction between a polypeptide comprising a maleimide functional group and a polypeptide comprising a thiol group forms a thio ether linkage; a reaction between a polypeptide comprising a vinyl sulfone functional group and a polypeptide comprising a thiol group forms a thio ether linkage; a reaction between a polypeptide comprising a thiol functional group and a polypeptide comprising a thiol group forms a di-sulfide linkage; a reaction between a polypeptide comprising a orthopyridyl disulfide functional group and a polypeptide comprising a thiol group forms a di-sulfide linkage; and a reaction between a polypeptide comprising an iodoacetamide functional group and a polypeptide comprising a thiol group forms a thio ether linkage.

In a specific embodiment, an amine-to-sulfhydryl crosslinker is used for preparing a conjugate. In one preferred embodiment, for example, the crosslinker is succinimidyl-4-(N- maleimidomethyl)cyclohexane-l-carboxylate (SMCC) (Thermo Scientific), which is a sulfhydryl crosslinker containing NHS-ester and maleimide reactive groups at opposite ends of a medium-length cyclohexane-stabilized spacer arm (8.3 angstroms). SMCC is a non-cleavable and membrane permeable crosslinker that can be used to create sulfhydryl-reactive, maleimide-activated agents (e.g., polypeptides) for subsequent reaction with the components of the conjugate. NHS esters react with primary amines at pH 7-9 to form stable amide bonds. Maleimides react with sulfhydryl groups at pH 6.5-7.5 to form stable thioether bonds. Thus, the amine reactive NHS ester of SMCC crosslinks rapidly with primary amines of a polypeptide and the resulting sulfhydryl-reactive maleimide group is then available to react with cysteine residues of the other polypeptide to yield specific conjugates of interest. In certain specific embodiments, a polypeptide is modified to contain exposed sulfhydryl groups to facilitate crosslinking, e.g., to facilitate crosslinking to a maleimide-activated polypeptide. In some specific embodiments, a polypeptide is modified with a reagent which modifies primary amines to add protected thiol sulfhydryl groups. In some embodiments, the reagent N-succinimidyl-S- acetylthioacetate (SATA) (Thermo Scientific) is used to produce thiolated polypeptides.

In certain embodiments, a maleimide-activated polypeptide is reacted under suitable conditions with a thiolated polypeptides to produce a conjugate. It will be understood that by manipulating the ratios of SMCC, SATA, agent, and polypeptides in these reactions it is possible to produce conjugates having differing stoichiometries, molecular weights and properties.

In some illustrative embodiments, conjugates are made using bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP), succinimidyl-4-(N- maleimidomethyl)cyclohexane-l-carboxylate, iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p- azidobenzoyl)hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)- ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4-dinitrobenzene). Particular coupling agents include N- succinimidyl-3-(2-pyridyldithio)propionate (SPDP) (Carlsson et al., Biochem. J. 173:723-737 [1978]) and N-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for a disulfide linkage.

The specific crosslinking strategies discussed herein are but a few of many examples of suitable conjugation strategies that may be employed in producing the conjugates described herein. It will be evident to those skilled in the art that a variety of other bifunctional or polyfimctional reagents, both homo- and hetero-functional (such as those described in the catalog of the Pierce Chemical Co., Rockford, IL), may be employed as the linker group. Coupling may be affected, for example, through amino groups, carboxyl groups, sulfhydryl groups or oxidized carbohydrate residues. There are numerous references describing such methodology, e.g., U.S. Patent No. 4,671,958, to Rodwell et al.

Conjugates can also be prepared by a various "click chemistry" techniques, including reactions that are modular, wide in scope, give very high yields, generate mainly inoffensive byproducts that can be removed by non-chromatographic methods, and can be stereospecific but not necessarily enantioselective (see Kolb et al., Angew Chem Int Ed Engl. 40:2004-2021, 2001).

Particular examples include conjugation techniques that employ the Huisgen 1,3 -dipolar cycloaddition of azides and alkynes, also referred to as "azide-alkyne cycloaddition" reactions (see Hein et al., Pharm Res. 25:2216-2230, 2008). Non-limiting examples of azide-alkyne cycloaddition reactions include copper-catalyzed azide-alkyne cycloaddition (CuAAC) reactions and ruthenium-catalyzed azide-alkyne cycloaddition (RuAAC) reactions.

CuAAC works over a broad temperature range, is insensitive to aqueous conditions and a pH range over 4 to 12, and tolerates a broad range of functional groups (see Himo et al, J Am Chem Soc. 127:210-216, 2005). The active Cu(I) catalyst can be generated, for example, from Cu(I) salts or Cu(II) salts using sodium ascorbate as the reducing agent. This reaction forms 1,4-substituted products, making it region-specific (see Hein et al., supra).

RuAAC utilizes pentamethylcyclopentadienyl ruthenium chloride [Cp*RuCl] complexes that are able to catalyze the cycloaddition of azides to terminal alkynes, regioselectively leading to 1,5- disubstituted 1,2,3-triazoles (see Rasmussen et al., Org. Lett. 9:5337-5339, 2007). Further, and in contrast to CuAAC, RuAAC can also be used with internal alkynes to provide fully substituted 1,2,3- triazoles.

Any one or more of the fusion or non-fusion techniques can be employed in the preparation of a conjugate, as described herein.

Methods of Use and Compositions

Also included are methods of using the conjugates described herein for treating a subject in need thereof, and compositions comprising the conjugates. For example, certain embodiments include methods of treating, ameliorating the symptoms of, or inhibiting the progression of, a cancer in a subject in need thereof, comprising administering to the subject a conjugate described herein, or a composition comprising the conjugate.

The methods and compositions described herein can be used in the treatment of any variety of cancers. In some embodiments, the cancer is selected from one or more of hepatocellular carcinoma (HCC), melanoma, metastatic melanoma, pancreatic cancer, prostate cancer, small cell lung cancer, mesothelioma, lymphocytic leukemia, chronic myelogenous leukemia, lymphoma, hepatoma, sarcoma, leukemia, acute myeloid leukemia, relapsed acute myeloid leukemia, B-cell malignancy, breast cancer, ovarian cancer, colorectal cancer, gastric cancer, glioma (e.g., astrocytoma, oligodendroglioma, ependymoma, or a choroid plexus papilloma), glioblastoma multiforme (e.g., giant cell gliobastoma or a gliosarcoma), meningioma, pituitary adenoma, vestibular schwannoma, primary CNS lymphoma, primitive neuroectodermal tumor (medulloblastoma), non-small cell lung cancer (NSCLC), kidney cancer, bladder cancer, uterine cancer, esophageal cancer, brain cancer, head and neck cancers, cervical cancer, testicular cancer, and stomach cancer.

In some embodiments, the cancer exhibits reduced expression and/or activity of

argininosuccinate synthetase-1 (ASS-1), or is otherwise argininosuccinate synthetase- 1 -deficient. In some of these and related embodiments, the cancer is ADI-sensitive or substantially ADI-sensitive. In some instances, reduced ASS-1 expression or activity is a reduction in expression and/or activity of about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, or more, relative to expression and/or activity in an appropriate control sample, for example, a normal cell or tissue. In certain embodiments, ASS or ASL expression or activity is reduced by at least two-fold relative to expression or activity in a control sample. In some embodiments, the cancer exhibits normal or increased expression and/or activity of argininosuccinate synthetase-1 (ASS-1). In certain of these and related embodiments, the cancer is ADI-resistant or substantially ADI-resistant, or ADI-non-sensitive.

ASS-1 expression or activity can be measured according to routine techniques the art, including, for example, quantitative PCR, immunohistochemistry, Western Blotting, enzyme activity assays (e.g., ADI activity assays to measure conversion of citrulline into argininosuccinate or conversion of argininosuccinate into arginine and fumarate), and the like.

In some embodiments, the methods or compositions described herein increase median survival time of a patient by 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 15 weeks, 20 weeks, 25 weeks, 30 weeks, 40 weeks, or longer. In certain embodiments, the methods or compositions described herein increase median survival time of a patient by 1 year, 2 years, 3 years, or longer. In some embodiments, the methods or compositions described herein increase progression- free survival by 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks or longer. In certain embodiments, the methods or compositions described herein increase progression-free survival by 1 year, 2 years, 3 years, or longer.

In certain embodiments, the composition administered is sufficient to result in tumor regression, as indicated by a statistically significant decrease in the amount of viable tumor, for example, at least a 10%, 20%, 30%, 40%, 50% or greater decrease in tumor mass, or by altered (e.g., decreased with statistical significance) scan dimensions. In certain embodiments, the composition administered is sufficient to result in stable disease. In certain embodiments, the composition administered is sufficient to result in stabilization or clinically relevant reduction in symptoms of a particular disease indication known to the skilled clinician.

The methods or compositions for treating cancers can be combined with other therapeutic modalities. For example, a compositions described herein can be administered to a subject before, during, or after other therapeutic interventions, including symptomatic care, chemotherapy, radiotherapy, surgery, transplantation, hormone therapy, photodynamic therapy, antibiotic therapy, or any combination thereof. Symptomatic care includes administration of corticosteroids, to reduce cerebral edema, headaches, cognitive dysfunction, and emesis, and administration of anti-convulsants, to reduce seizures. Radiotherapy includes whole-brain irradiation, fractionated radiotherapy, and radiosurgery, such as stereotactic radiosurgery, which can be further combined with traditional surgery.

Methods for identifying subjects with one or more of the diseases or conditions described herein are known in the art.

For in vivo use, for instance, for the treatment of human disease or testing, the conjugates described herein are generally incorporated into one or more pharmaceutical or therapeutic compositions prior to administration. In some instances, a pharmaceutical or therapeutic composition comprises one or more of the conjugates described herein in combination with a physiologically acceptable carrier or excipient.

To prepare a pharmaceutical or therapeutic composition, an effective or desired amount of one or more conjugates is mixed with any pharmaceutical carrier(s) or excipient known to those skilled in the art to be suitable for the particular conjugate and/or mode of administration. A pharmaceutical carrier may be liquid, semi-liquid or solid. Solutions or suspensions used for parenteral, intradermal, subcutaneous or topical application may include, for example, a sterile diluent (such as water), saline solution (e.g., phosphate buffered saline; PBS), fixed oil, polyethylene glycol, glycerin, propylene glycol or other synthetic solvent; antimicrobial agents (such as benzyl alcohol and methyl parabens); antioxidants (such as ascorbic acid and sodium bisulfite) and chelating agents (such as ethylenediaminetetraacetic acid (EDTA)); buffers (such as acetates, citrates and phosphates). If administered intravenously (e.g., by IV infusion), suitable carriers include physiological saline or phosphate buffered saline (PBS), and solutions containing thickening and solubilizing agents, such as glucose, polyethylene glycol, polypropylene glycol and mixtures thereof.

In certain aspects, the pH of the composition is near physiological pH or about pH 7.4, including about pH 6.5, about 7.0, about 7.1, about 7.2, about 7.3, about 7.4, about 7.5, about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.5, or any range thereof. In specific embodiments, the composition has one or more of the following determinations of purity: less than about 1 EU endotoxin/mg protein, less that about 100 ng host cell protein/mg protein, less than about 10 pg host cell DNA/mg protein, and/or greater than about 95% single peak purity by SEC HPLC.

Administration may be achieved by a variety of different routes, including oral, parenteral, intranasal, intravenous, intradermal, intramuscular, intrathecal, subcutaneous, sublingual, buccal, rectal, vaginal, and topical. Preferred modes of administration depend upon the nature of the condition to be treated or prevented. Particular embodiments include administration by IV infusion.

Carriers can include, for example, pharmaceutically acceptable carriers, excipients, or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as polysorbate 20 (TWEEN™) polyethylene glycol (PEG), and poloxamers (PLURONICS™), and the like.

In some embodiments, one or more conjugates can be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization (for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate)microcapsules, respectively), in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules), or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, 16th edition, Oslo, A., Ed., (1980). The particle(s) or liposomes may further comprise other therapeutic or diagnostic agents.

Typical routes of administering these and related pharmaceutical compositions thus include, without limitation, oral, topical, transdermal, inhalation, parenteral, sublingual, buccal, rectal, vaginal, and intranasal. The term parenteral as used herein includes subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques. Certain pharmaceutical or therapeutic compositions are formulated so as to allow the active ingredients contained therein to be bioavailable upon administration of the composition to a patient. Compositions that will be administered to a subject or patient may take the form of one or more dosage units, where for example, a tablet may be a single dosage unit, and a container of a herein described conjugate in aerosol form may hold a plurality of dosage units. Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art; for example, see Remington: The Science and Practice of Pharmacy, 20th Edition (Philadelphia College of Pharmacy and Science, 2000). The composition to be administered will typically contain a therapeutically effective amount of a conjugate described herein, for treatment of a disease or condition of interest.

A pharmaceutical or therapeutic composition may be in the form of a solid or liquid. In one embodiment, the carrier(s) are particulate, so that the compositions are, for example, in tablet or powder form. The carrier(s) may be liquid, with the compositions being, for example, an oral oil, injectable liquid or an aerosol, which is useful in, for example, inhalatory administration. When intended for oral administration, the pharmaceutical composition is preferably in either solid or liquid form, where semi-solid, semi-liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid.

As a solid composition for oral administration, the pharmaceutical composition may be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like. Such a solid composition will typically contain one or more inert diluents or edible carriers. In addition, one or more of the following may be present: binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, gum tragacanth or gelatin; excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, corn starch and the like; lubricants such as magnesium stearate or Sterotex; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; a flavoring agent such as peppermint, methyl salicylate or orange flavoring; and a coloring agent. When the pharmaceutical composition is in the form of a capsule, for example, a gelatin capsule, it may contain, in addition to materials of the above type, a liquid carrier such as polyethylene glycol or oil. The pharmaceutical or therapeutic composition may be in the form of a liquid, for example, an elixir, syrup, solution, emulsion or suspension. The liquid may be for oral administration or for delivery by injection, as two examples. When intended for oral administration, preferred composition contain, in addition to the present compounds, one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer. In a composition intended to be administered by injection, one or more of a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent may be included.

The liquid pharmaceutical or therapeutic compositions, whether they be solutions, suspensions or other like form, may include one or more of the following adjuvants: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. Physiological saline is a preferred adjuvant. An injectable pharmaceutical composition is preferably sterile.

A liquid pharmaceutical or therapeutic composition intended for either parenteral or oral administration should contain an amount of a conjugate such that a suitable dosage will be obtained. Typically, this amount is at least 0.01% of the conjugate of interest in the composition. When intended for oral administration, this amount may be varied to be between 0.1 and about 70% of the weight of the composition. Certain oral pharmaceutical compositions contain between about 4% and about 75% of the conjugate of interest. In certain embodiments, pharmaceutical compositions and preparations are prepared so that a parenteral dosage unit contains between 0.01 to 10% by weight of the conjugate of interest prior to dilution.

The pharmaceutical composition may be intended for topical administration, in which case the carrier may suitably comprise a solution, emulsion, ointment or gel base. The base, for example, may comprise one or more of the following: petrolatum, lanolin, polyethylene glycols, bee wax, mineral oil, diluents such as water and alcohol, and emulsifiers and stabilizers. Thickening agents may be present in a pharmaceutical composition for topical administration. If intended for transdermal administration, the composition may include a transdermal patch or iontophoresis device.

The pharmaceutical composition may be intended for rectal administration, in the form, for example, of a suppository, which will melt in the rectum and release the drug. The composition for rectal administration may contain an oleaginous base as a suitable nonirritating excipient. Such bases include, without limitation, lanolin, cocoa butter, and polyethylene glycol. The pharmaceutical composition may include various materials, which modify the physical form of a solid or liquid dosage unit. For example, the composition may include materials that form a coating shell around the active ingredients. The materials that form the coating shell are typically inert, and may be selected from, for example, sugar, shellac, and other enteric coating agents.

Alternatively, the active ingredients may be encased in a gelatin capsule. The pharmaceutical composition in solid or liquid form may include a component that binds to the conjugate and thereby assists in the delivery of the conjugate. Suitable components that may act in this capacity include monoclonal or polyclonal antibodies, one or more proteins or a liposome.

The pharmaceutical composition may consist essentially of dosage units that can be administered as an aerosol. The term aerosol is used to denote a variety of systems ranging from those of colloidal nature to systems consisting of pressurized packages. Delivery may be by a liquefied or compressed gas or by a suitable pump system that dispenses the active ingredients. Aerosols may be delivered in single phase, bi-phasic, or tri-phasic systems in order to deliver the active ingredient(s). Delivery of the aerosol includes the necessary container, activators, valves, subcontainers, and the like, which together may form a kit. One of ordinary skill in the art, without undue experimentation may determine preferred aerosols.

The compositions described herein may be prepared with carriers that protect the conjugates against rapid elimination from the body, such as time release formulations or coatings. Such carriers include controlled release formulations, such as, but not limited to, implants and microencapsulated delivery systems, and biodegradable, biocompatible polymers, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, polyorthoesters, polylactic acid and others known to those of ordinary skill in the art.

The pharmaceutical compositions may be prepared by methodology well known in the pharmaceutical art. For example, a pharmaceutical composition intended to be administered by injection may comprise one or more of salts, buffers and/or stabilizers, with sterile, distilled water so as to form a solution. A surfactant may be added to facilitate the formation of a homogeneous solution or suspension. Surfactants are compounds that non-covalently interact with the conjugate so as to facilitate dissolution or homogeneous suspension of the conjugate in the aqueous delivery system.

The compositions may be administered in a therapeutically effective amount, which will vary depending upon a variety of factors including the activity of the specific compound employed; the metabolic stability and length of action of the compound; the age, body weight, general health, sex, and diet of the patient; the mode and time of administration; the rate of excretion; the drug combination; the severity of the particular disorder or condition; and the subject undergoing therapy.

The precise dosage and duration of treatment is a function of the disease being treated and may be determined empirically using known testing protocols or by testing the compositions in model systems known in the art and extrapolating therefrom. Controlled clinical trials may also be performed. Dosages may also vary with the severity of the condition to be alleviated. A pharmaceutical composition is generally formulated and administered to exert a therapeutically useful effect while minimizing undesirable side effects. The composition may be administered one time, or may be divided into a number of smaller doses to be administered at intervals of time. For any particular subject, specific dosage regimens may be adjusted over time according to the individual need.

In some embodiments, a therapeutically effective amount or therapeutic dosage of a composition described herein is an amount that is effective to reduce or stabilize tumor growth. In certain instances, treatment is initiated with small dosages which can be increased by small increments until the optimum effect under the circumstances is achieved. In some instances, a therapeutically effective daily dose is (for a 70 kg mammal) from about 0.001 mg/kg (i.e., ~ 0.07 mg) to about 100 mg/kg (i.e., ~ 7.0 g); preferably a therapeutically effective dose is (for a 70 kg mammal) from about 0.01 mg/kg (i.e., ~ 0.7 mg) to about 50 mg/kg (i.e., ~ 3.5 g); more preferably a therapeutically effective dose is (for a 70 kg mammal) from about 1 mg/kg (i.e., ~ 70 mg) to about 25 mg/kg (i.e., - 1.75 g).

In some embodiments, a dosage is administered from about once a day to about once every two or three weeks. For example, in certain embodiments, a dosage is administered about once every 1, 2, 3, 4, 5, 6, or 7 days, or about once a week, or about twice a week, or about three times a week, or about once every two or three weeks.

In some embodiments, the dosage is from about 0.1 mg/kg to about 20 mg/kg, or to about 10 mg/kg, or to about 5 mg/kg, or to about 3 mg/kg. In some embodiments, the dosage is about 0.10 mg/kg, 0.15 mg/kg, 0.20 mg/kg, 0.25 mg/kg, 0.30 mg/kg, 0.35 mg/kg, 0.40 mg/kg, 0.45 mg/kg, 0.50 mg/kg, 0.55 mg/kg, 0.60 mg/kg, 0.65 mg/kg, 0.70 mg/kg, 0.75 mg/kg, 0.80 mg/kg, 0.85 mg/kg, 0.90 mg/kg, 0.95 mg/kg, 1.0 mg/kg, 1.5 mg/kg, 2.0 mg/kg, 2.5 mg/kg, 3.0 mg/kg, 3.5 mg/kg, 4.0 mg/kg, 4.5 mg/kg, 5.0 mg/kg, 5.5 mg/kg, 6.0 mg/kg, 6.5 mg/kg. 7.0 mg/kg, 7.5 mg/kg, 8.0 mg/kg, 8.5 mg/kg, 9.0 mg/kg, 9.5 mg/kg, 10 mg/kg, 11 mg/kg, 12 mg/kg, 13 mg/kg, 14 mg/kg, 15 mg/kg, 16 mg/kg, 17 mg/kg, 18 mg/kg, 19 mg/kg, or 20 mg/kg, including all integers and ranges in between. In specific embodiments, the dosage is about 1 mg/kg once a week as a 2 ml intravenous injection to about 20 mg/kg once every 3 days.

Also included are patient care kits, comprising one or more conjugates or compositions described herein. Certain kits also comprise one or more pharmaceutically -acceptable diluents or solvents, such as water (e.g., sterile water). In some embodiments, the conjugates are stored in vials, cartridges, dual chamber syringes, and/or pre-filled mixing systems.

The kits herein may also include a one or more additional therapeutic agents (e.g., conjugates) or other components suitable or desired for the indication being treated, or for the desired diagnostic application. The kits herein can also include one or more syringes or other components necessary or desired to facilitate an intended mode of delivery (e.g., stents, implantable depots, etc.). All publications, patent applications, and issued patents cited in this specification are herein incorporated by reference as if each individual publication, patent application, or issued patent were specifically and individually indicated to be incorporated by reference.

Although the foregoing has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to one of ordinary skill in the art in light of the teachings of this disclosure that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims. The following examples are provided by way of illustration only and not by way of limitation. Those of skill in the art will readily recognize a variety of noncritical parameters that could be changed or modified to yield essentially similar results.

Examples

Example 1

Combinations of ADI-PEG 20 and TRAIL

The ability of ADI to increase the anti-cancer activity of TRAIL, and in some instances vice versa, was tested by treating various cancer cell lines with ADI-PEG 20 (pegylated arginine deiminase from Mycoplasma hominis that is modified with Kl 12E and P210S substitutions), human rhTRAIL, or a combination thereof. The cellular assays were performed as described in Example 1.

The results for ADI-sensitive (most have low or undetectable expression of ASS1) cancer cell lines are shown in Table El below.

These results illustrate a synergistic or additive effect between the ADI-PEG 20 and rhTRAIL combination relative to ADI-PEG 20 and/or rhTRAIL alone in the cell-killing of a variety of cancer cell lines. These results also illustrate that ADI-PEG 20 potentiates the activity of rhTRAIL in cancer cell lines that are otherwise resistant to rhTRAIL. Significantly or synergistically increased cell- killing activity was observed in a variety of cancer cell lines, including breast cancer cells, Burkitt's Lymphoma cells, colon cancer cells, glioblastoma cancer cells, leukemic cells, melanoma cancer cells, non-small lung cell cancer (NSCLC) cells, ovarian cancer cells, pancreatic cancer cells, prostate cancer cells, and renal cancer cells.

Figures 1A-1D further illustrate the synergistic effects of the ADI-PEG 20 and rhTRAIL combination on the relative viability of various cancer cell lines, relative to ADI-PEG 20 and/or rhTRAIL alone. Figure 1A shows synergy in the HCT116 colon cancer cell line, Figure IB shows synergy in the Caki-1 renal cancer cell line, Figure 1C shows synergy in the ACHN renal cancer cell line, and Figure ID shows synergy in the A375 melanoma cell line.

Figures 2A-2C demonstrate the synergistic effects ADI-PEG 20 and rhTRAIL on caspase 3/7 activation (Fig. 2A), induction of cell death (Fig. 2B), and reduction in the percentage of viable cells that are not committed to apoptosis (cells in which caspase 3/7 is not activated; Fig. 2C), compared to each agent alone in Raji Burkitt's lymphoma cell line. Percentages of dead cells or cells with and without activated caspase 3/7 were determined by flow cytometry analysis after staining with fluorescent reagents detecting activated caspase 3/7 and dead cells (CellEvent Caspase 3/7 kit from ThermoFisher Scientific).

The results for ADI-resistant (relatively high expression of AS SI) cancer cell lines are shown in Table E2 below.

The results in Table E2 show that ADI-PEG 20 does not necessary potentiate the cancer cell- killing activity of rhTRAIL (or vice versa) in certain ADI-resistant cell lines (due to high ASS1). However, in some ADI-resistant cancer cell lines (for example, MDA-MB-453 and H1975, where ADI has at least some minimal activity), the combination of ADI-PEG 20 and rhTRAIL shows synergism, potentiation, and/or coalism in cancer cell-killing activity relative to ADI-PEG 20 and/or TRAIL alone. Examples 2 and 3 show some of the biological activities of ADI that are likely to contribute to its ability to potentiate or synergize with TRAIL.

Example 2

ADI-PEG 20 Upregulates DR5 Receptor

To explore potential mechanisms by which ADI increases or potentiates the activity of rhTRAIL, the expression of DR4 and DR5 receptors was measured by flow cytometry following treatment of cancer cell lines with ADI-PEG 20.

The experimental workflow consisted of cell treatment, collection, and staining with fixable Live/Dead stain (ThermoFisher) and antibodies recognizing TRAIL receptors for 30 minutes on ice. This was followed by washing away unincorporated Live/Dead dye and unbound antibodies and analysis by a multi-color flow cytometer. Live/dead stain and antibodies were labeled with distinct fluorophores detected in different channels of a flow cytometerlsotype control antibodies were used to assess and control for non-specific binding. Receptor expression was analyzed in a cell population gated on singlet and live cells. Figures 3A-3D show that expression of the DR5 receptor was upregulated by ADI-PEG 20 in the Panc-1, Jurkat, Raji, K562, 0-786, ACHN, Caki-1, Caki-2, WM-115 and HCT116 cell lines. Expression of the DR4 receptor was low or undetectable in these cell lines and was not noticeably affected by ADI-PEG 20 treatment.

Example 3

ADI-PEG 20 Downregulates Survivin

Figure 4 demonstrates reduction in survivin protein levels after treatment with ADI-PEG 20 of ADI-sensitive cell lines. Survivin has been shown to impede activity of TRAIL. Thus, lowering survivin levels (along with DR5 upregulation) may contribute to the ability of ADI to potentiate and/or increase apoptotic activity of TRAIL in cancer cell lines.

Example 4

Conjugates of ADI and TRAIL

Fusion proteins between the arginine deiminase (ADI) from M. columbinum and the extracellular domain (residues 114-281) of human TNF-related apoptosis-inducing ligand (TRAIL) were cloned, expressed, and purified according to routine techniques, and then tested for anti-cancer activity. Table E3 below provides a summary of the ADI-TRAIL fusion proteins tested.

In addition, ADI from other hexameric species as well as their swap domains were used to make fusion proteins with human TRAIL (aa 114-281) using the GGGGS linker (SEQ ID NO:76). Table E4 below provides a summary of the generated hexameric ADI-TRAIL fusion proteins as well as the activity of ADI hexamer as part of the ADI-TRAIL fusion protein.

To assess effect of the fusion proteins on cancer cell growth, viability, and apoptosis induction, various cancer cell lines were plated in 96-well plates and exposed to the fusion proteins. The suspension cell lines were treated right after plating, while the adherent cells were allowed to attach overnight prior to addition of an investigational protein therapeutic to the cultures.

Relative cell viability was calculated by dividing the cell viability signal from a test sample by that of a non-treated control. Cell viability was determined with a reagent that detects viable cells such as resazurin or CellTiter-Glo (Promega) and measured using a plate reader (colorimetric, fluorescent or luminescent signal). For apoptosis, Caspase 3/7 activation was assessed using Promega's caspase 3/7 Glo reagent and luminescence readout by a plate reader. Caspase 3/7 activation and cell viability were also assessed by flow cytometry analysis of cells stained with fluorescent reagents detecting activated caspase 3/7 and dead cells (CellEvent Caspase 3/7 kit from ThermoFisher Scientific).

Figure 5 depicts an exemplary ADI-TRAIL or TRAIL-ADI fusion protein schematic.

Figures 6A-6C show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptide with LI Linker (see Table E3) on caspase 3/7 induction (Fig. 6A) and relative cell viability (Figs. 6B and 6C) in the ADI-resistant Colo 205 cancer cell line, relative to rhTRAIL alone, M.col.ADI alone and the combination of rhTRAIL and M.col.ADI as separate polypeptides. In this cell line (high ASS1 expression), ADI is not significantly active, and the cancer cell-killing activity is due to the TRAIL component of the ADI-TRAIL fusion polypeptide.

Figures 7A-7C show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptide with LI linker (see Table E3) on caspase 3/7 induction (Fig. 7A) and relative cell viability (Figs. 7B and 7C) in the ADI-sensitive HCT116 tumor cell line, relative to rhTRAIL alone, M.col.ADI alone, and the combination of rhTRAIL and M.col.ADI as separate polypeptides.

Figures 8A-8B show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptide with LI linker (see Table E3) on caspase 3/7 induction (Fig. 8A) and relative cell viability (Fig. 8B) in the ADI-sensitive Jurkat tumor cell line, relative to rhTRAIL alone, M.col.ADI alone and the combination of of rhTRAIL and M.col.ADI as separate polypeptides. Figures 9A-9D show the effects of the exemplary M.col.ADI-TRAIL fusion polypeptides from Table E3 on caspase 3/7 induction (Figs. 9A and 9B) and relative cell viability (Figs. 9C and 9D) in the ADI-resistant Colo 205 cancer cell line. Figures lOA-lOC show the effects of exemplary M.col.ADI-TRAIL fusion polypeptides from Table E3 on caspase 3/7 induction (Fig. 10A) and relative cell viability (Figs. lOB-lOC) in the ADI-sensitive HCT116 cell line. Figures 11A-11B show the effects of exemplary M.col.ADI-TRAIL fusion polypeptides from Table E3 on caspase 3/7 induction (Fig. 11A) and relative cell viability (Fig. 11B) in the ADI-sensitive Jurkat cell line.

Figures 9-11 show that exemplary M.col.ADI-TRAIL fusion polypeptides from Table El have similar activities in three different cell lines, both ADI-sensitive and resistant.

Table E5 below summarizes the IC50 values of exemplary ADI-TRAIL fusion polypeptides from Table E4 on caspase 3/7 induction and relative cell viability reduction in the ADI-resistant Colo 205 cell line and the ADI-sensitive HCT116 cell line. These data show that the exemplary ADI- TRAIL fusion polypeptides have similar activities.

Figures 12A-12C show the effects of exemplary M.col.ADI-TRAIL fusion polypeptides with point mutation(s) in M.col.ADI (K192C or K287C), including non-PEGylated versus PEGylated with 2K or 20K PEG, on caspase 3/7 induction (Fig. 12A) and relative cell viability (Figs. 12B-12C) in the ADI-resistant Colo 205 cell line. Figures 13A-13C show the effects of exemplary M.col.ADI-TRAIL fusion polypeptides with point mutation in M.col.ADI (K192C or K287C), including non-PEGylated versus PEGylated with 2K or 20K PEG, on caspase 3/7 induction (Fig. 13A) and relative cell viability (Figs. 13B-13C) in the ADI-sensitive HCT116 cell line. ADI enzymatic activity was similar in the PEGylated versus non-PEGylated constructs described above.

Figures 14A-14C show the effects of exemplary TRAIL-M.col.ADI versus M.col.ADI - TRAIL fusion polypeptides on caspase 3/7 induction (Fig. 14A) and relative cell viability (Figs. 14B- 14C) in the ADI-resistant Colo 205 cell line. Because this Colo 205 cell line is resistant to ADI activity, the observed caspase 3/7 activation and subsequent reductions in viability are due to the pro- apoptotic activity of the TRAIL moiety. As shown in the Figs. 14A-14C, TRAIL activity is somewhat improved (approximately 2-fold) in TRAIL-M.col.ADI fusion protein versus M.col.ADI -TRAIL fusion proteins.

Figures 15A-15C show the effects of exemplary TRAIL-M.col.ADI versus M.col.ADI - TRAIL fusion polypeptides on caspase 3/7 induction (Fig. 15A) and relative cell viability (Figs. 15B- 15C) in the ADI-sensitive HCT116 cell line. In this cell line, the two fusion proteins have the same potencies for inducing caspase mediated apoptosis. ADI and TRAIL are synergistic in the HCT116 cell line. From this and other experiments (data not shown), it appears that ADI can enhance TRAIL effect to a certain level and that the combined effect of ADI and TRAIL is not significantly affected by small changes in the potency of the TRAIL moiety. In other words, a stronger synergy of ADI with a less potent preparation of TRAIL has been observed, and the effect of the combination has a certain threshold which it reaches even with optimal or suboptimal preparations of TRAIL.

Figures 16A-16B display PK profiles of M.col.ADI-TRAIL over time in serum of CD-I mice after a single dose of 30 mg/kg administered intravenously. M.col.ADI-TRAIL protein level (Figs. 16A-16B), arginine and citrulline levels (Fig. 16A) as well as antibody titers against the fusion protein M.col.ADI-TRAIL, and its components M. col. ADI and rhTRAIL (Fig. 16B) were measured in serum of CD-I mice after a single injection of the fusion protein.

The fusion protein concentration in serum was assessed by ELISA (Figs. 16A-16B).

Biological activity of ADI and TRAIL moieties in the serum samples were also assessed and concentrations of biologically active protein were determined based on a standard spiked into naive sera. Concentration of biologically active protein (based on both ADI and TRAIL activities) was very similar to the total ADI-TRAIL protein determined by the ELISA method.

Figures 17A-17F demonstrate the efficacy of the M.col.ADI-TRAIL in HCT116 xenograft model. Female athymic Nude mice were inoculated with HCT116 cells subcutaneously. On day 7 post inoculation mice were randomized into the treatment groups (to have similar starting tumor volumes between the groups) and administered rhTRAIL, M. col. ADI, M.col.ADI-TRAIL fusion protein or vehicle control (PBS buffer) by intravenous injection. Treatment with rhTRAIL was performed daily for 5 consecutive days (days 7-11 post tumor implantation). M.col.ADI and M.col.ADI-TRAIL fusion proteins were injected on days 7 and 15 post tumor implantation. The fusion protein did not cause any noticeable weight loss (Fig. 17A) and was able to reduce tumor growth (Figs. 17B-17F). * p<0.05, ** p<0.01, *** p<0.001. The statistical significance of the tumor reduction in the fusion protein treated group as compared to the vehicle treated control group was assessed by the 2-way ANOVA.

Serum M.col.ADI-TRAIL inversely correlated with the tumor volume as shown in Figs. 18A- 18B. Concentrations of fusion protein measured by ELISA (total protein) and in a biological assay (active protein) by were similar to one another. Serum was taken on days 21 and 28 post tumor implantation. The serum total fusion protein detected correlated between the two time points.

Arginine and citrulline levels in these serums samples are shown in Fig. 18D. Serum citrulline levels were higher and arginine levels were lower in M.col.ADI group compared to M.col.ADI-TRAIL group. This is likely due to the fusion protein localization to the tumor site due to its TRAIL moiety thereby decreasing its serum levels. Reverse correlation between the tumor volume and serum M.col.ADI-TRAIL supports this hypothesis.

Figure 19 demonstrates dose-dependent tumor growth reduction in the HCT116 xenograft model after treatment with M.col.ADI-TRAIL. Female athymic Nude mice were inoculated with HCT116 cells subcutaneously. On day 9 post inoculation mice were randomized into the treatment groups (to have similar starting tumor volumes between the groups) and administered M.col.ADI- TRAIL fusion protein or vehicle control (PBS buffer) by intravenous injection. M.col.ADI-TRAIL dose groups were as follows: 90mg/kg, 30mg/kg, 10 mg/kg and 5 mg/kg. The first three groups were dosed only on day 9 and the 5 mg/kg group was dosed on day 9 and day 12 post tumor implantation.

2-way ANOVA analysis revealed statistical significance of tumor volume reduction after M.col.ADI-TRAIL treatment. P values for treatment group versus vehicle control were as follows:

Day 12 p<0.0001 for 10 mg/kg, 30 mg/kg and 90 mg/kg groups, p=0.0001 for 5 mg/kg group.

Day 14 p<0.0001 for all groups

Day 16 p<0.0001 for all groups

On Day 16 (day 7 post treatment initiation) there were also statistically significant differences between high and low dose groups:

• 90 mg/kg group versus 10 mg/kg group p=0.0477

• 90 mg/kg group versus 5 mg/kg group p=0.0014

• 30 mg/kg group versus 5 mg/kg group p=0.0247