AU2906101A - Method of producing and purifying angiostatin protein - Google Patents

Description

WO 01/40260 PCT/USOO/32843 5 METHOD OF PRODUCING AND PURIFYING ANGIOSTATIN@ PROTEIN FIELD OF THE PRESENT INVENTION 10 The present invention relates to a novel method of recombinantly producing, recovering and purifying Angiostatin@ protein (EntreMed Inc., Rockville, MD). BACKGROUND OF THE INVENTION 15 Angiostatin@ is a protein which is a potent inhibitor of developing blood vessels and tumor growth. Angiostatin@ is believed to play an important role in the inhibition of the development of blood vessels to new tumor metastases. Isolation and purification of proteins, such as Angiostatin@ 20 protein, in high yield from biological material, such as tissue extracts, cell extracts, broth from incubation systems, and culture medium is often frought with problems in view of the numerous proteins and other undesirable molecules present in an homogenate or extract. What is needed are recombinant methods of producing Angiostatin® protein that will provide the 25 large amounts of Angiostatin® protein required for clinical use, including, but not limited to, cancer therapy. Such methods should produce Angiostatin® protein in an efficient and convenient manner in a culture broth which is amenable to procedures designed to recover and purify Angiostatin@ protein in high yields. Separating a specific protein of interest from potential 30 contaminants presents a challenge in view of numerous factors, such as contamination of cellular homogenates with proteolytic enzymes that may digest the protein. Other undesirable cellular constituents that may be present in homogenates, include but not limited to, pigments, cytochromes, lipids, free WO 01/40260 PCT/USOO/32843 2 radicals, oxidases and other lysosomal enzymes, and oxides. Some of these substances may affect the protein of interest by stripping electrons, affecting disulfide bonds and changing the conformation of the protein. Centrifugation of cells, including yeast, bacteria, insect and 5 other cells used for recombinant production of proteins, such as Angiostatin@ protein, could possibly result in damage to the cells with concomitant release of undesirable biological material. What is needed is a method for recovery and purification of protein, such as Angiostatin@ protein, which does not employ centrifugation. 10 Methods for recombinant production, recovery and purification of Angiostatin@ protein on a large scale are required to produce and isolate the amounts of purified Angiostatin@ protein needed for administration to patients and also for research purposes. Also needed is a method for purifying recombinantly-produced 15 Angiostatin@ protein which avoids the need for centrifugation of the culture broth, thereby avoiding problems associated with cell lysis. This method should be capable of use on a large scale to recover and purify Angiostatin@ protein in quantities needed for clinical administration and research. What is also needed is a method for purifying recombinantly 20 produced Angiostatin@ protein which minimizes contamination with cytochromes, pigments, enzymes, and other undesirable cellular constituents. Also needed are solutions for storage of Angiostatin@ protein following the recovery and purification process which optimizes solubility properties of Angiostatin@ protein. 25 SUMMARY OF THE INVENTION The present invention solves these problems inherent in the recovery and purification of proteins, particularly Angiostatin@ protein, by providing new and useful methods for recombinant production, recovery and 30 purification of proteins, especially Angiostatin® protein. The present invention provides new and useful methods for recombinantly producing Angiostatin@ protein in large amounts. The present invention provides a method for recovery and purification of Angiostatin@ protein. The present WO 01/40260 PCT/US00/32843 3 invention also provides new and useful solutions for storage of Angiostatin@ protein. These methods provide the benefit of preserving the biological activity of Angiostatin® protein. Preservation of the biological activity of Angiostatin® protein is crucial for administration of Angiostatin@ protein to 5 humans and animals for the purpose of inhibition of undesirable angiogenesis, for other biological activities, and for research investigations or other types of biological testing. Angiostatin@ protein is effective in treating diseases or processes that are mediated by, or involve, angiogenesis. The angiogenesis 10 mediated diseases include, but are not limited to, solid tumors; blood born tumors such as solid tumors, blood borne tumors, leukemias; tumor metastases; benign tumors, for example hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas; rheumatoid arthritis; psoriasis; ocular angiogenic diseases, for example, diabetic retinopathy, 15 retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, colon cancer, retrolental fibroplasia, rubeosis; Osler Webber Syndrome; myocardial angiogenesis; plaque neovascularization; telangiectasia; hemophiliac joints; angiofibroma; and wound granulation. In one embodiment, the present invention provides new and 20 improved methods for recombinant production of biologically active Angiostatin@ protein in high yield. In another embodiment, the method of the present invention is useful for recovery and purification of recombinantly-produced Angiostatin@ protein. 25 In another embodiment, the method of the present invention is useful for recovery and purification of Angiostatin@ protein from extracts of biological fluids, cells and tissues. An advantage of the present invention is that higher amounts of biologically active Angiostatin® protein are recombinantly produced. 30 Another advantage of the present invention is that greater amounts of Angiostatin® protein are recovered than obtained with prior art methods. Yet another advantage of the present invention is that higher yields of more purified, and biologically active Angiostatin® protein are obtained. Still WO 01/40260 PCT/USO0/32843 4 another advantage of the present invention is that Angiostatin@ protein may be stored in buffers for extended periods of time, and also subjected to lyophilization, while preserving biological activity. An advantage of the present invention is that it permits Angiostatin@ protein to be stored in vials 5 or other containers, either in a solution which may be liquid or frozen, or lyophilized, and optionally shipped to a recipient. Accordingly, an object of the present invention is to provide a an improved method for recombinant production of large amounts of biologically active Angiostatin@ protein. 10 Another object of the present invention is to provide a method for recovery and purification of recombinantly produced proteins. Yet another object of the present invention is to provide a method for recovery and purification of Angiostatin@ protein. Another object of the present invention is to provide a method 15 for recovery and purification of Angiostatin@ protein, particularly recombinantly produced Angiostatin@ protein. An advantage of the purification methods of the present invention is that undesirable proteins, lipids and pigments are efficiently separated from the desired protein, especially Angiostatin@ protein. 20 It is another object of the present invention to provide solutions which provide favorable solubility conditions for Angiostatin@ protein, particularly recombinantly-produced Angiostatin® protein while retaining biological activity of Angiostatin® protein. 25 Another advantage of the methods of the present invention is that centrifugation of the broth from fermentation steps in recombinant production of Angiostatin@ protein is avoided, thereby preventing unwanted cellular lysis and potential contamination of Angiostatin@ protein with additional proteins, pigments, enzymes and other cellular chemicals and 30 debris. Another object of the present invention is to provide methods amenable to large scale production, recovery and purification of recombinantly-produced Angiostatin® protein.

WO 01/40260 PCT/USOO/32843 5 Another advantage of the present invention is that the recovered and purified Angiostatin@ protein is provided in a solution which optimizes solubility of Angiostatin@ protein, while preserving the bioactivity of Angiostatin® protein. 5 These and other objects, features and advantages of the present invention will become apparent after a review of the following detailed description. 10 BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 is a process overview diagram for the large scale processing of purified Angiostatin@ protein. Figure 2 is a process flow diagram for fermentation inoculum preparation for Angiostatin® production. 15 Figure 3 is a process flow diagram for fermentation and streamline SP chromatography for Angiostatin@ production. Figure 4 is a process flow diagram for chromatography steps following streamline SP chromatography for Angiostatin® production. Figure 5 is a process flow diagram for chromatography, 20 ultrafiltration, diafiltration and formulated bulk processing steps following Toyopearl chromatography for Angiostatin@ production. DETAILED DESCRIPTION 25 Angiostatin® is a protein which is a potent inhibitor of developing blood vessels and tumor growth. Angiostatin@ is believed to play an important role in the inhibition of the development of blood vessels to new tumor metastases. The following pages of this patent application describe new procedures and protocols for the large scale production of human 30 recombinant Angiostatin® from Pichia pastoris fermentation of clones with nucleic acid sequences encoding for Angiostatin® protein or variants thereof. This application also provides new procedures for the large scale production, purification, characterization and storage of human recombinant WO 01/40260 PCT/USOO/32843 6 Angiostatin@. It is to be understood that the methods of the present invention are not limited to human recombinant Angiostatin@, and that the present methods apply to Angiostatin@ from other species, as well as fragments and conservatively substituted forms thereof. 5 The method can serve as a large scale purification protocol for obtaining a Angiostatin@ formulations which may be used in clinical human trials. Definitions 10 Definitions for other terms used herein are as follows. The terms "a", "an" and "the" as used herein are defined to mean "one or more" and include the plural unless the context is inappropriate. As used herein, the terms "detecting" or "detection" refer to qualitatively or quantitatively determining the presence of a molecule under investigation. 15 "Proteins", "peptides", "polypeptides" and "oligopeptides" are chains of amino acids (typically L-amino acids) whose alpha carbons are linked through peptide bonds formed by a condensation reaction between the carboxyl group of the alpha carbon of one amino acid and the amino group of the alpha carbon of another amino acid. The terminal amino acid at one end 20 of the chain (i.e., the amino terminal) has a free amino group, while the terminal amino acid at the other end of the chain (i.e., the carboxy terminal) has a free carboxyl group. As such, the term "amino terminus" (abbreviated N-terminus) refers to the free alpha-amino group on the amino acid at the amino terminal of the peptide, or to the alpha-amino group (imino group when 25 participating in a peptide bond) of an amino acid at any other location within the peptide. Similarly, the term "carboxy terminus" (abbreviated C-terminus) refers to the free carboxyl group on the amino acid at the carboxy terminus of a peptide, or to the carboxyl group of an amino acid at any other location within the peptide. 30 Typically, the amino acids making up a peptide are numbered in order, starting at the amino terminal and increasing in the direction toward the carboxy terminal of the peptide. Thus, when one amino acid is said to WO 01/40260 PCT/US00/32843 7 "follow" another, that amino acid is positioned closer to the carboxy terminal of the peptide than the preceding amino acid. The term "residue" is used herein to refer to an amino acid (D or L) or an amino acid mimetic that is incorporated into a peptide by an amide 5 bond. As such, the amino acid may be a naturally occurring amino acid or, unless otherwise limited, may encompass known analogs of natural amino acids that function in a manner similar to the naturally occurring amino acids (i.e., amino acid mimetics). Moreover, an amide bond mimetic includes peptide backbone modifications well known to those skilled in the art. 10 The term "Angiostatin@ protein" refers to proteins that may be synthesized and may be isolated from biological tissues, cells, cell culture medium, and from broth and media obtained from cellular and cell-free expression systems. Accordingly, the term Angiostatin@ protein includes Angiostatin@ protein produced from recombinant expression systems. The 15 term Angiostatin@ protein also includes precursor forms of the Angiostatin® protein. The term Angiostatin@ protein also includes fragments of the protein, and modified proteins and peptides thereof that have a substantially similar amino acid sequence, and that are capable of inhibiting proliferation of proliferation of blood vessels. For example, silent substitutions of amino 20 acids, wherein the replacement of an amino acid with a structurally or chemically similar amino acid does not significantly alter the structure, conformation or activity of the protein, are well known in the art. Such silent substitutions are intended to fall within the scope of the present invention. The term Angiostatin® protein also includes various post-translational 25 modifications or other modifications of Angiostatin@ protein, including, but not limited to, phosphorylation, glycosylation, sulfation, and disulfide bond formation or reduction. It will be appreciated that the term Angiostatin® protein, as used herein, includes shortened proteins or peptide fragments of Angiostatin® 30 protein wherein one or more amino acids, preferably 1 to 10 amino acids, are removed from either or both ends of Angiostatin® protein, or from an internal region of the protein, yet the resulting molecule retains bioactivity such as inhibiting proliferation of blood vessels. The term Angiostatin® protein also WO 01/40260 PCT/USOO/32843 8 includes lengthened proteins or peptides wherein one or more amino acids, preferably 1 to 10 amino acids, is added to either or both ends of Angiostatin@ protein, or to an internal location in the Angiostatin@ protein, yet the resulting molecule retains the ability to inhibit proliferation of blood 5 vessels. Also included in the definition of the term Angiostatin@ protein are modifications of the Angiostatin@ protein, its subunits and peptide fragments. Such modifications include substitutions of naturally occurring amino acids at specific sites with other molecules, including but not limited to 10 naturally and non-naturally occurring amino acids. Such substitutions may modify the bioactivity of Angiostatin@ protein and produce biological or pharmacological agonists or antagonists. Such substitutions may include conservative substitutions known to one of skill in the art, such as valine for alanine. Acceptable substitutions may also include modifications of amino 15 acids, such as norleucine for leucine. It is to be understood that substitution of D amino acids for L amino acids is encompassed within the scope of the present invention. Some substitutions are described in Dictionary of Biochemistry and Molecular Biology, 2 "d ed., J. Stenesh, John Wiley & Sons, 1989, the entirety of which is incorporated herein by reference. Additional 20 modifications include addition of an amino acid, such as a tyrosine or another amino acid at specific locations in Angiostatin@ protein or fragments thereof to enhance labeling potential with radioactive and non-radioactive labels, addition of molecules such as ricin, addition of radioactive and/or non radioactive labels. 25 "Substantial sequence homology" means at least approximately 70% homology between the acid residue sequence in the Angiostatin@ protein analog sequence and that of Angiostatin@ protein, preferably at least approximately 80% homology, more preferably at least approximately 90% homology. 30 Furthermore, one of skill in the art will recognize that individual substitutions, deletions or additions in the amino acid sequence of Angiostatin® protein, or in the nucleotide sequence encoding for the amino acids in the Angiostatin® protein, which alter, add or delete a single amino WO 01/40260 PCTIUSOO/32843 9 acid or a small percentage of amino acids (typically less than 5%, more typically less than 1%) in an encoded sequence are conservatively modified variations, wherein the alterations result in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables 5 providing functionally similar amino acids are well known in the art. The following six groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 10 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). 15 Methods of Producing Angiostatin@ Protein Angiostatin@ protein can be isolated from biological sources, including tissues, cells and biological fluids. Angiostatin@ protein may be produced from recombinant sources, from genetically altered cells implanted into animals, from tumors, and from cell cultures, as well as other sources. 20 Angiostatin@ protein can be isolated from body fluids including, but not limited to, serum, urine and ascites, or synthesized by chemical or biological methods (e.g. cell culture, recombinant gene expression, cellular and cell free expression systems, peptide synthesis, and in vitro and in vivo enzymatic catalysis of precursor molecules to yield active Angiostatin@V protein). 25 Recombinant techniques include gene amplification from DNA sources using the polymerase chain reaction (PCR), and gene amplification from RNA sources using reverse transcriptase/PCR. Angiostatin@ protein can be made by automated protein synthesis methodologies well known to one skilled in the art. Alternatively, 30 Angiostatin@ protein may be isolated from larger known proteins. Angiostatin® protein can also be produced synthetically by chemical reaction or by recombinant techniques in conjunction with expression systems. It is contemplated as part of the present invention that Angiostatin® protein can be isolated from a body fluid such as blood or urine WO 01/40260 PCT/USOO/32843 10 of patients. Angiostatin@ protein can also be produced by recombinant DNA methods or synthetic peptide chemical methods that are well known to those of ordinary skill in the art. In a preferred embodiment of the present invention, Angiostatin@ protein is recombinantly produced. A preferred 5 method of recombinant production of Angiostatin@ protein is a method employing Pichia pastoris. Novel methods of isolation and purification of Angiostatin® protein, especially recombinantly-produced Angiostatin@b protein are provided in the present invention. It is to be understood that a variety of expression systems may 10 be used for recombinant production of Angiostatin@ protein. These expression systems include, but are not limited to Pichia pastoris, yeast, E. coli, insect cells, baculovirus expressions systems, expression in transgenic animals, expression in transgenic plants, mammalian systems, and other systems commonly known to one of ordinary skill in the art of expressing 15 proteins. Some of these expression systems are described in U.S. Patent No. 5,854,205. Although the Pichia pastoris expression system was used for most of the recombinant Angiostatin@ protein production presented in the present application, it is to be understood that the present invention encompasses other systems for recombinant production of Angiostatin@ protein. Accordingly, 20 modifications of the Angiostatin@ protein production parameters presented herein can be made by one of ordinary skill in the art of recombinant production of proteins using specific expression systems. For example, when yeast are used for recombinant production of Angiostatin® protein, different induction methods may be used, as commonly known to one of skill in the art. 25 Yeast can be induced on methanol, or a mixture of methanol and glycerol, all optionally diluted with water, at feed rates commonly known to one of ordinary skill in the use of yeast expression systems for recombinant production of molecules, including proteins. 30 Culture Conditions The following description of a preferred embodiment of the culture conditions for Angiostatin® protein is not limiting to the invention, and it is to be understood that the conditions, described here and in the WO 01/40260 PCT/US0O/32843 11 examples may be scaled up or down to accommodate higher or lower requirements for production of Angiostatin@ protein. These conditions may be scaled up to accommodate Angiostatin@ protein production by 5, 10, 20 or 100 fold. It is also to be understood that the various concentrations of 5 solutions and reagents described herein, including description contained in the Tables) are not limiting and may be increased or decreased in a range of 0 to 20%, preferably 0 to 10%, without altering the spirit and scope of the present invention. 10 Seed Culture Inoculum cultures are prepared using a two stage seed process of Pichia pastoris. The first stage employs an enriched media (about 800mL in a 2.8L flask) and is incubated at 250 rpm and about 30'C for approximately 24 hours to a final optical density at 600 nm (OD 600 nm,) of greater than 30. 15 The second stage uses a similar media base (16 x IL in 2.8L shaker flasks) and is incubated at about 250 rpm and 30'C for approximately 16 hours to a final OD 6 00 nm of between about 20.0 and 30.0. Main Fermentation 20 The fermentation media consists of Calcium Sulfate, Potassium Sulfate, Magnesium Sulfate, Potassium Hydroxide, Phosphoric Acid and Glycerol. Post sterilization addition of Trace Salts Solution is necessary. The fermentation consists of four main phases; batch glycerol, fed-batch glycerol, methanol ramp and methanol soak. 25 The batch glycerol phase is the beginning phase which utilizes the initial charge of Glycerol as the carbon source. This phase lasts for approximately 30 hours. The end of this phase is characterized by a sharp DO spike. The spike indicates the depletion of the carbon source. 30 The fed-batch glycerol phase is initiated at a set flow (16.1 g/Kg/hr) immediately following the batch glycerol phase. The fed-batch glycerol phase lasts for 6 hours. During the final two hours of the fed-batch phase, the pH is WO 01/40260 PCT/US00/32843 12 allowed to decrease from 5.0 to 4.0. The temperature is also decreased from 30 0 C to 26'C during the last two hours of the phase. The methanol ramp phase is initiated immediately following the fed-batch 5 glycerol phase. The methanol is used as a carbon source and as a product inducer. Angiostatin is produced as a secreted protein. During this phase, the methanol flowrate to the fermentor is ramped linearly from 1.5 to 4.5 mL/Kg/hr at a rate of 1.0 mL/Kg/hr 2 . 10 The final phase of the fermentation is the methanol induction phase. The methanol continues to be used as a carbon source and product inducer. During this phase the methanol is fed to the fermentor at a set rate of 4.5mL/Kg/hr for -83 hours. Harvest conditions are then set, after the conditions have been achieved the fermentation process is ready for harvest. 15 To minimize foaming, the methanol and pH loops are not shutoff until the temperature is below 20"C. Final Angiostatin concentration is approximately 500mg/L in the supernatant. The final WCW is approximately 300g/L. Many of the solutions and other conditions used in the 20 incubation are shown in the following tables. It is to be understood that these conditions are not limiting, and that they may be increased or decreased to accommodate scale up or scale down of the procedure to attain a desired production level of Angiostatin@ protein.

WO 01/40260 PCTIUS0O/32843 13 Process Data Sheets Fermentation Seed Culture 1 " Stage Media Biotin 0.4 mg/L Components/Concentra Glycerol 10 g/L tion: Yeast Nitrogen Base 13.4 g/L Peptone 20 g/L Yeast Extract 10 g/L Potassium Phosphate Monobasic 10.9 g/L Potassium Phosphate Dibasic 3.5 g/L Shake Volume: 800 mL Inoculum Size: 1.OmL Incubation Conditions: 250 rpm and 30 0 C Incubation End OD600nm 20 - 30 (approximately 24 hours) Conditions: 2 " Stage Media Biotin 0.4 mg/L Components/Concentra Glycerol 10 g/L tion: Yeast Nitrogen Base 13.4 g/L Potassium Phosphate Monobasic 10.9 g/L Potassium Phosphate Dibasic 3.5 g/L Shake Volume: 16 x IL Inoculum Size: Such that initial OD600nm = 0.85 0.15 Incubation Conditions: 250 rpm and 30"C Incubation End OD600nm 6.0 - 12.0 Conditions: (approximately 16 hours) Testing: Non-host Contamination WO 01/40260 PCT/USOO/32843 14 Fermen tation Pre Inoculum Specifications Media Calcium Sulfate, dehydrate 0.93 gIL Components/Concentra (CaSO 4 *2H 2 O) 18.2 gIL tion: Potassium Sulfate (KS0 4 ) 14.9 gIL Magnesium Sulfate (MgSO 4 *7H 2 0) 4.13 g/L Potassium Hydroxide (KOH) 26.7 mL/L Phosphoric Acid (H 3 P0 4 ) 40 mL/L Glycerol Density: 1.05 Kg/L Pre SIP Volume: 900L (945Kg) Post SIP Volume 927L (973Kg) (Calculations based on Post SIP Volume): Sterile Additions: PTM 4 Trace Salts 4.0 mL/L Antifoam: KFO 880 2L required Testing: Media Hold (sterility)

PTM

4 Solution Component and Cupric Sulfate (CuSO 4 *5H 2 0) 2 g/L concentration: Sodium Iodide (Nal) 0.08 g/L Manganese Sulfate (MnSO 4

*H

2 0) 3 g/L Sodium Molybdate (Na 2

MO

4 *2H 2 0) 0.2 g/L Boric Acid (H 3 0 3 ) 0.02 g/L Cobalt Chloride (CoC1 2 *6H 2 0) 0.5 g/L Zinc Chloride (ZnCl 2 ) 7 g/L Ferric Sulfate (FeSO 4 *7H20) 22 g/L d-Biotin 0.2 gL Sulfuric Acid (H 2 SO4) 1 mL/L WO 01/40260 PCT/USOO/32843 15 Batch Glycerol Phase and Fermentation Conditions Carbon Source: Initial Charge of Glycerol Temperature: 30 0 C pH: 5.0 Agitation: 250 rpm Aeration: 0.666 vvm (per Post SIP weight) = 650slpm DO: 30% (controlled by oxygen supplementation) Back-pressure: 3 psig In Process Testing: Wet Cell Weight, OD600nm, offline pH, and methanol concentration Fed-Batch Glycerol Phase Purpose: Expansion of cell density Start: Approximately fermentation hour 30 Flowrate: 16.6 g/Kg/hr (per Kg of Post SIP weight) Duration: 6 hours Glycerol Specifics: 50% Glycerol Solution (by weight) with KFO 880 Antifoam (0.2 mL/Kg) pH Shift Start: 4 ti hour of Fed Batch Glycerol pH Shift Specifics: Linear Decrease from 5.0 to 4.0 pH Shift Duration: 2 hours Temperature Shift 4"' hour of Fed Batch Glycerol Start: Temperature Shift Linear Decrease from 30'C to 26'C Specifics: Temperature Shift 2 hours Duration: WO 01/40260 PCT/US0O/32843 16 Methanol Adaptation Phase Purpose: Methanol as inducer and carbon source Start: Immediately following Fed-Batch Glycerol Phase Initial Flowrate: 1.5 mL/Kg/hr (per Kg of Post SIP weight) Final Flowrate: 4.5 mL/Kg/hr (per Kg of Post SIP weight) Ramp Rate: 1.0 rL/Kg/hr 2 (-3 hours) Methanol Induction Phase Start: Immediately following Methanol Ramp Phase Flowrate: 4.5 mL/Kg/hr (per Kg of Post SIP weight) Duration: 83 hours Soa spcifcs: Oxygen consumption -Unknown at this time slpml-iKg (per Kg of Soak specifics:SIP weight) Harvest Conditions and Specifics Temperature: I 0 0 C Agitation: 50 rpm (250 rpm until 20 0 C is reached) Aeration: 50 slpm (650 slpm until 20 0 C is reached) DO Control: OFF Back-pressure: 3 psig Specifics: pH loop ON until <20'C is met Methanol flowrate reduced to 2.1 mL/Kg/hr, turned off when 20'C met Angiostatin Concentration 0.5 mg/L in supernatant Final Weight ofe 1450Kg Final WCW of 300 gL QC Testing: Non-Host Contamination Method4for Isolation and Fur/fication ofAngiostatin Protein WO 01/40260 PCT/USOO/32843 17 The present invention also provides a new and useful method for recovery and purification of proteins, particularly recombinantly-produced proteins. The methods of the present invention may be used for recovery and purification of Angiostatin@ protein from biological sources, including but 5 not limited to biological fluids, tissues, cells, culture media, and fermentation media. In one embodiment, the present invention provides a new and useful method for recovery and purification of Angiostatin@ protein, and more particularly, recombinantly-produced Angiostatin@ protein. This method may be employed for large scale recovery and purification of recombinantly 10 produced Angiostatin® protein. It is to be understood that the present invention is useful for recovery and purification of Angiostatin@ protein from any expression system. The basic recovery process of Angiostatin® protein is accomplished using four chromatography steps and a final concentration and 15 diafiltration step. These steps are shown schematically in Figures 1 through 5. Figure 1 presents an overview of the process. Upon completion of fermentation, the broth, which consists of all components (cells, nutrients, and buffer) within the fermenter, is diluted with water to a conductivity that favors binding of the target protein to the 20 first column in the process. The first chromatography step in the recovery and purification procedure is called the Angiostatin® protein purification capture step, and the specific resin used is called Streamline-SP (Pharmacia, Inc.). SP refers to the sulfopropyl functional groups that are attached to the support bead that give 25 the resin its cationic character. It is to be understood that besides Streamline SP resin, other resins that act as cation exchangers may be used in the practice of the present invention. Such cation exchangers include but are not limited to carboxymethylcellulose. Streamline refers to a relatively new format of chromatography that is designed to capture and separate target protein from a 30 milieu of broth, thus eliminating the need for centrifugation to separate cells from the protein-containing supernatant. This type of chromatography is also known as expanded bed absorption chromatography (EBA). In practice, the broth is typically pumped up into a Streamline column containing about 20- WO 01/40260 PCT/USOO/32843 18 30% by volume of settled resin and approximately 70-80% buffer. As the broth enters the column, the bed of resin expends and flows up, thereby accounting for the name EBA. As the bed flows up, protein is bound to the beads, which can only flow up a finite distance, to an equilibrium level. The 5 cells and non-bound protein however, flow up and out of the column to waste. Once all the broth has been pumped onto and traversed the column, the flow direction is reversed (now in the downward direction) and the resin is allowed to pack. What remains is a functional column that can be washed and eluted in the more conventional sense. Angiostatin@ protein is eluted from this 10 column with salt, and is ready for the next chromatographic step. The next chromatographic steps in the process are the Q sepharose and hydroxyapatite chromatography columns. These steps are followed by the phenyl column as shown in the figures. The final step in the purification procedure involved 15 concentration and dialysis using the approach of Ultrafiltration/Diafiltration (UF/DF). In this step, the sample from the preceding step is pushed through a membrane, preferably made from polyethersulfone, with a molecular cutoff chosen to retain Angiostatin@ protein or another protein of interest on the membrane. A preferred molecular cutoff for Angiostatin@ protein is about 20 3kDa. Several liters of formulation buffer are run over the membrane to recover retain Angiostatin@ protein, or another protein of interest remaining in the filters. This material recovered from the filters is added to the pool of Angiostatin@ protein. In another embodiment of the present invention, parallel flow concentrators employing porous tubes may be used instead of 25 flat membranes for concentration and dialysis. The following paragraphs describe the chromatography steps in greater detail. Streamline SP Chromatography 30 The expanded bed column (60cm x 18cm (settled height), 51L of Streamline SP Resin, expanded bed volume ~ 150L, expanded bed height of -54cm at 300 cm/hr) is sanitized with 0.5M NaOH (held for a minimum of 6 hours). The column is rinsed with WPU until neutral conditions are met.

WO 01/40260 PCT/US00/32843 19 The column is equilibrated with 50mM Sodium Phosphate, 24mM Citric Acid, pH 5.1 until the pH and conductivity of the column are that of the buffer. The Angiostatin Fermentation is loaded onto the column while performing inline dilution with WPU to maintain a load conductivity of 9-12 5 mS/cm. The column is washed with 15% Glycerol, 15mM Sodium Phosphate, pH 6.1. The Angiostatin is eluted from the column using 30mM Sodium Phosphate, 200mM NaCl, pH 7.2. Collection begins when the conductivity rises sharply (to > 4 mS/cm) and the UV rises above 0.5 AU. Collection ends 10 when UV returns to 0.2 AU. The volume of the eluate should be approximately 2-3CV's at an Angiostatin concentration of 3.3 g/L of eluate. The column is regenerated using 7 column volumes (CV's) of 2M NaCl. The 2M NaCl Regeneration is followed with 6M Urea. After an initial Urea Wash, Urea is recirculated for a minimum of 1 hour. The Urea dissolves 15 the cell paste and eases removal of the cell paste from the column. The regeneration is followed with a WPU flush until the UV returns to baseline. The column is sanitized with 0.5M NaOH then stored in 0.iM NaOH. The 0.iM NaOH may be prepared inline by mixing 0.5M NaOH and WPU so that the inlet conductivity is 23 ± 5mS/cm. 20 Q Sepharose FF and Ceramic Hydroxyapatite Chromatography The Q-Sepharose column (30cm x 15cm column, 10.6L CV) and Ceramic Hydroxyapatite (CHT) column (45cm x 37cm column, 58.8L CV) which were stored in 0.1M NaOH are rinsed with 5 CV's of 10mM Sodium Phosphate, pH 7.0. The maximum flowrate for this chromatography is 25 480LPH (300 cm/hr of CHT Column) and is performed at ambient temperature. The angiostatin flows through the Q Sepharose column and binds to the CHT column. The columns are charged with 0.5M Sodium Phosphate, pH 7.0 then equilibrated with 10mM Sodium Phosphate, pH 7.0 until the pH and conductivity are that of the equilibration buffer. The elution 30 from the Streamline SP Chromatography of Angiostatin is diluted inline with WFI (1 part elution: 3 part WFI) and loaded onto the column. The column is washed to baseline with 10mM Sodium Phosphate, pH 7.0. The Q Sepharose column is removed from the chromatography skid.

WO 01/40260 PCT/USOO/32843 20 The angiostatin is eluted from the CHT column with a 5CV linear gradient from 10mM Sodium Phosphate, pH 7.0 to 74mM Sodium Phosphate, pH 7.0. The 74mM Sodium Phosphate, pH 7.0 is continued until the UV returns to < 0.5 AU. The product is collected from peak beginning at 0.15 AU 5 to peak ending at 0.3 AU. The volume of the elution should be approximately 6-8 CV's at an Angiostatin concentration of ~0.8g/L. The CHT column is regenerated with 0.5M Sodium Phosphate, pH 7.0. The Q Sepharose FF column is regenerated with 2M NaCl. The columns are then cleaned with 0.5M NaOH and held for at least 1 hour (maximum of 24 10 hours). The columns are then stored in 0.1M NaOH which is prepared by blending 0.5M NaOH and WFI. Toyopearl Phenyl 650M Chromatography The Toyopearl Phenyl 650M Column (45cm x 25cm column, 40L CV) which was stored in 0.1M NaOH is rinsed with WFI until neutral conditions 15 have been met. The flowrate for this chromatography is 480LPH (300cm/hr) and is performed at ambient temperature. The column is equilibrated with 50mM Sodium Phosphate, 24mM Citric Acid, 1.4M Ammonium Sulfate, pH 5.1 until the pH and conductivity are that of the equilibration buffer. The elution from the CHT column is diluted inline with 50mM 20 Sodium Phosphate, 24mM Citric Acid, 2.8M Ammonium Sulfate, pH 4.5 (1 part elution: 1 part buffer) and loaded onto the Toyopearl 650M column. The loaded column is then washed with 50mM Sodium Phosphate, 24mM Citric Acid, 1.4M Ammonium Sulfate, pH 5.1. The Angiostatin is eluted from the column using a 20CV linear gradient from 50mM Sodium Phosphate, 24mM 25 Citric Acid, 1.4M Ammonium Sulfate, pH 5.1 to 50mM Sodium Phosphate, 24mM Citric Acid, 0.92M Ammonium Sulfate, pH 5.1. The 50mM Sodium Phosphate, 24mM Citric Acid, 0.92M Ammonium Sulfate is continued until UV returns to < 0.1 AU. The eluate is collected from peak beginning at 0.3 AU to peak ending at 0.1 AU. The elution volume is approximately 8CV's at 30 an Angiostatin concentration of ~ 0.7g/L. The column is regenerated with 50mM Sodium Phosphate, 24mM Citric Acid, pH 5.1. The column is rinsed with WFI and then cleaned with 0.5M NaOH. The column is then stored in 0.1M NaOH which may be prepared by blending 0.5M NaOH inline with WO 01/40260 PCT/USOO/32843 21 WFI. Note: If the Toyopearl Phenyl Elution will not be processed within 8 hours, the elution is to be diluted 1x with WFI and stored at 2-8"C for a maximum of 48 hours. 5 The Ultrafiltration/Diafiltration steps are described in great3er detail in the following paragraphs. 100sq. feet of 5Kd polyethersulfone filters are sanitized with 0.5M NaOH and held in 0.5M NaOH for a minimum of 1 hour (maximum of 2 hours). The filters are then rinsed with WFI until neutral conditions are 10 obtained. The filters are then equilibrated with 0.15M Sodium Chloride until the retentate pH and conductivity is that of the equilibration buffer. The Toyopearl Elution (if not diluted) is diafiltered Ix with 0.15M Sodium Chloride. The Diafiltered product is concentrated to 5 mg/mL then diafiltered again until the pH and conductivity is that of the formulation buffer (-7 15 volumes). The UF/DF skid is rinsed with 2 x 1 OL flushes which are added to the diafiltered product. Due to the hold up volume of the UF/DF skid, it is necessary to perform the final concentration on a table top unit with 25sq. feet of filter. The retentate is then concentrated to 20.0 mg/mL. The UF/DF filters are rinsed with 0.15M Sodium Chloride and the rinse is added to the 20 concentrated product. The UF/DF retentate is adjusted with 0.15M Sodium Chloride to a final concentration of 15 mg/ml. Note: If the Toyopearl Elution was diluted the lx diafiltration may be omitted. Formulation The formulated pool is then aseptically filtered through a 0.2micron 25 filter. The filtered Angiostatin is bulk filled into sterile bottles and then stored at -70 0 C. This invention is further illustrated by the following 30 examples, which are not to be construed in any way as imposing limitations upon the scope thereof. These conditions for Angiostatin@ protein production and/or purification may be scaled up, for example, by 5, 10, 20 or 100 fold to accommodate the need for large scale Angiostatin@ protein production. On WO 01/40260 PCT/USO0/32843 22 the contrary, it is to be clearly understood that resort may be had to various other embodiments, modifications, and equivalents thereof, which, after reading the description herein, may suggest themselves to those skilled in the art without departing from the spirit of the present invention. 5 EXAMPLE 1 Sequence of Human Angiostatin@ Protein The following is an example of a functional human Angiostatin@ protein of the present invention. This is the Angiostatin@9 10 protein amino acid sequence encoded by the gene sequence listed below as SEQ ID NO:1. ANGIOSTATIN@ Production Clone ENMA98: Angiostatin@ gene and protein sequences. SEQ ID NO:l shows the amino acid sequence of the 15 Angiostatin® protein produced from the production clone ENMA98 which contains the nucleotide sequence shown in SEQ ID NO:2 hASv3 protein sequence (260 aa) SEQ ID NO: 1 VYLSECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSE 20 GLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILECEEECMHCSGEN YDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDR ELRPWCFTTDPNKRWELCDIPRCTTPPPSSGPTYQCLKGTGENYRGNV AVTVSGHTCQHWSAQTPHTHERTPENFPCKNLDENYCRNPDGKRAP WCHTTNSQVRWEYCKIPSCDSSPV 25 hASv3 DNA sequence (780 bp) SEQ ID NO:2 GTGTATCTCTCAGAGTGCAAGACTGGGAATGGAAAGAATTACAGA GGGACGATGTCCAAAACAAAAAATGGCATCACCTGTCAAAAATGG AGTTCCACTTCTCCCCACAGACCTAGATTCTCACCTGCTACACACC 30 CCTCAGAGGGACTGGAGGAGAACTACTGCAGGAATCCAGACAACG ATCCGCAGGGGCCCTGGTGCTATACTACTGATCCAGAAAAGAGAT ATGACTACTGCGACATTCTTGAGTGTGAAGAGGAATGTATGCATTG CAGTGGAGAAAACTATGACGGCAAAATTTCCAAGACCATGTCTGG ACTGGAATGCCAGGCCTGGGACTCTCAGAGCCCACACGCTCATGG 35 ATACATTCCTTCCAAATTTCCAAACAAGAACCTGAAGAAGAATTAC

TGTCGTAACCCCGATAGGGAGCTGCGGCCTTGGTGTTTCACCACCG

WO 01/40260 PCT/US00/32843 23 ACCCCAACAA(CGCTGGGAACTTTGTGACATCCCCCGCTGCACAA CACCTCCACCATCTTCTGGTCCCACCTACCAGTGTCTGAAGGGAAC AGGTGAAAACTATCGCGGGAATGTGGCTGTTACCGTGTCCGGGCA CACCTGTCAGCACTGGAGTGCACAGACCCCTCACACACATGAAAG 5 GACACCAGAAAACTTCCCCTGCAAAAATTTGGATGAAAACTACTG CCGCAATCCTGACGGAAAAAGGGCCCCATGGTGCCATACAACCAA CAGCCAAGTGCGGTGGGAGTACTGTAAGATACCGTCCTGTGACTC CTCCCCAGTA 10 There is only one amino acid change (Asn-->Glu) in the protein sequence comparing to the wild type plasminogen K1-3, and one codon change in the nucleotide sequence (AAC-->GAA) corresponding to Angiostatin@9 protein. 15 EXAMPLE 2 Details concerning Chromatography, Diafiltration/Ultrafiltration, Bulk 20 Formulation and Various Buffers used in the Procedure for Purification of ANGIOSTA TIN® Protein Streamline SP Chromatography Column Specifications Resin: Streamline SP Type: Expanded Bed Adsorption Particle Size: 200micron Dimensions: 60cm x 18cm, 51L Resin, expanded bed volume ~ 150L, expande bed height of-54cm at 848 LPH Pressure 2.0 bar Limitation: Expected Flowrate: 848 LPH (660 - 740 LPH for load and wash) WO 01/40260 PCT/US0O/32843 24 Sanitization and Rinse Buffer: 0.5M NaOH Approximate 7CV (357L) Volume Required: Flow Direction: Up Hold Time: Minimum of 6 hours (maximum of 24 hours) WPU Rinse: Until conductivity < 1.0 mS/cm Equilibration Buffer: 50mM Sodium Phosphate, 24mM Citric Acid, pH 5.1 Approximate 14CV (714L) Volume Required: Flow Direction: Up Equilibration Conductivity 5.5 - 6.5mS/cm Specifics: pH=5.1 ±0.2 Load Capacity: > unknown at this time mg/mL Load Conductivity: 9 - 12 mS/cm WFI Dilution: -3 volumes of WPU Flow Direction: Up Loading Time: -5.5 hours Volume of Load: -4500L Wash Buffer: 15% Glycerol, 15mM Sodium Phosphate, pH 6.1 Approximate 14CV (714L) Volume Required: Flow Direction: Up then down (12cv up / 2cv down) Wash Specifics: Conductivity < 1.5 mS/cm pH = 6.1 ±0.2 WO 01/40260 PCT/USOO/32843 25 Elution Type: Step Elution Buffer: 30mM Sodium Phosphate, 200mM NaCl, pH 7.2. Approximate 11CV (561L) Volume Required: Flow Direction: Down Elution Specifics: Collection begins UV > 0.5AU and Conductivity > 6 mS/cm Angiostatin Concentration 2.5 - 3.3 g/L Approximate 2-3 CV Eluate Volume: Product Storage Ambient (< 8 hours) 2-8'C (< 24 hours) Conditions: Product Testing: LAL and UV Regeneration #1 Buffer: 2M NaCl Approximate 7CV (357L) Volume Required: Flow Direction: Up Regeneration #2 and Rinse Buffer: 6M Urea Approximate 1 OCV Total (51 OL) Volume Required: Flow Direction: Up for 8CV (408L). Recirculate down with 2CV (1OOL) for 60 minutes. WPU Rinse: Until UV return to baseline Cleaning Buffer: 0.5M NaOH Approximate 7CV (357L) Volume Required: WO 01/40260 PCT/USOO/32843 26 Flow Direction: Up Hold Time: Minimum 1 hour (maximum of 24 hours) Storage Buffer: 0.1M NaOH (inline dilution 0.5M NaOH / WPU) Approximate 7CV (357L total, 71L 0.5M NaOH) Volume Required: Flow Direction: Down WO 01/40260 PCT/USOO/32843 27 Purfication General Purification Storage Storage >8 hours at 2-8 0 C Conditions: No stability data has been generated. Therefore, storage time shoul be limited to less than 24 hours. Final product storage is -70"C, Extinction 2.08 Coefficient: Shear Sensitivity: Not Determined Concentration Not Determined Limit: In process Testing LAL, UV, PD and QC retains Q-Sepharose and Ceramic Hydroxyapatite Chromatography Column Specifications Resin: Q Sepharose FF (Pharmacia) Type: Ion Exchange (Flowthrough) Particle Size: 90micron Dimensions: 30 cm D x 15 cm H 10.6L CV Pressure 3.0 bar Limitation: Expected Flowrate: 480 LPH Resin: Ceramic Hydroxyapatite (Biorad) Type: Mixed Mode Particle Size: 40micron Dimensions: 45 cm D x 37 cm H 58L CV Pressure 2.5 bar Limitation: Expected Flowrate: 480 LPH Rinse Buffer: 10mM Sodium Phosphate, pH 7.0 WO 01/40260 PCTUSOO/32843 28 Specifics: Rinse until conductivity < 3.0 mS/cm Charge Buffer: 0.5M Sodium Phosphate, pH 7.0 Approximate 3CV (175L) Volume Required: Flow Direction: Up Equilibration Buffer: 10mM Sodium Phosphate, pH 7.0 Approximate 5 - 7CV (292 - 408L) Volume Required: Flow Direction: Up Equilibration pH = 7.0 ± 0.1 Specifics: Conductivity = 1.0 - 1.6 mS/cm Load Capacity: 6 - 13 mg/mL Conductivity: 4 - 6 mS/cm WFI Dilution: 3 Volumes Inline Flow Direction: Up Loading Time: 1.5 hr Volume of Load: 600L (4x Streamline Elution) Wash Buffer: 10mM Sodium Phosphate, pH 7.0 Approximate 3CV (175L) Volume Required: Flow Direction: Up Wash Specifics: pH = 7.0 ± 0.2 WO 01/40260 PCTIUS0O/32843 29 Elution (from CHT) Type: Linear Gradient 0 to 100% (A to B) Buffer A: 10mM Sodium Phosphate, pH 7.0 Buffer B: 74mM Sodium Phosphate, pH 7.0 Approximate 5CV (239L) Hold in B for 5CV (239L) Volume Required: Flow Direction: Up Product Collection: Start @ 0.15 AU pre Peak and end @ 0.3 AU post Peak Elution Specifics: pH = 7.0 ± 0.2 Volume ~ 4-5 CV Angiostatin concentration ~ 0.8 mg/mL Regeneration of CHT Column Buffer: 0.5M Sodium Phosphate, pH 7.0 Approximate 3CV (143L) Volume Required: Flow Direction: Down Regeneration of Q Sepharose Column Buffer: 2M NaCI Approximate 3CV (32L) Volume Required: Flow Direction: Down Cleaning (both columns) Buffer: 0.5M NaOH Approximate 5CV (292L) Volume Required: Flow Direction: Down Hold Time: Minimum 1 hour (Maximum of 24 hours) WO 01/40260 PCTIUS0O/32843 30 Storage Buffer: 0.1M NaOH Approximate 3CV (175L) Volume Required: Flow Direction: Down WO 01/40260 PCT/USOO/32843 31 Toyopearl Phenyl 650M Chromatography Toyopearl Phenyl 650M Column Specifications Resin: Toyopearl Phenyl 650M (TosoHaas) Type: Hydrophobic Interaction Particle Size: 65micron Dimensions: 45 cm D x 25 cm H 40L CV Pressure 2.5 bar Limitation: Expected 480 LPH Flowrate: Rinse WFI Rinse: Until conductivity < 1.0 mS/cm Rinse Specifics: Perform a 3CV gradient from 0.1M NaGH to WFI then continue rinsing Flow Direction: Up Equilibration Buffer: 50mM Sodium Phosphate, 24mM Citric Acid, 1.4M Ammonium Sulfate, pH 5.1 Transition Perform a 3CV gradient from WFJ to EQ buffer the continue with Specific: equilibration Approximate 4.5CV (I80L) Volume Required: Flow Direction: Up Equilibration Conductivity 154 - 171 mS/cm Specifics: Density = 1.10 Kg/L WO 01/40260 PCT/USOO/32843 32 Load Capacity: > 12 mg/mL Conductivity: 154 - 171 mS/cm Buffer Dilution: 1x (50mM Sodium Phosphate, 24mM Citric Acid, 2.8M Ammonium Sulfate, pH 4.6) Volume Buffer - 350L Required: Flow Direction: Up Loading Time: 1.25 hr Volume of Load: ~ 700L Wash Buffer: 50mM Sodium Phosphate, 24mM Citric Acid, 1.AM Ammonium Sulfate, pH 5.1 Approximate IOCV (400L) Volume Required: Flow Direction: Up Wash Specifics: Conductivity = 154 - 171 mS/cm pH = 5.1 ± 0.2 Elution Type: Linear Gradient from 0 to 100% (A to B), Hold in B for 5CV Buffer A: 50mM Sodium Phosphate, 24mM Citric Acid, I.4M Anmonium Sulfate, pH 5.1 Buffer B: 50mM Sodium Phosphate, 24mM Citric Acid, 0.92M Ammonium Sulfate, pH 5.1 Approximate 20CV (800L) Hold for 5CV(200L) B Volume Required: Flow Direction: Up Product Start @ 0.3 AU pre Peak and end @ 0.1 AU post Peak Collection: Elution Eluate Volume -8 CV's Specifics: Angiostatin Concentration - 0.6 g/L WO 01/40260 PCT/USOO/32843 33 Regeneration Buffer: 50mM Sodium Phosphate, 24mM Citric Acid, pH 5.1 Approximate 3CV (120L) Volume Required: Flow Direction: Down WFI Rinse: ~ 3CV Cleaning Buffer: 0.5M NaOH Approximate 4CV (1 60L) Volume Required: Flow Direction: Down Hold Time: Minimum 1 hour (Maximum of 24 hours) Storage Buffer: 0.1M NaOH Approximate 5CV (200 L) Volume Required: Flow Direction: Down UF/DF Filter Specifications Skid: UF Skid (25 - 45 LPM flowratc) and Table Top Unit (5 - 10 LPM) Membrane: 5Kd Polyethersulfone Membrane area: 100 sq. ft. (Skid) 25 sq. ft. (Table Top) Recirculation rate: 25 - 45 L/min (Skid) 5- 10 L/min (Table Top) Expected Flux rate: ~ 10 L/min (Skid) ~ I L/min (Table Top) Feed Pressure 10 - 25 psi (Skid) 5 - 10 psi (Table Top) Range: TMP Range: 10 - 20 psi (Skid) 5 - 10 psi (Table Top) WO 01/40260 PCT/USOO/32843 34 Equilibration Buffer: 0.15M Sodium Chloride Approximate 500L Volume Required: Equilibration Conductivity ~ 12 -14 mS/cm @ 18-22"C Specifics: Initial Diafiltration Buffer: 0.15M Sodium Chloride Approximate I1DV (400L) Volume Required: Initial Concentration Starting 0.6 g/L Concentration: Approximate 330 L Starting Volume: Intermediate 5 g/L Concentration: Approximate Final 30L Volume: Approximate 8 Concentration Factor: Final Diafiltration Buffer: 0.15M Sodium Chloride Diafiltration Until pH and conductivity are that of the 0.15M Sodium Chloride Specifics Approximate 7DV (280L) Volume Required: Rinse of UF/DF Skid Buffer: 0.1 5M Sodium Chloride Approximate 2 x 1OL Flushes Volume Required: Washout Specifics: Add both flushes to product tank WO 01/40260 PCT/USOO/32843 35 tank Final Concentration (Performed on Table Top Unit) Starting 3 g/L Concentration: Approximate 45 L Starting Volume: Intermediate 20 g/L Concentration: Approximate Final 10 L Volume: Approximate 4 Concentration Factor: Rinse of Table Top Unit Buffer: 0.15M Sodium Chloride Approximate 3L Volume Required: Washout specifics: Transfer all of rinse to the concentrated product Dilution (May not be required) Initial 15.4 mg/mL Concentration: Approximate Initial 13 L Volume: Final 15.0 mg/mL Concentration: Approximate Final 13.3 L Volume: Buffer: 0.15M Sodium Chloride Approximate 0.3 L Volume Required: WO 01/40260 PCT/USOO/32843 36 Angiostatin Formulated Bulk Bulk Filling Specifics Bottle Type: PETG Size: IL Fill per bottle: 800mL Total # of bottles: 25 Release Testing Quality - Appearance Clear, colorless'to slightly pink Quality - Osmolality Report Purity - Size Exclusion Report HPLC Strength - UV 10 - 20 mg/mL (based on I mg/mL = 2.08 AU @ 280nm) Absorbance Identity - SDS-Page Corresponds to reference (non-reduced) Safety - DNA Threshold Report Safety - LAL 0.50 EU/mg Safety - Bioburden 10 CFU/mL WO 01/40260 PCT/USOO/32843 37 Buffer Preparation General Buffer Preparation Specifics: Buffers made by volume 21 day expiration on all buffers (based on safety) In Process Testing: pH and Conductivity (measured @ 18-22'C) Density for Streamline Wash Buffer and Phenyl Buffers QC Testing: LAL and Bioburden 50mM Sodium Phosphate, 24mM Citric Acid, pH 5.1 Unit Op Streamline Equilibration and Toyopearl 650M Regeneration Description: Component and Sodium Phosphate, Dibasic 13.4 g/L Concentration: Citric Acid, Monohydrate 5.04 g/L pH Adjustment NaOH or HCl TBD Conductivity: 5 - 7 mS/cm pH: 4.9-5.3 Density: 1.00 Kg/L 30mM Sodium Phosphate, 200mM NaCl, pH 7.2 Unit Op Streamline Elution Description: Component and Sodium Phosphate, Dibasic 6.40 g/L Concentration: Sodium Phosphate, Monobasic 0.846 g/L Sodium Chloride 11.69 g/L pH Adjustment NaOH or HCl TBD Conductivity: 19-23mS/cm pH: 7.0 - 7.4 Density: 1.00 Kg/L WO 01/40260 PCT/USOO/32843 38 15% Glycerol, 15mM Sodium Phosphate, pH 6.1 Unit Op Streamline Wash Description: Component and Glycerol 189 g/L (15% v/v) Concentration: Sodium Phosphate, Dibasic 0.7 g/L Sodium Phosphate, Monobasic 2.08 g/L pH Adjustment NaOH or HCl TBD Conductivity: < 1.5 mS/cm pH: 5.9-6.3 Density: -1.04 Kg/L 10mM Sodium Phosphate, pH 7.0 Unit Op Q Sepharose and CHT Equilibration/Wash/Elution Description: Component and Sodium Phosphate, Dibasic 1.63 g/L Concentration: Sodium Phosphate, Monobasic 0.54 g/L pH Adjustment NaOH or HCI TBD Conductivity: 1.0 - 1.6 mS/cm pH: 6.9-7.1 Density: 1.00 Kg/L 74mM Sodium Phosphate, pH 7.0 Unit Op Q Sepharose and CHT Elution Description: Component and Sodium Phosphate, Dibasic 12.1 g/L Concentration: Sodium Phosphate, Monobasic 3.98 g/L pH Adjustment NaOH or HCl TBD Conductivity: 6.0 - 7.2 mS/cm pH: 6.9-7.1 Density: 1.00 Kg/L WO 01/40260 PCT/USOO/32843 39 0.5M Sodium Phosphate, pH 7.0 Unit Op Q Sepharose and CHT Regeneration Description: Component and Sodium Phosphate, Dibasic 81.8 g/L Concentration: Sodium Phosphate, Monobasic 26.9 g/L pH Adjustment NaOH or Phosphoric Acid TBD Conductivity: 35 - 41 mS/cm @ 18-20 0 C pH: 6.9-7.1 Density: 1.00 Kg/L 50mM Sodium Phosphate, 24mM Citric Acid, 1.4M Ammonium Sulfate, pH 5.1 Unit Op Toyopearl 650M Equilibration/Wash/Elution Description: Component and Sodium Phosphate, Dibasic 13.4 gIL Citric Acid 5.04 gIL Concentration: Ammonium Sulfate 185.0 g/L pH Adjustment: NaOH or HCJ Conductivity: 206 - 228 mS/cm pH: 4.9 - 5.3 Density: 1.092 - 1.112 Kg/L 50mM Sodium Phosphate, 24mM Citric Acid, 0.92M Ammonium Sulfate, pH 5.1 Unit Op Toyopearl 650M Elution Description: Component and Sodium Phosphate, Dibasic 13.4 g/L Concentration: Citric Acid, Monohydrate 5.04 g/L Ammonium Sulfate 121.6 g/L pH Adjustment: NaOH or HCl TBD Conductivity: 156 - 173 mS/cm pH: 4.9 - 5.3 Density: 1.068 - 1.084 g/L WO 01/40260 PCT/US00/32843 40 50mM Sodium Phosphate, 24mM Citric Acid, 2.8M Ammonium Sulfate, pH 4.5 Unit Op Toyopearl 650M Load Dilution Description: Component and Sodium Phosphate, Dibasic 13.4 g/L Citric Acid, Monohydrate 5.04 g/L Concentration: Ammonium Sulfate 370 g/L pH Adjustment: NaOH or HCl TBD Conductivity: 359 - 357 mS/cm pH: 4.3 - 4.7 Density: 1.167 - 1.204 Kg/L Formulation Buffer (0.15M NaCl) Unit Op Description: UF/DF Diafiltration Buffer Component and Sodium Chloride 8.76 g/L Concentration: Conductivity: 12 - 14 mS/cm Density: 1.00 Kg/L Example 3 Biochemical characterization verified the identity of the purified protein as human ANGIOSTATIN@ and indicated that the protein was over 5 95% pure. The initial step in purification, hydrophobic interaction chromatography (HIC), removed the majority of pigments and extraneous proteins; yielding 80-90% pure ANGIOSTATIN@. A number of resins and buffer systems were examined for ANGIOSTATIN@ binding capacity and specificity. The binding capacity of ANGIOSTATIN@ protein to Toyopearl 10 Phenyl 650m (TosoHaas) was 20-30% higher than the binding capacity of Phenyl Sepharose high sub (Pharmacia) in PBS containing 3.0 M NaCI [pH 7.4]. At pH 7.4, a buffer system utilizing sodium chloride dramatically increased the binding specificity of Phenyl 650m for ANGIOSTATIN@ versus an Ammonium Sulfate buffer system. 15 WO 01/40260 PCT/USOO/32843 41 Example 4 ANGIOSTA TIN® Purity and Identification of Glycosylation Site Purification of ANGIOSTATIN@ protein results in one major species as well as a number of minor species which can be separated by reverse phase 5 chromatography and SDS-PAGE. Western blot analysis using a polyclonal primary antibody indicated that all minor species were related to the major intact AngiostatinTM protein. Electrospray ionization mass spectrometry of the reduced protein detected two major components whose deconvoluted spectra indicated masses of 29788 Da and 29951 Da., consistent with an intact 10 AngiostatinTM molecule and an intact molecule with a single hexose sugar (+ 163 Da), respectively. Digestion of the molecule with lysyl endopeptidase followed by LC-MS indicated this modification is localized to Kringle domain 1 (residues 30-74). Analysis of a trypsin subdigest of this peptide by LC/MS/MS demonstrated that this sugar is linked to Serine 31. This was 15 confirmed by N-terminal sequencing. The peptide map and N-terminal sequencing were also useful in identifying an additional glycosylation site and minor cleavage products of the AngiostatinTM molecule. All patents, publications and abstracts cited above are 20 incorporated herein by reference in their entirety. The invention has been described in detail with particular reference to certain embodiments, but variations and modifications can be made without departing from the spirit and the scope of the present invention. 25

Claims (6)

1. A method for purifying recombinantly produced angiostatin 5 comprising: applying crude fermentation broth containing the recombinantly produced angiostatin to an expanded bed cation exchange column; collecting eluate from the expanded bed cation exchange 10 column and applying the eluate from the expanded bed cation exchange column to an anion exchange column; collecting eluate from the anion exchange column and applying the eluate from the anion exchange column to a hydroxyapatite column; collecting eluate from the hydroxyapatite column and applying the eluate from 15 the hydroxyapatite column to a hydrophobic column; collecting eluate from the hydrophobic column and applying the eluate from the hydrophobic column to a membrane; and collecting fluid passing through the membrane. 20

2. The method of Claim 1 further comprising: concentrating the fluid; diafiltering the fluid; concentrating the diafiltered fluid; and 25 passing the concentrated and diafiltered fluid through a second membrane.

3. The method of Claim 2, further comprising: collecting fluid passing through the second membrane; WO 01/40260 PCT/USOO/32843 43 concentrating the fluid passing through the second membrane; and aseptically filtering the concentrated fluid. 5

4. The method of Claim 1, wherein the recombinantly produced angiostatin is human angiostatin.

5. The method of Claim 4, wherein the recombinantly produced human angiostatin is produced from fermentation of Pichia pastoris. 10

6. The method of Claim 1, wherein the crude fermentation broth containing the recombinantly produced angiostatin is applied to the expanded bed cation exchange column in an upward direction, followed by application of elution buffer and elution of the column in a downward direction. 15 20