(19) TZZ¥Z¥_T (11) EP 3 095 793 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 23.11.2016 Bulletin 2016/47 C07K 16/06 (2006.01) (21) Application number: 16164203.8 (22) Date of filing: 24.06.2004 (84) Designated Contracting States: • McDONALD, Paul J. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR San Francisco, CA 94133 (US) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • O’LEARY, Rhona M. Designated Extension States: San Francisco, CA 94127 (US) AL HR LT LV MK (74) Representative: Kiddle, Simon John et al (30) Priority: 28.07.2003 US 490500 P Mewburn Ellis LLP City Tower (62) Document number(s) of the earlier application(s) in 40 Basinghall Street accordance with Art. 76 EPC: London EC2V 5DE (GB) 04777121.7 / 1 648 940 Remarks: (71) Applicant: GENENTECH, INC. •This application was filed on 07-04-2016 as a South San Francisco, CA 94080-4990 (US) divisional application to the application mentioned under INID code 62. (72) Inventors: •Claims filed after the date of filing of the application • FAHRNER, Robert L. / after the date of receipt of the divisional application San Mateo, CA 94403 (US) (Rule 68(4) EPC). • LAVERDIERE, Amy San Francisco, CA 94107 (US) (54) REDUCING PROTEIN A LEACHING DURING PROTEIN A AFFINITY CHROMATOGRAPHY (57) A method for reducing leaching of protein A during protein A affinity chromatography is described which involves reducing temperature of pH of, or by adding one or more protease inhibitors to, a composition that is subject to protein A affinity chromatography. EP 3 095 793 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 095 793 A1 Description [0001] This is a non-provisional application claiming priority under 35 USC §19 to provisional aplication number 60/490, 500 filed July 28, 2003, the entire disclosure of which is hereby incorporated by reference. 5 BACKGROUND OF THE INTENTION Field of the Invention 10 [0002] The present invention concerns protein purification. In particular, the invention concerns a method for reducing leaching of protein A during protein A affinity chromatography by reducing temperature or pH of, or by adding one or more protease inhibitors to, a composition that is subjected to protein A affinity chromatography. Description of Related Art 15 [0003] The large-scale, economic purification of proteins is increasingly an important problem for the biotechnology industry. Generally, proteins are produced by cell culture, using either mammalian or bacterial cell lines engineered to produce the protein of interest by insertion of a recombinant plasmid containing the gene for that protein. Since the cell lines used are living organisms, they must be fed with a complex growth medium, containing sugars, amino acids, and 20 growth factors, usually supplied from preparations of animal serum. Separation of the desired protein from the mixture of compounds fed to the cells and from the by-products of the cells themselves to a purity sufficient for use as a human therapeutic poses a formidable challenge. [0004] Procedures for purification of proteins from cell debris initially depend on the site of expression of the protein. Some proteins can be caused to be secreted directly from the cell into the surrounding growth media; others are made 25 intracellularly. For the latter proteins, the first step of a purification process involves lysis of the cell, which can be don e by a variety of methods, including mechanical shear, osmotic shock, or enzymatic treatments. Such disruption releases the entire contents of the cell into the homogenate, and in addition produces subcellular fragments that are difficult to remove due to their small size. These are generally removed by differential centrifugation or by filtration. The same problem arises, although on a smaller scale, with directly secreted proteins due to the natural death of cells and release 30 of intracellular host cell proteins in the course of the protein production run. [0005] Once a clarified solution containing the protein of interest has been obtained, its separation from the other proteins produced by the cell is usually attempted using a combination of different chromatography techniques. These techniques separate mixtures of proteins on the basis of their charge, degree of hydrophobicity, or size. Several different chromatography resins are available for each of these techniques, allowing accurate tailoring of the purification scheme 35 to the particular protein involved. The essence of each of these separation methods is that proteins can be caused either to move at different rates down a long column, achieving a physical separation that increases as they pass further down the column, or to adhere selectively to the separation medium, being then differentially eluted by different solvents. In some cases, the desired protein is separated from impurities when the impurities specifically adhere to the column, and the protein of interest does not, that is, the protein of interest is present in the "flow-thraugh." 40 [0006] Affinity chromatography, which exploits a specific interaction between the protein to be purified and an immo- bilized capture agent, may also be an option for some proteins. Protein A is a useful adsorbent for affinity chromatography of proteins, such as antibodies, which contain an Fc region. Protein A is a 41 kD cell wall protein from Staphylococcus aureas which binds with a high affinity (about 10 -8M to human IgG) to the Fc region of antibodies. [0007] US Patent Nos. 6,127,526 and 6,333,398 (Blank, G.) describe an intermediate wash step during protein A 45 affinity chromatography using hydrophobic electrolytes, e.g., tetramethylammonium chloride (TMAC) and tetraethylam- monium chloride (TEAC), to remove the impurities, but not the immobilized protein A or the protein of interest, bound to the protein A column. SUMMARY OF THE INVENTION 50 [0008] The present invention concerns a method of purifying a protein which comprises a C H2/CH3 region, comprising reducing the temperature of a composition comprising the protein and one or more impurities subjected to protein A affinity chromatography in the range from about 3°C to about 20°C, wherein protein A leaching is reduced. [0009] Preferably the protein is an antibody, e.g. one which binds an antigen selected from the group consisting of 55 HER2, vascular endothelial growth factor (VEGF), IgE, CD20, CD40, CD11a, tissue factor (TF), prostate stem cell antigen (PSCA), interleukin-8 (IL-8), epidermal growth factor receptor (EGFR), HER3, HER4, α4β7 or α5β3. In another embod- iment, the protein is an immunoadhesin, such as a TNF receptor immunoadhesin. [0010] The invention also concerns a method of purifying a protein which comprises a CH2/CH3 region by protein A 2 EP 3 095 793 A1 affinity chromatography comprising: (a) subjecting the protein to protein A affinity chromatography and measuring leached protein A in a composition comprising the protein which is recovered from the protein A affinity chromatography; 5 (b) if protein A leaching is detected in step (a), reducing the temperature of a composition comprising the protein and one or more impurities subjected to protein A affinity chromatography in the range from about 3°C to about 20°C, such that protein A leaching is reduced. [0011] The invention further provides a method for reducing leaching of protein A during protein A affinity chromatog- 10 raphy comprising reducing protease activity in a composition subjected to protein A affinity chromatography, wherein the composition comprises a protein which comprises a CH2/CH3 region and one or more proteases. Brief description of the Drawings 15 [0012] Figure 1 depicts protein A leaching as a function of temperature for various antibody products on PROSEP A™. Leached protein A is shown in ng/mg (ng protein A per mg antibody). Temperature on the x-axis refers to the temperature of the water bath. The column was equilibrated and washed with 25 mM Tris, 25mM NaCl, 5mM EDTA, 20 pH 7.1, washed with 25 mM Tris, 25 mM NaCl, 0.5 M TMAC, 5 mM EDTA pH 5.0 or 7.1, eluted with either 25 mM citrate pH 2.8, or 0.1 M acetic acid pH 2.9, regenerated with 0.1 M phosphoric acid, and stored in 0.2 M sodium acetate, 2 % benzyl alcohol pH 5.0. Trastuzumab was run on a bed height of 20 cm, loaded to 20 g Trastuzumab/ L resin, washed with TMAC pH 5.0, eluted with 25 mM citrate pH 2.8, and pooled from 0.1 AU to 2 CV’s. Humanized 2C4 was run on a 20 cm bed height column, loaded to 15 g humanized 2C4 per liter resin, washed with TMAC pH 25 7.1, eluted with 25 mM citrate pH 2.8, and pooled from 0.1 AU to 2 CV’s pool volume. Humanized VEGF antibody was run on 14cm bed height, loaded to 20 g humanized VEGF antibody per liter of resin, washed with TMAC pH 5.0, eluted with 0.1 M acetic acid pH 2.9, and pooled from 0.2 AU to 2 CV’s pool volume. Humanized CD11 a antibody was run on a 14 cm bed height, loaded to 20 g humanized CD11 a antibody per liter of resin, washed with TMAC pH 7.1, eluted with 0.1M acetic acid pH2.9, and pooled from 0.2 AU to 2CV’s. 30 Figure 2 depicts a comparison of temperature dependent protein A leaching from PROSEP A™ and PROSEP vA™ with Trastuzumab, humanized 2C4, and humanized CD11a antibody. Leached protein A is shown in ng/mg (ng protein A per mg antibody). Temperature on the x-axis refers to the temperature of the water bath.