# Patent

## Title
Analytical method for fab and fab′ molecules

## Abstract

A method of measuring acidic species generated by degradation of a Fab or Fab′ component of a Fab-PEG or a Fab′-PEG is provided. The method involves: a) cleaving PEG and a linker from the Fab-PEG or Fab′-PEG with an enzyme; b) optionally separating the PEG and linker from the Fab or Fab′ to provide isolated Fab or Fab′; and c) quantitatively analyzing acidic species associated with the cleaved Fab or Fab′ and/or the cleaved PEG.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 13/812,692, filed Apr. 3, 2013, now U.S. Pat. No. 8,722,353, which is the U.S. national stage application of International Patent Application No. PCT/GB2011/001135, filed Jul. 28, 2011.
The Sequence Listing for this application is labeled “Seq-List-replace.txt” which was created on Apr. 30, 2015 and is 8 KB. The entire contents of the sequence listing is incorporated herein by reference in its entirety.


The present invention relates to an improved assay method for measuring acidic species in PEGylated proteins. In particular, the present invention relates to an improved assay method for measuring acidic species for PEGylated Fab and PEGylated Fab′ antibody formats.
PEGylated Fab and PEGylated Fab′ antibody formats are useful in that they provide a circulating half-life in vivo similar to that of a whole antibody without the effector functions associated with a whole antibody. These formats have become useful in therapy and long term stability testing is required to support the regulatory approval process which licenses the sale of these therapeutic products. Furthermore, once approved for use by the general public manufactured product must be batch release tested before it can be made available for sale.
The presence of acidic species in the formulations, for example after storage may be indicative of degradation (in particular deamidation) of the Fab or Fab′. Deamidation is classed by regulatory authorities as a degradation route and as such limits for the levels of deamidation are set for the product. These levels should not be exceeded during the shelf-life of the product. Whilst not wishing to be bound by theory it is thought that asparagine residues may be degraded via a succinimide intermediate by deamidation to generate acidic species, such as isoaspartic acid/aspartic acid, as set out in Scheme 1:




This deamidation of asparagine residues may result in a change in the proteins overall charge and may increase immunogenicity of the Fab or Fab′. Additionally, this deamidation may result in changes in the function/efficacy of the Fab or Fab′, which may lead to unpredictable therapeutic effects/side effects or simply loss of activity. This can increase the adverse effects in patients after administration of the formulation. Thus degradation must be minimised and storage times and conditions must be limited to those when little or no degradation occurs. Therefore, it is important to be able to measure the deamidation in a given PEGylated Fab or Fab′ formulation. The analysis may impact on the shelf-life and storage conditions given on the product labelling. It is also important to be able to monitor the levels of deamidation in the product because if predefined limits are exceeded then this may result in marketed products being withdrawn from sale or a block on the release for sale of certain batches of the products. In theory deamidation in the protein could be measured by quantifying the acidic species generated therein.
At the present time the total acidic species content of PEGylated Fab or PEGylated Fab′ is measured using Cation Exchange (CEX)-HPLC.
The method measures an aggregate or total value of acidic species in the product. However, there are a number of routes by which the acidic species are generated and not all of those are associated with the deamidation (and hence degradation) of the protein. Thus the value obtained from the analysis is not a value for the actual amount of deamidation in the protein. In fact it includes acidic species generated by:

    
    
        degradation of the Fab′ and
        hydrolysis of the linker joining the Fab′ or Fab and the PEG molecule.
    
    


The hydrolysis of the PEG linker is thought to proceed through the succinimide ring as shown in FIG. 4. This hydrolysis may in fact be the dominant effect and generate a large component of the aggregate value of the acidic species when analysed. The total acidic species content is represented diagrammatically in FIG. 3, which shows acidic species generated in the protein by deamidation and acid species generated by hydrolysis of the linker. This can be represented diagrammatically as shown in FIG. 5, which shows the relative proportions of acidic species generated by hydrolysis of the linker by deamidation and a combination thereof.
The aggregate value of acidic species in a molecule is not of primary interest. Instead what is of interest is the amount of deamidation in the protein. However, the analysis of the total acidic species content does not provide a value representative of the deamidation in the protein.
The amount of deamidation can be measured, for example employing ISOQUANT® aspartate detection kits. The deamidation is represented diagrammatically in FIG. 2, which shows the deamidation in the protein only. However, this deamidation assay is not particularly robust (Alfaro et al., Anal. Chem., 2008, 80, 3882-3889).
To support the commercial manufacture of a therapeutic product, robust analytical techniques are required. The inventors believe that they have designed a robust and effective method for the analysis of the deamidation of PEGylated proteins, in particular PEGylated Fabs and Fab's.
The method of the present disclosure allows the direct measurement of acidic species in the Fab or Fab′ molecule resulting from deamidation/degradation in the Fab or Fab′ molecule and not in the PEG or the linker.
Thus there is provided a method of measuring acidic species generated by degradation of a Fab or Fab′ component of a Fab-PEG or a Fab′-PEG comprising the steps of:
a) cleaving the PEG and linker from the Fab-PEG or Fab′-PEG with an enzyme,
b) optionally separating the PEG and linker generated in step a) from the Fab or Fab′, to provide a Fab or Fab′ and
c) quantitatively analyzing acidic species associated with the cleaved Fab or Fab′ and/or the cleaved PEG.
By removing the PEG and linker from the Fab or Fab′ the amount of deamidation in the protein can be measured by quantifying the acidic species therein. The method is reproducible and robust and furthermore the cleavage of the PEG and linker does not interfere with or change the amount of deamidation in the protein. Thus the deamidation in the cleaved Fab or Fab′ should be representative of the deamidation in the protein portion of the PEGylated Fab or PEGylated Fab′.
In another embodiment the method also allows the extent of PEG linker hydrolysis to be determined by first determining the ‘total’ acidic species for the Fab-PEG or Fab′-PEG prior to cleavage in step (a) of the method and then subtracting the quantified acidic species associated with the Fab or Fab′ component determined in step (c) of the method from the ‘total’ acidic species.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows a diagrammatic representation of a PEGylated Fab′.
FIG. 2 shows a diagrammatic representation deamidation occurring in a PEGylated Fab′.
FIG. 3 shows a diagrammatic representation of deamidation and hydrolysis of the linker both of which generate acidic species.
FIG. 4 shows a diagrammatic representation of the chemical process of PEGylation of a Fab′ and subsequent ring opening to generate an acidic species.
FIG. 5 is a diagrammatic representation of the relative proportions of acidic species values which contribute to the total acidic species content.
FIG. 6 is a diagrammatic representation of the species generated from a PEGylated Fab′ after enzymatic digestion.
FIG. 7 shows efficiency of a trypsin digest of a PEGylated Fab′ over time.
FIG. 8 is a CEX-HPLC analysis of the crude product resulting from trypsin digest of a PEGylated Fab′.
FIG. 9 is an iCEF of a PEGylated Fab′ digested by trypsin.
FIG. 10 shows sequences 1 to 9.
FIG. 11 shows sequences 10 and 11.



BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO:1 shows the amino acid sequence of CDRH1 of CDP870.
SEQ ID NO:2 shows the amino acid sequence of CDRH2 of CDP870.
SEQ ID NO:3 shows the amino acid sequence of CDRH3 of CDP870.
SEQ ID NO:4 shows the amino acid sequence of CDRL1 of CDP870.
SEQ ID NO:5 shows the amino acid sequence of CDRL2 of CDP870.
SEQ ID NO:6 shows the amino acid sequence of CDRL3 of CDP870.
SEQ ID NO:7 shows the nucleotide and predicted amino acid sequence of the light chain variable region CDP870.
SEQ ID NO:8 shows the nucleotide and predicted amino acid sequence of the heavy chain variable region CDP870.
SEQ ID NO:9 shows the amino acid sequence of a grafted anti-TNFα Fab CDP870 light chain.
SEQ ID NO:10 shows the amino acid sequence of a grafted anti-TNFα Fab CDP870 heavy chain.
DETAILED DESCRIPTION OF THE INVENTION
Acidic species as employed herein is intended to refer to a moiety, molecule, comprising a carboxylic acid i.e. comprising the group —C(O)OH.
In one embodiment the enzyme is a protease, for example trypsin or chymotrypsin, such as trypsin. When the enzyme employed is trypsin then the cleavage point is expected to be between the K and T in, for example the sequence SCDKTHTCAA (SEQ ID NO:11) (C-terminus Heavy Chain) of the Fab′ fragment. Advantageously cleavage at this point does not result in a change in the value of deamidation in the protein because the small portion of the hinge that is cleaved does not contain any asparagine residues.
Fab's naturally have a sequence in the hinge which is a suitable substrate for the enzyme. Fab molecules do not naturally have a substrate sequence for the enzyme but if desired an appropriate sequence can be engineered into an appropriate position allowing for removal of the PEG attached to the Fab by enzymatic digestion.
The enzymatic digestion may he performed at a temperature in the range 20 to 40° C. such as 25 to 38° C., in particularly it is optimally performed at 37° C.
In one embodiment when the starting entity is a PEGylated Fab′ the enzyme cleaves the hinge portion of the Fab′ and releases the PEG and linker from the Fab′.
The enzymatic digestion, for example tryptic digestion may be effected over a period of 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160 minutes or more.
The entities generated by digestion need not be separated because if a technique such as HPLC/cIEF is employed for the quantification of acidic species the entities generated have different retention times and thus can be quantified individually without an additional separation step.
However, optionally the entities generated by step a) may be separated by known techniques, for example cation exchange chromatography, cIEF, size exclusion chromatography and the like.
In one embodiment the acidic species associated with the Fab, Fab′ and/or PEG is/are quantified.
In one embodiment the deamidation of the Fab or Fab′ is measured.
In one embodiment acidic species in step c) are analysed employing HPLC analysis, for example employing an elution gradient. In one embodiment the HPLC analysis is CEX-HPLC analysis.
Alternatively, the amount of deamidation in the cleaved protein may be measured by capillary electrophoresis.
In one embodiment acidic species in step c) are analysed employing cIEF analysis, suitable cartridges include iCE280 available from Convergent Bioscience.
All publications, including but not limited to patents and patent applications cited in this specification are herein incorporated by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein as though fully set forth.
In a preferred embodiment the antibody is an anti-TNF antibody, more preferably an anti-TNF Fab′ CDP870 , as described in WO01/094585 (the contents of which are incorporated herein by reference).
In a one embodiment the antibody having specificity for human TNFα, comprises a heavy chain wherein the variable domain comprises a CDR having the sequence shown in SEQ ID NO:1 for CDRH1 , the sequence shown in SEQ ID NO:2 for CDRH2 or the sequence shown in SEQ ID NO:3 for CDRH3.
In one embodiment the antibody comprises a light chain wherein the variable domain comprises a CDR having the sequence shown in SEQ ID NO:4 for CDRL1 , the sequence shown in SEQ ID NO:5 for CDRL2 or the sequence shown in SEQ ID NO:6 for CDRL3.
In one embodiment the antibody comprises a heavy chain wherein the variable domain comprises a CDR having the sequence shown in SEQ ID NO:1 for CDRH1 , the sequence shown in SEQ ID NO:2 for CDRH2 or the sequence shown in SEQ ID NO:3 for CDRH3 and a light chain wherein the variable domain comprises a CDR having the sequence shown in SEQ ID NO:4 for CDRL1 , the sequence shown in SEQ ID NO:5 for CDRL2 or the sequence shown in SEQ ID NO:6 for CDRL3.
In one embodiment the antibody comprises SEQ ID NO:1 for CDRH1 , SEQ ID NO: 2 for CDRH2 , SEQ ID NO:3 for CDRH3 , SEQ ID NO:4 for CDRL1 , SEQ ID NO:5 for CDRL2 and SEQ ID NO:6 for CDRL3.
The antibody is preferably a CDR-grafted antibody molecule and typically the variable domain comprises human acceptor framework regions and non-human donor CDRs.
Preferably, the antibody comprises the light chain variable domain CDP870 (SEQ ID NO:7) and the heavy chain variable domain CDP870 (SEQ ID NO:8).
It is preferred that the antibody is a modified Fab fragment wherein the modification is the addition to the C-terminal end of its heavy chain one or more amino acids to allow the attachment of an effector or reporter molecule. Preferably, the additional amino acids form a modified hinge region containing one or two cysteine residue to which the effector or reporter molecule may be attached. Such a modified Fab fragment preferably has a heavy chain comprising or consisting of the sequence given as SEQ ID NO:10 and the light chain comprising or consisting of the sequence given as SEQ ID NO:9.
The present disclosure explicitly discloses embodiment comprising certain combinations of integers. The present disclosure also extends to embodiments consisting or consisting essentially of the said combinations of integers.
Preferences and/or embodiments may be combined as technically feasible.
The invention will now be described with reference to the following examples, which are merely illustrative and should not in any way be construed as limiting the scope of the present invention.
EXAMPLE
Tryptic Digestion Method
To an eppendorf, 1.0 mg Fab′ PEG is added to 50mM NaOAc, 125mM NaCl pH 5.0 to 50 μL total volume. 50 μL 0.2M Na2HPO4 is added, followed by 40 μL trypsin resuspension buffer (50 mM Acetic Acid), the final pH should be in the region of pH 7.5 . Vortex for 10 seconds.
The reaction is incubated at 37° C. for 2 hours. Analyse by CEX HPLC or imaged capillary isoelectrophoresis.
Digest Efficiency Determined by HTRP HPLC
A tryptic digest using a Fab′PEG was set up using an Agilent 1100 series auto sampler incubated at 37° C., in order that the reaction could be injected directly onto HTRP HPLC assay. 9 injections of the Fab′ Peg and Fab′ control were carried out sequentially. Fab′ PEG gave a digest profile shown in FIG. 7. This demonstrates that within two hours, the Fab′ PEG product content is reduced to  ̃20%.
Analysis
After digestion, samples were removed and diluted to 1 mg/mL in sample dilution buffer (20 mM Sodium Acetate pH 4.5). The Fab′ PEG and cleaved Fab′ can be identified along with their respective acidic species without pre-processing of the mixture obtained from the digestion step, as shown in FIG. 8. The following as shown in FIG. 8 are eluted sequentially; undigested acidic Fab′ PEG species, undigested Fab′ PEG, acidic cleaved Fab′ species and cleaved Fab′.
Suitable Chromatographic Conditions for the Detection of Cleaved Fab′ Acidic species by CEX HPLC













Solvent A
equilibration buffer 10 mM 



2-(N-morpholino)Ethane Sulfonic acid pH 6.2


Solvent B
elution buffer 10 mM 



2-(N-morpholino)Ethane Sulfonic acid, 50 mM



sodium chloride pH 6.2


Column
Dionex Propac SCX-10 column


Flow Rate
0.5 mL/min


Stop Time
75 min


Max Pressure
250 bar


Method Run Pressure 
~60 bar


(guide) 



Column Temperature
25° C.


Injection Volume
100 μL


Autosampler Temperature
4° C.


Detection Wavelength 
280 nm (16 bandwidth), 4 nm slit width


Loading
100 μL at 1 mg/mL


























Solvent A
Solvent B
Flow Rate



Time
(%)
(%)
(mL/min)





















0.0
100
0
0.5



2.0
100
0
0.5



62.0
40
60
0.5



62.5
0
100
0.5



63.5
0
100
0.5



64.0
100
0
0.5



75.0
100
0
0.5










Data Analysis may be carried out using HP Chemstation software where the peaks are integrated, see FIG. 8 for an example of chromatogram of Fab′ PEG digest using the suitable chromatographic conditions described. The following are detected; undigested acidic Fab′ PEG, undigested Fab′ PEG, acidic cleaved Fab′, cleaved Fab′.
Alternative Method of Analysis Using Imaged Capillary Isoelectrophoresis
Sample Preparation for Analysis Using iCE280
A generic sample preparation of 200 μL volume is given below:

    
    
        Tryptic Digest (desalted and free from any free ions at a concentration of 1 mg/ml)-40 ul (General rule: final concentration of the protein should be around 0.1-0.3 mg/ml in final sample mixture).
        1% Methyl Cellulose: 70 μL (Methyl cellulose concentration in the final the mixture should be 0.35%).
        Carrier Ampholytes: (3-10 Pharmalytes)-8 μL (Carrier ampholytes should have a concentration of 4% in the final sample mix).
        pI markers: 1 μL each of two different pI markers are added whose pI values should lie on the either side of the protein and its related species.
        HPLC grade water: Add required amount of HPLC water to make up the volume to 200 μL.
    
    


Mix the above sample by vortexing for 15-30 second to ensure proper mixing of different components. Spin the mixture at 16000 g for 10 minutes to remove air bubbles and dust particles, which would interfere with the analysis.
Instrument Settings and Analysis Employing iCE280 Technology
iCE 280 from Convergent biosciences (Isogen in Europe) is an imaged capillary isoelectrophoresis instrument, which is used to determine pIs of various protein samples and their related species.
High voltage is applied across the capillary using an anode and cathode, which are dipped, in small reservoirs containing catholyte (OH−) and anolyte (H+). Samples are prepared with carrier ampholytes and on application of high voltage the protein molecules migrate according to their respective pIs and finally focus at it. The anolyte may be prepared by adding calculated amount of phosphoric acid to give a final solution of 0.08 M phosphoric acid in 0.1% methyl cellulose. The catholyte may be prepared by adding 10.4 μl of 50% w/w NaOH solution to 2 ml of 0.1% methyl cellulose. Catholyte must be freshly prepared and should not be reused. Generally 2 ml is enough for a single fill of the reservoir.
Generally for all non-PEGylated samples, a focusing period of 5-6 minutes at 3000 v should be enough, but since different proteins have different charge distribution, the focusing time would also vary accordingly. In that case the settings need to be optimised by running two or three samples.
Data analysis may be carried out using EZChrom software. Profiles can be compared by overlaying them using ‘Supercompare’ and electrophoregrams can be integrated using ‘Method development’ options within the EZChrom software. See FIG. 9 for an example of electrophoregram of Fab′ PEG digest. The following are detected; low pI marker, acidic cleaved Fab′ species, cleaved Fab′ species, basic cleaved Fab′ species, high pI marker.

## Claims

1. A method of quantitatively analyzing acidic species generated by degradation of a Fab or Fab′ component of a Fab-PEG or a Fab′-PEG comprising the steps of:
a) cleaving the PEG and linker from the Fab-PEG or Fab′-PEG with an enzyme,
b) optionally separating the PEG and linker generated in step a) from the Fab or Fab′, to provide a Fab or Fab′ and
c) quantitatively analyzing acidic species associated with the cleaved Fab or Fab′ and/or the cleaved PEG.

2. The method according to claim 1, wherein the enzyme is trypsin or chymotrypsin.

3. The method according to claim 1, wherein the cleaving in step a) is performed at a temperature in the range of 25° C. to 40° C.

4. The method according to claim 2, wherein step a) is performed at a temperature in the range of 25° C. to 40° C. with said enzyme.

5. The method according to claim 1, wherein the cleavage of step a) occurs between a lysine and a threonine in the C-terminal portion of the Fab or Fab′ heavy chain.

6. The method according to claim 5, wherein the lysine and threonine are found in the sequence SCDKTHTCAA (SEQ ID NO: 11) located at the C-terminal of a Fab′.

7. The method according to claim 6, wherein the enzyme cleaves the hinge portion of the Fab′ and releases the PEG and linker from the Fab′.

8. The method according to claim 1, wherein the PEG and linker generated in step a) is separated from the Fab or Fab′ to provide a Fab or Fab′.

9. The method according to claim 8, wherein the separation is effected by cation exchange chromatography, cIEF, and/or size exclusion chromatography.

10. The method according to claim 1, wherein the acidic species is quantitatively analyzed by cation exchange chromatography or imaged capillary isoelectrophoresis.

11. The method according to claim 1, wherein said Fab′ comprises SEQ ID NO: 9 and SEQ ID NO: 10.

12. The method according to claim 1, wherein said Fab′ consists of SEQ ID NO: 9 and SEQ ID NO: 10.