PROTEIN FOLDING
The present invention relates to a method for folding, or refolding, proteins into an active form. The invention particularly relates to folding of members of the Transforming growth factor beta superfamily.
The Transforming growth factor beta (TGF-Beta) superfamily of growth factors are involved in the regulation of many cellular processes including proliferation, migration, apoptosis, adhesion, differentiation, inflammation, immunosuppression and expression of extracellular proteins. The TGF-Beta superfamily include: TGF-Beta 1, TGF-Beta 2, TGF-Beta 3, TGF-Beta 4, TGF-Beta 5, bone morpbogenetic proteins (BMPs 1-16) growth and differentiation factors (GDFs 1-16), and activins/inhibins.
There are three mammalian isoforms of TGF-Beta, termed TGF-Beta 1, 2 and 3. TGF-Betas are produced by virtually all cell types (e.g., epithelial, endothelial, hematopoietic, neuronal, and connective tissue cells). TGF-Betas are secreted as 100-kDa latent inactive precursor molecules (LTGF-Beta). The LTGF-Beta molecules consist of: (a) a C-terminal 25kDa dimer signal peptide (active fragment) and (b) the latent-associated peptide (LAP). LTGF-Beta is activated by cleavage of LAP from the active fragment by endopeptidases such as furin, plasmin, thrombin and acidification of the pericellar space. The liberated active TGF-Beta dimeric fragment is stabilized by hydrophobic interactions and by an inter-subunit disulfide bridge. Furthermore each monomer comprises several extended beta strands interlocked by three of the four intra-disulfide bonds and forms a tight structure known as the "Cysteine knot".
TGF-Beta family proteins have been proposed for a number of medical purposes. These include the reduction of scarring, promotion of wound healing and the stimulation of the replacement of damaged or diseased tissue at a variety of sites. These sites include the skin, bone, cartilage, neural tissue, connective tissue (e.g. tendons and ligaments), ocular tissue, liver and blood vessels etc. TGF-Beta 1 and TGF-Beta 2 have been shown to accelerate wound healing in experimental animal models, whilst their inhibition reduces subsequent scar formation. TGF-Beta 3 also significantly reduces scarring both in animal models and in humans and, in 2006,
4 represents one of the members of the superfamily that is closest to gaining regulatory approval for use as a medicament.
It will be appreciated that such clinical uses of members of the TGF-Beta superfamily requires that efficient methods for producing significant quantities of active growth factors are made available.
Members of the TGF-Beta supcrlamily have been isolated or produced by recombinant means for a number of years. By way of example TGF-Beta 3 was originally purified from human platelets, human placenta and bovine kidney during the 1980s. In view of the therapeutic potential of TGF-Beta 3, numerous attempts have been made to produce this protein by recombinant methods. Due to the complexity of native biologically active TGF-Beta molecules (homodimeric protein with 8 intra-chain disulfide bonds and one inter-chain disulfide bond) they were originally expressed in eukaryotic organisms (e.g. see EP0200341B1). However, eukaryotic expression resulted in relatively low expression levels and was also associated with high process costs.
Prokaryotic hosts were therefore investigated. However it was found that microbial hosts were unable to correctly form the multiple disulfide bonds required for the growth factors to fold into an active form. The misfolded protein formed as insoluble inclusion bodies within the host cell and these bodies required solubilisation followed by renaturation to allow the protein to refold into its native biological active conformation.
A number of attempts have been made to overcome the problems associated with the formation of active growth factors from prokaryotic hosts. For instance, US 5,922,846, US 5,650,494 and EP-B-0433 225 propose methods for the renaturation of TGF-Beta family proteins from inclusion bodies. However none of these methods provide quick and efficient methods for the production of clinical grade growth factors. For instance the inventors have found that many of the prior art refolding methods contemplated in the abovementioned patents are ineffective. Further, the inventors have found that with even the most preferred prior art refolding conditions (e.g. 0.05M Tris, 1M NDSB-201, 20%(v/v) DMSO, 2%(w/v) CHAPS, 1M NaCl,
l%(w/v) GSH, 0.2mg/mL TGF-Beta 3, pH 9.3 at 2-8 °C) it can take about 7 days to refold growth factors. This folding time represents an unacceptable delay in cGMP manufacture and would result in undesirably high operational costs when large quantities of active growth factor are required.
It is therefore an object of the present invention to overcome the problems associated with prior art methods for folding, or refolding, members of the Transforming Growth Factor Beta superfamily.
According to a first aspect of the present invention there is provided a method for folding a Transforming Growth Factor Beta, or functional analogue thereof, into a dimeric, biologically active form comprising adding solubilized, unfolded monomelic growth factor to a solution containing:
(i) 2-(cylcohexylamino)-ethanesulfonic acid or a functional analogue thereof; and
(ii) a low molecular weight sulfhydryl/disulfide redox system; and incubating the growth factor in the solution until dimeric biologically active growth factor is formed.
The present invention is based on experiments conducted by the inventors that were conducted in an attempt to improve prior art folding methods.
The Transforming Growth Factor Beta (TGF-Beta) may be any TGF-Beta (e.g.. TGF-ß1, TGF-ß2 or TGF-ß3). However it is preferred that the TGF-Beta is TGF-Beta3 (TGF-ß3).
By "functional analogue thereof we mean variants of a TGF-beta that retain the biological activity of the wild type growth factor. The functional analogue is preferably a protein and, in mature form, may comprise a dimer of two monomelic polypeptides of about 112 amino acids in length although it will be appreciated that functional analogues may be truncated or elongated when compared to the wild-type. The term also encompasses mutants of wild -type TGF-beta and particularly of TGF-Beta 3 that retain, or even have improved, activity when compared to the wild-type.
The inventors have found that the methods of the invention are also applicable to folding or refolding of such mutants.
It will be appreciated that "folding", as defined in the present invention, encompasses the "re-folding" of previously folded proteins, and indeed this re-folding of proteins constitutes a preferred subset of the broader folding encompassed by the invention.
EP 0 433 225 contemplates a wide variety of "refolding conditions" that are alleged to permit a denatured monomer to dimerise and assume a biological active form. EP 0 433 225 discloses that such conditions should include the presence of a "solubilizing agent" and a redox system which permits the continuous oxidation and reduction of the thiol/disulfide pairs. It further contemplates a long list of such solubilizing agents including detergents; organic, water miscible, solvents; and phospholipids or a mixture of two or more such agents. Examples of the detergents contemplated in the specification include: surface active compounds, such as sodium dodecylsulfate (SDS), Triton or Tween, non-ionic mild detergents (e.g. digitonin), cationic mild detergents (e.g. N-[2,3-(Dioleyloxy)-propyl]-N,N,N-trimethylammonium), anionic mild detergents (e.g. sodium cholate, sodium deoxycholate) and zwitterionic ones (e.g. sulfobetaines (Zwittergent), 3-(3-chlolamidopropyl)dimethylammonio-l-propane-sulfonate (Chaps),
3-(3-chlolamidopropyl)dimethylammonio-2-hydroxy-1 -propane-sulfonate (Chapso).
The inventors decided to test out a variety of detergents, including those contemplated in EP 0 433 225, and were surprised to find that most of the detergents they tested were ineffective for folding or refolding members of the TGF-Beta superfamily whereas those that did work took an unacceptable amount of time to yield useful amount of active growth factor. Tables 1 and 2 of the Example illustrate that a number of such detergents were ineffective. However to the inventors' surprise they found that the use of 2-(cylcohexylamino)-ethanesulfonic acid (CHES), and analogues thereof, in combination with a low molecular weight sulfhydryl/disulfide redox system, in accordance with the first aspect of the invention, was particularly effective for producing correctly folded dimeric growth factor.
The inventors have found that the method according to the first aspect of the invention represents a significant improvement over prior art methods. The method results in signifioantly improved speed of the process compared to methods previously disclosed in the literature. In preferred embodiments of the method of the invention folding of the growth factor may be completed within 5 days; preferably within 3 days; more preferably within 2 days; and most preferably after approximately 24 hours of initiating the folding process.
By the term "2-(cylcohexylamino)-ethanesulfonic acid or analogues thereof we mean the detergent CHES and chemical analogues thereof that retain the refolding properties of CHES.
Suitable analogues of CHES that may be used in accordance with the methods of the invention may be defined by the following formula:
(Formula Removed)
wherein:
R1 and R2 are the same or different and are selected from the group consisting of hydrogen, substituted or unsubstituted C1-4 alkyl groups, substituted or unsubstituted C3-8 cycloalkyl groups, or a substituted or unsubstituted aromatic nucleus, or R1 and R2 together form a ring system having up to 10 atoms;
X1 and X2 are independently selected from -O-, -S-, -S(O), -S(O2)-, -NR3-, -CHR4- and CHR5 where R3, R4, and R5 are the same or different and are independently selected from the group consisting of hydrogen, substituted or unsubstituted C1-4 alkyl groups, substituted or unsubstituted C3-8 cycloalkyl groups, or a substituted or unsubstituted aromatic nucleus or any two of R3, R4 and R5 may together form a ring system having up to 6 carbon atoms, subject to the proviso that at least one of X1 and X2 is -CHR4- or -CHR5-; and
X3 is selected from C, S, S=O, or P-OH
If one or more of R1-5 are alkyl groups then, depending on the number of carbon atoms they contain, they may be normal, secondary, tertiary or iso-groups. Examples of suitable alkyl groups for R1-5 are Me, Et, n-Pr, i-Pr, n-Bu, sec-Bu and B-Bu groups.
If one or more of R1-5 are cycloaliphatic then they are preferably a substituted or unsubstituted cyclohexyl group, most preferably unsubstituted.
If one or more of R1-5 are aromatic then they are preferably a substituted or unsubstituted phenyl group.
Preferably R1 is hydrogen and R2 is cyclohexyl. Alternatively or additionally X1 and X2 are preferably -CH2-, alternatively or additionally X3 is -S=O.
Preferred examples of compounds of formula (I) that may be employed in the invention are:
(Formula Removed)
(i.e. a compound of formula (I) in. which X1 and X2 are both -CH2- and X3 is S=O);
(Formula Removed)
(i.e. a compound of formula (I) in which R1 is hydrogen, R2 is cyclohexyl and X3 is S=O); and
(Formula Removed)
(i.e. a compound of formula (I) in which R1 is hydrogen, R2 is cyclohexyl, and X1 and X2 are both -CH2-).
The preferred example of each of formula (la), (lb) and (Ic) is CHES, i.e.
(Formula Removed)
The inventors have established that CHES, and the low molecular weight sulfhydryl/disulfide redox system, may be used alone to fold the growth factor. However, in some embodiments of the invention, the inventors have found that CHES may also be advantageously combined with other agents that have detergent/folding activity. Examples of such agents include: Taurodeoxycholate, Isopropyl Alcohol, Argmine-HCl, Non-detergent Sulphobeatine-201 and Non-detergent Sulphobeatine-211.
It is preferred that the solution comprises a concentration of about 10mM to 2.0M CHES; more preferably 100mM-1.0M and most preferably about 0.7M CHES.
The abovementioned concentrations of CHES may also be used when CHES is combined with other agents. For instance a preferred combination of agents that promote refolding is about 30mM Taurodeoxycholate and 0.7M CHES.
By the term "low molecular weight sulfhydryl/disulfide redox system" we mean systems that allow the formation of disulfide bonds in the solution. Suitable systems include reagent combinations such as Glutathione in its oxidized and reduced form, dithiothreitol in its oxidized and reduced form, beta-mercaptoethanol or beta-mercaptomethanol in its oxidized and reduced form, Cystine and its reduced form, and Cystamine and its reduced form. These reagents may be used at a concentration of about 1µM to 250 mM, especially of about 100µM to 10 mM. The molar ratio of such systems for the oxidized and the reduced forms may be between 100: 1 and 1: 100, especially between 6: 1 and 1: 6.
It is preferred that the low molecular weight sulfhydryl/disulfide redox system comprises the use of Glutathione in its reduced (GSH) and oxidised (GSSG) forms. Preferably the solution contains about 20µM-200mM reduced Glutathione; more preferably 200µM-20mM reduced Glutathione; and most preferably about 2mM reduced Glutathione. The solution may also contain about 4µM-40mM oxidised Glutathione; more preferably 40µM-4mM oxidised Glutathione; and most preferably about 400µM oxidised Glutathione.
Accordingly, preferred low molecular weight sulfhydryl/disulfide redox systems may comprise 200µM-20mM reduced Glutathione and 40µM-4mM oxidised Glutathione. The exact ratio of GSH:GSSH will depend on a number of factors including: which growth factor is being folded; the pH of the solution and the CHES analogue employed in the method of the invention. By way of example, preferred low molecular weight sulfhydryl/disulfide redox systems for folding TGF-Beta 3 comprises about 2mM reduced Glutathione and either about 400µM or about 2mM reduced Glutathione.
As explained in more detail below, in preferred embodiments of the invention the low molecular weight sulfhydryl/disulfide redox system may be "aged" before used to refold the TGF-Beta.
Preferred methods for folding the growth factors involve the use of CHES in combination with GSH and GSSG as the low molecular weight sulfhydryl/disulfide
r redox system. Examples of preferred conditions include exposing unfolded growth factor to:
(a) 0.7M CHES, 2mM GSH and 0.4mM GSSG;
(h) 30mM Taurodeoxycholate, 0.7M CHES, 2mM GSH and 0.4mM GSSG;
or (c) 30mM Taurodeoxycholate, 0.7M CHES, 2mM GSH and 2mM GSSG.
It will be appreciated that the abovementioned agents may be dissolved in water to make a solution according to the invention. However it will also be appreciated that the agents may be dissolved in a solution comprising a number of other compounds. For instance, the solution may also further comprise salts. Salts that can be used in the solution include salts of sodium, potassium, and calcium with chloride, sulphate, phosphate, acetate etc. It is preferred that the solution is a sodium chloride solution at a concentration of 0.5 to 2 M. The solution may, for example, be phosphate buffered saline.
During their investigations the inventors also established that folding conditions could be optimised by adjusting the pH and the temperature at which folding is encouraged to proceed.
Optimal temperature depended on a number of factors such as the agents used, the pH and also the amount of growth factor to be refolded. Under most circumstances a temperature of below about 15°C is preferred (for example 2-8 °C or about 10°C). However higher temperatures (e.g. room temperature) were also effective for some conditions.
The inventors discovered that it was generally preferable to carry out the method of the invention at an alkaline pH. The pH is preferably above about pH 8.0. and more preferrably above a pH of about pH 8.5. A most preferred pH for the solution is a pH of about 9.5.
The amount of unfolded growth factor added to the solution was also found to influence the efficiency of the folding. In general about 0.005-0.75 mg/mL of a
growth factor may be added to the solution; preferably 0.01-0.5 mg/mL; more preferably about 0.12-0.25mg/mL of the growth factor; and most preferably about 0.25mg/mL (i.e. 250µg/ml).
The methods of the invention may be employed to fold any monomer of the Transforming Growth Factor Beta superfamily into a dimeric, biologically active form. It is preferred that the method is used to fold a TGF-Beta per se (for example TGF-Beta 1, TGF-Beta 2, or TGF-Beta 3).
It is also preferred that the method is used to fold monomelic precursors (into active dimer growth factor) that have been produced in prokaryotic hosts that have been transformed to express the growth factor. For instance the method is particularly useful for folding growth factors that are located within inclusion bodies of bacteria that have been transformed with an expression vector encoding a recombinant growth factor.
It is most preferred that the methods of the invention are used to fold monomelic TGF-Beta 3 that is located in an inclusion body of a bacterium transformed with a TGF-Beta 3 expression vector (e.g. as described in Example 1 or as known to the art). It is most preferred that the TGF-Beta 3 is human TGF-Beta 3, recombinant human TGF-Beta 3, or human TGF-Beta 3 that contains mutations that optimise the growth factor for clinical use in humans.
Examples of most preferred conditions employed to fold TGF-Beta 3 include:
(a) 0.7M 2-(cylcohexylamino) ethanesulfonic acid (CHES), 2mM reduced Glutathione (GSH), 0.4mM oxidised Glutathione (GSSG), 0.12mg/mL TGF-Beta 3, pH 9.5 at 2-8°C ;
(b) 30mM taurodeoxycholate, 0.7M CHES, 2mM GSH, 0.4mM GSSG, 0.12mg/mL TGF-Beta 3, pH 9.5 at 2-8°C;
(c) 30mM taurodeoxycholate, 0.7M CHES, 2mM GSH, 2mM GSSG, 0.12mg/mL TGF-Beta 3, pH 9.5 at 2-8°C; or
(d) 0.7M CHES, 1M NaCl, 2mM GSH, 0.4mM GSSG, 0.25mg/mL TGF-Beta 3, pH 9.5 at 2-8°C/room temperature.
The inventors developed the folding methods according to the invention in a laboratory (as described in Example 1) and then went on to scale-up the methodology as described in Example 2. It will be appreciated that the scale-up of the methods represent an important feature of the invention. Therefore according to a second aspect of the invention there is provided a method of producing an active member of the Transforming Growth Factor Beta superfamily from a prokaryotic host, the method comprising:
(a) fermentation of prokaryotic organisms that have been transformed to express a member of the Transforming Growth Factor Beta superfamily;
(b) isolation of inclusion bodies and recovery of expressed protein from the inclusion bodies;
(c) refolding of the member of the Transforming Growth Factor Beta superfamily according to the first aspect of the invention; and
(d) purification of the refolded member of the Transforming Growth Factor Beta superfamily.
It is preferred that step (a) involves the fermentation of bacteria that have been transformed with an expression vector encoding a member of the Transforming Growth Factor Beta superfamily. The vector preferably encodes a TGF-Beta and most preferably encodes a human TGF-Beta 3, or a functional analogue thereof. It will be appreciated that the transformed bacterium may be generated using molecular biology techniques known to the art. An example of such a bacterium is given in Example 1.
It is preferred that the organisms are fermented according to conventional techniques. This may involve fermentation of a cell paste and harvesting the cells by taking samples from the fermentation and centrifuging the sample to isolate the organisms.
Step (b) of the method of the second aspect of the invention may involve lysis of the organisms recovered by centrifugation. The inclusion bodies (IB) may then be recovered by further centrifugation and washing steps. Preferably the IBs are further
( processed by taking steps to solublize the protein within the IBs and then clarifying them.
The protein (i.e. the unfolded growth factor) from the isolated IBs is then subjected to the folding methods of the first aspect of the invention according to step (c) of the method of the second aspect of the invention.
The refolded growth factor should then be further purified according to step (d). Purification may involve a number of biochemical purification steps such as ultrafiltration and chromatography. Preferred purification procedures are illustrated in 1.15, 1.16 and 1.17 of Example 1. In a preferred embodiment the growth factor is first filtered; further purified by hydrophobic interaction chromatography; and then finally purified by cation exchange chromatography.
Optionally the method of the second aspect of the invention may further comprise a step (e) wherein the growth factor is formulated at a desired concentration in a solution and placed in vials. This solution may be the final formulation for clinical use or may be formulated for storage and/or transported. The growth factor may then be finished to form the final clinical product at a later date.
The inventors have recognised that W099/18196 discloses the use of CHES for refolding Bone Morphogenetic Proteins (BMPs). However the techniques disclosed in W099/18196 would not be considered by a skilled man to be useful for refolding TGF-Beta, and TGF-Beta3 in particular, according to the methods of the first or second aspects of the invention. The skilled person would come to this conclusion for a number of reasons. These include:
(a) W099/18196 discloses methods for the solubilisation of the BMP inclusion bodies should use denaturants such as Guanidine-HCL or by acidification with an acid such as Acetic Acid. The inventors have found that acidification resulted in low recoveries of TGF-Beta 3 from the inclusion bodies. They found that when TGF-Beta 3 was solubilised in acid and the pH was then titrated to 9.5 (the preferred pH for refolding according to the invention), that this change from acid to alkaline pH resulted in irreversible aggregation of TGF-Beta 3 (due to the TGF-Beta 3 crossing
its isoelectric point (pH 6.4)). This resulted in very low TGF-Beta 3 yields. The Guanidine-HCL was also examined as a solubihsation agent, though it gave very good recoveries of TGF-Beta 3 from inclusion bodies it was too strong a denaturant and prevented TGF-Beta 3 from refolding. Accordingly the inventors found the solubihsation steps of the prior art unsuitable. Experimentation did establish that solubihsation of inclusion bodies using 6M Urea and 0.1M DTT gave good recoveries of TGF-Beta 3 and allowed the TGF-Beta 3 to refold once it was diluted in the refold buffer. Accordingly it is preferred that TGF-Beta 3 is solubilised from inclusion bodies using Urea and DTT.
(b) W099/18196also states that the BMP can be clarified using size exclusion chromatography (SEC) or reverse phase high performance liquid chromatography (RP-HPLC). Both these methods would be unsuitable for the commercial scale manufacture of TGF-Beta 3. In SEC, sample volume influences the resolution of the sample (the smaller the sample volume the better the purification resolution). Commercial scale methods according to the second aspect of the invention may produce about 50L of solubilised inclusion bodies. It would be impractical to use SEC for such volumes because to process this volume in a single run would require a column (or multiple columns) with a single/combined bed-volume of 724 L. RP-HPLC is generally used as analytical tool due to the small column volume and again would be unpractical to use in the commercial scale manufacture of TGF-Beta 3 for the same reasons. It is preferred that the method of the second aspect of the invention uses Tangential Flow Filtration (TFF) which gives TGF-ß3 purities of 70% and above.
(c) It is known that purity of an expressed protein affects refold yields. As a general rule the higher the purity of the expressed protein the higher the refold yields. The inventors have found that TGF-ß3 purities of 70% (of total protein) and above give high refold yields and that low TGF-ß3 purities (<50% of total protein) gave low refold yields. Accordingly it is preferred that TGF-ß3 used in methods of the invention are greater than 50% pure and more preferably about 70% (or more) pure. This purity may be achieved by including washing steps of the inclusion bodies and clarification of the solublised TGF-Beta 3 using TFF (e.g. see Example 2).
(d) TGF-Beta 3 undergoes significant changes in conformation (secondary
structure) and solubility at different pHs. As the pH of a TGF-Beta 3 containing
solution is moved from acidic (