Title: Method of producing a recombinant polypeptide free of O-linked mannose residues.
Field of invention The present invention relates to a method for producing a therapeutic recombinant protein free of O-linked mannose residues and to the use of such proteins in therapy.
Background of the invention
Most proteins developed for pharmaceutical applications have oligosaccha des attached to their polypeptide backbone, when produced in an eukaryotic host cell. In general sugar chains of such glycoproteins may be attached by N-glycosidic bonds to the amide group of asparagine residues or O-glycosidic bonds to the hydroxyl group of serine or threonine residues.
O-carbohydrates added to recombinant proteins by e.g. fungal glycosylation/mannosylation could be recognized as antigenic structures by the human immune system and it is therefore desirable to completely remove O-linked mannose residues from proteins developed for pharmaceutical applications.
O. Letourneur et al. (2001 , Biotechnol. Appl. Biochem. 33:35-45) describes the enzymatic deglycosylation of a surface antigen I from Pichia pastoris using jack-bean (alpha 1 -2/1 -3/1-6)- mannosidase.
K.N. Neustroev et al. (1993, FEBS LETTERS, 316 (2):157-160) describes enzymatic deglycosilation of O-linked mannose by treatment of a glycoamylase from Aspergillus awamori with alpha-mannosidase. It is reported that the treatment results in removal of 24-26 % of total mannose.
Without complete removal of O-linked mannosyl, i.e. also removal of the mannose residue attached to the peptide backbone of proteins produced for therapy, it is necessary to remove the entire fraction of mannosylated proteins by purification steps, e.g. chromatographic purification steps, which will increase production costs an reduce production yield.
Summary of the invention
The present invention provides a method for the production of proteins developed for pharmaceutical applications in which such cost increasing steps, such as chromatographic
purification, can be avoided by providing a complete demannosylation of recombinant polypeptides produced in a fungal host.
In a first aspect the present invention relates to a method for producing a therapeutic recombinant polypeptide free of O-linked mannose residues, comprising the steps of
a) providing the polypeptide from a fungal host, and b) demannosylating the polypeptide, where in step (b) O-linked mannose residues on the polypeptide are completely removed by enzymatic treatment of the polypeptide with a glycosidase having mannosidase activity.
In a second aspect the present invention relates to a use of a therapeutic recombinant polypeptide expressed in a fungal host for the preparation of a medicament, wherein a therapeutic polypeptide free of O-linked mannose residues is provided by enzymatic treatment of the recombinant polypeptide with a glycosidase having mannosidase activity.
In a third aspect the present invention relates to a use of a glycosidase having mannosidase activity for complete demannosylation of a therapeutic recombinant polypeptide expressed in a fungal host.
Detailed description of the invention
O-mannosylation of recombinant human proteins/polypeptides produced in a non human host such as a fungal host will result in a mannosylation pattern, which is different from that seen in humans, and thus due to the possible antigenic properties of such recombinant proteins, the mannose residues have to be completely removed in proteins developed for therapeutic applications.
When the recombinant polypeptide is produced in a fungal host only a relatively small fraction of the total fraction of the polypeptide may comprise O-linked mannosyl, however, it is essential that this small fraction, usually between 1-10 %, is completely removed. Conventionally this is done by cost increasing chromatographic purification steps. Enzymatic demannosylation has never before been considered since such enzymatic removal of mannose residues was believed only to remove the mannose residues linked by alpha-1 ,2- linkages.
In the present context the term "polypeptide" is intended to cover amino acids linked together by peptide bonds ranging from the smallest polypeptide, i.e. dipeptide, to oligopeptides, polypeptides, as well as proteins as such.
"Therapeutic proteins" in the context of the present invention means that the proteins should be administrable to a human in pure form or comprised in a pharmaceutical formulation and therefore the protein should not be glycosylated. Especially the O-linked mannose residues should be completely removed.
"Completely removed" in the context of the present invention means that in the final product of the method according to the invention at I east 90 % is free of O-linked mannose residues, particularly at least 95%, more particularly at least 97%, even more particularly at least 99%, and even more particularly 99.9%.
In fungi such as the yeast Saccharomyces cerevisiae O-mannosylation occurs when expressing recombinant proteins comprising regions with serine and threonine.
It is known that enzymes like alpha-mannosidases belonging to the family EC 3.2.1.24, as well as mannosyl-oligosaccharide 1 ,2-alpha-mannosidases and mannosyl-oligosaccha de 1 ,3-1 ,6- alpha-mannosidases belonging to EC 3.2.1.113 and 3.2.1.114 respectively are capable of removing O-linked mannosyl. The mannose residue which is attached directly to the peptide backbone is, however, difficult to remove enzymatically and other means for complete removal of such residues have been applied. One possibility is to remove the entire fraction of mono- mannosylated protein or to use chemical deglycosylation.
Previous attempts to remove O-linked mannosyl by enzymatic treatment has resulted in removal of less than 30% of the total mannose (K.N. Neustroev et al., 1993, FEBS LETTERS, 316 (2): 157-160).
It has now been discovered that complete demannosylation is possible by a single enzymatic treatment of the recombinant polypeptide with an enzyme capable of removing O-linked mannose residues, thus avoiding steps for removing fractions that are not completely demannosylated or chemical demannosylation.
Optionally one or more purification steps can be applied before performing the enzymatic demannosylation in order to treat only the peptide of interest. Such steps are not essential in performing the present invention and will be obvious to the skilled person.
A first aspect of the present invention therefore relates to a method for producing a therapeutic recombinant polypeptide free of O-linked mannose residues, comprising the steps of
a) providing the polypeptide from a fungal host, and b) demannosylating the polypeptide, where in step (b) O-linked mannose residues on the polypeptide are completely removed by enzymatic treatment of the polypeptide with a glycosidase having mannosidase activity.
In a particular embodiment the glycosidase having mannosidase activity is chosen from the enzyme classes consisting of EC 3.2.1.24, EC 3.2.1.114 and EC 3.2.1.113.
In one embodiment the glycosyl hydrolase comprises jack-bean (alphal -2/1 -3/1-6)- mannosidase, Aspergillus oryzae GH47 α-mannosidase (SPTREMBL:Q8NKB3), Thermotoga maritima α-mannosidase (EMBLAE001822, TREMBLQ9X2G6), Mouse spermatozoal GH38, Arabidopsis GH38, Streptomyces coelicolor alpha-mannosidase and Saccharomyces cerevisiae vacuolar mannosidase (AMS1_YEAST).
In another embodiment of the invention the glycosyl hydrolase is jack-bean (alpha1-2/1-3/1-6)- mannosidase.
In a further embodiment the mannosidase enzyme is Streptomyces coelicolor α-mannosidase (SCM) or Thermotoga maritima α-mannosidase (TMM).
In one embodiment the enzymatic treatment is performed on the folded polypeptide.
The term "folded protein" means that the polypeptide has a secondary, and/or tertiary and/or quaternary structure during the enzymatic treatment.
Other steps or treatments that will render the polypeptide of interest more susceptible to the enzyme according to the invention can optionally be included. Such treatment includes e.g. denaturation by applying well known techniques, like e.g. heating, extreme pH, chemical treatment etc.
In a further embodiment the protein is a human protein.
The recombinant polypeptide according to the invention comprises hormones, cytokines, enzymes and antibodies.
In a particular embodiment the polypeptide is chosen from the group consisting of pro-insulin, miniproinsulin (miniproinsulins are single chain insulin molecules with a very short C-peptide or no C-peptide spacer between B29 and A1 as described in: Markussen et al., 1987, Biosynthesis of human insulin in yeast via single-chain precursors. In Peptides 1986, pp 189- 194. Edited D. Theodoropoulos. Berlin: Walter de Gruyter & Co.) and glucagon-like proteins (glucagon-like peptide 1 (GPL1 ), SWISSPROT:GLUC_HUMAN Prim, accession # P01275 ).
Host cell
The host cell according to the invention is a fungal cell. "Fungi" as used herein includes the phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (as defined by Hawksworth et al., In, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition, 1995, CAB International, University Press, Cambridge, UK) as well as the Oomycota (as cited in Hawksworth et al., 1995, In, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition, 1995, CAB International, University Press, Cambridge, UK, page 171 ) and all mitospohc fungi (Hawksworth et al., 1995, supra). Representative groups of Ascomycota include, e.g., Neurospora, Eupenicillium (=Penicillium), Emericella (=Aspergillus), Eurotium (= Aspergillus), and the true yeasts listed below. Examples of Basidiomycota include mushrooms, rusts, and smuts. Representative groups of Chytridiomycota include, e.g., Allomyces, Blastocladiella, Coelomomyces, and aquatic fungi. Representative groups of Oomycota include, e.g., Saprolegniomycetous aquatic f ungi (water m olds) such as Achlya. Examples of mitosporic fungi include Aspergillus, Penicillium, Candida, and Alternaria. Representative groups of Zygomycota include, e.g., Rhizopus and Mucor.
In a particular embodiment, the fungal host cell is a yeast cell. "Yeast" as used herein includes ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast belonging to the Fungi Imperfecti (Blastomycetes). The ascosporogenous yeasts are divided into the families Spermophthoraceae and Saccharomycetaceae. The latter is comprised of four subfamilies, Schizosaccharomycoideae (e.g., genus Schizosaccharomyces), Nadsonioideae, Lipomycoideae, and Saccharomycoideae (e.g., genera Pichia, Kluyveromyces and Saccharomyces). The basidiosporogenous yeasts include the genera Leucosporidim, Rhodosporidium, Sporidiobolus, Filobasidium, and Filobasidiella. Yeasts belonging to the Fungi Imperfecti are divided into two families, Sporobolomycetaceae (e.g., genera Sorobolomyces and Bullera) and Cryptococcaceae (e.g., genus Candida). Since the classification of yeast may change in the future, for the purposes of this invention, yeast shall
be defined as described in Biology and Activities of Yeast (Skinner, F.A., Passmore, S.M., and Davenport, R.R., eds, Soc. App. Bacteriol. Symposium Series No. 9, 1980). The biology of yeast and manipulation of yeast genetics are well known in the art (see, e.g., Biochemistry and Genetics of Yeast, Bacil, M., Horecker, B.J., and Stopani, A.O.M., editors, 2nd edition, 1987; The Yeasts, Rose, A.H., and Harrison, J.S., editors, 2nd edition, 1987; and The Molecular Biology of the Yeast Saccharomyces, Strathern er a/., editors, 1981 ).
In a more particular embodiment, the yeast host cell is a cell of a species of Candida, Kluyveromyces, Saccharomyces, Schizosaccharomyces, Pichia, or Yarrowia. In a particular embodiment, the yeast host cell is a Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis or Saccharomyces oviformis cell. In another embodiment, the yeast host cell is a Kluyveromyces lactis cell. In another embodiment, the yeast host cell is a Yarrowia lipolytica cell.
The fungal host cell is in a particular embodiment a filamentous fungal cell. "Filamentous fungi" include all filamentous forms of the subdivision Eumycota and Oomycota (as defined by Hawksworth et al., In, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition, 1995, CAB International, University Press, Cambridge, UK. The filamentous fungi are characterized by a vegetative mycelium composed of chitin, cellulose, glucan, chitosan, mannan, and other complex polysaccha des. Vegetative growth is by hyphal elongation and carbon catabolism is obligately aerobic. In contrast, vegetative growth by yeasts such as Saccharomyces cerevisiae is by budding of a unicellular thallus and carbon catabolism may be fermentative. In a more particular embodiment, the filamentous fungal host cell is a cell of a species of, but not limited to, Acremonium, Aspergillus, Fusarium, Humicola, Mucor, Myceliophthora, Neurospora, Penicillium, Thielavia, Tolypocladium, and Trichoderma or a teleomorph or synonym thereof. In a particular embodiment, the filamentous fungal host cell is an Aspergillus cell. In another particular embodiment, the filamentous fungal host cell is an Acremonium cell. In another particular embodiment, the filamentous fungal host cell is a Fusarium cell. In another particular embodiment, the filamentous fungal host cell is a Humicola cell. In another particular embodiment, the filamentous fungal host cell is a Mucor cell. In another particular embodiment, the filamentous fungal host cell is a Myceliophthora cell. In another particular embodiment, the filamentous fungal host cell is a Neurospora cell. In another particular embodyment, the filamentous fungal host cell is a Penicillium cell. In another even more particular embodiment, the filamentous fungal host cell is a Thielavia cell. In another particular embodiment, the filamentous fungal h ost cell i s a Tolypocladium cell. In a nother particular embodiment, the filamentous fungal host cell is a Trichoderma cell. In a particular
embodiment, the filamentous fungal host cell is an Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus, Aspergillus niger or Aspergillus oryzae cell. In another particular embodiment, the filamentous fungal host cell is a Fusarium cell of the section Discolor (also known as the section Fusarium). For example, the filamentous fungal parent cell may be a Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium s ulphureum, o r Fusarium trichothecioides cell. In a nother particular e mbodiment, the filamentous fungal cell is a Fusarium strain of the section Elegans, e.g., Fusarium oxysporum. In another particular embodiment, the filamentous fungal host cell is a Humicola insolens or Humicola lanuginosa cell. In another particular embodiment, the filamentous fungal host cell is a Mucor miehei cell. In another particular embodiment, the f ilamentous fungal host cell is a Myceliophthora thermophilum cell. In another particular embodiment, the filamentous fungal host cell is a Neurospora crassa cell. In another particular embodiment, the filamentous fungal host cell is a Penicillium purpurogenum cell. In another particular embodiment, the filamentous fungal host cell is a Thielavia terrestris cell. In another particular embodiment, the Trichoderma cell is a Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei or Trichoderma viride cell.
The demannosylated protein/polypeptide produced according to the invention is suited for therapeutic/pharmaceutical applications in pure form or comprised in a pharmaceutical composition.
In a further aspect the present invention therefore relates to a use of a therapeutic recombinant polypeptide expressed in a fungal host for the preparation of a medicament, wherein a therapeutic polypeptide free of O-linked mannose residues is provided by enzymatic treatment of the recombinant polypeptide with a glycosidase having mannosidase activity.
In a particular embodiment the glycosidase having mannosidase activity is chosen from the enzyme classes consisting of EC 3.2.1.24, EC 3.2.1.114 and EC 3.2.1.113.
Another embodiment of the invention relates to the use of a glycosidase having mannosidase activity for complete demannosylation of a therapeutic recombinant polypeptide expressed in a fungal host.
EXAMPLES
Example 1 Demannosylation of Di-O-mannosylated GLP1 7'37. K34R with Jack Bean 5 alpha-mannosidase.
Dimannosylated GLP1 7~37, K34R was dissolved in 50 ml NaAc-buffer (0.1 M pH 5.0) to a final concentration of 0.16 mg/ml . One ml of the GLP1 -substrate solution was mixed with 150 micro litre ZnCI2 (20 mM, 2.73 g/l), 25 micro litre alpha-mannosidase (19 units/ml, 95 mg Jack Bean ιo alpha-mannosidase from Sigma in 5.0 ml NaAc-buffer (0.1 M pH 5.0), 250 micro litre Complete protease inhibitor (One tablet in 2 ml water. Complete is available from Boeh nger) and incubation was carried o ut at 37°C. Previous experiments had revealed an urgent need for protease inhibitors due to protease contaminants in the jack bean preparation. At different time point samples were stopped with 2 M HAc (1 :1) and analyzed by HPLC.
15 HPLC analysis was performed on a LC1090 HPLC instrument (Agilent Technologies, Palo Alto, CA) using a VYDAC 214TP54 Protein C4 column with the dimensions 2.1 x 250 mm. The chromatography was performed at room temperature with the following gradient: 20-60% B in 15 minutes, where buffer A is 0.1% TFA in water and buffer B is 0.07% TFA in acetonitril.
20 The UV absorbance was measured at 214 nm, and the flow rate was 1 ml/min.
Mass spectrometric analysis was performed on a Voyager RP MALDI-TOF instrument (Perseptive Biosystems Inc., Framingham, MA) equipped with a nitrogen laser (337 nm). The instrument was operated in linear mode with delayed extraction, and the accelerating 25 voltage in the ion source was 25kV.
Sample preparation was done as follows: 1 micro litre sample-solution was mixed with 10 micro litre matrix-solution (Sinapinic acid dissolved in a 5:4:1 mixture of acetonitrile:water:3% TFA) and 1 micro litre of this mixture was deposited on the sample plate and allowed to dry
30 before insertion into the mass spectrometer. Calibration was performed using external standards (a range of standard peptides) and the resulting accuracy of the mass determinations is within 0.1%.
The results are shown in table 1 below and shows that the main part of the substrate (approx.
35 50%) is demannosylated after 5.25 hours of treatment, but only approx. 24% to the non- mannosylated form. The time-limiting step seems to be conversion of mono-mannosylated
GLP1 to non-mannosylated GLP1. Complete demannosylation of all the substrate therefore requires longer incubation.
Table 1 : Demannosylation of GLP1 with Jack Bean alpha-mannosidase.
Time course of demannosylated GLP1 shown in %.
Example 2 Demannosylation of O-mannosylated monoqlvcosylated human insulin. MG2 with Jack Bean alpha-mannosidase.
The experiment is performed as previously described under example 1 , with the following changes.
2000 micro litre substrate (MG-HI, 0.32 mg/ml), 300 micro litre ZnCI2 (20 mM), 500 micro litre Complete, 2000 micro litre alpha-mannosidase (19 units/ml).
Incubation temperature was 37°C, and incubation was continued for 100 hours.
The results are shown in table 2 below, and show that approximately 10 % of the substrate is completely demannosylated in 3 days.
Table 2: Demannosylation of MG2 with Jack Bean alpha-mannosidase.
Example 3 Cloning of Streptomyces coelicolor alpha-mannosidase (SCM) and 5 Thermotoga maritima alpha-mannosidase (TMM).
PCR: The ORF's encoding Streptomyces coelicolor alpha-mannosidase, SCM (Swiss Prot Ace: Q9RIV8) and the Thermotoga maritima alpha-mannosidase, TMM (Swiss Prot Ace: Q9X2G6) io comprises 3024 bp and 3033 bp, respectively from start to stop codon.
PCR amplification of SCM and TMM was done using primers designed to comprise the entire alpha-mannosidase encoding sequences retrieved from the published S. coelicolor and 7. maritima genome. Purified genomic DNA from S. coelicolor (Cat. No.:BAA-471 D) and 7. is maritima (Cat. No.: 43589D) was obtained from American Type Culture Collection (ATCC)
The SCM ORF was amplified with a 5'-end primer comprising a Ndel site and a 3'-end primer comprising a Xhol, Sacl and BamHI site. The TMM ORF was amplified with a 5'-end primer comprising a Ndel site and a 3'-end primer comprising the naturally occurring Xhol site present 20 16 bp downstream from the stop codon of TMM. A -3 kbp PCR product was amplified from genomic DNA from both bacteria with 15 PCR cycles using standard PCR conditions, except that 10% DMSO was added to the PCR mixture upon amplification of the GC-rich SCM.
Cloning and sequencing:
25 Purified PCR products of correct size were obtained after 1 % agarose gels separation (using GFX kit, Amersham) a nd l igated i nto the p CRTOPO2.1 a nd by standard TOPO TA cloning procedure (Invitrogen). E. coli competent cells (One Shot TOP10) were transformed with TOPO plasmids and blue/white colour selection for plasmids containing inserts was done on IPTG/X-Gal plates with ampicillin. Insert positive colonies were cultured overnight in LB
medium with ampicillin and plasmids are purified (Mini prep kit, Qiagen). Following sequence verification of selected plasmids, inserts comprising the correct sequences were released with Ndel/BamHI (SCM) or Ndel/Xhol (TCM) and ligated into the pET11a expression vector, thus yielding SCM-pET vector and TCM-pET encoding full length alpha-mannosidases. E. coli 5 competent cells (TOP10) were transformed with SCM-pET and TMM-pET and colonies having the desired inserts, as judged by RE cleavage, were cultivated overnight in LB/ampicillin medium to obtain plasmid for transformation into expression strains.
Expression in E. coli:0 E. coli BL21(DE3) or Rosetta (DE3) (Novagen) were transformed with SCM-pET and TMM- pET, respectively. Transformants were cultivated in LB medium with ampicillin (BL21 ) or ampicillin+chloramphinicol (Rosetta) until OD6oo 0.4-0.6 is reached. Protein induction with 0.1- 0.5 M IPTG was performed for 3 hours at 37°C or overnight at 18°C. Following induction, cultures were pelleted and cells were lysed by sonication in non-denaturing phosphate buffer.s After centrifugation, supernatants were evaluated for the presence of soluble alpha- mannosidase by separation on SDS-PAGE gels. For TMM, a heat precipitation step at 70°C for 30 minutes of the supernatant is included after sonication in order to remove the major bulk of E. coli contaminants. 0 Example 4 De-mannosylation with Thermotoga maritima alpha-mannosidase (TMM)
Supernatants (crude enzyme) from example 3 containing SCM or TCM were incubated with tetraglycosylated human GLP1 and monoglycosylated human insulin MG2 (see Example 2). 5 For TMM, a heat precipitated crude supernatant was tested using the following reaction mixture: 200 micro litre GLP1 (2 mg/ml) or MG2-insulin (0.32 mg/ml), 12.5 micro litre CoCI2, 200 m icro I itre c rude TMM , 87.5 m icro I itre o f 1 OmM p hosphate b uffer p H 7 i n a r eaction volume of 500 micro litre. o Samples were incubated at 40°C, 50°C, 60°C and 70°C and samples were evaluated by MALDI-TOF MS every hour. The crude TMM enzyme preparation was able to completely demannosylate up to 99% of GLP-1 within 1-2 hours at temperatures down to 40°C (Table 3). TMM was able to completely demannosylate approx. 50% of MG2 insulin after 3 hours incubation at 70°C (Table 4).5
Table 3: Glycosylation distribution of GLP1
Table 4: Glycosylation distribution of MG2 insulin