Title:  Processed polypeptides with IL-16 activity, process for preparing the same and their use

United States Patent:  6,506,582

Issued:  January 14, 2003

Inventors:  Kurth; Reinhard (Dreieich, DE); Baier; Michael (Frankfurt, DE); Bannert; Norbert (Frankfurt, DE); Werner; Albrecht (Weinheim, DE); Lang; Kurt (Penzberg, DE)

Assignee:  Bundesrepublik Deutschland vertreten durch den Bundesminister fur (Bonn, DE)

Appl. No.:  171962

Filed:  February 25, 1999

PCT Filed:  November 6, 1997

PCT NO:  PCT/EP97/02216

371 Date:  April 30, 1997

A nucleic acid which can be used to express a polypeptide with interleukin-16 activity in a prokaryotic or eukaryotic host cell wherein the nucleic acid codes for a polypeptide with the amino acid sequence SEQ ID NO:2 or a SEQ ID NO:2 elongated N-terminally by an aspartic acid residue or a form shortened at the C-terminus by up to 8 amino acids, and is suitable for the production of an active IL-16 polypeptide.

Description of the Invention

The invention concerns polypeptides with IL-16 activity, processes for their production and their use. The invention describes processed IL-16 with high activity.

IL-16 (interleukin-16) is a lymphokine which is also referred to as lymphocyte chemoattracting factor (LCF) or immunodeficiency virus suppressing lymphokine (ISL). IL-16 and its properties are described in WO 94/28134 and WO 96/31607 and by Cruikshank, W. W., et al., Proc. Natl. Acad. Sci. USA 91 (1994) 5109-5113 and by Baier, M., et al., Nature 378 (1995) 563. The recombinant production of IL-16 is also described in these references. According to these IL-16 is a protein with a molecular mass of 13,385 D. Cruikshank also found that ISL elutes in a molecular sieve chromatography as a multimeric form with a molecular weight of 50-60 and 55-60 kD. The chemoattractant activity has been attributed to this multimeric form which is a cationic homotetramer (product information AMS Biotechnology Ltd., Europe, Cat. No. 11177186). A homodimeric form of IL-16 with a molecular weight of 28 kD is described by Baier. However, the chemoattractant activity described by Cruikshank et al. in J. Immunol. 146 (1991) 2928-2934 and the activity of recombinant human IL-16 described by Baier are very small.

The object of the present invention is to improve the activity of IL-16 and to provide IL-16 forms which have a low immunogenicity and are advantageously suitable for a therapeutic application.

The object of the invention is achieved by a nucleic acid which can be used to express a polypeptide with interleukin-16 activity in a prokaryotic or eukaryotic host cell wherein the said nucleic acid

a) corresponds to the DNA sequence of SEQ ID NO:1 or to a DNA elongated at the 5' end by an aspartic acid codon (GAC), or to its complementary strand

b) hybridizes under stringent conditions with the DNA of SEQ ID NO:1 or with a DNA which is elongated at the 5' end by an aspartic acid codon,

c) or is a nucleic acid sequence which would hybridize under stringent conditions with the nucleic acid sequences defined by a) or b) without the degeneracy of the genetic code.

d) and at the 5' end codes for one of the amino acid sequences SEQ ID NO:7 to 10 or for analogous sequences which are elongated N-terminally by one aspartic acid.

Such a nucleic acid preferably codes for a polypeptide with the amino acid sequence SEQ ID NO:2 or for a polypeptide with a sequence which, compared to SEQ ID NO:2, is elongated N-terminally by one aspartic acid codon. In a further preferred embodiment the nucleic acid codes for a polypeptide with IL-16 activity which is shortened by up to 8 amino acids at the C-terminus.

Such a nucleic acid codes for a processed polypeptide with IL-16 activity, particularly preferably natural IL-16 from primates such as human IL-16 or IL-16 of an ape species or of another mammal such as the mouse.

It has surprisingly turned out that FIG. 2 of WO 94/28134 does not describe the correctly processed IL-16. The start codon "ATG" of the precursor form of the protein does not begin with nucleotide 783 but rather with nucleotide 54 or 174. This reading frame results when an A is inserted after nucleotide 156, a C is inserted after nucleotide 398 and a G is inserted after nucleotide 780. The sequence also shows further differences to FIG. 2 of WO 94/28134. These are for example nucleotide substitutions (313 G into A, 717 C into A). IL-16 is processed during the expression in eukaryotic cells. In this way a polypeptide according to SEQ ID NO:2 and/or a polypeptide with a sequence that is elongated N-terminally compared to SEQ ID NO:2 by one aspartic acid codon. Knowledge of the processed IL-16 enables the production of IL-16 and derivatives with high activity and low immunogenicity.

The sequence of IL-16 can differ to a certain extent from protein sequences coded by such DNA sequences. Such sequence variations may be amino acid substitutions, deletions or additions. However, the amino acid sequence of IL-16 is preferably at least 75% and particularly preferably at least 90% identical to the amino acid sequence of SEQ ID NO:2. Variants of parts of the amino and of the nucleic acid sequences SEQ ID NO:1/SEQ ID NO:2 are for example described in WO 96/31607 and the International Patent Applications PCT/EP96/05662 and PCT/EP96/05661. However, it is essential that the polypeptides have a correct N-terminus. Consequently proteins are preferred in which the first three to ten amino acids of the N-terminus are unchanged and thus begin N-terminally with the amino acid sequences SEQ ID NO:6 to 8 or with analogous sequences which are extended N-terminally by an aspartic acid residue. Proteins are also preferred which are shortened at the C-terminus by up to 8 amino acids.

Nucleic acids within the sense of the invention are understood for example as DNA, RNA and nucleic acid derivatives and analogues. Preferred nucleic acid analogues are those compounds in which the sugar phosphate backbone is replaced by other units such as e.g. amino acids. Such compounds are referred to as PNA and are described in WO 92/20702. Since PNA-DNA bonds are for example stronger than DNA-DNA bonds, the stringent conditions described below are not applicable to PNA-DNA hybridization. However, suitable hybridization conditions are described in WO 92/20703.

The term "IL-16" is understood within the sense of the invention as a polypeptide with the activity of IL-16. IL-16 preferably exhibits the stated action in the test procedure described in WO 96/31607 or stimulates cell division according to WO 94/28134.

IL-16 binds to CD4⁺ lymphocytes and can suppress the replication of viruses such as for example HIV-1, HIV-2 and SIV. The function of IL-16 is not limited by its presentation in the MHC complex.

In particular IL-16 exhibits one or several of the following properties:

binding to T cells via the CD4 receptor,

stimulation of the expression of the IL-2 receptor and/or HLA-DR antigen on CD4⁺ lymphocytes,

stimulation of the proliferation of T helper cells in the presence of IL-2,

suppression of the proliferation of T helper cells stimulated with anti-CD3 antibodies,

suppression of the replication of viruses preferably of HIV-1, HIV-2 or SIV.

Nucleic acids are preferred which hybridize with nucleic acids of the sequence SEQ ID NO:1 under stringent conditions. The term "hybridize under stringent conditions" means that two nucleic acid fragments hybridize with one another under standardized hybridization conditions as described for example in Sambrook et al., "Expression of cloned genes in E. coli" in Molecular Cloning: A laboratory manual (1989), Cold Spring Harbor Laboratory Press, New York, USA. Such conditions are for example hybridization in 6.0.times.SSC at about 45^oC. followed by a washing step with 2.times.SSC at 50^oC. In order to select the stringency the salt concentration in the washing step can for example be chosen between 2.0.times.SSC at 50^oC. for low stringency and 0.2.times.SSC at 50^oC. for high stringency. In addition the temperature of the washing step can be varied between room temperature, ca. 22^oC., for low stringency and 65^oC. for high stringency.

IL-16 is preferably produced recombinantly in prokaryotic or eukaryotic host cells. Such production processes are described for example in WO 94/28134 and WO 96/31607 which are also for this purpose a subject matter of the disclosure of the present invention. However, in order to obtain the forms according to the invention of IL-16 by recombinant production in a defined and reproducible manner, additional measures have to be taken beyond the processes for recombinant production familiar to a person skilled in the art.

Recombinant IL-16 can be produced by methods familiar to a person skilled in the art as heterologous expression or as homologous expression (after homologous recombination of the IL-16 nucleic acid into the genome of the host organism). For this a DNA is firstly produced which is able to produce a protein which has the activity of IL-16. The DNA is cloned into a vector which can be transferred into a host cell and can be replicated there. Such a vector contains regulator elements in addition to the IL-16 sequence which are necessary for the expression of the DNA sequence. This vector which contains the IL-16 sequence and the regulator elements is transferred into a vector which is able to express the DNA of IL-16. The host cell is cultured under conditions which are suitable for the amplification of the vector and IL-16 is isolated. In this process suitable measures ensure that the protein can adopt an active tertiary structure in which it exhibits IL-16 properties.

The nucleic acid sequence of the protein can also be modified. Such modifications are for example:

modification of the nucleic acid in order to introduce various recognition sequences of restriction enzymes to facilitate the steps of ligation, cloning and mutagenesis

modification of the nucleic acid to incorporate preferred codons for the host cell

extension of the nucleic acid by additional operator elements in order to optimize expression in the host cell.

The protein is preferably expressed in microorganisms in particular in prokaryotes and in this case in E. coli. The expression in prokaryotes yields an unglycosylated polypeptide.

The expression vectors must contain a promoter which allows expression of the protein in the host organism. Such promoters are known to a person skilled in the art and are for example the lac promoter (Chang et al., Nature 198 (1977) 1056), trp promoter (Goeddel et al., Nuc. Acids Res. 8 (1980) 4057), .lambda._PL promoter (Shimatake et al., Nature 292 (1981) 128) and T5 promoter (U.S. Pat. No. 4,689,406). Synthetic promoters such as for example the tac promoter (U.S. Pat. No. 4,551,433) are also suitable. Coupled promoter systems are equally suitable such as for example the T7-RNA polymerase/promoter system (Studier et al., J. Mol. Biol. 189 (1986) 113). Hybrid promoters composed of a bacteriophage promoter and the operator region of the microorganism (EP-A 0 267 851) are also suitable. An effective ribosome binding site is necessary in addition to the promoter. In the case of E. coli this ribosome binding site is referred to as the Shine-Dalgarno (SD) sequence (Sambrook et al., "Expression of cloned genes in E. coli" in Molecular Cloning: A laboratory manual (1989) Cold Spring Harbor Laboratory Press, New York, USA).

In order to improve expression it is possible to express the protein as a fusion protein. In this case a DNA sequence which codes for the N-terminal part of an endogenous bacterial protein or another stable protein is usually fused to the 5' end of the sequence coding for IL-16. Examples of this are for example lacZ (Phillips and Silhavy, Nature 344 (1990) 882-884), trpE (Yansura, Meth. Enzymol. 185 (1990) 161-166).

After expression of the vector which is preferably a biologically functional plasmid or a viral vector, the fusion proteins are preferably cleaved with enzymes (e.g. factor Xa) (Nagai et al., Nature 309 (1984) 810). Further examples of cleavage sites are the IgA protease cleavage site (WO 91/11520, EP-A 0 495 398), the ubiquitin cleavage site (Miller et al., Bio/Technology 7 (1989) 698) and the enterokinase cleavage site.

The proteins expressed in this manner in bacteria are obtained in the usual manner by disrupting the bacteria and isolating the protein.

In a further embodiment it is possible to secrete the proteins from the microorganisms as active proteins. For this a fusion product is preferably used which is composed of the signal sequence that is suitable for secretion of proteins in the host organisms used and of the nucleic acid that codes for the protein. In this case the protein is either secreted into the medium (in gram-positive bacteria) or into the periplasmatic space (in gram-negative bacteria). It is expedient to insert a cleavage site between the signal sequence and the sequence coding for IL-16 which allows cleavage of the protein either during processing or in an additional step. Such signal sequences are derived for example from ompA (Ghrayeb et al., EMBO J. 3 (1984) 2437), phoA (Oka et al., Proc. Natl. Acad. Sci. USA 82 (1985) 7212).

The vectors additionally contain terminators. Terminators are DNA sequences that signal the end of a transcription process. They are usually characterized by two structural features: a reversely repetitive G/C-rich region which can form a double helix intramolecularly as well as a number of U (or T) residues. Examples are the main terminator in the DNA of the phages fd (Beck and Zink, Gene 16 (1981) 35-38) and rrnB (Brosius et al., J. Mol. Biol. 148 (1981) 107-127).

In addition the expression vectors usually contain a selectable marker in order to select transformed cells. Such selectable markers are for example the resistance genes for ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracyclin (Davies et al., Ann. Rev. Microbiol. 32 (1978) 469). Selectable markers which are equally suitable are the genes for essential substances for the biosynthesis of substances necessary for the cell such as e.g. histidine, tryptophan and leucine.

Numerous suitable bacterial vectors are known. Vectors have for example been described for the following bacteria: Bacillus subtilis (Palva et al., Proc. Natl. Acad. Sci. USA 79 (1982) 5582), E. coli (Aman et al., Gene 40 (1985) 183; Studier et al., J. Mol. Biol. 189 (1986) 113), Streptococcus cremoris (Powell et al., Appl. Environ. Microbiol. 54 (1988) 655), Streptococcus lividans and Streptomyces lividans (U.S. Pat. No. 4,747,056).

Further genetic engineering methods for the production and expression of suitable vectors are described in J. Sambrook et al., Molecular cloning: a laboratory manual (1989), Cold Spring Harbor Laboratory Press, New York, N.Y.

In addition to prokaryotic microorganisms it is also possible to express recombinant IL-16 in eukaryotes (such as for example CHO cells, yeast or insect cells). The yeast system or insect cells are preferred as a eukaryotic expression system. Expression in yeast can be achieved by means of three types of yeast vectors: (integrating YI_P (yeast integrating plasmids) vectors, replicating YR_P (yeast replicon plasmids) vectors and episomal YE_P (yeast episomal plasmids) vectors. More details of this are described for example in S. M. Kingsman et al. Tibtech 5 (1987) 53-57.

The invention in addition concerns a prokaryotic or eukaryotic host cell which is transformed or transfected with a nucleic acid which codes for an IL-16 polypeptide according to the invention in such a way that the host cell expresses the said polypeptide. Such a host cell usually contains a biologically functional nucleic acid vector, preferably a DNA vector, a plasmid DNA, which contains this nucleic acid.

A monomeric IL-16 polypeptide is additionally preferred which cannot be cleaved into further subunits.

It has surprisingly turned out that the nucleic acid and the protein sequence of IL-16 described in WO 94/28134 do not correspond to the natural human sequences. It is merely a non-natural IL-16 analogue. However, a protein is preferably used for a therapeutic application which is either identical to the natural protein or only differs slightly from the natural protein and at least exhibits comparable activity and immunogenicity. The sequence of the protein is described in SEQ ID NO:2 (optionally with N-terminal elongation by an aspartic acid residue and/or shortening at the C-terminus by up to 8 amino acids).

The nucleic acid sequence of IL-16 can, within the scope of the invention contain deletions, mutations and additions. The monomeric form of IL-16 can be multimerized in a preferred embodiment. The activity of IL-16 can be increased in this manner. Such multimeric forms are preferably dimeric, tetrameric or octameric forms.

In a further embodiment the polypeptides of the invention can additionally contain a defined amount of metal ions, the number of metal ions per subunit being preferably 0.5 to 2.

Numerous metal ions are suitable as metal ions within the sense of the invention. It has turned out that alkaline earth metals as well as elements of the side groups are suitable. Alkaline earth metals, cobalt, zinc, selenium, manganese, nickel, copper, iron, magnesium, calcium, molybdenum and silver are particularly suitable. The ions may be monovalent, divalent, trivalent or tetravalent. Divalent ions are particularly preferred. The ions are preferably added as solutions of MgCl₂, CaCl₂, MnCl₂, BaCl₂, LiCl₂, Sr(NO₃)₂, Na₂ MoO₄, AgCl₂.

Such multimeric forms and forms of IL-16 containing metal ions are described in the International Patent Application PCT/EP96/05661.

The polypeptide according to the invention can be produced by culturing a prokaryotic or eukaryotic host cell which has been transformed or transfected with a nucleic acid sequence as claimed in claims 1 or 2 under suitable nutrient conditions and optionally isolating the desired polypeptide. If it is intended to produce the polypeptide in vivo in the context of a gene therapy treatment, the polypeptide is of course not isolated from the cell.

A further subject matter of the invention is a pharmaceutical composition which contains a polypeptide according to the invention in an amount and/or specific activity which is sufficient for a therapeutic application as well as optionally a pharmaceutically suitable diluent, adjuvant and/or carrier.

The polypeptides according to the invention are especially suitable for treating pathological states which are caused by viral replication, in particular retroviral replication, and for immunomodulation. Such therapeutic applications are also described in WO 96/31607. This also describes diagnostic test procedures.

The polypeptides according to the invention can also be preferably used for immunosuppression. This immunosuppression is preferably achieved by an inhibition of the helper function of the TH₀ and/or TH₁ and/or TH₂ cells. Hence the polypeptides according to the invention are of therapeutic value in all diseases in which an immunodysregulatory component is postulated in the pathogenesis and in particular a hyperimmunity. Diseases which can be treated by IL-16 in cardiology/angiology are for example diseases such as myocarditis, endocarditis and pericarditis, in pulmonology for example bronchitis, asthma, in haematology autoimmune neuropenias and transplant rejection, in gastroenterology chronic gastritis, in endocrinology diabetes mellitus type I, in nephrology glomerulonephritis, rheumatic diseases, diseases in ophthalmology, in neurology such as multiple sclerosis and eczemas in dermatology. The polypeptides according to the invention can be used in particular for autoimmune diseases, allergies and to avoid transplant rejections.

The invention furthermore concerns the use of the nucleic acids according to the invention within the context of gene therapy. Retroviral or non-viral vector systems are for example suitable vector systems for this.

In addition the invention concerns a polyclonal or monoclonal anti-IL-16 antibody or an immunoactive fragment thereof which binds to the first 3-20 amino acids of SEQ ID NO:2 or to SEQ ID NO:2 elongated N-terminally by an aspartic acid residue as well as processes for the production of such antibodies and their use for the determination of IL-16 and for determining viral infections in eukaryotic cells and in particular in mammalian cell material. Virus-activated mammalian cells and in particular T cells can also be determined with IL-16. The production of such antibodies is carried out by immunization with a polypeptide according to the invention. The production of such an antibody is carried out according to processes familiar to a person skilled in the art by immunizing with an immunogen which contains the first 3-20 amino acids of SEQ ID NO:2 or a SEQ ID NO:2 elongated N-terminally by an aspartic acid residue as the hapten. Subsequently the antibody can be isolated in the usual manner from the immunized mammal and optionally a monoclonal antibody can be produced.

Claim 1 of 18 Claims

What is claimed is:

1. An isolated nucleic acid encoding a polypeptide with interleukin-16 (IL-16) activity, wherein the IL-16 activity is at least one activity selected from the group consisting of (1) binding to T cells via the CD4 receptor, (2) stimulating the expression of the IL-2 receptor and/or HLA-DR antigen on CD4* lymphocytes, (3) stimulating the proliferation of T helper cells in the presence of IL-2, (4) suppressing the proliferation of T helper cells stimulated with anti-CD3 antibodies, and (5) suppressing the replication of viruses, wherein the nucleic acid sequence is selected from the group consisting of

(A) the nucleic acid sequence of SEQ ID NO:1,

(B) the nucleic acid sequence if SEQ ID NO:1 extended at the 5'-end by an aspartic acid codon, and

(C) the nucleic acid sequence of SEQ ID NO:1 shortened at the 3'-end by 1 to 8 amino acid codons.

 

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