# Patent

## Title
Derivatives of choline binding proteins for vaccines

## Abstract

The present invention provides bacterial immunogenic agents for administration to humans and non-human animals to stimulate an immune response. It particularly relates to the vaccination of mammalian species with pneumococcal derived polypeptides that include an alpha helix but exclude a choline binding region as a mechanism for stimulating production of antibodies that protect the vaccine recipient against infection by pathogenic bacterial species. In another aspect the invention provides antibodies against such proteins and protein complexes that may be used as diagnostics and/or as protective/treatment agents for pathogenic bacterial species.

## Background
This application is a Divisional of U.S. application Ser. No. 10/254,995, filed 25 Sep. 2002 now U.S. Pat. No. 6,863,893 which is a divisional of U.S. application Ser. No. 09/286,981, filed 6 Apr. 1999, now U.S. Pat. No. 6,503,511, which claims the benefit of U.S. Provisional Application Ser. No. 60/085,743, filed May 15, 1998 and U.S. Provisional Application Ser. No. 60/080,878, filed Apr. 7, 1998, the disclosures of all of which are hereby incorporated by reference in their entirety.


This invention relates generally to the field of bacterial antigens and their use, for example, as immunogenic agents in humans and animals to stimulate an immune response. More specifically, it relates to the vaccination of mammalian species with a polypeptide comprising an alpha helix-forming polypeptide obtained from a choline binding polypeptide as a mechanism for stimulating production of antibodies that protect the vaccine recipient against infection by pathogenic bacterial species. Further, the invention relates to antibodies and antagonists against such polypeptides useful in diagnosis and passive immune therapy with respect to diagnosing and treating such pneumococcal infections.
In a particular aspect, the present invention relates to the prevention and treatment of pneumonococcal infections such as infections of the middle ear, nasopharynx, lung and bronchial areas, blood, CSF, and the like, that are caused by pneumonococcal bacteria. In this regard, certain types of Streptococcus pneumoniae are of particular interest.
S. pneumoniae is a gram positive bacteria which is a major causative agent in invasive infections in animals and humans, such as sepsis, meningitis, otitis media and lobar pneumonia (Tuomanen, et al. NEJM 322:1280-1284 (1995)). As part of the infective process, pneumococci readily bind to non-inflamed human epithelial cells of the upper and lower respiratory tract by binding to eukaryotic carbohydrates in a lectin-like manner (Cundell et al., Micro. Path. 17:361-374 (1994)). Conversion to invasive pneumococcal infections for bound bacteria may involve the local generation of inflammatory factors which may activate the epithelial cells to change the number and type of receptors on their surface (Cundell, et al., Nature, 377:435-438 (1995)). Apparently, one such receptor, platelet activating factor (PAF) is engaged by the pneumococcal bacteria and within a very short period of time (minutes) from the appearance of PAF, pneumococci exhibit strongly enhanced adherence and invasion of tissue. Certain soluble receptor analogs have been shown to prevent the progression of pneumococcal infections (Idanpaan-Heikkila et al., J. Inf. Dis., 176:704-712 (1997)).
A family of choline binding proteins (CBPs), which are non-covalently bound to phosphorylcholine, are present on the surface of pneumococci and have a non-covalent association with teichoic acid or lipoteichoic acid. An example of such family is choline binding protein A (CbpA), an approximately 75 kD weight type of CBP which includes a unique N-terminal domain, a proline rich region, and a C-terminal domain comprised of multiple 20 amino acid repeats responsible for binding to choline. A segment of the N-terminal portion of CbpA protein forms an alpha helix as part of its three-dimensional structure.
Accordingly, it is an object of the present invention to provide a polypeptide having broad protection against pneumococcal infections.
Definitions
In order to facilitate understanding of the description below and the examples which follow certain frequently occurring methods and/or terms will be described.
“Plasmids” are designated by a lower case p preceded and/or followed by capital letters and/or numbers. The starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures. In addition, equivalent plasmids to those described are known in the art and will be apparent to the ordinarily skilled artisan.
“Digestion” of DNA refers to catalytic cleavage of the DNA with a restriction enzyme that acts only at certain sequences in the DNA. The various restriction enzymes used herein are commercially available and their reaction conditions, cofactors and other requirements were used as would be known to the ordinarily skilled artisan. For analytical purposes, typically 1 μg of plasmid or DNA fragment is used with about 2 units of enzyme in about 20 μl of buffer solution. For the purpose of isolating DNA fragments for plasmid construction, typically 5 to 50 μg of DNA are digested with 20 to 250 units of enzyme in a larger volume. Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer. Incubation times of about 1 hour at 37° C. are ordinarily used, but may vary in accordance with the supplier's instructions. After digestion the reaction is electrophoresed directly on a polyacrylamide gel to isolate the desired fragment.
Size separation of the cleaved fragments is performed using 8 percent polyacrylamide gel described by Goeddel, D. et al., Nucleic Acids Res., 8:4057 (1980).
“Oligonucleotides” refers to either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5′ phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide will ligate to a fragment that has not been dephosphorylated.
“Ligation” refers to the process of forming phosphodiester bonds between two double stranded nucleic acid fragments (Maniatis, T., et al., Id., p. 146). Unless otherwise provided, ligation may be accomplished using known buffers and conditions with 10 units to T4 DNA ligase (“ligase”) per 0.5 μg of approximately equimolar amounts of the DNA fragments to be ligated.
“HPS portion” as used herein refers to an amino acid sequence as set forth in SEQ ID NO:2 for a choline binding protein (“CBP”) of a pneumococcal bacteria that may be located amino terminal with respect to the proline rich portion of the overall amino acid sequence for such CBP.
The terms “identity”, “% identity” or “percent identity” as utilized in this application refer to a calculation of differences between two contiguous sequences which have been aligned for “best fit” (to provide the largest number of aligned identical corresponding sequence elements, wherein elements are either nucleotides or amino acids) and all individual differences are considered as individual difference with respect to the identity. In this respect, all individual element gaps (caused by insertions and deletions with respect to an initial sequence (“reference sequence”)) over the length of the reference sequence and individual substitutions of different elements (for individual elements of the reference sequence) are considered as individual differences in calculating the total number of differences between two sequences. Individual differences may be compared between two sequences where an initial sequences (reference sequence) has been varied to obtain a variant sequence (comparative sequence) or where a new sequence (comparative sequence) is simply aligned and compared to such a reference sequence. When two aligned sequences are compared all of the individual gaps in BOTH sequences that are caused by the “best fit” alignment over the length of the reference sequence are considered individual differences for the purposes of identity. If an alignment exists which satisfies the stated minimum identity, then a sequence has the stated minimum identity to the reference sequence. For example, the following is a hypothetical comparison of two sequences having 100 elements each that are aligned for best fit wherein one sequence is regarded as the “reference sequence” and the other as the comparative sequence. All of the individual alignment gaps in both sequences are counted over the length of the reference sequence and added to the number of individual element substitution changes (aligned elements that are different) of the comparative sequence for the total number of element differences. The total number of differences (for example 7 gaps and 3 substitutions) is divided by the total number of elements in the length of the reference sequence (100 elements) for the “percentage difference” (10/100). The resulting percentage difference (10%) is subtracted from 100% identity to provide a “% identity” of 90% identity. For the identity calculation all individual differences in both sequences are considered in the above manner over a discrete comparison length (the length of the reference sequence) of two best fit aligned sequences to determine identity. Thus, no algorithm is necessary for such an identity calculation.
“Isolated” in the context of the present invention with respect to polypeptides and/or polynucleotides means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living organism is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment. The polypeptides and polynucleotides of the present invention are preferably provided in an isolated form, and preferably are purified to homogeneity.
SUMMARY OF THE INVENTION
In one aspect the present invention relates to a vaccine for treating or preventing pneumococcal bacterial infections which utilizes as an immunogen at least one polypeptide truncate of a pneumococcal surface-binding protein, analog, or variant having a highly conserved immunogenic alpha-helical portion (corresponding generally to a “consensus” amino acid sequence as set forth in SEQ ID NO:1) with respect to different types of pneumococcal bacteria, which polypeptide does not include a choline-binding portion. Preferably, the C-terminal choline-binding portion is absent from such polypeptides. More preferred are such polypeptides wherein the HPS amino acid sequence is also absent. Even further preferred are polypeptides wherein the highly conserved immunogenic alpha-helical portion corresponding generally to a “consensus” amino acid sequence as set forth in SEQ ID NO:1 also corresponds generally to the amino acid sequence as set forth in SEQ ID NO:19 (amino acids 1 to 103 of SEQ ID NO:19 are identical to amino acids 1 to 103 of SEQ ID NO:1). Also preferred as vaccines are recombinantly-produced, isolated polypeptides that are missing both an HPS portion and the choline-binding portion.
More preferred as vaccines are one or more polypeptide truncates of pneumococcal surface-binding proteins, analogs or variants including a single highly conserved alpha-helix immunogenic portion with respect to different types of pneumococci, which polypeptides do not include a C-terminal choline-binding portion. Further preferred are isolated recombinantly produced polypeptides having such structure. Also preferred are such polypeptides that do not include either a C-terminal choline-binding portion or a HPS portion.
The present invention further provides a vaccine comprising a polypeptide including an immunogenic portion that is capable of forming an alpha helix, which polypeptide includes a sequence that has at least 85% identity and preferably at least 87% identity to the amino acid sequence of SEQ ID NO:1, wherein the isolated polypeptide does not include a C-terminal choline-binding portion. Further preferred are such polypeptides that comprise a polypeptide sequence that has at least 85% identity and preferably at least 87% identity to an amino acid sequence according SEQ ID NO:19. Preferably, the sequence of the isolated polypeptide includes neither an HPS portion (SEQ ID NO:2) nor a C-terminal choline-binding portion. Further preferred are isolated recombinantly produced polypeptides having such structure. In particular, such polypeptides corresponding to alpha helical structures of different types of S. pneumoniae bacteria are contemplated. Particularly preferred are the serotypes 1-5, 6A, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19F, 19A, 20, 22F, 23F and 33F of such S. pneumoniae bacteria. Examples of such serotypes of bacteria are readily available from standard ATCC catalogs.
In an additional aspect, the present invention further provides a vaccine against S. pneumoniae comprising a synthetic or recombinant polypeptide comprising a plurality of alpha-helical portions, each derived from different naturally occurring S. pneumoniae choline-binding polypeptides wherein such alpha-helical portions have at least 85% identity to the amino acid sequence of SEQ ID NO:1, and wherein the isolated polypeptide does not include a choline-binding portion. Further preferred are those wherein the amino acid sequence for the alpha-helix areas is at least 85% identical to the amino acid sequence of SEQ ID NO:19. Preferably, such synthetic polypeptide includes neither a HPS portion nor a choline-binding portion. Analogs and variants of such chain structure polypeptides wherein such alpha helical portions may be synthetic variant amino acid sequences (or may be a mixture of naturally occurring and variant sequences) are also contemplated and embraced by the present invention. In a preferred aspect, chain vaccines polypeptides having at least ten different alpha helical structures corresponding to S. pneumoniae serotypes 1-5, 6A, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19F, 19A, 20, 22F, 23F and 33F are provided. Further preferred are polypeptides including at least fifteen of such alpha-helical structures, more preferred are polypeptides including at least 20 such alpha-helical structures and more preferred are polypeptides including at least one alpha-helical structure corresponding to each of the S. pneumoniae serotypes 1-5, 6A, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19F, 19A, 20, 22F, 23F and 33F. Another preferred polypeptide comprises each of the alpha helical structures from the amino acid sequences of SEQ ID NOS:3-18 which correspond to SEQ ID NO:1.
In another aspect, the invention relates to passive immunity vaccines formulated from antibodies against a polypeptide including a highly conserved immunogenic portion with respect to different types of pneumococcal bacteria which portion is capable of forming an alpha-helix having the hereinbefore described identity to the amino acid sequence of SEQ ID NO:1, which polypeptide does not include a C-terminal choline-binding portion, wherein said antibodies will bind to at least one S. pneumoniae species. Preferably, if such polypeptide is a truncate of a native pneumococcal surface-binding protein both its HPS portion (where applicable) and its choline-binding portion are absent from such polypeptide. Such passive immunity vaccines can be utilized to prevent and/or treat pneumococcal infections in immunocompromised patients, patients having an immature immune system (such as young children) or patients who already have an ongoing infection. In this manner, according to a further aspect of the invention, a vaccine can be produced from a synthetic or recombinant polypeptide wherein the polypeptide includes the conserved alpha helical portions of two or more different choline binding polypeptides of S. pneumoniae. 
This invention also relates generally to the use of an isolated polypeptide having a highly conserved immunogenic portion with respect to different types of pneumococcal bacteria which portion is capable of forming an alpha-helix (corresponding generally to SEQ ID NO:1 or to SEQ ID NO:19) wherein the isolated polypeptide does not include a choline-binding portion, to raise antibodies in non-human mammalian species useful, for example, as diagnostic reagents and vaccines.
In yet another aspect, the present invention relates to the production of a polypeptide including a highly conserved immunogenic portion with respect to different types of pneumococcal bacteria which portion is capable of forming an alpha-helix whose sequence corresponds generally to the amino acid sequence of SEQ ID NO:1 or SEQ ID NO:19, wherein the isolated polypeptide does not include a choline-binding portion. Preferably, such recombinant production is of a truncated native pneumococcal surface-binding polypeptide wherein both the HPS portion (where applicable) and the choline-binding portion are absent.
In still another aspect, the present invention provides an isolated choline-binding polypeptide, wherein the non-choline binding region of such polypeptide has at least 90% identity to the corresponding amino acid sequence portion of a naturally occurring pneumococcal surface-binding protein which is a member selected from the group consisting of SEQ ID NOS:3-18. The invention relates to fragments of such polypeptides which include at least the conserved alpha-helical portion corresponding generally to SEQ ID NO:1, and which has at least 85% identity thereto, wherein the isolated polypeptide preferably is free of a choline binding region.
In another aspect the present invention provides an isolated polypeptide comprising an amino acid sequence which has at least 90% identity to one of the amino acid sequences selected from the group consisting of SEQ ID NO:3-18. Preferably, such isolated polypeptide comprises an amino acid sequence which has at least 95% identity, and more preferably 97% identity, to one of the amino acid sequences selected from the group consisting of SEQ ID NO:3-18. The invention further relates to fragments of such polypeptides.
In a yet further aspect, the present invention provides a S. pneumoniae CBP polypeptide encoded by a polynucleotide that will hybridize under highly stringent conditions to the complement of a polynucleotide encoding a polypeptide having an amino acid selected from the group consisting of SEQ ID NOS:1 and 3-18. Particularly preferred are polypeptides comprising an amino acid sequence segment that is at least 90% identical to the amino acid sequence of SEQ ID NO:1. Further preferred are such polypeptides comprising a contiguous amino acid sequence that has at least 95% identity with respect to the amino acid sequence of SEQ ID NO:1. And, even more preferred are polypeptides comprising an amino acid sequence that has at least 97% identity with respect to the amino acid sequence of SEQ ID NO:1.
In another aspect the present invention provides polynucleotides which encode the hereinabove described polypeptides of the invention. The polynucleotide of the present invention may be in the form of RNA or in the form of DNA, which DNA includes cDNA, genomic DNA, and synthetic DNA. The DNA may be double-stranded or single-stranded, and if single stranded may be the coding strand or non-coding (anti-sense) strand. The polynucleotides which encode polypeptides including the amino acid sequences of at least one of SEQ ID NOS:3-18 (or polypeptides that have at least 90% identity to the amino acid sequences of such polypeptides) may be one of the coding sequences shown in SEQ ID NOS:20-35 or may be of a different coding sequence which coding sequence, as a result of the redundancy or degeneracy of the genetic code, encodes the same polypeptides as the DNA of SEQ ID NOS:20-35.
The polynucleotides which encode the polypeptides of SEQ ID NOS:3-18 may include: only the coding sequence for the polypeptide; the coding sequence for the polypeptide (and optionally additional coding sequence) and non-coding sequence, such as introns or non-coding sequence 5′ and/or 3′ of the coding sequence for the polypeptide. The polypeptides encoded may comprise just a single alpha-helical portion or multiple alpha-helical portion and may independently or collectively include N-terminal sequences 5′ of such alpha helical areas and/or sequences corresponding to the “X” structures or proline rich areas (as set forth in FIG. 1, for example).
The invention further relates to a polynucleotide comprising a polynucleotide sequence that has at least 95% identity and preferably at least 97% identity to a polynucleotide encoding one of the polypeptides comprising SEQ ID NO:3-18. The invention further relates to fragments of such polynucleotides which include at least the portion of the polynucleotide encoding the polypeptide sequence corresponding to SEQ ID NO:1.
Thus, the term “polynucleotide encoding a polypeptide” encompasses a polynucleotide which includes only coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non-coding sequence. In particular, the polypeptides may include any or all of the types of structures set forth schematically in FIG. 1.
The present invention further relates to variants of the hereinabove described polynucleotides which encode for fragments, analogs and derivatives of the polypeptides including the amino acid sequences of SEQ ID NOS:3-18. The variants of the polynucleotides may be a naturally occurring allelic variant of the polynucleotides or a non-naturally occurring variant of the polynucleotides. Complements to such coding polynucleotides may be utilized to isolate polynucleotides encoding the same or similar polypeptides. In particular, such procedures are useful to obtain alpha helical coding segments from different serotypes of S. pneumoniae, which is especially useful in the production of “chain” polypeptide vaccines containing multiple alpha helical segments.
Thus, the present invention includes polynucleotides encoding polypeptides including the same polypeptides as shown in the Sequence Listing as SEQ ID NOS:3-18 as well as variants of such polynucleotides which variants encode for a fragment, derivative or analog of the polypeptides of SEQ ID NOS:3-18. Such nucleotide variants include deletion variants, substitution variants and addition or insertion variants.
As hereinabove indicated, the polynucleotides may have a coding sequence which is a naturally occurring allelic variant of the coding sequence shown in the Sequence Listing as SEQ ID NOS:20-35. As known in the art, an allelic variant is an alternate form of a polynucleotide sequence which may have a substitution, deletion or addition of one or more nucleotides, which does not substantially alter the function of the encoded polypeptide.
The polynucleotides of the present invention may also have the coding sequence fused in frame to a marker sequence which allows for purification of the polypeptides of the present invention. The marker sequence may be, for example, a hexa-histidine tag supplied by a pQE-9 vector to provide for purification of the mature polypeptides fused to the marker in the case of a bacterial host, or, for example, the marker sequence may be a hemagglutinin (HA) tag when a mammalian host, e.g. COS-7 cells, is used. The HA tag corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson, I., et al., Cell, 37:767 (1984)).
The present invention further relates to polynucleotides (hybridization target sequences) which hybridize to the complements of the hereinabove-described sequences if there is at least 70% and preferably 80% identity between the target sequence and the complement of the sequence to which the target sequence hybridizes, preferably at least 85% identity. More preferred are such sequences having at least 90% identity, preferably at least 95% and more preferably at least 97% identity between the target sequence and the sequence of complement of the polynucleotide to which it hybridizes. The invention further relates to the complements to both the target sequence and to the polynucleotide sequence that encodes an amino acid sequence selected from the group consisting of SEQ ID NOS:3 to 18. The present invention particularly relates to polynucleotides which hybridize under stringent conditions to the complements of the hereinabove-described polynucleotides as well as to those complements. As herein used, the term “stringent conditions” means hybridization will occur with the complement of a polynucleotide and a corresponding sequence only if there is at least 95% and preferably at least 97% identity between the target sequence and the sequence of complement of the polynucleotide to which it hybridizes. The polynucleotides which hybridize to the complements of the hereinabove described polynucleotides in a preferred embodiment encode polypeptides which retain an immunogenic portion that will cross-react with an antibody to at least one of the polypeptides having a sequence according to SEQ ID NOS:3-18, or to a polypeptide that includes an amino acid sequence which has at least 85% identity to that of SEQ ID NO:1.
In a still further aspect, the present invention provides for the production of such polypeptides and vaccines as set forth above having a histidine label (or other suitable label) such that the full-length proteins, truncates, analogs or variant discussed above can be isolated due to their label.
In another aspect the present invention relates to a method of prophylaxis and/or treatment of diseases that are mediated by pneumococcal bacteria that have surface-binding CBP proteins. In particular, the invention relates to a method for the prophylaxis and/or treatment of infectious diseases that are mediated by S. pneumoniae that have a CBP surface-binding protein that forms an alpha helix (comprising a sequence that has at least an 85% identity to the amino acid sequence of SEQ ID NO:1). In a still further preferred aspect, the invention relates to a method for the prophylaxis and/or treatment of such infections in humans.
In still another aspect the present invention relates to a method of using one or more antibodies (monoclonal, polyclonal or sera) to the polypeptides of the invention as described above for the prophylaxis and/or treatment of diseases that are mediated by pneumococcal bacteria that have CBP surface-binding proteins. In particular, the invention relates to a method for the prophylaxis and/or treatment of infectious diseases that are mediated by S. pneumoniae CBP proteins which include an alpha helical portion having the hereinbefore described identity to the consensus sequence of SEQ ID NO:1. In a still further preferred aspect, the invention relates to a method for the prophylaxis and/or treatment of otitis media, nasopharyngeal, bronchial infections, and the like in humans by utilizing antibodies to the alpha-helix containing immunogenic polypeptides of the invention as described above.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a diagram of a pneumococcal CBP protein which shows from the N-terminal to the C-terminal, respectively, (a) a N-terminal sequence, (b) one of a potential alpha-helical forming area conserved segment (R1) that may not be present in some CBP polypeptides, (c) an optional small bridging sequence of amino acids that may bridge two conserved alpha-helical segments (X), (d) a second of a potential alpha-helical forming area consensus sequence (R2) related to the first consensus sequence (which corresponds to SEQ ID NO:1), (e) a proline rich area sequence, (f) a choline binding repeats area, and (e) a C-terminal tail sequence. Where relevant, an optional HPS sequence may naturally occur 5′ of the proline rich sequence and 3′ of the R1, X, and/or R2 areas.
FIG. 2 reports the results for passive immunity protection against 1600 cfu virulent serotype 6B S. pneumoniae SP317 (in mice) that was provided by day 31 rabbit antisera to a pneumococcal CBP truncate polypeptide, NR1XR2 (truncate missing both the proline and the choline binding areas, but including two conserved alpha-helical areas R1 and R2). Eighty percent of the mice immunized with the truncate antisera prior to challenge survived the 14 day observation period. By contrast, all mice immunized with a control sera (pre-immune rabbit sera) were dead by day 7.
FIG. 3 reports the results for passive immunity protection against 3450 cfu virulent serotype 6B S. pneumoniae SP317 (in mice) that was provided by day 52 rabbit antisera to a pneumococcal CBP truncate polypeptide, NR1XR2 (truncate missing both the proline and the choline binding areas, but including two conserved alpha-helical areas R1 and R2). One hundred percent of the mice immunized with the truncate antisera prior to challenge survived the 10 day observation period. By contrast, ninety percent of the mice immunized with a control sera (pre-immune rabbit sera) were dead at day 10.
FIG. 4 reports the results for passive immunity protection against 580 cfu virulent serotype 6B S. pneumoniae SPSJ2 (in mice) that was provided by day 31 rabbit antisera to a pneumococcal CBP truncate polypeptide, NR1XR2 (truncate missing both the proline and the choline binding areas, but including two conserved alpha-helical areas R1 and R2). Fifty percent of the mice immunized with the truncate antisera prior to challenge survived the 10 day observation period. By contrast, all mice immunized with a control sera (pre-immune rabbit sera) were dead by day 8.
FIG. 5 reports the results for active immunity protection against 560 cfu virulent serotype 6B S. pneumoniae SPSJ2 (in mice) that was provided by immunization with a pneumococcal CBP truncate polypeptide, NR1X (truncate missing the second conserved alpha-helical area R2, as well as both the proline and the choline binding areas). Eighty percent of the mice actively immunized with the NR1X CBP truncate prior to challenge survived the 14 day observation period. By contrast, all mice immunized with a control (sham mice) of PBS and adjuvant were dead by day 8.
FIG. 6 reports the results for active immunity protection against 680 cfu virulent serotype 6B S. pneumoniae SPSJ2 (in mice) that was provided by immunization with a pneumococcal CBP truncate polypeptide, NR1XR2 (truncate missing both the proline and the choline binding areas, but including two conserved alpha-helical areas R1 and R2). Fifty percent of the mice actively immunized with the NR1XR2 CBP truncate prior to challenge survived the 14 day observation period. By contrast, all mice immunized with a control (SP90) protein and adjuvant were dead by day 9.
FIG. 7 is an alignment report of the amino terminus of CBP polypeptides from various types of S. pneumoniae (Norway 4 (SEQ ID NO: 9), ATCC33400(1) (SEQ ID NO: 3), ATCC11733(2) (SEQ ID NO: 4), ATCC2 (SEQ ID NO: 5), ATCC4 (SEQ ID NO: 6), ATCC6B (SEQ ID NO: 7), ATCC18C-3 (SEQ ID NO: 8), R6X(2) (SEQ ID NO: 10), SPB105(6B) (SEQ ID NO: 11), SPB328(23F) (SEQ ID NO: 12), SPB331(14) (SEQ ID NO: 13), SPB365(23F) (SEQ ID NO: 14), SPR332(9V) (SEQ ID NO: 15), SPSJ2(6B) (SEQ ID NO: 16), SPSJ9(14) (SEQ ID NO: 17), and SPSJ12(19A) (SEQ ID NO: 18) and a consensus sequence is reported at the top of each row (sets of lines) of the comparison. The consensus sequence for the comparison is listed as the “Majority” sequence (SEQ ID NO:36). One letter codes are utilized to represent the sequences which are aligned for a “best fit” comparison wherein dashes in a sequence indicate spacing gaps of the contiguous sequence.
FIG. 8 shows the sequence pair distances for the amino acid sequences as described for FIG. 7 and set forth therein. A Clustal method with identity residue weight table is used. The percent similarity for such a comparison is reported for the amino acid sequences set forth in FIG. 7.
FIG. 9 is an alignment report for a first helical region in the amino acid sequences of CBP polypeptides from various types of S. pneumoniae (Norway 4 (SEQ ID NO: 9), ATCC33400(1) (SEQ ID NO: 3), ATCC11733(2) (SEQ ID NO: 4), ATCC2 (SEQ ID NO: 5), ATCC4 (SEQ ID NO: 6), ATCC6B (SEQ ID NO: 7), ATCC18C-3 (SEQ ID NO: 8), R6X(2) (SEQ ID NO: 10), SPB105(6B) (SEQ ID NO: 11), SPB328(23F) (SEQ ID NO: 12), SPB331(14) (SEQ ID NO: 13), SPB365(23F) (SEQ ID NO: 14), SPR332(9V) (SEQ ID NO: 15), SPSJ2(6B) (SEQ ID NO: 16), SPSJ9(14) (SEQ ID NO: 17), and SPSJ12(19A) (SEQ ID NO: 18) and a consensus sequence is reported at the top of each row (sets of lines) of the comparison. The consensus sequence for the comparison is listed as the “Majority” sequence (SEQ ID NO:38). One letter codes are utilized to represent the sequences which are aligned for a “best fit” comparison wherein dashes in a sequence indicate spacing gaps of the contiguous sequence.
FIG. 10 shows the sequence pair distances for the amino acid sequences as described for FIG. 9 and set forth therein. A Clustal method with identity residue weight table is used. The percent similarity for such a comparison is reported for the amino acid sequences set forth in FIG. 9.
FIG. 11 is an alignment report for the region X in the amino acid sequences of CBP polypeptides from various types of S. pneumoniae (Norway 4 (SEQ ID NO: 9), ATCC33400(1) (SEQ ID NO: 3), ATCC11733(2) (SEQ ID NO: 4), ATCC2 (SEQ ID NO: 5), ATCC4 (SEQ ID NO: 6), ATCC6B (SEQ ID NO: 7), ATCC18C-3 (SEQ ID NO: 8), R6X(2) (SEQ ID NO: 10), SPB105(6B) (SEQ ID NO: 11), SPB328(23F) (SEQ ID NO: 12), SPB331(14) (SEQ ID NO: 13), SPB365(23F) (SEQ ID NO: 14), SPR332(9V) (SEQ ID NO: 15), SPSJ2(6B) (SEQ ID NO: 16), SPSJ9(14) (SEQ ID NO: 17), and SPSJ12(19A) (SEQ ID NO: 18) and a consensus sequence is reported at the top of each row (sets of lines) of the comparison. The consensus sequence for the comparison is listed as the “Majority” sequence (SEQ ID NO:37). One letter codes are utilized to represent the sequences which are aligned for a “best fit” comparison wherein dashes in a sequence indicate spacing gaps of the contiguous sequence.
FIG. 12 shows the sequence pair distances for the amino acid sequences as described for FIG. 11 and set forth therein. A Clustal method with identity residue weight table is used. The percent similarity for such a comparison is reported for the amino acid sequences set forth in FIG. 11.
FIG. 13 is an alignment report for the second helical region A in the amino acid sequences of CBP polypeptides from various types of S. pneumoniae (Norway 4 (SEQ ID NO: 9), ATCC33400(1) (SEQ ID NO: 3), ATCC11733(2) (SEQ ID NO: 4), ATCC2 (SEQ ID NO: 5), ATCC4 (SEQ ID NO: 6), ATCC6B (SEQ ID NO: 7), ATCC18C-3 (SEQ ID NO: 8), R6X(2) (SEQ ID NO: 10), SPB105(6B) (SEQ ID NO: 11), SPB328(23F) (SEQ ID NO: 12), SPB331(14) (SEQ ID NO: 13), SPB365(23F) (SEQ ID NO: 14), SPR332(9V) (SEQ ID NO: 15), SPSJ2(6B) (SEQ ID NO: 16), SPSJ9(14) (SEQ ID NO: 17), and SPSJ12(19A) (SEQ ID NO: 18) and a consensus sequence is reported at the top of each row (sets of lines) of the comparison. The consensus sequence for the comparison is listed as the “Majority” sequence (SEQ ID NO:1). One letter codes are utilized to represent the sequences which are aligned for a “best fit” comparison wherein dashes in a sequence indicate spacing gaps of the contiguous sequence.
FIG. 14 shows the sequence pair distances for the amino acid sequences as described for FIG. 13 and set forth therein. A Clustal method with identity residue weight table is used. The percent similarity for such a comparison is reported for the amino acid sequences set forth in FIG. 13.
FIG. 15 is an alignment report for the second helical region B in the amino acid sequences of CBP polypeptides from various types of S. pneumoniae (Norway 4 (SEQ ID NO: 9), ATCC33400(1) (SEQ ID NO: 3), ATCC11733(2) (SEQ ID NO: 4), ATCC2 (SEQ ID NO: 5), ATCC4 (SEQ ID NO: 6), ATCC6B (SEQ ID NO: 7), ATCC18C-3 (SEQ ID NO: 8), R6X(2) (SEQ ID NO: 10), SPB105(6B) (SEQ ID NO: 11), SPB328(23F) (SEQ ID NO: 12), SPB331(14) (SEQ ID NO: 13), SPB365(23F) (SEQ ID NO: 14), SPR332(9V) (SEQ ID NO: 15), SPSJ2(6B) (SEQ ID NO: 16), SPSJ9(14) (SEQ ID NO: 17), and SPSJ12(19A) (SEQ ID NO: 18) and a consensus sequence is reported at the top of each row (sets of lines) of the comparison. The consensus sequence for the comparison is listed as the “Majority”0 sequence (SEQ ID NO:19). One letter codes are utilized to represent the sequences which are aligned for a “best fit” comparison wherein dashes in a sequence indicate spacing gaps of the contiguous sequence.
FIG. 16 shows the sequence pair distances for the amino acid sequences as described for FIG. 15 and set forth therein. A Clustal method with identity residue weight table is used. The percent similarity for such a comparison is reported for the amino acid sequences set forth in FIG. 15.



DETAILED DESCRIPTION OF THE INVENTION
In accordance with an aspect of the present invention there is provided a vaccine to produce a protective response against S. pneumoniae infections which employs a polypeptide which comprises a member selected from the group consisting of:
(a) an amino acid sequence which produces an alpha helical structure and which is at least 85% identical to the amino acid sequence of SEQ ID NO:1 and which is free of a choline binding region, and
(b) an isolated truncate of a naturally occurring S. pneumoniae polypeptide that comprises an alpha helical portion that has at least 85% identity to the amino acid sequence of SEQ ID NO:1 and is free of a choline binding region,
(c) an isolated truncate of a naturally occurring S. pneumoniae polypeptide that comprises an alpha helical portion that has at least 90% identity to the amino acid sequence of SEQ ID NO:19 and is free of a choline binding region. In a preferred aspect, such isolated truncate polypeptide is a member selected from the group consisting of SEQ ID NOS:3-18 and said isolated polypeptide is free of a choline binding region and, if relevant, a HPS region; or a fragment thereof which includes at least the alpha helical segment which corresponds to the consensus sequence of SEQ ID NO:1. Particularly preferred are vaccines which utilize such truncate polypeptides that include at least such alpha helical area or utilize a recombinant immunogen polypeptide comprising at least two of such alpha-helical segments. Such polypeptide may be a recombinant polypeptide containing multiple alpha-helical areas from one or more trucates. Further preferred are recombinant immunogen polypeptides comprising at least two alpha-helical areas corresponding to the alpha helical areas of two or more truncates from different types of pneumococcal bacteria. Such polypeptide may be a recombinant polypeptide containing multiple alpha-helical areas from one or more different types of pneumococcal bacteria.
In accordance with the present invention, there is provided an isolated polypeptide comprising a truncated surface-binding polypeptide derived from S. pneumoniae, said isolated polypeptide containing an alpha-helical area whose amino acid sequence corresponds generally to the amino acid sequence of SEQ ID NO:1, but free of a choline binding area. Preferably, said isolated polypeptide also omits any naturally occurring repeats of the alpha-helical forming area and omits any HPS amino acid sequence that may be present.
It is an object of the present invention to utilize as immunogenic composition for a vaccine (or to produce antibodies for use as a diagnostic or as a passive vaccine) comprising an immunogenic polypeptide comprising a pneumococcal surface-binding polypeptide with an alpha helical portion from which a choline binding region has been omitted. In one embodiment, such truncated proteins (naturally or recombiantly produced, as well as functional analogs) from S. pneumoniae bacteria are contemplated. Even more particularly, S. pneumoniae polypeptides having a single alpha helical portion that omit any HPS areas that occur and choline binding areas of the native protein are contemplated.
A particularly preferred embodiment of such an immunogenic composition is for use as a vaccine (or as an immunogen for producing antibodies useful for diagnostics or vaccines) wherein the active component of the immunogenic composition is an isolated polypeptide comprising at least one member selected from the group consisting of:
(a) an amino acid sequence which is selected from SEQ ID NOS:3-19,
(b) a polypeptide which has at least 90% identity to (a), preferably at least 95% identity to (a), and even more preferred at least 97% identity to (a), or
(c) a fragment of (a) or (b) wherein such fragment includes at least one alpha helical portion that corresponds to the consensus sequence which is SEQ ID NO:1 and said fragment does not comprise a choline binding region. Preferably, such vaccines utilize a polypeptide that contains neither a choline binding region nor an HPS region that occurs as part of the amino acid sequences in the native proteins.
In another preferred embodiment, there is provided a vaccine which includes at least one isolated polypeptide which includes an amino acid sequence which has at least 85% identity (preferably 87% identity and more preferably at least 90% identity) to SEQ ID NO:1, which isolated polypeptide is free of a choline binding portion and, where applicable, is also preferably free of an HPS portion. The preferred polypeptide may also include one or more of the N-terminal sequences that are located 5′ of the alpha helical areas in the polypeptides having an amino acid sequence selected from the group consisting of SEQ ID NOS:3-18, or the like. The polypeptide truncate may also include one or more of the proline regions (region “P” in FIG. 1) and/or the spanning region (region “X” in FIG. 1).
In another aspect of the invention, such an immunogenic composition may be utilized to produce antibodies to diagnose pneumococcal infections, or to produce vaccines for prophylaxis and/or treatment of such pneumococcal infections as well as booster vaccines to maintain a high titer of antibodies against the immunogen(s) of the immunogenic composition.
While other antigens have been contemplated to produce antibodies for diagnosis and for the prophylaxis and/or treatment of pneumococcal infections, there is a need for improved or more efficient vaccines. Such vaccines should have an improved or enhanced effect in preventing bacterial infections mediated pneumococci having surface-binding polypeptides. Further, to avoid unnecessary expense and provide broad protection against a range of pneumococcal serotypes there is a need for polypeptides that comprise an immunogenic amino acid sequence corresponding to a portion of pneumococcal surface-binding polypeptides that is a highly conserved portion among various types of pneumococci. Preferably, such polypeptides avoid the inclusion of amino acid sequences corresponding to other portions of the native polypeptides, such as the choline binding region and/or the HPS region.
There is a need for improved antigenic compositions comprising highly conserved portions of polypeptides that bind to the surface of pneumococcal bacteria for stimulating high-titer specific antisera to provide protection against infection by pathogenic pneumococcal bacteria and also for use as diagnostic reagents.
In such respect, truncated polypeptides, functional variant analogs, and recombinantly produced truncated polypeptides of the invention are useful as immunogens for preparing vaccine compositions that stimulate the production of antibodies that can confer immunity against pathogenic species of bacteria. Further, preparation of vaccines containing purified proteins as antigenic ingredients are well known in the art.
Generally, vaccines are prepared as injectables, in the form of aqueous solutions or suspensions. Vaccines in an oil base are also well known such as for inhaling. Solid forms which are dissolved or suspended prior to use may also be formulated. Pharmaceutical carriers are generally added that are compatible with the active ingredients and acceptable for pharmaceutical use. Examples of such carriers include, but are not limited to, water, saline solutions, dextrose, or glycerol. Combinations of carriers may also be used.
Vaccine compositions may further incorporate additional substances to stabilize pH, or to function as adjuvants, wetting agents. or emulsifying agents, which can serve to improve the effectiveness of the vaccine.
Vaccines are generally formulated for parenteral administration and are injected either subcutaneously or intramuscularly. Such vaccines can also be formulated as suppositories or for oral administration, using methods known in the art.
The amount of vaccine sufficient to confer immunity to pathogenic bacteria is determined by methods well known to those skilled in the art. This quantity will be determined based upon the characteristics of the vaccine recipient and the level of immunity required. Typically, the amount of vaccine to be administered will be determined based upon the judgment of a skilled physician. Where vaccines are administered by subcutaneous or intramuscular injection, a range of 50 to 500 μg purified protein may be given.
The term “patient in need thereof” refers to a human that is infected with, or likely, to be infected with, pathogenic pneumococcal bacteria that produce CbpA, or the like, preferably S. pneumoniae bacteria (however a mouse model can be utilized to simulate such a patient in some circumstances).
In addition to use as vaccines, the polypeptides of the present invention can be used as immunogens to stimulate the production of antibodies for use in passive immunotherapy, for use as diagnostic reagents, and for use as reagents in other processes such as affinity chromatography.
The polynucleotides encoding the immunogenic polypeptides described above may also have the coding sequence fused in frame to a marker sequence which allows for purification of the polypeptides of the present invention. The marker sequence may be, for example, a hexa-histidine tag supplied by a pQE-9 vector to provide for purification of the mature polypeptides fused to the marker in the case of a bacterial host, or, for example, the marker sequence may be a hemagglutinin (HA) tag when a mammalian host, e.g. COS-7 cells, is used. The HA tag corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson, I., et al., Cell, 37:767 (1984)).
The identification of multiple coil structures of alpha helical amino acid segments in the S. pneumoniae polypeptides according to the invention may be determined by the location of proline rich areas with respect to one another. Further the “X” area optionally located between two or more alpha-helical structures can play a part in the formation of a coil within a coil structure. Standard three-dimensional protein modeling may be utilized for determining the relative shape of such structures. An example of a computer program, the Paircoil Scoring Form Program (“PairCoil program”), useful for such three-dimensional protein modelling is described by Berger et al. in the Proc. Natl. Acad. of Sci. (USA), 92:8259-8263 (August 1995). The PairCoil program is described as a computer program that utilizes a mathematical algorithm to predict locations of coiled-coil regions in amino acid sequences. A further example of such a computer program is described by Wolf et al., Protein Science 6:1179-1189 (June 1997) which is called the Multicoil Scoring Form Program (“Multicoil program”). The MultiCoil program is based on the PairCoil algorithm and is useful for locating dimeric and trimeric coiled coils.
In a preferred aspect, the invention provides for recombinant production of such polypeptides in a host bacterial cell other than a S. pneumoniae species host to avoid the inclusion of native surface-binding polypeptides that have a choline binding region. A preferred host is a species of such bacteria that can be cultured under conditions such that the polypeptide of the invention is secreted from the cell.
The present invention also relates to vectors which include polynucleotides encoding one or more of the polypeptides of the invention that include the highly conserved alpha-helical amino acid sequence in the absence of an area encoding a choline binding amino acid sequence, host cells which are genetically engineered with vectors of the invention and the production of such immunogenic polypeptides by recombinant techniques in an isolated and substantially immunogenically pure form.
Host cells are genetically engineered (transduced or transformed or transfected) with the vectors comprising a polynucleotide encoding a polypeptide comprising the highly conserved alpha-helical region but not having a choline binding region, or the like of this invention which may be, for example, a cloning vector or an expression vector. The vector may be, for example, in the form of a plasmid, a viral particle, a phage, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the polynucleotides which encode such polypeptides. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
Vectors include chromosomal, nonchromosomal and synthetic DNA sequences, e.g., derivatives of SV40; bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies. However, any other vector may be used as long as it is replicable and viable in the host.
The appropriate DNA sequence may be inserted into the vector by a variety of procedures. In general, the DNA sequence is inserted into an appropriate restriction endonuclease site(s) by procedures known in the art. Such procedures and others are deemed to be within the scope of those skilled in the art.
The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence(s) (promoter) to direct mRNA synthesis. As representative examples of such promoters, there may be mentioned: LTR or SV40 promoter, the E. coli, lac or trp, the phage lambda PL promoter and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression.
In addition, the expression vectors preferably contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli. 
The vector containing the appropriate DNA sequence as hereinabove described, as well as an appropriate promoter or control sequence, may be employed to transform an appropriate host to permit the host to express the proteins.
As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium; fungal cells, such as yeast; insect cells such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; adenoviruses; plant cells, etc. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.
More particularly, the present invention also includes recombinant constructs comprising one or more of the sequences as broadly described above. The constructs comprise a vector, such as a plasmid or viral vector, into which a sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art, and are commercially available. The following vectors are provided by way of example. Bacterial: pQE70, pQE60, pQE-9 (Qiagen, Inc.), pbs, pD10, phagescript, psiX174, pbluescript SK, pbsks, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene); ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia). Eukaryotic: pWLNEO, pSV2CAT, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, PSVL (Pharmacia). However, any other plasmid or vector may be used as long as they are replicable and viable in the host.
Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, PL and TRP. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-1. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art.
In a further embodiment, the present invention relates to host cells containing the above-described constructs. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, or electroporation (Davis, L., Dibner, M., Battey, I., Basic Methods in Molecular Biology, (1986)).
The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Alternatively, the polypeptides of the invention can be synthetically produced by conventional peptide synthesizers.
Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), the disclosure of which is hereby incorporated by reference.
Transcription of the DNA encoding the polypeptides of the present invention by higher eukaryotes is increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp that act on a promoter to increase its transcription. Examples including the SV40 enhancer on the late side of the replication origin bp 100 to 270, a cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiae TRP1 gene, and a promoter derived from a highly-expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), α-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences. Optionally, the heterologous sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.
Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include E. coli, Bacillus subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, although others may also be employed as a matter of choice.
As a representative but nonlimiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM1 (Promega Biotec, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed.
Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period.
Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.
Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, a french press, mechanical disruption, or use of cell lysing agents, such methods are well know to those skilled in the art. However, preferred are host cells which secrete the polypeptide of the invention and permit recovery of the polypeptide from the culture media.
Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described by Gluzman, Cell, 23:175 (1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements.
The polypeptides can be recovered and/or purified from recombinant cell cultures by well-known protein recovery and purification methods. Such methodology may include ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. In this respect, chaperones may be used in such a refolding procedure. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps.
The polypeptides that are useful as immunogens in the present invention may be a naturally purified product, or a product of chemical synthetic procedures, or produced by recombinant techniques from a prokaryotic or eukaryotic host (for example, by bacterial, yeast, higher plant, insect and mammalian cells in culture). Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. Particularly preferred immunogens are truncated pneumococcal polypeptides that comprise a single highly conserved alpha helical area, but do not comprise a choline binding region or a HPS region. Therefore, antibodies against such polypeptides should bind to other pneumococcal bacterial species (in addition to the S. pneumoniae species from which such polypeptides were derived) and vaccines against such S. pneumoniae should give protection against other pneumococcal bacterial infections.
Procedures for the isolation of the individually expressed alpha-helical containing polypeptides may be isolated by recombinant expression/isolation methods that are well-known in the art. Typical examples for such isolation may utilize an antibody to a conserved area of the protein or to a His tag or cleavable leader or tail that is expressing as part of the protein structure.
The polypeptides, their fragments or other derivatives, or analogs thereof, or cells expressing them can be used as an immunogen to produce antibodies thereto. These antibodies can be, for example, polyclonal or monoclonal antibodies. The present invention also includes chimeric, single chain, and humanized antibodies, as well as Fab fragments, or the product of an Fab expression library. Various procedures known in the art may be used for the production of such antibodies and fragments.
Antibodies generated against the polypeptides corresponding to a sequence of the present invention can be obtained by direct injection of the polypeptides into an animal or by administering the polypeptides to an animal, preferably a nonhuman. The antibody so obtained will then bind the polypeptides itself. In this manner, even a sequence encoding only a fragment of the polypeptides can be used to generate antibodies binding the whole native polypeptides.
For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler and Milstein, 1975, Nature, 256:495-497), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., 1983, Immunology Today 4:72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole, et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).
Techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies to immunogenic polypeptide products of this invention. Also, transgenic mice may be used to express humanized antibodies to immunogenic polypeptide products of this invention.
In order to facilitate understanding of the above description and the examples which follow below, as well as the Figures included herewith, Table 1 below sets forth the bacterial source for the polypeptides of SEQ ID NOS:3-18 and the polynucleotides encoding them (SEQ ID NOS:20-35, respectively). The name and/or type of bacteria is specified and a credit or source is named. The sequences from such types of bacteria are for illustrative purposes only since by utilizing probes and/or primers as described herein other sequences of similar type may be readily obtained by utilizing only routine skill in the art.









TABLE 1






Type Of



SEQ ID NO.
Pneumococcus
Source Credit or ATCC No.

















3
 1
ATCC 33400


4
 2
SPATCC 11733


5
 2
ATCC2 (catalog #6302)


6
 4
ATCC4 (catalog #6304)


7
 6B
ATCC 6B (catalog #6326)


8
18C
SPATCC 18C




(ATCC catalog #10356)


9
 4
Norway type 4; Nat'l. Inst. of Public




Health, Norway Ingeborg Aagerge


10
noncapsulated
R6X; Rockefeller Univ., Rob Masure




(from D39, type 2)


11
 6B
SPB 105; Boston Univ., Steve Pelton


12
23F
SPB 328; Boston Univ., Steve Pelton


13
14
SPB 331; Boston Univ., Steve Pelton


14
23F
SPB 365; Boston Univ., Steve Pelton


15
 9V
SPR 332; Rockefeller Univ., Rob




Masure


16
 6B
SPSJ 2p; St. Jude Children's Research




Hospital, Pat Flynn (clinical isolate




passaged 1× in mice for virulence)


17
14
SPSJ 9; St. Jude Children's Research




Hospital, Pat Flynn (clinical isolate -




nares, pneumonia)


18
19A
SPSJ 12; St. Jude Children's Research




Hospital, Pat Flynn (clinical isolate)









The present invention will be further described with reference to the following examples; however, it is to be understood that the present invention is not limited to such examples. All parts or amounts, unless otherwise specified, are by weight.
EXAMPLE 1
Generation of CbpA Truncate Protein Vectors
A. Vector for Full Length CbpA (NR1XR2PC)
A virulent serotype 4 S. pneumoniae strain, Norway 4 (obtained from I. Aaberge, National Instute of Public Health, Oslo, Norway) was used as a source of genomic DNA template for amplifying the polynucleotide encoding full-length CbPA. Full length CbpA was amplified with PCR primers SJ533 and SJ537 described below.
The degenerate forward primer SJ533 was designed based on the CbpA N-terminal sequence XENEG provided by H. R. Masure (St. Jude Childern's Research Hospital, Memphis, Tenn.). The SJ533 primer=5′ GGC GGA TCC ATG GA(A,G) AA(C,T) GA(A,G) GG 3′ (SEQ ID NO: 39). It incorporates both BamHI and Ncol restriction sites and an ATG start codon.
The 3′ reverse primer SJ537=5′-CC GTC GAC TTA GTT TCA CCA TTC ACC ATT GGC-3′ (SEQ ID NO: 40).
This primer incorporates a SaII restriction site for cloning purposes, and the natural stop codon from CbpA, and is based on type 4 and R6X sequence generated in-house.
PCR product generated from genomic DNA template with SJ533 and SJ537 was digested with BamHI and SaII, and cloned into the pQE30 expression vector (Qiagen, Inc.) digested with BamHI, XbaI, and SmaI. The type R6X template resulted in full-length vector PMI581 and the type 4 template DNA resulted in full-length vector PMI580.
B. Vector for CbpA Truncate Protein (NR1XR2)
The naturally occurring PvuII site in the end on the second amino repeat (nucleic acid 1228 of Type 4 sequence) was exploited to create a truncated version of CbpA, containing only the amino terminus of the gene. To create the truncate clone, the full-length clone PMI580 (Type 4) or PMI581 (R6X) was digested with PvuII and XbaI, and the amino terminus along with a portion of the expression vector was isolated by size on an agarose gel. pQE30 was digested with XbaI and SmaI, and the band corresponding to the other half of the vector was also size selected on an agarose gel. The two halves were ligated and clones identified by restriction digest, then expressed. In this instance, the stop codon utilized is in the expression vector, so the protein expressed is larger than the predicted size due to additional amino acids at the 5′ and 3′ end of the cloning site.
C. Vector for CbpA Truncate Protein (NR1X)
A similar strategy was used to express only the first amino repeat of CbpA. Here the naturally occurring XmnI site between the two amino repeats (nucleic acid 856 of Type 4 sequence) was utilized. CbpA full-length clone PMI580 was digested with XmnI and AatII. Expression vector pQE30 was digested with AatII and SmaI. Once again, the two sized fragments were ligated, and clones were screened by restriction digest and expressed.
EXAMPLE 2
Expression of CbpA Truncate Protein from Expression Vectors
All proteins are expressed from the vectors described in Examples 1A-1C in the Qia expressionist System (Qiagen) using the E. coli expression vector pQE30, and the amino terminus His6 tagged proteins are detected by western analysis using both anti-Histidine antibodies and gene specific antibodies.
The expressed CBP truncates were purified as follows.
A single colony was selected from plated bacteria containing the recombinant plasmid and grown overnight at 37° in 6.0 ml LB buffer with 50 ug/ml Kanamycin and 100 ug/ml Ampicillin. This 6.0 ml culture was added to 1 L LB with antibiotics at above concentrations. The culture was shaken at 37° C. until A600= ̃0.400. 1M IPTG was added to the 1 L culture to give a final concentration of 1 mM. The culture was then shaken at 37° C. for 3-4 h. The 1 L culture was spun 15 min. in 250 ml conical tubes at 4000 rpm in a model J-6B centrifuge. The supernatant was discarded and the pellet stored at −20° C. until use.
The 1 L pellet was resuspended in 25 ml 50 mM NaH2PO4, 10 mM Tris, 6M GuC1, 300 mM NaCl, pH 8.0 (Buffer A). This mixture was then rotated at room temperature for 30 minutes. The mixture was then subjected to sonication (VibraCell Sonicator, Sonics and Materials, Inc., Danbury, Conn.) using the microtip, two times, for 30 sec., at 50% Duty Cycle and with the output setting at 7. The mixture was spun 5 min. at 10K in a JA20 rotor and the supernatant removed and discarded. The supernatant was loaded on a 10 ml Talon (Clonetech, Palo Alto, Calif.) resin column attached to a GradiFrac System (Pharmacia Biotech, Upsala, Sweden). The column was equilibrated with 100 ml Buffer A and washed with 200 ml of this buffer. A volume based pH gradient using 100% 50 mM NaH2PO4, 8M Urea, 20 mM MES, pH 6.0 (Buffer B) as the final target buffer was run over a total volume of 100 ml. Protein eluted at  ̃30% Buffer B. Eluted peaks were collected and pooled.
For refolding, dialysis was carried out with a 2 L volume of PBS at room temperature for approximately 3 hr. using dialysis tubing with a molecular weight cutoff of 14,000. The sample was then dialyzed overnight in 2 L of PBS at 4° C. Additional buffer exchange was accomplished during the concentration of the protein using Centriprep-30 spin columns by adding PBS to the spun retentate and respinning. The protein concentration was determined using the BCA protein assay and the purity visualized using a Coomassie stained 4-20% SDS-PAGE gel.
EXAMPLE 3
Passive Protection with Anti-CbpA Truncate NR1XR2 Antisera
A. Generation of Rabbit Immune Serum
Rabbit immune serum against CbpA truncate was generated at Covance (Denver, Pa.). Following collection of preimmune serum, a New Zealand white rabbit (#ME101) was immunized with 250 μg CbpA truncate NR1XR2 (containing both alpha helix I and alpha helix II amino acid N-terminal repeats that are prepared from 483:58) in Complete Freund's Adjuvant. The rabbit was given a boost of 125 μg CbpA truncate in Incomplete Freund's Adjuvant on day 21 and bled on days 31 and 52.
B. Passive Protection in Mice
C3H/HeJ mice (5 mice/group) were passively immunized intraperitoneally with 100 μl of a 1:2 dilution of rabbit sera in sterile PBS (preimmune or day 31 immune sera). One hour after administration of serum, mice were challenged with 1600 cfu virulent serotype 6B S. pneumoniae, strain SP317 (obtained from H.R. Masure). Mice were monitored for 14 days for survival.
Eighty percent of the mice immunized with rabbit immune serum raised against CbpA truncate NR1XR2 protein survived the challenge for 14 days (FIG. 2). All mice immunized with preimmune rabbit serum were dead by day 7.
C. Passive Protection in Mice (Higher Challenge Dose)
C3H/HeJ mice (10 mice/group) were passively immunized intraperitoneally with 100 μl of a 1:2 dilution of rabbit sera in sterile PBS (preimmune or day 52 immune sera). One hour after administration of serum, mice were challenged with 3450 cfu virulent serotype 6B S. pneumoniae, strain SP317. Mice were monitored for 10 days for survival.
One hundred percent of the mice immunized with rabbit immune serum raised against CbpA truncate NR1XR2 protein survived the challenge for ten days (FIG. 3). Ninety percent of the mice immunized with preimmune rabbit serum were dead at day 10.
D. Passive Protection in Mice (Against High Virulence)
C3H/HeJ mice (10 mice/group) were passively immunized intraperitoneally with 100 μl of a 1:2 dilution of rabbit sera in sterile PBS (preimmune or day 52 immune sera). One hour after administration of serum, mice were challenged with 580 cfu virulent serotype 6B S. pneumoniae, strain SPSJ2 (provided by P. Flynn, St. Jude Children's Research Hospital, Memphis, Tenn.). Mice were monitored for 10 days for survival.
Fifty percent of the mice immunized with rabbit immune serum raised against CbpA truncate NR1XR2 protein survived the challenge for 10 days (FIG. 4). All of the mice immunized with preimmune rabbit serum were dead at day 8.
These data demonstrate that antibodies specific for CbpA are protective against systemic pneumococcal infection. The data further indicate that the choline-binding region is not necessary for protection, as antibody specific for truncated protein NR1XR2, lacking the choline-binding repeats, was sufficient for protection. In addition, serum directed against recombinant CbpA protein based on a serotype 4 sequence, was still protective against challenge with two different strains of serotype 6B.
EXAMPLE 4
Active Protection with Anti-CbpA Truncates NR1X and NR1XR2
A. Active Protection with NR1X Truncate Vaccination
C3H/HeJ mice (10/group) were immunized intraperitoneally with CbpA truncate protein NR1X (15 μg in 50 μl PBS, plus 50 μl Complete Freund's Adjuvant). A group of 10 sham immunized mice received PBS and adjuvant. A second immunization was administered four weeks later, 15 μg protein i.p. with Incomplete Freund's Adjuvant (sham group received PBS plus IFA). Blood was drawn (retro-orbital bleed) at weeks 3, 6, and 9 for analysis of immune response. The ELISA end point anti-CbpA truncate titer of pooled sera from the 10 CbpA immunized mice at 9 weeks was 4,096,000. No antibody was detected in sera from sham immunized mice. Mice were challenged at week 10 with 560 CFU serotype 6B S. pneumoniae strain SPSJ2. Mice were monitored for 14 days for survival.
Eighty percent of the mice immunized with CbpA truncate protein NR1X survived the challenge for 14 Days (results shown in FIG. 5). All sham immunized mice were dead by day 8.
B. Active Protection With NR1XR2 Truncate Vaccination
C3H/HeJ mice (10/group) were immunized intraperitoneally with CbpA truncate protein NR1XR2 (15 μg in 50 μl PBS, plus 50 μl Complete Freund's Adjuvant). A group of 10 control immunized mice received pneumococcal recombinant protein SP90 and adjuvant. A second immunization was administered four weeks later, 15 μg protein i.p. with Incomplete Freund's Adjuvant. Blood was drawn (retro-orbital bleed) at weeks 3, 6, and 9 for analysis of immune response. The ELISA end point anti-CbpA truncate titer of pooled sera from the 10 CbpA immunized mice at 9 weeks was 4,096,000. Mice were challenged at week 10 with 680 CFU serotype 6B S. pneumoniae strain SPSJ2. Mice were monitored for 14 days for survival.
Fifty percent of the mice immunized with CbpA truncate protein NR1XR2 survived the challenge for 14 days (results shown in FIG. 6). All control immunized mice were dead by day 9.
These data demonstrate that immunization with recombinant CbpA truncate proteins elicit production of specific antibodies capable of protecting against systemic pneumococcal infection and death. The data further indicate that the choline-binding region is not necessary for protection, as the immunogens were truncated proteins NR1X and NR1XR2. Additionally, the results suggest that a single amino terminal repeat may be sufficient to elicit a protective response. Cross protection is demonstrated as the recombinant pneumococcal protein was generated based on serotype 4 DNA sequence and protection was observed following challenge with a serotype 6B isolate.
Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore, within the scope of the appended claims, the invention may be practiced otherwise than as particularly described.

## Claims

1. A method for protecting against S. pneumoniae infections in a host comprising immunizing said host with a vaccine comprising a polypeptide having a plurality of alpha helical portions wherein at least one of said alpha helical portions is at least 90% identical to the sequence of SEQ ID NO: 1, wherein said polypeptide does not comprise a choline binding portion and is present in an amount sufficient to protect against infection by S. pneumoniae when said vaccine is administered to a mammal.

2. The method of claim 1, wherein said polypeptide is protective against otitis media, meningitis, and sepsis infections caused by S. pneumoniae.

3. The method of claim 1, wherein said S. pneumoniae is one or more of types 1-5, 6A, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19F, 19A, 20, 22F, 23F and 33F.

4. The method of claim 1, wherein said polypeptide does not comprise an HPS region.

5. The method of claim 1, wherein said polypeptide further comprises a proline rich region.

6. The method of claim 5, wherein said plurality of alpha helical portions are between the N-terminus of said polypeptide and said proline rich region.