WO2000029434A2 - PNEUMOCOCCAL CHOLINE BINDING PROTEINS, CbpG AND CbpD, DIAGNOSTIC AND THERAPEUTIC USES THEREOF - Google Patents

PNEUMOCOCCAL CHOLINE BINDING PROTEINS, CbpG AND CbpD, DIAGNOSTIC AND THERAPEUTIC USES THEREOF Download PDF

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WO2000029434A2
WO2000029434A2 PCT/US1999/027526 US9927526W WO0029434A2 WO 2000029434 A2 WO2000029434 A2 WO 2000029434A2 US 9927526 W US9927526 W US 9927526W WO 0029434 A2 WO0029434 A2 WO 0029434A2
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cbpg
choline binding
cbpd
polypeptide
seq
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PCT/US1999/027526
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French (fr)
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WO2000029434A3 (en
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Elaine I. Tuomanen
Khoosheh Gosink
Robert Masure
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St. Jude Children's Research Hospital
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Priority to AU20274/00A priority Critical patent/AU2027400A/en
Publication of WO2000029434A2 publication Critical patent/WO2000029434A2/en
Publication of WO2000029434A3 publication Critical patent/WO2000029434A3/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/12—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria
    • C07K16/1267—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria
    • C07K16/1275—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria from Streptococcus (G)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/315—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Streptococcus (G), e.g. Enterococci
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56911—Bacteria
    • G01N33/56944—Streptococcus
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/195—Assays involving biological materials from specific organisms or of a specific nature from bacteria
    • G01N2333/315—Assays involving biological materials from specific organisms or of a specific nature from bacteria from Streptococcus (G), e.g. Enterococci

Definitions

  • the present invention relates generally to choline binding polypeptides and to nucleic acids encoding such polypeptides.
  • the invention also relates to vaccines which provide protection or elicit protective antibodies to bacterial infection, and to antibodies and antagonists against or inhibitors of such polypeptides for use in diagnosis, therapy and passive immune therapy.
  • the choline binding polypeptides of the invention are useful as vaccines against Streptococcus, particularly pneumococcus.
  • a choline binding polypeptide of the present invention is also useful as a competitive inhibitor of bacterial adhesion, or to discover small molecule antagonists of adhesion.
  • Streptococcus pneumoniae is a gram positive bacteria which is a major cause of invasive infections such as sepsis, meningitis, otitis media and lobar pneumonia (Tuomanen et al NE 322:1280-1284, 1995). Vaccination has long been an important armament in the arsenal against infectious microorganisms. Prior to the introduction of antibiotics, vaccination was the major hope for protecting populations against viral or bacterial infection. With the advent of antibiotics, vaccination against bacterial infections became less important. However, the emerging problems with antibiotic resistance among such infectious bacteria, including S. pneumoniae strains, have raised an urgent need for a better understanding of the pathogenesis of these pathogens and has reestablished the importance of anti-bacterial vaccines (Appelbaum, P.C. (1992) Clin Infect Dis 15:77-83).
  • the capsular polysaccharide is a principal known virulence factor of the pneumococcus and induces an antibody response in adults.
  • Current vaccines against S. pneumoniae employ mixtures of the capsules of the 23 most common serotypes of this bacterium. After several comprehensive studies there is now overwhelming evidence that this vaccine is approximately 60% efficacious for the general population (Shapiro et ⁇ /.(1991) NEJM 325: 1453-60).
  • these vaccines are ineffective in individuals most susceptible to pathological infection - the young, the old, and the immune compromised - because of their inability to elicit a T cell immune response.
  • Conjugation of the capsule to a protein permits protection in the younger age group but is inherently limited in the number of capsules that can be conjugated at one time (approximately 5-8 capsules only).
  • Exported proteins in bacteria participate in many diverse and essential cell functions such as motility, signal transduction, macromolecular transport and assembly, and the acquisition of essential nutrients.
  • pathogenic bacteria such as S. pneumoniae
  • many exported proteins are virulence determinants that function as adhesins to colonize and thus infect the host, or as toxins to protect the bacteria against the host's immune system (for a review, see Hoepelman and Tuomanen (1992) Infect Immun 60:1729-33).
  • One alternative to current vaccines are subunit vaccines in which the antigen, or antigens, include a bacterial surface protein or proteins. These vaccines could overcome the deficiencies of whole bacterial or capsule-based vaccines.
  • these proteins are an important target for therapeutic intervention.
  • Pneumococci bind avidly to cells of the upper and lower respiratory tract. Like most bacteria, adherence of pneumococci to human cells is achieved by presentation of bacterial surface proteins that bind to eukaryotic cell surface carbohydrates in a lectin-like fashion (Cundell, D. & Tuomanen, E. ( ⁇ 994)Microb Pathog 17:361-374). Pneumococci bind to non-inflamed epithelium, a process that can be viewed as asymptomatic carriage. It has been proposed that the conversion to invasive disease involves the local generation of inflammatory factors which, activating the human epithelial cell, change the number and type of receptors available on the human cells (Cundell, D.
  • pneumococci appear to take advantage and engage one of these unregulated receptors, the platelet activating factor (PAF) receptor (Cundell et al. (1995) Nature, 377:435-438).
  • PAF platelet activating factor
  • pneumococci undergo waves of enhanced adherence and invasion.
  • Inhibition of bacterial binding to activated cells blocks the progression to disease in animal models (Idanpaan-Heikkila, I. et al. (1997) J. Infect. Dis., 176:704-712).
  • Particularly effective in this regard are soluble carbohydrates containing lacto-N-neotetraose with or without an additional sialic acid, which prevent pneumococcal attachment to human cells in vitro and prevent colonization in the lung in vivo.
  • Pneumococci display a family of surface proteins which bind to the bacterial surface by non-covalent association to the cell wall teichoic acid or lipoteichoic acid, specifically through its terminal component phosphorylcholine.
  • the surface of Streptococcus pneumoniae is decorated with twelve types of these choline binding proteins (Cbps).
  • the Cbps are represented by a family of molecules which decorate the surface of pneumococcus, each serving a unique function but bound to the surface by a common element.
  • These proteins consist of an N-terminal activity domain and a repeated C- terminal signature choline binding domain that contains two to greater than ten repeats of a 20 amino acid choline binding sequence that binds to phosphoryl choline and that anchors these molecules to the surface of the bacteria.
  • This motif has been identified in the C-terminal regions of a secreted glycoprotein from Clostridium acetobutylicum NCIB 88052 [Sanchez-Beato, et al., J Bacteriol 177: 1098-1103 (1995)], toxins A and B from Clostridium difficile [Non Eichel-Streiber and Sauerborn, Gene 96: 107-13 (1990); Non Eichel-Streiber et al., J Bacteriol.
  • a glucan-binding protein from Streptococcus mutans a glucan-binding protein from Streptococcus mutans, several glycosyltransferases from Streptococcus downei and S. mutans, the murein hydrolase (LytA) from pneumococcus and pneumococcal lytic phage [Ronda et al., Eur. J. Biochem. 164:621-4 (1987); Diaz et al., J. Bacteriol 174:5516-25 (1992); Romero et al., Microb. Lett. 108:87-92 (1993); Yother and White, J. Bacteriol. 176:2976-85 (1994)], and a surface antigen (PspA) also from pneumococcus.
  • the known pneumococcal Cbp family members are CbpA, LytA and PspA.
  • the choline binding domain was recognized and fully characterized by Lopez et al. in his studies of the autolytic enzyme, LytA (Ronda et al. (1987) Eur. J. Biochem, 164:621- 624). From studies of the sequences of the recognized choline binding proteins, consensus sequences have been reported, most particularly that of Garcia et al: GWLKDNGSWYYLNANGAMAT (SEQ ID NO:9) (Garcia, P. et al (1990) Gene 86:81- 88; Wren B. et al (1991) MolMicrobiol 5:797-803); Sanchez-Beato, A.R. et al (1995) J Bacteriol 177: 1098-1103).
  • Teichoic acid an integral part of the cell wall of Streptococcus pneumo iae, contains many terminal phosphorylcholine moieties. Choline affinity chromatography or Mono-Q Sepharose, a close relative of choline, were used to purify the CBPs. Previous studies have shown that PspA, as well as one other surface exposed protein, LytA, the autolytic amidase, bind in a choline-dependent manner. PspA, a protein having a molecular weight of 84 kDa, and which is highly variable, is released from the cell surface with high choline concentration (at least about 2% to about 10%). The function of PspA is unknown.
  • LytA or autolysin
  • choline binding proteins include those by Sanchez-Puelles et al Gene 89:69-75 (1990), Briese and HakenbackEwr. J. Biochem. 146:417-427, Yother and White J. of Bacteriol. 176:2976- 2985, Sanchez-Beato et alJ. of Bacteriol. 177:1098-1103, and WrenMicro. Review Mol Microbiol. 5:797-803 (1991), which are hereby incorporated by reference in their entirety.
  • CbpA is an adhesin (ligand) for the glycoconjugate containing receptors present on the surface of eucaryotic cells.
  • CbpA is a 663 amino acid protein with an apparent molecular mass of 112KDa.
  • CbpA has been shown to be critical to pneumococcal colonization and attachment to human cells. Mutants with defects in cbpA show reduced virulence in the infant rat model for nasopharyngeal colonization and fail to bind to eucaryotic cells found at the site of infection and to glycoconjugates that bind pneumococcus.
  • the CbpA protein cross reacts with human convalescent antisera, and antisera to the Cbps passively protected mice in a model for sepsis. Since the process of colonization and the progression to disease depend on pneumococcal attachment to human cells as a primary step, interruption of the function of surface choline binding proteins or the choline binding domain, for instance by cross reactive antibody or by inhibition with a competitive peptide mimicking this domain, may be relevant to blocking disease.
  • the cell wall associated choline binding protein, LytA a murein amidase
  • LytA a murein amidase
  • Expansion of the cell wall during bacterial growth and splitting of the septum for cell separation require enzymes that cleave the peptidoglycan network enclosing the cell.
  • some of these enzymes act as autolysins, thereby representing potentially suicidal enzymes. Regulation of these enzymes is therefore important and must take into consideration their extracytoplasmic location. Unlike other bacteria which have multiple autolysins, S. pneumoniae has only one major autolysin, LytA.
  • Antibiotics such as penicillin induce bacteriolysis by interfering with the control of the endogenous autolysins (Tomasz & Holtje, 1977, in Microbiology, D. Schlessinger, ed., pp. 202-215; Tomasz, 1983, in The Target of Penicillin, R.hackenback et al eds., pp. 155-172).
  • the binding of antibiotics to cell wall synthetic enzymes has been well characterized, the mechanism by which it induces autolysin mediated cell wall degradation is unknown. Tolerance to such antibiotics arises if the bacterial autolysins are not triggered as the antibiotic inhibits the cell wall synthetic machinery.
  • the question of whether antibodies raised against LytA are protective against infection by S.
  • PspA demonstrates antigenic variability between strains in the N- terminal half of the protein, which contains the immunogenic and protection eliciting epitopes (Yother et al., supra). This protein does not represent a common antigen for all strains of S. pneumoniae, and therefore is not an optimal vaccine candidate.
  • each Cbp while being bound to the surface by a common element, the choline binding domain, serves a unique function. This particular function is largely determined by the unique N-terminal activity domain of each Cbp.
  • N-terminal domain fragments of Cpbs, particularly CbpA have been shown to have activity in blocking adherence and are candidates for immunogenic vaccines, independent of the C-terminal choline binding domain.
  • Tuomanen et al U.S. Serial Number 09/056,019, which is hereby incorporated herein by reference in its entirety, provides isolated polypeptides comprising N-terminal choline binding protein A truncates, particularly wherein the polypeptides do not bind to choline.
  • Vaccines comprising such N-terminal truncates, DNA encoding such truncates, or antibodies directed against such truncates are also described in USSN 09/056,019.
  • ZmpB An additional surface exported protein that affects adherence and represents a virulence determinant for pneumococcus, ZmpB, has been identified and described by R. Novak and R. Masure in U.S. Serial No. 09/096,336 filed June 11, 1998 which is hereby incorporated by reference in its entirety.
  • ZmpB is a zinc metalloprotease, dependent on Zn 2+ for functional activity.
  • zmpB mutants show loss of adherence and colonization and are defective in the autolytic pathway.
  • a mutation in zmpB selectively alters the production of CbpA and generates covalently modified LytA.
  • ZmpB is proposed to be a master regulatory protein that controls the expression of multiple Cbps critical for bacterial survival in the human host.
  • ZmpB is a candidate for an S. pneumoniae vaccine or as one component of a multi-component vaccine.
  • the invention herein fills such a need in providing protective vaccines and therapies.
  • the present invention encompasses isolated polypeptides comprising an amino acid sequence of a choline binding protein, CbpG or CbpD.
  • the present invention is directed to an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein, CbpG or CbpD and wherein such polypeptide contains a choline binding domain sequence which is homologous to SEQ ID NO: 1.
  • the present invention provides an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein, CbpG or CbpD wherein such polypeptide contains a choline binding domain sequence which is homologous to GWLKDNGSWYYLNANGAMAT (SEQ ID NO: 9).
  • the present invention further provides an isolated polypeptide comprising an amino acid sequence of an N-terminal CbpG or CbpD choline binding protein truncate.
  • the present invention provides an N-terminal CbpG or CbpD truncate comprising the amino acid sequence as set forth in SEQ ID NO: 11, SEQ ID NO: 21, or SEQ ID NO: 23.
  • the invention particularly provides an N-terminal CbpG truncate consisting of amino acids 1- 90 of the CbpG choline binding protein.
  • the N-terminal CbpG truncate comprises less than amino acids 1-90 of the CbpG choline binding protein.
  • the invention provides an N-terminal CbpD truncate consisting of amino acids 2-280 of the CbpD choline binding protein.
  • the N-terminal CbpD truncates comprise amino acids 2-116 or 103-280 of the CbpD choline binding protein.
  • the present invention extends to vaccines based on the choline binding proteins described herein.
  • the present invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD.
  • the polypeptide comprises the amino acid sequence as set forth in SEQ ID NO: 2 or SEQ ID NO: 15 including fragments, mutants, variants, analogs, or derivatives, thereof.
  • the isolated polypeptide is suitable for use in immunizing animals and humans against bacterial infection, preferably pneumococci.
  • the present invention further provides an isolated polypeptide comprising an amino acid sequence of a N-terminal CbpG or CbpD choline binding protein truncate, particularly wherein the polypeptide does not bind to choline.
  • This invention provides an isolated immunogenic polypeptide comprising an amino acid sequence comprising an N-terminal truncate of a choline binding protein CbpG or CbpD.
  • this invention provides an isolated immunogenic N-terminal CbpG or CbpD truncate polypeptide comprising the amino acid sequence as set forth in SEQ ID NO: 11, SEQ ID NO: 21 or SEQ ID NO: 23.
  • the present invention further particularly provides an immunogenic N-terminal CbpG truncate polypeptide consisting of amino acids 1-90 of CbpG, or of less than amino acid 1-90 of CbpG.
  • the invention provides an N-terminal CbpD truncate consisting of amino acids 2-280 of the CbpD choline binding protein.
  • the N-terminal CbpD truncates comprise amino acids 2- 116 or 103- 280 of the CbpD choline binding protein.
  • the present invention extends to an immunogenic choline binding protein polypeptide CbpG or CbpD or a fragment thereof.
  • the present invention also extends to immunogenic choline binding protein polypeptides wherein such polypeptides comprise a combination of at least two choline binding polypeptides selected from the group consisting of CbpG or CbpD and at least one other choline binding polypeptide, including fragments thereof and N-terminal truncates thereof.
  • the present invention also relates to isolated nucleic acids, such as recombinant DNA molecules or cloned genes, or degenerate variants thereof, mutants, analogs, or fragments thereof, which encode the isolated polypeptide or which competitively inhibit the activity of the polypeptide.
  • the present invention further relates to isolated nucleic acids, such as recombinant DNA molecules or cloned genes, or degenerate variants thereof, mutants, analogs, or fragments thereof, which encode the choline binding protein CbpG or CbpD.
  • the isolated nucleic acid which includes degenerates, variants, mutants, analogs, or fragments thereof, has a sequence as set forth in SEQ ID NO: 3 or SEQ ID NO: 16.
  • the full DNA sequence of the recombinant DNA molecule or cloned gene so determined may be operatively linked to an expression control sequence which may be introduced into an appropriate host.
  • the invention accordingly extends to unicellular hosts transformed with the cloned gene or recombinant DNA molecule comprising a DNA sequence encoding the present invention, and more particularly, the DNA sequences or fragments thereof determined from the sequences set forth above.
  • the nucleic acid has the sequence selected from the group comprising SEQ ID NO:3 or SEQ ID NO: 16; a sequence complementary to SEQ ID NO:3 or SEQ ID NO: 16; or a homologous sequence which is substantially similar to SEQ ID NO:3 or SEQ ID NO: 16. In a further embodiment, the nucleic acid has the sequence consisting of SEQ ID NO:3 or SEQ ID NO: 16.
  • the present invention further relates to isolated nucleic acids encoding an N-terminal choline binding protein truncate, particularly wherein the encoded polypeptide does not bind to choline.
  • This invention particularly provides isolated nucleic acids encoding N- terminal choline binding protein truncates of choline binding protein CbpG or CbpD.
  • the invention further provides a nucleic acid encoding an N-terminal CbpG or CbpD truncate comprising SEQ ID NO: 12 , SEQ ID NO:22 or SEQ ID NO:24, a sequence complimentary to SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO:24, or a homologous sequence which is substantially similar to SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO: 24.
  • the nucleic acid encoding the N-terminal CbpG or CbpD truncate has the sequence consisting of SEQ ID NO: 12, SEQ ID NO: 22 or SEQ ID NO:24.
  • the nucleic acid encoding an N-terminal CbpG truncate is capable of encoding amino acids 1-90 of CbpG. In a still further embodiment, the nucleic acid encoding an N-terminal CbpG truncate encodes a truncate smaller than amino acids 1-90 of CbpG. In a particular embodiment, the nucleic acid encoding an N- terminal CbpD truncate is capable of encoding amino acids 2-280 of CbpD. In a still further embodiment, the nucleic acid encoding an N-terminal CbpD truncate encodes a truncate of amino acids 2-116 or 103-280 of CbpD.
  • Nucleic acid vaccines or DNA vaccines utilize nucleic acids encoding particular immunogenic polypeptides to induce immunity in a host against such encoded immunogenic vaccines.
  • Such nucleic acid based vaccines can be used directly as naked DNA, or can utilize well recognized expression vectors or retroviral vectors, as more particularly described herein, to encode such immunogenic polypeptide on expression in the host cell. Methods to generate and utilize such any such nucleic acid vaccines or DNA vaccines are well known in the art.
  • the present invention relates to nucleic acid vaccines or DNA vaccines comprising nucleic acids encoding immunogenic polypeptides of a choline binding protein CbpG or CbpD.
  • the present invention relates to nucleic acid vaccines or DNA vaccines comprising nucleic acids encoding immunogenic polypeptides of choline binding protein CbpG or CbpD or a fragment thereof or any combination of CbpG or CbpD with at least one other choline binding polypeptide.
  • this invention provides nucleic acid vaccines or DNA vaccines comprising nucleic acids encoding an immunogenic N-terminal polypeptide of choline binding protein CbpG or CbpD.
  • Antibodies against the isolated polypeptide include naturally raised and recombinantly prepared antibodies. These may include both polyclonal and monoclonal antibodies prepared by known genetic techniques, as well as bi-specific (chimeric) antibodies, and antibodies including other functionalities suiting them for diagnostic use. Such antibodies can be used in immunoassays to diagnose infection with a particular strain or species of bacteria. The antibodies can also be used for passive immunization to treat an infection with Gram positive bacteria, particularly pneumococcus. These antibodies may also be suitable for modulating bacterial adherence including but not limited to acting as competitive agents.
  • This invention provides pharmaceutical compositions for use in therapeutic methods which comprise or are based upon the isolated polypeptides, their subunits or their binding partners.
  • the invention further provides pharmaceutical compositions, vaccines, and diagnostic and therapeutic methods of use thereof.
  • the invention provides pharmaceutical compositions comprising a choline binding polypeptide CbpG or CbpD and a pharmaceutically acceptable carrier.
  • the present invention further provides pharmaceutical compositions comprising a choline binding polypeptide of a choline binding protein CbpG or CbpD, or a fragment thereof or any combination of CbpG or CbpD with at least one other choline binding polypeptide, and a pharmaceutically acceptable carrier.
  • this invention provides pharmaceutical compositions comprising N-terminal polypeptide of choline binding protein CbpG or CbpD and a pharmaceutically acceptable carrier.
  • the invention further relates to a vaccine for protection of an animal subject from infection with a Gram positive bacterium comprising a vector containing a gene encoding a choline binding protein CbpG or CbpD of a Gram positive bacterium operatively associated with a promoter capable of directing expression of the gene in the subject.
  • a vaccine for protection of an animal subject from infection with a Gram positive bacterium comprising a vector containing a gene encoding a choline binding protein CbpG or CbpD of a Gram positive bacterium operatively associated with a promoter capable of directing expression of the gene in the subject.
  • a vaccine contains a gene encoding a choline binding protein CbpG or CbpD of pneumococcus.
  • the invention is directed to a vaccine for protection of an animal subject from infection with a Gram positive bacterium, most preferably pneumococcus, comprising an immunogenic amount of a choline binding protein CbpG or CbpD, or a derivative or fragment thereof.
  • a vaccine may contain the protein conjugated covalently to a bacterial capsule or capsules from one or more strains of bacteria, including pneumococcus.
  • at least one of the bacterial capsules is derived from a mutant strain of bacteria which is non-adherent and non-virulent.
  • the non-adherent and non-virulent bacteria is a pneumococcus and is a CbpG or CbpD mutant bacteria.
  • Such non-adherent and non-virulent CbpG or CbpD mutant bacteria can further be utilized in expressing other immunogenic or therapeutic proteins for the purposes of eliciting immune responses to any such other proteins in the context of vaccines and in other forms of therapy.
  • the invention further provides a CbpG or CbpD mutant bacteria which is non-adherent to nasopharyngeal cells or to lung cells.
  • a CbpG or CbpD mutant is a gram positive bacteria.
  • such CbpG or CbpD mutant is Streptococcus.
  • such CbpG or CbpD mutant is Streptococcus pneumoniae.
  • the invention includes an assay system for screening of potential compounds effective to modulate the choline binding activity of the choline binding protein of the present invention.
  • the invention more particularly includes an assay system for screening of potential compounds effective to modulate the choline binding activity of the choline binding protein CbpG or CbpD.
  • the test compound, or an extract containing the compound could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein by comparison with a control.
  • test compound or an extract containing the compound, could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD, to determine the compound's effect upon the activity of the protein, and thereby on adherence of said cellular sample to host cells, by comparison with a control.
  • the invention includes an assay system for screening of potential compounds effective to modulate the activity of the N-terminal domain of the choline binding protein of the present invention.
  • the invention more particularly includes an assay system for screening of potential compounds effective to modulate the activity of the N-terminal domain of CbpG or CbpD.
  • the test compound, or an extract containing the compound could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein by comparison with a control.
  • test compound, or an extract containing the compound could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein, and thereby on adherence of said cellular sample to host cells, by comparison with a control.
  • test compound, or an extract containing the compound could be administered to a cellular sample expressing an N- terminal truncate (which lacks the C-terminal choline binding domain) of the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein by comparison with a control.
  • the cellular sample expresses an N-terminal CbpG truncate comprising amino acids 1-90 of CbpG or 2-280 of CbpD or a smaller N-terminal truncate comprising less than amino acids 1-90 of CbpG or 2-280 of CbpD.
  • the cellular sample expresses an N- terminal CbpD truncate comprising amino acids 2-116 or 103-280 of CbpD choline binding protein.
  • the N-terminal CbpG or CbpD truncate comprises the amino acid sequence set out in SEQ ID NO: 11, SEQ ID NO:21 or SEQ ID NO:23.
  • FIGURE 1 depicts the nucleic acid and amino acid sequence of the C-terminal 180 amino acids of CbpA. (amino acids 615-695).
  • FIGURE 2A-C depicts the nucleotide sequence and amino acid sequence for both CbpF and CbpG.
  • FIGURE 3 depicts the nucleotide sequence for CbpG including upstream promoter region.
  • FIGURE 4 depicts a Western Blot of a 10% SDS-PAGE on which choline binding proteins were separated and reacted with polyclonal antibody directed against CbpG.
  • Lane 1 is a ladder of recombinant choline binding proteins.
  • Lane 2 is a Cbp preparation from S. pneumoniae Type 4.
  • Lane 3 is a choline soak of S. pneumoniae Type 4.
  • Lane 4 is recombinant CbpG.
  • FIGURE 5 depicts the effect of the CbpG knockout, generated by insertion duplication mutagenesis, on colonization of infant rat nasopharynx at 48 hours by the method of Weiser, et al (Weiser JN et al (1994) 62(6):2582-2589).
  • WT depicts the colonization of wild type Type 4. Each bar presents the mean of four experiments on 10 rat pups per group.
  • FIGURE 6 is a graph of the CbpG knockout in a Type4R (T4R) genetic background (T4R is mutant Type4 pneumococcal strain which is unencapsulated) on the adhesion characteristics of Type 4R mutants on Detroit Nasopharyngeal Human Cell Line. T4R and the CbpG knockout are indicated (T4R and then CbpG- " ). Each bar represents an individual experiment shown as the mean of four wells.
  • FIGURE 7 presents a tabulation of characterization studies of CbpG.
  • the tabulation indicates the following: size of recombinantly prepared protein in kD; availability of N- terminal truncates (wherein the C-terminal choline binding domain is removed) (yes indicates available, blank indicates not available); recognition of recombinant protein by polyclonal anti-CbpG antibody on a Western Blot of a 4-15% gradient SDS-PAGE (** indicates recognition, - indicates no recognition); recognition of the corresponding CbpG protein on a Western Blot of a native choline binding protein preparation run on a 4- 15% gradient SDS-PAGE (** indicates recognition, - indicates no recognition); effects of a knockout of CbpG in rat nose colonization studies (N indicates no significant effect, Down indicates a significant reduction in colonization); In vitro adhesion to LNnT shows the effects of a knockout of CbpG on in vitro adhesion to LNnT (Lacto N-n
  • LYSIS w DOC provides the effect of the knockout of CbpG on the ability of Deoxycholate to lyse the particular knockout strains (Normal indicates no effect).
  • FIGURE 8 depicts the nucleic acid sequence and amino acid sequence for the N-terminal CbpG truncate.
  • FIGURE 9A depicts the expression of recombinant CbpG truncate and migration in SDS gel electrophoresis as detected by Coomassie blue staining. Lanes represent “not induced” and the "induced” soluble or insoluble fraction after induction of expression.
  • FIGURE 9B depicts migration of purified recombinant CbpG truncate on SDS gel electrophoresis as detected by Coomassie blue staining.
  • the CbpG truncate size is 13 kD as compared to MW Standards and is found in abundance in the soluble fraction of the cell preparation.
  • FIGURE 10 depicts the nucleotide sequence and predicted amino acid sequence of
  • FIGURE 11 depicts the effect of the CbpD knockout, generated by insertion duplication mutagenesis, on colonization of infant rat nasopharynx at 48 hours by the method of
  • FIGURE 12 is a graph of the CbpD knockout in a Type4R (T4R) genetic background (T4R is mutant Type4 pneumococcal strain which is unencapsulated) on the adhesion characteristics of Type 4R mutants to Detroit cells.
  • T4R Type4R
  • T4R is mutant Type4 pneumococcal strain which is unencapsulated
  • FIGURE 12 is a graph of the CbpD knockout in a Type4R (T4R) genetic background (T4R is mutant Type4 pneumococcal strain which is unencapsulated) on the adhesion characteristics of Type 4R mutants to Detroit cells.
  • Terasaki plates were coated with a monolayer of cells and fluorescein-labelled bacteria were placed in wells for 30 min, the wells were washed and adherent bacteria were counted. Values are expressed as a percentage of the T4R parent (100%).
  • T4R and the CbpD knockout are indicated (T4R and then Cb
  • FIGURE 13 presents a tabulation of characterization studies of CbpD.
  • the tabulation indicates the following: availability of N-terminal truncates (wherein the C-terminal choline binding domain is removed) (yes indicates available, blank indicates not available); effects of a knockout of CbpD in rat nose colonization studies (N indicates no significant effect, Down indicates a significant reduction in colonization);
  • In vitro adhesion to LNnT shows the effects of a knockout of CbpD on in vitro adhesion to LNnT (Lacto N- neotetraose-HSA) (reduced indicates significantly reduced from wild type);
  • TRSF w CSP depicts the effect of the knockout of CbpD on transformation of S.
  • LYSIS w DOC provides the effect of the knockout of CbpD on the ability of Deoxycholate to lyse the particular knockout strains (Normal indicates no effect).
  • FIGURE 14 depicts the amino acid sequence and nucleic acid sequences for the N- terminal CbpD truncates 2-116 (SEQ ID NO:21 and SEQ ID NO:22) and 103-280 (SEQ ID NO:23 and SEQ ID NO:24).
  • the present invention is directed to an isolated polypeptide comprising an amino acid sacid sequence of a choline binding protein CbpG or CbpD.
  • the present invention further provides an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein CbpG or CbpD wherein such polypeptide contains a choline binding domain sequence which is homologous to SEQ ID NO: 1.
  • the present invention further provides an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein CbpG or CbpD, wherein such polypeptide contains a choline binding domain sequence which is homologous to
  • the present invention is directed to an isolated polypeptide comprising an amino acid sequence of a choline binding polypeptide CbpG or CbpD.
  • the polypeptides of the present invention are suitable for use in immunizing animals against pneumococcal infection. These polypeptide or peptide fragments thereof, when formulated with an appropriate adjuvant, are used in vaccines for protection against pneumococci, and against other bacteria with cross-reactive proteins.
  • This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD.
  • the polypeptide has the amino acid sequence as set forth in SEQ ID NO: 2 or SEQ ED NO: 15 including fragments, mutants, variants, analogs, or derivatives, thereof.
  • This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD as set forth in Figure 2 and Figure 10.
  • the polypeptide is an analog, fragment, mutant, derivative or variant thereof.
  • This invention further provides an isolated polypeptide comprising an amino acid sequence of a N-terminal choline binding protein truncate, particularly wherein the polypeptide does not bind to choline.
  • This invention particularly provides an isolated immunogenic polypeptide comprising an amino acid sequence of a N-terminal choline binding protein CbpG or CbpD truncate.
  • this invention provides an N-terminal CbpG or CbpD truncate comprising amino acids 1-90 of CbpG or amino acids 2-280 of CbpD or an immunogenic fragment thereof.
  • the N-terminal CbpG or CbpD truncate may comprise less than amino acids 1-90 and the CbpD truncate may comprise less than amino acids 2-280.
  • the invention particularly provides an N-terminal CbpG or CbpD truncate comprising the amino acids set out in SEQ ID NO: 11, SEQ ID NO:21 or SEQ ID NO:23.
  • amino acid residues may be changed or modified to include variants such as, for example, deletions containing less than all of the residues specified for the protein, substitutions wherein one or more residues specified are replaced by other residues and additions wherein one or more amino acid residues are added to a terminal or medial portion of the polypeptide.
  • variants such as, for example, deletions containing less than all of the residues specified for the protein, substitutions wherein one or more residues specified are replaced by other residues and additions wherein one or more amino acid residues are added to a terminal or medial portion of the polypeptide.
  • These molecules include: the incorporation of codons "preferred" for expression by selected non-mammalian hosts; the provision of sites for cleavage by restriction endonuclease enzymes; and the provision of additional initial, terminal or intermediate DNA sequences that facilitate construction of readily expressed vectors.
  • this invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD, wherein the polypeptide has the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO: 15.
  • This invention is directed to a polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD, wherein the amino acid sequence is set forth in Figure 2 and Figure 10 and in SEQ ID NO:2 and SEQ ID NO:15.
  • This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD, wherein the polypeptide has choline binding activity.
  • the polypeptide has the amino acid sequence as set forth in SEQ ID NO:2 or SEQ ID NO: 15 including fragments, mutants, variants, analogs, or derivatives, thereof.
  • adheresion means noncovalent binding of a bacteria to a human cell or secretion that is stable enough to withstand washing.
  • CBP choline binding protein
  • CBP Choline binding protein
  • any variants not specifically listed may be used herein interchangeably, and as used throughout the present application and claims refer to proteinaceous material including single or multiple proteins, and extends to those proteins having the amino acid sequence data described herein and identified by SEQ ID NO:2 and SEQ ID NO: 15, and the profile of activities set forth herein and in the Claims. Accordingly, proteins displaying substantially equivalent or altered activity are likewise contemplated. These modifications may be deliberate, for example, such as modifications obtained through site-directed mutagenesis, or may be accidental, such as those obtained through mutations in hosts that are producers of the complex or its named subunits. Also, the term “choline binding protein (CBP)” is intended to include within its scope proteins specifically recited herein as well as all substantially homologous analogs and allelic variations.
  • This invention provides an isolated immunogenic polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. It is contemplated by this invention that the immunogenic polypeptide has the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO: 15, including fragments, mutants, variants, analogs, or derivatives, thereof.
  • the analog polypeptide may have an N-terminal methionine or a polyhistidine optionally attached to the N or COOH terminus of the polypeptide which comprise the amino acid sequence.
  • this invention contemplates peptide fragments of the polypeptide which result from proteolytic digestion products of the polypeptide.
  • the derivative of the polypeptide has one or more chemical moieties attached thereto.
  • the chemical moiety is a water soluble polymer.
  • the chemical moiety is polyethylene glycol
  • the chemical moiety is mon-, di-, tri- or tetrapegylated.
  • the chemical moiety is N-terminal monopegylated.
  • PEG polyethylene glycol
  • Attachment of polyethylene glycol (PEG) to compounds is particularly useful because PEG has very low toxicity in mammals (Carpenter et al, 1971).
  • a PEG adduct of adenosine deaminase was approved in the United States for use in humans for the treatment of severe combined immunodeficiency syndrome.
  • a second advantage afforded by the conjugation of PEG is that of effectively reducing the immunogenicty and antigenicity of heterologous compounds.
  • a PEG adduct of a human protein might be useful for the treatment of disease in other mammalian species without the risk of triggering a severe immune response.
  • the compound of the present invention may be delivered in a microencapsulation device so as to reduce or prevent an host immune response against the compound or against cells which may produce the compound.
  • the compound of the present invention may also be delivered microencapsulated in a membrane, such as a liposome.
  • PEG reagents for reaction with protein amino groups include active esters of carboxylic acid or carbonate derivatives, particularly those in which the leaving groups are N-hydroxysuccinimide, p-nitrophenol, imidazole or l-hydroxy-2- nitrobenzene-4-sulfonate.
  • PEG derivatives containing maleimido or haloacetyl groups are useful reagents for the modification of protein free sulfhydryl groups.
  • PEG reagents containing amino hydrazine or hydrazide groups are useful for reaction with aldehydes generated by periodate oxidation of carbohydrate groups in proteins.
  • amino acid residues of the polypeptide described herein are preferred to be in the "L" isomeric form.
  • residues in the "D" isomeric form can be substituted for any L-amino acid residue, as long as the desired functional property of lectin activity is retained by the polypeptide.
  • NH 2 refers to the free amino group present at the amino terminus of a polypeptide.
  • COOH refers to the free carboxy group present at the carboxy terminus of a polypeptide.
  • Abbreviations used herein are in keeping with standard polypeptide nomenclature, J. Biol. Chem. , 243:3552- 59 (1969).
  • amino-acid residue sequences are represented herein by formulae whose left and right orientation is in the conventional direction of amino- terminus to carboxy-terminus. Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino-acid residues.
  • Synthetic polypeptide prepared using the well known techniques of solid phase, liquid phase, or peptide condensation techniques, or any combination thereof, can include natural and unnatural amino acids.
  • Amino acids used for peptide synthesis may be standard Boc (N ⁇ -amino protected N ⁇ -t-butyloxycarbonyl) amino acid resin with the standard deprotecting, neutralization, coupling and wash protocols of the original solid phase procedure of Merrifield (1963, J Am. Chem. Soc. 85:2149-2154), or the base-labile N ⁇ -amino protected 9-fluorenylmethoxycarbonyl (Fmoc) amino acids first described by Carpino and Han (1972, J. Org. Chem. 37:3403-3409).
  • polypeptide of the invention may comprise D-amino acids, a combination of D- and L-amino acids, and various "designer" amino acids (e.g., ⁇ -methyl amino acids, C ⁇ -methyl amino acids, and N ⁇ -methyl amino acids, etc.) to convey special properties.
  • Synthetic amino acids include ornithine for lysine, fluorophenylalanine for phenylalanine, and norleucine for leucine or isoleucine. Additionally, by assigning specific amino acids at specific coupling steps, ⁇ - helices, ⁇ turns, ⁇ sheets, ⁇ -turns, and cyclic peptides can be generated.
  • the peptides may comprise a special amino acid at the C- terminus which incorporates either a CO 2 H or CONH 2 side chain to simulate a free glycine or a glycine-amide group. Another way to consider this special residue would be as a D or L amino acid analog with a side chain consisting of the linker or bond to the bead.
  • the pseudo-free C-terminal residue may be of the D or the L optical configuration; in another embodiment, a racemic mixture of D and L-isomers may be used.
  • pyroglutamate may be included as the N-terminal residue of the peptide.
  • pyroglutamate is not amenable to sequence by Edman degradation, by limiting substitution to only 50% of the peptides on a given bead with N- terminal pyroglutamate, there will remain enough non-pyroglutamate peptide on the bead for sequencing.
  • this technique could be used for sequencing of any peptide that incorporates a residue resistant to Edman degradation at the N-terminus.
  • Other methods to characterize individual peptides that demonstrate desired activity are described in detail infra. Specific activity of a peptide that comprises a blocked N-terminal group, e.g. , pyroglutamate, when the particular N- terminal group is present in 50% of the peptides, would readily be demonstrated by comparing activity of a completely (100%) blocked peptide with a non-blocked (0%) peptide.
  • peptides that have more well defined structural properties, and the use of peptidomimetics, and peptidomimetic bonds, such as ester bonds, to prepare peptides with novel properties.
  • a peptide may be generated that incorporates a reduced peptide bond, i.e., R ⁇ -CH 2 -NH-R 2 , where R j and R 2 are amino acid residues or sequences.
  • a reduced peptide bond may be introduced as a dipeptide subunit.
  • Such a molecule would be resistant to peptide bond hydrolysis, e.g. , protease activity.
  • Such peptides would provide ligands with unique function and activity, such as extended half-lives in vivo due to resistance to metabolic breakdown, or protease activity. Furthermore, it is well known that in certain systems constrained peptides show enhanced functional activity (Hruby, 1982, Life Sciences 31:189-199; Hruby et al., 1990, Biochem J. 268:249-262); the present invention provides a method to produce a constrained peptide that incorporates random sequences at all other positions.
  • a constrained, cyclic or rigidized peptide may be prepared synthetically, provided that in at least two positions in the sequence of the peptide an amino acid or amino acid analog is inserted that provides a chemical functional group capable of cross-linking to constrain, cyclise or rigidize the peptide after treatment to form the cross-link. Cyclization will be favored when a turn-inducing amino acid is incorporated.
  • Examples of amino acids capable of cross-linking a peptide are cysteine to form disulfide, aspartic acid to form a lactone or a lactase, and a chelator such as ⁇ -carboxyl-glutamic acid (Gla) (Bachem) to chelate a transition metal and form a cross-link.
  • Protected ⁇ -carboxyl glutamic acid may be prepared by modifying the synthesis described by Zee-Cheng and Olson (1980, Biophys. Biochem. Res. Commun. 94: 1128-1132).
  • a peptide in which the peptide sequence comprises at least two amino acids capable of cross-linking may be treated, e.g., by oxidation of cysteine residues to form a disulfide or addition of a metal ion to form a chelate, so as to cross-link the peptide and form a constrained, cyclic or rigidized peptide.
  • the present invention provides strategies to systematically prepare cross-links. For example, if four cysteine residues are incorporated in the peptide sequence, different protecting groups may be used (Hiskey, 1981, in The Peptides: Analysis, Synthesis, Biology, Vol. 3, Gross and Meienhofer, eds., Academic Press: New York, pp. 137-167; Ponsanti et al., 1990, Tetrahedron 46:8255-8266). The first pair of cysteine may be deprotected and oxidized, then the second set may be deprotected and oxidized. In this way a defined set of disulfide cross-links may be formed. Alternatively, a pair of cysteine and a pair of collating amino acid analogs may be incorporated so that the cross-links are of a different chemical nature.
  • non-classical amino acids may be incorporated in the peptide in order to introduce particular conformational motifs: l,2,3,4-tetrahydroisoquinoline-3-carboxylate (Kazmierski et al, 1991, J. Am. Chem. Soc.
  • LL-Acp LL-3-amino- 2-propenidone-6-carboxylic acid
  • ⁇ -turn inducing dipeptide analog Kemp et al, 1985, J. Org. Chem. 50:5834-5838
  • ⁇ -sheet inducing analogs Kemp et al., 1988, Tetrahedron Lett. 29:5081-5082
  • ⁇ -turn inducing analogs Kemp et al., 1988, Tetrahedron Lett.
  • the present invention further provides for modification or derivatization of the polypeptide or peptide of the invention.
  • Modifications of peptides are well known to one of ordinary skill, and include phosphorylation, carboxymethylation, and acylation. Modifications may be effected by chemical or enzymatic means.
  • glycosylated or fatty acylated peptide derivatives may be prepared. Preparation of glycosylated or fatty acylated peptides is well known in the art.
  • Fatty acyl peptide derivatives may also be prepared. For example, and not by way of limitation, a free amino group (N-terminal or lysyl) may be acylated, e.g. , myristoylated.
  • an amino acid comprising an aliphatic side chain of the structure -(CH 2 ) n CH 3 may be incorporated in the peptide.
  • This and other peptide-fatty acid conjugates suitable for use in the present invention are disclosed in U.K. Patent GB-8809162.4, International Patent Application PCT/AU89/00166, and reference 5, supra.
  • Mutations can be made in a nucleic acid encoding the polypeptide such that a particular codon is changed to a codon which codes for a different amino acid. Such a mutation is generally made by making the fewest nucleotide changes possible.
  • a substitution mutation of this sort can be made to change an amino acid in the resulting protein in a non-conservative manner (i.e., by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to another grouping) or in a conservative manner (i.e., by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to the same grouping).
  • the present invention should be considered to include sequences containing conservative changes which do not significantly alter the activity or binding characteristics of the resulting protein.
  • Substitutes for an amino acid within the sequence may be selected from other members of the class to which the amino acid belongs.
  • the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine.
  • Amino acids containing aromatic ring structures are phenylalanine, tryptophan, and tyrosine.
  • the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine.
  • the positively charged (basic) amino acids include arginine, lysine and histidine.
  • the negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Such alterations will not be expected to affect apparent molecular weight as determined by polyacrylamide gel electrophoresis, or isoelectric point.
  • substitutions are: - Lys for Arg and vice versa such that a positive charge may be maintained;
  • Synthetic DNA sequences allow convenient construction of genes which will express analogs or "muteins".
  • a general method for site-specific incorporation of unnatural amino acids into proteins is described in Noren, et al. Science, 244: 182-188 (April 1989). This method may be used to create analogs with unnatural amino acids.
  • pyroglutamate may be included as the N-terminal residue of the peptide.
  • pyroglutamate is not amenable to sequence by Edman degradation, by limiting substitution to only 50% of the peptides on a given bead with N- terminal pyroglutatamate, there will remain enough non-pyroglutamate peptide on the bead for sequencing.
  • this technique could be used for sequencing of any peptide that incorporates a residue resistant to Edman degradation at the N-terminus. Other methods to characterize individual peptides that demonstrate desired activity are described in detail infra.
  • Chemical Moieties for Derivatization may be selected from among water soluble polymers.
  • the polymer selected should be water soluble so that the component to which it is attached does not precipitate in an aqueous environment, such as a physiological environment.
  • the polymer will be pharmaceutically acceptable.
  • One skilled in the art will be able to select the desired polymer based on such considerations as whether the polymer/component conjugate will be used therapeutically, and if so, the desired dosage, circulation time, resistance to proteolysis, and other considerations. For the present component or components, these may be ascertained using the assays provided herein.
  • the water soluble polymer may be selected from the group consisting of, for example, polyethylene glycol, copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, poiyvinyl alcohol, poiyvinyl pyrrolidone, poly-1, 3-dioxolane, poly-1, 3, 6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co- polymers, polyoxyethylated polyols and poiyvinyl alcohol.
  • Polyethylene glycol propionaldenhyde may have advantages in manufacturing due to its stability in water.
  • the polymer may be of any molecular weight, and may be branched or unbranched.
  • the preferred molecular weight is between about 2kDa and about lOOkDa (the term "about” indicating that in preparations of polyethylene glycol, some molecules will weigh more, some less, than the stated molecular weight) for ease in handling and manufacturing.
  • Other sizes may be used, depending on the desired therapeutic profile (e.g. , the duration of sustained release desired, the effects, if any on biological activity, the ease in handling, the degree or lack of antigenicity and other known effects of the polyethylene glycol to a therapeutic protein or analog).
  • polymer molecules so attached may vary, and one skilled in the art will be able to ascertain the effect on function.
  • One may mono-derivative, or may provide for a di-, tri-, tetra- or some combination of derivatization, with the same or different chemical moieties (e.g., polymers, such as different weights of polyethylene glycols).
  • the proportion of polymer molecules to component or components molecules will vary, as will their concentrations in the reaction mixture.
  • the optimum ratio in terms of efficiency of reaction in that there is no excess unreacted component or components and polymer
  • the desired degree of derivatization e.g., mono, di-, tri-, etc.
  • the molecular weight of the polymer selected whether the polymer is branched or unbranched, and the reaction conditions.
  • polyethylene glycol molecules should be attached to the component or components with consideration of effects on functional or antigenic domains of the protein.
  • attachment methods available to those skilled in the art, e.g., EP 0 401 384 herein incorporated by reference (coupling PEG to G-CSF), see also Malik etal, 1992, Exp. Hematol. 20: 1028-1035 (reporting pegylation of GM-CSF using tresyl chloride).
  • polyethylene glycol may be covalently bound through amino acid residues via a reactive group, such as, a free amino or carboxyl group. Reactive groups are those to which an activated polyethylene glycol molecule may be bound.
  • amino acid residues having a free amino group include lysine residues and the - terminal amino acid residues; those having a free carboxyl group include aspartic acid residues glutamic acid residues and the C-terminal amino acid residue.
  • Sulfhydrl groups may also be used as a reactive group for attaching the polyethylene glycol molecule(s). Preferred for therapeutic purposes is attachment at an amino group, such as attachment at the N-terminus or lysine group.
  • This invention provides an isolated nucleic acid encoding a polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD.
  • This invention provides an isolated nucleic acid encoding a polypeptide comprising an amino acid sequence of a choline binding protein selected from the group of choline binding proteins CbpG or CbpD as set forth in Figure 2 or Figure 10.
  • the nucleic acid is set forth SEQ ID NO:3 or SEQ ID NO: 16, including fragments, mutants, variants, analogs, or derivatives, thereof.
  • the nucleic acid is DNA, cDNA, genomic DNA, RNA.
  • the isolated nucleic acid may be operatively linked to a promoter of RNA transcription. It is contemplated that the nucleic acid is used to competitively inhibit the lectin activity.
  • This invention further provides an isolated nucleic acid encoding an N-terminal CbpG or CbpD truncate.
  • the nucleic acid encodes an N-terminal CbpG or CbpD truncate comprising amino acids 1-90 of CbpG.
  • the nucleic acid encoding an N-terminal CbpG truncate comprising less than amino acids 1-90 of CbpG.
  • the nucleic acid encoding an N-terminal CbpD truncate is capable of encoding amino acids 2-280 of CbpD.
  • the nucleic acid encoding an N-terminal CbpD truncate encodes a truncate of amino acids 2-116 or 103-280 of CbpD.
  • the nucleic acid is set forth in SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO:24, including fragments, mutants, variants, analogs or derivatives thereof.
  • a "vector” is a replicon, such as plasmid, phage or cosmid, to which another DNA segment may be attached so as to bring about the replication of the attached segment.
  • a "DNA” refers to the polymeric form of deoxyribonucleotides (adenine, guanine, thymine, or cytosine) in its either single stranded form, or a double-stranded helix. This term refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear DNA molecules (e.g., restriction fragments), viruses, plasmids, and chromosomes.
  • linear DNA molecules e.g., restriction fragments
  • viruses e.g., plasmids, and chromosomes.
  • a DNA sequence is "operatively linked" to an expression control sequence when the expression control sequence controls and regulates the transcription and translation of that DNA sequence.
  • the term "operatively linked” includes having an appropriate start signal (e.g., ATG) in front of the DNA sequence to be expressed and maintaining the correct reading frame to permit expression of the DNA sequence under the control of the expression control sequence and production of the desired product encoded by the DNA sequence. If a gene that one desires to insert into a recombinant DNA molecule does not contain an appropriate start signal, such a start signal can be inserted in front of the gene.
  • this invention also provides a vector which comprises the above-described nucleic acid molecule.
  • the promoter may be, or is identical to, a bacterial, yeast, insect or mammalian promoter.
  • the vector may be a plasmid, cosmid, yeast artificial chromosome (YAC), bacteriophage or eukaryotic viral DNA.
  • vector backbones known in the art as useful for expressing protein may be employed.
  • Such vectors include, but are not limited to: adenovirus, simian virus 40 (SV40), cytomegalovirus (CMV), mouse mammary tumor virus (MMTV), Moloney murine leukemia virus, DNA delivery systems, i.e. liposomes, and expression plasmid delivery systems.
  • SV40 simian virus 40
  • CMV cytomegalovirus
  • MMTV mouse mammary tumor virus
  • Moloney murine leukemia virus DNA delivery systems
  • DNA delivery systems i.e. liposomes
  • expression plasmid delivery systems i.e. liposomes
  • one class of vectors comprises DNA elements derived from viruses such as bovine papilloma virus, polyoma virus, baculovirus, retroviruses or Semliki Forest virus.
  • Such vectors may be obtained commercially or assembled from the sequences described by methods well-known in the art.
  • This invention also provides a host vector system for the production of a polypeptide which comprises the vector of a suitable host cell.
  • Suitable host cells include, but are not limited to, prokaryotic or eukaryotic cells, e.g. bacterial cells (including gram positive cells), yeast cells, fungal cells, insect cells, and animal cells. Numerous mammalian cells may be used as hosts, including, but not limited to, the mouse fibroblast cell NTH 3T3, CHO cells, HeLa cells, Ltk " cells, Cos cells, etc.
  • a wide variety of host/expression vector combinations may be employed in expressing the DNA sequences of this invention.
  • Useful expression vectors for example, may consist of segments of chromosomal, non-chromosomal and synthetic DNA sequences.
  • Suitable vectors include derivatives of SV40 and known bacterial plasmids, e.g., E. coli plasmids col El, pCRl, pBR322, pMB9 and their derivatives, plasmids such as RP4; phage DNAS, e.g., the numerous derivatives of phage ⁇ , e.g., NM989, and other phage DNA, e.g., M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2 ⁇ plasmid or derivatives thereof; vectors useful in eukaryotic cells, such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or other expression control sequences; and the like.
  • phage DNAS e.g., the numerous derivatives of phage ⁇ , e.g.,
  • any of a wide variety of expression control sequences ⁇ sequences that control the expression of a DNA sequence operatively linked to it ⁇ may be used in these vectors to express the DNA sequences of this invention.
  • useful expression control sequences include, for example, the early or late promoters of SV40, CMN, vaccinia, polyoma or adenovirus, the lac system, the trp system, the TAC system, the TRC system, the LTR system, the major operator and promoter regions of phage ⁇ , the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase (e.g., Pho5), the promoters of the yeast ⁇ -mating factors, and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof.
  • a wide variety of unicellular host cells are also useful in expressing the D ⁇ A sequences of this invention.
  • These hosts may include well known eukaryotic and prokaryotic hosts, such as strains of E. coli, Pseudomonas, Bacillus, Streptomyces, fiingi such as yeasts, and animal cells, such as CHO, Rl.l, B-W and L-M cells, African Green Monkey kidney cells (e.g., COS 1, COS 7, BSC1, BSC40, and BMT10), insect cells (e.g., Sf9), and human cells and plant cells in tissue culture. It will be understood that not all vectors, expression control sequences and hosts will function equally well to express the DNA sequences of this invention.
  • Suitable unicellular hosts will be selected by consideration of, e.g., their compatibility with the chosen vector, their secretion characteristics, their ability to fold proteins correctly, and their fermentation requirements, as well as the toxicity to the host of the product encoded by the DNA sequences to be expressed, and the ease of purification of the expression products.
  • This invention further provides a method of producing a polypeptide which comprises growing the above-described host vector system under suitable conditions permitting the production of the polypeptide and recovering the polypeptide so produced.
  • the antibody may be a monoclonal or polyclonal antibody. Further, the antibody may be labeled with a detectable marker that is either a radioactive, calorimetric, fluorescent, or a luminescent marker.
  • the labeled antibody may be a polyclonal or monoclonal antibody. In one embodiment, the labeled antibody is a purified labeled antibody. Methods of labeling antibodies are well known in the art.
  • the term "antibody” includes, by way of example, both naturally occurring and non- naturally occurring antibodies. Specifically, the term “antibody” includes polyclonal and monoclonal antibodies, and fragments thereof. Furthermore, the term “antibody” includes chimeric antibodies and wholly synthetic antibodies, and fragments thereof. Such antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments, and an Fab expression library.
  • the polypeptide can be conjugated to an immunogenic carrier, e.g., bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH).
  • an immunogenic carrier e.g., bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH).
  • BSA bovine serum albumin
  • KLH keyhole limpet hemocyanin
  • Various adjuvant may be used to increase the immunological response, depending on the host species.
  • any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used (see, e.g., Antibodies — A Laboratory Manual, Harlow and Lane, eds., Cold Spring Harbor Laboratory Press: Cold Spring Harbor, Ne York, 1988).
  • monoclonal antibodies can be produced in germ- free animals utilizing recent technology (PCT/US90/02545).
  • human antibodies may be used and can be obtained by using human hybridomas (Cote et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:2026-2030) or by transforming human B cells with EBV virus in vitro (Cole et al, 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, pp. 77-96).
  • human hybridomas Cote et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:2026-2030
  • EBV virus Cold-d Antibodies
  • techniques developed for the production of "chimeric antibodies” (Morrison et al, 1984, J. Bacteriol.
  • Such human or humanized chimeric antibodies are preferred for use in therapy of human diseases or disorders (described infra), since the human or humanized antibodies are much less likely than xenogenic antibodies to induce an immune response, in particular an allergic response, themselves.
  • An additional embodiment of the invention utilizes the techniques described for the construction of Fab expression libraries (Huse et al, 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for the polypeptide, or its derivatives, or analogs.
  • Antibody fragments which contain the idiotype of the antibody molecule can be generated by known techniques.
  • such fragments include but are not limited to: the F(ab') 2 fragment which can be produced by pepsin digestion of the antibody molecule; the Fab' fragments which can be generated by reducing the disulfide bridges of the F(ab') 2 fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent.
  • screening for the desired antibody can be accomplished by techniques known in the art, e.g., radioimmunoassay, ELISA (enzyme-linked immunosorbant assay), "sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodif ⁇ usion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc.
  • radioimmunoassay e.g., ELISA (enzyme-linked immunosorbant assay), "sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodif ⁇ usion assays, in situ
  • antibody binding is detected by detecting a label on the primary antibody.
  • the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody.
  • the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
  • Antibodies can be labeled for detection in vitro, e.g., with labels such as enzymes, fluorophores, chromophores, radioisotopes, dyes, colloidal gold, latex particles, and chemiluminescent agents.
  • the antibodies can be labeled for detection in vivo, e.g., with radioisotopes (preferably technetium or iodine); magnetic resonance shift reagents (such as gadolinium and manganese); or radio-opaque reagents.
  • the labels most commonly employed for these studies are radioactive elements, enzymes, chemicals which fluoresce when exposed to ultraviolet light, and others.
  • a number of fluorescent materials are known and can be utilized as labels. These include, for example, fluorescein, rhodamine, auramine, Texas Red, AMCA blue and Lucifer Yellow.
  • a particular detecting material is anti-rabbit antibody prepared in goats and conjugated with fluorescein through an isothiocyanate.
  • the polypeptide can also be labeled with a radioactive element or with an enzyme.
  • the radioactive label can be detected by any of the currently available counting procedures.
  • the preferred isotope may be selected from 3 H, 14 C, 32 P, 35 S, 36 C1, 51 Cr, "Co, 58 Co, 59 Fe, 90 Y, 12 T, 131 I, and 186 Re.
  • Enzyme labels are likewise useful, and can be detected by any of the presently utilized calorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques.
  • the enzyme is conjugated to the selected particle by reaction with bridging molecules such as carbodiimides, diisocyanates, glutaraldehyde and the like. Many enzymes which can be used in these procedures are known and can be utilized. The preferred are peroxidase, ⁇ -glucuronidase, ⁇ -D-glucosidase, ⁇ -D-galactosidase, urease, glucose oxidase plus peroxidase and alkaline phosphatase.
  • U.S. Patent Nos. 3,654,090; 3,850,752; and 4,016,043 are referred to by way of example for their disclosure of alternate labeling material and methods. Diagnostic Applications
  • kits suitable for use by a medical specialist may be prepared to determine the presence or absence of predetermined binding activity or predetermined binding activity capability to suspected target cells.
  • one class of such kits will contain at least the labeled polypeptide or its binding partner, for instance an antibody specific thereto, and directions, of course, depending upon the method selected, e.g., "competitive,” “sandwich,” “DASP” and the like.
  • the kits may also contain peripheral reagents such as buffers, stabilizers, etc.
  • test kit may be prepared for the demonstration of the presence or capability of cells for predetermined bacterial binding activity, comprising:
  • choline binding protein CbpG or CbpD derive from the fact that the choline binding protein of the present invention is involved in or required for pneumococcal colonization and attachment, critical for bacterial survival and virulence in the human host.
  • an N- terminal CbpG or CbpD truncate acts as an immunotherapeutic fragment which binds to the cell target but prevents adhesion of the bacteria, particularly Streptococcus.
  • the N-terminal CbpG or CbpD truncate comprises the amino acid sequence as set forth in SEQ ID NO:ll, SEQ ID NO:21 or SEQ ID NO:23.
  • the N-terminal CbpG or CbpD truncate consists of amino acids 1-90 of the CbpG or amino acids 2-280 of the CbpD choline binding protein.
  • the N-terminal CbpG or CbpD truncate is a truncate of less than amino acids 1-90 of CbpG and less than amino acids 2-280, particularly consisting of amino acids 2- 116 or 103-280 of CbpD.
  • the present invention contemplates therapeutic intervention in the cascade of reactions, specifically colonization and attachment, in which the choline binding protein CbpG or CbpD is implicated, to thereby block or reduce the virulence of bacteria, particularly Streptococcus, most particularly pneumococcus.
  • an appropriate inhibitor of the choline binding protein CbpG or CbpD could be introduced to block the activity of the choline binding protein CbpG or CbpD.
  • the present invention contemplates screens for a modulator of the choline binding protein CbpG or CbpD, in particular, directly or indirectly through the choline binding site.
  • the present invention further contemplates screens for a modulator of the choline binding protein CbpG or CbpD, in particular, directly or indirectly through the N-terminal activity domain.
  • an expression vector containing the choline binding protein CbpG or CbpD of the present invention, or a derivative or analog thereof is placed into a cell in the presence of at least one agent suspected of exhibiting choline binding protein CbpG or CbpD modulator activity.
  • the cell is preferably a bacterial cell and most preferably a pneumococcal cell.
  • the amount of adhesion or binding activity is determined and any such agent is identified as a modulator when the amount of adhesion or binding activity in the presence of such agent is different than in its absence.
  • the vectors may be introduced by any of the methods described above.
  • the choline binding protein CbpG or CbpD is expressed and the step of determining the amount of adhesion or binding activity is performed by determining the amount of binding to nasopharyngeal cells in vitro.
  • an N-terminal choline binding protein truncate of the choline binding protein CbpG or CbpD is expressed and the step of determining the amount of adhesion or binding activity is performed by determining the amount of binding to nasopharyngeal cells in vitro.
  • the modulator When the amount of adhesion or binding activity in the presence of the modulator is greater than in its absence, the modulator is identified as an agonist or activator of the choline binding protein CbpG or CbpD, whereas when the amount of adhesion binding activity in the presence of the modulator is less than in its absence, the modulator is identified as an antagonist or inhibitor of the choline binding protein CbpG or CbpD.
  • the modulator is identified as an agonist or activator of the choline binding protein CbpG or CbpD
  • the modulator is identified as an antagonist or inhibitor of the choline binding protein CbpG or CbpD.
  • Natural effectors found in cells expressing choline binding protein CbpG or CbpD can be fractionated and tested using standard effector assays as exemplified herein, for example.
  • an agent that is identified can be a naturally occurring adhesion or binding modulator.
  • natural products libraries can be screened using the assays of the present invention for screening such agents.
  • This invention provides antagonist or blocking agents which include but are not limited to: peptide fragments, mimetic, a nucleic acid molecule, a ribozyme, a polypeptide, a small molecule, a carbohydrate molecule, a monosaccharide, an oligosaccharide or an antibody. Also, agents which competitively block or inhibit pneumococcal bacterium are contemplated by this invention.
  • This invention provides an agent which comprises an inorganic compound, a nucleic acid molecule, an oligonucleotide, an organic compound, a peptide, a peptidomimetic compound, or a protein which inhibits the polypeptide.
  • This invention provides a vaccine which comprises a polypeptide bacterial choline binding protein CbpG or CbpD and a pharmaceutically acceptable adjuvant or carrier.
  • This invention provides a vaccine which comprises a combination of at least two polypeptide bacterial choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein and a pharmaceutically acceptable adjuvant or carrier.
  • the polypeptide may comprise an amino acid sequence of a choline binding protein CbpG or CbpD as set forth in Figure 2 and SEQ ID NO:2 and Figure 10 and SEQ ID NO: 15.
  • the polypeptide may comprise an N-terminal truncate of a choline binding protein CbpG or CbpD.
  • the N-terminal CbpG or CbpD truncate comprises the amino acid sequence set forth in SEQID NOT 1, SEQ ID NO:21 or SEQ ID NO:23.
  • the N-terminal CbpG or CbpD truncate consists of amino acids 1-90 of the CbpG or amino acids 2-280 of CbpD choline binding protein.
  • the N-terminal truncate may comprise less than amino acids 1-90 of CbpG or amino acids 2-280 of CbpD.
  • the N-terminal truncate consists of amino acids 2-116 or 103-280 of CbpD.
  • This invention further provides a vaccine comprising an isolated nucleic acid encoding a bacterial choline binding protein CbpG or CbpD and a pharmaceutically acceptable adjuvant or carrier.
  • This invention further provides a vaccine comprising isolated nucleic acid encoding a combination of at least two polypeptide bacterial choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein and a pharmaceutically acceptable adjuvant or carrier.
  • This invention still further provides a vaccine comprising an isolated nucleic acid encoding a N-terminal truncate of choline binding protein CbpG or CbpD and a pharmaceutically acceptable adjuvant or carrier.
  • the nucleic acid may comprise a nucleic acid sequence of a choline binding protein CbpG or CbpD as set forth in Figure 2 and SEQ ID NO: 3 and Figure 10 and SEQ ID NO: 16.
  • Active immunity against Gram positive bacteria can be induced by immunization (vaccination) with an immunogenic amount of the polypeptide, or peptide derivative or immunogenic fragment thereof or N-terminal truncate thereof, and an adjuvant, wherein the polypeptide, or antigenic derivative or; fragment thereof, is the antigenic component of the vaccine.
  • the polypeptide, or antigenic derivative or fragment thereof may be one antigenic component, in the presence of other antigenic components in a vaccine.
  • the polypeptide of the present invention or immunogenic fragment thereof may be combined with other known pneumococcal polypeptides, or immunogenic fragments thereof or N-terminal truncates thereof, as for instance other choline binding protein(s), including for instance CbpA, LytA, and/or PspA in a multi-component vaccine.
  • the polypeptide of the present invention or immunogenic fragments thereof may be combined with bacterial zinc metalloprotease, ZmpB or immunogenic fragements thereof.
  • Such multi-component vaccine may be utilized to enhance immune response, even in cases where the polypeptide of the present invention elicits a response on its own.
  • the polypeptide of the present invention may also be combined with existing vaccines, whole bacterial or capsule-based vaccines, alone or in combination with other choline binding proteins or ZmpB, to enhance such existing vaccines.
  • the invention further provides a vaccine which comprises a non-adherent, non- virulent mutant, including but not limited to the CbpG or CbpD mutants herein described.
  • Medaglini et al (Madaglini et al (1995) Proc Natl Acad Sci USA 92;6868-6872) and Oggioni and Pozzi (Oggioni, M.R. and Pozzi, G. (1996) Gene 169:85-90) have previously described the use of Streptococcus gordonii, a commensal bacterium of the human oral cavity, as live vaccine delivery vehicles and for heterologous gene expression.
  • Such CbpG or CbpD mutant can therefore be utilized as a vehicle for expression of immunogenic proteins for the purposes of eliciting an immune response to such other proteins in the context of vaccines.
  • Active immunity against Gram positive bacteria, particularly pneumococcus can be induced by immunization (vaccination) with an immunogenic amount of the CbpG or CbpD vehicle expressing an immunogenic protein.
  • Also contemplated by the present invention is the use of any such CbpG or CbpD mutant in expressing a therapeutic protein in the host in the context of other forms of therapy.
  • polypeptide of the present invention can be prepared in an admixture with an adjuvant to prepare a vaccine.
  • the polypeptide or peptide derivative or fragment thereof, used as the antigenic component of the vaccine is an antigen common to all or many strains of a species of Gram positive bacteria, or common to closely related species of bacteria, for instance Streptococcus.
  • Vectors containing the nucleic acid-based vaccine of the invention can be introduced into the desired host by methods known in the art, e.g., transfection, electroporation, micro injection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, lipofection (lysosome fusion), use of a gene gun, or a DNA vector transporter (see, e.g., Wu et al, 1992, J. Biol. Chem. 267:963-967; Wu and Wu, 1988, J. Biol. Chem. 263: 14621-14624; Hartmut et al, Canadian Patent Application No. 2,012,311, filed March 15, 1990).
  • the vaccine can be administered via any parenteral route, including but not limited to intramuscular, intraperitoneal, intravenous, and the like.
  • parenteral route including but not limited to intramuscular, intraperitoneal, intravenous, and the like.
  • the desired result of vaccination is to elucidate an immune response to the antigen, and thereby to the pathogenic organism
  • administration directly, or by targeting or choice of a viral vector, indirectly, to lymphoid tissues, e.g., lymph nodes or spleen is desirable.
  • lymphoid tissues e.g., lymph nodes or spleen
  • Passive immunity can be conferred to an animal subject suspected of suffering an infection with a Gram positive bacterium, preferably streptococcal, and more preferably pneumoccal, by administering antiserum, polyclonal antibodies, or a neutralizing monoclonal antibody against a polypeptide of the invention to the subject.
  • a combination of antibodies can be, for instance, directed against at least two polypeptide bacterial choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein.
  • the antibodies administered for passive immune therapy are autologous antibodies.
  • the antibodies are of human origin or have been "humanized," in order to minimize the possibility of an immune response against the antibodies.
  • the active or passive vaccines of the invention can be used to protect an animal subject from infection of a Gram positive bacteria, preferably streptococcus, and more preferably, pneumococcus.
  • This invention provides a method for treating a subject infected with or exposed to pneumococcal bacterium comprising administering to the subject a therapeutically effective amount of the vaccine, thereby treating the subject.
  • This invention provides a pharmaceutical composition comprising an amount of the polypeptide as described and a pharmaceutically acceptable carrier or diluent.
  • This invention provides a pharmaceutical composition comprising an amount of a choline binding protein CbpG or CbpD and a pharmaceutically acceptable carrier or diluent.
  • This invention provides a pharmaceutical composition comprising an amount of at least two choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein and a pharmaceutically acceptable carrier or diluent.
  • the invention further provides a pharmaceutical composition comprising an amount of the polypeptide of SEQ ID NO: 2 or SEQ ID NO: 15, including fragments, mutants, variants, analogs or derivatives thereof, and a pharmaceutically acceptable carrier or diluent.
  • This invention still further provides a pharmaceutical composition
  • a pharmaceutical composition comprising an amount of an N- terminal truncate of a choline binding protein CbpG or CbpD.
  • the N-terminal CbpG or CbpD truncate comprises amino acids 1-90 of CbpG or amino acids 2-280, 2-116 or 103-280 of CbpD, as set out in SEQ ID NOT 1, SEQ ID NO:21 or SEQ ID NO:23, or active fragments, mutants, variants, analogs or derivatives thereof.
  • such pharmaceutical composition for preventing pneumococcal attachment to mucosal surface may include antibody to choline binding protein CbpG or CbpD or any combination of anti-CbpG or CbpD antibody and at least one other antibody directed against another choline binding protein. Blocking adherence using such antibody blocks the initial step in infection thereby reducing colonization. This in turn decreases person to person transmission and prevents development of symptomatic disease.
  • a further example of a pharmaceutical composition for preventing pneumococcal attachment may include an N-terminal CbpG or CbpD truncaate. In a particular embodiment, such N- terminal truncate comprises the amino acid set out in SEQ ID NOT 1, SEQ ID NO: 21 or SEQ ID NO: 23, or active fragments thereof.
  • This invention provides a method of inducing an immune response in a subject which has been exposed to or infected with a pneumococcal bacterium comprising administering to the subject an amount of the pharmaceutical composition, thereby inducing an immune response.
  • This invention provides a method for preventing infection by a pneumococcal bacterium in a subject comprising administering to the subject an amount of the pharmaceutical composition effective to block activity of the choline binding protein CbpG or CbpD, thereby preventing pneumococcal bacterium attachment, and further preventing infection by a pneumococcal bacterium.
  • This invention provides a method for preventing infection by a pneumococcal bacterium in a subject comprising administering to the subject an amount of a pharmaceutical composition comprising the antibody and a pharmaceutically acceptable carrier or diluent, thereby preventing infection by a pneumococcal bacterium.
  • This invention provides a method of inhibiting colonization of host cells in a subject which has been exposed to or infected with a pneumococcal bacterium comprising administering to the subject an amount of the pharmaceutical composition comprising the polypeptide consisting of the amino acid sequence as set forth in SEQ ID NO:2, SEQ ID NOT 1, SEQ ID NO:15, SEQ ID NO:21 or SEQ ID NO:23, or immunogenic fragments thereof thereby inducing an immune response.
  • the therapeutic peptide that blocks colonization is delivered via the respiratory mucosa.
  • the pharmaceutical composition comprises the polypeptide consisting of the amino acid sequence as set forth in SEQ ID NO:2, SEQ ID NOT 1, SEQ ID NO:15, SEQ ID NO:21 or SEQ ID NO:23.
  • pharmaceutical composition could mean therapeutically effective amounts of polypeptide products of the invention together with suitable diluents, preservatives, solubilizers, emulsifiers, adjuvant and/or carriers useful in therapy against bacterial infection or in inducing an immune response.
  • suitable diluents preservatives, solubilizers, emulsifiers, adjuvant and/or carriers useful in therapy against bacterial infection or in inducing an immune response.
  • a “therapeutically effective amount” as used herein refers to that amount which provides a therapeutic effect for a given condition and administration regimen.
  • compositions are liquids or lyophilized or otherwise dried formulations and include diluents of various buffer content (e.g., Tris- HCl, acetate, phosphate), pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts), solubilizing agents (e.g., glycerol, polyethylene glycerol), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), preservatives (e.g., Thimerosal, benzyl alcohol, parabens), bulking substances or tonicity modifiers (e.g., lactose, mannitol), covalent attachment of polymers such as polyethylene glycol to the protein, complexation with metal ions, or incorporation of the material into or onto particulate preparations of polymeric compounds such as polylactic acid, polglycolic acid
  • compositions will influence the physical state, solubility, stability, rate of in vivo release, and rate of in vivo clearance of choline binding protein CbpG or CbpD and the polypeptides of the present invention.
  • the choice of compositions will depend on the physical and chemical properties of the polypeptide.
  • Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils).
  • particulate compositions coated with polymers e.g., poloxamers or poloxamines
  • the polypeptides of the present invention coupled to antibodies directed against tissue-specific receptors, ligands or antigens or coupled to ligands of tissue-specific receptors.
  • Other embodiments of the compositions of the invention incorporate particulate forms, protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.
  • pharmaceutically acceptable carrier include, but are not limited to, 0.01-0.1M and preferably 0.05M phosphate buffer or 0.8%) saline.
  • pharmaceutically acceptable carriers may be aqueous or non-aqueous solutions, suspensions, and emulsions.
  • non- aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's or fixed oils.
  • Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Preservatives and other additives may also be present, such as, for example, antimicrobials, antioxidants, collating agents, inert gases and the like.
  • adjuvant refers to a compound or mixture that enhances the immune response to an antigen.
  • An adjuvant can serve as a tissue depot that slowly releases the antigen and also as a lymphoid system activator that non-specifically enhances the immune response (Hood et al, Immunology, Second Ed., 1984, Benjamin/Cummings: Menlo Park, California, p. 384).
  • a primary challenge with an antigen alone, in the absence of an adjuvant will fail to elicit a humoral or cellular immune response.
  • Adjuvant include, but are not limited to, complete Freund's adjuvant, incomplete Freund's adjuvant, saponin, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvant such as BCG (bacille Calmette-Gueri ⁇ ) and Corynebacterium parvum.
  • the adjuvant is pharmaceutically acceptable.
  • Controlled or sustained release compositions include formulation in lipophilic depots (e.g. fatty acids, waxes, oils). Also comprehended by the invention are particulate compositions coated with polymers (e.g. poloxamers or poloxamines) and the compound coupled to antibodies directed against tissue-specific receptors, ligands or antigens or coupled to ligands of tissue-specific receptors. Other embodiments of the compositions of the invention incorporate particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.
  • polymers e.g. poloxamers or poloxamines
  • Other embodiments of the compositions of the invention incorporate particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.
  • Such modifications may also increase the compound's solubility in aqueous solution, eliminate aggregation, enhance the physical and chemical stability of the compound, and greatly reduce the immunogenicity and reactivity of the compound.
  • the desired in vivo biological activity may be achieved by the administration of such polymer-compound abducts less frequently or in lower doses than with the unmodified compound.
  • the sufficient amount may include but is not limited to from about 1 ⁇ g/kg to about 1000 mg/kg.
  • the amount may be 10 mg/kg.
  • the pharmaceutically acceptable form of the composition includes a pharmaceutically acceptable carrier.
  • the present invention provides therapeutic compositions comprising pharmaceutical compositions comprising vectors, vaccines, polypeptides or fragments thereof, nucleic acids and antibodies, anti-antibodies, and agents, to compete with the pneumococcus bacterium for pathogenic activities, such as adherence to host cells.
  • compositions which contain an active component are well understood in the art.
  • such compositions are prepared as an aerosol of the polypeptide delivered to the nasopharynx or as injectables, either as liquid solutions or suspensions, however, solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared.
  • the preparation can also be emulsified.
  • the active therapeutic ingredient is often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof.
  • the composition can contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents which enhance the effectiveness of the active ingredient.
  • An active component can be formulated into the therapeutic composition as neutralized pharmaceutically acceptable salt forms.
  • Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the polypeptide or antibody molecule) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed from the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
  • a composition comprising "A” (where "A” is a single protein, DNA molecule, vector, etc.) is substantially free of “B” (where “B” comprises one or more contaminating proteins, DNA molecules, vectors, etc.) when at least about 75% by weight of the proteins, DNA, vectors (depending on the category of species to which A and B belong) in the composition is "A".
  • "A” comprises at least about 90% by weight of the A+B species in the composition, most preferably at least about 99% by weight.
  • terapéuticaally effective amount is used herein to mean an amount sufficient to reduce by at least about 15 percent, preferably by at least 50 percent, more preferably by at least 90 percent, and most preferably prevent, a clinically significant deficit in the activity, function and response of the host.
  • a therapeutically effective amount is sufficient to cause an improvement in a clinically significant condition in the host.
  • a deficit in the response of the host is evidenced by continuing or spreading bacterial infection.
  • An improvement in a clinically significant condition in the host includes a decrease in bacterial load, clearance of bacteria from colonized host cells, reduction in fever or inflammation associated with infection, or a reduction in any symptom associated with the bacterial infection.
  • the component or components of a therapeutic composition of the invention may be introduced parenterally, transmucosally, e.g., orally, nasally, pulmonarailly, orrectally, or transdermally.
  • administration is parenteral, e.g., via intravenous injection, and also including, but is not limited to, intra-arteriole, intramuscular, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial administration.
  • Oral or pulmonary delivery may be preferred to activate mucosal immunity; since pneumococci generally colonize the nasopharyngeal and pulmonary mucosa, mucosal immunity may be a particularly effective preventive treatment.
  • unit dose when used in reference to a therapeutic composition of the present invention refers to physically discrete units suitable as unitary dosage for humans, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent; i.e., carrier, or vehicle.
  • the active compound can be delivered in a vesicle, in particular a liposome (see Langer, Science 249:1527-1533 (1990); Treat et al. , in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
  • a liposome see Langer, Science 249:1527-1533 (1990); Treat et al. , in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
  • the therapeutic compound can be delivered in a controlled release system.
  • the polypeptide may be administered using intravenous infusion, an implantable osmotic pump, a transdermal patch, liposomes, or other modes of administration.
  • a pump may be used (see Langer, supra; Sefton, CRC Crit. Refi Biomed. Eng. 14:201 (1987); Buchwald et al, Surgery 88:507 (1980); Saudek et al, N. Engl. J. Med. 321 :574 (1989)).
  • polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Florida (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, J. Macromol. Sci. Rev. Macromol Chem. 23:61 (1983); see also Levy etal, Science 228:190 (1985); During et al, Ann. Neurol 25:351 (1989); Howard et al, J. Neurosurg. 71: 105 (1989)).
  • a controlled release system can be placed in proximity of the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)).
  • a controlled release device is introduced into a subject in proximity of the site of inappropriate immune activation or a tumor.
  • Other controlled release systems are discussed in the review by Langer (Science 249: 1527-1533 (1990)).
  • a subject in whom administration of an active component as set forth above is an effective therapeutic regimen for a bacterial infection is preferably a human, but can be any animal.
  • the methods and pharmaceutical compositions of the present invention are particularly suited to administration to any animal, particularly a mammal, and including, but by no means limited to, domestic animals, such as feline or canine subjects, farm animals, such as but not limited to bovine, equine, caprine, ovine, and porcine subjects, wild animals (whether in the wild or in a zoological garden), research animals, such as mice, rats, rabbits, goats, sheep, pigs, dogs, cats, etc., i.e., for veterinary medical use.
  • a therapeutically effective dosage of the active component is provided.
  • a therapeutically effective dosage can be determined by the ordinary skilled medical worker based on patient characteristics (age, weight, sex, condition, complications, other diseases, etc.), as is well known in the art. Furthermore, as further routine studies are conducted, more specific information will emerge regarding appropriate dosage levels for treatment of various conditions in various patients, and the ordinary skilled worker, considering the therapeutic context, age and general health of the recipient, is able to ascertain proper dosing. Generally, for intravenous injection or infusion, dosage may be lower than for intraperitoneal, intramuscular, or other route of administration. The dosing schedule may vary, depending on the circulation half-life, and the formulation used.
  • compositions are administered in a manner compatible with the dosage formulation in the therapeutically effective amount.
  • Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner and are peculiar to each individual.
  • suitable dosages may range from about 0.1 to 20, preferably about 0.5 to about 10, and more preferably one to several, milligrams of active ingredient per kilogram body weight of individual per day and depend on the route of administration.
  • Suitable regimes for initial administration and booster shots are also variable, but are typified by an initial administration followed by repeated doses at one or more hour intervals by a subsequent injection or other administration.
  • continuous intravenous infusion sufficient to maintain concentrations of ten nanomolar to ten micromolar in the blood are contemplated.
  • Administration with other compounds For treatment of a bacterial infection, one may administer the present active component in conjunction with one or more pharmaceutical compositions used for treating bacterial infection, including but not limited to (1) antibiotics; (2) soluble carbohydrate inhibitors of bacterial adhesin; (3) other small molecule inhibitors of bacterial adhesin; (4) inhibitors of bacterial metabolism, transport, or transformation; (5) stimulators of bacterial lysis, or (6) anti-bacterial antibodies or vaccines directed at other bacterial antigens.
  • Other potential active components include anti-inflammatory agents, such as steroids and non-steroidal anti-inflammatory drugs.
  • Administration may be simultaneous (for example, administration of a mixture of the present active component and an antibiotic), or may be in seriatim.
  • the therapeutic compositions may further include an effective amount of the active component, and one or more of the following active ingredients: an antibiotic, a steroid, etc.
  • active ingredients an antibiotic, a steroid, etc.
  • Polypeptide antagonist 5.0 sodium bisulfite USP 3.2 disodium edetate USP 0.1 water for injection q.s.a.d. 1.0 ml
  • the polypeptide is introduced to block the interaction of the bacteria with the host cell.
  • pulmonary delivery of an inhibitor of the polypeptide of the present invention having which acts as adhesin inhibitory agent (or derivatives thereof).
  • the adhesin inhibitory agent (or derivative) is delivered to the lungs of a mammal, where it can interfere with bacterial, i.e., streptococcal, and preferably pneumococcal binding to host cells.
  • adhesin inhibitory agent or derivative
  • each formulation is specific to the type of device employed and may involve the use of an appropriate propellant material, in addition to the usual diluents, adjuvant and/or carriers useful in therapy.
  • the use of liposomes, microcapsules or microspheres, inclusion complexes, or other types of carriers is contemplated.
  • Chemically modified adhesin inhibitory agent may also be prepared in different formulations depending on the type of chemical modification or the type of device employed.
  • Formulations suitable for use with a nebulizer will typically comprise adhesin inhibitory agent (or derivative) dissolved in water at a concentration of about 0.1 to 25 mg of biologically active adhesin inhibitory agent per ml of solution.
  • the formulation may also include a buffer and a simple sugar (e.g., for adhesin inhibitory agent stabilization and regulation of osmotic pressure).
  • the nebulizer formulation may also contain a surfactant, to reduce or prevent surface induced aggregation of the adhesin inhibitory agent caused by atomization of the solution in forming the aerosol.
  • Formulations for use with a metered-dose inhaler device will generally comprise a finely divided powder containing the adhesin inhibitory agent (or derivative) suspended in a propellant with the aid of a surfactant.
  • the propellant may be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon, or a hydrocarbon, including trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof.
  • Suitable surfactants include sorbitan trioleate and soya lecithin. Oleic acid may also be useful as a surfactant.
  • the liquid aerosol formulations contain adhesin inhibitory agent and a dispersing agent in a physiologically acceptable diluent.
  • the dry powder aerosol formulations of the present invention consist of a finely divided solid form of adhesin inhibitory agent and a dispersing agent. With either the liquid or dry powder aerosol formulation, the formulation must be aerosolized. That is, it must be broken down into liquid or solid particles in order to ensure that the aerosolized dose actually reaches the mucous membranes of the nasal passages or the lung.
  • aerosol particle is used herein to describe the liquid or solid particle suitable for nasal or pulmonary administration, i.e., that will reach the mucous membranes.
  • the mass median dynamic diameter will be 5 micrometers or less in order to ensure that the drug particles reach the lung alveoli [Wearley, L.L. (1991) Crit. Rev. in Ther. Drug Carrier Systems 8:333].
  • an aerosol formulation of the present invention can include other therapeutically or pharmacologically active ingredients in addition to adhesin inhibitory agent, such as but not limited to an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
  • the present invention provides aerosol formulations and dosage forms for use in treating subjects suffering from bacterial, e.g., streptococcal, in particularly pneumococcal, infection.
  • dosage forms contain adhesin inhibitory agent in a pharmaceutically acceptable diluent.
  • Pharmaceutically acceptable diluents include but are not limited to sterile water, saline, buffered saline, dextrose solution, and the like.
  • a diluent that may be used in the present invention or the pharmaceutical formulation of the present invention is phosphate buffered saline, or a buffered saline solution generally between the pH 7.0-8.0 range, or water.
  • the liquid aerosol formulation of the present invention may include, as optional ingredients, pharmaceutically acceptable carriers, diluents, solubilizing or emulsifying agents, surfactants and excipients.
  • the formulation may include a carrier.
  • the carrier is a macromolecule which is soluble in the circulatory system and which is physiologically acceptable where physiological acceptance means that those of skill in the art would accept injection of said carrier into a patient as part of a therapeutic regime.
  • the carrier preferably is relatively stable in the circulatory system with an acceptable plasma half life for clearance.
  • Such macromolecules include but are not limited to Soya lecithin, oleic acid and sorbitan trioleate, with sorbitan trioleate preferred.
  • the formulations of the present embodiment may also include other agents useful for pH maintenance, solution stabilization, or for the regulation of osmotic pressure.
  • agents include but are not limited to salts, such as sodium chloride, or potassium chloride, and carbohydrates, such as glucose, galactose or mannose, and the like.
  • the present invention further contemplates liquid aerosol formulations comprising adhesin inhibitory agent and another therapeutically effective drug, such as an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
  • another therapeutically effective drug such as an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
  • Aerosol Dry Powder Formulations It is also contemplated that the present aerosol formulation can be prepared as a dry powder formulation comprising a finely divided powder form of adhesin inhibitory agent and a dispersant.
  • Formulations for dispensing from a powder inhaler device will comprise a finely divided dry powder containing adhesin inhibitory agent (or derivative) and may also include a bulking agent, such as lactose, sorbitol, sucrose, or mannitol in amounts which facilitate dispersal of the powder from the device, e.g., 50 to 90% by weight of the formulation.
  • adhesin inhibitory agent (or derivative) should most advantageously be prepared in particulate form with an average particle size of less than 10 mm (or microns), most preferably 0.5 to 5 mm, for most effective delivery to the distal lung.
  • the dry powder formulation can comprise a finely divided dry powder containing adhesin inhibitory agent, a dispersing agent and also a bulking agent.
  • Bulking agents useful in conjunction with the present formulation include such agents as lactose, sorbitol, sucrose, or mannitol, in amounts that facilitate the dispersal of the powder from the device.
  • the present invention further contemplates dry powder formulations comprising adhesin inhibitory agent and another therapeutically effective drug, such as an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
  • another therapeutically effective drug such as an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
  • Solid dosage forms include tablets, capsules, pills, troches or lozenges, cachets or pellets.
  • liposomal or proteinoid encapsulation may be used to formulate the present compositions (as, for example, proteinoid microspheres reported in U.S. Patent No. 4,925,673).
  • Liposomal encapsulation may be used and the liposomes may be derivatized with various polymers (e.g., U.S. Patent No. 5,013,556).
  • the formulation will include the component or components (or chemically modified forms thereof) and inert ingredients which allow for protection against the stomach environment, and release of the biologically active material in the intestine.
  • oral dosage forms of the above derivatized component or components may be chemically modified so that oral delivery of the derivative is efficacious.
  • the chemical modification contemplated is the attachment of at least one moiety to the component molecule itself, where said moiety permits (a) inhibition of proteolysis; and (b) uptake into the blood stream from the stomach or intestine.
  • the increase in overall stability of the component or components and increase in circulation time in the body examples include: polyethylene glycol, copolymers of ethylene glycol and propylene glycol, carboxymethyl cellulose, dextran, poiyvinyl alcohol, poiyvinyl pyrrolidone and polyproline.
  • the location of release may be the stomach, the small intestine (the duodenum, the jejunem, or the ileum), or the large intestine.
  • the stomach the small intestine (the duodenum, the jejunem, or the ileum), or the large intestine.
  • One skilled in the art has available formulations which will not dissolve in the stomach, yet will release the material in the duodenum or elsewhere in the intestine.
  • the release will avoid the deleterious effects of the stomach environment, either by protection of the protein (or derivative) or by release of the biologically active material beyond the stomach environment, such as in the intestine.
  • a coating impermeable to at least pH 5.0 is essential.
  • examples of the more common inert ingredients that are used as enteric coatings are cellulose acetate trimellitate (CAT), hydroxypropylmethylcellulose phthalate (HPMCP), HPMCP 50, HPMCP 55, poiyvinyl acetate phthalate (PVAP), Eudragit L30D, Aquateric, cellulose acetate phthalate (CAP), Eudragit L, Eudragit S, and Shellac. These coatings may be used as mixed films.
  • a coating or mixture of coatings can also be used on tablets, which are not intended for protection against the stomach. This can include sugar coatings, or coatings which make the tablet easier to swallow.
  • Capsules may consist of a hard shell (such as gelatin) for delivery of dry therapeutic i.e. powder; for liquid forms, a soft gelatin shell may be used.
  • the shell material of cachets could be thick starch or other edible paper. For pills, lozenges, molded tablets or tablet triturates, moist massing techniques can be used.
  • the peptide therapeutic can be included in the formulation as fine multiparticulates in the form of granules or pellets of particle size about 1mm.
  • the formulation of the material for capsule administration could also be as a powder, lightly compressed plugs or even as tablets.
  • the therapeutic could be prepared by compression.
  • Colorants and flavoring agents may all be included.
  • the protein (or derivative) may be formulated (such as by liposome or microsphere encapsulation) and then further contained within an edible product, such as a refrigerated beverage containing colorants and flavoring agents.
  • diluents could include carbohydrates, especially mannitol, a-lactose, anhydrous lactose, cellulose, sucrose, modified dextran and starch.
  • Certain inorganic salts may be also be used as fillers including calcium triphosphate, magnesium carbonate and sodium chloride.
  • Some commercially available diluents are Fast-Flo, Emdex, STA-Rx 1500, Emcompress and Avicell
  • Disintegrants may be included in the formulation of the therapeutic into a solid dosage form.
  • Materials used as disintegrates include but are not limited to starch, including the commercial disintegrant based on starch, Explotab. Sodium starch glycolate, Amberlite, sodium carboxymethylcellulose, ultramylopectin, sodium alginate, gelatin, orange peel, acid carboxymethyl cellulose, natural sponge and bentonite may all be used.
  • Another form of the disintegrants are the insoluble cationic exchange resins.
  • Powdered gums may be used as disintegrants and as binders and these can include powdered gums such as agar, Karaya or tragacanth. Alginic acid and its sodium salt are also useful as disintegrants.
  • Binders may be used to hold the therapeutic agent together to form a hard tablet and include materials from natural products such as acacia, tragacanth, starch and gelatin. Others include methyl cellulose (MC), ethyl cellulose (EC) and carboxymethyl cellulose (CMC). Poiyvinyl pyrrolidone (PVP) and hydroxypropylmethyl cellulose (HPMC) could both be used in alcoholic solutions to granulate the therapeutic.
  • MC methyl cellulose
  • EC ethyl cellulose
  • CMC carboxymethyl cellulose
  • PVP polyvinyl pyrrolidone
  • HPMC hydroxypropylmethyl cellulose
  • Lubricants may be used as a layer between the therapeutic and the die wall, and these can include but are not limited to; stearic acid including its magnesium and calcium salts, polytetrafluoroethylene (PTFE), liquid paraffin, vegetable oils and waxes. Soluble lubricants may also be used such as sodium lauryl sulfate, magnesium lauryl sulfate, polyethylene glycol of various molecular weights, Carbowax 4000 and 6000.
  • the glidants may include starch, talc, pyrogenic silica and hydrated silicoaluminate.
  • surfactant might be added as a wetting agent.
  • Surfactants may include anionic detergents such as sodium lauryl sulfate, dioctyl sodium sulfosuccinate and dioctyl sodium sulfonate.
  • anionic detergents such as sodium lauryl sulfate, dioctyl sodium sulfosuccinate and dioctyl sodium sulfonate.
  • Cationic detergents might be used and could include benzalkonium chloride or benzethomium chloride.
  • nonionic detergents that could be included in the formulation as surfactants are lauromacrogol 400, polyoxyl 40 stearate, polyoxyethylene hydrogenated castor oil 10, 50 and 60, glycerol monostearate, polysorbate 40, 60, 65 and 80, sucrose fatty acid ester, methyl cellulose and carboxymethyl cellulose. These surfactants could be present in the formulation of the protein or derivative either alone or as a mixture in different ratios.
  • Additives which potentially enhance uptake of the polypeptide (or derivative) are for instance the fatty acids oleic acid, linoleic acid and linolenic acid.
  • Pulmonary Delivery also contemplated herein is pulmonary delivery of the present polypeptide (or derivatives thereof).
  • the polypeptide (or derivative) is delivered to the lungs of a mammal while inhaling and coats the mucosal surface of the alveoli.
  • Other reports of this include Adjei et al. (1990) Pharmaceutical Research 7:565-569; Adjei et al. (1990) International Journal of Pharmaceutics 63: 135-144 (leuprolide acetate); Braquet et ⁇ /.(1989) Journal of Cardiovascular Pharmacology, 13(suppl 5):143-146 (endothelin-1); Hubbard etal. (1989) Annals of Internal Medicine, Nol. in, pp.
  • Contemplated for use in the practice of this invention are a wide range of mechanical devices designed for pulmonary delivery of therapeutic products, including but not limited to nebulizers, metered dose inhalers, and powder inhalers, all of which are familiar to those skilled in the art.
  • Formulations suitable for use with a nebulizer will typically comprise polypeptide (or derivative) dissolved in water at a concentration of about 0.1 to 25 mg of biologically active protein per mL of solution.
  • the formulation may also include a buffer and a simple sugar (e.g., for protein stabilization and regulation of osmotic pressure).
  • the nebulizer formulation may also contain a surfactant, to reduce or prevent surface induced aggregation of the protein caused by atomization of the solution in forming the aerosol.
  • Formulations for use with a metered-dose inhaler device will generally comprise a finely divided powder containing the polypeptide (or derivative) suspended in a propellant with the aid of a surfactant.
  • the propellant may be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon, or a hydrocarbon, including trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof.
  • Suitable surfactants include sorbitan trioleate and soya lecithin. Oleic acid may also be useful as a surfactant.
  • Formulations for dispensing from a powder inhaler device will comprise a finely divided dry powder containing polypeptide (or derivative) and may also include a bulking agent, such as lactose, sorbitol, sucrose, or mannitol in amounts which facilitate dispersal of the powder from the device, e.g., 50 to 90% by weight of the formulation.
  • the protein (or derivative) should most advantageously be prepared in particulate form with an average particle size of less than 10 mm (or microns), most preferably 0.5 to 5 mm, for most effective delivery to the distal lung.
  • Nasal Delivery Nasal or nasopharyngeal delivery of the polypeptide (or derivative) is also contemplated. Nasal delivery allows the passage of the polypeptide directly over the upper respiratory tract mucosal after administering the therapeutic product to the nose, without the necessity for deposition of the product in the lung.
  • Formulations for nasal delivery include those with dextran or cyclodextran.
  • FIGURE 1 SEQ ID NO: 1
  • the pneumococcal database is publicly available at www.tigr.org/tdb/mdb/mdb.html and through the National Center for Biotechnology Information (at www.nih.ncbi.org).
  • the pneumococcal database is selected and searched by the following steps: (1) select "BLAST”; (2) under “Specialized Blast Pages", select “Unfinished Microbial Genomes”; (3) then click to choose individual genomes to search; and (4) under "Eubacteria” select "Streptococcus pneumoniae” .
  • a search of this public database using the search engine BLAST available at www.nih.ncbi.org, with the filter and other parameters set at default, using SEQ ID NO: 1 will yield the polypeptides and nucleic acids now identified in the present invention.
  • the search identifies eight contigs which contain nine encoded choline binding polypeptides, which are unique and distinct from the recognized pneumococcal choline binding proteins PspA, LytA and CbpA, and are designated CbpB, CbpC, CbpD, CbE, CbpF, CbpG, CbpH, Cbpl and CbpJ.
  • One contig encodes two Cbps, specifically CbpF and CbpG or CbpD, and required further visual analysis of the layout of the homologous choline binding domains to identify and distinguish the two unique Cbps.
  • the amino acid and nucleic acid sequences of choline binding protein CbpG is found in FIGURE 2, corresponding to SEQ ID NO: 2 (amino acid) and SEQ ID NO: 3 (nucleic acid).
  • CbpG is the smallest of the choline binding proteins with an open reading frame (ORF) that is 462 nucleotides long.
  • the CbpG gene has a 35%) GC content which is consistent with the 38.5%) GC content of pneumococcus. It is located upstream of the gene for
  • CbpF may be cotranscribed with CpbF.
  • FIGURE 2A-C SEQ ID NO:4.
  • FIGURE 2 CbpG polypeptide is shown in FIGURE 2 and FIGURE 3 (SEQ ID NO:2).
  • SEQ ID NO:2 The nucleic acid sequence of CbpG including upstream promoter sequence is presented in FIGURE
  • the CbpG gene encodes a peptide of 154 amino acids with a predicted size of 17kDa.
  • the protein has two domains: (i) an N-terminal domain (amino acids 1 to 93) with a high level of homology to a 50 amino acid region of the Enterococcus faecalis serine proteinase and (ii) a C-terminal domain which, like all other choline binding proteins, contains the 20 amino acid repeats required for choline binding.
  • CbpG has 2 such repeats.
  • cbpG loss of function mutants were constructed by insertion duplication mutagenesis.
  • An internal 220bp fragment at the N-terminus of CbpG was amplified from Type 4 chromosomal DNA using primers 939E (5' TTC TTG aAT TcC CAA GTT GAT ACT vTT (SEQ ID NO:5)) and 939B (5' ATA ATG Gat CCA ACT ACC ATT TAT TTT C (SEQIDNO: 6)).
  • the PCR product was digested with EcoRI and BamHI and cloned into pJDC9 and transformed into DH5 ⁇ E.coli. Insert was verified by size and restriction analysis and the plasmid was then transformed into S. pneumoniae wild type 4, selecting for erythromycin resistance. Such colonies were isolated and the position of the insert in the cbpG gene was verified by PCR.
  • the cbpG defective mutant was then assesssed for it's ability to colonize the infant rat nasopharynx, to adhere to Detroit cells as well as to immobilized carbohydrates LNnT and sialylactose, transformation, lysis in response to detergent (DOC) and pencillin sensitivity. All of these properties have been shown to be important in pneumococcal physiology.
  • TyR ⁇ Parent S. pneumoniae strain Type 4 Rough
  • the coding sequence of cbpG was amplified using primers to sequences immediately downstream of the AUG start codon, CbpGpura (5 ' CGC GGA TCC GCG TAT ACA GAT AAG AAA CAA G) (SEQIDNO:7) and sequences overlapping the TAA termination codon, CbpGpurb (5'TCC CCC GGG GAA CAT TAA ATC CAC TCA (SEQIDNO: 8)). These primers amplify out the entire CbpG coding sequence with the exception of the start codon and introduce a BamHI site at the N-terminus of the gene and a Smal site at the C-terminus of the gene.
  • the PCR product was then digested with BamHI and Smal and cloned into a pQE30 His-tag expression vector from Qiagen and transformed into E.coli strain Ml 5. This results in an in frame fusion of the N-terminus of the CbpG gene with the 6XHis tag of the plasmid.
  • the protein is then purified using a Nickel column following the Qiagen protocol.
  • the mixture was transferred to a small column and washed with 25-30 ml of washing buffer (8M Urea, 0.1M NaH 2 PO 4 , 0.01M Tris-Cl, 20 mM imidazole, pH8).
  • Column was eluted with four 500 ⁇ l fractions of elution buffer (8M Urea, 0.1M NaH 2 PO 4 , 0.01M Tris-Cl, 200 nN imidazole pH8).
  • This procedure resulted in relatively pure protein with minor contaminating bands.
  • This preparation was further separated on a 10%> acrylamide gel and a band migrating at 20 kDa, slightly larger than the predicted 17kDa, was excised and utilized for antibody production in rabbits (Covance Inc).
  • the N-terminus of CbpG was amplified from T4 chromosomal DNA by PCR using oligos B939f2 (5'-CGCGGATCCTATACAGATAAGAAACAAGTTTTAAGT) (SEQ ID NO:13) and B939r2 (5'-CGCGGTACCATGTTGTCTATAATGGTACCAACTACC) SEQ ID NO: 14).
  • the amplified fragment consisted of CbpG amino acids 1-90, deleting the C-terminal choline binding domain, and thus generating an N-terminal CbpG truncate.
  • the amino acid sequence (SEQ ID NO: 11) and nucleic acid sequence (SEQ ID NO: 12) of the N-terminal truncate of CbpG is depicted in FIGURE 8.
  • the oligos used introduced a BamHI site to the N-terminus of the gene and a Kpnl site to the C-te ⁇ ninus.
  • the PCR product was then digested with Bam HI and Kpnl.
  • the digested fragment was ligated into a Qiagen pQE-30 6-His tag expression vector and transformed into competent Ml 5 E. Coli cells.
  • Clones were screened by restriciton enzyme digestion with BamHI and Kpnl.
  • the clones positive for the CbpG truncted insert were sequenced to confirm an in-frame fusion between the His-tag and CbpG truncate coding region.
  • a 50ml culture of pQE939nt was grown in lxLB/Amp/Kan to an OD 600 of 0.7.
  • the culture was induced with 1.5mM IPTG and grown for an additional 2 hours.
  • the induced cells were harvested by centrifugation and lysed under native and denatured conditions in order to determine protein expression and solubility.
  • a 15% Tris-HCl gel showed that the 13.2kDa protein was soluble (FIGURE 9A).
  • the protein was purified under denatured conditions with 8M Urea using the His tag over a nickel column.
  • the resulting purified CbpG truncate protein was run on a 15% Tris-HCl gel Figure 9b, the bands excised, and utilized for antibody production in rabbits (Covance Inc.).
  • the polyclonal antibody raised against CbpG was used in experiments to test its ability to protect against challenge by S. pneumoniae in in vivo models of bacterial nose colonization and sepsis as described below in Materials and Methods.
  • the anti-CbpG antibody did not provide protection in a nose colonization test.
  • 6 of 9 animals injected with anti-CbpG antibody were dead versus 8 of 9 animals injected with pre-immune serum.
  • 7 of 12 animals injected with anti-CbpG antibody were dead versus 9 of 12 animals injected with pre-immune serum.
  • the polyclonal antibodies against CbpG recognize the recombinant protein but do not react well with the native CbpG protein.
  • FIGURE 7 presents a tabulation of the overall results of the experiments characterizing CbpG.
  • FIGURE 1 SEQ ID NOT
  • the pneumococcal database is publicly available at www.tigr.org/tdb/mdb/mdb.html and through the National Center for Biotechnology Information (at www.nih.ncbi.org).
  • the pneumococcal database is selected and searched by the following steps: (1) select "BLAST”; (2) under “Specialized Blast Pages", select “Unfinished Microbial Genomes”; (3) then click to choose individual genomes to search; and (4) under "Eubacteria” select "Streptococcus pneumoniae".
  • a search of this public database using the search engine BLAST available at www.nih.ncbi.org, with the filter and other parameters set at default, using SEQ ID NO: 1 will yield the polypeptides and nucleic acids now identified in the present invention.
  • the search identified eight contigs which contained nine encoded choline binding polypeptides, which are unique and distinct from the recognized pneumococcal choline binding proteins PspA, LytA and CbpA, and are designated CbpB, CbpC, CbpD, CbpE, CbpF, CbpD, CbpH, Cbpl and CbpJ.
  • the Cbp genes range in size from 390 bp to 2034 bp and encode proteins of approximately 20-80 KDa.
  • the proteins have between 2 and 10 choline binding repeats in their C- terminal region.
  • the amino acid and nucleic acid sequences of choline binding protein CbpD is found in FIGURE 10, corresponding to SEQ ID NO: 15 (amino acid) and SEQ ID NO: 16 (nucleic acid).
  • the CbpD open reading frame is 1347 nucleotides long and encodes a predicted protein of 449 amino acids.
  • the amino acid (SEQ ID NO: 15) and nucleic acid (SEQ ID NO: 16) sequence of the CbpD polypeptide is shown in FIGURE 10.
  • the CbpD gene encodes a peptide of 449 amino acids with a predicted size of approximately 50kDa.
  • the protein has two domains: (i) an N-terminal domain and (ii) a C-terminal domain which, like all other choline binding proteins, contains the 20 amino acid repeats required for choline binding.
  • CbpD has four such repeats. There were no other significant similarities to proteins in the current databases.
  • CbpD cbpD loss of function mutants were constructed by insertion duplication mutagenesis.
  • An internal fragment at the N-terminus of CbpD (amino acids 262-379) was amplified from Type 4 chromosomal DNA using primers 5' primer (ggaattcgatc TTTCTTCAACA GGTGGAACT) (SEQ ID NO: 17) and 3' primer (ggaattcgatcAGCTAGAACC GTCTTTCAG) (SEQ ID NO: 18).
  • the PCR product was digested with EcoRI and cloned into pJDC9 and transformed into DH5 ⁇ E.coli. Insert was verified by size and restriction analysis and the plasmid was then transformed into S. pneumoniae wild type 4, selecting for erythromycin resistance. Such colonies were isolated and the position of the insert in the CbpD gene was verified by PCR.
  • the CbpD defective mutant was then assesssed for it's ability to colonize the infant rat nasopharynx, to adhere to Detroit cells as well as to immobilized carbohydrates LNnT and sialylactose, transformation, lysis in response to detergent (DOC) and pencillin sensitivity. All of these properties have been shown to be important in pneumococcal physiology. There was no difference between the parent strain and the CbpD deficient mutant in efficiency of genetic transformation, lysis in stationary phase or lysis in response to penicillin.
  • the coding sequence of CbpD was amplified using primers to sequences immediately downstream of the AUG start codon, N-terminal Primer (5' cgaagatcttcgAAAA TTTTACCGTTTATAGCA 3' ) (SEQ ID NO: 19) and sequences overlapping the termination codon , C-terminal Primer (5' tcccccgggggaTGTCAAGGAAA CTGCTTACA 3' ) (SEQ ID NO:20) (Lower case letters indicate added linkers used for cloning).
  • the CbpD deficient mutant was also tested in an animal model for pneumoccal-induced sepsis. Most infant rats injected with the parental strain died within 16-24 hours and all were dead by 48 hours. Rats injected with the CbpD deficient strain exhibited less than 50% mortality in the first 16-24 hours, but survival at the 48 hour time point was not significantly different fromt the parental strain. The results of this experiment are depicted in TABLE 3. Thus, CbpD is directly implicated in pneumoccal virulence in sepsis.
  • Type 4 1/10 0/10 1/9 0/9 4/12 2/12 cbpD 10/10 2/10 5/9 3/9 9/12 4/12
  • Results are expressed as the number of surviving animals over the number of animals injected.
  • oligos 568F2 (5'- CGCGGATCCAAAATTTTACCGTTTATAGCAAGAGG-3') (SEQ IDNO:25) and 568KpnR3 (5'-GCGCGCGGTACCGTCGGTGTATTATC-3 ') (SEQ ID NO:26) for the first fragment, and oligos 568BamF3 (5'-
  • the first amplified fragment consisted of CbpD amino acids 2-116 while the second amplified fragment consisted of CbpD amino acids 103-280 deleting the C-terminal choline binding domain, and thus generating two N-terminal CbpD truncates.
  • the amino acid sequence (SEQ ID NO:21) and the nucleic acid sequence (SEQ ID NO:22) of fragment 1 (CbpD amino acids 2-116), and the amino acid sequence (SEQ ID NO: 23) and the nucleic acid sequence (SEQ ID NO: 24) of fragment 2 (CbpD amino acids 103-280) are depicted in FIGURE 14.
  • Both sets of oligos introduced a BamHI site to the N-terminus of the gene and a Kpnl site to the C-te ⁇ ninus. Both PCR products were then digested with BamHI and Kpnl. The digested fragments were ligated into a Qiagen pQE-30 6-His tag expression vector and transformed into competent Ml 5 E.coli cells.
  • Clones were screened by restriction enzyme digestion with BamHI and Kpnl. The clones positive for CbpD truncate insert 1 and for CbpD truncate insert 2 were sequenced to confirm an in-frame fusion between the His-tag and the CbpD truncated region. 50ml cultures of pQECbpDl and pQECbpD2 (containing fragments 1 and 2, respectively) were grown in IxLB/Amp/Kan to an OD600 of 0.7. The cultures were induced with 1.5mM IPTG and grown for an additional 2 hours. The induced cells were harvested by centrifugation and lysed under native and denatured conditions in order to determine protein expression and solubility.
  • S. pneumoniae type 4 is a clinical isolate obtained from Medlmmune Inc.
  • S. pneumoniae strain R6x (Tiraby et al (1973) Proc Natl Acad Sci USA 70:3541-3545) was obtained from the Rockefeller University collection.
  • S. pneumoniae type 4R is an unencapsulated mutant of Type 4 which was constructed by insertion duplication mutagenesis of capsule genes of Type4.
  • S. pneumoniae was plated on tryptic soy agar (TSA, Difco, Detroit, MI- USA) supplemented with sheep blood 3% (v/v).
  • bacteria For growth in liquid culture, the bacteria were grown without aeration at 37°C in 5% CO 2 in a semi-synthetic casein hydrolysate medium supplemented with yeast extract (C+Y medium, (Lacks, S and Hotchkiss, R.D. (1960) Biochem Biophys Acta 39:508-517).
  • C+Y medium yeast extract
  • bacteria were grown in the presence of 1 ⁇ g/ml erythromycin (Sigma, St. Louis, MO, USA).
  • DNA ligations, restriction endonuclease digestion and gel electrophoresis were performed according to standard protocols (Sambrook, J., Fritsh, E.F. and Maniatis, T. eds. (1989) Molecular Cloning: A Laboratory Manual (Second Edition) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). DNA purification and plasmid preparations were performed with kits from Qiagen and Wizard according to the manufacturer's instructions. Plasmids were introduced into E. coli strains by chemical transformation. Transformation in S. pneumoniae was performed according to standard protocols (Pearce et al (1993) MolMicrobiol 9: 1037-1050).
  • Bacterial adhesion assay The Detroit human nasopharyngeal cell line (American Type Culture Collection) was cultured in ATCC Vitacell Minimal Essential Eagle medium (ATCC Cat#30-2003) supplemented with Earles balanced salt solution, nonessential amino acids, lmM sodium pyruvate, 2mM L-glutamine and 1500 mg sodium bicarbonate. Cells were grown to confluence in Corning 100mm tissue culture dishes. At confluence, the cells were prepared for subculture with trypsin-0.05 % EDTA (Sigma), washed and resuspended in 5mls of the above media + 10%> FBS (Sigma).
  • lOul of the resuspended cells were added to Terasaki wells (Robbins Scientific, Sunnyvale, CA) and allowed to grow until a confluent monolayer formed. Prior to the adherence assay, culture fluid was removed by washing the monolayers twice with tissue culture medium.
  • the assay is modified such that monolayers are plated in 96 well dishes (Falcon) coated with 0.2% gelatin and at confluence are incubated with a range of concentrations of the mixture of CBPs (1 ⁇ g to 1 mg ml "1 ) for 15 min. After washing, the CBP-treated monolayers are challenged with 5 x 10 6 pneumococci for 30 min, washed and adherence is quantitated as fluorescence intensity measured in a Cytofluor II (Perseptive) with excitation at 485 nm and emission at 530 nm.
  • Cytofluor II Perseptive
  • Adherence to glyco conjugates was assessed by coating Terasaki plates overnight with 1 0 0 u M o f6 ' s i a l y l l a c t o s e - H S A , l a c t o - N - n e o t e t r a o s e - H S A , N-acetylglucosamine- ⁇ 1 ,4-glucose-HS A or N-acetylglucosamine- ⁇ 1 ,3-glucose-HSA (Neose Inc., Horsham, PA).
  • mice Passive protection against systemic challenge.
  • Outbred CF1 mice were housed under specific pathogen free conditions in accordance with institutional and NIH guidelines. Encapsulated pneumococci were grown for 5 hours in C+Y medium and diluted in PBS. Antibody (pre-immune serum for control or postimmune, 0.5ml diluted 1 : 10 in PBS) is incubated with the inoculum for 30 min at 37°C and then the entire mixture is injected. Two groups often mice received an inoculum of 3 x 10 7 cfu of Type 4 by injection into the peritoneal cavity. The number of animals alive or dead is scored over 4 days.
  • Nasopharyngeal challenge Nasopharyngeal colonization of 1 to 5-day old Sprague- Dawley rats by the parental strain serotype 4 and the Cbp deficient mutants was carrued out as described previously using Type4 (Weiser JN et al (1994) 62(6):2582- 2589).

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Abstract

The present invention provides isolated polypeptides comprising an amino acid sequence of a choline binding protein CbpG ou CbpD. This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding polypeptide CbpG or CbpD or N-terminal CbpG or CbpD truncate, including analogs, variants, mutants, derivatives and fragments thereof. This invention further provides an isolated immunogenic polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. This invention provides an isolated nucleic acid encoding a polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. This invention provides pharmaceutical compositions, vaccines, and disgnostic and therapeutic methods of use of the isolated polypeptides and nucleic acids. Assays for compounds which alter or inactivate the polypeptides of the present invention for use in therapy are also provided.

Description

IDENTIFICATION AND CHARACTERIZATION OF NOVEL
PNEUMOCOCCAL CHOLINE BINDING PROTEINS, CbpG AND CbpD,
AND DIAGNOSTIC AND THERAPEUTIC USES THEREOF
FIELD OF THE INVENTION
The present invention relates generally to choline binding polypeptides and to nucleic acids encoding such polypeptides. The invention also relates to vaccines which provide protection or elicit protective antibodies to bacterial infection, and to antibodies and antagonists against or inhibitors of such polypeptides for use in diagnosis, therapy and passive immune therapy. In particular, the choline binding polypeptides of the invention are useful as vaccines against Streptococcus, particularly pneumococcus. A choline binding polypeptide of the present invention is also useful as a competitive inhibitor of bacterial adhesion, or to discover small molecule antagonists of adhesion.
BACKGROUND OF THE INVENTION Streptococcus pneumoniae is a gram positive bacteria which is a major cause of invasive infections such as sepsis, meningitis, otitis media and lobar pneumonia (Tuomanen et al NE 322:1280-1284, 1995). Vaccination has long been an important armament in the arsenal against infectious microorganisms. Prior to the introduction of antibiotics, vaccination was the major hope for protecting populations against viral or bacterial infection. With the advent of antibiotics, vaccination against bacterial infections became less important. However, the emerging problems with antibiotic resistance among such infectious bacteria, including S. pneumoniae strains, have raised an urgent need for a better understanding of the pathogenesis of these pathogens and has reestablished the importance of anti-bacterial vaccines (Appelbaum, P.C. (1992) Clin Infect Dis 15:77-83).
There are over 90 different types of the pneumococcal organism, each with a different chemical structure of the capsular polysaccharide (i.e., each antigenically distinct). The capsular polysaccharide is a principal known virulence factor of the pneumococcus and induces an antibody response in adults. Current vaccines against S. pneumoniae employ mixtures of the capsules of the 23 most common serotypes of this bacterium. After several comprehensive studies there is now overwhelming evidence that this vaccine is approximately 60% efficacious for the general population (Shapiro et α/.(1991) NEJM 325: 1453-60). Importantly, these vaccines are ineffective in individuals most susceptible to pathological infection - the young, the old, and the immune compromised - because of their inability to elicit a T cell immune response. Conjugation of the capsule to a protein permits protection in the younger age group but is inherently limited in the number of capsules that can be conjugated at one time (approximately 5-8 capsules only).
Exported proteins in bacteria participate in many diverse and essential cell functions such as motility, signal transduction, macromolecular transport and assembly, and the acquisition of essential nutrients. For pathogenic bacteria such as S. pneumoniae, many exported proteins are virulence determinants that function as adhesins to colonize and thus infect the host, or as toxins to protect the bacteria against the host's immune system (for a review, see Hoepelman and Tuomanen (1992) Infect Immun 60:1729-33). One alternative to current vaccines are subunit vaccines in which the antigen, or antigens, include a bacterial surface protein or proteins. These vaccines could overcome the deficiencies of whole bacterial or capsule-based vaccines. Moreover, given the importance of exported or surface proteins to bacterial virulence, these proteins are an important target for therapeutic intervention.
Pneumococci bind avidly to cells of the upper and lower respiratory tract. Like most bacteria, adherence of pneumococci to human cells is achieved by presentation of bacterial surface proteins that bind to eukaryotic cell surface carbohydrates in a lectin-like fashion (Cundell, D. & Tuomanen, E. (\994)Microb Pathog 17:361-374). Pneumococci bind to non-inflamed epithelium, a process that can be viewed as asymptomatic carriage. It has been proposed that the conversion to invasive disease involves the local generation of inflammatory factors which, activating the human epithelial cell, change the number and type of receptors available on the human cells (Cundell, D. et al (1995) Nature, 377:435- 438). Presented with an opportunity in this new setting, pneumococci appear to take advantage and engage one of these unregulated receptors, the platelet activating factor (PAF) receptor (Cundell et al. (1995) Nature, 377:435-438). Within minutes of the appearance of the PAF receptor, pneumococci undergo waves of enhanced adherence and invasion. Inhibition of bacterial binding to activated cells, for instance by soluble receptor analogs, blocks the progression to disease in animal models (Idanpaan-Heikkila, I. et al. (1997) J. Infect. Dis., 176:704-712). Particularly effective in this regard are soluble carbohydrates containing lacto-N-neotetraose with or without an additional sialic acid, which prevent pneumococcal attachment to human cells in vitro and prevent colonization in the lung in vivo.
Pneumococci display a family of surface proteins which bind to the bacterial surface by non-covalent association to the cell wall teichoic acid or lipoteichoic acid, specifically through its terminal component phosphorylcholine. The surface of Streptococcus pneumoniae is decorated with twelve types of these choline binding proteins (Cbps). The Cbps are represented by a family of molecules which decorate the surface of pneumococcus, each serving a unique function but bound to the surface by a common element. These proteins consist of an N-terminal activity domain and a repeated C- terminal signature choline binding domain that contains two to greater than ten repeats of a 20 amino acid choline binding sequence that binds to phosphoryl choline and that anchors these molecules to the surface of the bacteria. This motif has been identified in the C-terminal regions of a secreted glycoprotein from Clostridium acetobutylicum NCIB 88052 [Sanchez-Beato, et al., J Bacteriol 177: 1098-1103 (1995)], toxins A and B from Clostridium difficile [Non Eichel-Streiber and Sauerborn, Gene 96: 107-13 (1990); Non Eichel-Streiber et al., J Bacteriol. 174:6707-6710 (1992)], a glucan-binding protein from Streptococcus mutans, several glycosyltransferases from Streptococcus downei and S. mutans, the murein hydrolase (LytA) from pneumococcus and pneumococcal lytic phage [Ronda et al., Eur. J. Biochem. 164:621-4 (1987); Diaz et al., J. Bacteriol 174:5516-25 (1992); Romero et al., Microb. Lett. 108:87-92 (1993); Yother and White, J. Bacteriol. 176:2976-85 (1994)], and a surface antigen (PspA) also from pneumococcus. The known pneumococcal Cbp family members are CbpA, LytA and PspA.
The choline binding domain was recognized and fully characterized by Lopez et al. in his studies of the autolytic enzyme, LytA (Ronda et al. (1987) Eur. J. Biochem, 164:621- 624). From studies of the sequences of the recognized choline binding proteins, consensus sequences have been reported, most particularly that of Garcia et al: GWLKDNGSWYYLNANGAMAT (SEQ ID NO:9) (Garcia, P. et al (1990) Gene 86:81- 88; Wren B. et al (1991) MolMicrobiol 5:797-803); Sanchez-Beato, A.R. et al (1995) J Bacteriol 177: 1098-1103).
Teichoic acid (TA), an integral part of the cell wall of Streptococcus pneumo iae, contains many terminal phosphorylcholine moieties. Choline affinity chromatography or Mono-Q Sepharose, a close relative of choline, were used to purify the CBPs. Previous studies have shown that PspA, as well as one other surface exposed protein, LytA, the autolytic amidase, bind in a choline-dependent manner. PspA, a protein having a molecular weight of 84 kDa, and which is highly variable, is released from the cell surface with high choline concentration (at least about 2% to about 10%). The function of PspA is unknown. LytA, or autolysin, is a 36 kDa protein, which lyses the pneumococcal cell wall (self lysis), but is not released from the cell by growth in high concentrations of choline, by washing in 10% choline, or by growth in ethanolamine. Reports on choline binding proteins include those by Sanchez-Puelles et al Gene 89:69-75 (1990), Briese and HakenbackEwr. J. Biochem. 146:417-427, Yother and White J. of Bacteriol. 176:2976- 2985, Sanchez-Beato et alJ. of Bacteriol. 177:1098-1103, and WrenMicro. Review Mol Microbiol. 5:797-803 (1991), which are hereby incorporated by reference in their entirety.
CbpA is an adhesin (ligand) for the glycoconjugate containing receptors present on the surface of eucaryotic cells. CbpA is a 663 amino acid protein with an apparent molecular mass of 112KDa. CbpA has been shown to be critical to pneumococcal colonization and attachment to human cells. Mutants with defects in cbpA show reduced virulence in the infant rat model for nasopharyngeal colonization and fail to bind to eucaryotic cells found at the site of infection and to glycoconjugates that bind pneumococcus. The CbpA protein cross reacts with human convalescent antisera, and antisera to the Cbps passively protected mice in a model for sepsis. Since the process of colonization and the progression to disease depend on pneumococcal attachment to human cells as a primary step, interruption of the function of surface choline binding proteins or the choline binding domain, for instance by cross reactive antibody or by inhibition with a competitive peptide mimicking this domain, may be relevant to blocking disease.
Choline-binding proteins for anti-pneumococcal vaccines are disclosed in International Patent Application WO 97/41151 of Masure, et al, which claims priority to U.S. patent application Serial Number 08/642,250, which are hereby incorporated by reference in their entirety. The International patent Application WO 97/41151 discloses partial polypeptide sequences of certain putative choline binding proteins and the polypeptide sequence of CbpA.
The cell wall associated choline binding protein, LytA, a murein amidase, is an autolysin that is responsible for remodeling the cell wall, the separation of daughter cells, cell death in stationary phase and penicillin induced cell lysis. Expansion of the cell wall during bacterial growth and splitting of the septum for cell separation require enzymes that cleave the peptidoglycan network enclosing the cell. In addition to acting as spacemaker enzymes for cell wall growth, some of these enzymes act as autolysins, thereby representing potentially suicidal enzymes. Regulation of these enzymes is therefore important and must take into consideration their extracytoplasmic location. Unlike other bacteria which have multiple autolysins, S. pneumoniae has only one major autolysin, LytA. Antibiotics such as penicillin induce bacteriolysis by interfering with the control of the endogenous autolysins (Tomasz & Holtje, 1977, in Microbiology, D. Schlessinger, ed., pp. 202-215; Tomasz, 1983, in The Target of Penicillin, R. Hackenback et al eds., pp. 155-172). Although the binding of antibiotics to cell wall synthetic enzymes has been well characterized, the mechanism by which it induces autolysin mediated cell wall degradation is unknown. Tolerance to such antibiotics arises if the bacterial autolysins are not triggered as the antibiotic inhibits the cell wall synthetic machinery. The question of whether antibodies raised against LytA are protective against infection by S. pneumoniae and its requirement for virulence remains controversial. In some cases, loss of LytA by deletion leads to less virulence, while others report no effect (Berry, A.M. et al (1992) Microb Pathog 12:87-93). PspA has been reported to be a candidate for a S. pneumoniae vaccine as it has been found in all pneumococci to date [see Yother et al., J. Bacteriol, 174:610 (1992)]; the purified protein can be used to elicit protective immunity in mice; and antibodies against the protein confer passive immunity in mice [Talkington et al., Microb. Pathog. 13:343- 355 (1992)]. However, PspA demonstrates antigenic variability between strains in the N- terminal half of the protein, which contains the immunogenic and protection eliciting epitopes (Yother et al., supra). This protein does not represent a common antigen for all strains of S. pneumoniae, and therefore is not an optimal vaccine candidate.
As described above, each Cbp, while being bound to the surface by a common element, the choline binding domain, serves a unique function. This particular function is largely determined by the unique N-terminal activity domain of each Cbp. N-terminal domain fragments of Cpbs, particularly CbpA, have been shown to have activity in blocking adherence and are candidates for immunogenic vaccines, independent of the C-terminal choline binding domain. In particular, Tuomanen et al, U.S. Serial Number 09/056,019, which is hereby incorporated herein by reference in its entirety, provides isolated polypeptides comprising N-terminal choline binding protein A truncates, particularly wherein the polypeptides do not bind to choline. Vaccines comprising such N-terminal truncates, DNA encoding such truncates, or antibodies directed against such truncates are also described in USSN 09/056,019.
An additional surface exported protein that affects adherence and represents a virulence determinant for pneumococcus, ZmpB, has been identified and described by R. Novak and R. Masure in U.S. Serial No. 09/096,336 filed June 11, 1998 which is hereby incorporated by reference in its entirety. ZmpB is a zinc metalloprotease, dependent on Zn2+for functional activity. zmpB mutants show loss of adherence and colonization and are defective in the autolytic pathway. A mutation in zmpB selectively alters the production of CbpA and generates covalently modified LytA. ZmpB is proposed to be a master regulatory protein that controls the expression of multiple Cbps critical for bacterial survival in the human host. ZmpB is a candidate for an S. pneumoniae vaccine or as one component of a multi-component vaccine. The deficiencies of whole bacterial or capsule-based vaccines and the emerging problems with antibiotic resistance among infectious bacteria, including S. pneumoniae strains, have raised an urgent need for alternative effective vaccines and therapies. The invention herein fills such a need in providing protective vaccines and therapies.
The citation of references herein shall not be construed as an admission that such is prior art to the present invention.
SUMMARY OF THE INVENTION
In its broadest aspect, the present invention encompasses isolated polypeptides comprising an amino acid sequence of a choline binding protein, CbpG or CbpD.
The present invention is directed to an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein, CbpG or CbpD and wherein such polypeptide contains a choline binding domain sequence which is homologous to SEQ ID NO: 1.
The present invention provides an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein, CbpG or CbpD wherein such polypeptide contains a choline binding domain sequence which is homologous to GWLKDNGSWYYLNANGAMAT (SEQ ID NO: 9).
The present invention further provides an isolated polypeptide comprising an amino acid sequence of an N-terminal CbpG or CbpD choline binding protein truncate. The present invention provides an N-terminal CbpG or CbpD truncate comprising the amino acid sequence as set forth in SEQ ID NO: 11, SEQ ID NO: 21, or SEQ ID NO: 23. The invention particularly provides an N-terminal CbpG truncate consisting of amino acids 1- 90 of the CbpG choline binding protein. In a further embodiment, the N-terminal CbpG truncate comprises less than amino acids 1-90 of the CbpG choline binding protein. The invention provides an N-terminal CbpD truncate consisting of amino acids 2-280 of the CbpD choline binding protein. In a further embodiment, the N-terminal CbpD truncates comprise amino acids 2-116 or 103-280 of the CbpD choline binding protein.
In a still further aspect, the present invention extends to vaccines based on the choline binding proteins described herein.
The present invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. The polypeptide comprises the amino acid sequence as set forth in SEQ ID NO: 2 or SEQ ID NO: 15 including fragments, mutants, variants, analogs, or derivatives, thereof. The isolated polypeptide is suitable for use in immunizing animals and humans against bacterial infection, preferably pneumococci.
The present invention further provides an isolated polypeptide comprising an amino acid sequence of a N-terminal CbpG or CbpD choline binding protein truncate, particularly wherein the polypeptide does not bind to choline. This invention provides an isolated immunogenic polypeptide comprising an amino acid sequence comprising an N-terminal truncate of a choline binding protein CbpG or CbpD. In a particular embodiment, this invention provides an isolated immunogenic N-terminal CbpG or CbpD truncate polypeptide comprising the amino acid sequence as set forth in SEQ ID NO: 11, SEQ ID NO: 21 or SEQ ID NO: 23. The present invention further particularly provides an immunogenic N-terminal CbpG truncate polypeptide consisting of amino acids 1-90 of CbpG, or of less than amino acid 1-90 of CbpG. The invention provides an N-terminal CbpD truncate consisting of amino acids 2-280 of the CbpD choline binding protein. In a further embodiment, the N-terminal CbpD truncates comprise amino acids 2- 116 or 103- 280 of the CbpD choline binding protein.
In a still further aspect, the present invention extends to an immunogenic choline binding protein polypeptide CbpG or CbpD or a fragment thereof. The present invention also extends to immunogenic choline binding protein polypeptides wherein such polypeptides comprise a combination of at least two choline binding polypeptides selected from the group consisting of CbpG or CbpD and at least one other choline binding polypeptide, including fragments thereof and N-terminal truncates thereof.
The present invention also relates to isolated nucleic acids, such as recombinant DNA molecules or cloned genes, or degenerate variants thereof, mutants, analogs, or fragments thereof, which encode the isolated polypeptide or which competitively inhibit the activity of the polypeptide. The present invention further relates to isolated nucleic acids, such as recombinant DNA molecules or cloned genes, or degenerate variants thereof, mutants, analogs, or fragments thereof, which encode the choline binding protein CbpG or CbpD. Preferably, the isolated nucleic acid, which includes degenerates, variants, mutants, analogs, or fragments thereof, has a sequence as set forth in SEQ ID NO: 3 or SEQ ID NO: 16. In a further embodiment of the invention, the full DNA sequence of the recombinant DNA molecule or cloned gene so determined may be operatively linked to an expression control sequence which may be introduced into an appropriate host. The invention accordingly extends to unicellular hosts transformed with the cloned gene or recombinant DNA molecule comprising a DNA sequence encoding the present invention, and more particularly, the DNA sequences or fragments thereof determined from the sequences set forth above.
In a particular embodiment, the nucleic acid has the sequence selected from the group comprising SEQ ID NO:3 or SEQ ID NO: 16; a sequence complementary to SEQ ID NO:3 or SEQ ID NO: 16; or a homologous sequence which is substantially similar to SEQ ID NO:3 or SEQ ID NO: 16. In a further embodiment, the nucleic acid has the sequence consisting of SEQ ID NO:3 or SEQ ID NO: 16.
The present invention further relates to isolated nucleic acids encoding an N-terminal choline binding protein truncate, particularly wherein the encoded polypeptide does not bind to choline. This invention particularly provides isolated nucleic acids encoding N- terminal choline binding protein truncates of choline binding protein CbpG or CbpD. The invention further provides a nucleic acid encoding an N-terminal CbpG or CbpD truncate comprising SEQ ID NO: 12 , SEQ ID NO:22 or SEQ ID NO:24, a sequence complimentary to SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO:24, or a homologous sequence which is substantially similar to SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO: 24. In a further embodiment, the nucleic acid encoding the N-terminal CbpG or CbpD truncate has the sequence consisting of SEQ ID NO: 12, SEQ ID NO: 22 or SEQ ID NO:24. In a particular embodiment, the nucleic acid encoding an N-terminal CbpG truncate is capable of encoding amino acids 1-90 of CbpG. In a still further embodiment, the nucleic acid encoding an N-terminal CbpG truncate encodes a truncate smaller than amino acids 1-90 of CbpG. In a particular embodiment, the nucleic acid encoding an N- terminal CbpD truncate is capable of encoding amino acids 2-280 of CbpD. In a still further embodiment, the nucleic acid encoding an N-terminal CbpD truncate encodes a truncate of amino acids 2-116 or 103-280 of CbpD.
Nucleic acid vaccines or DNA vaccines utilize nucleic acids encoding particular immunogenic polypeptides to induce immunity in a host against such encoded immunogenic vaccines. Such nucleic acid based vaccines can be used directly as naked DNA, or can utilize well recognized expression vectors or retroviral vectors, as more particularly described herein, to encode such immunogenic polypeptide on expression in the host cell. Methods to generate and utilize such any such nucleic acid vaccines or DNA vaccines are well known in the art.
The present invention relates to nucleic acid vaccines or DNA vaccines comprising nucleic acids encoding immunogenic polypeptides of a choline binding protein CbpG or CbpD. The present invention relates to nucleic acid vaccines or DNA vaccines comprising nucleic acids encoding immunogenic polypeptides of choline binding protein CbpG or CbpD or a fragment thereof or any combination of CbpG or CbpD with at least one other choline binding polypeptide. Still further, this invention provides nucleic acid vaccines or DNA vaccines comprising nucleic acids encoding an immunogenic N-terminal polypeptide of choline binding protein CbpG or CbpD.
Antibodies against the isolated polypeptide include naturally raised and recombinantly prepared antibodies. These may include both polyclonal and monoclonal antibodies prepared by known genetic techniques, as well as bi-specific (chimeric) antibodies, and antibodies including other functionalities suiting them for diagnostic use. Such antibodies can be used in immunoassays to diagnose infection with a particular strain or species of bacteria. The antibodies can also be used for passive immunization to treat an infection with Gram positive bacteria, particularly pneumococcus. These antibodies may also be suitable for modulating bacterial adherence including but not limited to acting as competitive agents.
It is still a further object of the present invention to provide a method for the treatment of mammals to control the amount or activity of the pneumococci bacteria or its subunits, so as to treat or avert the adverse consequences of invasive, spontaneous, or idiopathic pathological states. This invention provides pharmaceutical compositions for use in therapeutic methods which comprise or are based upon the isolated polypeptides, their subunits or their binding partners.
The invention further provides pharmaceutical compositions, vaccines, and diagnostic and therapeutic methods of use thereof.
The invention provides pharmaceutical compositions comprising a choline binding polypeptide CbpG or CbpD and a pharmaceutically acceptable carrier. The present invention further provides pharmaceutical compositions comprising a choline binding polypeptide of a choline binding protein CbpG or CbpD, or a fragment thereof or any combination of CbpG or CbpD with at least one other choline binding polypeptide, and a pharmaceutically acceptable carrier. Still further, this invention provides pharmaceutical compositions comprising N-terminal polypeptide of choline binding protein CbpG or CbpD and a pharmaceutically acceptable carrier.
The invention further relates to a vaccine for protection of an animal subject from infection with a Gram positive bacterium comprising a vector containing a gene encoding a choline binding protein CbpG or CbpD of a Gram positive bacterium operatively associated with a promoter capable of directing expression of the gene in the subject. Preferably, such vaccine contains a gene encoding a choline binding protein CbpG or CbpD of pneumococcus.
In another aspect, the invention is directed to a vaccine for protection of an animal subject from infection with a Gram positive bacterium, most preferably pneumococcus, comprising an immunogenic amount of a choline binding protein CbpG or CbpD, or a derivative or fragment thereof. Such a vaccine may contain the protein conjugated covalently to a bacterial capsule or capsules from one or more strains of bacteria, including pneumococcus. In one such embodiment, at least one of the bacterial capsules is derived from a mutant strain of bacteria which is non-adherent and non-virulent. In a further such embodiment, the non-adherent and non-virulent bacteria is a pneumococcus and is a CbpG or CbpD mutant bacteria. Such non-adherent and non-virulent CbpG or CbpD mutant bacteria can further be utilized in expressing other immunogenic or therapeutic proteins for the purposes of eliciting immune responses to any such other proteins in the context of vaccines and in other forms of therapy.
The invention further provides a CbpG or CbpD mutant bacteria which is non-adherent to nasopharyngeal cells or to lung cells. Particularly, such CbpG or CbpD mutant is a gram positive bacteria. More particularly, such CbpG or CbpD mutant is Streptococcus. Most particularly, such CbpG or CbpD mutant is Streptococcus pneumoniae.
The invention includes an assay system for screening of potential compounds effective to modulate the choline binding activity of the choline binding protein of the present invention. The invention more particularly includes an assay system for screening of potential compounds effective to modulate the choline binding activity of the choline binding protein CbpG or CbpD. In one instance, the test compound, or an extract containing the compound, could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein by comparison with a control. In a further instance the test compound, or an extract containing the compound, could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD, to determine the compound's effect upon the activity of the protein, and thereby on adherence of said cellular sample to host cells, by comparison with a control.
The invention includes an assay system for screening of potential compounds effective to modulate the activity of the N-terminal domain of the choline binding protein of the present invention. The invention more particularly includes an assay system for screening of potential compounds effective to modulate the activity of the N-terminal domain of CbpG or CbpD. In one instance, the test compound, or an extract containing the compound, could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein by comparison with a control. In a further instance the test compound, or an extract containing the compound, could be administered to a cellular sample expressing the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein, and thereby on adherence of said cellular sample to host cells, by comparison with a control. In another instance, the test compound, or an extract containing the compound, could be administered to a cellular sample expressing an N- terminal truncate (which lacks the C-terminal choline binding domain) of the choline binding protein CbpG or CbpD to determine the compound's effect upon the activity of the protein by comparison with a control. In a particular such instance, the cellular sample expresses an N-terminal CbpG truncate comprising amino acids 1-90 of CbpG or 2-280 of CbpD or a smaller N-terminal truncate comprising less than amino acids 1-90 of CbpG or 2-280 of CbpD. In a particular instance, the cellular sample expresses an N- terminal CbpD truncate comprising amino acids 2-116 or 103-280 of CbpD choline binding protein. In a further such instance, the N-terminal CbpG or CbpD truncate comprises the amino acid sequence set out in SEQ ID NO: 11, SEQ ID NO:21 or SEQ ID NO:23.
Other objects and advantages will become apparent to those skilled in the art from a review of the following description which proceeds with reference to the following illustrative drawings. BRIEF DESCRIPTION OF THE DRAWINGS
FIGURE 1 depicts the nucleic acid and amino acid sequence of the C-terminal 180 amino acids of CbpA. (amino acids 615-695).
FIGURE 2A-C depicts the nucleotide sequence and amino acid sequence for both CbpF and CbpG.
FIGURE 3 depicts the nucleotide sequence for CbpG including upstream promoter region.
FIGURE 4 depicts a Western Blot of a 10% SDS-PAGE on which choline binding proteins were separated and reacted with polyclonal antibody directed against CbpG. Lane 1 is a ladder of recombinant choline binding proteins. Lane 2 is a Cbp preparation from S. pneumoniae Type 4. Lane 3 is a choline soak of S. pneumoniae Type 4. Lane 4 is recombinant CbpG.
FIGURE 5 depicts the effect of the CbpG knockout, generated by insertion duplication mutagenesis, on colonization of infant rat nasopharynx at 48 hours by the method of Weiser, et al (Weiser JN et al (1994) 62(6):2582-2589). WT depicts the colonization of wild type Type 4. Each bar presents the mean of four experiments on 10 rat pups per group.
FIGURE 6 is a graph of the CbpG knockout in a Type4R (T4R) genetic background (T4R is mutant Type4 pneumococcal strain which is unencapsulated) on the adhesion characteristics of Type 4R mutants on Detroit Nasopharyngeal Human Cell Line. T4R and the CbpG knockout are indicated (T4R and then CbpG-"). Each bar represents an individual experiment shown as the mean of four wells.
FIGURE 7 presents a tabulation of characterization studies of CbpG. The tabulation indicates the following: size of recombinantly prepared protein in kD; availability of N- terminal truncates (wherein the C-terminal choline binding domain is removed) (yes indicates available, blank indicates not available); recognition of recombinant protein by polyclonal anti-CbpG antibody on a Western Blot of a 4-15% gradient SDS-PAGE (** indicates recognition, - indicates no recognition); recognition of the corresponding CbpG protein on a Western Blot of a native choline binding protein preparation run on a 4- 15% gradient SDS-PAGE (** indicates recognition, - indicates no recognition); effects of a knockout of CbpG in rat nose colonization studies (N indicates no significant effect, Down indicates a significant reduction in colonization); In vitro adhesion to LNnT shows the effects of a knockout of CbpG on in vitro adhesion to LNnT (Lacto N-neotetraose- HSA) (reduced indicates significantly reduced from wild type); TRSF w CSP depicts the effect of the knockout of CbpG on transformation of S. pneumoniae in the presence of competence stimulating protein (Normal indicates no effect; nd indicates not done); LYSIS w DOC provides the effect of the knockout of CbpG on the ability of Deoxycholate to lyse the particular knockout strains (Normal indicates no effect).
FIGURE 8 depicts the nucleic acid sequence and amino acid sequence for the N-terminal CbpG truncate.
FIGURE 9A depicts the expression of recombinant CbpG truncate and migration in SDS gel electrophoresis as detected by Coomassie blue staining. Lanes represent "not induced" and the "induced" soluble or insoluble fraction after induction of expression.
FIGURE 9B depicts migration of purified recombinant CbpG truncate on SDS gel electrophoresis as detected by Coomassie blue staining. The CbpG truncate size is 13 kD as compared to MW Standards and is found in abundance in the soluble fraction of the cell preparation.
FIGURE 10 depicts the nucleotide sequence and predicted amino acid sequence of
CbpD.
FIGURE 11 depicts the effect of the CbpD knockout, generated by insertion duplication mutagenesis, on colonization of infant rat nasopharynx at 48 hours by the method of
Weiser, et al (Weiser JN et al (1994) 62(6):2582-2589). WT depicts the colonization of wild type Type 4. Each bar presents the mean of four experiments on 10 rat pups per group.
FIGURE 12 is a graph of the CbpD knockout in a Type4R (T4R) genetic background (T4R is mutant Type4 pneumococcal strain which is unencapsulated) on the adhesion characteristics of Type 4R mutants to Detroit cells. Terasaki plates were coated with a monolayer of cells and fluorescein-labelled bacteria were placed in wells for 30 min, the wells were washed and adherent bacteria were counted. Values are expressed as a percentage of the T4R parent (100%). T4R and the CbpD knockout are indicated (T4R and then CbpD"). Each bar represents an individual experiment shown as the mean of four wells.
FIGURE 13 presents a tabulation of characterization studies of CbpD. The tabulation indicates the following: availability of N-terminal truncates (wherein the C-terminal choline binding domain is removed) (yes indicates available, blank indicates not available); effects of a knockout of CbpD in rat nose colonization studies (N indicates no significant effect, Down indicates a significant reduction in colonization); In vitro adhesion to LNnT shows the effects of a knockout of CbpD on in vitro adhesion to LNnT (Lacto N- neotetraose-HSA) (reduced indicates significantly reduced from wild type); TRSF w CSP depicts the effect of the knockout of CbpD on transformation of S. pneumoniae in the presence of competence stimulating protein (Normal indicates no effect; nd indicates not done); LYSIS w DOC provides the effect of the knockout of CbpD on the ability of Deoxycholate to lyse the particular knockout strains (Normal indicates no effect).
FIGURE 14 depicts the amino acid sequence and nucleic acid sequences for the N- terminal CbpD truncates 2-116 (SEQ ID NO:21 and SEQ ID NO:22) and 103-280 (SEQ ID NO:23 and SEQ ID NO:24). DETAILED DESCRIPTION
The present invention is directed to an isolated polypeptide comprising an amino acid sacid sequence of a choline binding protein CbpG or CbpD. The present invention further provides an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein CbpG or CbpD wherein such polypeptide contains a choline binding domain sequence which is homologous to SEQ ID NO: 1. The present invention further provides an isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein CbpG or CbpD, wherein such polypeptide contains a choline binding domain sequence which is homologous to
GWLKDNGSWYYLNANGAMAT (SEQ ID NO:9).
The present invention is directed to an isolated polypeptide comprising an amino acid sequence of a choline binding polypeptide CbpG or CbpD. The polypeptides of the present invention are suitable for use in immunizing animals against pneumococcal infection. These polypeptide or peptide fragments thereof, when formulated with an appropriate adjuvant, are used in vaccines for protection against pneumococci, and against other bacteria with cross-reactive proteins.
This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. In a particular embodiment the polypeptide has the amino acid sequence as set forth in SEQ ID NO: 2 or SEQ ED NO: 15 including fragments, mutants, variants, analogs, or derivatives, thereof.
This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD as set forth in Figure 2 and Figure 10. In one embodiment the polypeptide is an analog, fragment, mutant, derivative or variant thereof.
This invention further provides an isolated polypeptide comprising an amino acid sequence of a N-terminal choline binding protein truncate, particularly wherein the polypeptide does not bind to choline. This invention particularly provides an isolated immunogenic polypeptide comprising an amino acid sequence of a N-terminal choline binding protein CbpG or CbpD truncate. In a particular embodiment, this invention provides an N-terminal CbpG or CbpD truncate comprising amino acids 1-90 of CbpG or amino acids 2-280 of CbpD or an immunogenic fragment thereof. In a further embodiment, the N-terminal CbpG or CbpD truncate may comprise less than amino acids 1-90 and the CbpD truncate may comprise less than amino acids 2-280. The invention particularly provides an N-terminal CbpG or CbpD truncate comprising the amino acids set out in SEQ ID NO: 11, SEQ ID NO:21 or SEQ ID NO:23.
The identity or location of one or more amino acid residues may be changed or modified to include variants such as, for example, deletions containing less than all of the residues specified for the protein, substitutions wherein one or more residues specified are replaced by other residues and additions wherein one or more amino acid residues are added to a terminal or medial portion of the polypeptide. These molecules include: the incorporation of codons "preferred" for expression by selected non-mammalian hosts; the provision of sites for cleavage by restriction endonuclease enzymes; and the provision of additional initial, terminal or intermediate DNA sequences that facilitate construction of readily expressed vectors.
Further, this invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD, wherein the polypeptide has the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO: 15.
This invention is directed to a polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD, wherein the amino acid sequence is set forth in Figure 2 and Figure 10 and in SEQ ID NO:2 and SEQ ID NO:15.
This invention provides an isolated polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD, wherein the polypeptide has choline binding activity. In one embodiment the polypeptide has the amino acid sequence as set forth in SEQ ID NO:2 or SEQ ID NO: 15 including fragments, mutants, variants, analogs, or derivatives, thereof.
As defined herein, "adhesion" means noncovalent binding of a bacteria to a human cell or secretion that is stable enough to withstand washing.
The term "choline binding protein (CBP)" and any variants not specifically listed, may be used herein interchangeably, and as used throughout the present application and claims refer to proteinaceous material including single or multiple proteins, and extends to those proteins having the amino acid sequence data described herein and identified by SEQ ID NO:2 and SEQ ID NO: 15, and the profile of activities set forth herein and in the Claims. Accordingly, proteins displaying substantially equivalent or altered activity are likewise contemplated. These modifications may be deliberate, for example, such as modifications obtained through site-directed mutagenesis, or may be accidental, such as those obtained through mutations in hosts that are producers of the complex or its named subunits. Also, the term "choline binding protein (CBP)" is intended to include within its scope proteins specifically recited herein as well as all substantially homologous analogs and allelic variations.
This invention provides an isolated immunogenic polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. It is contemplated by this invention that the immunogenic polypeptide has the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO: 15, including fragments, mutants, variants, analogs, or derivatives, thereof.
This invention is directed to analogs of the polypeptide which comprise the amino acid sequence as set forth above. The analog polypeptide may have an N-terminal methionine or a polyhistidine optionally attached to the N or COOH terminus of the polypeptide which comprise the amino acid sequence. In another embodiment, this invention contemplates peptide fragments of the polypeptide which result from proteolytic digestion products of the polypeptide. In another embodiment, the derivative of the polypeptide has one or more chemical moieties attached thereto. In another embodiment the chemical moiety is a water soluble polymer. In another embodiment the chemical moiety is polyethylene glycol In another embodiment the chemical moiety is mon-, di-, tri- or tetrapegylated. In another embodiment the chemical moiety is N-terminal monopegylated.
Attachment of polyethylene glycol (PEG) to compounds is particularly useful because PEG has very low toxicity in mammals (Carpenter et al, 1971). For example, a PEG adduct of adenosine deaminase was approved in the United States for use in humans for the treatment of severe combined immunodeficiency syndrome. A second advantage afforded by the conjugation of PEG is that of effectively reducing the immunogenicty and antigenicity of heterologous compounds. For example, a PEG adduct of a human protein might be useful for the treatment of disease in other mammalian species without the risk of triggering a severe immune response. The compound of the present invention may be delivered in a microencapsulation device so as to reduce or prevent an host immune response against the compound or against cells which may produce the compound. The compound of the present invention may also be delivered microencapsulated in a membrane, such as a liposome.
Numerous activated forms of PEG suitable for direct reaction with proteins have been described. Useful PEG reagents for reaction with protein amino groups include active esters of carboxylic acid or carbonate derivatives, particularly those in which the leaving groups are N-hydroxysuccinimide, p-nitrophenol, imidazole or l-hydroxy-2- nitrobenzene-4-sulfonate. PEG derivatives containing maleimido or haloacetyl groups are useful reagents for the modification of protein free sulfhydryl groups. Likewise, PEG reagents containing amino hydrazine or hydrazide groups are useful for reaction with aldehydes generated by periodate oxidation of carbohydrate groups in proteins. In one embodiment, the amino acid residues of the polypeptide described herein are preferred to be in the "L" isomeric form. In another embodiment, the residues in the "D" isomeric form can be substituted for any L-amino acid residue, as long as the desired functional property of lectin activity is retained by the polypeptide. NH2 refers to the free amino group present at the amino terminus of a polypeptide. COOH refers to the free carboxy group present at the carboxy terminus of a polypeptide. Abbreviations used herein are in keeping with standard polypeptide nomenclature, J. Biol. Chem. , 243:3552- 59 (1969).
It should be noted that all amino-acid residue sequences are represented herein by formulae whose left and right orientation is in the conventional direction of amino- terminus to carboxy-terminus. Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino-acid residues.
Synthetic polypeptide, prepared using the well known techniques of solid phase, liquid phase, or peptide condensation techniques, or any combination thereof, can include natural and unnatural amino acids. Amino acids used for peptide synthesis may be standard Boc (Nα-amino protected Nα-t-butyloxycarbonyl) amino acid resin with the standard deprotecting, neutralization, coupling and wash protocols of the original solid phase procedure of Merrifield (1963, J Am. Chem. Soc. 85:2149-2154), or the base-labile Nα-amino protected 9-fluorenylmethoxycarbonyl (Fmoc) amino acids first described by Carpino and Han (1972, J. Org. Chem. 37:3403-3409). Thus, polypeptide of the invention may comprise D-amino acids, a combination of D- and L-amino acids, and various "designer" amino acids (e.g., β-methyl amino acids, Cα-methyl amino acids, and Nα-methyl amino acids, etc.) to convey special properties. Synthetic amino acids include ornithine for lysine, fluorophenylalanine for phenylalanine, and norleucine for leucine or isoleucine. Additionally, by assigning specific amino acids at specific coupling steps, α- helices, β turns, β sheets, γ-turns, and cyclic peptides can be generated. In one aspect of the invention, the peptides may comprise a special amino acid at the C- terminus which incorporates either a CO2H or CONH2 side chain to simulate a free glycine or a glycine-amide group. Another way to consider this special residue would be as a D or L amino acid analog with a side chain consisting of the linker or bond to the bead. In one embodiment, the pseudo-free C-terminal residue may be of the D or the L optical configuration; in another embodiment, a racemic mixture of D and L-isomers may be used.
In an additional embodiment, pyroglutamate may be included as the N-terminal residue of the peptide. Although pyroglutamate is not amenable to sequence by Edman degradation, by limiting substitution to only 50% of the peptides on a given bead with N- terminal pyroglutamate, there will remain enough non-pyroglutamate peptide on the bead for sequencing. One of ordinary skill would readily recognize that this technique could be used for sequencing of any peptide that incorporates a residue resistant to Edman degradation at the N-terminus. Other methods to characterize individual peptides that demonstrate desired activity are described in detail infra. Specific activity of a peptide that comprises a blocked N-terminal group, e.g. , pyroglutamate, when the particular N- terminal group is present in 50% of the peptides, would readily be demonstrated by comparing activity of a completely (100%) blocked peptide with a non-blocked (0%) peptide.
In addition, the present invention envisions preparing peptides that have more well defined structural properties, and the use of peptidomimetics, and peptidomimetic bonds, such as ester bonds, to prepare peptides with novel properties. In another embodiment, a peptide may be generated that incorporates a reduced peptide bond, i.e., Rι-CH2-NH-R2, where Rj and R2 are amino acid residues or sequences. A reduced peptide bond may be introduced as a dipeptide subunit. Such a molecule would be resistant to peptide bond hydrolysis, e.g. , protease activity. Such peptides would provide ligands with unique function and activity, such as extended half-lives in vivo due to resistance to metabolic breakdown, or protease activity. Furthermore, it is well known that in certain systems constrained peptides show enhanced functional activity (Hruby, 1982, Life Sciences 31:189-199; Hruby et al., 1990, Biochem J. 268:249-262); the present invention provides a method to produce a constrained peptide that incorporates random sequences at all other positions.
A constrained, cyclic or rigidized peptide may be prepared synthetically, provided that in at least two positions in the sequence of the peptide an amino acid or amino acid analog is inserted that provides a chemical functional group capable of cross-linking to constrain, cyclise or rigidize the peptide after treatment to form the cross-link. Cyclization will be favored when a turn-inducing amino acid is incorporated. Examples of amino acids capable of cross-linking a peptide are cysteine to form disulfide, aspartic acid to form a lactone or a lactase, and a chelator such as γ-carboxyl-glutamic acid (Gla) (Bachem) to chelate a transition metal and form a cross-link. Protected γ -carboxyl glutamic acid may be prepared by modifying the synthesis described by Zee-Cheng and Olson (1980, Biophys. Biochem. Res. Commun. 94: 1128-1132). A peptide in which the peptide sequence comprises at least two amino acids capable of cross-linking may be treated, e.g., by oxidation of cysteine residues to form a disulfide or addition of a metal ion to form a chelate, so as to cross-link the peptide and form a constrained, cyclic or rigidized peptide.
The present invention provides strategies to systematically prepare cross-links. For example, if four cysteine residues are incorporated in the peptide sequence, different protecting groups may be used (Hiskey, 1981, in The Peptides: Analysis, Synthesis, Biology, Vol. 3, Gross and Meienhofer, eds., Academic Press: New York, pp. 137-167; Ponsanti et al., 1990, Tetrahedron 46:8255-8266). The first pair of cysteine may be deprotected and oxidized, then the second set may be deprotected and oxidized. In this way a defined set of disulfide cross-links may be formed. Alternatively, a pair of cysteine and a pair of collating amino acid analogs may be incorporated so that the cross-links are of a different chemical nature.
The following non-classical amino acids may be incorporated in the peptide in order to introduce particular conformational motifs: l,2,3,4-tetrahydroisoquinoline-3-carboxylate (Kazmierski et al, 1991, J. Am. Chem. Soc. 113:2275-2283); (2S,3S)-methyl- phenylalanine, (2S,3R)-methyl-phenylalanine, (2R,3S)-methyl-phenylalanine and (2R,3R)- methyl-phenylalanine (Kazmierski and Hruby, 1991, Tetrahedron Lett); 2- aminotetrahydronaphthalene-2-carboxylic acid (Landis, 1989, Ph.D. Thesis, University of Arizona); hydroxy-l,2,3,4-tetrahydroisoquinoline-3-carboxylate (Miyake et al, 1989, J. TakedaRes. Labs. 43:53-76); β-carboline (D and L) (Kazmierski, 1988, Ph.D. Thesis, University of Arizona); HIC (histidine isoquinoline carboxylic acid) (Zechel et al, 1991, Int. J. Pep. Protein Res. 43); and HIC (histidine cyclic urea) (Dharanipragada).
The following amino acid analogs and peptidomimetics may be incorporated into a peptide to induce or favor specific secondary structures: LL-Acp (LL-3-amino- 2-propenidone-6-carboxylic acid), a β-turn inducing dipeptide analog (Kemp et al, 1985, J. Org. Chem. 50:5834-5838); β-sheet inducing analogs (Kemp et al., 1988, Tetrahedron Lett. 29:5081-5082); β-turn inducing analogs (Kemp et al., 1988, Tetrahedron Lett. 29:5057-5060); «-helix inducing analogs (Kemp et al, 1988, Tetrahedron Lett. 29:4935- 4938); γ-turn inducing analogs (Kemp et al, 1989, J. Org. Chem. 54:109: 115); and analogs provided by the following references: Nagai and Sato, 1985, Tetrahedron Lett. 26:647-650; DiMaio et al, 1989, J. Chem. Soc. Perkin Trans, p. 1687; also a Gly-Ala turn analog (Kahn et al, 1989, Tetrahedron Lett. 30:2317); amide bond isostere (Jones et al, 1988, Tetrahedron Lett. 29:3853-3856); tretrazol (Zabrocki et al., 1988, J. Am. Chem. Soc. 110:5875-5880); DTC (Samanen et al, 1990, Int. J. Protein Pep. Res. 35:501 :509); and analogs taught in Olson et al, 1990, J. Am. Chem. Sci. 112:323-333 and Garvey et al., 1990, J Org. Chem. 56:436. Conformationally restricted mimetics of beta turns and beta bulges, and peptides containing them, are described in U.S. Patent No. 5,440,013, issued August 8, 1995 to Kahn.
The present invention further provides for modification or derivatization of the polypeptide or peptide of the invention. Modifications of peptides are well known to one of ordinary skill, and include phosphorylation, carboxymethylation, and acylation. Modifications may be effected by chemical or enzymatic means. In another aspect, glycosylated or fatty acylated peptide derivatives may be prepared. Preparation of glycosylated or fatty acylated peptides is well known in the art. Fatty acyl peptide derivatives may also be prepared. For example, and not by way of limitation, a free amino group (N-terminal or lysyl) may be acylated, e.g. , myristoylated. In another embodiment an amino acid comprising an aliphatic side chain of the structure -(CH2)nCH3 may be incorporated in the peptide. This and other peptide-fatty acid conjugates suitable for use in the present invention are disclosed in U.K. Patent GB-8809162.4, International Patent Application PCT/AU89/00166, and reference 5, supra.
Mutations can be made in a nucleic acid encoding the polypeptide such that a particular codon is changed to a codon which codes for a different amino acid. Such a mutation is generally made by making the fewest nucleotide changes possible. A substitution mutation of this sort can be made to change an amino acid in the resulting protein in a non-conservative manner (i.e., by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to another grouping) or in a conservative manner (i.e., by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to the same grouping). Such a conservative change generally leads to less change in the structure and function of the resulting protein. A non-conservative change is more likely to alter the structure, activity or function of the resulting protein. The present invention should be considered to include sequences containing conservative changes which do not significantly alter the activity or binding characteristics of the resulting protein. Substitutes for an amino acid within the sequence may be selected from other members of the class to which the amino acid belongs. For example, the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. Amino acids containing aromatic ring structures are phenylalanine, tryptophan, and tyrosine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Such alterations will not be expected to affect apparent molecular weight as determined by polyacrylamide gel electrophoresis, or isoelectric point.
Particularly preferred substitutions are: - Lys for Arg and vice versa such that a positive charge may be maintained;
- Glu for Asp and vice versa such that a negative charge may be maintained;
- Ser for Thr such that a free -OH can be maintained; and
- Gin for Asn such that a free NH2 can be maintained.
Synthetic DNA sequences allow convenient construction of genes which will express analogs or "muteins". A general method for site-specific incorporation of unnatural amino acids into proteins is described in Noren, et al. Science, 244: 182-188 (April 1989). This method may be used to create analogs with unnatural amino acids.
In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook et al, "Molecular Cloning: A Laboratory Manual" (1989); "Current Protocols in Molecular Biology" Volumes I-III [Ausubel, R. M., ed. (1994)]; "Cell Biology: A Laboratory Handbook" Volumes I-HI [J. E. Celis, ed. (1994))]; "Current Protocols in Immunology" Volumes I- III [Coligan, J. E., ed. (1994)]; "Oligonucleotide Synthesis" (M.J. Gait ed. 1984); "Nucleic Acid Hybridization" [B.D. Hames & S.J. Higgins eds. (1985)]; "Transcription And Translation" [B.D. Hames & S.J. Higgins, eds. (1984)]; "Animal Cell Culture" [R.I. Freshney, ed. (1986)]; "Immobilized Cells And Enzymes" [IRL Press, (1986)]; B. Perbal, "A Practical Guide To Molecular Cloning" (1984).
In an additional embodiment, pyroglutamate may be included as the N-terminal residue of the peptide. Although pyroglutamate is not amenable to sequence by Edman degradation, by limiting substitution to only 50% of the peptides on a given bead with N- terminal pyroglutatamate, there will remain enough non-pyroglutamate peptide on the bead for sequencing. One of ordinary skill in would readily recognize that this technique could be used for sequencing of any peptide that incorporates a residue resistant to Edman degradation at the N-terminus. Other methods to characterize individual peptides that demonstrate desired activity are described in detail infra. Specific activity of a peptide that comprises a blocked N-terminal group, e.g., pyroglutamate, when the particular N-terminal group is present in 50% of the peptides, would readily be demonstrated by comparing activity of a completely (100%) blocked peptide with a non- blocked (0%) peptide.
Chemical Moieties For Derivatization. Chemical moieties suitable for derivatization may be selected from among water soluble polymers. The polymer selected should be water soluble so that the component to which it is attached does not precipitate in an aqueous environment, such as a physiological environment. Preferably, for therapeutic use of the end-product preparation, the polymer will be pharmaceutically acceptable. One skilled in the art will be able to select the desired polymer based on such considerations as whether the polymer/component conjugate will be used therapeutically, and if so, the desired dosage, circulation time, resistance to proteolysis, and other considerations. For the present component or components, these may be ascertained using the assays provided herein.
The water soluble polymer may be selected from the group consisting of, for example, polyethylene glycol, copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, poiyvinyl alcohol, poiyvinyl pyrrolidone, poly-1, 3-dioxolane, poly-1, 3, 6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co- polymers, polyoxyethylated polyols and poiyvinyl alcohol. Polyethylene glycol propionaldenhyde may have advantages in manufacturing due to its stability in water.
The polymer may be of any molecular weight, and may be branched or unbranched. For polyethylene glycol, the preferred molecular weight is between about 2kDa and about lOOkDa (the term "about" indicating that in preparations of polyethylene glycol, some molecules will weigh more, some less, than the stated molecular weight) for ease in handling and manufacturing. Other sizes may be used, depending on the desired therapeutic profile (e.g. , the duration of sustained release desired, the effects, if any on biological activity, the ease in handling, the degree or lack of antigenicity and other known effects of the polyethylene glycol to a therapeutic protein or analog).
The number of polymer molecules so attached may vary, and one skilled in the art will be able to ascertain the effect on function. One may mono-derivative, or may provide for a di-, tri-, tetra- or some combination of derivatization, with the same or different chemical moieties (e.g., polymers, such as different weights of polyethylene glycols). The proportion of polymer molecules to component or components molecules will vary, as will their concentrations in the reaction mixture. In general, the optimum ratio (in terms of efficiency of reaction in that there is no excess unreacted component or components and polymer) will be determined by factors such as the desired degree of derivatization (e.g., mono, di-, tri-, etc.), the molecular weight of the polymer selected, whether the polymer is branched or unbranched, and the reaction conditions.
The polyethylene glycol molecules (or other chemical moieties) should be attached to the component or components with consideration of effects on functional or antigenic domains of the protein. There are a number of attachment methods available to those skilled in the art, e.g., EP 0 401 384 herein incorporated by reference (coupling PEG to G-CSF), see also Malik etal, 1992, Exp. Hematol. 20: 1028-1035 (reporting pegylation of GM-CSF using tresyl chloride). For example, polyethylene glycol may be covalently bound through amino acid residues via a reactive group, such as, a free amino or carboxyl group. Reactive groups are those to which an activated polyethylene glycol molecule may be bound. The amino acid residues having a free amino group include lysine residues and the - terminal amino acid residues; those having a free carboxyl group include aspartic acid residues glutamic acid residues and the C-terminal amino acid residue. Sulfhydrl groups may also be used as a reactive group for attaching the polyethylene glycol molecule(s). Preferred for therapeutic purposes is attachment at an amino group, such as attachment at the N-terminus or lysine group.
This invention provides an isolated nucleic acid encoding a polypeptide comprising an amino acid sequence of a choline binding protein CbpG or CbpD. This invention provides an isolated nucleic acid encoding a polypeptide comprising an amino acid sequence of a choline binding protein selected from the group of choline binding proteins CbpG or CbpD as set forth in Figure 2 or Figure 10. In one embodiment the nucleic acid is set forth SEQ ID NO:3 or SEQ ID NO: 16, including fragments, mutants, variants, analogs, or derivatives, thereof. The nucleic acid is DNA, cDNA, genomic DNA, RNA. Further, the isolated nucleic acid may be operatively linked to a promoter of RNA transcription. It is contemplated that the nucleic acid is used to competitively inhibit the lectin activity.
This invention further provides an isolated nucleic acid encoding an N-terminal CbpG or CbpD truncate. In one embodiment the nucleic acid encodes an N-terminal CbpG or CbpD truncate comprising amino acids 1-90 of CbpG. In a further embodiment, the nucleic acid encoding an N-terminal CbpG truncate comprising less than amino acids 1-90 of CbpG. In a particular embodiment, the nucleic acid encoding an N-terminal CbpD truncate is capable of encoding amino acids 2-280 of CbpD. In a still further embodiment, the nucleic acid encoding an N-terminal CbpD truncate encodes a truncate of amino acids 2-116 or 103-280 of CbpD. In a particular embodiment the nucleic acid is set forth in SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO:24, including fragments, mutants, variants, analogs or derivatives thereof.
A "vector" is a replicon, such as plasmid, phage or cosmid, to which another DNA segment may be attached so as to bring about the replication of the attached segment.
A "DNA" refers to the polymeric form of deoxyribonucleotides (adenine, guanine, thymine, or cytosine) in its either single stranded form, or a double-stranded helix. This term refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear DNA molecules (e.g., restriction fragments), viruses, plasmids, and chromosomes. In discussing the structure of particular double-stranded DNA molecules, sequences may be described herein according to the normal convention of giving only the sequence in the 5' to 3' direction along the nontranscribed strand of DNA (i.e., the strand having a sequence homologous to the mRNA). A DNA sequence is "operatively linked" to an expression control sequence when the expression control sequence controls and regulates the transcription and translation of that DNA sequence. The term "operatively linked" includes having an appropriate start signal (e.g., ATG) in front of the DNA sequence to be expressed and maintaining the correct reading frame to permit expression of the DNA sequence under the control of the expression control sequence and production of the desired product encoded by the DNA sequence. If a gene that one desires to insert into a recombinant DNA molecule does not contain an appropriate start signal, such a start signal can be inserted in front of the gene.
Further this invention also provides a vector which comprises the above-described nucleic acid molecule. The promoter may be, or is identical to, a bacterial, yeast, insect or mammalian promoter. Further, the vector may be a plasmid, cosmid, yeast artificial chromosome (YAC), bacteriophage or eukaryotic viral DNA.
Other numerous vector backbones known in the art as useful for expressing protein may be employed. Such vectors include, but are not limited to: adenovirus, simian virus 40 (SV40), cytomegalovirus (CMV), mouse mammary tumor virus (MMTV), Moloney murine leukemia virus, DNA delivery systems, i.e. liposomes, and expression plasmid delivery systems. Further, one class of vectors comprises DNA elements derived from viruses such as bovine papilloma virus, polyoma virus, baculovirus, retroviruses or Semliki Forest virus. Such vectors may be obtained commercially or assembled from the sequences described by methods well-known in the art.
This invention also provides a host vector system for the production of a polypeptide which comprises the vector of a suitable host cell. Suitable host cells include, but are not limited to, prokaryotic or eukaryotic cells, e.g. bacterial cells (including gram positive cells), yeast cells, fungal cells, insect cells, and animal cells. Numerous mammalian cells may be used as hosts, including, but not limited to, the mouse fibroblast cell NTH 3T3, CHO cells, HeLa cells, Ltk" cells, Cos cells, etc. A wide variety of host/expression vector combinations may be employed in expressing the DNA sequences of this invention. Useful expression vectors, for example, may consist of segments of chromosomal, non-chromosomal and synthetic DNA sequences. Suitable vectors include derivatives of SV40 and known bacterial plasmids, e.g., E. coli plasmids col El, pCRl, pBR322, pMB9 and their derivatives, plasmids such as RP4; phage DNAS, e.g., the numerous derivatives of phage λ, e.g., NM989, and other phage DNA, e.g., M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2μ plasmid or derivatives thereof; vectors useful in eukaryotic cells, such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or other expression control sequences; and the like.
Any of a wide variety of expression control sequences ~ sequences that control the expression of a DNA sequence operatively linked to it ~ may be used in these vectors to express the DNA sequences of this invention. Such useful expression control sequences include, for example, the early or late promoters of SV40, CMN, vaccinia, polyoma or adenovirus, the lac system, the trp system, the TAC system, the TRC system, the LTR system, the major operator and promoter regions of phage λ, the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase (e.g., Pho5), the promoters of the yeast α-mating factors, and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof.
A wide variety of unicellular host cells are also useful in expressing the DΝA sequences of this invention. These hosts may include well known eukaryotic and prokaryotic hosts, such as strains of E. coli, Pseudomonas, Bacillus, Streptomyces, fiingi such as yeasts, and animal cells, such as CHO, Rl.l, B-W and L-M cells, African Green Monkey kidney cells (e.g., COS 1, COS 7, BSC1, BSC40, and BMT10), insect cells (e.g., Sf9), and human cells and plant cells in tissue culture. It will be understood that not all vectors, expression control sequences and hosts will function equally well to express the DNA sequences of this invention. Neither will all hosts function equally well with the same expression system. However, one skilled in the art will be able to select the proper vectors, expression control sequences, and hosts without undue experimentation to accomplish the desired expression without departing from the scope of this invention. For example, in selecting a vector, the host must be considered because the vector must function in it. The vector's copy number, the ability to control that copy number, and the expression of any other proteins encoded by the vector, such as antibiotic markers, will also be considered.
In selecting an expression control sequence, a variety of factors will normally be considered. These include, for example, the relative strength of the system, its controllability, and its compatibility with the particular DNA sequence or gene to be expressed, particularly as regards potential secondary structures. Suitable unicellular hosts will be selected by consideration of, e.g., their compatibility with the chosen vector, their secretion characteristics, their ability to fold proteins correctly, and their fermentation requirements, as well as the toxicity to the host of the product encoded by the DNA sequences to be expressed, and the ease of purification of the expression products.
This invention further provides a method of producing a polypeptide which comprises growing the above-described host vector system under suitable conditions permitting the production of the polypeptide and recovering the polypeptide so produced.
This invention further provides an antibody capable of specifically recognizing or binding to the isolated polypeptide. The antibody may be a monoclonal or polyclonal antibody. Further, the antibody may be labeled with a detectable marker that is either a radioactive, calorimetric, fluorescent, or a luminescent marker. The labeled antibody may be a polyclonal or monoclonal antibody. In one embodiment, the labeled antibody is a purified labeled antibody. Methods of labeling antibodies are well known in the art. The term "antibody" includes, by way of example, both naturally occurring and non- naturally occurring antibodies. Specifically, the term "antibody" includes polyclonal and monoclonal antibodies, and fragments thereof. Furthermore, the term "antibody" includes chimeric antibodies and wholly synthetic antibodies, and fragments thereof. Such antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments, and an Fab expression library.
Various procedures known in the art may be used for the production of polyclonal antibodies to polypeptide or derivatives or analogs thereof (see, e.g., Antibodies — A Laboratory Manual, Harlow and Lane, eds., Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York, 1988). For the production of antibody, various host animals can be immunized by injection with the choline binding polypeptide CbpG or CbpD, an immunogenic fragment thereof, or a derivative (e.g., fragment or fusion protein) thereof, including but not limited to rabbits, mice, rats, sheep, goats, etc. In one embodiment, the polypeptide can be conjugated to an immunogenic carrier, e.g., bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH). Various adjuvant may be used to increase the immunological response, depending on the host species.
For preparation of monoclonal antibodies, or fragment, analog, or derivative thereof, any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used (see, e.g., Antibodies — A Laboratory Manual, Harlow and Lane, eds., Cold Spring Harbor Laboratory Press: Cold Spring Harbor, Ne York, 1988). These include but are not limited to the hybridoma technique originally developed by Kohler and Milstein (1975, Nature 256:495-497), as well as 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). In an additional embodiment of the invention, monoclonal antibodies can be produced in germ- free animals utilizing recent technology (PCT/US90/02545). According to the invention, human antibodies may be used and can be obtained by using human hybridomas (Cote et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:2026-2030) or by transforming human B cells with EBV virus in vitro (Cole et al, 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, pp. 77-96). In fact, according to the invention, techniques developed for the production of "chimeric antibodies" (Morrison et al, 1984, J. Bacteriol. 159-870; Neuberger et a , 1984, Nature 312:604-608; Takeda et /., 1985, Nature 314:452-454) by splicing the genes from a mouse antibody molecule specific for a polypeptide together with genes from a human antibody molecule of appropriate biological activity can be used; such antibodies are within the scope of this invention. Such human or humanized chimeric antibodies are preferred for use in therapy of human diseases or disorders (described infra), since the human or humanized antibodies are much less likely than xenogenic antibodies to induce an immune response, in particular an allergic response, themselves. An additional embodiment of the invention utilizes the techniques described for the construction of Fab expression libraries (Huse et al, 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for the polypeptide, or its derivatives, or analogs.
Antibody fragments which contain the idiotype of the antibody molecule can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab')2 fragment which can be produced by pepsin digestion of the antibody molecule; the Fab' fragments which can be generated by reducing the disulfide bridges of the F(ab')2 fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent.
In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art, e.g., radioimmunoassay, ELISA (enzyme-linked immunosorbant assay), "sandwich" immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodifϊusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc. In one embodiment, antibody binding is detected by detecting a label on the primary antibody. In another embodiment, the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody. In a further embodiment, the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
Antibodies can be labeled for detection in vitro, e.g., with labels such as enzymes, fluorophores, chromophores, radioisotopes, dyes, colloidal gold, latex particles, and chemiluminescent agents. Alternatively, the antibodies can be labeled for detection in vivo, e.g., with radioisotopes (preferably technetium or iodine); magnetic resonance shift reagents (such as gadolinium and manganese); or radio-opaque reagents.
The labels most commonly employed for these studies are radioactive elements, enzymes, chemicals which fluoresce when exposed to ultraviolet light, and others. A number of fluorescent materials are known and can be utilized as labels. These include, for example, fluorescein, rhodamine, auramine, Texas Red, AMCA blue and Lucifer Yellow. A particular detecting material is anti-rabbit antibody prepared in goats and conjugated with fluorescein through an isothiocyanate. The polypeptide can also be labeled with a radioactive element or with an enzyme. The radioactive label can be detected by any of the currently available counting procedures. The preferred isotope may be selected from 3H, 14C, 32P, 35S, 36C1, 51Cr, "Co, 58Co, 59Fe, 90Y, 12T, 131I, and 186Re.
Enzyme labels are likewise useful, and can be detected by any of the presently utilized calorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques. The enzyme is conjugated to the selected particle by reaction with bridging molecules such as carbodiimides, diisocyanates, glutaraldehyde and the like. Many enzymes which can be used in these procedures are known and can be utilized. The preferred are peroxidase, β-glucuronidase, β-D-glucosidase, β-D-galactosidase, urease, glucose oxidase plus peroxidase and alkaline phosphatase. U.S. Patent Nos. 3,654,090; 3,850,752; and 4,016,043 are referred to by way of example for their disclosure of alternate labeling material and methods. Diagnostic Applications
In a further embodiment of this invention, commercial test kits suitable for use by a medical specialist may be prepared to determine the presence or absence of predetermined binding activity or predetermined binding activity capability to suspected target cells. In accordance with the testing techniques discussed above, one class of such kits will contain at least the labeled polypeptide or its binding partner, for instance an antibody specific thereto, and directions, of course, depending upon the method selected, e.g., "competitive," "sandwich," "DASP" and the like. The kits may also contain peripheral reagents such as buffers, stabilizers, etc.
Accordingly, a test kit may be prepared for the demonstration of the presence or capability of cells for predetermined bacterial binding activity, comprising:
(a) a predetermined amount of at least one labeled immunochemically reactive component obtained by the direct or indirect attachment of the present polypeptide or a specific binding partner thereto, to a detectable label;
(b) other reagents; and
(c) directions for use of said kit.
Therapeutic Applications
The therapeutic possibilities that are raised by the existence of the choline binding protein CbpG or CbpD derive from the fact that the choline binding protein of the present invention is involved in or required for pneumococcal colonization and attachment, critical for bacterial survival and virulence in the human host.
Thus, a mutation in such choline binding protein CbpG or CbpD leads to the inability to adhere to the host cells and the failure to colonize in said host. In a further aspect, an N- terminal CbpG or CbpD truncate, acts as an immunotherapeutic fragment which binds to the cell target but prevents adhesion of the bacteria, particularly Streptococcus. In a particular embodiment, the N-terminal CbpG or CbpD truncate comprises the amino acid sequence as set forth in SEQ ID NO:ll, SEQ ID NO:21 or SEQ ID NO:23. In a further embodiment, the N-terminal CbpG or CbpD truncate consists of amino acids 1-90 of the CbpG or amino acids 2-280 of the CbpD choline binding protein. In a still further embodiment, the N-terminal CbpG or CbpD truncate is a truncate of less than amino acids 1-90 of CbpG and less than amino acids 2-280, particularly consisting of amino acids 2- 116 or 103-280 of CbpD.
As suggested earlier and elaborated further on herein, the present invention contemplates therapeutic intervention in the cascade of reactions, specifically colonization and attachment, in which the choline binding protein CbpG or CbpD is implicated, to thereby block or reduce the virulence of bacteria, particularly Streptococcus, most particularly pneumococcus.
Modulators of Choline Binding Protein
Thus, in instances where it is desired to reduce or inhibit the effects resulting from the choline binding protein CbpG or CbpD of the present invention, an appropriate inhibitor of the choline binding protein CbpG or CbpD could be introduced to block the activity of the choline binding protein CbpG or CbpD.
The present invention contemplates screens for a modulator of the choline binding protein CbpG or CbpD, in particular, directly or indirectly through the choline binding site. The present invention further contemplates screens for a modulator of the choline binding protein CbpG or CbpD, in particular, directly or indirectly through the N-terminal activity domain. In one such embodiment, an expression vector containing the choline binding protein CbpG or CbpD of the present invention, or a derivative or analog thereof, is placed into a cell in the presence of at least one agent suspected of exhibiting choline binding protein CbpG or CbpD modulator activity. The cell is preferably a bacterial cell and most preferably a pneumococcal cell. The amount of adhesion or binding activity is determined and any such agent is identified as a modulator when the amount of adhesion or binding activity in the presence of such agent is different than in its absence. The vectors may be introduced by any of the methods described above.
In a related embodiment the choline binding protein CbpG or CbpD is expressed and the step of determining the amount of adhesion or binding activity is performed by determining the amount of binding to nasopharyngeal cells in vitro. In a further embodiment an N-terminal choline binding protein truncate of the choline binding protein CbpG or CbpD is expressed and the step of determining the amount of adhesion or binding activity is performed by determining the amount of binding to nasopharyngeal cells in vitro.
When the amount of adhesion or binding activity in the presence of the modulator is greater than in its absence, the modulator is identified as an agonist or activator of the choline binding protein CbpG or CbpD, whereas when the amount of adhesion binding activity in the presence of the modulator is less than in its absence, the modulator is identified as an antagonist or inhibitor of the choline binding protein CbpG or CbpD. As any person having skill in the art would recognize, such determinations as these and those below could require some form of statistical analysis, which is well within the skill in the art.
Natural effectors found in cells expressing choline binding protein CbpG or CbpD can be fractionated and tested using standard effector assays as exemplified herein, for example. Thus an agent that is identified can be a naturally occurring adhesion or binding modulator. Alternatively, natural products libraries can be screened using the assays of the present invention for screening such agents.
Another approach uses recombinant bacteriophage to produce large libraries. Using the "phage method" [Scott and Smith, 1990, Science 249:386-390 (1990); Cwirla, et al., Proc. Natl. Acad. Sci., 87:6378-6382 (1990); Devlin et al., Science, 249:404-406 (1990)], very large libraries can be constructed (106-108 chemical entities). Yet another approach uses primarily chemical methods, of which the Geysen method [Geysen et al., Molecular Immunology 23:709-715 (1986); Geysen et al. J. Immunologic Method 102:259-274 (1987)] and the method of Fodor et al. [Science 251:767-773 (1991)] are examples. Furka et al. [14th International Congress of Biochemistry, Volume 5, Abstract FR:013 (1988); Furka, Int. J. Peptide Protein Res. 37:487-493 (1991)], Houghton [U.S. Patent No. 4,631,211, issued December 1986] and Rutter et al. [U.S. Patent No. 5,010,175, issued April 23, 1991] describe methods to produce a mixture of peptides that can be tested.
In another aspect, synthetic libraries [Needels et al, Proc. Natl. Acad. Sci. USA 90:10700-4 (1993); Ohlmeyer et al., Proc. Natl. Acad. Sci. USA 90: 10922-10926 (1993); Lam et al., International Patent Publication No. WO 92/00252; Kocis et al., International Patent Publication No. WO 9428028, each of which is incorporated herein by reference in its entirety], and the like can be used to screen for such an agent.
This invention provides antagonist or blocking agents which include but are not limited to: peptide fragments, mimetic, a nucleic acid molecule, a ribozyme, a polypeptide, a small molecule, a carbohydrate molecule, a monosaccharide, an oligosaccharide or an antibody. Also, agents which competitively block or inhibit pneumococcal bacterium are contemplated by this invention. This invention provides an agent which comprises an inorganic compound, a nucleic acid molecule, an oligonucleotide, an organic compound, a peptide, a peptidomimetic compound, or a protein which inhibits the polypeptide.
Vaccines
This invention provides a vaccine which comprises a polypeptide bacterial choline binding protein CbpG or CbpD and a pharmaceutically acceptable adjuvant or carrier. This invention provides a vaccine which comprises a combination of at least two polypeptide bacterial choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein and a pharmaceutically acceptable adjuvant or carrier. The polypeptide may comprise an amino acid sequence of a choline binding protein CbpG or CbpD as set forth in Figure 2 and SEQ ID NO:2 and Figure 10 and SEQ ID NO: 15.
The polypeptide may comprise an N-terminal truncate of a choline binding protein CbpG or CbpD. In a particular embodiment, the N-terminal CbpG or CbpD truncate comprises the amino acid sequence set forth in SEQID NOT 1, SEQ ID NO:21 or SEQ ID NO:23. In a further embodiment, the N-terminal CbpG or CbpD truncate consists of amino acids 1-90 of the CbpG or amino acids 2-280 of CbpD choline binding protein. Still further, the N-terminal truncate may comprise less than amino acids 1-90 of CbpG or amino acids 2-280 of CbpD. In a further particular embodiment the N-terminal truncate consists of amino acids 2-116 or 103-280 of CbpD.
This invention further provides a vaccine comprising an isolated nucleic acid encoding a bacterial choline binding protein CbpG or CbpD and a pharmaceutically acceptable adjuvant or carrier. This invention further provides a vaccine comprising isolated nucleic acid encoding a combination of at least two polypeptide bacterial choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein and a pharmaceutically acceptable adjuvant or carrier. This invention still further provides a vaccine comprising an isolated nucleic acid encoding a N-terminal truncate of choline binding protein CbpG or CbpD and a pharmaceutically acceptable adjuvant or carrier. The nucleic acid may comprise a nucleic acid sequence of a choline binding protein CbpG or CbpD as set forth in Figure 2 and SEQ ID NO: 3 and Figure 10 and SEQ ID NO: 16.
Active immunity against Gram positive bacteria, particularly pneumococcus, can be induced by immunization (vaccination) with an immunogenic amount of the polypeptide, or peptide derivative or immunogenic fragment thereof or N-terminal truncate thereof, and an adjuvant, wherein the polypeptide, or antigenic derivative or; fragment thereof, is the antigenic component of the vaccine. The polypeptide, or antigenic derivative or fragment thereof, may be one antigenic component, in the presence of other antigenic components in a vaccine. For instance, the polypeptide of the present invention or immunogenic fragment thereof may be combined with other known pneumococcal polypeptides, or immunogenic fragments thereof or N-terminal truncates thereof, as for instance other choline binding protein(s), including for instance CbpA, LytA, and/or PspA in a multi-component vaccine. In addition, the polypeptide of the present invention or immunogenic fragments thereof may be combined with bacterial zinc metalloprotease, ZmpB or immunogenic fragements thereof. Such multi-component vaccine may be utilized to enhance immune response, even in cases where the polypeptide of the present invention elicits a response on its own. The polypeptide of the present invention may also be combined with existing vaccines, whole bacterial or capsule-based vaccines, alone or in combination with other choline binding proteins or ZmpB, to enhance such existing vaccines.
The invention further provides a vaccine which comprises a non-adherent, non- virulent mutant, including but not limited to the CbpG or CbpD mutants herein described. Medaglini et al (Madaglini et al (1995) Proc Natl Acad Sci USA 92;6868-6872) and Oggioni and Pozzi (Oggioni, M.R. and Pozzi, G. (1996) Gene 169:85-90) have previously described the use of Streptococcus gordonii, a commensal bacterium of the human oral cavity, as live vaccine delivery vehicles and for heterologous gene expression. Such CbpG or CbpD mutant can therefore be utilized as a vehicle for expression of immunogenic proteins for the purposes of eliciting an immune response to such other proteins in the context of vaccines. Active immunity against Gram positive bacteria, particularly pneumococcus, can be induced by immunization (vaccination) with an immunogenic amount of the CbpG or CbpD vehicle expressing an immunogenic protein. Also contemplated by the present invention is the use of any such CbpG or CbpD mutant in expressing a therapeutic protein in the host in the context of other forms of therapy.
The polypeptide of the present invention, or fragments thereof, can be prepared in an admixture with an adjuvant to prepare a vaccine. Preferably, the polypeptide or peptide derivative or fragment thereof, used as the antigenic component of the vaccine is an antigen common to all or many strains of a species of Gram positive bacteria, or common to closely related species of bacteria, for instance Streptococcus. Vectors containing the nucleic acid-based vaccine of the invention can be introduced into the desired host by methods known in the art, e.g., transfection, electroporation, micro injection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, lipofection (lysosome fusion), use of a gene gun, or a DNA vector transporter (see, e.g., Wu et al, 1992, J. Biol. Chem. 267:963-967; Wu and Wu, 1988, J. Biol. Chem. 263: 14621-14624; Hartmut et al, Canadian Patent Application No. 2,012,311, filed March 15, 1990).
The vaccine can be administered via any parenteral route, including but not limited to intramuscular, intraperitoneal, intravenous, and the like. Preferably, since the desired result of vaccination is to elucidate an immune response to the antigen, and thereby to the pathogenic organism, administration directly, or by targeting or choice of a viral vector, indirectly, to lymphoid tissues, e.g., lymph nodes or spleen, is desirable. Since immune cells are continually replicating, they are ideal target for retroviral vector-based nucleic acid vaccines, since retroviruses require replicating cells.
Passive immunity can be conferred to an animal subject suspected of suffering an infection with a Gram positive bacterium, preferably streptococcal, and more preferably pneumoccal, by administering antiserum, polyclonal antibodies, or a neutralizing monoclonal antibody against a polypeptide of the invention to the subject. A combination of antibodies can be, for instance, directed against at least two polypeptide bacterial choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein. Although passive immunity does not confer long term protection, it can be a valuable tool for the treatment of a bacterial infection in a subject who has not been vaccinated. Passive immunity is particularly important for the treatment of antibiotic resistant strains of Gram positive bacteria, since no other therapy may be available. Preferably, the antibodies administered for passive immune therapy are autologous antibodies. For example, if the subject is a human, preferably the antibodies are of human origin or have been "humanized," in order to minimize the possibility of an immune response against the antibodies. The active or passive vaccines of the invention can be used to protect an animal subject from infection of a Gram positive bacteria, preferably streptococcus, and more preferably, pneumococcus.
This invention provides a method for treating a subject infected with or exposed to pneumococcal bacterium comprising administering to the subject a therapeutically effective amount of the vaccine, thereby treating the subject.
Pharmaceutical Compositions
This invention provides a pharmaceutical composition comprising an amount of the polypeptide as described and a pharmaceutically acceptable carrier or diluent. This invention provides a pharmaceutical composition comprising an amount of a choline binding protein CbpG or CbpD and a pharmaceutically acceptable carrier or diluent. This invention provides a pharmaceutical composition comprising an amount of at least two choline binding proteins comprising CbpG or CbpD and at least one other choline binding protein and a pharmaceutically acceptable carrier or diluent. The invention further provides a pharmaceutical composition comprising an amount of the polypeptide of SEQ ID NO: 2 or SEQ ID NO: 15, including fragments, mutants, variants, analogs or derivatives thereof, and a pharmaceutically acceptable carrier or diluent. This invention still further provides a pharmaceutical composition comprising an amount of an N- terminal truncate of a choline binding protein CbpG or CbpD. In a particular embodiment, the N-terminal CbpG or CbpD truncate comprises amino acids 1-90 of CbpG or amino acids 2-280, 2-116 or 103-280 of CbpD, as set out in SEQ ID NOT 1, SEQ ID NO:21 or SEQ ID NO:23, or active fragments, mutants, variants, analogs or derivatives thereof.
For example, such pharmaceutical composition for preventing pneumococcal attachment to mucosal surface may include antibody to choline binding protein CbpG or CbpD or any combination of anti-CbpG or CbpD antibody and at least one other antibody directed against another choline binding protein. Blocking adherence using such antibody blocks the initial step in infection thereby reducing colonization. This in turn decreases person to person transmission and prevents development of symptomatic disease. A further example of a pharmaceutical composition for preventing pneumococcal attachment may include an N-terminal CbpG or CbpD truncaate. In a particular embodiment, such N- terminal truncate comprises the amino acid set out in SEQ ID NOT 1, SEQ ID NO: 21 or SEQ ID NO: 23, or active fragments thereof.
This invention provides a method of inducing an immune response in a subject which has been exposed to or infected with a pneumococcal bacterium comprising administering to the subject an amount of the pharmaceutical composition, thereby inducing an immune response.
This invention provides a method for preventing infection by a pneumococcal bacterium in a subject comprising administering to the subject an amount of the pharmaceutical composition effective to block activity of the choline binding protein CbpG or CbpD, thereby preventing pneumococcal bacterium attachment, and further preventing infection by a pneumococcal bacterium.
This invention provides a method for preventing infection by a pneumococcal bacterium in a subject comprising administering to the subject an amount of a pharmaceutical composition comprising the antibody and a pharmaceutically acceptable carrier or diluent, thereby preventing infection by a pneumococcal bacterium.
This invention provides a method of inhibiting colonization of host cells in a subject which has been exposed to or infected with a pneumococcal bacterium comprising administering to the subject an amount of the pharmaceutical composition comprising the polypeptide consisting of the amino acid sequence as set forth in SEQ ID NO:2, SEQ ID NOT 1, SEQ ID NO:15, SEQ ID NO:21 or SEQ ID NO:23, or immunogenic fragments thereof thereby inducing an immune response. The therapeutic peptide that blocks colonization is delivered via the respiratory mucosa. The pharmaceutical composition comprises the polypeptide consisting of the amino acid sequence as set forth in SEQ ID NO:2, SEQ ID NOT 1, SEQ ID NO:15, SEQ ID NO:21 or SEQ ID NO:23. As used herein, "pharmaceutical composition" could mean therapeutically effective amounts of polypeptide products of the invention together with suitable diluents, preservatives, solubilizers, emulsifiers, adjuvant and/or carriers useful in therapy against bacterial infection or in inducing an immune response. A "therapeutically effective amount" as used herein refers to that amount which provides a therapeutic effect for a given condition and administration regimen. Such compositions are liquids or lyophilized or otherwise dried formulations and include diluents of various buffer content (e.g., Tris- HCl, acetate, phosphate), pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts), solubilizing agents (e.g., glycerol, polyethylene glycerol), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), preservatives (e.g., Thimerosal, benzyl alcohol, parabens), bulking substances or tonicity modifiers (e.g., lactose, mannitol), covalent attachment of polymers such as polyethylene glycol to the protein, complexation with metal ions, or incorporation of the material into or onto particulate preparations of polymeric compounds such as polylactic acid, polglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, unilamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts. Such compositions will influence the physical state, solubility, stability, rate of in vivo release, and rate of in vivo clearance of choline binding protein CbpG or CbpD and the polypeptides of the present invention. The choice of compositions will depend on the physical and chemical properties of the polypeptide. Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). Also comprehended by the invention are particulate compositions coated with polymers (e.g., poloxamers or poloxamines) and the polypeptides of the present invention coupled to antibodies directed against tissue-specific receptors, ligands or antigens or coupled to ligands of tissue-specific receptors. Other embodiments of the compositions of the invention incorporate particulate forms, protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.
Further, as used herein "pharmaceutically acceptable carrier" are well known to those skilled in the art and include, but are not limited to, 0.01-0.1M and preferably 0.05M phosphate buffer or 0.8%) saline. Additionally, such pharmaceutically acceptable carriers may be aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non- aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Preservatives and other additives may also be present, such as, for example, antimicrobials, antioxidants, collating agents, inert gases and the like.
The term "adjuvant" refers to a compound or mixture that enhances the immune response to an antigen. An adjuvant can serve as a tissue depot that slowly releases the antigen and also as a lymphoid system activator that non-specifically enhances the immune response (Hood et al, Immunology, Second Ed., 1984, Benjamin/Cummings: Menlo Park, California, p. 384). Often, a primary challenge with an antigen alone, in the absence of an adjuvant, will fail to elicit a humoral or cellular immune response. Adjuvant include, but are not limited to, complete Freund's adjuvant, incomplete Freund's adjuvant, saponin, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvant such as BCG (bacille Calmette-Gueriή) and Corynebacterium parvum. Preferably, the adjuvant is pharmaceutically acceptable.
Controlled or sustained release compositions include formulation in lipophilic depots (e.g. fatty acids, waxes, oils). Also comprehended by the invention are particulate compositions coated with polymers (e.g. poloxamers or poloxamines) and the compound coupled to antibodies directed against tissue-specific receptors, ligands or antigens or coupled to ligands of tissue-specific receptors. Other embodiments of the compositions of the invention incorporate particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.
When administered, compounds are often cleared rapidly from mucosal surfaces or the circulation and may therefore elicit relatively short-lived pharmacological activity. Consequently, frequent administrations of relatively large doses of bioactive compounds may by required to sustain therapeutic efficacy. Compounds modified by the covalent attachment of water-soluble polymers such as polyethylene glycol, copolymers of polyethylene glycol and polypropylene glycol, carboxymethyl cellulose, dextran, poiyvinyl alcohol, polyvinylpyrrolidone or polyproline are known to exhibit substantially longer half-lives in blood following intravenous injection than do the corresponding unmodified compounds (Abuchowski et al, 1981; Newmark et al, 1982; and Katre et al, 1987). Such modifications may also increase the compound's solubility in aqueous solution, eliminate aggregation, enhance the physical and chemical stability of the compound, and greatly reduce the immunogenicity and reactivity of the compound. As a result, the desired in vivo biological activity may be achieved by the administration of such polymer-compound abducts less frequently or in lower doses than with the unmodified compound.
Dosages. The sufficient amount may include but is not limited to from about 1 μg/kg to about 1000 mg/kg. The amount may be 10 mg/kg. The pharmaceutically acceptable form of the composition includes a pharmaceutically acceptable carrier.
As noted above, the present invention provides therapeutic compositions comprising pharmaceutical compositions comprising vectors, vaccines, polypeptides or fragments thereof, nucleic acids and antibodies, anti-antibodies, and agents, to compete with the pneumococcus bacterium for pathogenic activities, such as adherence to host cells.
The preparation of therapeutic compositions which contain an active component is well understood in the art. Typically, such compositions are prepared as an aerosol of the polypeptide delivered to the nasopharynx or as injectables, either as liquid solutions or suspensions, however, solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared. The preparation can also be emulsified. The active therapeutic ingredient is often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the composition can contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents which enhance the effectiveness of the active ingredient.
An active component can be formulated into the therapeutic composition as neutralized pharmaceutically acceptable salt forms. Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the polypeptide or antibody molecule) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed from the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
A composition comprising "A" (where "A" is a single protein, DNA molecule, vector, etc.) is substantially free of "B" (where "B" comprises one or more contaminating proteins, DNA molecules, vectors, etc.) when at least about 75% by weight of the proteins, DNA, vectors (depending on the category of species to which A and B belong) in the composition is "A". Preferably, "A" comprises at least about 90% by weight of the A+B species in the composition, most preferably at least about 99% by weight.
The phrase "therapeutically effective amount" is used herein to mean an amount sufficient to reduce by at least about 15 percent, preferably by at least 50 percent, more preferably by at least 90 percent, and most preferably prevent, a clinically significant deficit in the activity, function and response of the host. Alternatively, a therapeutically effective amount is sufficient to cause an improvement in a clinically significant condition in the host. In the context of the present invention, a deficit in the response of the host is evidenced by continuing or spreading bacterial infection. An improvement in a clinically significant condition in the host includes a decrease in bacterial load, clearance of bacteria from colonized host cells, reduction in fever or inflammation associated with infection, or a reduction in any symptom associated with the bacterial infection.
According to the invention, the component or components of a therapeutic composition of the invention may be introduced parenterally, transmucosally, e.g., orally, nasally, pulmonarailly, orrectally, or transdermally. Preferably, administration is parenteral, e.g., via intravenous injection, and also including, but is not limited to, intra-arteriole, intramuscular, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial administration. Oral or pulmonary delivery may be preferred to activate mucosal immunity; since pneumococci generally colonize the nasopharyngeal and pulmonary mucosa, mucosal immunity may be a particularly effective preventive treatment. The term "unit dose" when used in reference to a therapeutic composition of the present invention refers to physically discrete units suitable as unitary dosage for humans, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent; i.e., carrier, or vehicle.
In another embodiment, the active compound can be delivered in a vesicle, in particular a liposome (see Langer, Science 249:1527-1533 (1990); Treat et al. , in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
In yet another embodiment, the therapeutic compound can be delivered in a controlled release system. For example, the polypeptide may be administered using intravenous infusion, an implantable osmotic pump, a transdermal patch, liposomes, or other modes of administration. In one embodiment, a pump may be used (see Langer, supra; Sefton, CRC Crit. Refi Biomed. Eng. 14:201 (1987); Buchwald et al, Surgery 88:507 (1980); Saudek et al, N. Engl. J. Med. 321 :574 (1989)). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Florida (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, J. Macromol. Sci. Rev. Macromol Chem. 23:61 (1983); see also Levy etal, Science 228:190 (1985); During et al, Ann. Neurol 25:351 (1989); Howard et al, J. Neurosurg. 71: 105 (1989)). In yet another embodiment, a controlled release system can be placed in proximity of the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)). Preferably, a controlled release device is introduced into a subject in proximity of the site of inappropriate immune activation or a tumor. Other controlled release systems are discussed in the review by Langer (Science 249: 1527-1533 (1990)).
A subject in whom administration of an active component as set forth above is an effective therapeutic regimen for a bacterial infection is preferably a human, but can be any animal. Thus, as can be readily appreciated by one of ordinary skill in the art, the methods and pharmaceutical compositions of the present invention are particularly suited to administration to any animal, particularly a mammal, and including, but by no means limited to, domestic animals, such as feline or canine subjects, farm animals, such as but not limited to bovine, equine, caprine, ovine, and porcine subjects, wild animals (whether in the wild or in a zoological garden), research animals, such as mice, rats, rabbits, goats, sheep, pigs, dogs, cats, etc., i.e., for veterinary medical use.
In the therapeutic methods and compositions of the invention, a therapeutically effective dosage of the active component is provided. A therapeutically effective dosage can be determined by the ordinary skilled medical worker based on patient characteristics (age, weight, sex, condition, complications, other diseases, etc.), as is well known in the art. Furthermore, as further routine studies are conducted, more specific information will emerge regarding appropriate dosage levels for treatment of various conditions in various patients, and the ordinary skilled worker, considering the therapeutic context, age and general health of the recipient, is able to ascertain proper dosing. Generally, for intravenous injection or infusion, dosage may be lower than for intraperitoneal, intramuscular, or other route of administration. The dosing schedule may vary, depending on the circulation half-life, and the formulation used. The compositions are administered in a manner compatible with the dosage formulation in the therapeutically effective amount. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner and are peculiar to each individual. However, suitable dosages may range from about 0.1 to 20, preferably about 0.5 to about 10, and more preferably one to several, milligrams of active ingredient per kilogram body weight of individual per day and depend on the route of administration. Suitable regimes for initial administration and booster shots are also variable, but are typified by an initial administration followed by repeated doses at one or more hour intervals by a subsequent injection or other administration. Alternatively, continuous intravenous infusion sufficient to maintain concentrations of ten nanomolar to ten micromolar in the blood are contemplated.
Administration with other compounds. For treatment of a bacterial infection, one may administer the present active component in conjunction with one or more pharmaceutical compositions used for treating bacterial infection, including but not limited to (1) antibiotics; (2) soluble carbohydrate inhibitors of bacterial adhesin; (3) other small molecule inhibitors of bacterial adhesin; (4) inhibitors of bacterial metabolism, transport, or transformation; (5) stimulators of bacterial lysis, or (6) anti-bacterial antibodies or vaccines directed at other bacterial antigens. Other potential active components include anti-inflammatory agents, such as steroids and non-steroidal anti-inflammatory drugs. Administration may be simultaneous (for example, administration of a mixture of the present active component and an antibiotic), or may be in seriatim.
Accordingly, in specific embodiment, the therapeutic compositions may further include an effective amount of the active component, and one or more of the following active ingredients: an antibiotic, a steroid, etc. Exemplary formulations are given below:
Formulations Intravenous Formulation I
Ingredient mg/ml cefotaxime 250.0
Polypeptide 10.0 dextrose USP 45.0 sodium bisulfite USP 3.2 edetate disodium USP 0.1 water for injection q.s.a.d. 1.0 ml
Intravenous Formulation II
Ingredient mg/ml ampicillin 250.0
Polypeptide 10.0 sodium bisulfite USP 3.2 disodium edetate USP 0.1 water for injection q.s.a.d. 1.0 ml
Intravenous Formulation III
Ingredient mg/ml gentamicin (charged as sulfate) 40.0 Polypeptide 10.0 sodium bisulfite USP 3.2 disodium edetate USP 0.1 water for injection q.s.a.d. 1.0 ml
Intravenous Formulation IN
Ingredient mg/ml
Polypeptide 10.0 dextrose USP 45.0 sodium bisulfite USP 3.2 edetate disodium USP 0.1 water for injection q.s.a.d. 1.0 ml Intravenous Formulation V
Ingredient mg/ml
Polypeptide antagonist 5.0 sodium bisulfite USP 3.2 disodium edetate USP 0.1 water for injection q.s.a.d. 1.0 ml
Thus, in a specific instance where it is desired to reduce or inhibit the infection resulting from a bacterium mediated binding of bacteria to a host cell, or an antibody thereto, or a ligand thereof or an antibody to that ligand, the polypeptide is introduced to block the interaction of the bacteria with the host cell.
Also contemplated herein is pulmonary delivery of an inhibitor of the polypeptide of the present invention having which acts as adhesin inhibitory agent (or derivatives thereof). The adhesin inhibitory agent (or derivative) is delivered to the lungs of a mammal, where it can interfere with bacterial, i.e., streptococcal, and preferably pneumococcal binding to host cells. Other reports of preparation of proteins for pulmonary delivery are found in the art [Adjei et α/.(1990) Pharmaceutical Research, 7:565-569; Adjei et α/.(1990) InternationalJournal of Pharmaceutics, 63: 135-144 (leuprolide acetate); Braquet et al (1989), Journal of Cardiovascular Pharmacology, 13(suppl 5): 143-146 (endothelin-1); Hubbard et al. (1989) Annals of Internal Medicine, Vol. m, pp. 206-212 (αl-antitrypsin); Smith et /.(1989) J. Clin. Invest. 84:1145-1146 (α-1-proteinase); Oswein et al, "Aerosoli-zation of Proteins", Proceedings of Symposium on Respiratory Drug Delivery II, Keystone, Colorado, March, (1990) (recombinant human growth hormone); Debs et /.(1988) J. Immunol. 140:3482-3488 (interferon-γ and tumor necrosis factor alpha); Platz et al, U.S. Patent No. 5,284,656 (granulocyte colony stimulating factor)]. A method and composition for pulmonary delivery of drugs is described in U.S. Patent No. 5,451,569, issued September 19, 1995 to Wong et al.
All such devices require the use of formulations suitable for the dispensing of adhesin inhibitory agent (or derivative). Typically, each formulation is specific to the type of device employed and may involve the use of an appropriate propellant material, in addition to the usual diluents, adjuvant and/or carriers useful in therapy. Also, the use of liposomes, microcapsules or microspheres, inclusion complexes, or other types of carriers is contemplated. Chemically modified adhesin inhibitory agent may also be prepared in different formulations depending on the type of chemical modification or the type of device employed.
Formulations suitable for use with a nebulizer, either jet or ultrasonic, will typically comprise adhesin inhibitory agent (or derivative) dissolved in water at a concentration of about 0.1 to 25 mg of biologically active adhesin inhibitory agent per ml of solution. The formulation may also include a buffer and a simple sugar (e.g., for adhesin inhibitory agent stabilization and regulation of osmotic pressure). The nebulizer formulation may also contain a surfactant, to reduce or prevent surface induced aggregation of the adhesin inhibitory agent caused by atomization of the solution in forming the aerosol.
Formulations for use with a metered-dose inhaler device will generally comprise a finely divided powder containing the adhesin inhibitory agent (or derivative) suspended in a propellant with the aid of a surfactant. The propellant may be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon, or a hydrocarbon, including trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof. Suitable surfactants include sorbitan trioleate and soya lecithin. Oleic acid may also be useful as a surfactant.
The liquid aerosol formulations contain adhesin inhibitory agent and a dispersing agent in a physiologically acceptable diluent. The dry powder aerosol formulations of the present invention consist of a finely divided solid form of adhesin inhibitory agent and a dispersing agent. With either the liquid or dry powder aerosol formulation, the formulation must be aerosolized. That is, it must be broken down into liquid or solid particles in order to ensure that the aerosolized dose actually reaches the mucous membranes of the nasal passages or the lung. The term "aerosol particle" is used herein to describe the liquid or solid particle suitable for nasal or pulmonary administration, i.e., that will reach the mucous membranes. Other considerations, such as construction of the delivery device, additional components in the formulation, and particle characteristics are important. These aspects of pulmonary administration of a drug are well known in the art, and manipulation of formulations, aerosolization means and construction of a delivery device require at most routine experimentation by one of ordinary skill in the art. In a particular embodiment, the mass median dynamic diameter will be 5 micrometers or less in order to ensure that the drug particles reach the lung alveoli [Wearley, L.L. (1991) Crit. Rev. in Ther. Drug Carrier Systems 8:333].
Systems of aerosol delivery, such as the pressurized metered dose inhaler and the dry powder inhaler are disclosed in Newman, S.P., Aerosols and the Lung, Clarke, S.W. and Davia, D. editors, pp. 197-22 and can be used in connection with the present invention.
In a further embodiment, as discussed in detail infra, an aerosol formulation of the present invention can include other therapeutically or pharmacologically active ingredients in addition to adhesin inhibitory agent, such as but not limited to an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
Liquid Aerosol Formulations. The present invention provides aerosol formulations and dosage forms for use in treating subjects suffering from bacterial, e.g., streptococcal, in particularly pneumococcal, infection. In general such dosage forms contain adhesin inhibitory agent in a pharmaceutically acceptable diluent. Pharmaceutically acceptable diluents include but are not limited to sterile water, saline, buffered saline, dextrose solution, and the like. In a specific embodiment, a diluent that may be used in the present invention or the pharmaceutical formulation of the present invention is phosphate buffered saline, or a buffered saline solution generally between the pH 7.0-8.0 range, or water.
The liquid aerosol formulation of the present invention may include, as optional ingredients, pharmaceutically acceptable carriers, diluents, solubilizing or emulsifying agents, surfactants and excipients. The formulation may include a carrier. The carrier is a macromolecule which is soluble in the circulatory system and which is physiologically acceptable where physiological acceptance means that those of skill in the art would accept injection of said carrier into a patient as part of a therapeutic regime. The carrier preferably is relatively stable in the circulatory system with an acceptable plasma half life for clearance. Such macromolecules include but are not limited to Soya lecithin, oleic acid and sorbitan trioleate, with sorbitan trioleate preferred.
The formulations of the present embodiment may also include other agents useful for pH maintenance, solution stabilization, or for the regulation of osmotic pressure. Examples of the agents include but are not limited to salts, such as sodium chloride, or potassium chloride, and carbohydrates, such as glucose, galactose or mannose, and the like.
The present invention further contemplates liquid aerosol formulations comprising adhesin inhibitory agent and another therapeutically effective drug, such as an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
Aerosol Dry Powder Formulations. It is also contemplated that the present aerosol formulation can be prepared as a dry powder formulation comprising a finely divided powder form of adhesin inhibitory agent and a dispersant.
Formulations for dispensing from a powder inhaler device will comprise a finely divided dry powder containing adhesin inhibitory agent (or derivative) and may also include a bulking agent, such as lactose, sorbitol, sucrose, or mannitol in amounts which facilitate dispersal of the powder from the device, e.g., 50 to 90% by weight of the formulation. The adhesin inhibitory agent (or derivative) should most advantageously be prepared in particulate form with an average particle size of less than 10 mm (or microns), most preferably 0.5 to 5 mm, for most effective delivery to the distal lung. In another embodiment, the dry powder formulation can comprise a finely divided dry powder containing adhesin inhibitory agent, a dispersing agent and also a bulking agent. Bulking agents useful in conjunction with the present formulation include such agents as lactose, sorbitol, sucrose, or mannitol, in amounts that facilitate the dispersal of the powder from the device.
The present invention further contemplates dry powder formulations comprising adhesin inhibitory agent and another therapeutically effective drug, such as an antibiotic, a steroid, a non-steroidal anti-inflammatory drug, etc.
Contemplated for use herein are oral solid dosage forms, which are described generally in Remington's Pharmaceutical Sciences, 18th Ed.1990 (Mack Publishing Co. Easton PA 18042) at Chapter 89, which is herein incorporated by reference. Solid dosage forms include tablets, capsules, pills, troches or lozenges, cachets or pellets. Also, liposomal or proteinoid encapsulation may be used to formulate the present compositions (as, for example, proteinoid microspheres reported in U.S. Patent No. 4,925,673). Liposomal encapsulation may be used and the liposomes may be derivatized with various polymers (e.g., U.S. Patent No. 5,013,556). A description of possible solid dosage forms for the therapeutic is given by Marshall, K. In: Modern Pharmaceutics Edited by G.S. Banker and CT. Rhodes Chapter 10, 1979, herein incorporated by reference. In general, the formulation will include the component or components (or chemically modified forms thereof) and inert ingredients which allow for protection against the stomach environment, and release of the biologically active material in the intestine.
Also specifically contemplated are oral dosage forms of the above derivatized component or components. The component or components may be chemically modified so that oral delivery of the derivative is efficacious. Generally, the chemical modification contemplated is the attachment of at least one moiety to the component molecule itself, where said moiety permits (a) inhibition of proteolysis; and (b) uptake into the blood stream from the stomach or intestine. Also desired is the increase in overall stability of the component or components and increase in circulation time in the body. Examples of such moieties include: polyethylene glycol, copolymers of ethylene glycol and propylene glycol, carboxymethyl cellulose, dextran, poiyvinyl alcohol, poiyvinyl pyrrolidone and polyproline. Abuchowski and Davis, 1981, "Soluble Polymer-Enzyme Abducts" In: Enzymes as Drugs, Hocenberg and Roberts, eds., Wiley-Interscience, New York, NY, pp. 367-383; Newmark, etal. (1982) J. Appl. Biochem. 4: 185-189. Other polymers that could be used are poly-1, 3 -dioxolane and poly-1, 3, 6-tioxocane. Preferred for pharmaceutical usage, as indicated above, are polyethylene glycol moieties.
For the component (or derivative) the location of release may be the stomach, the small intestine (the duodenum, the jejunem, or the ileum), or the large intestine. One skilled in the art has available formulations which will not dissolve in the stomach, yet will release the material in the duodenum or elsewhere in the intestine. Preferably, the release will avoid the deleterious effects of the stomach environment, either by protection of the protein (or derivative) or by release of the biologically active material beyond the stomach environment, such as in the intestine.
To ensure full gastric resistance a coating impermeable to at least pH 5.0 is essential. Examples of the more common inert ingredients that are used as enteric coatings are cellulose acetate trimellitate (CAT), hydroxypropylmethylcellulose phthalate (HPMCP), HPMCP 50, HPMCP 55, poiyvinyl acetate phthalate (PVAP), Eudragit L30D, Aquateric, cellulose acetate phthalate (CAP), Eudragit L, Eudragit S, and Shellac. These coatings may be used as mixed films.
A coating or mixture of coatings can also be used on tablets, which are not intended for protection against the stomach. This can include sugar coatings, or coatings which make the tablet easier to swallow. Capsules may consist of a hard shell (such as gelatin) for delivery of dry therapeutic i.e. powder; for liquid forms, a soft gelatin shell may be used. The shell material of cachets could be thick starch or other edible paper. For pills, lozenges, molded tablets or tablet triturates, moist massing techniques can be used.
The peptide therapeutic can be included in the formulation as fine multiparticulates in the form of granules or pellets of particle size about 1mm. The formulation of the material for capsule administration could also be as a powder, lightly compressed plugs or even as tablets. The therapeutic could be prepared by compression. Colorants and flavoring agents may all be included. For example, the protein (or derivative) may be formulated (such as by liposome or microsphere encapsulation) and then further contained within an edible product, such as a refrigerated beverage containing colorants and flavoring agents.
One may dilute or increase the volume of the therapeutic with an inert material. These diluents could include carbohydrates, especially mannitol, a-lactose, anhydrous lactose, cellulose, sucrose, modified dextran and starch. Certain inorganic salts may be also be used as fillers including calcium triphosphate, magnesium carbonate and sodium chloride. Some commercially available diluents are Fast-Flo, Emdex, STA-Rx 1500, Emcompress and Avicell
Disintegrants may be included in the formulation of the therapeutic into a solid dosage form. Materials used as disintegrates include but are not limited to starch, including the commercial disintegrant based on starch, Explotab. Sodium starch glycolate, Amberlite, sodium carboxymethylcellulose, ultramylopectin, sodium alginate, gelatin, orange peel, acid carboxymethyl cellulose, natural sponge and bentonite may all be used. Another form of the disintegrants are the insoluble cationic exchange resins. Powdered gums may be used as disintegrants and as binders and these can include powdered gums such as agar, Karaya or tragacanth. Alginic acid and its sodium salt are also useful as disintegrants. Binders may be used to hold the therapeutic agent together to form a hard tablet and include materials from natural products such as acacia, tragacanth, starch and gelatin. Others include methyl cellulose (MC), ethyl cellulose (EC) and carboxymethyl cellulose (CMC). Poiyvinyl pyrrolidone (PVP) and hydroxypropylmethyl cellulose (HPMC) could both be used in alcoholic solutions to granulate the therapeutic.
An antifrictional agent may be included in the formulation of the therapeutic to prevent sticking during the formulation process. Lubricants may be used as a layer between the therapeutic and the die wall, and these can include but are not limited to; stearic acid including its magnesium and calcium salts, polytetrafluoroethylene (PTFE), liquid paraffin, vegetable oils and waxes. Soluble lubricants may also be used such as sodium lauryl sulfate, magnesium lauryl sulfate, polyethylene glycol of various molecular weights, Carbowax 4000 and 6000.
Glidants that might improve the flow properties of the drug during formulation and to aid rearrangement during compression might be added. The glidants may include starch, talc, pyrogenic silica and hydrated silicoaluminate.
To aid dissolution of the therapeutic into the aqueous environment a surfactant might be added as a wetting agent. Surfactants may include anionic detergents such as sodium lauryl sulfate, dioctyl sodium sulfosuccinate and dioctyl sodium sulfonate. Cationic detergents might be used and could include benzalkonium chloride or benzethomium chloride. The list of potential nonionic detergents that could be included in the formulation as surfactants are lauromacrogol 400, polyoxyl 40 stearate, polyoxyethylene hydrogenated castor oil 10, 50 and 60, glycerol monostearate, polysorbate 40, 60, 65 and 80, sucrose fatty acid ester, methyl cellulose and carboxymethyl cellulose. These surfactants could be present in the formulation of the protein or derivative either alone or as a mixture in different ratios.
Additives which potentially enhance uptake of the polypeptide (or derivative) are for instance the fatty acids oleic acid, linoleic acid and linolenic acid.
Pulmonary Delivery. Also contemplated herein is pulmonary delivery of the present polypeptide (or derivatives thereof). The polypeptide (or derivative) is delivered to the lungs of a mammal while inhaling and coats the mucosal surface of the alveoli. Other reports of this include Adjei et al. (1990) Pharmaceutical Research 7:565-569; Adjei et al. (1990) International Journal of Pharmaceutics 63: 135-144 (leuprolide acetate); Braquet et α/.(1989) Journal of Cardiovascular Pharmacology, 13(suppl 5):143-146 (endothelin-1); Hubbard etal. (1989) Annals of Internal Medicine, Nol. in, pp. 206-212 (al- antitrypsin); Smith et al. (1989) J. Clin. Invest. 84:1145-1146 (a-1-proteinase); Oswein et al. (1990) "Aerosolization of Proteins", Proceedings of Symposium on Respiratory Drug Delivery II, Keystone, Colorado, March, (recombinant human growth hormone); Debs et al (1988) J. Immunol. 140:3482-3488 (interferon-g and tumor necrosis factor alpha) and Platz et al., U.S. Patent No. 5,284,656 (granulocyte colony stimulating factor). A method and composition for pulmonary delivery of drugs for systemic effect is described in U.S. Patent No. 5,451,569, issued September 19, 1995 to Wong et al.
Contemplated for use in the practice of this invention are a wide range of mechanical devices designed for pulmonary delivery of therapeutic products, including but not limited to nebulizers, metered dose inhalers, and powder inhalers, all of which are familiar to those skilled in the art.
Formulations suitable for use with a nebulizer, either jet or ultrasonic, will typically comprise polypeptide (or derivative) dissolved in water at a concentration of about 0.1 to 25 mg of biologically active protein per mL of solution. The formulation may also include a buffer and a simple sugar (e.g., for protein stabilization and regulation of osmotic pressure). The nebulizer formulation may also contain a surfactant, to reduce or prevent surface induced aggregation of the protein caused by atomization of the solution in forming the aerosol.
Formulations for use with a metered-dose inhaler device will generally comprise a finely divided powder containing the polypeptide (or derivative) suspended in a propellant with the aid of a surfactant. The propellant may be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon, or a hydrocarbon, including trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof. Suitable surfactants include sorbitan trioleate and soya lecithin. Oleic acid may also be useful as a surfactant.
Formulations for dispensing from a powder inhaler device will comprise a finely divided dry powder containing polypeptide (or derivative) and may also include a bulking agent, such as lactose, sorbitol, sucrose, or mannitol in amounts which facilitate dispersal of the powder from the device, e.g., 50 to 90% by weight of the formulation. The protein (or derivative) should most advantageously be prepared in particulate form with an average particle size of less than 10 mm (or microns), most preferably 0.5 to 5 mm, for most effective delivery to the distal lung.
Nasal Delivery. Nasal or nasopharyngeal delivery of the polypeptide (or derivative) is also contemplated. Nasal delivery allows the passage of the polypeptide directly over the upper respiratory tract mucosal after administering the therapeutic product to the nose, without the necessity for deposition of the product in the lung. Formulations for nasal delivery include those with dextran or cyclodextran.
The invention may be better understood by reference to the following non-limiting Examples, which are provided as exemplary of the invention. The following examples are presented in order to more fully illustrate the preferred embodiments of the invention and should in no way be construed, however, as limiting the broad scope of the invention.
EXAMPLE 1
IDENTIFICATION AND CHARACTERIZATION OF CHOLINE BINDING PROTEINS
We have used the C-terminal 180 amino acids of CbpA (the choline binding domain), shown in FIGURE 1 (SEQ ID NO: 1 ) to search the pneumococcal genome to identify new members of the choline binding family of proteins. The pneumococcal database is publicly available at www.tigr.org/tdb/mdb/mdb.html and through the National Center for Biotechnology Information (at www.nih.ncbi.org). The pneumococcal database is selected and searched by the following steps: (1) select "BLAST"; (2) under "Specialized Blast Pages", select "Unfinished Microbial Genomes"; (3) then click to choose individual genomes to search; and (4) under "Eubacteria" select "Streptococcus pneumoniae" . A search of this public database using the search engine BLAST available at www.nih.ncbi.org, with the filter and other parameters set at default, using SEQ ID NO: 1 will yield the polypeptides and nucleic acids now identified in the present invention. The search identifies eight contigs which contain nine encoded choline binding polypeptides, which are unique and distinct from the recognized pneumococcal choline binding proteins PspA, LytA and CbpA, and are designated CbpB, CbpC, CbpD, CbE, CbpF, CbpG, CbpH, Cbpl and CbpJ. One contig encodes two Cbps, specifically CbpF and CbpG or CbpD, and required further visual analysis of the layout of the homologous choline binding domains to identify and distinguish the two unique Cbps. The amino acid and nucleic acid sequences of choline binding protein CbpG is found in FIGURE 2, corresponding to SEQ ID NO: 2 (amino acid) and SEQ ID NO: 3 (nucleic acid).
CHARACTERIZATION OF CbpG
CbpG is the smallest of the choline binding proteins with an open reading frame (ORF) that is 462 nucleotides long. The CbpG gene has a 35%) GC content which is consistent with the 38.5%) GC content of pneumococcus. It is located upstream of the gene for
CbpF and may be cotranscribed with CpbF. The DNA sequence for both CbpG and
CbpF is shown in FIGURE 2A-C (SEQ ID NO:4). The amino acid sequence of the
CbpG polypeptide is shown in FIGURE 2 and FIGURE 3 (SEQ ID NO:2). The nucleic acid sequence of CbpG including upstream promoter sequence is presented in FIGURE
3 (SEQ ID NO: 10). Analysis of sequences directly upstream of CbpG indicate the presence of a putative E. coli like promoter with a consensus -10 (TAT AAT) and a -35 containing two mismatches (GTGACT). There are only 35 nucleotides between the end of the CbpG ORF and the start codon for CbpF. Sequence analysis failed to reveal a promoter in this intervening region. Therefore, CbpG and CbpF are likely cotranscribed from the promoter in front of CbpG.
The CbpG gene encodes a peptide of 154 amino acids with a predicted size of 17kDa.
The protein has two domains: (i) an N-terminal domain (amino acids 1 to 93) with a high level of homology to a 50 amino acid region of the Enterococcus faecalis serine proteinase and (ii) a C-terminal domain which, like all other choline binding proteins, contains the 20 amino acid repeats required for choline binding. CbpG has 2 such repeats. There were no other significant similarities to proteins in the current databases.
Functional analysis of CbpG
cbpG loss of function mutants were constructed by insertion duplication mutagenesis. An internal 220bp fragment at the N-terminus of CbpG was amplified from Type 4 chromosomal DNA using primers 939E (5' TTC TTG aAT TcC CAA GTT GAT ACT vTT (SEQ ID NO:5)) and 939B (5' ATA ATG Gat CCA ACT ACC ATT TAT TTT C (SEQIDNO: 6)). The PCR product was digested with EcoRI and BamHI and cloned into pJDC9 and transformed into DH5α E.coli. Insert was verified by size and restriction analysis and the plasmid was then transformed into S. pneumoniae wild type 4, selecting for erythromycin resistance. Such colonies were isolated and the position of the insert in the cbpG gene was verified by PCR.
The cbpG defective mutant was then assesssed for it's ability to colonize the infant rat nasopharynx, to adhere to Detroit cells as well as to immobilized carbohydrates LNnT and sialylactose, transformation, lysis in response to detergent (DOC) and pencillin sensitivity. All of these properties have been shown to be important in pneumococcal physiology.
The ability to colonize the nasopharynx of 1 to 5 day old Sprague-Dawley rat pups was determined as described previously (Wieser JN et al (1994) Infect Immun 62(6): 2582- 2589). For each experiment 8 to 10 rat pups were inoculated intranasally with 2.5-8 x 103 cfu of the cδpG-deficient mutant or the isogenic Type 4 in PBS. Colonization was assessed 48 and 96hrs post inoculation. The results of these experiments are presented in Table 1. In four independent experiments, the cbpG defective mutant showed decreased colonization ranging from 9-35 % of wild type 4. These data indicate that the cέpG-deficient mutant has an approximately 3-10 fold reduced ability to colonize the rat nasopharynx. The effect of the CbpG knockout mutant on colonization of infant rat nasopharynx at 48 hrs is presented graphically in FIGURE 5.
TABLE 1 Effect of CbpG deletion on intranasal virulence
Figure imgf000068_0001
* = P value **= % of wild type nd = not done
We have tested the ability of this mutant to adhere to human Detroit cells, and to carbohydrates in vitro. The in vitro adhesion experiments were done as previously described (Cundell D.R. et al (1995) Infect Immun 63(3):757-761) and the data shown in Table 2 indicate that there is a 40%> reduction in adhesion to Detroit human nasopharyngeal cell line by the C >/?G-deficient mutant and a 80-90%) reduction in adhesion to both lacto-N-neotrose (LNnT) and sialylactose in vitro. These data along with the in vivo colonization data suggest that CbpG plays a role in adherence to cells of the nasopharynx and that the binding may occur through sugars on the eukaryotic cells. TABLE 2
Adherence of CbpG Mutant to Various Substrates
Figure imgf000069_0001
Substrate Key
TyR =► Parent S. pneumoniae strain Type 4 Rough
3' Sialyl Lactose-HSA - 3' SL
6' Sialyl Lactose-HSA - 6' SL
Lacto N-neotetraose-HSA =» LNnT
Detroit 562 Nasopharyngeal Cell Line -» Detroit
The effect of the cbpG mutant on the adhesion characteristics of Type 4R mutants on Detroit Nasopharyngeal Human Cells is graphically presented in FIGURE 6. To rule out an activity of CbpG similar to the choline binding protein LytA, the response of the CbpG-deficient mutant (cbpG) to penicillin was determined. There were no differences between the CbpG-deficient mutant and it's isogenic parental strain Type 4 in autolysin dependent lysis in response to the detergent DOC or penicillin or in efficiency of genetic transformation.
Cloning and purification of CBPG
The coding sequence of cbpG was amplified using primers to sequences immediately downstream of the AUG start codon, CbpGpura (5 ' CGC GGA TCC GCG TAT ACA GAT AAG AAA CAA G) (SEQIDNO:7) and sequences overlapping the TAA termination codon, CbpGpurb (5'TCC CCC GGG GAA CAT TAA ATC CAC TCA (SEQIDNO: 8)). These primers amplify out the entire CbpG coding sequence with the exception of the start codon and introduce a BamHI site at the N-terminus of the gene and a Smal site at the C-terminus of the gene. The PCR product was then digested with BamHI and Smal and cloned into a pQE30 His-tag expression vector from Qiagen and transformed into E.coli strain Ml 5. This results in an in frame fusion of the N-terminus of the CbpG gene with the 6XHis tag of the plasmid. The protein is then purified using a Nickel column following the Qiagen protocol.
100 ml of culture of E.coli containing the CbpG expressing plasmid was grown to OD620 of 0.7-0.9 and induced with 1.5mM IPTG. The bacterial pellet was lysed overnight in 20 ml of lysis buffer (6M GuHCl, 0.1M NaH2PO4, 0.01M Tris-Cl, pH8). Sample was centrifuged at 10,000g for 20 minutes at 4 degrees and the supernatant was collected and filtered through a .45 micron filter. 1.5 ml of the NINTA resin was added per 10 ml of sample and mixed gently at room temperature for 1 hr. The mixture was transferred to a small column and washed with 25-30 ml of washing buffer (8M Urea, 0.1M NaH2PO4, 0.01M Tris-Cl, 20 mM imidazole, pH8). Column was eluted with four 500 μl fractions of elution buffer (8M Urea, 0.1M NaH2PO4, 0.01M Tris-Cl, 200 nN imidazole pH8). This procedure resulted in relatively pure protein with minor contaminating bands. This preparation was further separated on a 10%> acrylamide gel and a band migrating at 20 kDa, slightly larger than the predicted 17kDa, was excised and utilized for antibody production in rabbits (Covance Inc). Polyclonal antibodies against the protein recognize the recombinant protein (FIGURE 4). These antibodies do not react well with the native CbpG protein in a choline binding protein preparation derived from Type 4. The recombinant protein and the native 17kD protein from pneumococcus eluted with 10% choline do not react with the antibody described by Rosenow et al. (Rosenow, C. et al. (1997) MolMicrobiol 25:819-829).
Construction of CbpG N-terminal Truncate
The N-terminus of CbpG was amplified from T4 chromosomal DNA by PCR using oligos B939f2 (5'-CGCGGATCCTATACAGATAAGAAACAAGTTTTAAGT) (SEQ ID NO:13) and B939r2 (5'-CGCGGTACCATGTTGTCTATAATGGTACCAACTACC) SEQ ID NO: 14). The amplified fragment consisted of CbpG amino acids 1-90, deleting the C-terminal choline binding domain, and thus generating an N-terminal CbpG truncate. The amino acid sequence (SEQ ID NO: 11) and nucleic acid sequence (SEQ ID NO: 12) of the N-terminal truncate of CbpG (amino acids 1-90) is depicted in FIGURE 8. The oligos used introduced a BamHI site to the N-terminus of the gene and a Kpnl site to the C-teπninus. The PCR product was then digested with Bam HI and Kpnl. The digested fragment was ligated into a Qiagen pQE-30 6-His tag expression vector and transformed into competent Ml 5 E. Coli cells. Clones were screened by restriciton enzyme digestion with BamHI and Kpnl. The clones positive for the CbpG truncted insert were sequenced to confirm an in-frame fusion between the His-tag and CbpG truncate coding region.
A 50ml culture of pQE939nt was grown in lxLB/Amp/Kan to an OD600 of 0.7. The culture was induced with 1.5mM IPTG and grown for an additional 2 hours. The induced cells were harvested by centrifugation and lysed under native and denatured conditions in order to determine protein expression and solubility. A 15% Tris-HCl gel showed that the 13.2kDa protein was soluble (FIGURE 9A). The protein was purified under denatured conditions with 8M Urea using the His tag over a nickel column. The resulting purified CbpG truncate protein was run on a 15% Tris-HCl gel Figure 9b, the bands excised, and utilized for antibody production in rabbits (Covance Inc.).
Antibodies Raised Against CbpG are Protective
The polyclonal antibody raised against CbpG (described above) was used in experiments to test its ability to protect against challenge by S. pneumoniae in in vivo models of bacterial nose colonization and sepsis as described below in Materials and Methods. The anti-CbpG antibody did not provide protection in a nose colonization test. In the sepsis model, in one experiment, at 24 hours, 6 of 9 animals injected with anti-CbpG antibody were dead versus 8 of 9 animals injected with pre-immune serum. In a second experiment, at 24 hours, 7 of 12 animals injected with anti-CbpG antibody were dead versus 9 of 12 animals injected with pre-immune serum. As noted above, the polyclonal antibodies against CbpG recognize the recombinant protein but do not react well with the native CbpG protein.
FIGURE 7 presents a tabulation of the overall results of the experiments characterizing CbpG.
EXAMPLE 2
IDENTIFICATION AND CHARACTERIZATION OF CHOLINE BINDING PROTEINS
We have used the C-terminal 180 amino acids of CbpA (the choline binding domain), (amino acids 514 to 694 of S. pneumoniae type 4 strain), shown in FIGURE 1 (SEQ ID NOT ) to search the pneumococcal genome to identify new members of the choline binding family of proteins. The pneumococcal database is publicly available at www.tigr.org/tdb/mdb/mdb.html and through the National Center for Biotechnology Information (at www.nih.ncbi.org). The pneumococcal database is selected and searched by the following steps: (1) select "BLAST"; (2) under "Specialized Blast Pages", select "Unfinished Microbial Genomes"; (3) then click to choose individual genomes to search; and (4) under "Eubacteria" select "Streptococcus pneumoniae". A search of this public database using the search engine BLAST available at www.nih.ncbi.org, with the filter and other parameters set at default, using SEQ ID NO: 1 will yield the polypeptides and nucleic acids now identified in the present invention. The search identified eight contigs which contained nine encoded choline binding polypeptides, which are unique and distinct from the recognized pneumococcal choline binding proteins PspA, LytA and CbpA, and are designated CbpB, CbpC, CbpD, CbpE, CbpF, CbpD, CbpH, Cbpl and CbpJ. The Cbp genes range in size from 390 bp to 2034 bp and encode proteins of approximately 20-80 KDa. The proteins have between 2 and 10 choline binding repeats in their C- terminal region. The amino acid and nucleic acid sequences of choline binding protein CbpD is found in FIGURE 10, corresponding to SEQ ID NO: 15 (amino acid) and SEQ ID NO: 16 (nucleic acid).
CHARACTERIZATION OF CbpD
The CbpD open reading frame (ORF) is 1347 nucleotides long and encodes a predicted protein of 449 amino acids. The amino acid (SEQ ID NO: 15) and nucleic acid (SEQ ID NO: 16) sequence of the CbpD polypeptide is shown in FIGURE 10.
The CbpD gene encodes a peptide of 449 amino acids with a predicted size of approximately 50kDa. The protein has two domains: (i) an N-terminal domain and (ii) a C-terminal domain which, like all other choline binding proteins, contains the 20 amino acid repeats required for choline binding. CbpD has four such repeats. There were no other significant similarities to proteins in the current databases.
Functional analysis of CbpD cbpD loss of function mutants were constructed by insertion duplication mutagenesis. An internal fragment at the N-terminus of CbpD (amino acids 262-379) was amplified from Type 4 chromosomal DNA using primers 5' primer (ggaattcgatc TTTCTTCAACA GGTGGAACT) (SEQ ID NO: 17) and 3' primer (ggaattcgatcAGCTAGAACC GTCTTTCAG) (SEQ ID NO: 18). (Lower case letters indicate added linkers used for cloning.) The PCR product was digested with EcoRI and cloned into pJDC9 and transformed into DH5α E.coli. Insert was verified by size and restriction analysis and the plasmid was then transformed into S. pneumoniae wild type 4, selecting for erythromycin resistance. Such colonies were isolated and the position of the insert in the CbpD gene was verified by PCR.
The CbpD defective mutant was then assesssed for it's ability to colonize the infant rat nasopharynx, to adhere to Detroit cells as well as to immobilized carbohydrates LNnT and sialylactose, transformation, lysis in response to detergent (DOC) and pencillin sensitivity. All of these properties have been shown to be important in pneumococcal physiology. There was no difference between the parent strain and the CbpD deficient mutant in efficiency of genetic transformation, lysis in stationary phase or lysis in response to penicillin.
The ability to colonize the nasopharynx of 1 to 5 day old Sprague-Dawley rat pups was determined as described previously (Wieser JN et al (1994) Infect Immun 62(6): 2582- 2589). For each experiment 8 to 10 rat pups were inoculated intranasally with 2.5-8 x 103 cfu of the C6/7E>-deficient mutant or the isogenic Type 4 in PBS. Colonization was assessed 48 and 96 hrs post inoculation. The CbpD deflective mutant showed a two fold reduction in colonization after 48 hours. The number of bacteria in the nasal wash increased between 48 and 96 hours but remained significantly below wild type. The effect of the CbpD knockout mutant on colonization of infant rat nasopharynx at 48 hrs is presented graphically in FIGURE 11.
We have tested the ability of this mutant to adhere to carbohydrates in vitro. The in vitro adhesion experiments were done as previously described (Cundell D.R. et al (1995) Infect Immun 63(3):757-761) and the data shown in FIGURE 12 indicate that there is no significant affect on adherence to Detroit cells in vitro in the CbpD mutant.
To rule out an activity of CbpD similar to the choline binding protein LytA, the response of the CbpD-deficient mutant (cbpD) to penicillin was determined. There were no differences between the CbpD-deficient mutant and it's isogenic parental strain Type 4 in autolysin dependent lysis in response to the detergent DOC or penicillin or in efficiency of genetic transformation.
Cloning and purification of CbpD
The coding sequence of CbpD was amplified using primers to sequences immediately downstream of the AUG start codon, N-terminal Primer (5' cgaagatcttcgAAAA TTTTACCGTTTATAGCA3' ) (SEQ ID NO: 19) and sequences overlapping the termination codon , C-terminal Primer (5' tcccccgggggaTGTCAAGGAAA CTGCTTACA3' ) (SEQ ID NO:20) (Lower case letters indicate added linkers used for cloning). These primers amplify out the entire CbpD coding sequence with the exception of the start codon and introduce a BamHI site at the N-terminus of the gene and a Smal site at the C-terminus of the gene. The PCR product was then digested with BamHI and Smal and cloned into a pQE30 His-tag expression vector from Qiagen and transformed into E.coli strain Ml 5. This results in an in frame fusion of the N-terminus of the CbpD gene with the 6XHis tag of the plasmid. The protein can then be purified using a Nickel column following the Qiagen protocol. Overexpression of CbpD proved lethal to E.coli.
Virulence of CbpD deficient strain in an infant rat sepsis model
The CbpD deficient mutant was also tested in an animal model for pneumoccal-induced sepsis. Most infant rats injected with the parental strain died within 16-24 hours and all were dead by 48 hours. Rats injected with the CbpD deficient strain exhibited less than 50% mortality in the first 16-24 hours, but survival at the 48 hour time point was not significantly different fromt the parental strain. The results of this experiment are depicted in TABLE 3. Thus, CbpD is directly implicated in pneumoccal virulence in sepsis.
TABLE 3
Virulence of CbpD deficient strain in an infant rat sepsis model Experiment 1 Experiment 2 Experiment 3
Strain 16 hrs 48 hrs 24 hrs 48 hrs 24 hrs 48 hrs
Type 4 1/10 0/10 1/9 0/9 4/12 2/12 cbpD 10/10 2/10 5/9 3/9 9/12 4/12
Results are expressed as the number of surviving animals over the number of animals injected.
Construction of CbpD N-terminal Truncate
Two fragments of the CbpD N-terminus were amplified from T4 chromosomal DNA by PCR using oligos 568F2 (5'- CGCGGATCCAAAATTTTACCGTTTATAGCAAGAGG-3') (SEQ IDNO:25) and 568KpnR3 (5'-GCGCGCGGTACCGTCGGTGTATTATC-3 ') (SEQ ID NO:26) for the first fragment, and oligos 568BamF3 (5'-
GCGCGCGGATCCCATCGTGCTCGG-3') (SEQ ID NO:27) and 568R2 (5'- CGCGGTACCTTCAGTTTTGATAGCAGACTTGGTCTT-3') (SEQ ID NO:28) for the second fragment. The first amplified fragment consisted of CbpD amino acids 2-116 while the second amplified fragment consisted of CbpD amino acids 103-280 deleting the C-terminal choline binding domain, and thus generating two N-terminal CbpD truncates. The amino acid sequence (SEQ ID NO:21) and the nucleic acid sequence (SEQ ID NO:22) of fragment 1 (CbpD amino acids 2-116), and the amino acid sequence (SEQ ID NO: 23) and the nucleic acid sequence (SEQ ID NO: 24) of fragment 2 (CbpD amino acids 103-280) are depicted in FIGURE 14. Both sets of oligos introduced a BamHI site to the N-terminus of the gene and a Kpnl site to the C-teπninus. Both PCR products were then digested with BamHI and Kpnl. The digested fragments were ligated into a Qiagen pQE-30 6-His tag expression vector and transformed into competent Ml 5 E.coli cells. Clones were screened by restriction enzyme digestion with BamHI and Kpnl. The clones positive for CbpD truncate insert 1 and for CbpD truncate insert 2 were sequenced to confirm an in-frame fusion between the His-tag and the CbpD truncated region. 50ml cultures of pQECbpDl and pQECbpD2 (containing fragments 1 and 2, respectively) were grown in IxLB/Amp/Kan to an OD600 of 0.7. The cultures were induced with 1.5mM IPTG and grown for an additional 2 hours. The induced cells were harvested by centrifugation and lysed under native and denatured conditions in order to determine protein expression and solubility.
MATERIALS AND METHODS
The following details the material and methods used in the above described experimental examples:
Strains of pneumococci and growth conditions
S. pneumoniae type 4 is a clinical isolate obtained from Medlmmune Inc. S. pneumoniae strain R6x (Tiraby et al (1973) Proc Natl Acad Sci USA 70:3541-3545) was obtained from the Rockefeller University collection. S. pneumoniae type 4R is an unencapsulated mutant of Type 4 which was constructed by insertion duplication mutagenesis of capsule genes of Type4. S. pneumoniae was plated on tryptic soy agar (TSA, Difco, Detroit, MI- USA) supplemented with sheep blood 3% (v/v). For growth in liquid culture, the bacteria were grown without aeration at 37°C in 5% CO2 in a semi-synthetic casein hydrolysate medium supplemented with yeast extract (C+Y medium, (Lacks, S and Hotchkiss, R.D. (1960) Biochem Biophys Acta 39:508-517). For the selection and maintenance of pneumococci containing chromosomally integrated plasmids, bacteria were grown in the presence of 1 μg/ml erythromycin (Sigma, St. Louis, MO, USA).
Recombinant DNA methods DNA ligations, restriction endonuclease digestion and gel electrophoresis were performed according to standard protocols (Sambrook, J., Fritsh, E.F. and Maniatis, T. eds. (1989) Molecular Cloning: A Laboratory Manual (Second Edition) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). DNA purification and plasmid preparations were performed with kits from Qiagen and Wizard according to the manufacturer's instructions. Plasmids were introduced into E. coli strains by chemical transformation. Transformation in S. pneumoniae was performed according to standard protocols (Pearce et al (1993) MolMicrobiol 9: 1037-1050).
Bacterial adhesion assay. The Detroit human nasopharyngeal cell line (American Type Culture Collection) was cultured in ATCC Vitacell Minimal Essential Eagle medium (ATCC Cat#30-2003) supplemented with Earles balanced salt solution, nonessential amino acids, lmM sodium pyruvate, 2mM L-glutamine and 1500 mg sodium bicarbonate. Cells were grown to confluence in Corning 100mm tissue culture dishes. At confluence, the cells were prepared for subculture with trypsin-0.05 % EDTA (Sigma), washed and resuspended in 5mls of the above media + 10%> FBS (Sigma). lOul of the resuspended cells were added to Terasaki wells (Robbins Scientific, Sunnyvale, CA) and allowed to grow until a confluent monolayer formed. Prior to the adherence assay, culture fluid was removed by washing the monolayers twice with tissue culture medium.
Bacteria at an OD620 of 0.4 or 0.6 were washed in 1 ml carbonate buffer (0.05 M sodium carbonate, 0.1 M sodium chloride), resuspended in the same buffer and labeled with FITC (Sigma; 1 mg ml"1) for 20 min in the dark at room temperature (LO). After 3 washes with carbonate buffer, the bacteria were resuspended in medium Ml 99 without antibiotics and 5 x 107 pneumococci were incubated per well for 30 min at 37°C in the presence of 5%> CO2. After the removal of unbound bacteria by washing the monolayers five times with Ml 99, the cells and bacteria were fixed in 2.5%) glutaraldehyde for 3 min and washed five times with PBS. Adherent pneumococci were counted visually with an inverted microscope (Diaphot-TDM; Nikon Inc., Melville, NY) equipped for epifluorescence with an IF DM-510 filter and expressed as the number of attached bacteria per 100 lung cells. Values for 6-9 wells were averaged and each experiment was performed 3-6 times. To test the ability of the mixture of CBPs to affect adherence to eucaryotic cells, the assay is modified such that monolayers are plated in 96 well dishes (Falcon) coated with 0.2% gelatin and at confluence are incubated with a range of concentrations of the mixture of CBPs (1 μg to 1 mg ml"1) for 15 min. After washing, the CBP-treated monolayers are challenged with 5 x 106 pneumococci for 30 min, washed and adherence is quantitated as fluorescence intensity measured in a Cytofluor II (Perseptive) with excitation at 485 nm and emission at 530 nm.
Adherence to glyco conjugates was assessed by coating Terasaki plates overnight with 1 0 0 u M o f6 ' s i a l y l l a c t o s e - H S A , l a c t o - N - n e o t e t r a o s e - H S A , N-acetylglucosamine-β 1 ,4-glucose-HS A or N-acetylglucosamine-β 1 ,3-glucose-HSA (Neose Inc., Horsham, PA). Wells were washed and 1 x 107 FITC labelled pneumococci were added for 30 min at 37°C. Unbound cells were washed away three times with PBS and adherence was quantitated visually as described above. Each glycoconjugate was tested in 18 wells during three experiments.
Passive protection against systemic challenge. Outbred CF1 mice were housed under specific pathogen free conditions in accordance with institutional and NIH guidelines. Encapsulated pneumococci were grown for 5 hours in C+Y medium and diluted in PBS. Antibody (pre-immune serum for control or postimmune, 0.5ml diluted 1 : 10 in PBS) is incubated with the inoculum for 30 min at 37°C and then the entire mixture is injected. Two groups often mice received an inoculum of 3 x 107 cfu of Type 4 by injection into the peritoneal cavity. The number of animals alive or dead is scored over 4 days.
Nasopharyngeal challenge. Nasopharyngeal colonization of 1 to 5-day old Sprague- Dawley rats by the parental strain serotype 4 and the Cbp deficient mutants was carrued out as described previously using Type4 (Weiser JN et al (1994) 62(6):2582- 2589). For each experiment, litters were randomized and sorted into groups of eight to ten pups. Each pup received equal intranasal inocula of 2.5-8xl03 cfu in 10 ul of PBS of either the parent strain (Type 4) or the isogenic mutant containing a defined mutation in CbpG or CbpD. Colonization was assessed at 48 and 96 hours post- inoculation. To insure accurate evaluation of recovered bacteria, the fluid from the nasal washes were diluted in series, plated and colony counts determined. Results are expressed as the geometric mean of each group ± the standard deviation (n=20). The experiment was repeated at least 3 independent times.
To assess virulence in a model of sepsis, two to five day old infant rats were injected intraperitoneally with 2-4 x 107 cfu of parental strain serotype 4 or a Cbp deficient mutant. Survival was assessed at 16-24 hours and 48 hours post injection.
This invention may be embodied in other forms or carried out in other ways without departing from the spirit or essential characteristics thereof. The present disclosure is therefore to be considered as in all aspects illustrate and not restrictive, the scope of the invention being indicated by the appended Claims, and all changes which come within the meaning and range of equivalency are intended to be embraced therein.
Various references are cited throughout this Specification, each of which is incorporated herein by reference in its entirety.

Claims

WHAT IS CLAIMED IS:
1. An isolated streptococcal choline binding polypeptide wherein the polypeptide is expressed by Streptococcus and wherein such polypeptide is CbpG or CbpD.
2. The choline binding polypeptide of Claim 1 having the following characteristics: a. choline-binding activity; and b. elution from a chromatographic column in the presence of at least about 2% choline.
3. The choline binding polypeptide of Claim 1 which is isolated from Streptococcus pneumoniae .
4. An isolated polypeptide comprising an amino acid sequence of a pneumococcal choline binding protein CbpG or CbpD, wherein such polypeptide contains a choline binding domain sequence which is homologous to SEQ ID NO: 1.
5. An isolated streptococcal CbpG or CbpD choline binding polypeptide comprising the amino acid sequence set out as SEQ ID NO: 2 or SEQ ID
NO:15.
6. An N-terminal truncate polypeptide of a choline binding protein CbpG or CbpD.
7. The N-terminal truncate of Claim 6 comprising the amino sequence set out as SEQ ID NOT 1, SEQ ID NO:21 or SEQID NO:23.
8. The streptococcal choline binding protein of Claim 1 labeled with a detectable label.
9. A vaccine comprising the polypeptide of Claim 1 or Claim 6 and a pharmaceutically acceptable adjuvant.
10. The vaccine of Claim 9, further comprising an antigen selected from the group consisting of: a. a different streptococcal choline binding protein; b. PspA; c. autolysin (LytA); d. CbpA; and d. any combination of one or more of the foregoing.
11. A pharmaceutical composition comprising a choline binding polypeptide of Claim 1 or Claim 6 and a pharmaceutically acceptable carrier.
12. The pharmaceutical composition of Claim 11, further comprising an active ingredient selected from the group consisting of: e. PspA, CbpA or autolysin (LytA); f an antibiotic; g. an anti-streptococcal choline binding protein vaccine, wherein the choline binding protein is not PspA, CbpA or autolysin (LytA); and h. an anti-streptococcal vaccine.
13. A purified antibody to a streptococcal choline binding polypeptide CbpG or CbpD.
14. A monoclonal antibody to the streptococcal choline binding protein of Claim 1 or Claim 6.
15. An immortal cell line that produces a monoclonal antibody according to Claim 14.
16. The antibody of any of Claims 13 or 14 labeled with a detectable label.
17. The antibody of Claim 16 wherein the label is selected from the group consisting of an enzyme, a chemical which fluoresces, and a radioactive elements.
18. A pharmaceutical composition comprising an antibody to a choline binding protein of Claim 1 or Claim 6 and a pharmaceutically acceptable carrier.
19. A pharmaceutical composition comprising a combination of at least two antibodies to choline binding proteins, wherein one of such antibodies is directed to the choline binding protein of Claim 1 or Claim 6, and a pharmaceutically acceptable carrier.
20. An isolated nucleic acid which encodes the streptococcal choline binding protein of Claim 1 or Claim 6, or a fragment thereof.
21. The isolated nucleic acid of Claim 20, wherein the nucleic acid is selected from the group consisting of: a. the DNA sequence of SEQ ID NO:3 or SEQ ID NO: 16; b. DNA sequences that hybridize to the DNA sequence of SEQ ID NO: 3 or SEQ ID NO: 16 under standard hybridization conditions; c. degenerate variants thereof; d. alleles thereof; and e. hybridizable fragments thereof.
22. The isolated nucleic acid of Claim 20, wherein the nucleic acid is selected from the group consisting of: a. the DNA sequence of SEQ ID NO: 12, SEQ ic acid is selected from the group consisting of: a. the DNA sequence of SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO:24; b. DNA sequences that hybridize to the DNA sequence of SEQ ID NO: 12, SEQ ID NO:22 or SEQ ID NO:24 under standard hybridization conditions; c. degenerate variants thereof; d. alleles thereof; and e. hybridizable fragments thereof.
23. The nucleic acid of Claim 20 which is a DNA molecule having a nucleotide sequence selected from the group consisting of: a. a DNA sequence encoding a polypeptide comprising the amino acid sequence set out in SEQ ID NO:2 or SEQ ID NO: 15; b. a DNA sequence that hybridizes to the DNA sequence of (a) under moderately stringent hybridization conditions; and c. a DNA sequence capable of encoding the amino acid sequence encoded by any of the foregoing DNA sequences of (a) or (b).
24. A vector which comprises the nucleic acid of Claim 20 and a promoter.
25. The vector of Claim 24, wherein the promoter comprises a bacterial, yeast, insect or mammalian promoter.
26. The vector of Claim 24, wherein the vector is a plasmid, cosmid, yeast artificial chromosome (YAC), bacteriophage or eukaryotic viral DNA.
27. A host vector system for the production of a polypeptide which comprises the vector of Claim 24 in a suitable host cell.
28. The host vector system of Claim 27, wherein the suitable host cell comprises a prokaryotic or eukaryotic cell.
29. The nucleic acid of Claim 20 which is a recombinant DNA molecule.
30. The recombinant DNA molecule of Claim 29, wherein the DNA molecule is operatively linked to an expression control sequence..
31 A unicellular host transformed with a recombinant DNA molecule of Claim 29.
32. A nucleic acid vaccine comprising the recombinant DNA molecule of Claim 29.
33. A method for detecting the presence of a streptococcal choline binding polypeptide of Claim 1, wherein the streptococcal choline binding polypeptide is measured by: a. contacting a sample in which the presence or activity of the choline binding polypeptide CbpG and/or CbpD is suspected with an antibody to the choline binding polypeptide CbpG and/or CbpD under conditions that allow binding of the choline binding polypeptide CbpG and/or CbpD to the binding partner to occur; and b. detecting whether binding has occurred between the choline binding polypeptide CbpG and/or CbpD from the sample and the antibody; wherein the detection of binding indicates the presence or activity of the choline binding polypeptide CbpG or CbpD in the sample.
34. A method for detecting the presence of a bacterium having a gene encoding a choline binding polypeptide of Claim 1, comprising: a. contacting a sample in which the presence or activity of the bacterium is suspected with an oligonucleotide which hybridizes to the choline binding polypeptide CbpG or CbpD gene under conditions that allow specific hybridization of the oligonucleotide to the gene to occur; and b. detecting whether hybridization has occurred between the oligonucleotide and the gene; wherein the detection of hybridization indicates that presence or activity of the bacterium in the sample. .
35. A method for preventing infection with a bacterium that expresses a streptococcal choline binding polypeptide comprising administering an immunogenically effective dose of a vaccine of Claim 9 to a subject.
36. A method for preventing infection with a bacterium that expresses a streptococcal choline binding polypeptide comprising administering an immunogenically effective dose of a vaccine of Claim 10 to a subject.
37. A method for treating infection with a bacterium that expresses a streptococcal choline binding polypeptide comprising administering a therapeutically effective dose of a pharmaceutical composition of Claim 11 to a subject.
38. A method for treating infection with a bacterium that expresses a streptococcal choline binding polypeptide comprising administering a therapeutically effective dose of a pharmaceutical composition of Claim 18 to a subject.
39. A method for treating infection with a bacterium that expresses a streptococcal choline binding polypeptide comprising administering pulmonarily an adhesion inhibitory agent wherein said agent is a choline binding polypeptide CbpG or CbpD or fragment thereof.
40. A method of inducing an immune response in a subject which has been exposed to or infected with a pneumococcal bacterium comprising administering to the subject an amount of the pharmaceutical composition of Claim 11, thereby inducing an immune response.
1. A method for preventing infection by a pneumococcal bacterium in a subject comprising administering to the subject an amount of a pharmaceutical composition of Claim 18 and a pharmaceutically acceptable carrier or diluent, thereby preventing infection by a pneumococcal bacterium.
PCT/US1999/027526 1998-11-19 1999-11-19 PNEUMOCOCCAL CHOLINE BINDING PROTEINS, CbpG AND CbpD, DIAGNOSTIC AND THERAPEUTIC USES THEREOF WO2000029434A2 (en)

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