WO2023137519A1 - Chimeric polypeptides - Google Patents

Chimeric polypeptides Download PDF

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Publication number
WO2023137519A1
WO2023137519A1 PCT/AU2023/050028 AU2023050028W WO2023137519A1 WO 2023137519 A1 WO2023137519 A1 WO 2023137519A1 AU 2023050028 W AU2023050028 W AU 2023050028W WO 2023137519 A1 WO2023137519 A1 WO 2023137519A1
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WIPO (PCT)
Prior art keywords
chimeric
fusion protein
polypeptide
sequence
amino acid
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Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
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PCT/AU2023/050028
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English (en)
French (fr)
Inventor
Eric Charles Reynolds
Nada Slakeski
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Oral Health Australia Pty Ltd
Denteric Pty Ltd
Original Assignee
Oral Health Australia Pty Ltd
Denteric Pty Ltd
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Publication date
Priority claimed from AU2022900101A external-priority patent/AU2022900101A0/en
Priority to KR1020247027669A priority Critical patent/KR20240149404A/ko
Priority to CN202380027380.5A priority patent/CN118891059A/zh
Priority to IL314282A priority patent/IL314282A/en
Priority to AU2023209795A priority patent/AU2023209795A1/en
Priority to JP2024543301A priority patent/JP2025503079A/ja
Application filed by Oral Health Australia Pty Ltd, Denteric Pty Ltd filed Critical Oral Health Australia Pty Ltd
Priority to EP23742622.6A priority patent/EP4466011A4/en
Priority to CA3248847A priority patent/CA3248847A1/en
Publication of WO2023137519A1 publication Critical patent/WO2023137519A1/en
Priority to MX2024008983A priority patent/MX2024008983A/es
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/52—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from bacteria or Archaea
    • 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
    • A61K39/02—Bacterial antigens
    • A61K39/0216—Bacteriodetes, e.g. Bacteroides, Ornithobacter, Porphyromonas
    • 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
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A61K39/40—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum bacterial
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/12—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from bacteria
    • C07K16/1203—Gram-negative bacteria
    • 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
    • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55505—Inorganic adjuvants
    • 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
    • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55511—Organic adjuvants
    • A61K2039/55522—Cytokines; Lymphokines; Interferons
    • 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
    • A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
    • 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
    • A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
    • A61K2039/575—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 humoral response
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y304/00—Hydrolases acting on peptide bonds, i.e. peptidases (3.4)
    • C12Y304/22—Cysteine endopeptidases (3.4.22)
    • C12Y304/22037—Gingipain R (3.4.22.37)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y304/00—Hydrolases acting on peptide bonds, i.e. peptidases (3.4)
    • C12Y304/22—Cysteine endopeptidases (3.4.22)
    • C12Y304/22047—Gingipain K (3.4.22.47)

Definitions

  • the invention relates to chimeric polypeptides that are useful for inducing an immune response to P. gingivalis, compositions comprising same and uses thereof for the prevention and treatment of P. gingivalis- related conditions and diseases.
  • Periodontitis Periodontal pathogen Porphyromonas gingivalis
  • Periodontitis an inflammatory disease of the supporting tissues of the teeth leading to resorption of alveolar bone and eventual tooth loss. The disease is a major public health problem in all societies and is estimated to affect up to 30% of the adult population with severe forms affecting 12-15% of the adult population.
  • periodontitis has been linked to an increased risk of inflammatory diseases including cardiovascular diseases, certain cancers, preterm birth, rheumatoid arthritis and dementia. More recent research has linked chronic infection by P. gingivalis with dementia and rheumatoid arthritis. For example, in one study, 96% of Alzheimer's disease (AD) brain samples showed the presence of P. ginigvalis. Another study shows that chronic oral infection of mice with P. gingivalis resulted in the brain plaques associated with AD in humans and that the P. gingivalis proteases could cleave amyloid precursor and tau proteins to form the plaques and tangles associated with AD.
  • AD Alzheimer's disease
  • P. gingivalis gingipains A number of virulence factors have been reported to contribute to the pathogenicity of P. gingivalis including; LPS, fimbriae, hemagglutinin, hemolysin and extracellular hydrolytic enzymes (especially the Arg-X and Lys-X specific proteinases), otherwise known as "P. gingivalis gingipains”.
  • the magnitude of the public health problem is such that there is a need for a vaccine that provides a strong protective response to P. gingivalis infection and means for providing same.
  • the present invention provides a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide and a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto; and B) the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis., wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to some or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20, (ABM2) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2) SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, most preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18, or 22 or 27 or sequences at least 80% identical thereto; and wherein the second polypeptide: a) does not comprise: a sequence of a cleaved adhesin domain (CAD) or part thereof, preferably a sequence of a CAD having a sequence set forth in SEQ ID NOs: 12 or 13 or sequences at least 80% identical
  • CAD cleaved adhes
  • the chimeric or fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide or C-terminally to the second polypeptide.
  • At least two further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys- gingipain of P. gingivalis, or sequences that are at least 80% identical thereto may be present.
  • the two further polypeptides may be located N-terminally to the second polypeptide, C-terminally to the second polypeptide, or N and C terminally to the second polypeptide.
  • the one or more further polypeptides may be linked to the first or second polypeptide of the chimeric or fusion protein, preferably via a linker of no more than 50 amino acids, or directly linked to the first or second polypeptide.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the present invention provides a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide and a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis', wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to some or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, most preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18, or 22 or 27 or a sequence at least 80% identical thereto; and wherein the second polypeptide: a) does not comprise a sequence of a cleaved adhesin domain (CAD), the CAD preferably having the sequence set forth in SEQ ID NO: 12 or 13 or sequences at least 80% identical thereto; preferably, wherein the
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C-terminally to the first polypeptide, N-terminally to the second polypeptide of C-terminally to the second polypeptide.
  • the one or more further polypeptides may be linked to the first or second polypeptide of the chimeric or fusion protein, preferably via a linker of no more than 50 amino acids, or directly linked to the first or second polypeptide.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 85%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P.
  • gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the present invention provides a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide linked to a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis; wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to some or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM2) or sequences at least 80% identical thereto, most preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18 or 22 or a sequence at least 80% identical thereto; and wherein the second polypeptide: a) does not comprise: a sequence of a cleaved adhesin domain (CAD) or part thereof, the CAD preferably having a sequence set forth in SEQ ID NOs: 12 or 13 or sequences at least 80% identical thereto; and
  • CAD cleaved adhesin
  • an amino acid sequence corresponding substantially to the full length of the DUF2436 domain, or a sequence at least 80% identical thereto refers to a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the length of a DUF2436 domain of an Arg- or Lys-gingipain.
  • the amino acid sequence of the DUF2436 domain of an Arg- or Lys-gingipain is the sequence set forth in SEQ ID NO: 23 or is a sequence at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the second polypeptide comprises or consists of the sequence set forth in SEQ ID NO: 34 or a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the second polypeptide comprises the sequence set forth in SEQ ID NO: 76, or a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric or fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide of C-terminally to the second polypeptide.
  • the one or more further polypeptides may be linked to the first or second polypeptide of the chimeric or fusion protein, preferably via a linker of no more than 50 amino acids, or directly linked to the first polypeptide.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the chimeric or fusion protein comprises or consists of an amino acid sequence as set forth in any one of SEQ ID NOs: 28, 50, 51 , 52, 53 or 54, or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the present invention provides a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide and a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis; wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to some or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2) SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, most preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18 or 22 or SEQ ID NO: 27 or a sequence at least 80% identical thereto; and wherein the second polypeptide comprises one or more amino acid substitutions selected from: a) one or more cysteine amino acid substitutions in the adhesin domain, compared to the naturally occurring Arg- or Lys-gingipain sequences in corresponding regions; and/
  • the one or more cysteine amino acid substitutions may be a substitution to a serine residue or to a valine residue.
  • the one or more cysteine substitutions may comprise one or more substitutions to a serine residue.
  • cysteine residues are substituted to a combination of valine and serine residues. In other embodiments, all substituted cysteine residues are substituted to serine or all substitute cysteine residues are substituted to valine.
  • the adhesin domain comprises the DUF2436 domain or part thereof, and the cysteine residue in the DUF2436 domain is substituted to a serine or valine, preferably a serine.
  • the adhesin domain comprises the DUF2436 domain, and the cysteine residue in the DUF2436 domain is not substituted and preferably, one or more cysteine residues in the remainder of the adhesin domain are substituted.
  • the adhesin domain comprises or consists of the sequence set forth in SEQ ID NO: 23 or a sequence at least 80% identical thereto, wherein the cysteine residue at position 115 is substituted to a serine or valine residue.
  • the adhesin domain comprises or consists of the sequence set forth in SEQ ID NO: 25 or a sequence at least 80% identical thereto, wherein the cysteine residue at position 77 is substituted to a serine or valine residue.
  • the adhesin domain comprises or consists of the sequence set forth in SEQ ID NO: 34 or SEQ ID NO: 76 or a sequence at least 80% identical thereto, wherein one or more cysteine residues are substituted to a serine or valine residue.
  • a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide and a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis’, wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to some or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18 or 22 or SEQ ID NO: 27 or a sequence at least 80% identical thereto; and wherein the second polypeptide c) comprises one or more cysteine to serine amino acid substitutions compared to the naturally occurring adhesin domain sequence; and d) comprises a proline substitution and/or an asparagine substitution, in the sequence PxxN corresponding, or at a position equivalent to, residues at positions 6 to 9 of the sequence of SEQ ID NO: 14 or 19.
  • the chimeric or fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide of C-terminally to the second polypeptide.
  • the second polypeptide comprises an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis, wherein the adhesin domain comprises the sequence set forth in SEQ ID NO: 18 or 22 or a sequence at least 80% identical thereto; and wherein one or both cysteine residues in SEQ ID NO: 18 or 22 are substituted to a serine residue and wherein the proline and/or asparagine residues in the sequence PxxN at positions 63 to 66 of SEQ ID NO: 18 or SEQ ID NO: 22 (corresponding to positions 6 to 9 of SEQ ID NOs: 14 or 19), or positions equivalent to, are substituted.
  • the proline residue is substituted to an alanine residue and/or the asparagine residue is substituted to a proline or alanine residue, preferably wherein the proline is substitute to alanine, and the asparagine is substituted to proline, such that the sequence at positions 63 to 66 of SEQ ID NO: 18 or SEQ ID NO: 22 is AxxP (eg AVQP).
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 34 or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues.
  • the cysteine residue at residue 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 34, or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues and wherein the proline and asparagine residues in the sequence PxxN at positions 235 to 238, or positions equivalent to, are substituted.
  • the cysteine residue at residue 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues, and wherein the proline residue at position 235, or position equivalent thereto, is substituted to an alanine residue and the asparagine residue at position 238, or a position equivalent thereto, is substituted to a proline.
  • the second polypeptide comprises or consists of a sequence as set forth in any one of SEQ ID NOs: 35 to 49, or sequences at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the chimeric or fusion protein comprises or consists of the amino acid sequence as set forth in any of SEQ ID NO: 55, 56, or 57, or sequences at 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the present invention provides: a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide and a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis; wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to some or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18 or 22 or a sequence at least 80% identical thereto; and wherein the second polypeptide: a) comprises an amino acid sequence corresponding substantially to the full length of the DUF2436 domain of an Arg- or Lys-gingipain, preferably as set forth in SEQ ID NO: 23, or a sequence at least 80% identical thereto; and one or more amino acid substitutions selected from: b) one or more cysteine amino acid substitutions in the adhesin domain, compared to the naturally occurring Arg- or Lys-gingipain sequences in corresponding regions; and/or d
  • the one or more cysteine amino acid substitutions may be a substitution to a serine residue or a valine residue.
  • the one or more cysteine substitutions may comprise one or more substitutions to a serine residue.
  • cysteine residues are substituted to a combination of valine and serine residues. In other embodiments, all substituted cysteine residues are substituted to serine or all substitute cysteine residues are substituted to valine.
  • the adhesin domain comprises the DUF2436 domain, and the cysteine residue in the DUF2436 domain is substituted to a serine or valine, preferably a serine.
  • the adhesin domain comprises the DUF2436 domain, and the cysteine residue in the DUF2436 domain is not substituted and preferably, one or more cysteine residues in the remainder of the adhesin domain are substituted.
  • the adhesin domain comprises or consists of the sequence set forth in SEQ ID NO: 34 or SEQ ID NO: 76, or a sequence at least 80% identical thereto, wherein one or more cysteine residues are substituted to a serine or valine residue.
  • the sequence PxxN corresponding to or at a position equivalent to residues 235 to 238 of SEQ ID NO: 34, comprises a substitution of the proline and asparagine residues.
  • the substitution is from PxxN to AxxP.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 34, or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues.
  • the cysteine residue at residue 115 of SEQ ID NO: 34, or a position equivalent thereto, is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 34 or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues and wherein the proline and asparagine residues in the sequence PxxN at positions 235 to 238, or positions equivalent to, are substituted.
  • the cysteine residue at residue 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues, and wherein the proline residue at position 235, or position equivalent thereto, is substituted to an alanine residue and the asparagine residue at position 238, or a position equivalent thereto, is substituted to a proline.
  • the second polypeptide comprises or consists of a sequence as set forth in any one of SEQ ID NOs: 35 to 49, or sequences at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric or fusion protein comprises or consists of a sequence as set forth in any one of SEQ ID NOs: 62 to 63, or sequences at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric of fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide of C-terminally to the second polypeptide.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the present invention provides: a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide linked to a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis; wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to part or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, most preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18 or 22 or a sequence at least 80% identical thereto; and wherein the second polypeptide: a) does not comprise: a sequence of a cleaved adhesin domain (CAD), or part thereof, preferably a sequence of a CAD having the amino acid sequence set forth in SEQ ID NO: 12 or 13 or sequences at least 80% identical
  • CAD cleaved adhes
  • the one or more cysteine amino acid substitutions may be a substitution to a serine residue or a valine residue.
  • the one or more cysteine substitutions may comprise one or more substitutions to a serine residue.
  • cysteine residues are substituted to a combination of valine and serine residues. In other embodiments, all substituted cysteine residues are substituted to serine or all substitute cysteine residues are substituted to valine.
  • the adhesin domain comprises the DUF2436 domain, and the cysteine residue in the DUF2436 domain is substituted to a serine or valine, preferably a serine.
  • the adhesin domain comprises the DUF2436 domain, and the cysteine residue in the DUF2436 domain is not substituted and preferably, one or more cysteine residues in the remainder of the adhesin domain are substituted.
  • the adhesin domain comprises or consists of the sequence set forth in SEQ ID NO: 34 or a sequence at least 80% identical thereto, wherein one or more cysteine residues are substituted to a serine or valine residue.
  • the sequence PxxN corresponding to or at a position equivalent to residues 235 to 238 of SEQ ID NO: 34, comprises a substitution of the proline and asparagine residues.
  • the substitution is from PxxN to AxxP.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 34 or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues.
  • the cysteine residue at residue 115 of SEQ ID NO: 34, or a position equivalent thereto, is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 34, or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues and wherein the proline and asparagine residues in the sequence PxxN at positions 235 to 238, or positions equivalent to, are substituted.
  • the cysteine residue at residue 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues, and wherein the proline residue at position 235, or position equivalent thereto, is substituted to an alanine residue and the asparagine residue at position 238, or a position equivalent thereto, is substituted to a proline.
  • the second polypeptide comprises or consists of a sequence as set forth in any one of SEQ ID NOs: 35 to 49, or sequences at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric or fusion protein comprises or consists of a sequence as set forth in any one of SEQ ID NOs: 58 to 61 , or sequences at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric or fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide of C-terminally to the second polypeptide.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the present invention provides: a chimeric or fusion protein for inducing an immune response to P. gingivalis, the protein comprising a first polypeptide linked to a second polypeptide, wherein:
  • the first polypeptide comprises or consists of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or a sequence that is at least 80% identical thereto;
  • the second polypeptide comprises or consists of an amino acid sequence of an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis; wherein the second polypeptide comprises the sequence of one or more adhesin binding motifs (ABMs), preferably wherein the ABMs correspond to part or all of the ABMs between the DUF2436 domain and cleaved adhesin domain (CAD) of a P.
  • ABSMs adhesin binding motifs
  • the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, more preferably wherein the one or more ABMs comprise the sequence as set forth in SEQ ID NO: 15 or 20 (ABM2), SEQ ID NO: 14 or 19 (ABM1) and/or SEQ ID NO: 17 or 21 (ABM3) or sequences at least 80% identical thereto, most preferably wherein the one or more ABMs comprise the sequence set forth in any of SEQ ID NO: 16 or SEQ ID NO: 18 or 22 or a sequence at least 80% identical thereto; and wherein the second polypeptide: a) does not comprise: a sequence of a cleaved adhesin domain (CAD), or part thereof, preferably a sequence of a CAD having the amino acid sequence set forth in SEQ ID NO: 12 or 13 or sequences at least 80% identical
  • CAD cleaved adhes
  • the chimeric or fusion protein not comprise an amino acid sequence corresponding to or derived from a DUF2436 domain of an Arg- or Lys-gingipain, such as set forth in SEQ ID NO: 23, or a sequence at least 80% identical thereto.
  • the one or more cysteine amino acid substitutions may be a substitution to a serine residue or a valine residue.
  • the one or more cysteine substitutions may comprise one or more substitutions to a serine residue.
  • cysteine residues are substituted.
  • cysteine residues are substituted to a combination of valine and serine residues.
  • all substituted cysteine residues are substituted to serine or all substitute cysteine residues are substituted to valine.
  • the adhesin domain comprises or consists of the sequence set forth in SEQ ID NO: 18 or 22 or a sequence at least 80% identical thereto, wherein one or more cysteine residues are substituted to a serine or valine residue.
  • the sequence PxxN (eg PVQN), corresponding to or at a position equivalent to residues 63 to 66 of SEQ ID NO: 18, comprises a substitution of the proline and asparagine residues.
  • the substitution is from PxxN to AxxP, (eg AVQP).
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 18 or a sequence at least 80% identical thereto, wherein one or two cysteine residues are substituted to serine residues.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 18, or a sequence at least 80% identical thereto, wherein one or two cysteine residues are substituted to serine residues and wherein the proline and asparagine residues in the sequence PxxN at positions 63 to 66, or positions equivalent to, are substituted.
  • the first and second polypeptides may be joined directly, or joined with a linker.
  • the linker comprises a series of amino acid sequences, preferably of between about 1 amino acid residue to about 20 amino acid residues, preferably no more than about 5 amino acids or no more than about 10 amino acids in length or no more than about 15 amino acids in length.
  • the first and second polypeptides may be linked via a peptide sequence having the amino acid sequence DMEVEDDSP.
  • the chimeric or fusion protein comprises or consists of a sequence as set forth in any one of SEQ ID NOs: 80 or 81 , or sequences at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric or fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide of C-terminally to the second polypeptide.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an amino acid sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or wherein the amino acid sequences are identical.
  • the first polypeptide and the further polypeptide may be derived from the active site of heterologous gingipains (e.g., from gingipains of different strains of P. gingivalis).
  • the first polypeptide and the further polypeptide may have an amino acid sequence that is derived from different gingipains (e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • different gingipains e.g., wherein one of the polypeptides has an amino acid sequence of an active site from a Kgp and the other polypeptide has an amino acid sequence of an active site from an Rgp; or alternatively wherein one of the polypeptides has an amino acid sequence of an active site from a RgpA and the other polypeptide has an amino acid sequence of an active site from an RgpB).
  • the chimeric or fusion protein consists or consists essentially of the sequences of the first and second polypeptides as defined herein. It will be appreciated therefore that the chimeric or fusion proteins comprise an arrangement or configuration of domains that differs to the configuration of those domains in naturally occurring gingipain polyprotein sequences. In other words, the first and second polypeptides and domains therein have a differential spatial configuration to naturally occurring gingipain polyproteins.
  • the first and second polypeptides are linked.
  • the first and second polypeptides may be linked directly, via a linker, or via a polypeptide sequence of no more than 100, preferably no more than 50 amino acids.
  • the first and second polypeptides are directly linked, or linked by no more than about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acids.
  • the first and second polypeptides are directly linked.
  • the C-terminal residue of the first polypeptide may be linked to the N-terminal residue of the second polypeptide, directly, via a linker, or via a polypeptide sequence of no more than 50 amino acids.
  • the N-terminal residue of the first polypeptide may be linked to the C- terminal residue of the second polypeptide, directly, via a linker, or via a polypeptide sequence of no more than 50 amino acids.
  • the DUF2436 domain and ABM domains derived from an Arg- or Lys-gingipain may be directly linked or joined via a linker, or via a polypeptide sequence.
  • the DUF2436 and ABM domains are linked via a short linker sequence comprising about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acids.
  • the DUF and ABM domains are linked via a short linker sequence of no more than about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acids.
  • the DUF2436 and ABM domains may be linked via a peptide sequence having the amino acid sequence EVEDDSP.
  • the further polypeptide may be joined directly or via a linker to the chimeric or fusion protein comprising the first and second polypeptides.
  • the further polypeptide is joined to the C terminal region of the fusion protein via the second polypeptide, preferably the C terminus of the second polypeptide is joined directly to the N terminus of the further polypeptide.
  • the C terminus of the adhesin domain is preferably joined directly to the N terminus of the active site amino acid sequence).
  • the copies of the further polypeptide may be directly joined to each other or joined via a linker sequence.
  • the linker region is an amino acid sequence of no more than 15 amino acids, and preferably greater than 2 amino acids.
  • Suitable linkers for use in protein constructs, including those with minimal impact on solubility are known in the art.
  • Useful linkers include glycine-serine (GlySer) linkers, which are well-known in the art and comprise glycine and serine units combined in various orders. Examples include, but are not limited to, (GS), (GSGGS)n, (GGGS)n and (GGGGS)n, where n is an integer of at least one, typically an integer between 1 and about 10, for example, between 1 and about 8, between 1 and about 6, or between 1 and about 5.
  • Other useful linkers include DSSG, DSSGAS, KLDSSG or others described herein.
  • the linker region may be derived from the native ginigipain polyprotein sequence.
  • the present invention also provides a nucleic acid encoding any chimeric or fusion protein as defined herein.
  • the nucleic acid has a nucleotide sequence that encodes any one or more of the amino acid sequences define in Table 1 herein.
  • such a nucleic acid is included in an expression construct in which the nucleic acid is operably linked to a promoter.
  • an expression construct can be in a vector, e.g., a plasmid, or viral vector.
  • the present invention also provides a cell comprising a nucleic acid, or nucleic acid vector as herein described.
  • cells of the present invention include bacterial cells, yeast cells, insect cells or mammalian cells.
  • the cell is isolated, substantially purified or recombinant.
  • the present invention also provides a composition comprising a chimeric or fusion protein as described herein, optionally in combination with a pharmaceutically acceptable carrier.
  • composition may also comprise an adjuvant for potentiating an immune response to the chimeric or fusion protein.
  • the present invention accordingly further provides for a vaccine or immune stimulating composition for inducing an immune response to P. gingivalis in a subject, the composition comprising: i) an immunogen in the form of a chimeric or fusion protein as described herein, and ii) an adjuvant, for potentiating the immune response to the immunogen in the subject.
  • the sole immunogen provided in the compositions, vaccines or immune stimulating compositions of the invention is a chimeric or fusion protein as herein described.
  • the present invention also provides a method for inducing an immune response in a subject to P. gingivalis, the method comprising administering to a subject in need thereof, a chimeric or fusion protein, vaccine or immune stimulating composition as described herein.
  • the present invention also provides a method of inducing a humoural immune response to P. gingivalis in a subject, the method comprising administering to the subject, a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined.
  • the immune response that is induced comprises a switch from a Th1 to a Th2 immune response.
  • the immune response elicited by administration of a chimeric or fusion protein described herein, or vaccine or other composition comprising the same is preferably antigen-specific.
  • the methods and compositions and chimeric proteins described herein are for inducing an immune response, preferably a protective immune response, to P. gingivalis gingipain antigens.
  • compositions, chimeric proteins and methods of the invention may be for strengthening an immune response (such as a protective immune response) of a subject to P. gingivalis.
  • the present invention also provides for methods of immunising a subject against P. gingivalis infection, the method comprising administering to the subject, a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined.
  • a subject who has received or has been administered a chimeric or fusion protein of the invention, or composition or vaccine including the same has an increased level of protection against infection with P. gingivalis, or severity of one or more symptoms of P. gingivalis infection, compared to a subject who has not received the protein, composition or vaccine.
  • the invention provides a method of treating a P. gingivalis infection in a subject, the method comprising administering to a subject in need thereof, a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined, thereby treating the P. gingivalis infection in the subject.
  • the present invention provides a method for reducing or minimising the severity of a symptom associated with an infection with P. gingivalis, comprising administering to an individual in need thereof, a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined, wherein the symptoms are selected from the group consisting of swollen or puffy gums, gums that bleed easily, receding gums, periodontal pockets around the teeth, loss of tooth supporting tissues (periodontal ligament, cementum and/or alveolar bone) pus between gums and teeth, and gingivitis.
  • the present invention also provides a method for treating P. gingivalis-related disease in a subject, the method comprising administering to an individual in need thereof, a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined.
  • a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined.
  • the P. gingivalis-related disease comprises periodontal disease.
  • the present invention provides for a method of treatment comprising administration of a chimeric or fusion protein, composition, vaccine or immune stimulating composition of the invention may also comprise administration of one or more of: an antimicrobial compound, an anti-inflammatory agent.
  • the invention also provides use of a chimeric or fusion protein as herein defined, in the manufacture of a medicament for:
  • the invention also provides a chimeric or fusion protein, composition, vaccine or immune stimulating composition as herein defined, for use in:
  • the subject may be any subject that has or is at risk of having an infection with P. gingivalis.
  • the subject may be a human.
  • the subject may be a veterinary subject, such as a companion animal that has, or is at risk of having an infection with P. gingivalis.
  • the present invention also provides a method for obtaining an antibody directed to P. gingivalis, the method comprising administering a chimeric or fusion protein, composition, vaccine or immune stimulating composition of the invention, to a non-human animal, thereby generating antibodies directed to P. gingivalis in the animal.
  • the method further comprises isolating the antibody from the animal (eg, extracting from the blood of the animal) or from an egg thereof (in the case where the animal is an avian species, preferably chicken).
  • the present invention also provides an antibody preparation comprising an antibody directed to P. gingivalis, wherein the antibody preparation is obtained by administering a chimeric or fusion protein, composition, vaccine or immune stimulating composition of the invention, to a non-human animal, thereby generating antibodies directed to P. gingivalis in the animal, and isolating the antibodies from the animal or egg thereof.
  • the antibody directed to P. gingivalis may be used therapeutically to eliminate or reduce P. gingivalis infection or prophylactically, to prevent or reduce the severity of P. gingivalis infection.
  • the present invention also provides a kit comprising a composition comprising a chimeric or fusion protein as herein defined, wherein optionally the kit comprises one or more cytokines and/or adjuvants in sealed containers.
  • the kit comprises a label or package insert indicating that the composition is used for immunising an individual, optionally wherein the label or package insert includes instructions for use.
  • phrases including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements.
  • the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements (e.g., 1 , 2, 3, 4, 5, 6,7, 8,9 ,10, 11 , 12 13, 14, 15, 16, 17,18, 19, 20, or more than 20 additional amino acid residues at the N-terminus or C- terminus of a polypeptide sequence) are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.
  • FIG. 1 A. Mouse periodontitis model - therapeutic vaccination.
  • B Schematic showing the domain structure of Kgp gingipain polyprotein and components derived therefrom for generating the chimeric or fusion proteins of the invention.
  • FIG. 1 SDS-PAGE of E coli fractions expressing recombinant variants with or without a K1 domain and containing either a full length or truncated DUF domain. Low temperature and low IPTG conditions used. A full length DUF is essential for solubility. A full length K1 is detrimental to solubility. B. Native PAGE of chimera structures KDA and KDAK1 in the presence of absence of DTT. Addition of K1 domain to KDA reduces solubility but the proteins multimerise.
  • FIG. 3 Elimination of multimerisation
  • A Diagrammatic representation of Kgp polyprotein showing positions of ABM 1 and ABM2 domains.
  • B-D NATIVE_PAGE analysis of purified recombinant protein variants subject to electrophoresis in the presence or absence of DTT.
  • B Study of "PVQN” mutant variants.
  • C Study of "PVQN” mutant variants with additional Cys>Ser mutations.
  • D Study of mutations in loop proceeding "PVQN" motif (lanes 2-4) and highly conserved hydrophobic Tyr and Trp residues in ABM2 and ABM1 respectively (lanes 5-7).
  • E Diagrammatic representation of Kgp polyprotein showing positions of ABM 1 and ABM2 domains.
  • B-D NATIVE_PAGE analysis of purified recombinant protein variants subject to electrophoresis in the presence or absence of DTT.
  • B Study of "PVQN” mutant variants.
  • C Study of "PVQN” mutant
  • Lanes 1 & 2 KDAK-3S-AVQP (1 : unreduced; 2: reduced); Lanes 3 & 4: KDAK-1V-2S-AVQP(3: unreduced; 4:reduced); Lanes 5 & 6: KDAK-1V-AVQP (5: unreduced; 6: reduced); Lanes 7 & 8: KDAK-AVQP (7: unreduced; 8: reduced); Lanes 9 & 10: KDcAKIn (9: unreduced; 10: reduced). Gels were stained with Coomassie blue.
  • Figure 4 Bone loss study. Statistical analysis - One-way ANOVA and post- hoc Dunnet's T3. # significantly different from the Control Challenge group.
  • Figure 7 Bone loss study Statistical analysis - One-way ANOVA and post-hoc Dunnet's T3. #p ⁇ 0.01 ; ##p ⁇ 0.05 (T test) significantly different from the Control Challenge group.
  • Figure 9 Bone loss study study following immunisation of animals with various fusion protein constructs. Statistical analysis: one-way ANOVA and post hoc Dunnet's T3 Significantly different from the Control Challenge group # p ⁇ 0.05 ## p ⁇ 0.01 ### p ⁇ 0.001 #### p ⁇ 0.0001.
  • Figure 10 Bone loss study study following immunisation of animals with various fusion protein constructs. Statistical analysis: one-way ANOVA and post-hoc Dunnet's T3. ### (p ⁇ 0.05); #### (p ⁇ 0.01); significantly different from the Control Challenge group.
  • Figure 11 Bone loss study following immunisation of animals with various fusion protein constructs. Statistical analysis: one-way ANOVA and post-hoc Dunnet's T3. # (p ⁇ 0.05) significantly different from the Control Challenge group.
  • Figure 12 Bone loss study following immunisation of animals with various fusion protein constructs.
  • Statistical analysis one-way ANOVA and post-hoc Dunnet's T3. * (p ⁇ 0.05) significantly different from the naive (ie Control Non-Challenged group).
  • FIG. 13 Purity of the final products of the P. gingivalis antigens tested in Example 4.
  • PAGE analysis of His-tagged antigens A and B) and tagless KDAK-3S- AVQP (C).
  • A SDS-PAGE;
  • B Native PAGE or on native gels.
  • C SDS- and native PAGE or on native gel with loaded samples being heated (95°C) or unheated.
  • R gel loaded samples reduced;
  • His-tagged KDAK-3S-AVQP was purified in parallel with the other His-tagged proteins.
  • Figure 14 Bone loss study following immunisation of animals with various fusion protein constructs. Statistical analysis - One-way ANOVA and post-hoc Dunnet's T3. # (p ⁇ 0.05, compared to naive control (ie Control Non-Challenge)); ## (p ⁇ 0.05, compared to infected control (ie Control Challenge)).
  • Figure 15 Antibody titres in mouse sera (individual) towards heat-killed P. gingivalis whole cells.
  • A Total IgG Titres;
  • B lgG1 Subtype titres;
  • C lgG2a Subtype titres.
  • Figure 16 Dose response trend of exemplary fusion protein of invention, with periodontal bone loss protection with Kgpcat cross-reactive Ab titre.
  • the inventors investigated various chimeric or fusion proteins for use in inducing immune responses to P. gingivalis and methods for large-scale production of such chimeras for use as vaccine candidates.
  • the inventors identified various problems associated with large-scale manufacturing and production of chimeric or fusion proteins derived from components of P. gingivalis gingipains. Firstly, the chimeric or fusion proteins described in the prior art are difficult to produce at sufficiently high quantities, as soluble proteins. More specifically, the chimeric proteins of the prior art are typically produced in inclusion bodies in E. coli, making it challenging to produce large amounts of soluble protein for downstream clinical product development.
  • Reduced solubility when produced in E. coli also substantially contributes to time and scale of manufacturing, as well as poor stability of the proteins once solubilised and refolded from inclusion bodies.
  • gingipain-derived chimeric proteins described in the prior art also suffer from multimerisation.
  • the formation of beta-sheets between domains in the chimeric proteins makes an assessment of the final vaccine product challenging, from a regulatory perspective, as well as contributing to potentially reduced immune responses once administered.
  • the present invention is therefore concerned with improved design of chimeric or fusion proteins for use in inducing an immune response to P. gingivalis, and methods and uses comprising the same.
  • the chimeric or fusion proteins of the present invention have improved solubility and/or stability compared to chimeric or fusion proteins described in the prior art. Improved solubility and/or stability provides for significant advantages when it comes to large-scale production of fusion proteins for use in a clinical setting.
  • the chimeric or fusion proteins of the invention have a reduced propensity to aggregate and multimerise compared to chimeric or fusion proteins of the prior art. Aggregation and multimerisation may hinder large-scale manufacturing and production of therapeutic/prophylactic proteins. Consequently, reducing propensity for aggregation and/or multimerisation of the chimeric proteins of the invention provides for a significant improvement over prior art chimeric proteins for use in inducing immune responses to P. gingivalis.
  • the chimeric or fusion proteins of the invention have increased immunogenicity compared to chimeric or fusion proteins of the prior art.
  • the inventors have identified various new approaches for obtaining a chimeric or fusion protein for inducing an immune response to P. gingivalis and which results in a chimeric or fusion protein with one or more advantages over the prior art.
  • the inventors believe that one or more of the new approaches for generating chimeric or fusion proteins for inducing an immune response to P. gingivalis, as described herein, may result in advantages including: increased ease of manufacturing of a suitable immunogenic composition for inducing an immune response to P. gingivalis; improved shelf-life and/or improved immunogenicity.
  • the pathogenicity of P. gingivalis is attributed to a number of surface-associated virulence factors that include cysteine proteinases (gingipains), fimbriae, haem-binding proteins, and outer membrane transport proteins amongst others.
  • cysteine proteinases gingipains
  • fimbriae fimbriae
  • haem-binding proteins haem-binding proteins
  • outer membrane transport proteins outer membrane transport proteins amongst others.
  • the extracellular Arg- and Lys-specific proteinases 'gingipains' (RgpA/B and Kgp) of P. gingivalis have been implicated as major virulence factors that are critical for colonisation, penetration into host tissue, dysregulation of the immune response, dysbiosis and disease.
  • the gingipains in particular the Lys-specific proteinase Kgp are essential for P. gingivalis to induce alveolar bone resorption in the mouse periodontitis model.
  • the gingipains have also been found in gingival tissue at sites of severe periodontitis at high concentrations proximal to the subgingival plaque and at lower concentrations at distal sites deeper into the gingival tissue.
  • Lys-specific and Arg-specific proteinases have been shown to degrade a variety of host proteins in vitro, e.g., fibrinogen, fibronectin, and laminin.
  • Plasma host defence and regulatory proteinase inhibitors a-trypsin, ⁇ 2- macroglobulin, anti-chymotrypsin, antithrombin III and antiplasmin are also degraded by Lys- and Arg- proteinases from P. gingivalis. This has led to the development of a cogent mechanism to explain the keystone role played by P. gingivalis in the development of chronic periodontitis.
  • the RgpA, RgpB and Kgp genes all encode an N-terminal signal peptide of ⁇ 22 amino acids in length, an unusually long propeptide of ⁇ 200 amino acids in length, and a catalytic domain of ⁇ 480 amino acids.
  • C-terminal to the catalytic domain is a large hemagglutinin-adhesin (HA) domain which is comprised of adhesin binding domains (ABMs, or which 5 distinct sequences have been described), a "Domain of Unknown Function" (termed DUF2436 which is defined as conserved Pfam Domain of Unknown Function; IPR018832) and C-terminal adhesin domains or cleaved adhesin domains (or CADs).
  • HA hemagglutinin-adhesin
  • DUF2436 which is defined as conserved Pfam Domain of Unknown Function; IPR018832
  • Kgp comprises (N terminus to C terminus): a catalytic domain, a first ABM (ABM1), DUF2436, a domain comprising ABM2, ABM1 , ABM3, two CAD domains (termed K1 and K2), a further domain comprising ABM2 and ABM 1 , a further CAD domain (termed K3), ABM2, and a C-terminal domain.
  • ABMs 1 , 2 and 3 will be understood to generally refer to the ABMs found in the order ABM2, ABM1 and ABM3 in the sequence immediately C terminal to DUF2436 of Kgp, as depicted in Figure 1 B.
  • RgpB and RgpA share a high-degree of sequence homology.
  • RgpB lacks the HA domains and is located in a monomeric form on the outer membrane.
  • Some of the HA domains have been alternatively described as C- terminal adhesin domains or cleaved adhesin domains (CADs) and some are DUF ("Domain of Unknown Function") 2436 domains (conserved Pfam Domain of Unknown Function; IPR018832).
  • the RgpA and Kgp precursor proteins are cleaved into multiple domains that remain non-covalently associated forming large outer membrane protein complexes.
  • Arg- and Lys-specific proteinases are therefore found in a cell-associated complex of non-covalently associated proteinases and adhesins.
  • One such complex has been designated the RgpA-Kgp proteinase-adhesin complex (previously referred to as the PrtR-PrtK proteinase-adhesin complex).
  • the complex is composed of a 45kDa Arg- specific calcium-stabilised cysteine proteinase and seven sequence-related adhesin domains,
  • a Lys-gingipain catalytic domain may also be referred to a KAS domain or PAS domain.
  • an Arg-gingipain catalytic domain may also be referred to as a RAS domain or PAS domain.
  • the catalytic domain of the Lys- gingipain or Arg-gingipains is located in the N-terminal ⁇ 480 amino acid region of the protein.
  • the active site within the catalytic domain is typically located at amino acid residues 426-446 (for RgpA) and 432-453 (for Kgp).
  • Exemplary active site peptides, as found within the catalytic domains are set out in in Table 1 as SEQ ID NOs: 1-11.
  • an adhesin domain of an Arg- or Lys-gingipain of P. gingivalis will be understood to typically refer to the region of an Arg- or Lys-gingipain that is C-terminal to the catalytic or active site domain.
  • the adhesin domain also referred to as the HA domain
  • the adhesin domain typically comprise a Domain of Unknown Function (DUF) domain (especially DUF 2436 conserved Pfam Domain of Unknown Function; IPR018832) and several adhesin binding motifs (ABM) domains and a cleaved adhesin domain (CAD).
  • DUF Domain of Unknown Function
  • ABM adhesin binding motifs
  • the chimeric or fusion proteins of the present invention comprise a first polypeptide that comprises or consists of an amino acid sequence of the active site of an Arg-X or Lys-X proteinase (also referred to herein as Arg- or Lys-gingipain, respectively) of P. gingivalis, or a sequence that is at least 80% identical thereto.
  • the first polypeptide comprises or consists of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the chimeric or fusion protein comprises one or more further polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the one or more further polypeptides comprising or consisting of the active site of an Arg- or Lys-gingipain of P. gingivalis may be located N-terminally to the first polypeptide, C- terminally to the first polypeptide, N-terminally to the second polypeptide or C-terminally to the second polypeptide.
  • the one or more further polypeptides may be linked to the first or second polypeptide of the chimeric or fusion protein, preferably via a linker of no more than 50 amino acids, or directly linked to the first polypeptide.
  • the one or more further polypeptides preferably comprise or consist of an amino acid sequence selected from the group of: SEQ ID NOs: 1 to 11 , or sequences at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the first polypeptide and the further polypeptide that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis comprise or consist of an identical amino acid sequence, or sequences that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to each other.
  • the chimeric or fusion proteins of the invention comprise no more than 2 or nor more than 3 or no more than 4 polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the chimeric or fusion proteins of the invention have fewer than 5, more preferably fewer than 4, most preferably fewer than 3 polypeptides that comprise or consist of an amino acid sequence of the active site of an Arg- or Lys-gingipain of P. gingivalis, or sequences that are at least 80% identical thereto.
  • the chimeric or fusion proteins of the present invention comprise a second polypeptide that comprises or consists of an amino acid sequence of an adhesin domain of an ArgX or Lys-X proteinase of P. gingivalis, or a sequence that is at least 80% identical thereto.
  • the second polypeptide will typically comprise at least a sequence corresponding to one or more of the adhesin-binding motifs (ABM) that are recognised domains/motifs in the adhesin domains of ArgX or Lys-X proteinases of P. gingivalis (such as Kgp and RgpA).
  • ABSM adhesin-binding motifs
  • ABMs There are five ABMs that have been defined for Kgp and RgpA (ABM 1-5). Exemplary sequences for these ABMs are set forth in Table 1 .
  • the second polypeptide comprises more than one ABM, preferably wherein the second polypeptide comprises at least ABM1 and ABM2, or a sequence at least 80% identical to each of ABM1 or ABM2.
  • the second polypeptide may also comprise the sequence of ABM3 or a sequence at least 80% identical thereto.
  • the arrangement of the ABM peptides in the second polypeptide need not correspond to the arrangement of the ABM peptides as found in naturally occurring adhesin domains.
  • the ABM peptides may be arranged in the second polypeptide in the sequence (N-terminus to C-terminus) ABM1 , ABM2, ABM3 etc.
  • the ABM peptides may be arranged to reflect the arrangement in naturally occurring adhesin domains, such as ABM2, ABM1 and ABM3, such as occurs in Adhesin domain 1 of Kgp.
  • the ABMs in the second polypeptide may be arranged contiguously or may be separated from each other by an amino acid sequence of no more than 50 amino acids. It will be appreciated by the skilled person that the spacing between the ABMs is not critical in the design of the chimeric or fusion proteins of the invention.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 16 or a sequence at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical thereto.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 18 or SEQ ID NO: 27 or a sequence at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical thereto.
  • the second polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 22 or SEQ ID NO: 27 or a sequence at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical thereto.
  • the inventors have established that the methods of the prior art, which include simply selecting various domains found in naturally occurring gingipains for use in a chimeric or fusion protein typically result in the generation of a protein that is poorly expressed in recombinant systems, and which has a propensity to be expressed as insoluble protein (for example in inclusion bodies in E. coli).
  • the inventors recognised that the sequence set forth in SEQ ID NO: 13 (ie, a truncated form of the CAD domain), represents how the Kgp polyprotein is proteolytically processed and assembled on the cell surface.
  • the inclusion of such a sequence was therefore thought to be critical to the induction of an immune response to P. gingivalis.
  • the inventors surprisingly found that when present, this sequence contributed to poor solubility and formation of inclusion bodies of recombinant proteins when expressed in E. coli.
  • the inventors sought to rectify this issue by including the full sequence of the CAD in the fusion proteins. Surprisingly, this did not improve solubility and in fact contributed to lower solubility.
  • CADs cleaved adhesin domains
  • the second polypeptide does not comprise the sequence set forth in SEQ ID NO: 13 or a sequence at least 80 % identical thereto.
  • the second polypeptide does not comprise a sequence as set forth in SEQ ID NO: 12 or a sequence at least 80 % identical thereto or part thereof.
  • the inventors have also found that the solubility of the chimeric or fusion proteins of the invention is reduced when the chimeric or fusion proteins of the invention comprise only part of the DUF2436 domain (ie an N-terminally truncated DUF2436 domain).
  • the inventors recognised prior art approaches to P. gingivalis vaccine design included an N-terminally truncated form of the DUF2436 domain.
  • the truncated DUF2436 domain represents how the Kgp polyprotein is proteolytically processed and assembled on the cell surface, the inventors found that providing the sequence of the full length of the DUF2436 domain (ie including the N-terminal portion of the DUF2436 domain) substantially improved production of soluble recombinant protein.
  • the second polypeptide in the chimeric or fusion proteins of the invention comprises residues 1 to 37 of a DUF2436 domain, preferably wherein the chimeric protein comprises an amino acid sequence corresponding substantially to the full length of the DUF2436 domain of an Arg- or Lys- gingipain, or a sequence at least 80% identical thereto.
  • an amino acid sequence corresponding substantially to the full length of the DUF2436 domain, or a sequence at least 80% identical thereto refers to a sequence that is at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the length of a DUF2436 domain of an Arg- or Lys-gingipain.
  • the DUF2436 domain comprises the sequence set forth in SEQ ID NO: 23, or sequences at least 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical thereto.
  • the inventors have also established that various domains in gingpains have a propensity to multimerise, contributing to reduced solubility of the chimeric or fusion proteins and reduced immunogenicity when multimerised or aggregated.
  • the formation of multimers has implications for ease of large-scale production of chimeric proteins derived from ginigipain sequences and for use as vaccines, but may also affect the generation of protective responses.
  • the inventors have identified two mechanisms for multimer formation: the formation of disulphide bridges between cysteine residues and beta-strand exchange between ABM domains.
  • ABM 1 may interact with its next available neighbour, ABM2, during folding of the Kgp polyprotein in vivo.
  • the inventors show that co-expression of recombinant ABM1 and ABM2 as separate proteins, was able to form a stable beta sheet complexed structure.
  • the inventors targeted the cysteine residues of the DUF and ABM domains, in addition to specific motifs within ABMs 2 and 1 , which may be responsible for beta sheet formation.
  • c) comprises one or more cysteine amino acid substitutions in the amino acid sequence of the DUF 2436 domain and ABMs compared to the naturally occurring Arg- or Lys-gingipain sequences in corresponding regions; and/or d) comprises one or more amino acid motif substitutions selected from: i) substitution of the proline and/or an asparagine residues in the sequence PxxN corresponding to, or at a position equivalent to, residues 6 to 9 of the sequence of SEQ ID NO: 14 or 19 (ABM1); ii) substitution of the motif NxFA to SxYQ in the sequence, corresponding to, or at a position equivalent to residues 2 to 5 of the sequence of SEQ ID NO: 14 or 19 (ABM1); iii) substitution of the second tyrosine residue, corresponding to or at a position equivalent to residues at position 5 of
  • the second polypeptide comprises one or more cysteine amino acid substitutions compared to the naturally occurring adhesin domain sequence.
  • Cysteine residues are found (at least) in the DUF2436 domain, ABM 2 and in the K1 CAD sequence in the P. gingivalis Kgp sequence.
  • the cysteine amino acid substitution may be a substitution to a serine residue or a valine residue.
  • the one or more cysteine substitutions comprise one or more substitutions to a serine residue.
  • the cysteine residue in the DUF2436 domain is not substituted, while one or more cysteine residues in the region of the adhesin domain between the C-terminus of the DUF2436 domain and N-terminal to the K1 CAD domain, may be substituted.
  • An exemplary sequence of the region between the DUF domain and CAD domain is set forth in SEQ ID NO: 18.
  • one or both of the cysteine residues at positions 36 and 50, or positions equivalent thereto are substituted, optionally to a serine or valine residue, preferably to a serine residue.
  • An exemplary sequence of the DUF2436 domain plus ABM2+1+3 region is set forth in SEQ ID NO: 34.
  • one or both of the cysteine residues at positions 208 and 222, or positions equivalent thereto are substituted, optionally to a serine or valine residue, preferably to a serine residue.
  • the cysteine residue in the DUF2436 domain is substituted to a serine or valine residue, preferably a serine residue, and one or both cysteine residues in the region of the adhesin domain between the C-terminus of the DUF2436 domain and N-terminal to the K1 CAD domain, may be substituted.
  • An exemplary sequence of the region between the DUF domain and the CAD domain is set forth in SEQ ID NO: 18.
  • one or both of the cysteine residues at positions 36 and 50, or positions equivalent thereto are substituted, optionally to a serine or valine residue, preferably to a serine residue.
  • cysteine residue at position 115 and one or both of the cysteine residues at positions 208 and 222, or positions equivalent thereto, are substituted, optionally to a serine or valine residue, preferably to a serine residue.
  • the chimeric or fusion protein of the invention comprises an amino acid sequence corresponding to the sequence as set forth in any one of SEQ ID NOs: 35 to 49, or sequences at least 80% identical thereto (but for the cysteine substitutions therein).
  • the inventors have further established that multimerisation is also reduced by the mutation of a conserved motifs present in the ABM domains 2, 1 and 3.
  • the inventors considered modification of the domain at the N terminus of ABM 1 of the adhesin domain. More specifically, substitution of the motif PxxN (eg PVQN in ABM1 of P. gingivalis Kgp, as set forth in SEQ ID NO: 14), was found to substantially contribute to reduced multimerisation and reduction in beta-strand exchange between ABM domains.
  • substitution of the motif PxxN eg PVQN in ABM1 of P. gingivalis Kgp, as set forth in SEQ ID NO: 14
  • the chimeric or fusion proteins of the invention therefore comprise a modification of the ABM1 PxxN motif in the region of the chimeric or fusion protein corresponding to the adhesin domain of P. gingivalis gingipain.
  • the second polypeptide preferably comprises a proline substitution and an asparagine substitution, in the sequence PxxN corresponding, or at a position equivalent to positions 6 to 9 of the sequence of SEQ ID NO: 14 or 19 defining ABM 1.
  • the proline amino acid substitution is preferably a substitution to an alanine residue.
  • the asparagine amino acid substitution may be a substitution to a proline residue or an alanine residue.
  • the asparagine residue is substituted to a proline residue. In other embodiments, the asparagine residue is not substituted.
  • the inventors considered the motif NEFA in the sequence in ABM1 in the Kgp/Rgp polyprotein. This sequence is defined at residues 2 to 5 of SEQ ID NO: 14 and 19 herein. As demonstrated further in the examples, modification of the motif NEFA to SEQY, through substitution of the asparagine, phenylalanine and alanine residues to serine, glutamine and tyrosine, respectively, significantly reduces multimerisation.
  • the inventors determined that substitution of the tyrosine residue in ABM2 corresponding or at a position equivalent to residues at position 5 of SEQ ID NOs: 15 or 20, and of the tryptophan residue in ABM1 , corresponding or at a position equivalent to residue at position 23 of SEQ ID NOs: 14 or 19, to alanine residues, also significantly reduced multimerisation.
  • the inventors found that the combination of one or more cysteine modifications, preferably at least 2 cysteine substitutions to serine, and modification of the PXXN motif of ABM1 to AXXP, eliminated multimerisation of the resulting recombinant chimeric protein.
  • the present invention therefore provides for chimeric or fusion proteins as described herein, wherein the second polypeptide of the chimeric protein, corresponding to a region of an adhesin domain of a P. gingivalis Arg or Lys gingipain, comprises or consists of an amino acid sequence as set forth in SEQ ID NO: 34, or a sequence at least 80% identical thereto, wherein one, two or three cysteine residues are substituted to serine residues and/or wherein the proline and asparagine residues in the sequence PXXN at positions 235 to 238, or positions equivalent to, are substituted.
  • cysteine residue at residue 115 of SEQ ID NO: 34 is not substituted to either a serine or a valine residue.
  • the cysteine residue at position 115 of SEQ ID NO: 34, or a position equivalent thereto is not substituted to either a serine or a valine residue, while the cysteine residues at positions 208 and 222 of SEQ ID NO: 34, or at positions equivalent thereto, are substituted to serine residues, and wherein the proline residue at position 235, or position equivalent thereto, is substituted to an alanine residue and the asparagine residue at position 238, or a position equivalent thereto, is substituted to a proline.
  • the C-terminal residue of the first polypeptide may be covalently linked to the N-terminal residue of the second polypeptide (corresponding to an adhesin domain polypeptide) or the N-terminal residue of the first peptide may be covalently linked to the C-terminal residue of the second polypeptide (corresponding to an adhesin domain polypeptide).
  • the first peptide and adhesin domain polypeptide are said to be "directly linked” or "adjacent".
  • the chimeric or fusion protein includes a linker for linking the first peptide to an adhesin domain polypeptide.
  • the linker may be any linker able to join a peptide to a polypeptide, including both amino acid and non-amino acid linkers.
  • the linker is non-immunogenic.
  • the linker is comprised of amino acids, and may therefore be termed a peptide linker.
  • a linker is usually a peptide having a length of up to 20 amino acids, although may be longer.
  • the term "linked to” or “fused to” refers to a covalent bond, e.g., a peptide bond, formed between two moieties. Accordingly, in the context of the present invention the linker may have a length of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 or 22 or more amino acids.
  • the herein provided chimeric or fusion proteins may comprise a linker between the first polypeptide comprising or consisting of an amino acid sequence of a P. gingivalis gingipain active domain, and the second polypeptide corresponding to the adhesin domain of a P.
  • Suitable linkers may be up to 50 amino acids in length, although less than 20, less than 15 or less than five amino acids is preferred.
  • the linker may function to bring the first peptide and adhesin domain polypeptide into a closer spatial arrangement than normally observed in a P. gingivalis trypsin-like enzyme. Alternatively, it may space the first polypeptide and the second polypeptide (corresponding to an adhesin domain polypeptide) apart.
  • linker for use in protein constructs, including those with minimal impact on solubility are known in the art.
  • the linker may be any linker known in the art to the skilled person and may be a flexible linker (such as those comprising repeats of glycine and serine residues), a rigid linker (such as those comprising glutamic acid and lysine residues, flanking alanine repeats) and/or a cleavable linker (such as sequences that are susceptible by protease cleavage). Examples of such linkers are known to the skilled person and are described for example, in Chen et al., (2013) Advanced Drug Delivery Reviews, 65: 1357-1369.
  • Useful linkers include glycine-serine (GlySer) linkers, which are well-known in the art and comprise glycine and serine units combined in various orders. Examples include, but are not limited to, (GS), (GSGGS)n, (GGGS)n and (GGGGS)n, where n is an integer of at least one, typically an integer between 1 and about 10, for example, between 1 and about 8, between 1 and about 6, or between 1 and about 5.
  • the peptide linker may include the amino acids glycine and serine in various lengths and combinations.
  • the peptide linker can include the sequence Gly-Gly-Ser (GGS), Gly-Gly-Gly-Ser (GGGS) or Gly-Gly-Gly-Gly- Ser (GGGGS) and variations or repeats thereof.
  • the peptide linker can include the amino acid sequence GGGGS (a linker of 6 amino acids in length) or even longer.
  • the linker may a series of repeating glycine and serine residues (GS) of different lengths, i.e. , (GS)n where n is any number from 1 to 15 or more.
  • the linker may be (GS)3 (i.e., GSGSGS) or longer (GS)11 or longer. It will be appreciated that n can be any number including 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or more. Fusion proteins having linkers of such length are included within the scope of the present invention.
  • the linker may be a series of repeating glycine residues separated by serine residues. For example (GGGGS)3 (i.e., the linker may comprise the amino acid sequence GGGGSGGGGSGGGGS (G4S)3.) and variations thereof.
  • the peptide linker can include the amino acid sequence GGGGS (a linker of 6 amino acids in length) or even longer.
  • the linker may a series of repeating glycine and serine residues (GS) of different lengths, i.e., (GS)n where n is any number from 1 to 15 or more.
  • the linker may be (GS)3 (i.e., GSGSGS) or longer (GS)11 or longer. It will be appreciated that n can be any number including 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or more.
  • linkers include DSSG, DSSGAS, KLDSSG and variations thereof. Examples of other suitable linkers are described in Chen et al., (2013) Advanced Drug Delivery Reviews, 65: 1357-1369. Chimeric or fusion proteins and recombinant proteins
  • the chimeric or fusion proteins of the invention can be prepared by any of a number of conventional techniques although typically, the polypeptides are made using recombinant technology.
  • a DNA fragment encoding a desired peptide can be subcloned into an appropriate vector using well-known molecular genetic techniques (see, e.g., Maniatis et al., Molecular Cloning: A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory, 1982); Sambrook et al., Molecular Cloning A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory, 1989).
  • the fragment can be transcribed and the polypeptide subsequently translated in vitro.
  • kits e.g., such as manufactured by Clontech, Palo Alto, Calif.; Amersham Pharmacia Biotech Inc., Piscataway, N.J.; InVitrogen, Carlsbad, Calif., and the like).
  • the polymerase chain reaction optionally can be employed in the manipulation of nucleic acids.
  • a “fragment” is a portion of a polypeptide of the present invention that retains substantially similar functional activity or substantially the same biological function or activity as the polypeptide, which can be determined using assays described herein.
  • Percent (%) amino acid sequence identity or “percent (%) identical” with respect to a polypeptide sequence, i.e. a polypeptide of the invention defined herein, is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific polypeptide of the invention, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • Reference herein to variants having "at least x% sequence identity" to a recited sequence means that the variant is at least x% identical to the recited sequence.
  • the defined polypeptides are described by reference to variants having at least 80% homology to a reference sequence or more.
  • Percentage (%) homology generally refers to a polypeptide of the invention defined herein, defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific polypeptide of the invention, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • amino acids glycine, alanine, valine, leucine and isoleucine can often be substituted for one another (amino acids having aliphatic side chains). Of these possible substitutions it is preferred that glycine and alanine are used to substitute for one another (since they have relatively short side chains) and that valine, leucine and isoleucine are used to substitute for one another (since they have larger aliphatic side chains which are hydrophobic).
  • amino acids which can often be substituted for one another include: phenylalanine, tyrosine and tryptophan (amino acids having aromatic side chains); lysine, arginine and histidine (amino acids having basic side chains); aspartate and glutamate (amino acids having acidic side chains); asparagine and glutamine (amino acids having amide side chains); and cysteine and methionine (amino acids having sulphur containing side chains).
  • Amino acid deletions or insertions can also be made relative to the native sequence of the P. gingivalis protein.
  • amino acids which do not have a substantial effect on the activity of the polypeptide, or at least which do not eliminate such activity can be deleted.
  • Such deletions can be advantageous, particularly with longer polypeptides since the overall length and the molecular weight of a polypeptide can be reduced whilst still retaining activity. This can enable the amount of polypeptide required for a particular purpose to be reduced - for example, dosage levels can be reduced.
  • Amino acid insertions relative to the sequence of the native polypeptide can also be made. This can be done to alter the properties of a polypeptide for use in the present invention (e.g. to enhance antigenicity).
  • Amino acid changes can be made using any suitable technique e.g. by using site- directed mutagenesis or solid-state synthesis.
  • amino acid substitutions or insertions within the scope of the present invention can be made using naturally occurring or non-naturally occurring amino acids. Whether or not natural or synthetic amino acids are used, it is preferred that only L-amino acids are present.
  • PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra.
  • the default parameters of the respective programs e.g., BLASTX and BLASTN
  • Alignment may also be performed manually by inspection.
  • Another non- limiting example of a mathematical algorithm utilized for the comparison of sequences is the ClustalW algorithm (Higgins et al. (1994) Nucleic Acids Res. 22:4673- 4680).
  • ClustalW compares sequences and aligns the entirety of the amino acid or DNA sequence, and thus can provide data about the sequence conservation of the entire amino acid sequence.
  • the ClustalW algorithm is used in several commercially available DNA/amino acid analysis software packages, such as the ALIGNX module of the Vector NTI Program Suite (Invitrogen Corporation, Carlsbad, CA). After alignment of amino acid sequences with ClustalW, the percent amino acid identity can be assessed.
  • a non-limiting examples of a software program useful for analysis of ClustalW alignments is GENEDOCTM or JalView (http://www.jalview.org/). GENEDOCTM allows assessment of amino acid (or DNA) similarity and identity between multiple proteins.
  • the polypeptide desirably comprises an amino end and a carboxyl end.
  • the polypeptide can comprise D-amino acids, L-amino acids or a mixture of D- and L-amino acids.
  • the D-form of the amino acids is particularly preferred since a polypeptide comprised of D-amino acids is expected to have a greater retention of its biological activity in vivo.
  • conservative substitution refers to the replacement of an amino acid present in the native sequence in the peptide with a naturally or non- naturally occurring amino acid or a peptidomimetic having similar steric properties.
  • side-chain of the native amino acid to be replaced is either polar or hydrophobic
  • the conservative substitution should be with a naturally occurring amino acid, a non- naturally occurring amino acid or with a peptidomimetic moiety which is also polar or hydrophobic (in addition to having the same steric properties as the side-chain of the replaced amino acid).
  • Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that may be considered to be conservative substitutions for one another:
  • conservative substitutions by naturally occurring amino acids can be determined bearing in mind the fact that replacement of charged amino acids by sterically similar non-charged amino acids are considered as conservative substitutions.
  • amino acid analogues synthetic amino acids
  • a peptidomimetic of the naturally occurring amino acid is well documented in the literature known to the skilled person and non-natural or unnatural amino acids are described further below.
  • the substituting amino acid should have the same or a similar functional group in the side chain as the original amino acid.
  • non-conservative substitution or a “non-conservative residue” as used herein refers to replacement of the amino acid as present in the parent sequence by another naturally or non-naturally occurring amino acid, having different electrochemical and/or steric properties.
  • the side chain of the substituting amino acid can be significantly larger (or smaller) than the side chain of the native amino acid being substituted and/or can have functional groups with significantly different electronic properties than the amino acid being substituted.
  • non-conservative substitutions of this type include the substitution of phenylalanine or cyclohexylmethyl glycine for alanine, isoleucine for glycine, or -NH-CH[(-CH2)5-COOH]-CO- for aspartic acid.
  • Non-conservative substitution includes any mutation that is not considered conservative.
  • a non-conservative amino acid substitution can result from changes in: (a) the structure of the amino acid backbone in the area of the substitution; (b) the charge or hydrophobicity of the amino acid; or (c) the bulk of an amino acid side chain.
  • Substitutions generally expected to produce the greatest changes in protein properties are those in which: (a) a hydrophilic residue is substituted for (or by) a hydrophobic residue; (b) a proline is substituted for (or by) any other residue; (c) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine; or (d) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histadyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl.
  • Alterations of the native amino acid sequence to produce mutant polypeptides can be done by a variety of means known to those skilled in the art.
  • site-specific mutations can be introduced by ligating into an expression vector a synthesized oligonucleotide comprising the modified site.
  • oligonucleotide-directed site-specific mutagenesis procedures can be used, such as disclosed in Walder et al., Gene 42: 133 (1986); Bauer et al., Gene 37: 73 (1985); Craik, Biotechniques, 12-19 (January 1995); and U.S. Pat. Nos. 4,518,584 and 4,737,462.
  • a preferred means for introducing mutations is the QuikChange Site- Directed Mutagenesis Kit (Stratagene, LaJolla, Calif.).
  • Any appropriate expression vector e.g., as described in Pouwels et al., CIoning Vectors: A Laboratory Manual (Elsevier, N.Y.: 1985)
  • suitable host can be employed for production of recombinant polypeptides.
  • Expression hosts include, but are not limited to, bacterial species within the genera Escherichia, Bacillus, Pseudomonas, Salmonella, mammalian or insect host cell systems including baculovirus systems (e.g., as described by Luckow et al., Bio/Technology 6: 47 (1988)), and established cell lines such as the COS-7, C127, 3T3, CHO, HeLa, and BHK cell lines, and the like.
  • polypeptides produced in yeast or mammalian cells will differ from that of polypeptides produced in bacterial cells, such as Escherichia coli.
  • a polypeptide of the invention can be synthesized using standard peptide synthesizing techniques well-known to those of ordinary skill in the art (e.g., as summarized in Bodanszky, Principles of Peptide Synthesis (Springer-Verlag, Heidelberg: 1984)).
  • the polypeptide can be synthesized using the procedure of solid- phase synthesis (see, e.g., Merrifield, J. Am. Chem. Soc. 85: 2149-54 (1963); Barany et al., Int. J. Peptide Protein Res. 30: 705-739 (1987); and U.S. Pat. No. 5,424,398). If desired, this can be done using an automated peptide synthesizer.
  • t-BOC t-butyloxycarbonyl
  • Fmoc 9-fluorenylmethyloxycarbonyl
  • the polypeptide-containing mixture can then be extracted, for instance, with dimethyl ether, to remove non-peptidic organic compounds, and the synthesized polypeptide can be extracted from the resin powder (e.g., with about 25% w/v acetic acid).
  • further purification e.g., using high performance liquid chromatography (HPLC)
  • HPLC high performance liquid chromatography
  • Amino acid and/or HPLC analysis can be performed on the synthesized polypeptide to validate its identity.
  • the chimeric or fusion protein of the invention may comprise additional amino acid residues to facilitate expression in a recombinant expression system and/or to facilitate purification of the protein.
  • the proteins defined herein may include additional amino acids such as one, two, three, four, or five amino acids in the N-terminal region.
  • the additional amino acids will include an N- terminal methionine for facilitating expression in recombinant expression systems although it will be appreciated that typically such N-terminal residues are cleaved following translation of the protein.
  • the N-terminal amino acids include at least methionine and an alanine residue.
  • a chimeric or fusion protein according to the invention may include additional amino acids such as one, two, three, four, or five amino acids in the N or C- terminal region, preferably to facilitate purification. It will be understood that such amino acid residues may facilitate the inclusion of a purification tag in the protein (such as histidine tags and the like). Such residues may not be included where untagged versions of the protein are produced.
  • a polypeptide of the invention may also be modified by, conjugated or fused to another moiety to facilitate purification, or increasing the in vivo half-life of the polypeptides, or for use in immunoassays using methods known in the art.
  • a polypeptide of the invention may be modified by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc.
  • nucleic acid molecules that encode any of the chimeric or fusion proteins or polypeptides of the invention are also within the scope of the invention.
  • the nucleic acids are useful, for example, in making the polypeptides of the present invention and as therapeutic agents. They may be administered to cells in culture or in vivo and may include a secretory signal that directs or facilitates secretion of the polypeptide of the invention from the cell. Also within the scope of the invention are expression vectors and host cells that contain or include nucleic acids of the invention (described further below).
  • nucleic acids of the invention may be referred to as “isolated,” by definition, the polypeptides of the invention are not wild-type polypeptides and, as such, would not be encoded by naturally occurring nucleic acids.
  • polypeptides and nucleic acids of the present invention may be “purified,” “substantially purified,” “isolated,” “recombinant” or “synthetic” they need not be so in order to be distinguished from naturally occurring materials.
  • An “isolated” nucleic acid molecule is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the nucleic acid.
  • an isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the nucleic acid molecule as it exists in natural cells. However, an isolated nucleic acid molecule includes nucleic acid molecules contained in cells that ordinarily express Kgp where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • nucleic acid molecule and “polynucleotide” are used interchangeably herein and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogues thereof.
  • Non-limiting examples of polynucleotides include a gene, a gene fragment, messenger RNA (mRNA), cDNA, recombinant polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • a polynucleotide of the invention may be provided in isolated or purified form.
  • a nucleic acid sequence which "encodes" a selected polypeptide is a nucleic acid molecule which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vivo when placed under the control of appropriate regulatory sequences.
  • the boundaries of the coding sequence are determined by a start codon at the 5' (amino) terminus and a translation stop codon at the 3' (carboxy) terminus.
  • such nucleic acid sequences can include, but are not limited to, cDNA from viral, prokaryotic or eukaryotic mRNA, genomic sequences from viral or prokaryotic DNA or RNA, and even synthetic DNA sequences.
  • a transcription termination sequence may be located 3' to the coding sequence.
  • Polynucleotides of the invention can be synthesised according to methods well known in the art, as described by way of example in Sambrook et al (1989, Molecular CIoning — a laboratory manual; Cold Spring Harbor Press).
  • the polynucleotide molecules of the present invention may be provided in the form of an expression cassette which includes control sequences operably linked to the inserted sequence, thus allowing for expression of the polypeptide of the invention in vivo in a targeted subject.
  • These expression cassettes are typically provided within vectors (e.g., plasmids or recombinant viral vectors) which are suitable for use as reagents for nucleic acid immunization.
  • vectors e.g., plasmids or recombinant viral vectors
  • Such an expression cassette may be administered directly to a host subject.
  • a vector comprising a polynucleotide of the invention may be administered to a host subject.
  • the polynucleotide is prepared and/or administered using a genetic vector.
  • a suitable vector may be any vector which is capable of carrying a sufficient amount of genetic information and allowing expression of a polypeptide of the invention.
  • the present invention thus includes expression vectors that comprise such polynucleotide sequences.
  • the present invention provides a vector for use in preventing or treating an inflammatory disease or condition comprising a polynucleotide sequence which encodes a polypeptide of the invention and optionally one or more further polynucleotide sequences which encode different polypeptides as defined herein.
  • compositions and products of the invention may comprise a mixture of polypeptides and polynucleotides. Accordingly, the invention provides a composition or product as defined herein, wherein in place of any one of the polypeptide is a polynucleotide capable of expressing said polypeptide.
  • Expression vectors are routinely constructed in the art of molecular biology and may for example involve the use of plasmid DNA and appropriate initiators, promoters, enhancers and other elements, such as for example polyadenylation signals which may be necessary, and which are positioned in the correct orientation, in order to allow for expression of a peptide of the invention.
  • Other suitable vectors would be apparent to persons skilled in the art.
  • a polypeptide of the invention may be provided by delivering such a vector to a cell and allowing transcription from the vector to occur.
  • a polynucleotide of the invention or for use in the invention in a vector is operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector.
  • operably linked refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function.
  • a given regulatory sequence, such as a promoter, operably linked to a nucleic acid sequence is capable of effecting the expression of that sequence when the proper enzymes are present.
  • the promoter need not be contiguous with the sequence, so long as it functions to direct the expression thereof.
  • intervening untranslated yet transcribed sequences can be present between the promoter sequence and the nucleic acid sequence and the promoter sequence can still be considered "operably linked" to the coding sequence.
  • a number of expression systems have been described in the art, each of which typically consists of a vector containing a gene or nucleotide sequence of interest operably linked to expression control sequences. These control sequences include transcriptional promoter sequences and transcriptional start and termination sequences.
  • the vectors of the invention may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter.
  • a "plasmid” is a vector in the form of an extra-chromosomal genetic element.
  • the vectors may contain one or more selectable marker genes, for example an ampicillin resistance gene in the case of a bacterial plasmid or a resistance gene for a fungal vector.
  • Vectors may be used in vitro, for example for the production of DNA or RNA or used to transfect or transform a host cell, for example, a mammalian host cell.
  • the vectors may also be adapted to be used in vivo, for example to allow in vivo expression of the polypeptide.
  • a “promoter” is a nucleotide sequence which initiates and regulates transcription of a polypeptide-encoding polynucleotide. Promoters can include inducible promoters (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), repressible promoters (where expression of a polynucleotide sequence operably linked to the promoter is repressed by an analyte, cofactor, regulatory protein, etc.), and constitutive promoters. It is intended that the term “promoter” or “control element” includes full-length promoter regions and functional (e.g., controls transcription or translation) segments of these regions.
  • a polynucleotide, expression cassette or vector according to the present invention may additionally comprise a signal peptide sequence.
  • the signal peptide sequence is generally inserted in operable linkage with the promoter such that the signal peptide is expressed and facilitates secretion of a polypeptide encoded by coding sequence also in operable linkage with the promoter.
  • a signal peptide sequence encodes a peptide of 10 to 30 amino acids for example 15 to 20 amino acids. Often the amino acids are predominantly hydrophobic. In a typical situation, a signal peptide targets a growing polypeptide chain bearing the signal peptide to the endoplasmic reticulum of the expressing cell. The signal peptide is cleaved off in the endoplasmic reticulum, allowing for secretion of the polypeptide via the Golgi apparatus.
  • the invention further provides compositions comprising the chimeric or fusion proteins defined herein, and the use of such chimeric or fusion proteins in immunogenic or vaccine compositions in the treatment or prevention of P. gingivalis infection.
  • vaccine composition used herein is defined as a composition used to elicit an immune response against an antigen (immunogen) within the composition in order to protect or treat an organism against disease.
  • immunological composition As used herein, the terms “immunostimulating composition”, “vaccine composition” and “immunogenic composition” may generally be used interchangeably.
  • the immunostimulating compositions or vaccines of the invention may suitably include a pharmaceutically acceptable carrier, excipient, diluent, adjuvant, vehicle, buffer or stabiliser in addition to one or more peptides of the invention as the therapeutically or prophylactically active ingredient.
  • a pharmaceutically acceptable carrier include, but are not limited to, saline, buffered saline, dextrose, liposomes, water, glycerol, polyethylene glycol, ethanol and combinations thereof.
  • the immunostimulating compositions or vaccine compositions can be adapted for administration by any appropriate route, for example by the parenteral (including subcutaneous, intramuscular, intravenous or intradermal or by injection into the cerebrospinal fluid), oral (including buccal or sublingual), nasal, topical (including buccal, sublingual or transdermal), vaginal or rectal route.
  • Such compositions can be prepared by any method known in the art of pharmacy, for example by admixing peptides with the carrier(s) or excipient(s) under sterile conditions.
  • the vaccine composition is adapted for administration by the subcutaneous, intramuscular, intravenous or intradermal route, typically by injection.
  • the vaccine composition may be adapted for oral or nasal administration.
  • An immunostimulating composition or vaccine composition adapted for parenteral administration may be an aqueous and non-aqueous sterile injection solution which can contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation substantially isotonic with the blood of the intended recipient; and aqueous and non- aqueous sterile suspensions which can include suspending agents and thickening agents.
  • Excipients which can be used for injectable solutions include water, alcohols, polyols, glycerine and vegetable oils, for example.
  • composition can be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carried, for example water for injections, immediately prior to use.
  • sterile liquid carried, for example water for injections, immediately prior to use.
  • Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules and tablets.
  • An immunostimulating or vaccine composition adapted for oral administration can be presented as discrete units such as capsules or tablets or lozenges; as powders or granules; as solutions, syrups or suspensions (in aqueous or non-aqueous liquids; or as edible foams or whips; or as emulsions).
  • Suitable excipients for tablets or hard gelatine capsules include lactose, maize starch or derivatives thereof, stearic acid or salts thereof.
  • Suitable excipients for use with soft gelatine capsules include for example vegetable oils, waxes, fats, semi-solid, or liquid polyols etc.
  • excipients which can be used include for example water, polyols and sugars.
  • oils e.g. vegetable oils
  • oil-in-water or water in oil suspensions can be used.
  • An immunostimulating or vaccine composition adapted for nasal administration wherein the carrier is a solid include a coarse powder having a particle size for example in the range 20 to 500 microns which is administered in the manner in which snuff is taken, i.e. by rapid inhalation through the nasal passage from a container of the powder held close up to the nose.
  • a suitable composition wherein the carrier is a liquid, for administration as a nasal spray or as nasal drops, may comprise an aqueous or oil solution of the active ingredient.
  • Compositions adapted for administration by inhalation include fine particle dusts or mists that can be generated by means of various types of metered dose pressurised aerosols, nebulizers or insufflators.
  • An immunostimulating or vaccine composition adapted for transdermal administration may be presented as a discrete patch intended to remain in intimate contact with the epidermis of the recipient for a prolonged period of time.
  • the active ingredient can be delivered from the patch by iontophoresis as generally described in Pharmaceutical Research. 3(6):318 (1986).
  • a composition adapted for topical administration may be formulated as an ointment, cream, suspension, lotion, powder, solution (eg mouth wash) paste, gel, spray, aerosol or oil.
  • the composition may be applied as a topical ointment or cream.
  • the active ingredient can be employed with either a paraffinic or a water- miscible ointment base.
  • the active ingredient can be formulated in a cream with an oil-in-water cream base or a water-in-oil base.
  • a pharmaceutical composition adapted for topical administration to the eye may comprise eye drops wherein the active ingredient is dissolved or suspended in a suitable carrier, especially an aqueous solvent.
  • a pharmaceutical composition adapted for topical administration in the mouth may comprise lozenges, pastilles or mouth washes.
  • the immunostimulating or vaccine composition may contain preserving agents, solubilising agents, stabilising agents, wetting agents, emulsifiers, sweeteners, colourants, odourants, salts (substances of the present invention can themselves be provided in the form of a pharmaceutically acceptable salt), buffers, coating agents or antioxidants.
  • the vaccine composition of the invention may also contain one or more other prophylactically or therapeutically active agents in addition to the chimeric or fusion protein as defined herein.
  • a chimeric or fusion protein for use in the vaccine compositions of the invention may or may not be lyophilised.
  • the vaccine compositions of the invention may also include a pharmaceutically acceptable adjuvant in addition to the peptide(s) as defined herein.
  • Adjuvants are added in order to enhance the immunogenicity of the vaccine composition.
  • Suitable adjuvants for inclusion in a vaccine composition include incomplete Freund's adjuvant, complete Freund's adjuvant, Freund's adjuvant with MDP (muramyldipeptide), alum (aluminium hydroxide), alum plus Bordatella pertussis and immune stimulatory complexes (ISCOMs, typically a matrix of Quil A containing viral proteins), QS- 21 , Detox-PC, MPL-SE, MoGM-CSF, TiterMax-G, CRL- 1005, GERBU, TERamide, PSC97B, Adjumer, PG-026, GSK-I, GcMAF, B-alethine, MPC-026, Adjuvax, CpG ODN, Betafectin, and MF59.
  • incomplete Freund's adjuvant include incomplete Freund's adjuvant, complete Freund's adjuvant, Freund's adjuvant with MDP (muramyldipeptide), alum (aluminium hydroxide), a
  • the vaccine compositions of the invention may also include or be co-administered with one or more co-stimulatory molecules.
  • Dosages of the vaccine composition of the present invention can vary between wide limits, depending upon the age and condition of the individual to be treated, etc. and a physician will ultimately determine appropriate dosages to be used.
  • This dosage can be repeated as often as appropriate. For example, an initial dose of the vaccine may be administered and then a booster administered at a later date.
  • the daily dosage of the active agent will be from 1 ⁇ g/kg to 10 mg/kg body weight, typically around 10 ⁇ g /kg to 1 mg/kg body weight.
  • the physician in any event will determine the actual dosage which will be most suitable for an individual which will be dependent on factors including the age, weight, sex and response of the individual.
  • the above dosages are exemplary of the average case. There can, of course, be instances where higher or lower dosages are merited, and such are within the scope of this invention.
  • the vaccine composition of the invention can be administered by any convenient route as described herein, such as via the intramuscular, intravenous, by inhalation, intraperitoneal or oral routes or by injection into the cerebrospinal fluid.
  • the vaccine composition of the invention can be provided in unit dosage form, will generally be provided in a sealed container and may be provided as part of a kit. Such a kit would normally (although not necessarily) include instructions for use. It can include a plurality of said unit dosage forms.
  • the present invention provides a kit of parts comprising a vaccine composition of the invention and one or more cytokines and/or adjuvants in sealed containers.
  • the present invention provides methods and compositions for treating or preventing infection or minimising the likelihood of infection with P. gingivalis, in an individual in need thereof, the methods comprising administering a fusion or chimeric protein of the invention.
  • the present invention also provides for methods and compositions for inducing a a humoural immune response in a subject to P. gingivalis.
  • the humoural response may be for the purposes of obtaining protective/therapeutic anti-P. gingivalis antibodies directly in the individual requiring protection/therapy.
  • the humoural response may be for the purpose of generating antibodies which are then isolated from the subject (or egg thereof), such that the antibodies can then be directly administered to an individual requiring treatment/protection with the antibodies.
  • the present invention includes methods and compositions for preventing infection with P. gingivalis, minimising the likelihood of infection and/or reducing the severity and duration of P. gingivalis infection in a subject.
  • the present invention also provides a method for obtaining an antibody directed to P. gingivalis, the method comprising administering a chimeric or fusion protein, composition, vaccine or immune stimulating composition of the invention, to a non-human animal, thereby generating antibodies directed to P. gingivalis in the animal.
  • the method further comprises isolating the antibody from the animal (eg from the blood of the animal) or from an egg of the animal (eg in the case of generating IgY antibodies from chickens).
  • the present invention also provides an antibody preparation comprising an antibody directed to P. gingivalis, wherein the antibody preparation is obtained by administering a chimeric or fusion protein, composition, vaccine or immune stimulating composition of the invention, to a non-human animal, thereby generating antibodies directed to P. gingivalis in the animal, and isolating the antibodies from the animal or egg thereof.
  • the antibody directed to P. gingivalis may be used therapeutically to eliminate or reduce P. gingivalis infection or prophylactically, to prevent or reduce the severity of P. gingivalis infection.
  • treatment or “treating” of a subject includes the application or administration of a composition of the invention to a subject (or application or administration of a compound of the invention to a cell or tissue from a subject) with the purpose of delaying, slowing, stabilizing, curing, healing, alleviating, relieving, altering, remedying, less worsening, ameliorating, improving, or affecting the disease or condition, the symptom of the disease or condition, or the risk of (or susceptibility to) the disease or condition.
  • treating refers to any indication of success in the treatment or amelioration of an injury, pathology or condition, including any objective or subjective parameter such as abatement; remission; lessening of the rate of worsening; lessening severity of the disease; stabilization, diminishing of symptoms or making the injury, pathology or condition more tolerable to the subject; slowing in the rate of degeneration or decline; making the final point of degeneration less debilitating; or improving a subject's physical or mental well-being.
  • preventing or “prevention” is intended to refer to at least the reduction of likelihood of the risk of (or susceptibility to) acquiring a disease or disorder (i.e. , causing at least one of the clinical symptoms of the disease not to develop in a subject that may be exposed to or predisposed to the disease but does not yet experience or display symptoms of the disease).
  • Biological and physiological parameters for identifying such subjects are provided herein and are also well known by physicians.
  • the vaccine compositions of the invention can be administered to subjects felt to be in greatest need thereof, for example in the context of human patients, to children or the elderly or individuals at risk of exposure to P. gingivalis.
  • the vaccine compositions of the invention can also be administered to subjects suspected of having or diagnosed with having infection with P. gingivalis.
  • compositions and methods of the present invention extend equally to uses in both human and/or veterinary medicine, generation of diagnostic agents or the generation of other treatment reagents.
  • the term "subject” shall be taken to mean any animal including humans, for example a mammal. Exemplary subjects include but are not limited to humans and non-human primates. For example, the subject may be a human. In further examples, the subject may be a veterinary subject, such as a companion animal (cat, dog, guinea pig, and the like).
  • the skilled person will be familiar with methods for determining successful vaccination/immunisation with a chimeric or fusion protein or composition as described herein.
  • the skilled person will be familiar with methods for quantifying the antibodies generated following immunisation and/or for quantifying the extent of the humoural (Th2) response induced following immunisation.
  • kit or article of manufacture including one or more proteins, polypeptides or polynucleotides of the invention and/or immunogenic composition as described above.
  • the present invention provides a kit of parts comprising a vaccine composition of the invention and one or more adjuvants for separate, subsequent or simultaneous administration to a subject.
  • kits for use in a therapeutic or prophylactic application mentioned above including: - a container holding a protein, polypeptide, polynucleotide or immunogenic composition of the invention;
  • kit may contain one or more further active principles or ingredients for eliciting an immune response to P. gingivalis in a subject.
  • the kit or "article of manufacture” may comprise a container and a label or package insert on or associated with the container.
  • Suitable containers include, for example, bottles, vials, syringes, blister pack, etc.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a therapeutic composition which is effective for treating the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the label or package insert indicates that the therapeutic composition is used for treating the condition of choice.
  • the label or package insert includes instructions for use and indicates that the therapeutic or prophylactic composition can be used to treat an inflammatory disease or condition described herein.
  • the kit may comprise (a) a therapeutic or prophylactic composition; and (b) a second container with a second active principle or ingredient contained therein.
  • the kit in this embodiment of the invention may further comprise a package insert indicating the composition and other active principle can be used to treat a disorder or prevent a complication stemming from an inflammatory disease or condition described herein.
  • the kit may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
  • BWFI bacteriostatic water for injection
  • the therapeutic composition may be provided in the form of a device, disposable or reusable, including a receptacle for holding the therapeutic, prophylactic or immunogenic composition.
  • the device is a syringe, autoinjector or nanopatch.
  • the device may hold between 0.1 to 2 mL of the therapeutic or immunogenic composition.
  • the therapeutic or prophylactic composition may be provided in the device in a state that is ready for use or in a state requiring mixing, dissolution or resuspension or addition of further components.
  • Example 1 describes the materials and methods used in the studies described in Examples 2 and 3.
  • Example 2 describes the results of in vitro studies and
  • Example 3 describes the results of in vivo studies.
  • Example 1 Materials and methods
  • Recombinant proteins i.e., different chimeric or fusion proteins as described herein
  • pET28 vector or pDUET-1 for rABM1 + rABM2 co- expression from one vector
  • IPTG isopropyl p-D-thiogalactosidase
  • Nucleic acids encoding different chimeras and components of the chimeras and fusion proteins were produced by standard PCR or DNA splicing via overlap extension ("SOEing") PCR using P. gingivalis W50 genomic DNA template and specifically designed oligonucleotide primers.
  • SOEing overlap extension
  • PCR fragments or SOEn PCR fragments were purified and ligated into cloning vectors pGEMTeasy or pBHA and transformed into chemically competent E. coli a-Gold cells (Bioline, New South Wales, Australia).
  • DNA sequences encoding single additional KAS (i.e. active site) residues containing either a "DSSG" amino acid linker region or no linker were sequentially added to the recombinant chimera and Kgp adhesin domains, one at a time, essentially as follows: restriction enzyme sites were introduced onto the ends of DNA insert fragments in chimera and adhesin variant motherclones by PCR with oligonucleotide primers containing nucleotides specific for restriction enzymes. Synthetic DNA fragments encoding an individual KAS sequence with corresponding restriction sequence were ligated onto the insert ends of DNA constructs from motherclones and recombinant clones were purified.
  • KAS active site
  • Residues within ABM1 and ABM2 and Cysteine residues were mutated using the QuickChange II Site Directed Mutagenesis kit (Stratagene, La Jolla, CA) following the manufacturer's instructions.
  • Cultures (200 mL) were subjected to IPTG induction at various temperatures (e.g., 5 h at 30°C or 16 h at 16°C). Cells were harvested and resuspended in lysis buffer (20 mM sodium phosphate, 500 mM NaCI, 0.5% v/v Triton X-100, 5mg/ml DNAsel, 1X proteinase inhibitor cocktail, 1mg/ml lysozyme, 10 mM imidazole, pH 8).
  • lysis buffer (20 mM sodium phosphate, 500 mM NaCI, 0.5% v/v Triton X-100, 5mg/ml DNAsel, 1X proteinase inhibitor cocktail, 1mg/ml lysozyme, 10 mM imidazole, pH 8).
  • Recombinant proteins subject to SDS PAGE were subject to staining using Invision In Gel His Stain kit (Invitrogen) following manufacturers' instructions. This stain is highly specific for His-tagged proteins. This procedure was used to identify N-terminal degradation of recombinant proteins since all candidates contained a C-terminal His tag. Large scale purification of chimera for study in animal models
  • All recombinant proteins identified for use as vaccine candidates for animal models were expressed as recombinant C-terminally His-tagged fusion proteins or as "tagless" proteins, in E. coli BL21 (DE3) as previously described.
  • the cells were lysed for 1.5 h on-ice in lysis buffer [0.35 mg/mL lysozyme, 40 ⁇ g/mL DNAse I in TBS150 (50 mM Tris Ci, 150 mM NaCI, pH 7.5], plus 1% Triton X-100 and EDTA-free protease inhibitors (Complete ULTRA Tablets, Sigma- Aldrich) unless indicated otherwise.
  • lysis buffer [0.35 mg/mL lysozyme, 40 ⁇ g/mL DNAse I in TBS150 (50 mM Tris Ci, 150 mM NaCI, pH 7.5], plus 1% Triton X-100 and EDTA-free protease inhibitors (Complete ULTRA Tablets, Sigma- Aldrich) unless indicated otherwise.
  • the cell lysate was clarified by centrifugation for 40 min at 23,500 g at 4°C.
  • Initiator Met residue (aa 1) on all recombinant proteins denoted in Table 1 beginning with the translated sequence MA is removed in vivo by E. coli N terminal Methionine processing enzymes that cleave Methionine when the penultimate residue is a small residue. This was confirmed by mass spectrometric analyses of KDAK and KDAK-variant recombinant proteins.
  • Ni-affinity chromatography Cell lysates were clarified by centrifugation at 20,000 g at 4 °C to remove the cell debris. After filtration through a 0.22 ⁇ m filter, lysates were loaded to a HisTrap Ni-affinity column (GE Healthcare) in loading buffer TBS300 (50 mM Tris Ci, 300 mM NaCI, pH 7.5), plus 10 mM imidazole and 1 % Triton X-100. Columns were washed extensively with the loading buffer and then 20 mM imidazole in TBS300. Bound proteins were eluted with a 20-350 mM imidazole gradient in TBS300 with the absorbance being monitored at 280 nm.
  • Peak fractions were analysed with SDS- and/or native PAGE. Eluted target proteins were concentrated using the Amicon filter units with a molecular weight cutoff of 3 kDa or 10 kDa depending on the protein sizes. The resulting protein solutions were stored at -70 °C for further purification.
  • the isoelectric points (pls) of all candidate proteins were predicted to be in the acidic range using online analysing ProtParam tool - ExPASy (https://web.expasy.org/protparam/), thus anion exchange chromatography was applied for further purification when necessary.
  • the concentrated proteins from Ni-affinity purification were diluted into buffer A (50 mM Tris. CI, 20 mM NaCI, pH 7.5) to reduce ionic strength and then loaded to an anion exchange HiTrap Q column (GE Healthcare) in buffer A.
  • the proteins were eluted with a NaCI gradient from 20 to 400 mM in the Tris buffer with the absorbance at 280 nm monitored.
  • Target proteins in the peak fractions were verified with SDS- and/or native PAGE and concentrated using the Amicon filter units of an appropriate molecular weight cut-off.
  • the protein solutions were stored at -70 °C for further purification or buffer exchange using size exclusion chromatography or dialysis.
  • Size exclusion chromatography was performed on a HiLoad Superdex 200 or a HiLoad Superdex 75 column (GE Healthcare) at 4°C.
  • the proteins from Ni affinity purification or the further step of anion exchange chromatography were loaded to an appropriate column and eluted in the buffer of TBS150 or TBS100 (100 mM NaCI in 50 mM Tris.CI, pH 7.5) with absorbance at 280 nm monitored.
  • Target proteins in the peak fractions were verified with SDS- and/or native PAGE.
  • second or further rounds of size exclusion purification were performed. The fractions containing the best protein purity were pooled and concentrated.
  • the target protein fractions were simply pooled and concentrated. Protein identities were confirmed by determination of intact protein molar masses using liquid chromatography-electrospray ionisation spectrometry (LC-MS, Agilent) or by sequence analysis using liquid chromatography Orbitrap tandem mass spectrometry (LC-MS/MS, Agilent) where necessary. Protein concentration was quantitated by determination of the absorbance at 280 nm using calculated extinction coefficients before submission for animal model experiments.
  • LC-MS liquid chromatography-electrospray ionisation spectrometry
  • Agilent sequence analysis using liquid chromatography Orbitrap tandem mass spectrometry
  • the insoluble pellet was washed twice with TBS150.
  • the proteins expressed as inclusion bodies were solubilised with 8 M urea at room temperature on a rolling platform for 1 hour in TBS300 or 20 mM NaPi, 500 mM NaCI, pH 7.4 (PBS500).
  • the protein extracts were centrifuged at 20,000 g and filtered through a 0.22 pm filter unit and then loaded to the HisTrap affinity column in the urea containing buffer TBSU (8 M urea in TBS300 plus 20 mM imidazole) or PBSU (8 M urea, 20 mM NaPi pH 7.8, 500 mM NaCI, plus 20 mM imidazole).
  • the column was extensively washed with the same 8 M urea buffer. A further wash with PBSU at pH 6.5 was applied for the columns with proteins loaded in PBSU. For removal of urea, the target proteins were eluted with a gradient of 20-500 mM imidazole in PBSU. When loose Ni-NTA resin (Thermofisher) was used, the urea extracts were mixed with the resin for 2 hours with gentle stirring in PBSU. After extensive wash with PBSU (pH 7.8 and then pH 6.5) and the bound proteins were eluted off the resin with 500 mM imidazole in the same buffer.
  • PBSU pH 7.8 and then pH 6.5
  • the eluted proteins were stepwise dialysed into 6 M, 4 M and then 2 M urea phosphate buffers in a dialysis tube with molecular weight cut- off of 3.5 kDa (Fisher Biotec, Australia).
  • the proteins in the 2 M urea buffer were further dialysed into saline only and kept at 4 °C before submission to animal model experiments or otherwise submitted in 2 M urea buffer without further dialysis.
  • the proteins were extracted from inclusion bodies with 6 M urea buffer in the presence of 5 mM TCEP and loaded to a HisTrap column in the same buffer. After the column was washed with 4 M urea buffer containing 2 M TCEP, the target proteins were refolded on column with a decreasing concentration gradient of urea from 4 to 0 M in the presence of 2 M TCEP. The proteins were then eluted with an increasing concentration gradient of imidazole from 20-350 mM in TBS300 plus 2 mM TCEP.
  • the eluted proteins were then concentrated for size exclusion chromatography in the reducing buffer (2 mM TCEP in TBS150) the same way as described in the section for purification of the protein dimer or multimers from soluble fractions under nondenaturing conditions. After analysis with SDS- and native PAGE, mass spectrometry and quantitation, the samples were stored at -70 °C in the reducing buffer or submitted for animal model experiments.
  • Anion exchange chromatography This is the first chromatographic step for purification of the tagless proteins. Like their His-tagged counterparts, pls of the tagless candidates were predicted to also be in the acidic range using online analysing ProtParam tool - ExPASy (https://web.expasy.org/protparam/). Therefore, anion exchange chromatography was applied, and two rounds were performed. In the first round, the clarified cell lysates were filtered through a 0.22 pm filter disc and loaded to an anion exchange HiTrap Q column (GE Healthcare) in Buffer AA (20 mM NaPi, pH 6.5, supplemented with 0.05x protease inhibitor cocktails).
  • the bound proteins were eluted with a NaCI gradient of 0-100% Buffer BA (1M NaCI in 20 mM NaPi pH 6.5) and the absorbance at 280 nm was monitored. Target proteins in the peak fractions were verified with SDS- and/or native PAGE.
  • the best fractions from the first round of anion exchange step were pooled and diluted by 6 folds with Buffer AA and were then re-loaded to the anion exchange HiTrap Q column (GE Healthcare) in the same buffer. Bound proteins were eluted with a NaCI gradient of 0-50% Buffer BA with the absorbance at 280 nm being monitored.
  • Target proteins in the peak fractions were verified with SDS- and/or native PAGE and the best fractions were concentrated using the Amicon filter units of a 10 kDa molecular weight cut-off.
  • the protein solutions were stored at -20 °C for further purification with size exclusion chromatography.
  • First-round size exclusion chromatography Size exclusion chromatography was performed on a HiLoad Superdex 200 column (GE Healthcare) at room temperature. The proteins from purification via anion exchange chromatography were loaded to the size exclusion column and eluted in the buffer of AS (1 M (NH 4 ) 2 SO 4 , 50 mM NaPi pH 7.0, supplemented with 0.05x protease inhibitor cocktails) with absorbance at 280 nm monitored. Target proteins in the peak fractions were verified with SDS- and/or native PAGE. The fractions of the best protein purity were pooled for further purification with hydrophobic interaction chromatography.
  • Second-round size exclusion chromatoqraphy The concentrated samples from the purification step with hydrophobic interactions were loaded to the size exclusion column as used in first-round size exclusion chromatography and eluted in the buffer of BTS (20 mM Bis-Tris, 150 mM NaCI, pH 6.5). Peak fractions were analysed with SDS- and/or native PAGE. The fractions of best purity were pooled and concentrated. After identification with liquid chromatography-electrospray ionisation mass spectrometry (LC- MS, Agilent) and quantitation, the antigens were aliquoted and stored at -80 °C for future use. Protein identification and quantitation of tagless candidates
  • P. gingivalis strain; W50 (serotype C); was obtained from the culture collection of the Oral Health Cooperative Research Centre, The Melbourne Dental School, University of Melbourne, Australia.
  • P. gingivalis W50 was grown on Horse Blood Agar (HBA) (20 g/L HBA; Oxoid Ltd., Hampshire, UK) supplemented with 10% v/v lysed horse blood (37 °C) in an anaerobic N2 atmosphere containing 5% CO 2 in a MK3 Anaerobic Workstation (Don Whitley Scientific Ltd., Sydney, Australia).
  • Colonies were inoculated into starter culture comprised of 20 mL sterilised brain heart infusion (37 g/L BHI; Oxoid Ltd., Hamsphire, UK) medium supplemented with 5 mg/L hemin and 0.5 mg/L cysteine [McKee et al. (1986) Infect Immun 52: 349-355] and incubated anaerobically (24 h, 37 °C). Absorbance of batch cultures were monitored at OD650nm using a spectrophotometer (model 295E, Perkin-Elmer, Germany). Bacterial cells were harvested during late exponential growth by centrifugation (7,000 g, 20 min, 4 °C).
  • P. gingivalis W50 culture was harvested (6,500 g, 4 °C), washed once with phosphate buffered saline (PBS) (0.01 M Na2HPO4, 1.5 mM KH 2 PO 4 and 0.15 M NaCI, pH 7.4) then pelleted by centrifugation (7,000 g, 20 min 4°C). Bacterial cells were resuspended in PBS and heated to 65°C for 15 minutes. The suspension was centrifuged (7,000 g, 20 min 4°C) and resuspended in sterile PBS and this was repeated once.
  • PBS phosphate buffered saline
  • the cell pellet was resuspended in sterile PBS to obtain a cell density of 2 x 10 10 cells/mL, and protein concentration determined using Biorad Protein Assay Dye Reagent Concentrate (Life Science, NSW, Australia).
  • mice The mouse periodontitis experiments were modified from Baker et al.'s mode (1994). Arch Oral Biol 39: 1035-1040) and performed as described previously by O'Brien- Simpson et al. (2005 J Immunol 175: 3980-3989).
  • Mice female BALB/c; 6-8 weeks old, 10 mice/group), on Day 0 were intra-orally inoculated with P. gingivalis consisting of four doses of P. gingivalis W50 [1 x 10 10 viable P.
  • gingivalis W50 cells suspended in 20 pL PG buffer (50 mM Tris-HCL, 150 mM NaCI, 10 mM MgSO 4 and 14.3 mM Mercaptoethanol, pH 7.4) containing 2% w/v carboxymethylcellulose (CMC, Sigma, New South Wales, Australia)], given two days apart.
  • the inocula were prepared anaerobically and then immediately applied to the gingival margin of the maxillary molar teeth. The number of viable bacteria in each inoculum was verified by flow cytometry and CFU counts on blood agar. Groups of animals consisted of; P. gingivalis W50 orally inoculated (infected control), a non-bacterial inoculated control, and immunised groups.
  • mice were immunised on day 19 after the first oral inoculation with 50 ⁇ g of vaccine candidate in saline/alum (Alhydrogel; 2% aluminium hydroxide wet gel suspension; Invivogen) via the intraperitoneal route.
  • Mice received a second immunisation (50 ⁇ g in saline/alum) on day 40 via the subcutaneous route.
  • mice were bled by cardiac puncture and killed. Maxillae were removed and halved through the midline, with 10 halves used to determine alveolar bone loss. Sera were used to determine the antibody profile using ELISA.
  • gingivalis- induced alveolar bone loss in mm 2 was calculated by subtracting the total visible CEJ-ABC area of the uninoculated (N-C) group from the total visible CEJ-ABC area of each experimental group. Alveolar bone loss measurements were determined twice in a random and blinded protocol. Data are expressed as the mean +/- standard deviation in mm 2 and were analysed using a one-way ANOVA and Dunnetts T3 post-hoc test.
  • ELISAs were performed to evaluate subclass antibody in sera as described in Pathirana et al. (2007). Infect Immun 75: 1436-1442) using a solution (1 ⁇ g/mL) of either HK W50 cells, domain subunits or epitopes in 0.1 M PBS (pH 7.4) to coat wells (16 h, 4 °C) of flat-bottom polyvinyl microtiter plates (Microtiter; Dynatech Laboratories, McLean, VA, US).
  • the ELISA was developed with 1/4000 goat anti-mouse IgG and 1/4000 horseradish peroxidase-conjugated swine anti-goat IgG antibody. All optical density measurements were conducted on a Wallac VICTORS 1420 Multilabel counter (Perkin Elmer) at 405nm.
  • KDcAKIn SEQ ID NO: 64 and may also be referred to herein as "original chimera” or “chimera” in comparison to the chimeric and fusion proteins of the present invention.
  • the KDcAKIn protein is produced as inclusion bodies in E. coli and is poorly soluble and poorly stable.
  • the truncated DUF and K1 domains of the A1 adhesin fragment represent how the Kgp polyprotein is naturally proteolytically processed and assembled on the P. gingivalis cell surface during infection. It follows that truncated DUF and K1 domains make obvious candidates for inclusion in a vaccine for generating immune responses to gingipains.
  • KAS motif conjugated to a ABM213 domain ie, "KA”
  • KDA KAS motif conjugated to both DUF and ABM213 domains
  • KDAKI n (SEQ ID NO: 65) and KDAK1 (SEQ ID NO: 66) proteins require more fastidious growth conditions for soluble expression, at significantly lower levels than for KDA (ie the same protein excluding truncated or full length CAD).
  • K1 (CAD) domain is a contributor to poor solubility of chimera-based recombinants.
  • Truncation of the DUF domain in chimeric protein constructs resulted in elimination of soluble protein expression. This result indicates that a full DUF domain containing the extra 38 N-terminal residues is desirable for optimising soluble expression and efficient stabilization of the recombinant protein.
  • a construct expressing a chimera variant with an extended De domain (chimera with De extended by 38 N terminal residues) was created.
  • This recombinant was designated KDAKI n and results show that chimera solubility is significantly enhanced with a full DUF domain.
  • Expression of KDAKIn in large scale at 30 °C with 0.2- 0.5 mM IPTG resulted in expression of a soluble recombinant protein of good yield.
  • K1 n/K1 in KDAK1 n/KDAK1 did appear to make preparation more problematic than that for the KDA variants lacking K1 n/K1 , such that these variants involving K1 may be less desirable for scale up and commercial development.
  • K1 and K1n domain containing variants had an increased tendency for aggregation at higher concentrations and after freeze-thaw of purified samples. K1 domain was responsible for this instability. However, all variants lacking K1 or K1 n were very stable upon freeze-thaw and at higher concentrations (eg concentrations above 30 mg/ml) Variants containing a full length or truncated K1 domain were very insoluble and the small level of soluble recombinant protein produced was prone to instability and aggregation after purification. Efficient upscale of soluble K1 containing variants was not possible.
  • Extension of DUF to full length and/or removal of K1 (or K1 n) domains, preferably both, are therefore important for solubility and stability of the recombinant protein.
  • a recombinant protein comprising ABM2(1), ABM2(2) and ABM3 domains was readily able to form a multimer.
  • Subsequent expression of a smaller recombinant protein encoding ABM2(1), ABM1 (2) and ABM3 (designated rABM213) and a recombinant protein encoding ABM2(1) and ABM1 (2) (designated rABM21) showed that both recombinants were readily able to multimerize. This multimerization was evident by the presence of a neat ladder of bands on Native PAGE.
  • ABM 1 domains interact with the ABM2 domains to form an Fnlll like stable beta sheet complexed structure.
  • rABM1 and rABM2 were capable of interacting to form a stable beta sheet complexed structure.
  • rABM2(1) was able to form a stable structure with either rABM1 (1) or rABM1 (2).
  • NMR spectroscopic analysis of the folded ABM domain indicates that the domain multimerizes through beta-strand exchange involving the ABM1 and ABM2 motifs. Together these results provide evidence that the chimera and variants containing the ABM domain will multimerize through an interaction between the ABM1 and ABM2 motifs of a properly folded ABM domain.
  • the inventors aimed to mutate specific residues of ABM1 or ABM2 within a recombinant ABM21 (rABM21) protein that encompasses residues 878-968 on the Kgp W50 polyprotein.
  • the inventors mutated residues within the PVQN motif of rABM21 as well as mutating residues within the loop immediately prior to the PVQN.
  • the residues within the loop were targeted as it was believed that the size and shape of the loop preceding beta sheet structures can influence the strength of adjacent beta sheet folding.
  • the number and location of Proline residues within such "loop" structures are reported to be relevant to adjacent beta sheet interaction.
  • the inventors mutated highly conserved hydrophobic residues Y(878) and W(968) present in ABM2 and ABM1 respectively.
  • the inventors also introduced substitutions into the sequence of the motif NxFA in ABM1 , to SxYQ (see SSEYQ variant mentioned in Table 2 below).
  • the mutated rABM21 variants were purified and assessed for their ability to multimerise. The inventors sought to identify mutations that would result in a stable soluble recombinant molecule that could be purified as a stable monomer.
  • KDAK-1V-AVQP SEQ ID NO: 70
  • KDAK-AVQP SEQ ID NO: 71
  • the two proteins shared essentially the same profiles on the native gel either reduced or unreduced ( Figure 3G).
  • the DUF cysteine residue did not contribute to the laddering multimerisation but the presence of the two ABM cysteine residues was critical for the formation of the laddering multimers in these two variants. This suggests that the DUF domain cysteine residue is not a significant contributor to multimerisation.
  • KAS motifs were engineered onto recombinant chimera variants to determine if this would have an impact on immunogenicity.
  • Single KAS or two successive KAS were added to variants at their N terminus or at both termini.
  • a linear sequence of 4 KAS residues containing DSSG linker sequence between each KAS motif was also added to the N terminus of selected variants.
  • K1 is insoluble and that the addition of K1 or K1n to KDA or DA decreases solubility of recombinant variants on large scale purification, as stated above it seems likely that the K1 region may be responsible for instability of K1 -containing chimera variants such that exclusion of K1 would be preferred if the domain is not necessary for protection.
  • the chimera mutant KDcAKIn PVQN>AVQP / 4 Cys> Ser variant (SEQ ID NO: 57) exhibited a higher solubility than KDcAKIn under identical non-reducing denaturing conditions in urea.
  • the concentrations of some soluble proteins such as His-tagged KDAK-1V2S- AVQP were able to reach at least 40 mg/mL.
  • the two lead tagless candidates SEQ ID NO: 59 and SEQ ID NO: 69 (KDAK-1V2S-AVQP and KDAK-3S-AVQP) have been concentrated up to over 30 mg/mL and 16 mg/mL in well buffering solutions at pH 6.5, respectively, and these concentrations are not yet the maximum.
  • the C-term His-tagged original chimera (KDcAKI n) and its variant KDcAK1 n-4S which were purified from inclusion bodies were the least stable in unbuffered saline.
  • KDcAKI n and KDcAK1 n-4S in saline were 1.35 mg/mL and 2.3 mg/mL, respectively.
  • non-specific disulphide bond formation was one of the factors for significant protein aggregation and low solubility of the Chimera.
  • the removal of Cys residues in KDcAK1 n-4S disabled the formation of intermolecular disulfide bonds and improved the protein solubility.
  • the C-term His-tag was not seen to have considerable effects on protein production and solubility when the proteins were expressed under the same conditions.
  • both lead tagless candidates were purified to a purity of 99% with a high homogeneity, which were evidenced by SDS-/native PAGE and SEC-MALS analyses.
  • the inventors tested various constructs (antigens) to determine the importance of the DUF domain in the chimeric fusion proteins, and to compare it to the solubility/stability of a construct comprising an active site sequence derived from an Arginine-dependent gingipain.
  • the constructs produced were: KDAK-3S-AVQP ; KDAK- 2S-AVQP (His tag), KAK-2S-AVQP (His tag) and KDAR-3S-AVQP (His tag).
  • the RAS containing candidate KDAR-3S-AVQP was less soluble than the other antigens, indicating an interference of the RAS sequence with the protein structure, but was still able to be used in subsequent mouse model experiments and could be purified under non-reducing conditions from soluble fractions.
  • All the antigens were purified under non-reducing conditions from soluble fractions.
  • the three His-tagged proteins were purified through Ni affinity, anion exchange and size exclusion chromatography.
  • KDAK-3S-AVQP untagged was purified through anion exchange, hydrophobic interaction and size exclusion chromatography. The yields of purified antigens were high.
  • KDAK-2S-AVQP-His6 had the highest yield (>160 mg/L culture, 20 mg/g wet cells).
  • the KDAR-3S-AVQP-His6 antigen had a lower yield (55 mg/L culture, 7.2 mg/g wet cells) due to its lower solubility.
  • the higher solubility of KAS only antigens relative to the RAS containing antigen was reflected from the peak intensities in the elution profiles of the His-tagged proteins at the Ni-affinity purification step. Nevertheless, when the RAS antigen was pure, it was also highly soluble, able to be concentrated up to at least 15 mg/mL.
  • KAK-2S-AVQP-His6 Two species in KAK-2S-AVQP-His6 and the species of laddering molecular weights below the monomeric form in KDAR-3S-AVQP-His6 co-eluted in one predominant peak in AIEX as also seen from previous Ni-affinity chromatography.
  • KAK-2S-AVQP-His6 and KDAR-3S- AVQP-His6 in their size exclusion tailing profiles may also be an indication of the presence of degradants.
  • KAK-2S- AVQP-His6 had a high purity and high homogeneity, which was also supported by SEC- MALS analysis.
  • SEC-MALS exhibited predominant existence of monomer in solution at 2 mg/mL for all these proteins (data not shown).
  • KDAK-3S-AVQP and KDAK-2S-AVQP- His6 appeared to have a higher quality among the four antigens and KAK-2S-AVQP-His6 seemed to be the least homogeneous according to the SDS-PAGE analysis although the minor species was not resolved in SEC-MALS analysis (eg Figure 13).
  • Antigens tested KDcAKIn 50 ⁇ g; KDcAKI n 0.5 ⁇ g; KDA 50 ⁇ g; KDA 0.5 ⁇ g; KDAK1 50 ⁇ g; KDAK1 0.5 ⁇ g. All antigens absorbed onto alum in PBS (pH 7.4).
  • KDcAKIn from inclusion bodies, batch purified with Ni-NTA resin followed by dialysis into 2 M urea-PBS under non-reducing conditions.
  • KDA and KDAK1 from soluble fractions, Ni-affinity (prepacked column) and anion exchange chromatography with gradient elution followed by dialysis into PBS, under non- reducing conditions.
  • KDcAKI n and KDA protected against bone loss in the animal model.
  • KDcAKI n protected against bone loss at both concentrations tested while KDA only protected at 50 ⁇ g ( Figure 4). Data for KDAK1 not shown.
  • Serum antibody subclass responses of immunised mice in the periodontitis model were examined by ELISA.
  • Antisera was used to probe heat killed P. gingivalis strain W50 as the absorbed antigen.
  • Antibody responses are expressed as the ELISA titre obtained minus triple the background level, with each titre representing the mean ⁇ s.d. of the 10 individual mice ( Figure 5).
  • KDcAKI n (referred to in Figure 5 as "chimera") and KDA induced the strongest total IgG and lgG1 responses against P. gingivalis whole cells followed by KDAK1. There was no significant difference in IgG and lgG1 antibody responses at 50 ⁇ g between the antigens tested. 2.
  • Antigens tested KDcAKIn 50 ⁇ g; KDcAKI n 0.5 ⁇ g; KDA 50 ⁇ g; KDA 0.5 ⁇ g; KDAK1 50 ⁇ g; KDAK1 0.5 ⁇ g. All antigens absorbed onto alum in saline (pH 7.4).
  • Antigens were purified in the same way as for Experiment 1.
  • KDcAKIn antigens tested: all antigens except KDcAKIn were fractionated as described: KDcAKIn (dimer); KDcAKIn (multimer); KDcAKIn (Chimera, original); KDcAK1 n-4S- AVQP; KDA (dimer); KDA (multimer).
  • KDcAK1 n-4S-AVQP, KDcAKIn dimer and multimers urea extracted from inclusion bodies, Ni-affinity column purified followed by gel filtration, with the two KDcAKI n samples under reducing conditions.
  • KDA dimer and multimers from soluble fractions, Ni-affinity column purified followed by anion exchange and gel filtration, under non-reducing conditions.
  • Pre-screen of vaccine candidates with mAbs to P. gingivalis epitopes In an attempt to develop a pre-screening assay to determine antigen suitability for animal models, antigens were screened by ELISA using mAbs against KAS2, ABM2, ABM3 and EP1. All vaccine candidates were able to bind the KAS2, ABM3 and EP1 mAbs, as seen by the large titration curve compared to the negative control muBM4 mAb.
  • Serum antibody subclass responses of immunised mice in the periodontitis model were examined by ELISA. Antisera was used to probe heat killed P. gingivalis strain W50 as the adsorbed antigen. All antigens tested generated an IgG response to varying degrees. KDcAKI n multimer and KDA multimer generated strong lgG1 isotype responses.
  • Antigens tested KKDAI nKK; KDAKI n; KDAK1 nK-4S-AVQP; KKDAKK.
  • All the antigens were purified from soluble fractions under non-reducing conditions with Ni-affinity column, anion exchange and gel filtration chromatography except KDAK1 nK-4S-AVQP without using anion exchange chromatography.
  • Alhydrogel 2% The ability of Alhydrogel 2% to absorb antigens was tested by incubating antigens with alum for 60 minutes at 4°C with gentle mixing. Alum was pelleted and a Bradford protein assay was then conducted on the antigens pre- and post- alum adsorption. All antigens bound to alum at percentages of 91.7% to 99.3%. An SDS-PAGE gel was also run on samples pre- and post- alum absorption and was in agreeance with the Bradford Assay protein determination.
  • Serum antibody subclass responses of immunised mice in the periodontitis model were examined by ELISA. Antisera was used to probe heat killed P. gingivalis strain W50 as the adsorbed antigen. All antigens tested generated an IgG response to varying degrees. The protective KKDAKInKK and KKDAKK induced robust total IgG and lgG1 responses against heat-killed P. gingivalis. Interestingly, KDAK1nK-4S-AVQP, which protected against bone loss, had a lower antibody response to the whole cell P. gingivalis than some of the less protective antigens (KDAKIn).
  • KDcAKI n - from inclusion body using urea and affinity column purified (IB, Urea, AC); KDA - from soluble fraction and affinity column purified (S, AC); KDA - from soluble fraction, using urea and affinity column purified (S, Urea, AC); KDA - from soluble fraction, using urea and batch purification method (S, Urea, Batch); KDAK1 - from soluble fraction, using urea and affinity column purified (S, Urea, AC); KDAK1 - from inclusion body, using urea and affinity column purified (IB, Urea, AC); KDAK1 - from inclusion body, using urea and batch purification method (IB, Urea, Batch).
  • Pre-screen of vaccine candidates with mAbs to P. gingivalis epitopes Pre-screen of vaccine candidates with mAbs to P. gingivalis epitopes.
  • KDcAKI n (IB, Urea, AC), KDA (S, AC), KDAK1 (S, Urea, AC), KDAK1 (IB, Urea, AC) KDAK1 (IB, Urea, Batch) and KDA (S, Urea, Batch) showed significant protection against bone loss with KDcAKIn (IB, Urea, AC), KDA (S, AC), and KDAK1 (IB, Urea, Batch) providing the best protection. It should be noted that the significant protection observed with KDA (S, AC) was lost on denaturation with urea, e.g. KDA (S, Urea, AC) ( Figure 8).
  • affinity-purified antigens provided protection of bone loss, in particular good protection was observed with affinity purified soluble KDA but this protection was partially lost on treatment with urea under oxidizing conditions that would promote disulphide cross links of denatured D and A domains. Again these results suggest that disulphide cross linking of denatured domains may destroy antigen-induced protection, such that urea should be avoided and preparation of soluble, folded domains should be preferred.
  • Antigens tested were: KDcAKI n - from inclusion body, using urea and affinity column purified (IB, Urea, AC); KDAK-3S-AVQP, KDAKInK, KDAK1 n-4S-AVQP, KDAK, KKDAKK, KKDAKI nKK.
  • KDcAKI n prior art chimera
  • KDcAK1n-4S KDAK
  • KDAK-3S KDAK-3S-AVQP
  • KDAK1nK-4S-AVQP KDAK1nK-4S-AVQP.
  • All the antigens possessed a His-tag and were purified using affinity chromatography. Antigens were absorbed onto alum by the addition of equal volumes of Alum to protein on a weight-to-weight ratio. The Alum: Protein compound was adjusted to the appropriate concentration for IP or SC injection (0.5mg/mL), prior to incubation at 4 °C with constant mixing. Mice were then injected IP (Vaccination 1) or SC (Vaccination 2). All the antigens were purified under non-reducing conditions using Ni-affinity chromatography followed by dialysis into saline.
  • KDcAKI n prior art chimera
  • KDAK-3S-AVQP KDAK- 1V-2S- AVQP
  • KDAK-1V-AVQP KDAK-AVQP
  • All the antigens possessed a His-tag and were purified using affinity chromatography. Antigens were absorbed onto alum by the addition of equal volumes of Alum to protein on a weight-to-weight ratio.
  • mice immunised with Chimera KDAK-3S-AVQP, KDAK-1 V-2S- AVQP, KDAK-1 V-AVQP nor KDAK-AVQP developed significantly less bone loss than the mice in the infected control group (Figure 11).
  • the infected control mice developed significant levels of alveolar bone loss compared to the naive mice.
  • * p ⁇ 0.05; in comparison to the Control Challenge Group).
  • the Alum:Protein compound was adjusted to the appropriate antigen concentration for IP and SC injection (1.0 mg/mL, 0.5mg/mL or 0.25mg/mL), prior to incubation at 4°C with constant mixing. Mice were then injected IP (Vaccination 1) and SC (Vaccination 2).
  • Antigens tested were: KDcAKIn - His-tagged, from inclusion body, using urea and affinity column purified (IB, Urea, AC); KDAK-3S-AVQP untagged (100 ⁇ g, 50 ⁇ g and 25 ⁇ g doses) KDAK-1 V-2S-AVQP untagged (100 ⁇ g, 50 ⁇ g and 25 ⁇ g doses), KDAK-3S- AVQP His-tagged (100 ⁇ g dose), KDAK-3S-AVQP untagged and without alum.
  • KDcAKIn - His-tagged from inclusion body, using urea and affinity column purified (IB, Urea, AC)
  • KDAK-3S-AVQP untagged 100 ⁇ g, 50 ⁇ g and 25 ⁇ g doses
  • KDAK-1 V-2S-AVQP untagged 100 ⁇ g, 50 ⁇ g and 25 ⁇ g doses
  • KDAK-3S- AVQP His-tagged 100 ⁇ g dose
  • mice treated with the prior art chimera (KDcAKIn) at 100 ⁇ g did not develop significant bone loss.
  • mice treated with all concentration of the KDAK-3S-AVQP 100 ⁇ g, 50 ⁇ g and 25 ⁇ g
  • mice treated with all concentration of the KDAK-3S-AVQP 100 ⁇ g, 50 ⁇ g and 25 ⁇ g
  • mice treated with all concentration of the KDAK-3S-AVQP 100 ⁇ g, 50 ⁇ g and 25 ⁇ g
  • mice treated with all concentration of the KDAK-3S-AVQP 100 ⁇ g, 50 ⁇ g and 25 ⁇ g
  • mice that received the KDAK-1V-2S-AVQP vaccination were protected from alveolar bone loss at the highest dose of 100 ⁇ g but did develop significant bone loss when vaccinated with 50 ⁇ g and 25 ⁇ g or protein.
  • Serum antibody subclass responses of immunised mice in the periodontitis model were examined by ELISA. Antisera was used to probe heat killed P. gingivalis strain W50 as the adsorbed antigen. All antigens tested generated a total IgG response towards P. gingivalis, with KDA (S, Urea, AC), followed by KDAK1 (IB, Urea, Batch) and KDcAKIn (IB, Urea, AC) having strong lgG1 responses to P. gingivalis whole cells. Only KDAK1 (IB, Urea, AC) induced a strong lgG2a response to P. gingivalis whole cells.
  • KDA S, Urea, AC
  • KDAK1 IB, Urea, Batch
  • KDAK1 IB, Urea, AC
  • KDA induced a strong IgG response to the KAS and ABM3 epitopes.
  • KDA S, Urea, AC
  • KDA also induced IgG antibodies to the EP1 and ABM2a epitopes. All antigen groups with the exception of KDAK1 (S, Urea, AC) induced a response to the EP1 epitope. None of the protective antigens generated antisera that bound to the K1 epitope ABM5.
  • the inventors further tested the in vivo activity of constructs previously tested in Examples 6, 7, 8 and 9, and compared the activity with a construct that did not comprise the DUF domain and a construct comprising an active site sequence derived from an Arginine-dependent gingipain.
  • KDAK-3S-AVQP previously tested in Experiments 6, 7, 8 and 9
  • KDAK-2S-AVQP His tag
  • KAK-2S-AVQP His tag
  • KDAR-3S-AVQP His tag
  • the antigen KDAK-3S-AVQP was used at two concentrations in this experiment: the previously tested 100 ⁇ g/mouse and a two fold increase at 200 ⁇ g/mouse. There was a dose dependent increase in protection against alveolar bone loss, with the mice that received the 200 ⁇ g dose developing less bone loss than the 100 ⁇ g group ( Figure 14).
  • Serum antibody subclass responses of immunised mice in the periodontitis model were examined by ELISA against several different antigens, including whole P. gingivalis, purified RgpA/Kgp complex, the purified catalytic domain Kgpcat as well as several different protective epitopes including KAS, and the protective epitopes of the ABM domain, ABM3 and ABM2.
  • the RgpA/Kgp complex and purified catalytic domain Kgpcat were purified from P. gingivalis, and confirmed to be folded and enzymatically active when assayed).
  • the work described in this report compares production and efficacy of various vaccine candidates in order to identify the components of a chimera vaccine that promote ease of production (such as components contributing to improved solubility, stability and reduced propensity to multimerise) and which are most effective in eliciting immune responses to P. gingivalis and/or in reducing P. gingivalis-induced alveolar bone loss.
  • KDcAKI n While efficacious in preventing periodontal bone loss in the animal periodontitis model, a prior art vaccine, KDcAKI n, is expressed by E. coli as inclusion bodies and exhibits variable solubility and stability.
  • KDcAKIn was based on a fusion between the active site sequence (KAS or K) of the Lys-specific gingipain Kgp and the processed adhesin fragment (A1) of the Kgp polyprotein. From structural analysis of the Kgp polyprotein domains it is now clear that the A1 adhesin fragment found on the cell surface comprises three discrete structural domains, the DUF domain (D), the ABM domain (A) and the K1 domain (K1).
  • the processing of the Kgp polyprotein on the surface of P. gingivalis to release the proteinase catalytic domain and adhesins involves N-terminal truncation of the DUF domain by 38 amino acid residues.
  • KDcAKI n also included a C-terminally truncated K1 domain (K1 n) again based on the cell surface processing of the Kgp polyprotein to produce the A1 adhesin fragment.
  • K1 n C-terminally truncated K1 domain
  • KDcAKI n contains four cysteine residues, one in DUF, two in ABM and one in K1. These cysteine residues are thought to contribute to the problem with the formation of inclusion bodies.
  • P. gingivalis is an obligate anaerobe and requires a highly reduced environment to be pathogenic.
  • the known or modelled structures of the Kgp domains indicate that the cysteine residues are reduced on the cell surface and not involved in disulphide bridges.
  • Expression in E coli under more oxidizing conditions results in disulphide bridge formation between denatured domains and inclusion body formation.
  • the disulphide bridges between denatured domains of the chimera can be seen on non- reducing Native-PAGE which changes upon reduction.

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WO2025019900A1 (en) * 2023-07-26 2025-01-30 Denteric Pty Ltd Chimeric protein vaccine
WO2025019901A1 (en) * 2023-07-26 2025-01-30 Denteric Pty Ltd Rna vaccines

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001047961A1 (en) * 1999-12-24 2001-07-05 Csl Limited P. gingivalis antigenic composition
WO2010022463A1 (en) * 2008-08-29 2010-03-04 Oral Health Australia Pty Ltd Prevention, treatment and diagnosis of p.gingivalis infection
WO2014183168A1 (en) * 2013-05-14 2014-11-20 Oral Health Australia Pty Ltd Inhibitory propeptides

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001047961A1 (en) * 1999-12-24 2001-07-05 Csl Limited P. gingivalis antigenic composition
WO2010022463A1 (en) * 2008-08-29 2010-03-04 Oral Health Australia Pty Ltd Prevention, treatment and diagnosis of p.gingivalis infection
WO2014183168A1 (en) * 2013-05-14 2014-11-20 Oral Health Australia Pty Ltd Inhibitory propeptides

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP4466011A4 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2025019900A1 (en) * 2023-07-26 2025-01-30 Denteric Pty Ltd Chimeric protein vaccine
WO2025019901A1 (en) * 2023-07-26 2025-01-30 Denteric Pty Ltd Rna vaccines

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