# Patent

## Title
Immunogenic compositions and methods therefor

## Abstract

The present invention provides compositions relating to viral capsomeres which comprise foreign immunogenic sequences for use in pharmaceutical compositions and methods of producing such compositions, and related isolated or purified protein and nucleic acid molecules, vectors, host cells, compositions, and methods of use to augment an immune response, immunize an animal and prophylactically or therapeutically treat a disease, disorder or condition. The viral capsomere may be derived from a polyomavirus and comprise an immunogen of interest at the N-terminus and further at the C-terminus and/or at one or more exposed loops of the capsomere.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is the U.S. National Stage of International Application PCT/AU2012/000952, filed Aug. 13, 2012, which designates the U.S. and was published by the International Bureau in English on Feb. 14, 2013, and which claims the benefit of Australian Application No. 2011903217, filed Aug. 11, 2011, both of which are hereby incorporated by reference in their entirety.
FIELD OF THE INVENTION
THIS invention relates to immunogenic compositions generally. In particular, this invention relates to viral capsomeres which comprise foreign immunogenic sequences for use in pharmaceutical compositions and more particularly, vaccine preparations. This invention also relates to use of novel adjuvants to augment immune responses.
BACKGROUND TO THE INVENTION
Subunit vaccines based on self-assembled major capsid proteins synthesised in heterologous cells, have proven effective in preventing infection by several pathogenic viruses, including hepatitis B virus and human papillomavirus. The use of viral capsomeres as subunit vaccines affords a number of advantages because they should result in highly homogeneous vaccine compositions. Moreover, capsomeres are considered to be a cost-effective alternative to VLP-based vaccines because they can be produced in relatively cost effective expression systems (such as bacterial expression systems) and because of their high degree of stability. In particular, if the capsomeres do not give rise to virus-like particles (VLPs) or other aggregates to any significant extent, compositions comprising such capsomeres should be substantially free of higher molecular weight forms of the capsid proteins. This is advantageous from a clinical standpoint wherein supplying a product of high consistency may be very important, indeed essential. That is, capsomeres may give rise to pharmaceutical compositions and in particular vaccines, of enhanced homogeneity. Also, since capsomeres are significantly smaller than VLPs, they may be easier to purify on conventional chromatographic media, thereby increasing the ease of manufacture.
Vaccine formulations comprising chimeric capsomeres can provide an advantage of increased antigenicity of both protein components of the fusion protein from which the capsomere is formed. For example, in a VLP, protein components of the underlying capsomere may be buried in the overall structure as a result of internalized positioning within the VLP itself. Similarly, epitopes of the protein components may be sterically obstructed as a result of capsomere-to-capsomere contact, and therefore unaccessible for eliciting an immune response. Capsomere vaccines potentially offer the additional advantage of increased antigenicity against any protein component.
The formulation of immunotherapeutic compositions and in particular vaccines with different adjuvants may affect the antibody response differently. Formulations that have been used to adjuvant capsomeres include cholera toxin, Escherichia coli enterotoxin, CpG, complete Freund's, and alum or alum in combination with monophosphoryl A. The most important issue in any adjuvant is its safety. Due to the toxicity, some adjuvants, such as complete Freund's adjuvant which causes strong local reaction, are only used in preclinical studies although they are very efficient in adjuvanting weak antigens.
Currently, only very few vaccine adjuvants are licensed for use in humans. Although both MF59 and aluminum salts have been approved in Europe, only aluminum salts have been used in licensed human vaccines in the United States. Billions of doses of vaccines containing aluminum salts have been shown to elicit early, high and long lasting antibody titers after a single immunization.
Aluminium salts have several disadvantages for use as adjuvants inclusive of a bias in the type of immune response elicited by aluminum salt adjuvants, instability to freezing and drying and inconsistencies in producing humoral immunity. Additionally, despite maintaining a good safety profile for more than seven decades, there have still been safety concerns regarding the use of aluminum salts. Symptoms such as erythema, allergic responses, hypersensitivity to contact, granulomatous inflammation and subcutaneous nodules as well as macrophagic myofascitis have been reported for patients who received an aluminum salt-containing vaccine. While aluminum salts offer an appropriate immune enhancement for some types of vaccines, they are clearly not adequate for all. This can also apply to MF59. MF59 consists of squalene, Tween 80, and Span 85 in sodium citrate buffer. There have been two reported cases of hypersensitivity reaction to the Tween 80.
SUMMARY OF THE INVENTION
The development of new and efficacious immunogen delivery vehicles and/or adjuvants is an ever evolving process in vaccinology.
In broad aspects, the invention relates to isolated proteins and capsomeres derived therefrom which comprise an addition at one or both termini of an immunogenic amino acid sequence of interest.
In a first aspect, the invention provides an isolated protein comprising a viral capsomere-forming amino acid sequence wherein the amino-terminus of said viral capsomere-forming amino acid sequence comprises an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence.
In a preferred embodiment, the viral capsomere-forming amino acid sequence further comprises at its carboxy-terminus an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence.
Suitably, the isolated protein of the first aspect further comprises an immunogenic amino acid sequence in one or more exposed loops of said viral capsomere-forming amino acid sequence.
In a particularly preferred embodiment of the first aspect, the isolated protein comprises a viral capsomere-forming amino acid sequence comprising at the amino-terminus and the carboxy-terminus of an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence; and an insertion of an immunogenic amino acid sequence in one or more exposed loops of said viral capsomere-forming amino acid sequence. More preferably, the immunogenic amino acid sequence is identical to or substantially identical to the immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence.
Preferably, the viral capsomere forming sequence is derived from a polyomavirus and more preferably a murine polyomavirus. In preferred embodiments, the viral capsomere forming sequence derived from polyomavirus is VP1.
In a second aspect, the invention provides an isolated nucleic acid encoding an isolated protein of the first aspect.
In one embodiment of the second aspect, the invention provides an isolated nucleic acid encoding a viral capsomere-forming amino acid sequence, wherein the amino terminus of the viral capsomere-forming amino acid sequence has been adapted to receive at its amino terminus an isolated nucleic acid encoding an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag sequence. In preferred embodiments, the carboxy terminus of the viral capsomere forming sequence is also adapted to receive an isolated nucleic acid encoding an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag sequence.
In a third aspect, the invention provides a genetic construct comprising an isolated nucleic acid according to the second aspect.
Preferably, the genetic construct comprises an isolated nucleic acid according to the second aspect together with one or more other nucleotide sequences in a vector, and more preferably, operably-linked to one or more regulatory sequences in a vector.
Preferably, the genetic construct is an expression construct. According to these embodiments, the isolated nucleic acid is operably-linked to one or more regulatory sequences in an expression vector.
In a fourth aspect, the invention provides a host cell comprising the genetic construct of the third aspect.
Preferably, the host cell is selected from a prokaryotic cell and a eukaryotic cell.
More preferably, the host cell is a prokaryotic cell. Even more preferably, the prokaryotic cell is E. coli. 
In a fifth aspect, the invention provides a capsomere comprising one or more isolated proteins of the first aspect.
Preferably, the capsomere is a chimeric capsomere.
In a sixth aspect, the invention provides a method of producing an isolated nucleic acid including the step of inserting at one or more nucleotide sequences adjacent or substantially adjacent the amino-terminus of a viral capsomere protein, a nucleotide sequence encoding an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag sequence, or a fragment thereof.
Also included within the sixth aspect is an isolated nucleic acid produced by the method.
In a seventh aspect, the invention provides a method of producing a capsomere, including the steps of:
(a) introducing the isolated nucleic acid of the first aspect or the genetic construct of the third aspect into a host cell;
(b) culturing said host cell under conditions which facilitate production of the isolated protein of the first aspect;
(c) optionally purifying the isolated protein of the first aspect; and
(d) assembling the isolated protein to thereby produce the capsomere.
Also included within the seventh aspect, is a capsomere produced by the method.
In an eighth aspect, the invention provides a pharmaceutical composition comprising one or more agents selected from the group consisting of an isolated protein, isolated nucleic acid and a capsomere according to any one of the aforementioned aspects, together with a pharmaceutically-acceptable carrier, diluent or excipient.
Preferably, the pharmaceutical composition is an immunotherapeutic composition.
More preferably, the pharmaceutical composition is a vaccine.
Compositions according to the eighth aspect may be used either prophylactically or therapeutically.
In a ninth aspect, the invention provides a method of treating an animal including the step of administering the pharmaceutical composition of the eighth aspect, or the capsomere of the fifth aspect, or a capsomere produced by the method of the seventh aspect to prophylactically or therapeutically treat a disease, disorder or condition.
It will be appreciated that the immunogenic amino acid sequence may be derived from, of, or corresponds to an immunogen from a pathogenic organism such as a virus, a bacteria, a fungi and a parasite, a cancer immunogen, an allergic reaction immunogen (i.e., an allergen), a transplantation immunogen and an autoantigen.
Preferably, the immunogenic amino acid sequence is derived from a virus, preferably influenza, Hendra virus or papillomavirus.
In a tenth aspect, the invention provides a method of immunising an animal including the step of administering the pharmaceutical composition of the eighth aspect, or the capsomere of the fifth aspect, or a capsomere produced by the method of the seventh aspect to said animal to thereby induce immunity in said animal.
In an eleventh aspect, the invention provides a pharmaceutical composition comprising an immunogen of interest and an adjuvant selected from the group consisting of a protein-surfactant stabilised emulsion, a solid particle substantially free of the immunogen of interest and a virus-like particle, together with a pharmaceutically-acceptable diluent, carrier or excipient.
Preferably, the pharmaceutical composition of the eleventh aspect is an immunotherapeutic composition.
More preferably, the pharmaceutical composition is a vaccine.
Compositions according to the eleventh aspect may be used either prophylactically or therapeutically.
In a twelfth aspect, the invention provides a method of augmenting an immune response in an animal, said method including the step of administering a pharmaceutical composition of the eleventh aspect or the capsomere of the fifth aspect, or a capsomere produced by the method of the seventh aspect to thereby augment an immune response in said animal.
In a thirteenth aspect, the invention provides a method of treating an animal including the step of administering the pharmaceutical composition of the eleventh aspect to prophylactically or therapeutically treat a disease, disorder or condition.
Preferably, the immunogen of interest and the adjuvant are mixed prior to administration to produce a formulation that does not subsequently undergo processing, purification or modification prior to administration.
Preferably, the protein-surfactant stabilised emulsion has a mean size of less than 200 nm and more preferably, a mean diameter size of less than 200 nm.
In preferred embodiments, the protein-surfactant stabilised emulsion is a peptide-surfactant stabilised emulsion.
Preferably, the protein-surfactant stabilised emulsion is an oil-in-water emulsion.
Suitably, the protein-surfactant stabilised emulsion further comprises a pharmaceutically-approved oil in mild buffer conditions.
Preferably, the solid particle is a silica particle.
Preferably, the immunogen of interest is a capsomere, more preferably the capsomere of the fifth aspect and even more preferably the chimeric capsomere of the fifth aspect.
The immune response of any one of the aforementioned aspects is a B cell and/or T cell response.
An animal of any of the aforementioned aspects can be selected from the group consisting of humans, domestic livestock, laboratory animals, performance animals, companion animals, poultry and other animals of commercial importance, although without limitation thereto.
Preferably, the animal is a mammal.
More preferably, the animal is a human.
In a fourteenth aspect, the invention provides a capsomere produced by the method of the seventh aspect.
In a fifteenth aspect, the invention provides an isolated nucleic acid produced by the method of the sixth aspect.
Throughout this specification, unless the context requires otherwise, the words “comprise”, “comprises” and “comprising” will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.



BRIEF DESCRIPTION OF FIGURES
In order that the invention may be readily understood and put into practical effect, preferred embodiments will now be described by way of example with reference to the accompanying:
FIG. 1 Sequence alignment of generic vectors (SEQ ID NOs: 1, 2, 3, 4 and 5).
FIG. 2 Sequence alignment of vectors carrying HA epitope from loop A of H1N1 (SEQ ID NOs: 1, 4 and 6).
FIG. 3 Chromatogram of chimeric VP1 dNdC 1011A from GST purification.
FIG. 4 S200 purification of chimeric VP1 dNdC 1011A.
FIG. 5 Antibody response against H1 A peptide.
FIG. 6 Sequence alignment of VP1 constructs with M2e insert (SEQ ID NOs: 1, 4, 7 and 8).
FIG. 7A SDS-gel electrophoresis analysis of expression. Lane designations from left to right: Lane 1: Protein molecular weight marker; Lane 2: Wildtype VP1 total expression; Lane 3: Wildtype VP1 soluble expression; Lane 4: 1011M2e total expression; Lane 5: 1011M2e soluble expression.
FIG. 7B Left to right: Lane 1: Protein molecular weight marker; Lane 2: Wildtype VP1 total expression; Lane 3: Wildtype VP1 soluble expression; Lane 4: 2022M2e total expression; Lane 5: 2022M2e soluble expression.
FIG. 8 Load profile of bound GST fusions of 1011M2e (FIG. 8A) and 2022M2e (FIG. 8B).
FIG. 9 Elution profile of bound GST fusions of 1011M2e (FIG. 9A) and 2022M2e (FIG. 9B).
FIG. 10 S200 purification of chimeric VP1 dNdC 1011M2e and VP1 dNdC 2022M2e.
FIG. 11 Antibody response against H1 M2e peptide.
FIG. 12 The amino acid sequences of VP1 dNdC 0000 with inserted peptides from Hendra Virus antigenic sequences (SEQ ID NOs: 1, 4, 9, 10, 11, 12 and 13).
FIG. 13 The amino acid sequences of VP1 dNdC 0000 with inserted peptides from GAS antigenic sequences (SEQ ID NOs: 1, 4, 14, 15 and 16).
FIG. 14 The amino acid sequences of chimeric VP1 with inserted peptides: M2e and HA epitopes A and B (SEQ ID NOs: 1, 17 and 18).
FIG. 15 SDS-PAGE analysis of expression. Left to right: Lane 1: Protein molecular weight marker; Lane 2: M2e-VP1-S1A total expression; Lane 3: M2e-VP1-S1A soluble expression; Lane 4: M2e-VP1-S1B-S4A total expression; Lane 5: M2e-VP1-S1B-S4A soluble expression.
FIG. 16 GST affinity purification for M2e-VP1-S1A.
FIG. 17 S200 purification for M2e-VP1-S1A.
FIG. 18 GST affinity purification for M2e-VP1-S1B-S4A.
FIG. 19 S200 purification for M2e-VP1-S1B-S4A.
FIG. 20 The amino acid sequences of VP1 dNdC 0000 with inserted peptides from HPV E7 antigenic sequences (SEQ ID NOs: 1, 4, 19 and 20).
FIG. 21 Expression of chimeric VP1 capsomeres with M2e peptide inserted into N and/or C termini and/or surface loops S1 and S4 analysed using Calliper LabChip GXII.
FIG. 22 Expression of chimeric VP1 capsomeres with M2e peptide inserted into N and/or C termini and/or surface loops S1 and S4 analysed using Calliper LabChip GXII.
FIG. 23 Isotherm adsorption of both VP1 delta C63 capsomeres and chimeric 1011M2e capsomeres.
FIG. 24 Antibody response to H1 M2e peptide.
FIG. 25 Antibody response to peptide epitopes from Hendra virus.
FIG. 26 Antibody response to peptide epitopes from Group A Streptococcus (GAS).
FIG. 27 Viral antigens: A. amino acid sequence of Arginine deiminase (ADI) from Streptococcus pyogenes (SEQ ID NO: 42; and B. amino acid sequence of trigger factor (TF) from Streptococcus pyogenes (SEQ ID NO: 43).
FIG. 28 Expression of chimeric VP1 capsomeres with large antigen inserted on the N-terminal (Left to right: Lane 1. Molecular weight marker; Lane 2. VP1 dNdC 0000 total protein; Lane 3. VP1 dNdC 0000 soluble protein; Lane 4. ADI-VP1 dNdC total protein; Lane 5. ADI-VP1 dNdC soluble protein; Lane 6. TF-VP1 dNdC total protein; and Lane 7. TF-VP1 dNdC soluble protein).
FIG. 29 Chimeric capsomere sequences: A. ADI-VP1 dNdC (SEQ ID NO: 21); and B. TF-VP1 dNdC (SEQ ID NO: 22).



BRIEF DESCRIPTION OF SEQUENCE LISTING
Wild-Type and Chimeric Capsomere Sequences


    SEQ ID NO: 1 Amino acid sequence VP1 wildtype
    SEQ ID NO: 2 Amino acid sequence VP1 S1
    SEQ ID NO: 3 Amino acid sequence VP1 S1 S4
    SEQ ID NO: 4 Amino acid sequence VP1 dNdC 0000
    SEQ ID NO: 5 Amino acid sequence VP1 dNdC S1 S4
    SEQ ID NO: 6 Amino acid sequence VP1 dNdC 1011A
    SEQ ID NO: 7 Amino acid sequence VP1dNdC 1011M2e
    SEQ ID NO: 8 Amino acid sequence VP1dNdC 2022M2e
    SEQ ID NO: 9 Amino acid sequence VP1dNdC 1011G1-2
    SEQ ID NO: 10 Amino acid sequence VP1dNdC 1011G4
    SEQ ID NO: 11 Amino acid sequence VP1dNdC 1011G5
    SEQ ID NO: 12 Amino acid sequence VP1dNdC 1011G9
    SEQ ID NO: 13 Amino acid sequence VP1dNdC 1011G10
    SEQ ID NO: 14 Amino acid sequence 1011GAS1
    SEQ ID NO: 15 Amino acid sequence 1011GAS2
    SEQ ID NO: 16 Amino acid sequence 1011GAS3
    SEQ ID NO: 17 Amino acid sequence M2e-VP1-S1A
    SEQ ID NO: 18 Amino acid sequence M2e-VP1-S1B-S4A
    SEQ ID NO: 19 Amino acid sequence VP1 dNdC 1011E7
    SEQ ID NO: 20 Amino acid sequence VP1 dNdC 1011CTL
    SEQ ID NO: 21 Amino acid sequence ADI-VP1 dNdC
    SEQ ID NO: 22 Amino acid sequence TF-VP1 dNdC

Epitope sequences

    SEQ ID NO: 23 Amino acid sequence M2e peptide (SLLTEVETPTRSEWECRCSDSSD)
    SEQ ID NO: 24 Amino acid sequence Hendra virus epitopes G1-2 (GLPNQIMLQKTTS)
    SEQ ID NO: 25 Amino acid sequence Hendra virus epitope G4 (VRPKSDSGDYN)
    SEQ ID NO: 26 Amino acid sequence Hendra virus epitope G5 (PIIHSKYSKAE)
    SEQ ID NO: 27 Amino acid sequence Hendra virus epitope G9 (VEIYDTGDSVIRPKL)
    SEQ ID NO: 28 Amino acid sequence Hendra virus epitope G10 (LEKIGSCTRGIAKQ)
    SEQ ID NO: 29 Amino acid sequence GAS peptide BSA101-28 (NSKTPAPAPAVPVKKEATKSKLSEAELH)
    SEQ ID NO: 30 Amino acid sequence GAS peptide 20321-19 (NSKNPVPVKKEAKLSEAEL)
    SEQ ID NO: 31 Amino acid sequence GAS peptide 204050-69 (LKMLNRDLEQAYNELSGEAH)
    SEQ ID NO: 32 Amino acid sequence HA epitope A of H1N1 (DSNKGVTAACPHAGAKS)
    SEQ ID NO: 33 Amino acid sequence HA epitope A (PYNGKSS)
    SEQ ID NO: 34 Amino acid sequence HA epitope B (GNDAAEQTKLYQNPTTY)
    SEQ ID NO: 35 Amino acid sequence HPV E7 peptides (QAEPDRAHYNIVTFCCKCD)
    SEQ ID NO: 36 Amino acid sequence HPV E7 peptide (RAHYNIVTF)
    SEQ ID NO: 37 Amino acid sequence-antigenic epitope of loop B (PNDAAEQTKLYQNPTTY)
    SEQ ID NO: 38 Amino acid sequence-antigenic epitope of loop A (KRGPGSG)
    SEQ ID NO: 39 Amino acid sequence antigenic epitope of loop B (PSTNQEQTSLYVQASGR)
    SEQ ID NO: 40 Amino acid sequence antigenic epitope of loop A (SHKGKSS)
    SEQ ID NO: 41 Amino acid sequence-loop B (PSNIEDQKTIYRKENAY)
    SEQ ID NO: 42 Amino acid sequence of the viral antigen Arginine deiminase (ADI) from Streptococcus pyogenes (FIG. 27-A)
    SEQ ID NO: 43 Amino acid sequence of the viral antigen trigger factor (TF) from Streptococcus pyogenes (FIG. 27-B)

Other

    SEQ ID NO: 44 Amino acid sequence LATSDTED (VP1 wildtype sequence, amino acids 82-89)
    SEQ ID NO: 45 Amino acid sequence LATSAGTED (VP1 S1 sequence, amino acids 82-90)
    SEQ ID NO: 46 Amino acid sequence TRNYDV (VP1 wildtype, amino acids 92-97)
    SEQ ID NO: 47 Amino acid sequence TRSAYDV (VP1 S1S4 amino acids 92-98)
    SEQ ID NO: 48 Amino acid sequence (common name AM1) MKQLADSLHQLARQVSRLEHA
    SEQ ID NO: 49 Amino acid sequence (common name Lac21) MKQLADSLMQLARQVSRLESA


DETAILED DESCRIPTION OF THE INVENTION
The present invention is predicated, at least in part, on the finding that chimeric capsomeres with an N-terminal addition of an immunogenic protein are particularly advantageous for stimulating or eliciting a desired immune response and in particular, an effective immune response using a multiplicity of immunogenic protein sequences. Also particularly efficacious are capsomere with additions of immunogenic amino acid sequences at N and C termini and optional insertions of immunogenic amino acid sequences in one or more exposed loops of the capsomeres.
Therefore in broad aspects, the invention relates to isolated proteins, isolated nucleic acids and capsomeres derived therefrom which comprise an addition at one or both termini of an immunogenic amino acid sequence of interest. In particular, the addition is at the N-terminus and in preferred embodiments, at the N- and C-terminus. In particularly preferred embodiments, the isolated protein, isolated nucleic acids and capsomeres derived therefrom which comprise an addition at the N- and C-terminus also comprise an insertion of an immunogenic amino acid sequence at one or more exposed loops of the capsomere.
The present invention is also predicated on the notion that an immune response to immunogens of interest and more preferably, chimeric capsomeres may be augmented by certain classes of adjuvant.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this, invention belongs. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.
The term “capsomere” is well-known in the art as a morphological unit of the capsid of a virus. A “capsomere” comprises monomeric or oligomeric viral structural proteins. In nature, capsomeres typically self-assemble into a virus-like particle. The capsomeres of the present invention are substantially incapable of assembly into VLPs due to the deletion of VLP assembly-related parts of the sequence and/or addition, of a foreign or heterologous sequence at the amino-terminus of the capsomere-forming amino acid sequence, and thus retain a capsomere morphology. By way of example for polyomavirus VP1 VLPs, five VP1 units self-associate to create a basic capsomeric unit. The VP1 VLP comprises 72 capsomeres associated into a capsid. In other examples, “capsomere” may refer to a papillomavirus capsomere, and preferably human papillomavirus, and in particular, refers to an oligomeric configuration of the L1 protein which is constituted of L1 pentamers. In other preferred embodiments, the capsomere is a hepatitis B virus capsomere, and more preferably, a hepatitis B virus surface antigen (HBsAg) capsomere.
A “viral capsomere-forming amino acid sequence” refers to an amino acid sequence which is capable of forming a capsomere. Such a sequence may correspond to, be derived from or related to a capsid-derived protein and more suitably, one or more viral structural proteins forming part of a viral capsid. It will be understood that by “capsid” is meant the structural portion of a virus which is comprised of capsomeres. The capsomere sequence is not limited to a virus of human origin but may be a sequence derived from any suitable virus. The capsomere forming sequence of the invention may be a chimera between two different viral structural or capsid proteins. The “viral capsomere-forming amino acid sequence” can be derived from or correspond to a suitable amino acid sequence from a virus such as, but not limited to, polyomavirus and papillomavirus, hepatitis B virus (HBV), hepatitis C virus (HCV), rotavirus, tobacco mosaic virus (TMV), cow pea mosaic virus (CPMV), bacteriophage MS2 and HIV.
In preferable embodiments, the viral capsomere-forming amino acid sequence is derived from or corresponds to a protein selected from the group consisting of polyomavirus VP1, papillomavirus L1, HBV surface antigen, HCV core, E1 or E2, VP1, 2, 3, 4, 5, 6 or 7 from rotavirus, TMV capsid protein, L and S protein of CPMV, MS2 coat protein and p24 protein of HIV.
Unless contraindicated or noted otherwise, in these descriptions and throughout this specification, the terms “a” and “an” mean one or more.
By “consisting of” is meant including, and limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory, and that no other elements may be present.
By “consisting essentially of” is meant 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. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.
For the purposes of this invention, by “isolated” is meant material that has been removed from its natural state or otherwise been subjected to human manipulation. Isolated material may be substantially or essentially free from components that normally accompany it in its natural state, or may be manipulated so as to be in an artificial, state together with components that normally accompany it in its natural state. Isolated material may be in native, chemical synthetic or recombinant form.
By “protein” is meant an amino acid polymer. The amino acids may be natural or non-natural amino acids, D- or L-amino acids or chemically-derivatized amino acids as are well understood in the art.
A “peptide” is a protein having less than fifty (50) amino acids.
A “polypeptide” is a protein having fifty (50) or more amino acids.
Proteins, polypeptides and peptides may be useful in native, chemical synthetic or recombinant synthetic form.
The present invention is particularly amenable to generation of a chimera. A “chimera” or a “chimeric” gene, nucleic acid, protein, peptide or polypeptide is meant a gene, nucleic acid, protein, peptide or polypeptide that comprises two or more genes, nucleic acids, proteins, peptides or polypeptides not normally associated together. A “chimera” includes within its scope a fusion between fragments. Typically, although not exclusively, the chimera is a fusion between unrelated sequences however it is readily contemplated that the sequences may be homologues. Preferred embodiments of the present invention relate to a chimeric capsomere, isolated proteins encoding a chimeric capsomere and an isolated nucleic acid encoding said isolated proteins.
As used herein, by “synthetic” is meant not naturally occurring but made through human technical intervention. In the context of synthetic proteins and nucleic acids, this encompasses molecules produced by recombinant or chemical synthetic and combinatorial techniques as are well understood in the art.
The term “foreign” or “exogenous” or “heterologous” refers to any molecule (e. g., a polynucleotide or polypeptide) which is introduced into a host by experimental manipulations and may include gene/nucleic acid sequences found in that host so long as the introduced gene contains some modification (e.g., a point mutation, the presence of a selectable marker gene, the presence of a recombination site, etc.) relative to the naturally-occurring gene.
By “corresponds to” or “corresponding to” in the context of the present invention, is meant an amino acid sequence or nucleic acid sequence which shares primary sequence characteristics of another amino acid sequence or nucleic acid sequence but is not necessarily derived or obtained from the same source as said another amino acid sequence or said nucleic acid sequence.
By “an immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence” is meant that said immunogenic sequence does not act as an amino acid sequence that is utilised for protein purification and/or does not act as an amino acid sequence that is utilised for enhancing expression of a recombinant protein. In preferred embodiments, the immunogenic amino acid sequence that is not a purification tag amino acid sequence.
A “purification tag amino acid sequence” is any amino acid sequence that is specifically fused to or associated with a second amino acid sequence to assist with purification, and in particular chromatographic purification (and more suitably, affinity chromatography) of a protein, peptides etc. The term may also be referred to as a “purification tag molecule”. Non-limiting examples of a purification tag include 6×HIS, glutathione S-transferase and c-myc. Inclusive of such sequences are sequences which specifically allow cleavage of the fusion partner from the capsomere-forming sequence, as normal protein engineering approaches would tend to incorporate a method for removal of the purification tag. An “expression enhancing sequence” is any amino acid sequence which aids with the recombinant expression of proteins and includes SUMO protein or fragments thereof.
The terms “immunogenic amino acid sequence”, “immunogenic sequence”, “immunogenic protein, “immunogenic amino acid sequence of interest”,” or “immunogen of interest” are used interchangeably herein with immunogen, antigen, epitope, antigenic sequence, polytope, immunogenic peptide, peptide, antigenic epitope etc as is known in the art to denote or refer to a sequence capable of eliciting an immune response, and more particularly a specific or desired immune response such as protective immune response or memory immune response. The term immunogen broadly includes any type of molecule which is recognized by a host immune system as being foreign. Immunogenic sequences of the invention may comprise B and/or T-cell epitopes. The immunogenic sequence may be fused with a purification tag sequence or expression enhancing tag to facilitate purification/expression but in itself, does not act as an purification tag molecule or expression enhancing tag; in these embodiments, the purification tag sequence may not be added to the amino-terminus of the viral capsomere forming sequence but is added to the amino-terminus of the immunogenic sequence e.g., tag molecule-immunogenic sequence-viral capsomere sequence. The immunogenic sequence can be an immunogen of an infectious agent, a cancer immunogen, an allergic reaction immunogen (i.e., an allergen), a transplantation immunogen, an autoantigen, and the like as are known in the art.
The term “native” nucleic acid or protein also refers to “wild-type” or “normal” nucleic acid or protein, which are normally obtainable from a selected organism or part thereof. These terms are used interchangeably.
The term “non-native” nucleic acid or protein refers to a nucleic acid or protein not normally obtainable from a selected organism or part thereof. For example, a non-native protein preferably comprises a chimeric protein that may comprise two peptides or proteins not normally associated with each other as a contiguous protein and accordingly comprise non-native proteins. Likewise, a chimeric nucleic acid may comprise two or more non-native nucleic acids.
Additions at termini contemplated by the invention may be directly adjacent to the terminus (ie. contiguous between the last nucleotide of the terminus sequence and the first nucleotide of the added sequence). Alternatively, there may be a spacer sequence between the capsomere sequence and the immunogenic sequence, such as a spacer sequence generated by a restriction enzyme site although without limitation thereto.
Therefore the capsomeres and isolated proteins thereof of the present invention may comprise a viral protein expressed as a fusion protein adjacent amino acid residues from a second protein, namely the desired immunogen of the present invention. Amino acids of the second protein can be derived from numerous sources as described herein as long as the addition of the second protein amino acid residues to the first protein permits formation of capsomeres. Amino acid residues of the second protein can be derived from numerous sources, including amino acid residues from the first protein.
The present invention also extends to use of fragments. In one embodiment, a “fragment” includes a protein comprising an amino acid sequence that constitutes less than 100% of an amino acid sequence of an entire protein. A fragment preferably comprises less than 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%, 60%, 50%, 40%, 30%, 20% or as little as even 10%, 5% or 3% of the entire protein.
In particular aspects, a protein fragment may comprise, for example, at least 5, 10, 20, 30, 40, 50 60, 70, 80, 90, 100, 120, 140, 150, 200, 250, 300, 350, 400, 450 or 500 contiguous amino acids of a protein.
In particular embodiments, the fragment may be a “biologically-active fragment” is a fragment, portion, region or segment of a protein, or a nucleic acid encoding the same, which displays at least 10%, preferably at least 25%, more preferably at least 50% and even more preferably at least 70%, 80% or 90% of the biological activity of the entire or full length protein from which it is derived. In preferred embodiments, a “biologically-active fragment” may be a fragment of a virus structural protein and/or virus capsid protein which retains the ability to self-assemble into capsomere, wherein the capsomere is substantially incapable of assembly into a VLP.
In other preferred embodiments, a “biologically-active fragment” is, a truncated protein including those having one or more amino acid residues deleted from the carboxy terminus of the protein, or one or more amino acid residues deleted from the amino terminus of the protein, or one or more amino acid residues deleted from an internal region (i.e., not from either terminus) of the protein. Preferred capsomeres are comprised of proteins truncated at the carboxy- and amino-terminus.
In preferred embodiments that relate to murine polyomavirus VP1, a suitable biologically-active fragment lacks the C-terminal 63 amino acids residues of wild-type VP1. Such a truncated VP1 is described in Garcea et al (1987), Nature 329: 86. In other preferred embodiments, a suitable biologically active fragment has the first 28 amino acids of wild-type VP1 are removed. In particularly preferred embodiments, a biologically active fragment is a murine polyomavirus VP1 sequence with the first 28 amino acids and the last 63 amino acids of wild-type VP1 missing. Such a sequence is exemplified in FIG. 1 and particularly an amino acid sequence as set forth in SEQ ID NO: 5. In other preferred embodiments, the suitable fragment is a fragment of the immunogenic protein of the invention. In particular suitable embodiments, such a fragment is an antigenic epitope.
Proteins, polypeptides, polytopes and peptides may be useful in native, chemical synthetic or recombinant synthetic form and may be produced by any means known in the art, including but not limited to, chemical synthesis, recombinant DNA technology and proteolytic cleavage to produce peptide fragments.
In one embodiment, proteins of the invention are produced by chemical synthesis. Chemical synthesis techniques are well known in the art, although the skilled person may refer to Chapter 18 of CURRENT PROTOCOLS IN PROTEIN SCIENCE Eds. Coligan et. al., John Wiley & Sons NY (1995-2009) for examples of suitable methodology.
In another preferred embodiment of the invention, isolated proteins of the invention may comprise intact viral or other proteins isolated from natural sources. Such proteins isolated from natural sources may be modified in vitro to include additional amino acid residues to provide a fusion protein of the invention using covalent modification techniques well known and routinely practiced in the art. Similarly, in formulations comprising truncated viral proteins, the proteins may be isolated from natural sources as intact proteins and hydrolyzed in vitro using chemical hydrolysis or enzymatic digestion with any of a number of site-specific or general proteases, the truncated protein subsequently modified to include additional amino acid resides as described above to provide a truncated fusion protein of the invention.
In another embodiment, proteins as described herein may be prepared as a recombinant protein.
A recombinant protein or peptide may be conveniently prepared by a person skilled in the art using standard protocols as for example described in Sambrook et al., MOLECULAR CLONING. A Laboratory Manual (Cold Spring Harbor Press, 1989), incorporated herein by reference, in particular Sections 16 and 17; CURRENT PROTOCOLS IN MOLECULAR BIOLOGY Eds. Ausubel et al., (John Wiley & Sons, Inc. 1995-2009), incorporated herein by reference, in particular Chapters 10 and 16; and CURRENT PROTOCOLS IN PROTEIN SCIENCE Eds. Coligan et al., (John Wiley & Sons, Inc. 1995-2009) which is incorporated by reference herein, in particular Chapters 1, 5 and 6. In producing capsomeres, recombinant molecular biology techniques can be utilized to produce DNA encoding either the desired intact protein, the truncated protein, or the truncated fusion protein. Recombinant methodologies required to produce a DNA encoding a desired protein are well known and routinely practiced in the art.
It is readily contemplated that any recombinant protein expression system may be used for the present invention such as bacterial, yeast, plant, insect cells, mammalian cell lines such as lymphoblastoid cell lines and splenocytes isolated from transformed host organisms such as humans and mice and insect-based expression systems but is not limited thereto. It will be appreciated that the recombinant protein expression system employed may be chosen on the basis of suitability for expression of soluble and stable protein.
In one preferred embodiment, recombinant protein expression occurs in cells of prokaryotic origin. Suitable host cells for recombinant protein expression are bacterial cells such as Escherichia coli (BL21 and various derivative strains thereof which have been optimised for certain applications, such as Rosetta and DE3, for example) and Bacillus subtilis, although without limitation thereto. Preferably the host cell is Escherichia coli BL21 Rosetta (DE3).
In another preferred embodiment, recombinant expression occurs in insect cells which are suited to viral-based recombinant expression e.g. Sf9 cells.
The present invention contemplates recombinant expression of capsomeres in plant cells. By way of example, according to these embodiments a capsomere-forming sequence from a plant virus eg TMV or CPMV may be modified according to the methods of the present invention. Waheed et al (2011) Transgenic Research 20: 271-282 describes suitable methodology for capsomere expression in tobacco and is incorporated herein by reference.
To facilitate recombinant protein purification, a fusion partner sequence may be included with the protein of the present invention. That is, a genetic construct of the present invention may also include a fusion partner (typically provided by a vector or an expression vector) so that the recombinant protein of the invention is expressed as a fusion protein with said fusion partner. The main advantage of fusion partners is that they assist identification and/or purification of said fusion protein. However it will also be appreciated that the choice of fusion partner may also assist with protein properties such as stability, solubility and the like. Non-limiting examples of such proteins include Protein A, glutathione S-transferase (GST), green fluorescent protein (GFP) maltose-binding protein (MBP), hexahistidine (HIS6) and epitope tags such as V5, FLAG, haemagglutinin and c-myc tags.
The fusion partner sequence facilitates fusion protein binding to an affinity matrix to enable protein purification and/or detection. For the purposes of fusion polypeptide purification by affinity chromatography, relevant matrices for affinity chromatography are antibody, protein A- or G-, glutathione-, amylose-, and nickel- or cobalt-conjugated resins respectively. Many such matrices are available in “kit” form, such as the QIAexpressTM system (Qiagen) useful with (HIS6) fusion partners and the Pharmacia GST purification system. In many cases, the fusion partner can be cleaved by an appropriate protease or chemical reagent to release the protein of interest from the fusion partner.
By “purify”, “purified” and “purification”, particularly in the context of recombinant protein purification, is meant enrichment of a recombinant protein so that the relative abundance and/or specific activity of said recombinant protein is increased compared to that before enrichment.
In those embodiments which contemplate peptides, said peptides may be in the form of peptides prepared by chemical synthesis, inclusive of solid phase and solution phase synthesis. Such methods are well known in the art, although reference is made to examples of chemical synthesis techniques as provided in Chapter 9 of SYNTHETIC VACCINES Ed. Nicholson (Blackwell Scientific Publications) and Chapter 15 of CURRENT PROTOCOLS IN PROTEIN SCIENCE Eds. Coligan et al., (John Wiley & Sons, Inc. NY USA 1995-2009). In this regard, reference is also made to International Publication WO 99/02550 and International Publication WO 97/45444.
By “chromatography” such as in the context of chromatographic steps of the invention, is meant any technique used for the separation of biomolecules (e.g., protein and/or nucleic acids) from complex mixtures that typically employs at least two phases: a stationary bed phase and a mobile phase that moves through the stationary bed. Molecules may be separated on the basis of a particular physicochemical property such as charge, size, affinity and hydrophobicity, or a combination thereof.
When recombinant proteins are used to provide capsomeres of the invention, the proteins may first be isolated from the host cell of its expression and incubated under conditions which permit self-assembly to provide capsomeres. Alternatively, the proteins may be expressed under conditions wherein capsomeres are formed in the host cell.
The present invention also contemplates the use of variants of any protein and/or nucleic acid encompassed by the invention. “Variants” include within their scope naturally-occurring variants such as allelic variants, orthologs and homologs and artificially created mutants, for example.
The terms “mutant”, “mutation” and “mutated” are used herein generally to encompass conservative or non-conservative amino acid substitutions, deletions and/or insertions introduced into an isolated protein or fragment thereof.
It is well understood in the art that some amino acids may be changed to others with broadly similar properties without changing the nature of the activity of the protein or the structure of the protein (conservative substitutions).
Generally, non-conservative substitutions which are likely to produce the greatest changes in protein structure and function are those in which (a) a hydrophilic residue (e.g. Ser or Thr) is substituted for, or by, a hydrophobic residue (e.g. Ala, Leu, Ile, Phe or Val); (b) a cysteine or proline is substituted for, or by, any other residue; (c) a residue having an electropositive side chain (e.g. Arg, His or Lys) is substituted for, or by, an electronegative residue (e.g. Glu or Asp) or (d) a residue having a bulky hydrophobic or aromatic side chain (e.g. Val, Ile, Phe or Trp) is substituted for, or by, one having a smaller side chain (e.g. Ala, Ser) or no side chain (e.g. Gly).
With regard to protein variants and in particular those which are artificially-created mutants, these can be created by mutagenising a protein or by mutagenising an encoding nucleic acid, such as by random mutagenesis or site-directed mutagenesis. Examples of nucleic acid mutagenesis methods are provided in Chapter 9 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel et al., supra which is incorporated herein by reference.
It will be appreciated by the skilled person that site-directed mutagenesis is best performed where knowledge of the amino acid residues that contribute to biological activity is available. In many cases, this information is not available, or can only be inferred by molecular modelling approximations, for example.
In such cases, random mutagenesis is contemplated. Random mutagenesis methods include chemical modification of proteins by hydroxylamine (Ruan et al., 1997, Gene 188 35), incorporation of dNTP analogs into nucleic acids (Zaccolo et al., 1996, J. Mol. Biol. 255 589) and PCR-based random mutagenesis such as described in Stemmer, 1994, Proc. Natl. Acad. Sci. USA 91 10747 or Shafikhani et al., 1997, Biotechniques 23 304, each of which references is incorporated herein. It is also noted that PCR-based random mutagenesis kits are commercially available, such as the DiversifyTM kit (Clontech).
The invention therefore also contemplates variants which share an appropriate level of sequence identity with isolated proteins and encoding nucleic acids as set forth herein. As generally used herein, a “homolog” shares a definable nucleotide or amino acid sequence relationship with a nucleic acid or protein of the invention as the case may be.
The term “sequence identity” is used herein in its broadest sense to include the number of exact nucleotide or amino acid matches having regard to an appropriate alignment using a standard algorithm, having regard to the extent that sequences are identical over a window of comparison. Thus, a “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U) or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. For example, “sequence identity” may be understood to mean the “match percentage” calculated by the DNASIS computer program (Version 2.5 for windows; available from Hitachi Software engineering Co., Ltd., South San Francisco, Calif., USA).
In particular embodiments, variants will share at least 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90% and more preferably at least 95%, 96%, 97%, 98% or 99% sequence identity with the isolated proteins and/or isolated nucleic acids of the invention. It will be appreciated that a variant comprises all integer values less than 100%, for example the percent value as set forth above and others.
The invention also contemplates protein derivatives. By “derivative” is meant a polypeptide that has been derived from the basic sequence by modification, for example by conjugation or complexing with other chemical moieties or by post-translational modification techniques as would be understood in the art.
The term “derivative” also includes within its scope alterations that have been made to a parent sequence including additions or deletions that provide for functional equivalent molecules. The invention also contemplates chemical derivatives of the chimera of the present invention, such as produced using techniques described in CURRENT PROTOCOLS IN PROTEIN SCIENCE Chapter 15, for example. With regard to chemical modification of amino acids, this includes but is not limited to, modification by acylation, amidination, pyridoxylation of lysine, reductive alkylation, trinitrobenzylation of amino groups with 2,4,6-trinitrobenzene sulphonic acid (TNBS), amide modification of carboxyl groups and sulphydryl modification by performic acid oxidation of cysteine to cysteic acid, formation of mercurial derivatives, formation of mixed disulphides with other thiol compounds, reaction with maleimide, carboxymethylation with iodoacetic acid or iodoacetamide and carbamoylation with cyanate at alkaline pH, although without limitation thereto.
The invention further contemplates isolated proteins, isolated nucleic acids and capsomeres derived therefrom comprising an addition, and optionally an insertion, of the sequence of interest (and preferably the immunogenic sequence) at one or a plurality of the sites contemplated herein (a plurality being two, three or more). That is, encompassed in the invention is a single copy at one or a plurality of sites, multiple copies at one or a plurality of sites, or combinations thereof. Insertion or addition may be a single copy of a sequence of interest at one or a plurality of sites. Alternatively, multiple copies of a sequence of interest (preferably as tandem repeats) may be included at one or a plurality of sites. Also contemplated is a combination of a single copy inserts and a multiplicity of copies at different sites, in which a single isolated protein may comprise a single copy of the sequence of interest at one or more sites as well as multiple copies of an insert at one or more other sites. It will be appreciated that embodiments that contemplate a plurality, the sequence of interest may be the same sequence or different sequences. A particular advantage conferred by a multiplicity of inserts is the elicitation of an enhanced immune response.
In preferred embodiments, there is addition of a single copy or a plurality of copies of the sequence of interest at both the amino- and carboxy-terminus of the capsomere-forming sequence. In further particularly preferred embodiments, the invention contemplates an insertion of one or a plurality of copies of the sequence of interest at one or more exposed loops of the capsomere together with additions at either the amino-terminus or the amino- and carboxy-terminus as described hereinbefore. Non-limiting examples of such chimeric proteins are provided in Table 1.
In light of the foregoing, it will be appreciated that the present invention also contemplates isolated proteins, such as polypeptides or “polytope” proteins, comprising one or a plurality of isolated immunogenic fragments or sequences contemplated by the invention, and/or an isolated nucleic acid encoding the same. For example, said sequences or fragments may be present singly or as repeats, which also includes tandemly repeated fragments. “Spacer” amino acids may also be included between one or the plurality of the immunogenic sequences or fragments thereof present in said isolated protein. In one embodiment, an isolated polytope protein may comprise one or a plurality of isolated immunogenic fragments of the invention. In another embodiment, the isolated polytope protein may consist of one or a plurality of isolated immunogenic fragments of the invention. In yet another embodiment, an isolated protein may consist essentially of one or a plurality of isolated immunogenic fragments of the invention.
The isolated immunogenic proteins, fragments and/or polytopes of the present invention may be produced by any means known in the art, including but not limited to, chemical synthesis, recombinant DNA technology and proteolytic cleavage to produce peptide fragments.
The immunogenic sequences of the present invention possess the ability or potential to generate an immune response upon administration to an animal. It is envisaged that the immune response may be either mucosal, B-lymphocyte or T-lymphocyte mediated, or a combination thereof. The T-lymphocyte mediated response may be a specific cytotoxic T lymphocyte response. In preferred embodiments, the immunogenic sequences induce a neutralising antibody response. Preferably, the immune response is a protective immune response.
Suitably, the immunogenic proteins/sequences that are part of the isolated proteins and capsomeres of the present invention are derived from a pathogenic organism that causes or is related to an infectious disease of an animal, preferably a mammal and more preferably a human. Said pathogenic organisms include, but are not limited to, a virus, bacteria, a fungi, a mycobacterium and a parasite.
In the preferred embodiments that contemplate an immunogen from a virus and/or a viral capsomere sequence, the invention contemplates any member of the dsDNA Viruses group including (and without limitation thereto) any member of the family Adenoviridae inclusive of a mastadenovirus (eg, a human adenovirus) and an aviadenovirus (eg, a fowl adenovirus), although without limitation thereto; any member of the family Herpesviridae inclusive of an Alphaherpesvirinae such as, but not limited to, a simplexvirus (e.g., a human herpesvirus 1) and a varicellovirus (e.g. a human herpesvirus 3); a Betaherpesvirinae such as, but not limited to, a cytomegalovirus (e.g., human herpesvirus 5), a muromegalovirus (e.g., a mouse cytomegalovirus 1), a roseolovirus (e.g., a human herpesvirus 6); a Gammaherpesvirinae such as, but not limited to, a lymphocryptovirus (e.g., a human herpesvirus 4), a rhadinovirus (e.g., an ateline herpesvirus 2); any member of the family Papillomaviridae inclusive of a papillomavirus, preferably human papillomavirus, and preferably subtypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, and 59, although without limitation thereto; any member of the family Iridoviridae inclusive of a ranavirus and such as, epizootic haematopoietic necrosis virus, but not limited to; any member of the family Polyomaviridae inclusive of a polyomavirus and preferably murine polymavirus; any member of the family Poxviridae inclusive of an orthopoxvirus (e.g., a vaccinia virus), a parapoxvirus (e.g., a orf virus), an avipoxvirus (e.g., a fowlpox virus), an capripoxvirus (e.g., a sheep pox virus), a leporipoxvirus (e.g., a myxoma virus) and a suipoxvirus (e.g., a swinepox virus). A virus of the invention further contemplates any member of the ssDNA Viruses group including (and without limitation thereto) any member of the family Parvoviridae inclusive of a parvovirus (e.g., Rheumatoid arthritis virus, B19).
In the preferred embodiments that contemplate an immunogen from a virus and/or a viral capsomere sequence, the invention further contemplates any member of the dsRNA Viruses group including (and without limitation thereto) any member of the family Birnaviridae inclusive of an aquabirnavirus (e.g., an infectious pancreatic necrosis virus) and an avibirnavirus (e.g., infectious bursal disease virus); any member of the family Reoviridae inclusive of an orthoreovirus (e.g., a reovirus 3), a orbivirus (e.g., a bluetongue virus 1), a rotavirus, a coltivirus (e.g., a Colorado tick fever virus and an aquareovirus.
In the preferred embodiments that contemplate an immunogen from a virus and/or a viral capsomere sequence, the invention contemplates any member of the (+) sense RNA Virus group including (and without limitation thereto) any member of the family Astroviridae inclusive of an astrovirus (e.g., a human astrovirus) and an arterivirus (e.g., an equine arteritis virus); any member of the family Caliciviridae inclusive of a Norwalk virus, a Hepatitis E virus; any member of the family Coronaviridae inclusive of Corona Virus and SARS and a torovirus; any member of the family Flaviviridae inclusive of a flavivirus such as, but not limited to, yellow fever virus, dengue virus and West Nile virus; a pestivirus (e.g. bovine diarrhea virus) and hepatitis C-like viruses (e.g. a hepatitis C virus); any member of the family Picornaviridae inclusive of an enterovirus, a rhinovirus (e.g. a human rhinovirus 1A), a hepatovirus (e.g. a hepatitis A virus), a cardiovirus (e.g. a encephalomyocarditis virus) and an aphtovirus (e.g. foot-and-mouth disease virus); any member of the family Togaviridae inclusive of an alphavirus (e.g., a Sindbis virus) and a rubivirus (e.g. a rubella virus).
In the preferred embodiments that contemplate an immunogen from a virus and/or a viral capsomere sequence, the invention contemplates any member of the (−) negative sense RNAVirus group including (and without limitation thereto) any member of the family Filoviridae inclusive of a filovirus (e.g. Marburg virus, Ebola virus); any member of the family Paramyxoviridae inclusive of a paramyxovirus (e.g. a human parainfluenza virus 1), a morbillivirus (e.g. a measles virus), a rubulavirus (a mumps virus), a Hendra virus and a Nipah virus; any member of the family Pneumovirinae inclusive of a pneumovirus (eg. a human respiratory syncytial virus); any member of the family Rhabdoviridae inclusive of a vesiculovirus (e.g. a vesicular stomatitis virus, Indiana virus), a lyssavirus (e.g. a rabies virus) and an ephemerovirus (e.g. a bovine ephemeral fever virus); any member of the ambisense RNA Virus group inclusive of any member of the family Arenaviridae such as an arenavirus (e.g. lymphocytic choriomeningitis virus); any member of the family Bunyaviridae inclusive of a bunyavirus (e.g. Bunyamwera virus) and a hantavirus (e.g. a Hantaan virus); any member of the family Orthomyxoviridae inclusive of an influenzavirus A (such as an influenza A virus, an avian influenza A virus), an influenzavirus B (such as an influenza B virus), an influenzavirus C (such as an influenza C virus) and a “Thogoto-like viruses” (e.g. Thogoto virus).
In the preferred embodiments that contemplate an immunogen from a virus and/or a viral capsomere sequence, the invention contemplates any member of the RNA Reverse Transcribing Viruses group including any member of the family Retroviridae inclusive of a mammalian type B retrovirus (e.g. a mouse mammary tumor virus), a mammalian type C retrovirus (e.g. a murine leukemia virus), an avian type C retrovirus (e.g. a avian leukosis virus), a type D retrovirus (eg a Mason-Pfizer monkey virus), a BLV-HTLV retrovirus (e.g. a bovine leukemia virus), a lentivirus (e.g. a human immunodeficiency virus 1) and a spumavirus (e.g. a human spumavirus).
In relation to a virus, the invention contemplates any member of the DNA Reverse Transcribing Viruses group including any member of the family Hepadnaviridae inclusive of an orthohepadnavirus (e.g. a hepatitis B virus) and an avihepadnavirus (e.g. a duck hepatitis B virus), although without limitation thereto.
In the preferred embodiments that contemplate an immunogen from a virus and/or a viral capsomere sequence, the invention contemplates any member of the un-classified group of subviral agents such as satellites (e.g. tobacco necrosis virus), Viroids (hepatitis delta virus) and Agents of Spongiform Encephalopathies (e.g. prions, scrapie agent).
In a particularly preferred embodiment, the immunogen sequence corresponds to or is derived from a protein derived from an influenza virus. In preferable embodiments, the influenza virus protein is selected from the group consisting of hemagglutinin (HA), neuraminidase (NA), nuclear protein (NP), matrix protein M1 and matrix protein M2.
Preferably, the influenza virus protein is selected from the group consisting of HA and M2.
More preferably, the immunogenic protein or fragment thereof derived from an influenza virus is HA. Advantageously, the immunogenic protein derived from an influenza virus corresponds to a hypervariable region of HA. In another preferred embodiment, the immunogen is a domain of M2 and more preferably, M2e. Typically, although not exclusively, the domain of M2 is an ectodomain. In particularly preferred embodiments, the M2 immunogenic sequence comprises an amino acid sequence as set forth in SEQ ID NO: 23.
In particular preferred embodiments that relate to the HA protein, the immunogenic protein or fragment thereof corresponds to an exposed loop of HA selected from the group consisting of loop A, loop B, loop C, loop D and loop E, or a fragment thereof. Preferably, the exposed loop of HA is selected from the group consisting of loop A, loop B, loop C and loop E. More preferably, the exposed loop of HA is selected from the group consisting of loop A and loop B.
In more preferred embodiments, the fragment is an antigenic epitope of HA. In even more preferred embodiments, the fragment is an antigenic epitope of an exposed loop of HA selected from the group consisting of loop A, loop B, loop C and loop E.
A person skilled in the art will appreciate that viruses have evolved a number of mechanisms to evade the host cell immune response and, as a consequence, lead to generation of escape mutants. One such mechanism is the presence of a region within a virus protein/s with a high degree of variability, the so named hypervariable region. It will further be appreciated that the variability within an antigenic epitope between virus subtypes, and in particular influenza virus subtypes, can be substantial. Advantageously, although not exclusively, loop A and loop B comprise a minimal region which display a high degree of variability across virus subtypes.
Therefore in general embodiments where HA is derived from a H5 subtype of influenza virus, at least one consensus amino acid sequence for an antigenic epitope of loop A is PYqGKSS (SEQ ID NO: 33) (there is common q<-->N and K<-->R variability) whereas at least one consensus sequence for an antigenic epitope of loop B is PNDAAEQTKLYQNPTTY (SEQ ID NO: 37) (there is common K<-->R variability), although without limitation thereto.
In other general embodiments where HA derived from a H3 subtype of influenza virus, at least one consensus amino acid sequence for an antigenic epitope of loop A is KRGPgSG (SEQ ID NO: 38) (there is common PgS<-->PaS variability) whereas at least one consensus amino acid sequence for an antigenic epitope of loop B is PSTNQEQTsLYVQASGR (SEQ ID NO: 39) (there is common TsL<-->TNL variability), although without limitation thereto.
In yet other general embodiments where HA is derived from a H1 subtype of influenza virus, at least one consensus amino acid sequence for an antigenic epitope of loop A is SHKGKSS (SEQ ID NO: 40), whereas at least one consensus amino acid sequence of loop B is PSNIEDQKTIYRKENAY (SEQ ID NO: 41), although without limitation thereto.
In preferred embodiments, the HA immunogenic sequence comprises or has an amino acid sequence selected from the group consisting of SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41.
Other particularly preferred embodiments relate to an immunogenic protein derived from or corresponding to a protein from Hendra virus or Nipah virus. According to these preferred embodiments, the immunogenic protein or fragment thereof from Hendra virus or Nipah virus is derived from or corresponds to attachment-envelope glycoprotein G. More preferably, the G protein fragment comprises or has an amino sequence selected from the group consisting of SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ. ID NO: 27 and SEQ ID NO: 28.
Other preferred embodiments relate to use of immunogens that elicit an immune response against human papillomavirus (HPV) and more preferably, a HPV type selected from the group consisting of HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 66 and 68. In preferable embodiments, the HPV type is HPV16. It is also contemplated that HPV types, especially high risk HPV types, that have yet to be identified are encompassed by the invention. According to particularly preferred embodiments, HPV immunogenic sequence is derived from or corresponds to the E7 protein of HPV or a fragment thereof. Preferably, E7 protein fragment comprises or has an amino acid sequence selected from SEQ ID NO: 35 and SEQ ID NO: 36.
Examples of infectious fungi include: Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Candida albicans, although without limitation thereto.
The invention also contemplates immunogenic proteins from a parasite inclusive of a protozoan, a roundworm, a fluke and a tapeworm. Protozoans are inclusive of an Amebiasis sp, a Babesia sp, a Cryptosporidium sp, a Cyclosporia sp, a Giardia sp, a Leishmania sp, a Microsporidia sp, a Toxoplasma sp and a Plasmodium sp, although without limitation thereto. In embodiments that relate to the genus Plasmodium, contemplated are any Plasmodium species that is the causative agent of or is related to malaria such as Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale and Plasmodium malaria. Preferred embodiments relate to Plasmodium falciparum. A roundworm is inclusive of a filarial sp, a strongyloidial sp, a trichinellosis sp and a toxocariasis sp. A fluke is inclusive of a Paragonimus sp and a Schistosoma sp, although without limitation thereto. A tapeworm is inclusive of a Cysticercosis sp and an Echinococcosis sp although without limitation thereto.
The invention also encompasses use of immunogenic proteins from bacteria and in particular, Gram-positive and Gram-negative bacteria inclusive of a Salmonella sp (eg. Salmonella typhi), a Neisseria sp (eg. Neisseria gonorrhoeae, N. meningitidis), a Legionella sp, a Mycobacterium (Mycobacterium tuberculosis), eg Chlamydia sp, and Chlamydophila spp, (eg. Chlamydia trachomatis, Chlamydophila pneumoniae, C. psittaci), a Listeria spp, a Brucella sp, a Streptococcus sp (eg. Streptococcus pneumoniae, Streptococcus pyogenes (group A Streptococcus; GAS), S. agalactiae (group B Streptococcus; GBS, and S. mutans), a Haemopholia sp (eg. Haemophilus influenzae), Pasteurella species, a Vibrio sp (eg. Vibrio cholera), Escherichia coli, a Coxiellaceae sp (eg. Coxiella bumetii) pathogenic Campylobacter sp., Enterococcus sp., a Bacillus sp (eg Bacillus antracis; anthrax toxin), a Helicobacter sp and in particular Helicobacter pyloris, Clostridium sp (eg Clostridium perfringers, Clostridium tetani), a Borelia sp (eg. Borelia burgdorferi), and a Rickettsiales sp, although without limitation thereto.
In preferred embodiments that relate to Streptococcus pyogenes, the immunogenic protein is derived from or corresponds to a Streptococcus pyogenes protein selected from the group consisting of M protein, C5a peptidase, SpeB, group A carbohydrate, the fibronectin binding proteins Sfb1, SOF and FBP54, trigger factor (TF), ketopantoate reductase (KPR), arginine deiminase (ADI), ornithine carbamoyltransferase (OCTase), phosphotransacetylase (PTA), ribosome recycling factor (RRF), branched-chain-amino-acid aminotransferase (BCAT), carbamate kinase (CK), adenylate kinase (AK), elongation factor P (EF-P), high temperature requirement A serine protease (HtrA), phosphoglycerate kinase (PGK), 6-phosphofructokinase (PFK), NADP dependent glyceraldehyde 3 phosphate dehydrogenase (NADP-GAPDH) and Spy1262.
Preferably, the immunogenic protein or fragment corresponds to or is derived from M protein and more preferably, the amino terminal region of M protein which corresponds to any one or more amino acid residues up to and inclusive of about residue number 100 of wild-type M protein. In particularly preferred embodiments that relate to M protein, the immunogen comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 29, SEQ ID NO: 30 and SEQ ID NO: 31. Other suitable immunogenic peptides from M protein are provided in Brandt et al, Infect Immun. 2000 December; 68(12): 6587-6594, which is incorporated herein by reference.
Other medically relevant microorganisms have been described extensively in the literature, e.g., see C. G. A Thomas, Medical Microbiology, Bailliere Tindall, Great Britain 1983, the entire contents of which is hereby incorporated by reference.
The invention also contemplates use of immunogenic proteins derived from a protein associated with or causative of a cancer, a neurological disease, (and more preferably a degenerative neurological disease), an allergy and an autoimmune disease. Such proteins may be self-antigens.
Therefore the invention contemplates tumour antigens and tumour associated antigens (may collectively be referred to as ‘cancer antigens’) found in or associated with a germ cell tumour, a bowel cancer, a breast cancer, an ovarian cancer, a genitourinary cancer such as a prostate cancer and a testicular cancer, a brain cancer, a liver cancer, a pancreatic cancer, an oesophageal cancer, B cell lymphoma, T cell lymphoma, myeloma, leukemia, hematopoietic neoplasias, thymoma, lymphoma, sarcoma, lung cancer, non-Hodgkins lymphoma, Hodgkins lymphoma, uterine cancer, adenocarcinoma, pancreatic cancer, colon cancer, lung cancer, renal cancer, bladder cancer, a primary or metastatic melanoma, squamous cell carcinoma, basal cell carcinoma, angiosarcoma, hemangiosarcoma, head and neck carcinoma, thyroid carcinoma, soft tissue sarcoma, bone sarcoma, uterine cancer, cervical cancer, gastrointestinal cancer, biliary tract cancer, choriocarcinoma, colon cancer, endometrial cancer, esophageal cancer, gastric cancer, intraepithelial neoplasms, lymphomas, lung cancer (e.g. small cell and non-small cell), neuroblastomas, oral cancer, rectal cancer; skin cancer, as well as other carcinomas and sarcomas, although without limitation thereto and any other cancer now known or later identified (see, e.g., Rosenberg (1996) Ann. Rev. Med. 47:481-491, the entire contents of which are incorporated by reference herein). It will be appreciated that the cancer may be a malignant or nonmalignant cancer.
Non-limiting examples of tumour and/or tumour-associated antigens are alphafetoprotein, carcinoembryonic antigen (CEA), CA-125, MUC-1, ras, p53, epithelial tumor antigen (ETA), tyrosinase, HER2/neu and BRCA1 antigens for breast cancer, MART-1/MelanA, gp100, TRP-1, TRP-2, NY-ESO-1, CDK-4, |3-catenin, MUM-1, Caspase-8, KIAA0205, HPVE7, SART-1, PRAME, and p 15 antigens, members of the Melanoma-associated antigen (MAGE) family, the BAGE family (such as BAGE-1), the DAGE/PRAME family (such as DAGE-1), the GAGE family, the RAGE family (such as RAGE-1), the SMAGE family, NAG, TAG-72, CA125, mutated proto-oncogenes such as p21 ras, mutated tumor suppressor genes such as p53, tumor associated viral antigens (e.g., HPV16 E7), the SSX family, HOM-MEL-55, NY-COL-2, HOM-HD-397, HOM-RCC1.14, HOM-HD-21, HOM-NSCLC-11, HOM-MEL-2.4, HOM-TES-11, RCC-3.1.3, NY-ESO-1, and the SCP family. Members of the MAGE family include, but are not limited to, MAGE-1, MAGE-2, MAGE-3, MAGE4 and MAGE-11. Members of the GAGE family include, but are not limited to, GAGE-1, GAGE-6. See, e.g., review by Van den Eynde and van der Bruggen (1997) in Curr. Opin. Immunol. 9: 684-693, Sahin et al. (1997) in Curr. Opin. Immunol. 9: 709-716, and Shawler et al. (1997), the entire contents of which are incorporated by reference herein for their teachings of cancer antigens.
The cancer antigen can also be, but is not limited to, human epithelial cell mucin (Muc-1; a 20 amino acid core repeat for Muc-1 glycoprotein, present on breast cancer cells and pancreatic cancer cells), MUC-2, MUC-3, MUC-18, the Ha-ras oncogene product, carcino-embryonic antigen (CEA), the raf oncogene product, CA-125, GD2, GD3, GM2, TF, sTn, gp75, EBV-LMP 1 & 2, HPV-F4, 6, 7, prostatic serum antigen (PSA), prostate-specific membrane antigen (PSMA), C017-1A, GA733, gp72, p53, the ras oncogene product, 13-HCG, gp43, HSP-70, pi 7 mel, HSP70, gp43, HMW, HOJ-1, melanoma gangliosides, TAG-72, mutated proto-oncogenes such as p21 ras, mutated tumor suppressor genes such as p53, estrogen receptor, milk fat globulin, telomerases, nuclear matrix proteins, prostatic acid phosphatase, protein MZ2-E, polymorphic epithelial mucin (PEM), folate-binding-protein LK26, truncated epidermal growth factor receptor (EGFR), Thomsen-Friedenreich (T) antigen, GM-2 and GD-2 gangliosides, polymorphic epithelial mucin, folate-binding protein LK26, human chorionic gonadotropin (HCG), pancreatic oncofetal antigen, cancer antigens 15-3, 19-9, 549, 195, squamous cell carcinoma antigen (SCCA), ovarian cancer antigen (OCA), pancreas cancer associated antigen (PaA), mutant K-ras proteins, mutant p53, and chimeric protein p210BCR_ABL and tumor associated viral antigens (e.g., HPV16 E7).
The cancer antigen can also be an antibody produced by a B cell tumor (e.g., B cell lymphoma; B cell leukemia; myeloma; hairy cell leukemia), a fragment of such an antibody, which contains an epitope of the idiotype of the antibody, a malignant B cell antigen receptor, a malignant B cell immunoglobulin idiotype, a variable region of an immunoglobulin, a hypervariable region or complementarity determining region (CDR) of a variable region of an immunoglobulin, a malignant T cell receptor (TCR), a variable region of a TCR and/or a hypervariable region of a TCR. In one embodiment, the cancer antigen of this invention can be a single chain antibody (scFv), comprising linked VH, and VL domains, which retains the conformation and specific binding activity of the native idiotype of the antibody.
The cancer antigens that can be used in accordance with the present invention are in no way limited to the cancer antigens listed herein. Other cancer antigens can be identified, isolated and cloned by methods known in the art such as those disclosed in U.S. Pat. No. 4,514,506, the entire contents of which are incorporated by reference herein.
In relation to degenerative neurological diseases associated with dementia, the invention contemplates Alzheimer's disease and Lewy body dementia, although without limitation thereto. An immunogenic protein for Alzheimer's disease includes (and without limitation thereto) Amyloid beta (Aβ or Abeta), which is a peptide of 36-43 amino acids that appears to be the main constituent of amyloid plaques, which are deposits found in the brains of patients with Alzheimer's disease).
Immunogenic proteins that are associated with or causative of autoimmune diseases such as rheumatoid arthritis and diabetes are particularly amenable for use in the present invention. In suitable embodiments that relate to rheumatoid arthritis, the immunogenic protein may be derived from arthritogenic auto-antigen.
The immunogen can further be an autoantigen (for example, to enhance self-tolerance to an autoantigen in a subject, e.g., a subject in whom self-tolerance is impaired). Exemplary autoantigens include, but are not limited to, myelin basic protein, islet cell antigens, insulin, collagen and human collagen glycoprotein, muscle acetylcholine receptor and its separate polypeptide chains and peptide epitopes, glutamic acid decarboxylase and muscle-specific receptor tyrosine kinase.
The present invention also relates to use of immunogenic sequences in chimeric capsomeres that are allergens. An “allergen” refers to a substance (antigen) that tan induce an allergic or asthmatic response in a susceptible subject. An “allergy” refers to acquired hypersensitivity to a substance (allergen). Allergic conditions include but are not limited to eczema, allergic rhinitis or coryza, conjunctivitis, hay fever, bronchial asthma, urticaria (hives) and food allergies, and other atopic conditions. Allergies are generally caused by IgE antibody generation against harmless allergens. “Asthma” refers to a disorder of the respiratory system characterized by inflammation, narrowing of the airways and increased reactivity of the airways to inhaled agents. Asthma is frequently, although not exclusively associated with atopic or allergic symptoms.
The list of allergens is enormous and can include pollens, insect venoms, plant proteins, animal dander dust, fungal spores and drugs (e.g. penicillin). Examples of natural, animal and plant allergens include but are not limited to proteins specific to the following genuses: Canine (Canis familiaris); Dermatophagoides (e.g. Dermatophagoides farinae); Felis (Felis domesticus); Ambrosia ((Ambrosia artemiisfolia); Lolium (e.g. Lolium perenne OK Lolium multiflorum); Cryptomeria (Cryptomeria japonica); Altemaria (Altemaria altemata); Alder; Alnus (Alnus gultinoasa); Betula (Betula verrucosa); Quercus (Quercus alba); Olea (Olea europa); Artemisia (Artemisia vulgaris); Plantago (e.g. Plantago lanceolata); Parietaria (e.g. Parietaria officinalis or Parietaria judaica); Blattella (e.g. Blattella germanica); Apis (e.g. Apis multiflorum); Cupressus (e.g. Cupressus sempervirens, Cupressus arizonica and Cupressus macrocarpa); Juniperus (e.g. Juniperus sabinoides, Juniperus virginiana, Juniperus communis and Juniperus ashei); Thuya (e.g. Thuya orientalis); Chamaecyparis (e.g. Chamaecyparis obtusa); Periplaneta (e.g. Periplaneta americana); Agropyron (e.g. Agropyron repens); Secale (e.g. Secale cereale); Triticum (e.g. Triticum aestivum); Dactylis (e.g. Dactylis glomerata); Festuca (e.g. Festuca elatior); Poa (e.g. Poapratensis or Poa compressa); Avena (e.g. Avena sativa); Holcus (e.g. Holcus lanatus); Anthoxanthum (e.g. Anthoxanthum odoratum); Arrhenatherum (e.g. Arrhenatherum elatius); Agrostis (e.g. Agrostis alba); Phleum (e.g. Phleum pratense); Phalaris (e.g. Phalaris arundinacea); Paspalum (e.g. Paspalum notatum); Sorghum (e.g. Sorghum halepensis); Ricinus (eg. Ricinus communis and more preferably, ricin protein) and Bromus (e.g. Bromus inermis).
The invention also contemplates chimeric capsomeres comprising designed bioweapons or other toxic proteins.
Although many of the pathogenic or toxic antigens or sequences described above relate to human disorders, the invention is also useful for treating other nonhuman vertebrates. Nonhuman vertebrates are also capable of developing infections which can be prevented or treated with proteins, nucleic acid and capsomeres of the present invention. For instance, in addition to the treatment of infectious human diseases, the methods of the invention are useful for treating infections of animals.
As hereinbefore described the invention contemplates capsomeres with insertion of an immunogenic sequence into one or more surface exposed loops of a viral capsomere sequence in conjunction with addition/s of immunogenic sequences at the terminus. A particular advantage conferred by chimeric capsomeres with insertion into exposed loops is enhanced and/or more efficient surface presentation of the immunogen to the immune system. Reference is made to International Publication No. WO2008/040060 in the name of the University of Queensland which provides non-limiting examples of insertion into exposed loops and is incorporated herein by reference.
In those embodiments which relate to a viral capsomere forming sequence that is derived from VP1, it is understood that VP1 comprises four surface exposed loops which span around about residues 82-89, 221-224, 247-249 and 292-297 and are referred to as site 1, site 2, site 3 and site 4 respectively. In the context of the present invention, typically, although not exclusively, at least one exposed loop site has an insertion. It can be appreciated that to facilitate generation of a more potent or, alternatively a broad-spectrum capsomere vaccine, one, two, three or four sites may comprise an insertion. This equally applies to capsomeres other than VP1 capsomeres.
Preferably, one, two or three exposed loops comprise an insertion. More preferably, the one or more exposed loops comprising an insertion are selected from the group consisting of site 1, site 3 and site 4. In more preferred embodiments, the one or more exposed loops comprising an insertion are selected from the group consisting of site 1 and site 4: Preferable examples of suitable VP1 chimeras of the present invention are provided in the Examples section and in particular, FIGS. 2, 6, 12, 13, 14 and 20.
In light of the foregoing it would be readily appreciated that the present invention contemplates isolated nucleic acids encoding isolated proteins, or fragments thereof, of the present invention.
The term “nucleic acid” as used herein designates single- or double-stranded mRNA, RNA, cRNA and DNA inclusive of cDNA, genomic DNA and DNA-RNA hybrids. Nucleic acids may also be conjugated with fluorochromes, enzymes and peptides as are well known in the art.
The term “gene” is used herein to describe a discrete nucleic acid locus, unit or region within a genome that may comprise one or more of introns, exons, splice sites, open reading frames and 5′ and/or 3′ non-coding regulatory sequences such as a polyadenylation sequence.
The present invention also contemplates nucleic acids that have been modified such as by taking advantage of codon sequence redundancy. In a more particular example, codon usage may be modified to optimize expression of a nucleic acid in a particular organism or cell type. The invention also contemplates use of modified purines (for example, inosine, methylinosine and methyladenosine) and modified pyrimidines (for example, thiouridine and methylcytosine) in nucleic acids of the invention.
It will be well appreciated by a person of skill in the art that the isolated nucleic acids of the invention can be conveniently prepared by a person of skill in the art using standard protocols such as those described in Chapter 2 and Chapter 3 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (Eds. Ausubel et al. John Wiley & Sons NY, 1995-2008).
In one particular embodiment, an isolated nucleic acid of the present invention is operably-linked to one or more regulatory nucleotide sequences in a genetic construct. A person skilled in the art will appreciate that a genetic construct is a nucleic acid comprising any one of a number of nucleotide sequence elements, the function of which depends upon the desired use of the construct. Uses range from vectors for the general manipulation and propagation of recombinant DNA to more complicated applications such as prokaryotic or eukaryotic expression of the isolated nucleic acid. Typically, although not exclusively, genetic constructs are designed for more than one application. By way of example only, a genetic construct whose intended end use is recombinant protein expression in a eukaryotic system may have incorporated nucleotide sequences for such functions as cloning and propagation in prokaryotes in addition to sequences required for expression. An important consideration when designing and preparing such genetic constructs are the required nucleotide sequences for the intended application.
In view of the foregoing, it is evident to a person of skill in the art that genetic constructs are versatile tools that can be adapted for any one of a number of purposes. Methods for the generation of said genetic constructs are well known to those of skill in the art.
In a preferred embodiment, the genetic construct is an expression construct which is suitable for recombinant expression. Preferably, the expression construct comprises at least a promoter and in addition, one or more other regulatory nucleotide sequences which are required for manipulation, propagation and expression of recombinant DNA.
In particular aspects, the invention contemplates an expression construct comprising an isolated nucleic acid, operably-linked to one or more regulatory nucleotide sequences in an expression vector. A person skilled in the art will appreciate that the isolated nucleic acid may be inserted into the expression vector by a variety of recombinant techniques using standard protocols as for example described in Sambrook et al., MOLECULAR CLONING, A Laboratory Manual (Cold Spring Harbor Press, 1989), which is incorporated herein by reference.
An “expression vector” may be either a self-replicating extra-chromosomal vector such as a plasmid, or a vector that integrates into a host genome, inclusive of vectors of viral origin such as adenovirus, lentivirus, poxvirus and flavivirus vectors as are well known in the art.
By “operably linked” is meant that said regulatory nucleotide sequence(s) is/are positioned relative to the recombinant nucleic acid of the invention to initiate, control, regulate or otherwise direct transcription and/or other processes associated with expression of said nucleic acid.
Regulatory nucleotide sequences will generally be appropriate for the host cell used for expression. Numerous types of appropriate expression vectors and suitable regulatory sequences are known in the art for a variety of host cells.
Preferable vectors include any of the well known prokaryotic expression vectors, recombinant baculoviruses, COS cell specific vectors, vaccinia recombinants, or yeast-specific expression constructs. Among expression vectors preferred for use in cells of prokaryotic origin include pQE60 available from Qiagen, pGEX series of vectors available from GE Life Sciences and pET vector system available from Novagen.
Typically, said one or more regulatory nucleotide sequences may include, but are not limited to, promoter sequences, leader or signal sequences for secretion of a translated protein, ribosomal binding sites, transcriptional start and termination sequences, translational start and termination sequences, splice donor/acceptor sequences, enhancer or activator sequences and nucleic acid packaging signals.
Preferably, said promoter is operable in a bacterial cell. Non-limiting examples include T7 promoter, tac promoter and T5 promoter.
Inducible/repressible promoters (such as tet-repressible promoters and IPTG-, alcohol-, metallothionine- or ecdysone-inducible promoters) are well known in the art and are contemplated by the invention, as are tissue-specific promoters such as α-crystallin promoters. It will also be appreciated that promoters may be hybrid promoters that combine elements of more than one promoter (such as SRα promoter).
The expression construct may also include a fusion partner (typically provided by the expression vector) so that the protein (or fragment thereof) of the invention is expressed as a fusion protein with said fusion partner, as hereinafter described.
Expression constructs may also include a selection marker nucleic acid that confers transformed host cell resistance to a selection agent. Selection markers useful for the purposes of selection of transformed bacteria include bla, kanR and tetR while transformed eukaryotic cells may be selected by markers such as hygromycin, G418 and puromycin, although without limitation thereto.
Expression constructs may be introduced into cells or tissues, inclusive of cells capable of recombinant protein production, by any of a number of well known methods typically referred to as “transfection” “transduction”, “transformation” and the like. Non-limiting examples of such methods include transformation by heat shock, electroporation, DEAE-Dextran transfection, microinjection, liposome-mediated transfection (e.g. lipofectamine, lipofectin), calcium phosphate precipitated transfection, viral transformation, protoplast fusion, microparticle bombardment and the like.
It is readily contemplated that any recombinant protein expression system may be used for the present invention such as bacterial, yeast, plant, mammalian and insect-based expression systems but is not limited thereto.
In one preferred embodiment, recombinant protein expression occurs in cells of prokaryotic origin. Suitable host cells for recombinant protein expression are bacterial cells such as Escherichia coli (BL21 and various derivative strains thereof which have been optimised for certain applications, such as Rosetta and DE3, for example) and Bacillus subtilis, although without limitation thereto.
In another preferred embodiment, recombinant expression occurs in insect cells which are suited to viral-based recombinant expression e.g. Sf9 cells.
Formation of capsomeres can be monitored by electron microscopy or other techniques including size-exclusion chromatography optimally hyphenated with light scattering and, in instances wherein capsomeres are comprised of fusion proteins, the presence of various protein components in the assembled capsomere can be confirmed by Western blot analysis using specific antisera.
Pharmaceutical Compositions and Methods Thereof
In broad aspects, the invention relates to pharmaceutical compositions and therapeutic/prophylactic methods comprising the capsomeres as hereinbefore described.
In other general aspects, the invention relates to pharmaceutical compositions and methods of augmenting an immune response, comprising an immunogenic protein of interest and an adjuvant selected from the group consisting of a protein-stabilised surfactant emulsion adjuvant, a solid particle substantially-free of an immunogen of interest and a virus-like particle.
In preferred embodiments, the methods include inducing or augmenting an antigen specific immune response in a subject. Methods of the present invention may be prophylactic or therapeutic.
In a preferred embodiment, the pharmaceutical composition of the present invention is an immunogenic composition.
More preferably, the immunogenic composition is an immunotherapeutic composition.
In a particular preferred embodiment, the immunotherapeutic composition is a vaccine. Any suitable procedure is contemplated for producing vaccine compositions. Exemplary procedures include, for example, those described in New Generation Vaccines (1997, Levine et al., Marcel Dekker, Inc. New York, Basel, Hong Kong), which is incorporated herein by reference. Alternatively, a vaccine may be in the form of a nucleic acid vaccine and in particular, a DNA vaccine. A useful reference describing DNA vaccinology is DNA Vaccines, Methods and Protocols, Second Edition (Volume 127 of Methods in Molecular Medicine series, Humana Press, 2006) and is incorporated herein by reference.
According to the methods using a protein-stabilised surfactant emulsion adjuvant, a solid particle substantially-free of an immunogen of interest and a virus-like particle as an adjuvant to immunogens of interest, and preferably capsomeres, the immunogen is mixed with the adjuvant and suitably this co-formulation is administered to the subject without further purification and/or processing prior to administration and without covalent attachment.
Adjuvants
As well as the use of conventional adjuvants, the invention particularly contemplates in other general aspects of the present invention relate to methods and compositions for augmenting an immune response against an immunogen of interest, and preferably a capsomere carrying one or more immunogens of interest and in particular, a chimeric capsomere as hereinbefore described by administration of the immunogen of interest with an adjuvant selected from the group a protein-surfactant stabilised emulsion, a solid particle substantially-free of the immunogen of interest and a virus-like particle. According to preferred forms, once combined the immunogen of interest and the adjuvant does not undergo further processing, modification and/or purification prior to administration. According to particularly preferred forms, after combining the immunogen of interest and adjuvant, we do not expect the immunogen of interest and adjuvant do not become substantially associated thus most of the immunogen remains in solution and not be attached to the surface of the adjuvant.
By “augment” or “augmenting” is meant to enhance, stimulate, boost, potentiate or otherwise improve an immune response against an immunogen. By “augment” is not meant to initiate an immune response but rather, increase or potentiate an immune response. The response is a immunogen-specific immune response and may be a neutralising, B-cell and/or T-cell response. Preferably, it is an IgG response.
As used herein, the term “adjuvant” has its ordinary meaning as understood by those in the art. For example, an adjuvant can be defined as a substance that increases the ability of an immunogen to stimulate an immune response against the immunogen in the subject. In particular embodiments, the adjuvant increases the immune response against the immunogen by at least about 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 75, 100, 150, 500, 1000-fold or more. In other embodiments, the adjuvant reduces the amount of immunogen required to achieve a particular level of immune response (cellular and/or humoral and/or mucosal), e.g., a reduction of at least about 15%, 25%, 35%, 50%, 65%, 75%, 80%, 85%, 90%, 95%, 98% or more. An adjuvant can further be a substance that prolongs the time over which an immune response, optionally protective immune response, is sustained (e.g., by at least about a 2-fold, 3-fold, 5-fold, 10-fold, 20-fold longer time period or more).
Protein-Surfactant Stabilised Emulsion Adjuvant
As used herein, the term “emulsion” refers to a suspension or dispersion of a first liquid suspended or dispersed in a second liquid in which the first liquid is poorly soluble or non-miscible. The first liquid is referred to as the dispersed phase and the second liquid is referred to as the continuous phase. The dispersed phase may form droplets which are dispersed throughout the continuous phase in a heterogenous or homogeneous manner. Illustrative examples of emulsions include oil-in-water emulsions in which the oil forms the dispersed phase and the water forms the continuous phase, and water-in-oil emulsions in which the water forms the dispersed phase and the oil forms the continuous phase. In addition, “multiple emulsions” may be formed in which droplets of a first discontinuous phase contain smaller droplets of a second discontinuous phase, which may or may not be similar in composition to the continuous phase containing the first discontinuous phase. Illustrative examples of multiple emulsions include water-in-oil-in-water emulsions in which the oil forms the first discontinuous phase and water forms the second discontinuous phase, and oil-in-water-in-oil emulsions in which the water forms the first discontinuous phase and oil forms the second discontinuous phase. Suitably, the emulsion of the present invention may be a water-in-oil (W/O) emulsion or an oil-in-water (O/W) emulsion.
The protein-surfactant stabilised emulsions of the present invention are formed from a protein-surfactant that, when emulsified to form the adjuvant, will substantially prevent the breakdown of the capsomere structure. The protein-surfactants are emulsified in an oil phase and suitably, with an appropriate buffer. In preferred embodiments, the protein-stabilised surfactant emulsion of the present invention is an oil-in-water emulsion (O/W).
It will be appreciated that the protein component of the protein-surfactant stabilised emulsion may be a peptide, a polypeptide or a mixture of the two.
Particularly excluded from these embodiments of the invention are emulsion adjuvants (and more preferably emulsion adjuvants with a mean size of less than 200 nm) which comprise non-proteinaceous surfactants and in particular, one or more of a chemical surfactants, a lipid or synthetic chemical polymer and/or are specifically formulated to destroy and inactivate virus structure. Preferably, the emulsion adjuvant is not a squalene-based adjuvant and more preferably, is not MF59 and its equivalents or alternatives. In other particular embodiments, the emulsion is not an emulsion adjuvant which kills or inactivates viruses (such as by membrane structure destabilisation) such as W805EC (supplied by NanoBio Corporation (Ann Arbor, Mich.)). W805EC is an oil-in-water emulsion manufactured by high speed emulsification and typically, although not exclusively, contains Tween 80, ethanol, soybean oil, cetylpyridinium chloride and water.
The emulsion of the present invention can be prepared by conventional techniques as is known in the art.
Particular advantages conferred by the protein-surfactant stabilised emulsion employed in the present invention include that it is a “structure-friendly” adjuvant meaning that it substantially retains the structure of the capsomere. This advantage stems from inclusion of a peptide or protein surfactant molecule in an appropriate buffer and an oil phase that will not break down capsomere structure. This is unlike other adjuvants such as W805EC which destroys and inactivates virus structure. The protein stabilised surfactant emulsion ensures efficient antigen presenting cells (APCs) uptake due to, at least in part, an average emulsion size of less than 200 nm, which is similar to some viruses. Furthermore, the emulsion is manufactured from biodegradable compounds, and is thus less toxic and less reactogenic than some other emulsion adjuvants.
Protein surfactants of the present invention may be designed (or otherwise engineered) or alternatively, may be naturally-derived. Designed peptide surfactants (may be commonly referred to as ‘pepfactants’) are facially amphipathic molecules that self-assemble at fluid interfaces to give cohesive films stabilizing foams and emulsions. A change in the bulk solution conditions can switch off the interfacial film, leading to rapid foam or emulsion collapse. Designed peptide surfactants can be genetically engineered and produced using standard methods. Reference is made to International Publication No. 2006/089364 (in the name of the University of Queensland), Dexter et al (2006) Nature Materials 5: 502-506 and Dexter and Middelberg (2008) Industrial & Engineering Chemistry Research, 4717: 6391-6398 for non-limiting examples of designed peptide surfactants that suitable for use in the present invention and methods of production thereof. International Publication No. 2006/089364, Dexter et al (2006) and Dexter and Middelberg (2008) are incorporated herein by reference.
Preferably, the peptide surfactant comprises a peptide sequence selected from MKQLADSLHQLARQVSRLEHA (SEQ ID NO: 48; common name AM1) and MKQLADSLMQLARQVSRLESA (SEQ ID NO: 49; common name Lac21). More preferably, the peptide sequence is MKQLADSLHQLARQVSRLEHA (SEQ ID NO: 48).
Other preferred embodiments contemplate a peptide-surfactant comprising a plurality of peptides wherein either the same peptide or different peptides associate to create a peptide-surfactant. By way of example, Middelberg and Dimitrijev-Dwyer (2011) Chem Phys Chem 12:1426-1429 (incorporated herein by reference) describes a peptide-surfactant (referred to as DAMP4) which is composed of four AM1 peptide surfactant units joined together to create a suitable peptide-surfactant for use in the present invention.
Protein hydrolysates are an example of a naturally-derived peptide surfactant involves digesting native proteins to obtain short peptide sequences that may have useful surface activity. In this approach, intact proteins are subjected to chemical or enzymatic hydrolysis; often with a reagent that has selectivity for particular sequence sites within the protein. After peptide bond cleavage has proceeded to a given level, usually involving cleavage of 1-10% of all monomer links, the reaction is terminated. The partial digest, a highly complex mixture, is subjected to tests to determine its surfactant properties and may undergo fractionation to obtain peptides with improved functionality relative to the native protein or the initial mixture. In rare cases, it may be possible to attribute the improved surfactant properties to a particular peptide or peptides in the hydrolysate. Proteins used for the preparation of surfactant peptide mixtures are generally low-cost food proteins, including casein, whey, soy, seed residues, and fishery by products.
It is commonly, although not universally, observed that the surfactant properties of native proteins are improved by partial hydrolysis. Because different proteolytic enzymes have different cleavage site specificities, the products of partial digestion with each enzyme will be different for the same starting protein, even at the same degree of hydrolysis. For a given protein/protease combination, there appears to exist an optimal degree of hydrolysis beyond which surfactant functionality decreases, as amphipathic peptides are degraded to single amino acids. In some cases, the surfactant properties of short peptides can be improved by chemical acylation. Fractionation of peptide products may be achieved by ultrafiltration, selective precipitation or chromatography, based on differences in size, hydrophobicity, charge, or solubility. Analysis of the products of digestion has identified peptide structural features important to improved surfactant properties. However, for good surface activity, peptides may contain distinct clusters of hydrophobic and hydrophilic residues. It appears to be particularly favorable if they possess distinct hydrophobic and hydrophilic faces in an α-helical or β-sheet conformation. Sequence patterns suitable to this outcome are well-known.
Digest peptides may be smaller than 2 kDa or as high as 7 kDa or more, as can be deemed suitable by a person of skill in the art.
The protein-surfactant stabilised emulsion is preferably formulated with a pharmaceutically-acceptable oil. Non-limiting examples of suitable pharmaceutically-acceptable oils include oils derived from plant fatty acids and more suitably, triglycerides of the fractionated plant fatty acids C8 and C10 and more particularly, saturated coconut and palmkernel oil-derived caprylic and capric fatty acids and glycerin or propylene glycol. Such oils are sold under trade name of MIGLYOL® 810, 812, 818, 829, 840 by Sasol (Germany).
The protein-surfactant stabilised emulsion of the present invention preferably has a mean size (particle size) that is equivalent to the size of a virus particle. Preferably, protein-surfactant stabilised emulsion has a mean size of less than about 300 nm, 200 nm or less. In particularly preferred embodiments, the protein-surfactant stabilised emulsion has a mean size of less than 200 nm.
A Solid Particle Substantially-Free of an Immunogen of Interest as an Adjuvant
According to these embodiments, the invention is predicated, at least in part, on the finding that it is not necessary to covalently attach an immunogen either in or on the surface of a solid particle (sometimes referred to colloquially herein as “nanoparticles”), and in particular a solid silica particle, to act as an effective adjuvant for the immunogen. The invention is also predicated on the finding that it is not necessary to achieve a high level of saturation of the surface of the solid particle with immunogen for there to be an effective adjuvanting effect the surface of the solid particle can be substantially free of the immunogen of interest, with most of the immunogen present in the administered sample being in an unconjugated state and thus free in solution. As described in the Examples section herein, the inventors have demonstrated that the co-administration of capsomeres in presence of solid silica particles (in which there is no substantial association between the solid silica particle and the capsomere) gives a better immune response than administration of capsomeres alone. This is a surprising and unexpected result and directly challenges the dogma that an immunogen must be attached to a particle to give a positive benefit. Moreover, the immunogen is not covalently attached to the solid particle and any association that occurs is through non-covalent linkage. In preferred embodiments, after combining the immunogen and solid particle, a substantial fraction of the immunogen remains in solution and not attached to the surface of the solid particle. It is contemplated that a small fraction of the immunogen may non-specifically bind through, for example, non-covalent bonds, to the solid particle.
By “solid particle substantially-free of an immunogen of interest” is meant a particulate structure not found in nature, and is preferably pre-fabricated, formed from one or more solid carrier materials and is either free or substantially-free of an immunogen of interest associated with its surface. The present invention avoids specific conjugation or attachment of the immunogen of interest to the solid particle for use as an adjuvant. It may be that the solid particle is substantially-free of covalently associated immunogen of interest either at its surface, encapsulated therein or a combination thereof. That is, the solid particles of the invention are not used for delivery of the substantial amount of immunogen since the immunogen of interest is not covalently attached to the solid particle since the immunogen of interest is not conjugated to the particle and any association that occurs is through non-covalent linkage. Accordingly to those embodiments that contemplate capsomeres, the immunogen carrier or interest is the capsomere and preferably the chimeric capsomere as herein described.
By “substantially-free of an immunogen of interest”, is where about 15%, preferably about 10%, and more preferably about 5%, 4%, 3%, 2%, 1% or lower of the available immunogen of interest is bound to the solid particle. It is contemplated that in certain embodiments, the immunogen of interest may constitute no more than about 50%, preferably no more than about 40% and even more preferably no more than about 30%, about 25%, 20%, 15%, 10%, 5% or lower of the surface coverage that would correspond to a closely packed saturated monolayer of the immunogen on the surface of the solid particle. Surface coverage may be defined an a mg/m2 basis and according to these embodiments, reference is made to Daly et al, Langmuir (2003), 19, 3848-3857, which provides useful methodology for measuring protein adsorption to a solid surface and is incorporated herein by reference.
In particular embodiments, the pharmaceutical composition comprises a solid particle substantially-free of an immunogen of interest and substantially unbound antigen. By “substantially unbound immunogen”, in relation to this invention, is where the majority of the immunogen remains in solution when the solid particle as an adjuvant and immunogen are combined, such that less than 20% of the immunogen capable of associating with the solid particle binds to the surface and preferably not more than 10% and more preferably not more than 9%, 8%, 7%, 6%, 5% or lower.
Routine assays, apparent to the person of skill in the art, could be used to determine whether and at what level the immunogen of interest is associated with solid particles, including but not limited to separation into distinct fractions by free flow of the formulation within an electric field, isotherm adsorption, or techniques such as sedimentation rate analysis which are particularly suited to non-particulate antigens, followed by assaying for immunogen of interest in the fractions.
The term solid in the context of the present invention is meant a material that is characterized by structural rigidity and resistance to changes of shape or volume. The “solid particle” of the present invention preferably has a solid surface/core and may be porous or non-porous. The solid particles may be a variety of different shapes including but not limited to, spheroidal, cubic, pyramidal, oblong, cylindrical, toroidal and the like.
Included within the scope of a solid particle for use of as an adjuvant are particles differentiated by size such as a nanoparticle whose mean particle size falls within the nano-scale and a microparticle whose mean particle size falls within the micron-scale. Suitably, the particles are no larger than the upper limit of the micron scale. In particular embodiments, the solid particle has a mean particle size of less than 1 micron. In some preferred embodiments, the solid particles used as an adjuvant of the invention have a mean particle diameter size of less than 200 nm. In other preferred embodiments, the mean particle diameter size is between about 5 nm and about 100 μm, more preferably between about 50 nm and 50 μm, even more preferably about 100 nm and 20 μm, yet even more preferably between 150 nm and 10 μm and even more preferably, about 200 nm. It is contemplated that the mean particle diameter size of the unconjugated solid particle is less than about 50 nm, 100 nm, 150 nm, 200 nm, 250 nm, 300 nm, 350 nm, 400 nm, 450 nm, 500 nm, 550 nm, 600 nm, 650 nm, 700 nm, 750 nm, 800 nm, 850 nm, 900 nm, 950 nm, 1 μm, 1.5 μm, 2 μm, 2.5 μm, 3 μm, 4 μm, 5 μm, 10 μm, 15 μm, 20 μm, 25 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm and 100 μm.
In particular preferred embodiments, the solid particle of the invention has a mean diameter size of between about 40 nm and 60 nm.
In particular embodiments, the solid particle used as an adjuvant is a non-polymeric with a mean particle size of less than 1 micron.
The solid particles of the invention may be made from degradable and non-degradable carrier materials. Degradable materials include synthetic polymers such as polycyanoacrylate, poly(D, L-lactide), poly(lactide-co-glycolide) (PLGA) and poly(lactic acid); natural polymers such as polysaccharides inclusive of chitosan, gelatine, and sodium alginate, although without limitation thereto. Non-degradable carrier materials include latex, silica, polystyrene and metal such as gold and silver. Particles can be prepared by different techniques, such as spray drying, freeze drying or solvent evaporation as will be known to a person of skill in the art.
The invention contemplates solid particles as adjuvants that have been surface-modified. For example, a solid particle can be polymer-coated silica where the surface has been designed or engineered using techniques known in the art to modify the surface in such a way that protein adsorption is resisted. This same approach could be used for polymer particles.
In particularly preferred embodiments, the solid particles of the invention are manufactured from silica. Such solid silica particles are available commercially from Polysciences, Inc. In particularly, preferred embodiments, the invention contemplates a solid particle substantially-free of an immunogen of interest being a silica particle of a mean diameter size of less than about 250 nm, more preferably less than about 100 nm and even more preferably having a mean diameter size of less between about 40 nm and 60 nm.
According to preferred methods of use, the immunogen of interest is not substantially absorbed to or encapsulated within the solid particle. Preferably, once combined the immunogen of interest and the adjuvant does not undergo further processing, modification and/or purification prior to administration to a subject.
The state of the particle may be ascertained by methods such as isotherm calorimetry, dynamic light, x-ray scattering, zeta potential measurement or indirectly by HPLC analysis of formulated supernatant as are known in the art.
According to particularly preferred embodiments that relate to utilising a solid particle substantially-free of an immunogen of interest as an adjuvant, the solid particle and the immunogen of interest is combined as a pharmaceutical composition without further processing prior to administration, such that the bound and unbound immunogen of interest are not separated. Therefore when administered, the pharmaceutical composition comprises a substantial proportion of unbound immunogen of interest (and thereby present free in the solution) and a proportion of the immunogen of interest is bound to the solid particle. In particularly preferred embodiments, the pharmaceutical composition is formulated by combining a solid particle and an immunogen of interest without further processing prior to administration and comprises a solid particle in which the immunogen of interest is less than 50% of surface saturation of the particle.
Virus-Like Particles (VLPs) as Adjuvants
The present inventors assert that virus-like particles can act as potent adjuvants to enhance an immune response, which effect is unrelated to their ability to act as vaccine vectors. The VLP adjuvants of the invention can stimulate and enhance an immune response against an immunogen that is independent of the VLP adjuvant, i.e., is not presented by the VLP adjuvant or expressed by the VLP adjuvant. That is according to the present invention, VLPs are not used as an immunogen against the parental virus or as an antigen carrier against the targeted virus. In the context of the present invention, the VLP is used as an immunisation partner to capsomere, i.e. as an adjuvant instead of as an immunogen or antigen carrier. Suitably, the VLP is an unconjugated VLP. In particularly preferred embodiments, the VLP adjuvant is a wild-type VP1 VLP. The conjugation state of the particle may be ascertained by methods such as calorimetry, size-exclusion chromatography or HPLC as are known in the art.
In particular embodiment, by “pharmaceutically-acceptable carrier, diluent or excipient” is meant a solid or liquid filler, diluent or encapsulating substance that may be safely used in systemic administration. Depending upon the particular route of administration, a variety of carriers, well known in the art may be used. These carriers may be selected from a group including sugars, starches, cellulose and its derivatives, malt, gelatine, talc, calcium sulfate, vegetable oils, synthetic oils, polyols, alginic acid, phosphate buffered solutions, emulsifiers, isotonic saline and salts such as mineral acid salts including hydrochlorides, bromides and sulfates, organic acids such as acetates, propionates and malonates and pyrogen-free water.
A useful reference describing pharmaceutically acceptable carriers, diluents and excipients is Remington's Pharmaceutical Sciences (Mack Publishing Co. N.J. USA, 1991) which is incorporated herein by reference.
Any safe route of administration may be employed for providing a patient with the composition of the invention. For example, enteral, oral, rectal, parenteral, sublingual, buccal, intravenous, intra-articular, intra-muscular, intra-dermal, subcutaneous, inhalational, intraocular, intraperitoneal, intracerebroventricular, transdermal and the like may be employed.
Dosage forms include tablets, dispersions, suspensions, injections, solutions, oils, syrups, troches, capsules, suppositories, aerosols, transdermal patches and the like. These dosage forms may also include injecting or implanting controlled releasing devices designed specifically for this purpose or other forms of implants modified to act additionally in this fashion. Controlled release of the therapeutic agent may be effected by coating the same, for example, with hydrophobic polymers including acrylic resins, waxes, higher aliphatic alcohols, polylactic and polyglycolic acids and certain cellulose derivatives such as hydroxypropylmethyl cellulose. In addition, the controlled release may be effected by using other polymer matrices, liposomes and/or microspheres.
Compositions of the present invention suitable for enteral, oral or parenteral administration may be presented as discrete units such as capsules, sachets or tablets each containing a pre-determined amount of one or more therapeutic agents of the invention, as a powder or granules or as a solution or a suspension in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion or a water-in-oil liquid emulsion. Such compositions may be prepared by any of the methods of pharmacy but all methods include the step of bringing into association one or more agents as described above with the carrier which constitutes one or more necessary ingredients. In general, the compositions are prepared by uniformly and intimately admixing the agents of the invention with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product into the desired presentation.
The above compositions may be administered in a manner compatible with the dosage formulation, and in such amount as is pharmaceutically-effective. The dose administered to a patient, in the context of the present invention, should be sufficient to effect a beneficial response in a patient over an appropriate period of time. The quantity of agent(s) to be administered may depend on the subject to be treated inclusive of the age, sex, weight and general health condition thereof, factors that will depend on the judgement of the practitioner.
It will also be appreciated that treatment methods and pharmaceutical compositions may be applicable to prophylactic or therapeutic treatment of mammals, inclusive of humans and non-human mammals such as livestock (e.g. horses, cattle and sheep), companion animals (e.g. dogs and cats), laboratory animals (e.g. mice, rats and guinea pigs) and performance animals (eg racehorses, greyhounds and camels), although without limitation thereto.
So that the invention may be readily understood and put into practical effect, the following non-limiting Examples are provided.
EXAMPLES
Example 1
Construction of Generic Vectors Carrying VP1 Sequences Able to Accept Antigenic Peptide Sequences on the N-Terminal and/or C-Terminal and/or the Surface Loops
Murine polyomavirus VP1 sequence (GenBank accession number: M34958) was cloned between the BamHI and XhoI sites within the multiple cloning site of the commercial vector pGEX-4T-1 (GE healthcare). Generic vectors carrying VP1 sequences able to accept antigenic sequences on the surface-exposed loops of polyomavirus VP1 were previously constructed and documented in International Publication No. WO/2008/040060.
The amino acid sequence of VP1 present in the generic vectors is depicted in FIG. 1. S1 of VP1 was mutated to include NaeI restriction site (LATSDTED (SEQ ID NO: 44) mutated to LATSAGTED (SEQ ID NO: 45)). S4 of VP1 was mutated to include AfeI restriction site (TRNYDV (SEQ ID NO: 46) mutated to TRSAYDV (SEQ ID NO: 47)). A delta N28 and delta C63 VP1 along with mutated S1 and S4 sites is generated by recloning the truncated VP1 S1/S4. The first 28 amino acid residues of VP1 and the last 63 amino acids of VP1 are removed to generate the truncated VP1 S1/S4. Restriction site PmlI is introduced at the N-terminus of truncated VP1 S1/S4 and restriction site SnaBI is introduced at the C-terminus during the recloning.
Resulting generic vectors with modified VP1 sequences to enable the insertion of one or multiple foreign peptides are: pGEX4T1-VP1 S1, pGEX4T1-VP1 S4, pGEX4T1-VP1 S1/S4 and pGEX4T1-VP1 dNdC 0000.
Example 2
Production of Chimeric VP1 Capsomeres with Antigenic Peptide Sequences on the N-Terminal, C-Terminal and the Surface Loops
Construction and Sequencing of Vector Carrying HA Epitope from Loop A of H1N1:
E. coli codon optimised oligonucleotides were designed for epitope A (17 amino acids, DSNKGVTAACPHAGAKS (SEQ ID NO: 32)) for insertion into generic vector pGEX4T1-VP1 dNdC 0000. The sequence of epitope A is of H1N1 (A/California/07/2009).
Resulting constructs carrying HA epitope A is pGEX4T1-VP1 dNdC 1011A (FIG. 2).
Expression of Chimeric VP1 dNdC 1011A:
VP1 dNdC 1011A protein were expressed in Rosetta (DE3) pLysS (Novagen) as a glutathione-s-transferase-VP1-dNdC 1011A (GST-VP1-dNdC 1011A) fusion protein using the pGEX-4T-1-VP1 dNdC 1011A expression vector. For solid agar medium, 15 g/L of agar was added to Luria-Bertani (LB) medium (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.0). Liquid medium used for cell cultures was Terrific Broth (TB) containing 12 g/L peptone, 24 g/L yeast extract, 0.4% (v/v) glycerol, 2.31 g/L KH2PO4 and 12.54 g/L K2HPO4. All media used were supplemented with 50 μg/mL of ampicillin and 34 μg/mL of chloramphenicol. Overnight cultures were set up by inoculating single colonies of the transformed, cells into 5 mL of TB medium and cultivated at 30° C. on a rotary shaker at 180 rpm. After incubation of 16 hours, the overnight cultures were diluted 1000 times into 400 mL cultures in 2 L baffled flasks. These cultures were cultivated to an OD600 of 0.5 at 37° C. and then cooled to 26° C. under running tap water and subsequently induced with IPTG at final concentration of 0.2 mM. The induced cultures were then cultivated at 26° C. for a further 16 hours and harvested by centrifugation at 8000 g, 4° C. for 30 mins.
Purification of Chimeric VP1 dNdC 1011A:
Two pellets from 2×400 mL cultures were re-suspended in 40 mL of buffer L (200 mM NaCl, 40 mM Tris, 5 mM dithiothreitol, 1 mM EDTA, 5% v/v glycerol, pH 8 with HCl). The cell suspension was sonicated at output 30 using a Branson Sonifier 450 (Sonifier, USA) for 4×40 seconds. The resulting cell lysate was centrifuged at 27000 g, 4° C. for 30 mins and the supernatant which contained soluble chimeric proteins was filtered through an 0.45 μm syringe filters (Millipore) giving a recovery of  ̃35 mL.
Protein purification was performed with an Äkta Explorer system from GE Healthcare. GST-VP1 dNdC 1011A in the clarified lysate was captured using a GSTrapTM HP 5 mL column from GE Healthcare pre-equilibrated with buffer L (illustrated in FIG. 3A). The bound GST fusion proteins was eluted with elution buffer (Buffer L with 10 mM reduced glutathione) as illustrated in FIG. 3B. Eluted samples were stored at −80° C. until required.
40 μL of Thrombin was added to 1 mL of purified GST fusion proteins followed by 2 hours incubation at room temperature. 1 mL of thrombin treated capsomere was injected onto a Superdex S200 10/300 GL size exclusion column (GE Healthcare) equilibrated in buffer L, to separate capsomeres from aggregates, GST and thrombin (FIG. 4). Capsomere fractions eluting at a volume of 11-13 mL were pooled, aliquoted and frozen at −80° C. for subsequent use. The capsomere sample was analysed by TEM (data not shown) which showed that the sample comprised distinct non-aggregated and non-assembled capsomeres suitable for use.
Animal Testing of Chimeric VP1 dNdC 1011A Capsomeres:
Adjuvant Formulation
Adjuvanted samples were prepared by mixing protein sample with alum adjuvant in 1:1 volume ratio, followed by incubation for one hour at room temperature on a roller mixer prior to immunisation.
Mice Immunisation
Mice were immunised with vaccine sample containing 50 μg of protein (<2 EU/ml) and 250 μg of alum adjuvant in a total of 50 μl volume through subcutaneous injections into the tail bases using 25-gauge needles. After the first immunisation on day 0, two other immunisations were given to the mice on days 21 and 42. Blood samples were taken by tail snip before the first immunisation (day 0), as well as on days 14, 35 and 56.
















Groups
1. PBS + alum




2. VP1dC63




3. VP1dC63 + alum




4. VP1dNdC 1011A + alum



Dose
50 μg of capsomeres



Volume
Total 50 μL



Adjuvant
Alum (250 μg)



Immunisation and bleeds
Inject days: 0, 21, 42




Bleed days: 0, 14, 35, 56










ELISA

H1 A peptide at 10 μg/mL in carbonate coating buffer (50 mM Na2CO3NaHCO3, pH 9.6) was adsorbed to 96-well NUNC immunoplates (Thermo Fisher Scientific, MA, USA), 1004 per well overnight at 4° C. Plates were blocked with PBST (137 mM NaCl, 2.7 mM KCl, 10.15 mM Na2HPO4, 1.76 mM KH2PO4, pH 7.4, 0.05% (v/v) Tween 20) containing 5% skim milk (37° C., 90 min) and washed twice with PBST. Plates were incubated with mouse sera at 100-fold dilution followed by 2-fold serial dilutions (90 min, 37° C.). After washing 4 times with PBST, HRP-conjugated goat anti-mouse antibody (Sigma-Aldrich, USA) was added at 10000-fold dilution (90 min, 37° C.). Plates were washed 4 times with PBST and developed (0.4 mg/ml o-Phenylenediamine dihydrochloride (Sigma-Aldrich, USA), 50 mM Phosphate citrate buffer, 0.03% sodium perborate) prior to absorbance measurement at 450 nm. End point titers were determined as the highest dilution of serum for which the OD was 3SD above the mean OD of blank wells. The end point titers of each group are shown in FIG. 5. Specific immune response against H1 A peptide is observed.
Construction of Vectors Carrying M2e:
E. coli codon optimised oligonucleotides were designed to insert M2e peptide (SLLTEVETPTRSEWECRCSDSSD (SEQ ID NO: 23)) into the generic vectors.
Resulting constructs carrying M2e are designated pGEX4T1-VP1 dNdC 1011M2e and pGEX4T1-VP1 dNdC 2022M2e. The sequence of M2e is of H1N1 (A/California/07/2009).
The amino acid sequences of VP1 dNdC 0000 with inserted peptides are exemplified in FIG. 6.
Expression of Chimeric VP1 dNdC 1011M2e and VP1 dNdC 2022M2e:
VP1 dNdC 1011M2e and VP1 dNdC 2022M2e proteins were expressed in Rosetta (DE3) pLysS (Novagen) as a glutathione-s-transferase-VP1-dNdC 1011M2e (GST-VP1-dNdC 1011M2e) and glutathione-s-transferase-VP1-dNdC63 1011M2e (GST-VP1-dNdC 2022M2e) fusion protein using the pGEX-4T-1-VP1 dNdC 1011M2e and pGEX-4T-1-VP1 dNdC 2022M2e expression vectors. For solid agar medium, 15 g/L of agar was added to Luria-Bertani (LB) medium (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.0). Liquid medium used for cell cultures was Terrific Broth (TB) containing 12 g/L peptone, 24 g/L yeast extract, 0.4% (v/v) glycerol, 2.31 g/L KH2PO4 and 12.54 g/L K2HPO4. All media used were supplemented with 50 μg/mL of ampicillin and 34 μg/mL of chloramphenicol. Overnight cultures were set up by inoculating single colonies of the transformed cells into 5 mL of TB medium and cultivated at 30° C. on a rotary shaker at 180 rpm. After incubation of 16 hours, the overnight cultures were diluted 1000 times into 400 mL cultures in 2 L baffled flasks. These cultures were cultivated to an OD600 of 0.5 at 37° C. and then cooled to 26° C. under running tap water and subsequently induced with IPTG at final concentration of 0.2 mM. The induced cultures were then cultivated at 26° C. for a further 16 hours and harvested by centrifugation at 8000 g, 4° C. for 30 mins. The expression was analysed on SDS-PAGE (FIGS. 7A and 7B).
Purification of Chimeric VP1 dNdC 1011M2e and VP1 dNdC 2022M2e:
Two pellets from 2×400 mL cultures were re-suspended in 40 mL of buffer L (200 mM NaCl, 40 mM Tris, 5 mM dithiothreitol, 1 mM EDTA, 5% v/v glycerol, pH 8 with HCl). The cell suspension was sonicated at output 30 using a Branson Sonifier 450 (Sonifier, USA) for 4×40 seconds. The resulting cell lysate was centrifuged at 27000 g, 4° C. for 30 mins and the supernatant which contained soluble chimeric proteins was filtered through a 0.45 μm syringe filters (Millipore) giving a recovery of  ̃35 mL.
Protein purification was performed with an Äkta Explorer system from GE Healthcare. GST fusion proteins in the clarified homogenate were captured using a GSTrapTM HP 5 mL column from GE Healthcare pre-equilibrated with buffer L. The bound GST fusion proteins were eluted with elution buffer (Buffer L with 10 mM reduced glutathione) (FIGS. 8 and 9). Eluted samples were stored at −80° C. until required. 40 μL of Thrombin was added to 1 mL of purified GST fusion proteins followed by 2 hours incubation at room temperature. 1 mL of thrombin treated capsomere was injected onto a Superdex S200 10/300 GL size exclusion column (GE Healthcare) equilibrated in buffer L, to separate capsomeres from aggregates, GST and thrombin (FIG. 10). Capsomere fractions eluting at a volume of 11-13 mL were pooled, aliquoted and frozen at −80° C. for subsequent use. Capsomere sample was analysed by TEM (results not shown) and comprised distinct non-aggregated and non-assembled capsomeres suitable for use.
Animal Testing of VP1 dNdC 1011M2e and VP1 dNdC 2022M2e Capsomeres:
Adjuvant Formulation
Adjuvanted samples were prepared by mixing protein sample with alum adjuvant in 1:1 volume ratio, followed by incubation for one hour at room temperature on a roller mixer prior to immunisation.
Mice Immunisation
Mice were immunised with vaccine sample containing 50 μg of protein (<2 EU/ml) and 250 μg of alum adjuvant in a total of 50 μl volume through subcutaneous injections into the tail bases using 25-gauge needles. After the first immunisation on day 0, two other immunisations were given to the mice on days 21 and 42. Blood samples were taken by tail snip before the first immunisation (day 0), as well as on days 14, 35 and 56.
















Groups
1. PBS + alum




2. VP1dC63




3. VP1dC63 + alum




4. VP1dNdC 1011M2e + alum




5. VP1dNdC 2022M2e




6. VP1 dNdC 2022M2e + alum



Dose
50 μg of capsomeres



Volume
Total 50 μL



Adjuvant
Alum (250 μg)



Immunisation and bleeds
Inject days: 0, 21, 42




Bleed days: 0, 14, 35, 56










ELISA

H1 M2e peptide at 10 μg/mL in carbonate coating buffer (50 mM Na2CO3NaHCO3, pH 9.6) was adsorbed to 96-well NUNC immunoplates (Thermo Fisher Scientific, MA, USA), 100 μl per well overnight at 4° C. Plates were blocked with PBST (137 mM NaCl, 2.7 mM KCl, 10.15 mM Na2HPO4, 1.76 mM KH2PO4, pH 7.4, 0.05% (v/v) Tween 20) containing 5% skim milk (37° C., 90 min) and washed twice with PBST. Plates were incubated with mouse sera at 100-fold dilution followed by 2-fold serial dilutions (90 min, 37° C.). After washing 4 times with PBST, HRP-conjugated goat anti-mouse antibody (Sigma-Aldrich, USA) was added at 10000-fold dilution (90 min, 37° C.). Plates were washed 4 times with PBST and developed (0.4 mg/ml o-Phenylenediamine dihydrochioride (Sigma-Aldrich, USA), 50 mM Phosphate citrate buffer, 0.03% sodium perborate) prior to absorbance measurement at 450 nm. End point titers were determined as the highest dilution of serum for which the OD was 3SD above the mean OD of blank wells. The end point titers of each group are shown in FIG. 11. Antibodies specific to H1 M2e peptide are detected in mice immunised with 1011M2e and 2022M2e capsomeres. Higher end point titres were obtained from mice immunised with adjuvanted 1011M2e capsomeres than with unadjvanted 2022M2e capsomeres.
Example 3
Construction and Sequencing of Vectors Expressing Epitopes from Hendra Virus
E. coli codon optimised oligonucleotides were designed to insert epitopes G1-2 (GLPNQIMLQKTTS) SEQ ID NO: 24, G4 (VRPKSDSGDYN) SEQ ID NO: 25, G5 (PIIHSKYSKAE) SEQ ID NO: 26, G9 (VEIYDTGDSVIRPKL) SEQ ID NO: 27 and G10 (LEKIGSCTRGIAKQ) SEQ ID NO: 28 into the generic vector pGEX4T1-VP1 dNdC 0000.
Resulting constructs carrying Hendra Virus peptides are designated pGEX4T1-VP1 dNdC 1011G1-2, pGEX4T1-VP1 dNdC 1011G4, pGEX4T1-VP1 dNdC 1011G5, pGEX4T1-VP1 dNdC 1011G9 and pGEX4T1-VP1 dNdC 0.1011G10.
The amino acid sequences of VP1 dNdC 0000 with inserted peptides from Hendra Virus antigenic sequences are exemplified in FIG. 12.
Example 4
Construction and Sequencing of Vectors Expressing Antigenic Peptides from Group A Streptococcus (GAS)
E. coli codon optimised oligonucleotides were designed to insert GAS peptides BSA101-28 (NSKTPAPAPAVPVKKEATKSKLSEAELH) SEQ ID NO: 29, 20321-19 (NSKNPVPVKKEAKLSEAEL) SEQ ID NO: 30 and 204080-69 (LKMLNRDLEQAYNELSGEAH) SEQ ID NO: 31 into the generic vector pGEX4T1-VP1 dNdC 0000. These peptides are from the paper by Brandt et al (Infection and Immunity, December 2000, p 6587-6594, 68(12)). Resulting constructs carrying GAS peptides are designated pGEX4T1-VP1 dNdC 1011GAS1, pGEX4T1-VP1 dNdC 1011GAS2, pGEX4T1-VP1 dNdC 1011GAS3. The amino acid sequences of VP1 dNdC 0000 with inserted peptides from GAS antigenic sequences are exemplified in FIG. 13.
Example 5
Production of Chimeric VP1 Capsomere with M2e Inserted on N-Terminus and HA Epitopes on Surface Loops S1 and S4
Construction of Vectors Carrying M2e and HA Epitopes a and B:
E. coli codon optimised oligonucleotides were designed to insert M2e peptide (SLLTEVETPTRNEWECRCSDSSD) SEQ ID NO: 23, HA epitopes A (PYNGKSS) SEQ ID NO: 33 and B (GNDAAEQTKLYQNPTTY) SEQ ID NO: 34 into the generic vectors. M2e oligo was inserted on the N-terminal of VP1 using the BamHI restriction site upstream of VP1 gene. Oligo for HA epitope A is inserted into the surface loop S1 for construct pGEX4T1-M2e-VP1-S1A. Oligos for HA epitopes B and A are inserted into the surface loops S1 and S4, respectively, to generate construct pGEX4T1-M2e-VP1-S1B-S4A.
Resulting constructs carrying M2e and HA epitopes A and B are designated pGEX4T1-M2e-VP1-S1A and pGEX4T1-M2e-VP1-S1B-S4A. The sequence of M2e and HA epitopes A and B are of H5N1 (A/Vietnam/3028/2004). The amino acid sequences of chimeric VP1 with inserted peptides are exemplified in FIG. 14.
Expression of M2e-VP1-S1A and M2e-VP1-S1B-S4A:
Expression was conducted as outlined in Example 2. The cell pellets were analysed on SDS-PAGE for total and soluble expression (FIG. 15).
Purification of M2e-VP1-S1A and M2e-VP1-S1B-S4A Capsomeres:
Chimeric capsomeres were purified as in protocol outlined in Example 2. The GST affinity purification profiles are shown in FIGS. 16 and 18. Chimeric capsomeres were obtained after S200 purification (FIGS. 17 and 19).
Example 6
Construction and Sequencing of Vectors Expressing Antigenic Peptides from HPV E7
E. coli codon optimised oligonucleotides were designed to insert E7 peptides (QAEPDRAHYNIVTFCCKCD—SEQ ID NO: 35 and RAHYNIVTF SEQ ID NO: 36) into the generic vector pGEX4T1-VP1 dNdC 0000. Resulting constructs carrying E7 peptides are designated pGEX4T1-VP1 dNdC 1011E7 and pGEX4T1-VP1 dNdC 1011CTL. The amino acid sequences of VP1 dNdC 0000 with inserted peptides from HPV E7 antigenic sequences are exemplified in FIG. 20.
Example 7
Expression of Chimeric VP1 Capsomeres with M2e Peptide Inserted into N and/or C Termini and/or Surface Loops S1 and S4
Chimeric VP1 with M2e peptide inserted into N and/or C termini and/or surface loops were constructed as described in Example 2. All constructs were expressed according to the protocol outlined in Example 2. Table 1 below illustrates the insertions on various constructs and the final OD during expression. The total and soluble expression of all constructs were analysed using Calliper LabChip GXII as shown in FIGS. 21 and 22.
Example 8
Capsomere Vaccines Adjuvanted with VLPs, Nanoparticles, Alum and Nanoemulsion
Adjuvant Preparation
VLPs:
Wild-type capsomeres were prepared as described hereinbefore. Endotoxin in capsomere samples was removed through Vivapure® Q spin column (Sartorius, Germany). Capsomeres were then dialysed against GL1 assembly buffer at room temperature for 15 hours to promote VLP assembly, and then dialysed against PBS at 4° C. for 24 hours. VLP concentration was adjusted to a protein VP1 concentration of 2 mg/ml.
Nanoparticles:
Commercial silica nanoparticles of nominal diameter 50 nm and 1 μm (Cat.#24040 and 24326, Polysciences, Inc., US) were dialysed against PBS at 4° C. for 24 hours. Both solutions were adjusted to a nominal silica concentration of 2 mg/ml.
Alum:
Commercial alum hydroxide Alhydrogel® adjuvant (Brenntag, Germany) was used. Alum was prepared at concentration of 10 mg/ml (as received) and 2 mg/ml (by dilution with PBS).
Nanoemulsion.
A mixture containing 400 μM of peptide surfactant AM1 and 800 μM ZnCl2 in 25 mM HEPES pH 7.0 was prepared. 20 μl of Miglyol 812 (Sasol, Germany) was added into 980 μl of the mixture and then sonicated using Branson Sonifier 450 (Sonifier, US) for 2×45 seconds at output 15. The resulting nanoemulsion was then added drop by drop into 80 mg/ml BSA in 1:1 volume. The size of emulsion ( ̃200 nm) was confirmed with Dynamic Light Scattering (Malvern Instruments Ltd, UK). All protocols were prepared using endotoxin free reagents and apparatus.
Vaccine Preparation
1011 H1 M2e vaccine sample, prepared as described hereinbefore, was processed to give a sample in PBS having a VP1 protein concentration of 2 mg/ml and an endotoxin level of 0.980 EU/ml, measured using Endosafe® (Charles-River Laboratories, US). Samples were stored at 80° C.
Immunisations
Vaccine samples were thawed gently on ice few hours before injection. Thawed samples were mixed with each adjuvant preparation at 1:1 volume. Samples adjuvanted with nanoparticles, nanoemulsion and alum were incubated at room temperature for 1 h prior to use, Mice were immunised with 50 μl of vaccine sample through subcutaneous tail base injection on days 0, 21 and 42. Blood samples (504 each) were taken by tail snip before the first immunisation (day 0), and on days 14, 35 and 56.
Isotherm adsorption of both VP1 dC63 capsomeres and chimeric. 1011M2e capsomeres were measured. FIG. 23 indicates that chimeric 1011M2e capsomeres did not attach substantially to the nanoparticles (silica 50 nm).
Animal testing results are shown in FIGS. 24, 25 and 26. FIG. 24 shows the end point titers of each group. Antibodies specific to H1 M2e peptide are detected in all groups except for negative control (PBS). Higher antibody titres are detected after second injection. Also demonstrated in FIG. 24 is that the presence of 50 nm nanoparticles gives a better response than the free capsomeres. Based on data in FIG. 23, it is expected that less than 5% of the antigen is attached to the 50 nm nanoparticles. Thus there is no substantial association. This is a very unexpected result and directly challenges the dogma of conjugation or adsorption. It also is unexpected in the context of the conventional thinking which believes that there is a positive benefit of adsorption. What is also noted from FIG. 24 is the following:

    
    
        the silica formulation is beneficial versus the free capsomeres.
        the immunogenicity of the 50 nm silica formulation does not differ substantially from the alum preparation, even though Ag is not substantially associated with the silica, yet we expect the Ag to be fully associated with the 250 μg alum.
        a comparison of the peptide+dC63+alum 250 μg vs alum 250 μg data shows a clear benefit of functionally linking the antigen to the N-, C- and loop of VP1. The former is a formulation of free peptide (9.7 μg), non-chimeric VP1 dC63 (40.3 μg) and alum (250 μg). The latter is chimeric VP1 dNdC 1011 (50 μg, comprising 9.7 μg of M2e peptide equivalent within a chimeric 1011 capsomere). The chimeric capsomere is clearly superior (surprisingly so) versus the peptide antigen.
    
    


FIG. 25 shows capsomere vaccines expressing epitopes from Hendra virus, adjuvanted with 50 nm nanoparticles. VP1dNdC 1011G4 (SEQ ID NO: 10), VP1dNdC 1011G5 (SEQ ID NO: 11), VP1dNdC 1011G9 (SEQ ID NO: 12), VP1dNdC 1011G10 (SEQ ID NO: 13), and VP1dNdC 1011G1-2 (SEQ ID NO: 9) vaccine samples and 50 nm silica nanoparticles adjuvant were prepared as described hereinbefore (see Example 8). Immunisations of mice were also as described hereinbefore (see Example 8). FIG. 25 shows the endpoint titers of peptide-specific antibody of each group at the last bleed. FIG. 26 shows capsomere vaccines expressing epitopes from Group A Streptococcus (GAS), adjuvanted with 50 nm nanoparticles. 1011GAS1 (SEQ ID NO: 14), 1011GAS2 (SEQ ID NO: 15), and 1011GAS3 (SEQ ID NO: 16) vaccine samples were prepared as described hereinbefore (Example 8). 50 nm silica nanoparticles, prepared as described hereinbefore (Example 8), were adjusted to nominal silica concentration of 10 mg/ml. Immunisations of mice were as described hereinbefore as well (Example 8). FIG. 26 shows the endpoint titers of peptide-specific antibody of each group at the last bleed.
Arginine deimonase (ADI) and trigger factor (TF) from Streptococcus pyogenes (FIGS. 27 A and B—SEQ ID NOs: 42 and 43) were cloned into the N-terminus of VP1 dNdC S1 S4 (SEQ ID NO: 5), separately. The resulting constructs were ADI-VP1 dNdC (SEQ ID NO: 21) and TF-VP1 dNdC (SEQ ID NO: 22) as detailed in FIG. 29. The expression of both constructs was investigated as described hereinbefore (Example 2). The cell pellets were analysed on SDS-PAGE for total and soluble expression (FIG. 28). High levels of soluble expression were detected for both constructs as shown in FIG. 28.
Throughout the specification the aim has been to describe the preferred embodiments of the invention without limiting the invention to any one embodiment or specific collection of features. It will therefore be appreciated by those of skill in the art that, in light of the instant disclosure, various modifications and changes can be made in the particular embodiments exemplified without departing from the scope of the present invention.
All computer programs, algorithms, patent and scientific literature referred to herein is incorporated herein by reference.
TABLES







TABLE 1







Insertions on various constructs and the final OD during expression.


1-3 copies of M2e are inserted into N and/or C and/or surface


loops S1 and S4 of VP1 dNdC 0000 vector. For example, a construct


designated as 1000 has 1 copy of M2e inserted into the N terminus


of truncated VP1, and a construct designated as 1111 has 1


copy of M2e insert into N and C termini, as well as into surface


loop sites 1 and 4.



















M2e
OD600
OD600


Constructs
N-term
S1
S4
C-term
copy
Induction
Harvest

















WT-VP1





0.54
9.89


0000
0
0
0
0
0
0.73
9.81


1000
1
0
0
0
1
0.67
8.34


1001
1
0
0
1
2
0.80
10.54


1011
1
0
1
1
3
0.61
6.82


1111
1
1
1
1
4
0.49
9.54


1211
1
2
1
1
5
0.50
8.41


1311
1
3
1
1
6
0.51
10.05


1021
1
0
2
1
4
0.49
8.90


1121
1
1
2
1
5
0.52
9.12


1221
1
2
2
1
6
0.67
6.20


1321
1
3
2
1
7
0.54
5.74


1031
1
0
3
1
5
0.67
9.62


1131
1
1
3
1
6
0.69
6.84


1231
1
2
3
1
7
0.57
4.77


2000
2
0
0
0
2
0.52
7.69


2002
2
0
0
2
4
0.49
6.06


2012
2
0
1
2
5
0.59
6.30


2112
2
1
1
2
6
0.53
5.31


2212
2
2
1
2
7
0.60
5.70


2312
2
3
1
2
8
0.69
4.46


2022
2
0
2
2
6
0.53
8.01


2122
2
1
2
2
7
0.50
10.12


2222
2
2
2
2
8
0.51
10.86


2322
2
3
2
2
9
0.62
9.55


2032
2
0
3
2
7
0.68
6.16


2132
2
1
3
2
8
0.51
3.79


2332
2
3
3
2
10
0.78
6.41


3000
3
0
0
0
3
0.49
9.93


3003
3
0
0
3
6
0.49
7.93


3013
3
0
1
3
7
0.76
6.60


3113
3
1
1
3
8
0.62
6.71


3033
3
0
3
3
9
0.48
11.01


3133
3
1
3
3
10
0.66
4.89


3333
3
3
3
3
12
0.65
11.20

## Claims

1. An isolated protein comprising:
a viral capsomere-forming amino acid sequence, wherein said viral capsomere-forming amino acid sequence comprises an amino acid sequence of a polyomavirus capsomere lacking at least part of the amino-terminus and/or the carboxy-terminus that is normally present in the amino acid sequence of the polyomavirus capsomere; and
a heterologous immunogenic amino acid sequence at the amino-terminus of the polyomavirus capsomere amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence,
wherein said isolated protein is essentially incapable of assembly into virus-like particles (VLPs) as a result of lacking VLP assembly-related parts of the viral capsomere-forming amino acid sequence and/or the addition of said immunogenic amino acid sequence at the amino-terminus of said viral capsomere-forming amino acid sequence, and thereby retains a capsomere morphology.

2. The isolated protein of claim 1, wherein the virus is a murine polyomavirus.

3. The isolated protein of claim 1, wherein the protein is polyomavirus VP1.

4. The isolated protein of claim 3, wherein the protein is a murine polyomavirus VP1.

5. The isolated protein of claim 1, wherein the viral capsomere-forming amino acid sequence comprises an amino acid sequence as set forth in any one of SEQ ID NOs: 4 to 22.

6. The isolated protein of claim 1, wherein the viral capsomere-forming amino acid sequence further comprises a heterologous immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence at the carboxy-terminus of the viral capsomere amino acid sequence, wherein said immunogenic amino acid sequence is the same as or different to the heterologous immunogenic amino acid sequence at the amino-terminus of the viral capsomere amino acid sequence.

7. The isolated protein of claim 1, further comprising a heterologous immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence in one or more exposed loops of said viral capsomere-forming amino acid sequence, wherein said immunogenic amino acid sequence is the same as or different to the heterologous immunogenic amino acid sequence at the amino-terminus of the viral capsomere amino acid sequence.

8. The isolated protein of claim 1, wherein the immunogenic amino acid sequence is of an immunogen from a pathogenic organism selected from the group consisting of a virus, a bacteria, a fungi, a parasite, a cancer immunogen, an allergic reaction immunogen a transplantation immunogen and an autoantigen.

9. The isolated protein of claim 8, wherein the immunogenic amino acid is of a virus.

10. The isolated protein of claim 9, wherein the virus is selected from the group consisting of influenza, Hendra and papillomavirus.

11. The isolated protein of claim 10, wherein the immunogenic amino acid sequence is as set forth in any one of SEQ ID NOs: 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40 and 41.

12. The isolated protein of claim 8, wherein the immunogenic amino acid is of a bacterium.

13. An isolated nucleic acid encoding an isolated protein or amino acid sequence of claim 1.

14. A genetic construct comprising the isolated nucleic acid of claim 13.

15. An isolated host cell comprising the genetic construct of claim 14.

16. A capsomere comprising one or more isolated proteins of claim 1.

17. A method of producing a capsomere, comprising the steps of
(a) introducing into a host cell:
an isolated nucleic acid encoding the isolated protein of claim 1;
a genetic construct comprising an isolated nucleic acid encoding the isolated protein of claim 1;

(b) culturing said host cell under conditions which facilitate production of the isolated protein encoded by the isolated nucleic acid;
(c) optionally purifying the isolated protein; and
(d) assembling the isolated protein to thereby produce the capsomere.

18. A pharmaceutical composition comprising one or more agents selected from the group consisting of:
an isolated protein comprising a viral capsomere-forming amino acid sequence wherein said viral capsomere-forming amino acid sequence comprises an amino acid sequence of a polyomavirus capsomere lacking at least part of the amino-terminus and/or the carboxy-terminus that is normally present in the amino acid sequence of the polyomavirus capsomere; and a heterologous immunogenic amino acid sequence at the amino-terminus of the polyomavirus capsomere amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence, wherein said isolated protein is essentially incapable of assembly into VLPs as a result of lacking VLP assembly-related parts of the viral capsomere-forming amino acid sequence and/or the addition of said immunogenic amino acid sequence at the amino-terminus of said viral capsomere-forming amino acid sequence, and thereby retains a capsomere morphology; and
an isolated nucleic acid encoding an isolated protein comprising a viral capsomere-forming amino acid sequence wherein said viral capsomere-forming amino acid sequence comprises an amino acid sequence of a polyomavirus capsomere lacking at least part of the amino-terminus and/or the carboxy-terminus that is normally present in the amino acid sequence of the polyomavirus capsomere; and a heterologous immunogenic amino acid sequence at the amino-terminus of the polyomavirus capsomere amino acid that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence, wherein said isolated protein encoded by said isolated nucleic acid is essentially incapable of assembly into VLPs as a result of lacking VLP assembly-related parts of the viral capsomere-forming amino acid sequence and/or the addition of said immunogenic amino acid sequence at the amino-terminus of said viral capsomere-forming amino acid sequence, and thereby retains a capsomere morphology; and
a capsomere comprising one or more isolated proteins comprising a viral capsomere-forming amino acid sequence wherein said viral capsomere-forming amino acid sequence comprises an amino acid sequence of a polyomavirus capsomere lacking at least part of the amino-terminus and/or the carboxy-terminus that is normally present in the amino acid sequence of the polyomavirus capsomere; and a heterologous immunogenic amino acid sequence at the amino-terminus of the viral capsomere amino acid that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence, wherein said one or more isolated proteins of said capsomere are essentially incapable of assembly into VLPs as a result of lacking VLP assembly-related parts of the viral capsomere-forming amino acid sequence and/or the addition of said immunogenic amino acid sequence at the amino-terminus of said viral capsomere-forming amino acid sequence, and thereby retain a capsomere morphology; and,
a pharmaceutically-acceptable carrier, diluent or excipient.

19. The pharmaceutical composition of claim 18, wherein the pharmaceutical composition is an immunotherapeutic composition.

20. The pharmaceutical composition of claim 18, wherein the pharmaceutical composition is a vaccine.

21. A method of eliciting or augmenting an immune response in an animal, said method comprising the step of administering a pharmaceutical composition comprising one or more agents selected from the group consisting of the isolated protein of claim 1, an isolated nucleic acid encoding the isolated protein of claim 1, and a capsomere comprising the isolated protein of claim 1; and, a pharmaceutically-acceptable carrier, diluent or excipient; to thereby elicit or augment an immune response in said animal.

22. The method of claim 21, wherein the animal is thereby immunised.

23. The method of claim 21, wherein a disease, disorder or condition of the animal is thereby prophylactically or therapeutically treated.

24. The isolated protein of claim 12, wherein the immunogenic amino acid sequence is as set forth in any one of SEQ ID NOs: 29, 30, 31, 42 and 43.

25. The isolated protein of claim 1, wherein the viral capsomere-forming amino acid sequence comprises an amino acid sequence of a polyomavirus capsomere lacking at least part of the amino-terminus and the carboxy-terminus that is normally present in the amino acid sequence of the polyomavirus capsomere.

26. The isolated protein of claim 6, wherein the viral capsomere-forming amino acid sequence comprises an amino acid sequence of a polyomavirus capsomere lacking at least part of the amino-terminus and the carboxy-terminus that is normally present in the amino acid sequence of the polyomavirus capsomere.

27. The isolated protein of claim 26 further comprising a heterologous immunogenic amino acid sequence that is not a purification tag amino acid sequence and/or expression-enhancing tag amino acid sequence in one or more exposed loops of the viral capsomere-forming amino acid sequence, wherein said immunogenic amino acid sequence is the same as or different to the heterologous immunogenic amino acid sequence at the amino-terminus of the viral capsomere amino acid sequence.

28. The isolated protein of claim 1, consisting essentially of non-aggregated protein with capsomere morphology.