Patent Application
20240156942
The present application relates to the field of norovirus vaccines. In particular, it relates to a peptide comprising a neutralizing epitope for a norovirus, an antibody that recognizes the peptide, a polynucleotide encoding the peptide, a composition for treating a norovirus, and a method for identifying a neutralizing epitope.
Norovirus infections occur throughout the year, but are known to become epidemic particularly during the winter months. Symptoms include abdominal pain, diarrhea, nauseous feeling, vomiting, and fever. The routes of infection include ingestion of food or water contaminated with norovirus, contact with humans or objects that harbor norovirus, and droplets from persons infected with norovirus. Since noroviruses are generally resistant to disinfection and heat and are highly contagious, secondary infections can easily occur.
Antibiotics are an effective treatment for bacterial infections. However, with norovirus infections, the circumstances are different from bacterial infections, and there are no specific drugs. Therefore, when infected with norovirus, one has to wait for the virus to be excreted out of the body and recover naturally.
Against this background, vaccines are being developed with the purpose of preventing norovirus infection. Patent Literature 1 discloses a method for administering parenterally a vaccine composition to humans to induce protective immunity to a norovirus. Here, the vaccine composition comprises virus-like proteins (sometimes also referred to as “VLP”) of genogroup I genotype 1 (GI.1) and/or genogroup II genotype 4 (GII.4) norovirus.
Noroviruses are currently classified into 10 genogroups based on their genome and capsid protein sequences (Non Patent Literature 1). Then there are one or more genotypes in each genogroup. For example, there are 27 genotypes (GII.1, GII.2, GII.27) in genogroup II (GII). In this regard, Non Patent Literature 2 discloses the identification of a blockade epitope (also referred to as an inhibitory epitope) for GII.4. However, noroviruses are known to differ antigenically from one another among different genotypes, even if the genogroup is the same. Much of the research on noroviruses has been directed toward GII.4, which accounts for the majority of norovirus infections.
The genotypes of GII are diverse. Therefore, vaccine compositions of prior art may not be effective in inducing protective immunity to noroviruses belonging to GII. The present invention provides a peptide that can be used to induce protective immunity to a norovirus belonging to a GII genotype.
In light of the above, the inventor of the present application focused on the P (protruding) domain of the VP1 (viral protein 1) protein of norovirus and conducted extensive studies from the aspect of three-dimensional structure. This led to the identification of a plurality of potential epitope regions. Based on such findings, the inventor of the present application has completed the present invention.
The present invention provides, but is not limited to the following.
<Peptide>
The present invention provides a peptide comprising a specific amino acid sequence. The specific amino acid sequence comprises a portion of an amino acid sequence of a P domain of a VP1 protein of a norovirus or an amino acid sequence derived from the P domain. However, the specific amino acid sequence does not comprise the whole P domain of a VP1 protein of a norovirus.
Norovirus is a virus belonging to the family Caliciviridae. Norovirus is known to have 10 genogroups (GI, GII, GIII, GIV, GV, GVI, GVII, GVIII, GIX, and GX). Noroviruses belonging to GI, GII, GIV, GVIII, and GIX are known to infect humans, noroviruses belonging to GIII infect cattle, noroviruses belonging to GV infect mice, noroviruses belonging to GVI infect cats, noroviruses belonging to GVII infect dogs, and noroviruses belonging to GX infect bats. Each genogroup has genotypes, classified or clustered based on the gene sequence of the norovirus. For example, with respect to GI and GII, various genotypes are known to exist. At present, GI has nine genotypes (GI.1 to 9) and GII has 27 genotypes (GII.1 to 27).
The specific amino acid sequence constituting the peptide provided by the present invention comprises a portion of an amino acid sequence of a P domain of a VP1 protein of a norovirus belonging to any of genotypes of GII. Here, genotype 4 is excluded from any of genotypes of GII. Any of genotypes of GII can be selected, for example, from the group consisting of 1, 2, 3, 5, 6, 7, 12, 13, 14, 17, and 21, but is not limited thereto.
Furthermore, the portion of an amino acid sequence of a P domain of a VP1 protein comprises the whole or a portion of an amino acid sequence corresponding to a neutralizing epitope selected from the group consisting of epitope A, epitope D, epitope E, epitope F, and combinations thereof. Here, the combination of epitope A, epitope D, epitope E, and epitope F can be a plurality of combinations of these epitopes, for example, two, three, four, and more. Furthermore, the combination may be a combination of the same epitope or a combination of different epitopes. The plurality of combinations of these epitopes can be directly linked epitopes or epitopes linked via any amino acid sequence. A method for linking a plurality of peptides or epitopes and a method for designing any amino acid sequence are well known and can be appropriately performed by those skilled in the art.
Epitope A comprises an amino acid sequence selected from the group consisting of A1 region, A2 region, A3 region, and combination thereof, in amino acid sequences of a P domain of a VP1 protein of any of genotypes of naturally occurring GII (except GII.4) noroviruses. Here, the combination is a combination of the A1 and A2 regions, a combination of the A1 and A3 regions, a combination of the A2 and A3 regions, or a combination of the A1, A2, and A3 regions. For example, the A1, A2, and A3 regions can exist at the following positions in the amino acid sequence of the VP1 protein, counting from the N-terminus.
(1) GII.1
(2) GII.2
(3) GII.3
(4) GII.5
(5) GII.6
(6) GII.7
(7) GII.12
(8) GII.13
(9) GII.14
(10) GII.17
(11) GII.21
The amino acid sequence of epitope A may have mutations such as substitutions, deletions, truncations, insertions, and modifications introduced into the corresponding natural amino acid sequence, or may not have such mutations introduced. If the amino acid sequence of epitope A has such mutations, mutations that do not substantially affect the three-dimensional structure are preferred, and examples thereof include conservative substitutions. Those skilled in the art are familiar with conservative substitutions and can perform them as appropriate. In addition, the amino acid sequence of epitope A may have 70% or more, 80% or more, 90% or more, 95% or more, 98% or more, or 99% or more homology to the corresponding natural amino acid sequence. The introduction of mutations and/or variations in sequence homology to the amino acid sequence of epitope A are acceptable to the extent that an immune response to a norovirus can be induced. Although not limited, epitope A can have, for example, an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 267 (Table 1), an amino acid sequence in which a mutation described above is introduced into the amino acid sequence, or an amino acid sequence having the above sequence homology to the amino acid sequence.
More specific examples of the amino acid sequence constituting epitope A comprise, but are not limited to the following:
When two or three of the A1 region, A2 region, and A3 region are combined, they may be adjacent to each other or separated via any amino acid sequence within epitope A.
Epitope D comprises a portion of the amino acid sequence of the P domain of the VP1 protein of any of genotypes of GII (except GII.4) in a naturally occurring norovirus. For example, epitope D can exist at the following positions in the amino acid sequence of the VP1 protein, counting from the N-terminus.
The amino acid sequence of epitope D may have mutations such as substitutions, deletions, truncations, insertions, and modifications introduced into the corresponding natural amino acid sequence, or may not have such mutations introduced. If the amino acid sequence of epitope D has such mutations, mutations that do not substantially affect the three-dimensional structure are preferred, and examples thereof include conservative substitutions. Those skilled in the art are familiar with conservative substitutions and can perform them as appropriate. In addition, the amino acid sequence of epitope D may have 70% or more, 80% or more, 90% or more, 95% or more, 98% or more, or 99% or more homology to the corresponding natural amino acid sequence. The introduction of mutations and/or variations in sequence homology to the amino acid sequence of epitope D are acceptable to the extent that an immune response to a norovirus can be induced. Although not limited, epitope D can have, for example, an amino acid sequence selected from the group consisting of SEQ ID NOs: 268 to 351 (Table 1), 426, 429, and 431, an amino acid sequence in which a mutation described above is introduced into the amino acid sequence, or an amino acid sequence having the above sequence homology to the amino acid sequence.
Epitope E comprises a portion of the amino acid sequence of the P domain of the VP1 protein of any of genotypes of GII (except GII.4) in a naturally occurring norovirus. For example, epitope E can exist at the following positions in the amino acid sequence of the VP1 protein, counting from the N-terminus.
The amino acid sequence of epitope E may have mutations such as substitutions, deletions, truncations, insertions, and modifications introduced into the corresponding natural amino acid sequence, or may not have such mutations introduced. If the amino acid sequence of epitope E has such mutations, mutations that do not substantially affect the three-dimensional structure are preferred, and examples thereof include conservative substitutions. Those skilled in the art are familiar with conservative substitutions and can perform them as appropriate. In addition, the amino acid sequence of epitope E may have 70% or more, 80% or more, 90% or more, 95% or more, 98% or more, or 99% or more homology to the corresponding natural amino acid sequence. The introduction of mutations and/or variations in sequence homology to the amino acid sequence of epitope E are acceptable to the extent that an immune response to a norovirus can be induced. Although not limited, epitope E can have, for example, an amino acid sequence selected from the group consisting of SEQ ID NOs: 352 to 390 (Table 1), 427, and 430, an amino acid sequence in which a mutation described above is introduced into the amino acid sequence, or an amino acid sequence having the above sequence homology to the amino acid sequence.
Epitope F comprises an amino acid sequence selected from the group consisting of F1 region, F2 region, and combination thereof, in amino acid sequences of a P domain of a VP1 protein of any of genotypes of naturally occurring GII (except GII.4) noroviruses. For example, the F1 and F2 regions can exist at the following positions in the amino acid sequence of the VP1 protein, counting from the N-terminus.
(1) GII.1
(2) GII.2
(3) GII.3
(4) GII.5
(5) GII.6
(6) GII.7
(7) GII.12
(8) GII.13
(9) GII.14
(10) GII.17
(11) GII.21
The amino acid sequence of epitope F may have mutations such as substitutions, deletions, truncations, insertions, and modifications introduced into the corresponding natural amino acid sequence, or may not have such mutations introduced. If the amino acid sequence of epitope F has such mutations, mutations that do not substantially affect the three-dimensional structure are preferred, and examples thereof include conservative substitutions. Those skilled in the art are familiar with conservative substitutions and can perform them as appropriate. In addition, the amino acid sequence of epitope F may have 70% or more, 80% or more, 90% or more, 95% or more, 98% or more, or 99% or more homology to the corresponding natural amino acid sequence. The introduction of mutations and/or variations in sequence homology to the amino acid sequence of epitope F are acceptable to the extent that an immune response to a norovirus can be induced. Although not limited, epitope F can have, for example, an amino acid sequence selected from the group consisting of SEQ ID NOs: 391 to 425 (Table 1), an amino acid sequence in which a mutation described above is introduced into the amino acid sequence, or an amino acid sequence having the above sequence homology to the amino acid sequence.
More specific examples of the amino acid sequence constituting epitope F include, but are not limited to the following:
When the F1 region and F2 region are combined, they may be adjacent to each other or separated via any amino acid sequence within epitope F.
In addition to the amino acid sequences described above for epitopes A to F, the peptide of the present invention can have any amino acid sequence within the epitopes A to F or at their N-terminal or C-terminal side. For example, the peptide can have an amino acid sequence other than the P domain of the VP1 protein derived from naturally occurring noroviruses (noroviruses belonging to any of genotypes of GII (except genotype 4), e.g., norovirus belonging to a genotype selected from the group consisting of GII.1, 2, 3, 5, 6, 7, 12, 13, 14, 17, and 21), an amino acid sequence not derived from naturally occurring noroviruses (noroviruses belonging to any of genotypes of GII (except genotype 4), e.g., norovirus belonging to a genotype selected from the group consisting of GII.1, 2, 3, 5, 6, 7, 12, 13, 14, 17, and 21), or a non-natural amino acid sequence. The use of any amino acid sequence is acceptable as long as the peptide of the present invention can induce an immune response to a norovirus. Therefore, the amino acid sequence of the peptide of the present invention, taken as a whole, can be an amino acid sequence that does not occur naturally.
The peptide of the present invention can be obtained by chemical synthesis. Peptide synthesis can be performed in-house or outsourced to an external institution. The peptide can be synthesized by any known method. For example, liquid-phase peptide synthesis methods or solid-phase peptide synthesis methods are well known. Examples of solid-phase peptide synthesis methods include the Boc solid-phase method and the Fmoc solid-phase method. Those skilled in the art are familiar with the methods and conditions for peptide synthesis.
Alternatively, the peptide of the present invention can be biologically produced using a polynucleotide encoding the peptide. The peptide of the present invention can be produced by introducing such polynucleotide into appropriate host cells and culturing the host cells. The polynucleotide (nucleic acid sequence) encoding the peptide of the present invention, the expression vector comprising the polynucleotide, and the host cells into which the polynucleotide is introduced are described elsewhere in the present description.
The obtained peptide can also be purified if necessary. Purification can be performed based on the physicochemical properties such as the size, charge, and hydrophobicity of the peptide. Examples thereof include size exclusion chromatography, ion exchange chromatography, partition chromatography, and high-performance liquid (normal or reversed phase) chromatography. Those skilled in the art are familiar with the methods and conditions for peptide purification.
<Antibody>
The present invention provides an antibody that recognizes at least one peptide of the present invention. Here, “recognize” means that the antibody selectively interacts (binds) with the target peptide, and is distinguished from non-selective interaction. The interaction between the antibody and the target peptide can be evaluated by known means. Examples thereof include ELISA, immunoblotting, and immunoprecipitation. Those skilled in the art can use these means as appropriate.
The antibody may be a polyclonal antibody or a monoclonal antibody. Furthermore, the antibody may be a chimeric antibody such as humanized antibodies. Chimeric antibodies can be produced by any method known to those skilled in the art. The antibody can be at least one selected from the group consisting of IgG, IgA, IgY, IgD, IgM, IgE, and fragments thereof, but is not limited thereto. The fragments can include, for example, heavy chains, light chains, Fc, or F(ab). In addition, the antibody may consist of a single antibody or fragment thereof, or it may consist of two or more antibodies or fragments thereof.
The antibody of the present invention can recognize at least one norovirus belonging to any of genotypes of GII (except GII.4). For example, the antibody of the present invention can recognize at least one norovirus belonging to a specific genotype of GII. For example, the antibody can recognize noroviruses belonging to at least one selected from the group consisting of GII.1, GII.2, GII.3, GII.5, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17, and GII.21.
The antibody is expected to bind to the P domain of the VP1 protein of the norovirus. For example, the antibody can bind to at least one of epitope A, epitope D, epitope E, and epitope F in the P domain of the VP1 protein of the norovirus.
The antibody of the present invention can be produced using the peptide of the present invention. The methods for producing antibodies using peptides are well known to those skilled in the art. A method for producing antibodies is provided that comprises, but is not limited to, the following steps.
The method for producing antibodies comprises a step of administering the peptide of the present invention to a subject. This step can immunize the subject and make it produce antibodies to the peptide. Here, the subject can be clinically and/or experimentally used and is capable of producing antibodies. Examples of the subject include, but are not limited to, humans, pigs, cattle, rodents (mice, rats, guinea pigs, etc.), dogs, cats, sheep, rabbits, and birds (chickens, ostriches, etc.). The conditions of immunization (dosage of antigen peptide, frequency of administration, timing of administration, site of administration, etc.) are well known to those skilled in the art and can be set appropriately without requiring explanation.
The method for producing antibodies further comprises a step of collecting the antibodies produced in the subject. In the collection step, the antibody of interest can be obtained by collecting body fluids (e.g., blood, serum, plasma, and ascites) from the immunized subject. Alternatively, in the collection step, the antibody of interest can also be obtained by collecting antibody-producing cells from the immunized subject. In this case, a hybridoma strain with the ability to proliferate can be established by fusing the antibody-producing cells with other cells and the like, as necessary. The method for generating hybridoma cells is well known to those skilled in the art and requires no particular explanation.
The method for producing antibodies can further comprises a step of purifying the collected antibodies and/or a step of evaluating the interaction between the collected antibodies and the target peptide, if necessary. The purification of the antibodies and/or the evaluation of the interaction between the antibodies and the target peptide can be performed by known means.
<Polynucleotide, Expression Vector, and Host Cells>
The present invention provides a polynucleotide encoding the peptide of the present invention. Since the correspondence between amino acid residues and gene codons has already been established, it is easy to convert a peptide sequence into its corresponding polynucleotide sequence. The polynucleotide may be either RNA or DNA, but from the aspect of handling and storage, DNA is more convenient.
The polynucleotide of the present invention can be obtained by chemical synthesis. Polynucleotide synthesis can be performed in-house or outsourced to an external institution. The polynucleotide may be synthesized by any known method. For example, solid-phase synthesis methods are well known. Those skilled in the art are familiar with the methods and conditions for polynucleotide synthesis.
Alternatively, the polynucleotide of the present invention can be obtained by a biological method. For example, the nucleic acid sequence encoding the amino acid sequence of the peptide of the present invention can be amplified by reverse transcribing RNA encoding a P domain of a VP1 protein of a norovirus into cDNA, and performing a gene amplification reaction (reverse transcription PCR) using the cDNA as the template. The primers for the PCR are designed so that the region comprising the nucleic acid sequence encoding the amino acid sequence of the peptide of the present invention is amplified. That is, the primers should be designed to anneal to nucleic acid sequences that are upstream and/or downstream of the nucleic acid sequence encoding the amino acid sequence of the peptide of the present invention. For example, since the polynucleotide encoding the amino acid sequence represented by any of the SEQ ID NOs: 1 to 425 (Table 1) is present on the gene for the P domain of the VP1 protein of norovirus, the primers can be created based on the nucleic acid sequences upstream and/or downstream thereof.
Information on the gene sequence comprising the gene encoding the P domain of the VP1 protein of norovirus can be obtained from databases publicly available on the Internet and the like (including, but not limited to, GenBank, EMBL, and DDBJ (Japanese DNA database)).
The polynucleotide described above can be subjected to extraction and/or purification as necessary at any time during its preparation. Those skilled in the art can appropriately select a known method for the extraction and/or purification of the polynucleotide.
The polynucleotide of the present invention can be incorporated into an expression vector. Therefore, the present invention also provides such expression vector. Examples of expression vectors include pET for E. coli expression, pAUR for yeast expression, pIEx-1 for insect cell expression, and pBApo-CMV for animal cell expression, but other known vectors can also be used. The incorporation of the polynucleotide into an expression vector can be performed by a known method.
The expression vector of the present invention can be introduced into appropriate host cells. Therefore, the present invention provides the host cells into which the polynucleotide has been introduced. The host cells are not particularly limited as long as they are capable of producing the peptide of the present invention. For example, insect-derived cells (e.g., Sf9 and Hi5 cells), E. coli, yeasts (e.g., Saccharomyces cerevisiae, Saccharomyces pombe, and Pichia pastoris), mammalian cells (CHO, HEK, etc.) and any other cells can be used as host cells. The peptide of the present invention can be produced by culturing the host cells of the present invention. The introduction of the expression vector into the host cells and the culture of the host cells can be performed by a known method.
<Composition>
The present invention provides a composition comprising at least one peptide of the present invention described above. Moreover, the present invention provides a composition comprising at least one polynucleotide described above. Furthermore, the present invention provides a composition comprising at least one antibody of the present invention described above. In the following description, simply referring to “the composition of the present invention” is intended to comprehensively describe these three compositions.
The composition of the present invention may comprise additional components as long as the effects of the invention are exhibited. The additional components include, but are not limited to, excipients, diluents, pH adjusters, preservatives, carriers, suspending agents, solubilizers, thickeners, stabilizers, antiseptic agents, penetrating agents, and adjuvants. Known components can be appropriately selected as additional components.
The composition of the present invention may be for either oral or parenteral use, and may be formulated in a form suitable for the intended route of administration. A parenteral composition can be administered by any route, including intravenous, intraarterial, intramuscular, intraperitoneal, intranasal, transdermal, subcutaneous, buccal, sublingual, rectal, oral, ocular, vaginal, and pulmonary.
The form of the composition of the present invention is not limited, but can be, for example, a tablet, a capsule, a pill, a syrup, an elixir, an emulsion, an aerosol, an aqueous or non-aqueous injectable solution, or a powder, granules, or tablet for an injectable solution (the injectable solution is prepared by adding an aqueous or non-aqueous liquid excipient to the powder, the granules, or the tablet).
The composition of the present invention can prevent, treat, alleviate, or ameliorate (improve) norovirus infection, disease induced by norovirus, or at least one symptom associated with the infection and/or disease. Here, norovirus infection, disease induced by norovirus, or at least one symptom associated with the infection and/or disease includes acute gastroenteritis and the associated symptoms (at least one of nausea, diarrhea, loose stool, vomiting, nauseous feeling, fever, malaise, fatigue, stomach cramps, chills, myalgia, and headache). Norovirus infections, or diseases or conditions resulting therefrom, are known to those skilled in the art, but it should be understood that they may not be limited to those listed here. The above prevention, treatment, alleviation, or amelioration may be accomplished by, but is not limited to, neutralizing the infectious agent, inhibiting entry of the infectious agent into the cell, inhibiting replication of the infectious agent, protecting host cells from infection or destruction, or stimulating antibody production. Therefore, the composition of the present invention can be a pharmaceutical composition for use in the treatment of norovirus.
The norovirus to which the composition of the present invention can be applied may be a norovirus belonging to GII, but GII. 4 can be excluded. Examples thereof include noroviruses belonging to at least one selected from the group consisting of GII.1, GII.2, GII.3, GII.5, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17, and GII.21.
The composition of the present invention can be administered to a subject in an amount effective to prevent, treat, alleviate, or ameliorate norovirus infection, disease induced by norovirus, or at least one symptom associated with the infection and/or disease. The subject can be any subject that can be infected with norovirus, and for example, can be a mammal (human, pig, cattle, rodent, dog, cat, etc.). The effective amount can be appropriately set in consideration of the subject to which the composition is applied, the route of administration, the form of administration, and the like.
The composition of the present invention can also be administered in combination with another protein and/or peptide, and the like. The other protein or peptide may be administered as an additional component blended in the composition of the present invention. Alternatively, the other protein or peptide may be administered at the same time or at a different time as the composition of the present invention, as a component blended in a separate composition. Furthermore, the other protein or peptide may be administered to a subject with the intent to prevent, treat, alleviate, or ameliorate norovirus infection, but may also be administered to a subject with the intent to prevent, treat, alleviate, or ameliorate another disease.
Of the compositions of the present invention, the composition comprising the peptide of the present invention or the polynucleotide encoding the peptide can be, for example, a vaccine composition. The vaccine composition can be used to induce protective immunity to a norovirus, and thereby prevent, treat, alleviate, or ameliorate norovirus infection, disease induced by norovirus, or at least one symptom associated with the infection and/or disease.
The norovirus here may be a norovirus belonging to any of genotypes of GII, but GII. 4 can be excluded. Examples thereof include noroviruses belonging to at least one selected from the group consisting of GII.1, GII.2, GII.3, GII.5, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17, and GII.21.
Furthermore, induction of “protective immunity” to a norovirus means inducing immunity or an immune response to the infectious agent (norovirus, substances derived therefrom, or substances produced thereby). The protective immune response may result from either a humoral or cell-mediated immune response. When protective immunity to a norovirus is induced, the antibody titers against the norovirus can become higher in a subject compared to before the induction. Antibody titers can be measured by a known method. Examples thereof include a neutralizing activity test, as described in the examples.
The vaccine composition can be administered to a subject in an amount effective to induce protective immunity to a norovirus. The subject can be any subject that can be infected with norovirus, and for example, can be a mammal (human, pig, cattle, rodent, dog, cat, etc.). The effective amount to induce protective immunity can be appropriately set in consideration of the subject to which the vaccine composition is applied, the route of administration, the form of administration, and the like.
The vaccine composition can be a peptide vaccine comprising the peptide of the present invention. The peptide vaccine may comprise a single epitope or two or more different epitopes. Each of the epitopes in the peptide vaccine may be present in a free state, or with two or more linked together (multi-epitope peptide).
Alternatively, the vaccine composition can be a virus-like particle (VLP) vaccine. Examples thereof include a VLP vaccine in which the peptide of the present invention is expressed in VLPs. For example, VLPs of papillomavirus, human hepatitis B virus (HBV), norovirus, and the like can be used as VLPs, but are not limited thereto. Methods for preparing VLP vaccines are well known, and those skilled in the art can appropriately select the necessary materials, such as the VLPs, vectors for their expression, expression vectors, and hosts.
Alternatively, the vaccine composition can be a gene vaccine comprising the polynucleotide encoding the peptide of the present invention. Examples thereof include a recombinant vector vaccine comprising a vector into which the polynucleotide is incorporated.
Alternatively, the vaccine composition can comprise particles having the peptide of the present invention or the polynucleotide encoding the peptide. The peptide of the present invention or the polynucleotide encoding the peptide may be present on the surface of the particles or inside the particles. In addition, the peptide of the present invention or the polynucleotide encoding the peptide may be covalently or non-covalently bound to the particles, or may even be bound to the particles via a linker.
<Method for Identifying Neutralizing Epitope>
The present invention provides a method for identifying a neutralizing epitope for a norovirus.
The method for identifying a neutralizing epitope of the present invention comprises a step of collecting genome sequences of one or more norovirus strains belonging to a specific genotype, and extracting gene sequences of a capsid protein VP1 (VP1 protein) from the genome sequence. The specific genotype may belong to any of GI, GII, GIII, GIV, GV, GVI, GVII, GVIII, GIX, and GX, but preferably belongs to GII. For example, it is possible to collect genome sequences from one or more norovirus strains belonging to a genogroup selected from the group consisting of GII.2, GII.3, GII.5, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17, and GII.21, and extract gene sequences of the VP1 protein. In this step, the genome sequences are preferably collected from as many norovirus strains as possible to extract many VP1 protein gene sequences. Information on the genome sequences of the norovirus strains and the gene sequences of VP1 proteins can be obtained from databases publicly available on the Internet and the like (including, but not limited to, GenBank, EMBL, and DDBJ (Japanese DNA database)).
Next is included a step of aligning the extracted gene sequences of the VP1 protein, and classifying the norovirus strains into one or more clusters based on the similarity of these gene sequences, the phylogenetic closeness of the strains from which these gene sequences are derived, or a combination thereof. For example, if there is similarity in the gene sequences and/or the strains from which the gene sequences are derived are phylogenetically close, the gene sequences can be classified into the same cluster. Then, any norovirus strain is selected from the classified cluster, and a three-dimensional structure of a P domain of the VP1 protein of the strain is predicted by homology modeling. This operation does not necessarily need to be performed for all of the norovirus strains classified in a cluster. This is because once the neutralizing epitope is predicted for some of the norovirus strains, e.g., about three to five strains, the neutralizing epitopes of other norovirus strains belonging to the same cluster can also be predicted by comparing amino acid sequences. Software for predicting three-dimensional structure is generally accessible or available. Examples thereof include Swiss-model.
The neutralizing epitope is then determined from the predicted three-dimensional structure of the P domain of the VP1 protein. The neutralizing epitope is determined by comparing the predicted three-dimensional structure with a three-dimensional structure of a P domain of a VP1 protein of a reference strain of norovirus. A portion of the predicted three-dimensional structure that structurally corresponds to a neutralizing epitope of the P domain of the reference strain is determined as the neutralizing epitope. Here, the reference strain of norovirus refers to a norovirus strain belonging to the same genogroup as the strain subject to the identification of the neutralizing epitope. For example, if the strain subject to the identification of the neutralizing epitope is a norovirus strain belonging to GII, the reference strain can be a norovirus strain belonging to GII (but different from the subject strain). To give a more specific example, if the subject strain is a norovirus strain belonging to GII.1, GII.2, GII.3, GII.5, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17, or GII.21, the reference strain can be a norovirus strain belonging to GII.4. In addition, the presence of a neutralizing epitope on the P domain of the VP1 protein is better to be known (previously confirmed) for the reference strain. The neutralizing epitope can be identified by a method of analyzing crystals of antigen-antibody conjugates by X-ray, epitope mapping, or other known methods. Alternatively, a norovirus strain for which the presence of a neutralizing epitope on the P domain of the VP1 protein has already been reported can also be used as the reference strain. For example, a GII.4 norovirus strain with an identified epitope on the P domain of the VP1 protein (Non Patent Literature 2 (Lindesmith L C, Baric R S: Immunity 50, 1530, 2019)) can be used as the reference strain.
Furthermore, an amino acid sequence of the P domain of the VP1 protein, which comprises the identified neutralizing epitope as described above, is compared with an amino acid sequence of a P domain of a VP1 protein from a different strain that belongs to the same genotype as the above-described strain from which the amino acid sequence is derived and whose three-dimensional structure was not compared above, to determine a portion in the amino acid sequence of the P domain of the VP1 protein of the different strain corresponding to the amino acid sequence of the neutralizing epitope, and identify that portion as the neutralizing epitope of the P domain of the VP1 protein of the different strain.
The following examples describe the present invention in more detail. The examples are provided for the purpose of better understanding the invention and are not intended to limit the scope of the invention.
The neutralizing epitope for a GII.6 norovirus was identified as follows. From the NCBI (National Center for Biotechnology Information: www.ncbi.nlm.nih.gov) database, the data (99 data) that could be confirmed to be the gene sequences of the VP1 protein of noroviruses belonging to GII.6 based on the annotation information were collected and translated into amino acid sequences. Clustering of these amino acid sequences based on sequence homology revealed that they can be classified into three major clusters. From these three clusters, three strains were selected as representatives of each. The NCBI accession numbers for the genetic information of the three strains are AB078337, MI-1279838, and JX989075, respectively.
The three-dimensional structures of the P domain of the VP1 protein of these representative strains were predicted by homology modeling based on the amino acid sequences. The predicted three-dimensional structure of the P domain of the VP1 protein of the representative strains of GII.6 was compared by three-dimensional structure alignment with the three-dimensional structure of the P domain of the VP1 protein of GII.4 (reference strain) (for details, reference literature: Lindesmith L C, Baric R S: Immunity 50, 1530, 2019 (Non Patent Literature 2)), for which the neutralizing epitope is known. The identification of epitope D of AB078337 is shown as an example (
The gene sequences of all of the GII.6 VP1 proteins obtained above were converted to amino acid sequences, and the amino acid sequences were compared by multiple sequence alignment. This allowed to calculate the degree of conservation of each amino acid residue of the VP1 proteins within GII.6 (between the same genotypes) to identify a region with low conservation (highly mutated) of the amino acid residues of the P domain of the VP1 protein.
The amino acid sequence identified as described above, comprising a predicted portion of the P domain of the GII.6 representative strain and the region of low amino acid conservation (high mutation) in the vicinity of that portion, was identified as the neutralizing epitope of the GII.6 representative strain (The neutralizing epitope of GII.6 is considered to have a three-dimensional structure similar to the neutralizing epitope of GII.4). In addition, neutralizing epitopes are generally prone to amino acid mutation to evade host immunity. Thus, the portion that meet these conditions can be presumed to be the neutralizing epitope.). Known neutralizing epitopes of GII.4 include A (divided into three regions, which are designated as the A1, A2, and A3 regions for convenience), D, E, and F (divided into two regions, which are designated as the F1 and F2 regions for convenience). The neutralizing epitopes identified in the corresponding GII.6 representative strain were confirmed to correspond to the following amino acid positions in the amino acid sequence of the VP1 protein, counting from the N-terminus.
AB078337
MI-1279838
JX989075
Furthermore, based on the results of the comparison of the amino acid sequences of the GII.6 VP1 proteins performed above by multiple sequence alignment, the amino acid sequences (i.e., neutralizing epitopes) of GII.6 other than the GII.6 representative strains (AB078337, MI-1279838, and JX989075) corresponding to the identified neutralizing epitopes of the representative strains were identified (Table 1).
The neutralizing epitopes for GII.1, GII.2, GII.3, GII.5, GII.7, GII.12, GII.13, GII.14, GII.17, and GII.21 noroviruses were identified according to the method described in Example 1 (Table 1).
GII.2 VLPs, GII.6 VLPs, and GII.17 VLPs were prepared as follows.
The VP1 genes derived from the following norovirus strains were used:
These VP1 genes were incorporated into baculovirus genomic DNA, introduced into Sf9 cells, and recombinant baculovirus was recovered. Recombinant baculovirus was inoculated into High Five cells at the appropriate MOI (Multiplicity of Infection). Four to seven days after infection, the culture solution was collected and centrifuged at 10,000×g for 60 minutes, and the culture supernatant was subjected to density gradient centrifugation using cesium chloride to obtain VLPs. The obtained VLPs were used in the evaluation of neutralizing activity shown below.
Peptides having the amino acid sequences of GII.6 epitope A, GII.6 epitope D, GII.6 epitope E, GII.17 epitope A, GII.17 epitope D, and GII.17 epitope E identified in Example 1 or 2 were synthesized by the Fmoc solid phase synthesis method.
Examples of the synthesized peptides include the following. The position of the amino acids determined for each epitope corresponds to the position of the amino acids counted from the N-terminus of the amino acid sequence of the VP1 protein.
GII.6 (GZ2010 (JX989075))
GII.17 (Kawasaki308 (LC037415))
The following describes the tests using the synthetic peptides listed above.
Rabbits were immunized four times by intradermal administration using each of the synthesized peptides, and serum was collected 49 days after the first immunization. Serum was also collected before immunization.
Neutralizing activity tests were performed using the collected sera. With reference to Haynes, J et al., Viruses 2019; 11(5):392, the neutralizing activity tests were performed under the following conditions.
Porcine gastric mucin (PGM) solution (1.0 μg/mL, PBS) was prepared and 100 μL was added to each well and then allowed to stand for 2 hours at 25° C. Then, the liquid was removed and 300 μL of washing buffer (PBS with 0.05% Tween 20) was added to wash the wells (this washing procedure was repeated three times thereafter). 200 μL of 5% skim milk-PBS solution was added to each well, and then allowed to stand overnight at 4° C. A mixed solution (with serum) was prepared by mixing 50 μL each of GII.6 or GII.17 VLP solution and rabbit serum collected as described above, which was diluted from 1 to 128 times, and was allowed to stand at 25° C. for one hour. After washing the wells, 100 μL of the above mixed solution was added to the wells and allowed to stand at 25° C. for one hour. After washing the wells, 100 μL of primary antibody solution (Mouse anti-NoV VLP Antibody in PBS with 0.05% Tween 20 and 5% skim milk) was added to each well and allowed to stand at 25° C. for one hour. After washing, 100 μL of secondary antibody solution (Anti-Mouse IgG Antibody, HRP conjugated in PBS with 0.05% Tween 20 and 5% skim milk) was added to each well and allowed to stand at 25° C. for one hour. After washing, 100 μL of TMB (3,3′,5,5′-tetramethylbenzidine) solution was added to each well and allowed to stand at 25° C. for 30 minutes, shielded from light. The reaction was stopped by adding 100 μL of Stop Solution, and the absorbance at a wavelength of 450 nm was measured.
PBS with 0.05% Tween 20 and 5% skim milk alone was mixed with VLPs to prepare a mixed solution (without serum). The mixed solution (without serum) was used instead of the above mixed solution (with serum) to perform the same operations as above. The same operations as above were also performed using PBS with 0.05% Tween 20 and 5% skim milk (without VLPs or rabbit serum) as a blank, instead of the above mixed solution (with serum).
The binding blockade activity was calculated by applying the OD [with serum] obtained using the mixed solution with serum, the OD [without serum] obtained using the mixed solution without serum, and the OD [blank] obtained using the blank to the following equation (
Binding blockade activity=100(%)−[(OD [with serum]−OD [blank])(OD [without serum]−OD [blank])]×100(%)
The presence of neutralizing activity is based on the Blocking Titer (BT) 50 value. BT50 is the value of the maximum serum dilution factor at which binding blockade activity exceeds 50%. The BT50 values for the present test are shown in Table 2, and neutralizing activity was considered to be present if the BT50 value of the serum after immunization was twice or more the BT50 value of the serum before immunization. However, if the BT50 value of the serum before immunization was outside the detection range, neutralizing activity was considered to be present if the BT50 value of the serum after immunization could be detected. As shown in Table 2, all of the sera collected from rabbits immunized with the epitope peptides were found to have neutralizing activity. This suggests that immunization with the epitope peptides of GII.6 induced antibodies with neutralizing activity against GII.6 and immunization with the epitope peptides of GII.17 induced antibodies with neutralizing activity against GII.17.
Peptides with the amino acid sequences of GII.2 epitope A and GII.2 epitope D identified in Example 1 or 2 were synthesized by the Fmoc solid phase synthesis method.
Examples of the synthesized peptides include the following. The position of the amino acids determined for each epitope corresponds to the position of the amino acids counted from the N-terminus of the amino acid sequence of the VP1 protein.
GII.2 (MK04 (DQ456824))
The following describes the tests using the synthetic peptides listed above.
Rabbits were immunized four times by intradermal administration using each of the synthesized peptides, and serum was collected 49 days after the first immunization. Serum was also collected before immunization.
Neutralizing activity tests were performed using the collected sera. With reference to Haynes, J et al., Viruses 2019; 11(5):392, the neutralizing activity tests were performed under the following conditions.
Porcine gastric mucin (PGM) solution (1.0 μg/mL, PBS) was prepared and 100 μL was added to each well and then allowed to stand for 2 hours at 25° C. Then, the liquid was removed and 300 μL of washing buffer (PBS with 0.05% Tween 20) was added to wash the wells (this washing procedure was repeated three times thereafter). 200 μL of 5% skim milk-PBS solution was added to each well, and then allowed to stand overnight at 4° C. After washing, 100 μL of glycosyltransferase reaction solution (0.25 μg/mL B-type glycosyltransferase, 50 mM HEPES, pH 6.5, 1.5 mM UDP-galactose, 5 mM MnCl2) was added to each well and allowed to stand at 37° C. for 2 hours. While performing the transglycosylation reaction, a mixed solution (with serum) was prepared by mixing 50 μL each of GII.2 VLP solution and rabbit serum collected as described above, which was diluted from 1 to 128 times, and was allowed to stand at 25° C. for one hour. After washing the wells, 100 μL of the above mixed solution was added to the wells and allowed to stand at 25° C. for one hour. After washing the wells, 100 μL of primary antibody solution (Mouse anti-NoV VLP Antibody in PBS with 0.05% Tween 20) was added to each well and allowed to stand at 25° C. for one hour. After washing, 100 μL of secondary antibody solution (Anti-Mouse IgG Antibody, HRP conjugated in PBS with 0.05% Tween 20) was added to each well and allowed to stand at 25° C. for one hour. After washing, 100 μL of TMB (3,3′,5,5′-tetramethylbenzidine) solution was added to each well and allowed to stand at 25° C. for 30 minutes, shielded from light. The reaction was stopped by adding 100 μL of Stop Solution, and the absorbance at a wavelength of 450 nm was measured.
PBS with 0.05% Tween 20 and 5% skim milk alone was mixed with VLPs to prepare a mixed solution (without serum). The mixed solution (without serum) was used instead of the above mixed solution (with serum) to perform the same operations as above. The same operations as above were also performed using PBS with 0.05% Tween 20 and 5% skim milk (without VLPs or rabbit serum) as a blank, instead of the above mixed solution (with serum).
The binding blockade activity was calculated by applying the OD [with serum] obtained using the mixed solution with serum, the OD [without serum] obtained using the mixed solution without serum, and the OD [blank] obtained using the blank to the following equation (
Binding blockade activity=100(%)−[(OD [with serum]−OD [blank])(OD [without serum]−OD [blank])]×100(%)
The presence of neutralizing activity is based on the Blocking Titer (BT) 50 value. BT50 is the value of the maximum serum dilution factor at which binding blockade activity exceeds 50%. The BT50 values for the present test are shown in Table 3, and neutralizing activity was considered to be present if the BT50 value of the serum after immunization was twice or more the BT50 value of the serum before immunization. However, if the BT50 value of the serum before immunization was outside the detection range, neutralizing activity was considered to be present if the BT50 value of the serum after immunization could be detected. As shown in Table 3, the sera collected from rabbits immunized with the epitope peptides were found to have neutralizing activity. This suggests that immunization with the epitope peptides of GII.2 induced antibodies with neutralizing activity against GII.2.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2021-055049 | Mar 2021 | JP | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/JP2022/015581 | 3/29/2022 | WO |
