Patent Grant
10973909
This application claims the benefit of priority to UK Application No. 2004974.8 filed on Apr. 3, 2020, the content of which are incorporated herein by reference in its entirety.
The invention relates to polypeptides that find use in the prevention or treatment of Coronaviridae viral infection.
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 29, 2020, is named 52895708201_SL.txt and is 43,351 bytes in size.
Disclosed herein, in certain embodiments, are polypeptide vaccines, comprising a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 17, and a pharmaceutically-acceptable adjuvant, diluent, carrier, preservative, excipient, buffer, stabilizer, or combination thereof. In some embodiments, the polypeptide vaccines comprise two or more polypeptides, each polypeptide comprising a different amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 17. In some embodiments, the polypeptide vaccines comprise at least one polypeptide from at least two of the following groups: (a) SEQ ID NOs: 1 to 11; (b) SEQ ID NOs: 12 to 15; (c) SEQ ID NO: 16; and (d) SEQ ID NO: 17. In some embodiments, the polypeptide vaccines comprise at least two polypeptides, wherein each polypeptide comprises a different one of the amino acid sequences of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17. In some embodiments, the polypeptide vaccines comprise at least four polypeptides, wherein each polypeptide comprises a different one of the amino acid sequences of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17. In some embodiments, the polypeptide vaccines comprise at least six polypeptides, wherein each polypeptide comprises a different one of the amino acid sequences of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17. In some embodiments, the polypeptide vaccines comprise at least eight polypeptides, wherein each polypeptide comprises a different one of the amino acid sequences of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17. In some embodiments, the polypeptide vaccines comprise at least ten polypeptides, wherein each polypeptide comprises a different one of the amino acid sequences of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17. In some embodiments, the one or more of the polypeptides comprises a fragment of a Coronaviridae protein that is a CD8+ T cell epitope that is restricted to at least two HLA class I alleles of the individual. In some embodiments, the one or more of the polypeptides comprises a fragment of a Coronaviridae protein that is a CD4+ T cell epitope restricted to at least two HLA class II alleles of the individual. In some embodiments, the one or more of the polypeptides comprises a linear B cell epitope.
Disclosed herein, in certain embodiments, are methods treating or preventing a Coronaviridae infection in an individual in need thereof, comprising administering to the individual a polypeptide vaccine disclosed herein. In some embodiments, the Coronaviridae infection is a SARS-CoV-2 infection.
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
SEQ ID NOs: 1 to 17 set forth 30 mer T cell epitopes described in Table 2A.
SARS-CoV-2 is similar to SARS-CoV, for which previous research data exist on protective immune responses. Both the humoral and cell-mediated immune responses appear to play a protective role against SARS-CoV. Antibody responses generated against the spike (S) and nucleocapsid (N) protein of SARS-CoV are particularly prevalent in SARS-CoV-infected patients. While being effective, the antibody response is short-lived in convalescent SARS-CoV patients. In contrast, T cell responses provide long-term memory post-infection in recovered patients.
One of the challenges of producing an effective vaccine is that there is tremendous variability in the way the immune systems of different human individuals interact with the different antigens expressed by an infecting virus. Previously, it has been shown that the immune response of an individual is predicted by the ability of single antigen T cell epitopes to be recognized by multiple HLA alleles of the individual. T cell epitopes that are restricted to multiple HLA alleles of an individual act as genetic biomarkers that predict peptide-specific T cell responses of individual patients. These genetic biomarkers are referred to as “personal epitopes” or “PEPIs”. Multi-HLA allele-binding PEPIs induce T cell responses at a significantly higher rate than T cell epitopes that are restricted to a single HLA allele of a vaccinated individual. The identification of T cell epitopes in the polypeptides of a vaccine composition that are multi-HLA allele-binding PEPIs for individuals in a model human population has been shown to predict the immune response rates reported in clinical trials (WO 2018/158456, WO 2018/158457 and WO 2018/158455).
A second challenge in the development of an effective vaccine is the continuing evolution of the virus through mutation and the potential for infecting virus heterogeneity.
A third challenge is the need to quickly develop, safety test, and verify efficacy of a vaccine for the new emergent SARS-CoV-2 coronavirus virus, and subsequently manufacture the vaccine on a very large scale, to meet immediate population demands. Conventional vaccine development is a complex and challenging process. Peptide vaccines provide several advantages in comparison to conventional vaccines made of dead or attenuated pathogens, inactivated toxins, and recombinant subunits. Short polypeptides can be synthesized rapidly and peptide vaccine production is relatively inexpensive. Additionally, peptide vaccines avoid the inclusion of unnecessary components possessing high reactogenicity to the host, such as lipopolysaccharides, lipids, and toxins.
Peptide vaccine development strategy typically targets the selection of a combination of HLA allele-restricted epitopes that seek to maximize population coverage globally. According to this approach, multiple peptides are selected having different HLA binding specificities to afford increased coverage of the patient population targeted by peptide (epitope)-based vaccines, taking also in consideration that different HLA types are expressed at dramatically different frequencies in different ethnicities.
One recent approach proposed to screen a set of T cell epitopes estimated to provide broad coverage of global population as well as in China against SARS-CoV-2. This approach used HLA-restricted SARS-CoV-derived epitopes and the publicly available IEDB Population Coverage Tool (tools.iedb.org/population) to guide experimental efforts towards the development of vaccines against SARS-CoV-2. This approach attempts to take in consideration HLA polymorphism and frequency in different ethnic populations. In practice, however, most often HLA-restricted epitopes do not induce an immune response in HLA-matched individuals, and clinical trials result in lower immune response rates than expected. In addition, peptides recognized by CD8 T cells have been shown to be both selective and extremely sensitive; one amino acid change can alter the specific epitope into a non-immunogenic peptide.
Other approaches include the whole sequence of S protein in mRNA or pDNA vectors.
Accordingly, there is an immediate need for a vaccine that is effective in a high proportion of the global human population, robust to viral antigen mutation, and could proceed rapidly through the necessary steps for clinical validation and manufacture.
Disclosed herein, in certain embodiments, are polypeptide vaccines against SARS-CoV-2 that addresses the dual challenges of heterogeneity in the immune responses of different individuals, and potential heterogeneity in the infecting virus. In some embodiments, the peptides disclosed herein merge personal epitope design with the further selection of B cell epitope sequences resulting in overlapping, multi-HLA binding epitopes within an individual aiming to induce CD4+, CD8+ and antibody-producing B-cell responses. In some embodiments, the peptide vaccines comprise a selection of 30mer polypeptide fragments of the conserved regions of SARS-CoV-2 viral antigens that comprise (i) maximum CD8+ personal epitopes (PEPIs) in a model population of human individuals having HLA genotypes that are representative of the global population; (ii) maximum CD4+ personal epitopes (PEPIs) in the global population; and (iii) linear B cell epitopes. In some embodiments, the vaccines disclosed herein induce cytotoxic T cell, helper T cell and B cell responses in a surprisingly high proportion of individuals in the human population.
Disclosed herein, in certain embodiments, are polypeptide vaccines comprising at least one polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 1 to 17, and a pharmaceutically-acceptable excipient. In some embodiments, the polypeptide vaccine comprises at least two different polypeptides comprising an amino acid sequence selected from SEQ ID NOs: 1 to 17.
Disclosed herein, in certain embodiments, are polypeptide vaccines comprising at least one polypeptide comprising a fragment of a Coronaviridae, Betacoronavirus or SARS-CoV-2 protein. In some embodiments, the polypeptide vaccine comprises at least one amino acid sequence selected from SEQ ID NOs: 1 to 17. In some embodiments, the polypeptide vaccine comprises at least one sequence from at least two of the following groups: (a) SEQ ID NOs: 1 to 11 (fragments of SARS-CoV-2 surface protein); (b) SEQ ID NOs: 12 to 15 (fragments of SARS-CoV-2 nucleocapsid protein); (c) SEQ ID NO: 16 (fragment of SARS-CoV-2 membrane protein); and (d) SEQ ID NO: 17 (fragment of SARS-CoV-2 envelope protein). In some embodiments, the polypeptide vaccine comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 different polypeptides, each comprising a different amino acid sequence selected from SEQ ID NOs: 1 to 17. In some embodiments, the polypeptide vaccine comprises ten polypeptides comprising an amino acid sequence of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17.
Disclosed herein, in certain embodiments, are methods of treating or preventing a SARS-CoV-2 infection in an individual in need thereof, comprising administering to the individual a polypeptide vaccine comprising at least one polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 1 to 17, and a pharmaceutically-acceptable excipient. In some embodiments, the polypeptide vaccine comprises at least two different polypeptides comprising an amino acid sequence selected from SEQ ID NOs: 1 to 17. In some embodiments, at least one polypeptide comprises a CD8+ T cell epitope that is restricted to at least two, or in some cases three or at least three, HLA class I alleles of the individual. In some embodiments, at least one polypeptide comprises a CD4+ T cell epitope that is restricted to at least two, or in some cases at least three, or in some cases four or at least four, HLA class II alleles of the individual. In some embodiments, at least one polypeptide comprises a linear B cell epitope. In some cases, the method further comprises the step of determining the HLA class I and/or class II genotype of the individual.
Disclosed herein, in certain embodiments, are methods of treating or preventing a Coronaviridae, Betacoronavirus or SARS-CoV-2 infection in an individual in need thereof, comprising administering to the individual a polypeptide vaccine comprising at least one polypeptide comprising a fragment of a Coronaviridae, Betacoronavirus or SARS-CoV-2 protein. In some embodiments, at least one polypeptide comprises a CD8+ T cell epitope that is restricted to at least two, or in some cases three or at least three, HLA class I alleles of the individual. In some embodiments, at least one polypeptide comprises a CD4+ T cell epitope that is restricted to at least two, or in some cases at least three, or in some cases four or at least four, HLA class II alleles of the individual. In some embodiments, at least one polypeptide comprises a linear B cell epitope. In some embodiments, the polypeptide vaccine comprises at least one amino acid sequence selected from SEQ ID NOs: 1 to 17. In some embodiments, the polypeptide vaccine comprises at least one sequence from at least two of the following groups: (a) SEQ ID NOs: 1 to 11 (fragments of SARS-CoV-2 surface protein); (b) SEQ ID NOs: 12 to 15 (fragments of SARS-CoV-2 nucleocapsid protein); (c) SEQ ID NO: 16 (fragment of SARS-CoV-2 membrane protein); and (d) SEQ ID NO: 17 (fragment of SARS-CoV-2 envelope protein). In some embodiments, the polypeptide vaccine comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 different polypeptides, each comprising a different amino acid sequence selected from SEQ ID NOs: 1 to 17. In some embodiments, the polypeptide vaccine comprises ten polypeptides comprising an amino acid sequence of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17. In some cases, the method further comprises the step of determining the HLA class I and/or class II genotype of the individual.
The disclosure will now be described in more detail, by way of example and not limitation, and by reference to the accompanying drawings. Many equivalent modifications and variations will be apparent, to those skilled in the art when given this disclosure. Accordingly, the exemplary embodiments of the disclosure set forth are considered to be illustrative and not limiting. Various changes to the described embodiments may be made without departing from the scope of the disclosure. All documents cited herein, whether supra or infra, are expressly incorporated by reference in their entirety.
The present disclosure includes the combination of the aspects and preferred features described except where such a combination is clearly impermissible or is stated to be expressly avoided. As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “a peptide” includes two or more such peptides.
Section headings are used herein for convenience only and are not to be construed as limiting in any way.
HLA Genotypes
HLAs are encoded by the most polymorphic genes of the human genome. Each person has a maternal and a paternal allele for the three HLA class I molecules (HLA-A*, HLA-B*, HLA-C*) and four HLA class II molecules (HLA-DP*, HLA-DQ*, HLA-DRB1*, HLA-DRB3*/4*/5*). Practically, each person expresses a different combination of 6 HLA class I and 8 HLA class II molecules that present different epitopes from the same protein antigen.
The nomenclature used to designate the amino acid sequence of the HLA molecule is as follows: gene name*allele:protein number, which, for instance, can look like: HLA-A*02:25. In this example, “02” refers to the allele. In most instances, alleles are defined by serotypes—meaning that the proteins of a given allele will not react with each other in serological assays. Protein numbers (“25” in the example above) are assigned consecutively as the protein is discovered. A new protein number is assigned for any protein with a different amino acid sequence (e.g. even a one amino acid change in sequence is considered a different protein number). Further information on the nucleic acid sequence of a given locus may be appended to the HLA nomenclature.
The HLA class I genotype or HLA class II genotype of an individual may refer to the actual amino acid sequence of each class I or class II HLA of an individual, or may refer to the nomenclature, as described above, that designates, minimally, the allele and protein number of each HLA gene. An HLA genotype may be determined using any suitable method. For example, the sequence may be determined via sequencing the HLA gene loci using methods and protocols known in the art. Alternatively, the HLA set of an individual may be stored in a database and accessed using methods known in the art.
Some individuals may have two HLA alleles that encode the same HLA molecule (for example, two copies for HLA-A*02:25 in case of homozygosity). The HLA molecules encoded by these alleles bind all of the same T cell epitopes. For the purposes of this disclosure “binding to at least two HLA molecules of the individual” as used herein includes binding to the HLA molecules encoded by two identical HLA alleles in a single individual. In other words, “binding to at least two HLA molecules of the individual” and the like could otherwise be expressed as “binding to the HLA molecules encoded by at least two HLA alleles of the individual”.
Polypeptides
Disclosed herein, in certain embodiments, are polypeptide vaccines that are derived from SARS-CoV-2 antigens and that are immunogenic for a high proportion of the human population.
As used herein, the terms “peptide” and “polypeptide” refer to chains of amino acids comprising between 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15 and 10, or 11, or 12, or 13, or 14, or 15, or 20, or 25, or 30, or 35, or 40, or 45, or 50 or 55 or 60 amino acids. The terms “peptide”
and “polypeptide” are used interchangeably. In some embodiments, the polypeptides disclosed herein comprise 30 amino acids.
As used herein, the term “epitope” or “T cell epitope” refers to a sequence of contiguous amino acids contained within a protein antigen that possess a binding affinity for (is capable of binding to) one or more HLAs. An epitope is HLA- and antigen-specific (HLA-epitope pairs, predicted with known methods), but not individual specific. An epitope, a T cell epitope, a polypeptide, a fragment of a polypeptide or a composition comprising a polypeptide or a fragment thereof is “immunogenic” for a specific human individual if it is capable of inducing a T cell response (a cytotoxic T cell response or a helper T cell response) in that individual. In some cases, the helper T cell response is a Th1-type helper T cell response. The terms “T cell response” and “immune response” are used herein interchangeably, and refer to the activation of T cells and/or the induction of one or more effector functions following recognition of one or more HLA-epitope binding pairs. In some cases, an “immune response” includes an antibody response, because HLA class II molecules stimulate helper responses that are involved in inducing both long lasting CTL responses and antibody responses. Effector functions include cytotoxicity, cytokine production and proliferation. According to the present disclosure, an epitope, a T cell epitope, or a fragment of a polypeptide is immunogenic for a specific individual if it is capable of binding to at least two, or in some cases at least three, class I or at least two, or in some cases at least three or at least four class II HLAs of the individual.
A “personal epitope” (or “PEPI”) is a fragment of a polypeptide consisting of a sequence of contiguous amino acids of the polypeptide that is a T cell epitope capable of binding to one or more HLA class I molecules of a specific human individual. In other cases, a “PEPI” is a fragment of a polypeptide consisting of a sequence of contiguous amino acids of the polypeptide that is a T cell epitope capable of binding to one or more HLA class II molecules of a specific human individual. In other words, a “PEPI” is a T cell epitope that is recognized by the HLA set of a specific individual, and is consequently specific to the individual in addition to the HLA and the antigen. In contrast to an “epitope”, which is specific only to HLA and the antigen, PEPIs are specific to an individual because different individuals have different HLA molecules which each bind to different T cell epitopes.
“PEPI1” as used herein refers to a peptide, or a fragment of a polypeptide, that can bind to one HLA class I molecule (or, in specific contexts, HLA class II molecule) of an individual. “PEPI1+” refers to a peptide, or a fragment of a polypeptide, that can bind to one or more HLA class I molecule of an individual. “PEPI2” refers to a peptide, or a fragment of a polypeptide, that can bind to two HLA class I (or II) molecules of an individual. “PEPI2+” refers to a peptide, or a fragment of a polypeptide, that can bind to two or more HLA class I (or II) molecules of an individual. “PEPI3” refers to a peptide, or a fragment of a polypeptide, that can bind to three HLA class I (or II) molecules of an individual. “PEPI3+” refers to a peptide, or a fragment of a polypeptide, that can bind to three or more HLA class I (or II) molecules of an individual. “PEPI4” refers to a peptide, or a fragment of a polypeptide, that can bind to three HLA class I (or II) molecules of an individual. “PEPI4+” refers to a peptide, or a fragment of a polypeptide, that can bind to three or more HLA class I (or II) molecules of an individual.
Generally speaking, epitopes presented by HLA class I molecules are about nine amino acids long and epitopes presented by HLA class II molecules are about fifteen amino acids long. For the purposes of this disclosure, however, an epitope may be more or less than nine (for HLA Class I) or fifteen (for HLA Class II) amino acids long, as long as the epitope is capable of binding HLA. For example, an epitope that is capable of binding to class I HLA may be between 7, or 8 or 9 and 9 or 10 or 11 amino acids long. An epitope that is capable of binding to a class II HLA may be between 13, or 14 or 15 and 15 or 16 or 17 amino acids long.
A given HLA of an individual will only present to T cells a limited number of different peptides produced by the processing of protein antigens in an antigen presenting cell (APC). As used herein, “display” or “present”, when used in relation to HLA, references the binding between a peptide (epitope) and an HLA. In this regard, to “display” or “present” a peptide is synonymous with “binding” a peptide.
Any suitable method is used to determine the epitopes that will bind to a known HLA. For example, biochemical analysis may be used. It is also possible to use lists of epitopes known to be bound by a given HLA. It is also possible to use predictive or modelling software to determine which epitopes may be bound by a given HLA. Examples are provided in Table 1. In some cases, a T cell epitope is capable of binding to a given HLA if it has an IC50 or predicted IC50 of less than 5000 nM, less than 2000 nM, less than 1000 nM, or less than 500 nM.
In some embodiments, the peptides disclosed herein comprise or consist of one or more fragments of one or more Coronaviridae, a Betacoronavirus or SARS-CoV-2 antigens selected from surface glycoprotein, alias Spike, nucleocapsid phosphoprotein, envelope protein and membrane glycoprotein. Reference sequences are provided herein.
In some embodiments, the amino acid sequence is flanked at the N and/or C terminus by additional amino acids that are not part of the sequence of the Coronaviridae, Betacoronavirus or SARS-CoV-2 antigen, in other words that are not the same sequence of consecutive amino acids found adjacent to the selected fragments in the target polypeptide antigen. In some embodiments, the sequence is flanked by up to 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 additional amino acids at the N and/or C terminus.
It has been shown that the presence in a cancer vaccine of at least two polypeptide fragments (epitopes) that can bind to at least three HLA class I of an individual (≥2 PEPI3+) is predictive for a clinical response. In other words, if ≥2 PEPI3+ can be identified within the active ingredient polypeptide(s) of a vaccine, then an individual is a likely clinical responder.
Without wishing to be bound by theory, it is believed that one reason for the increased likelihood of deriving clinical benefit from a vaccine/immunotherapy comprising at least two multiple-HLA binding PEPIs, is that diseased cell populations, such as cancer or tumor cells or cells infected by viruses or pathogens such as HIV, are often heterogeneous both within and between affected individuals. In addition, the likelihood of developing resistance is decreased when more multiple HLA-binding PEPIs are included or targeted by a vaccine because a patient is less likely to develop resistance to the composition through mutation of the target PEPI(s).
Likewise, in the context of a vaccine for a viral infection, where the viral infection may be heterologous, it is advantageous to administer to an individual vaccine peptide(s) that are predicted to comprise multiple individual-specific multi-HLA allele-binding PEPIs (for treatment of an individual having a known HLA genotype) or multiple population bestEPIs, i.e. amino acid sequences that are or comprise multi-HLA allele-binding PEPIs in a high proportion of the target population. Including more bestEPI sequences also increases the total proportion of human individuals that will respond to treatment. Accordingly, in some embodiments, the polypeptide vaccine comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 polypeptides, each comprising a different amino acid sequence selected from SEQ ID NOs: 1 to 17. In some embodiments, the combination of polypeptides excludes one or more of the following combinations: SEQ ID NOs: 1 and 2; SEQ ID NOs: 3 and 4; SEQ ID NOs: 7 and 8; and/or SEQ ID NOs: 9 and 10; and/or excludes one or more of the following combinations: SEQ ID NOs: 2 and 3; and/or SEQ ID NOs: 13 and 14.
In some embodiments, the polypeptide vaccine comprises fragments of the same or different viral antigens. Different viral structural proteins may tend to mutate at different rates. Hence, in some embodiments, each polypeptide comprises an amino acid sequence selected from SEQ ID NOs: 1 to 17 that is a fragment of a different Coronaviridae, a Betacoronavirus or SARS-CoV-2 protein. In some embodiments, the polypeptide vaccine includes at least one sequence from at least two, three or all four of the following groups: (a) SEQ ID NOs: 1 to 11 (fragments of SARS-CoV-2 surface protein), optionally excluding the combination of SEQ ID NOs: 1 and 2, SEQ ID NOs: 2 and 3, SEQ ID NOs: 3 and 4, SEQ ID NOs: 7 and 8, and/or SEQ ID NOs: 9 and 10; (b) SEQ ID NOs: 12 to 15 (fragments of SARS-CoV-2 nucleocapsid protein), optionally excluding the combination of SEQ ID NOs: 13 and 14; (c) SEQ ID NO: 16 (fragment of SARS-CoV-2 membrane protein); and (d) SEQ ID NO: 17 (fragment of SARS-CoV-2 envelope protein). In some embodiments, the combination of polypeptides comprises or consists of ten polypeptides comprising or consisting of the amino acid sequences of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17.
Selection of Polypeptides and Patients
In some embodiments, the peptides described herein induce T cell responses or provide vaccination in an individual in need therefore. In some embodiments, the peptides treat or prevent a Coronaviridae infection, a Betacoronavirus infection or SARS-CoV-2 infection (COVID-19) in an individual. More than one peptide will typically be selected for treatment of an individual. In some cases, the peptide(s) used for treatment may be selected based on (i) the disease or condition to be treated in the individual; (ii) the HLA genotype of the individual; and/or (iii) the genetic background of the individual (e.g. nationality or ethnic group).
Polypeptide antigens, and particularly short peptides derived from polypeptide antigens, that are commonly used in vaccination and immunotherapy, induce immune responses in only a fraction of human individuals. The peptides of the present disclosure are specifically selected to induce immune responses in a high proportion of the global population. However, but they may not be effective in all individuals due to HLA genotype heterogeneity.
The present inventors have discovered that multiple HLA expressed by an individual generally need to present the same peptide in order to trigger a T cell response. Therefore, the fragments of a polypeptide antigen (epitopes) that are predicted to be immunogenic for a specific individual (PEPIs) are those that can bind to multiple class I (activate cytotoxic T cells) or class II (activate helper T cells) HLAs expressed by that individual. In general, a cytotoxic T-cell response in an individual to a specific vaccine peptide is best predicted by the presence in the vaccine peptide of ≥1 PEPI3+(epitope that binds to three or more class I HLA alleles of the individual). A helper T cell response is generally best predicted by ≥1 PEPI3+ or ≥1 PEPI4+(epitope that binds to three or more or four or more class II HLA alleles of the individual).
Accordingly, disclosed herein, in certain embodiments, are methods of predicting that a human individual will have a T cell response (cytotoxic and/or helper) to administration of a panel of polypeptides or a pharmaceutical composition as described herein. In some embodiments, the methods comprise (A) (i) determining that the panel of polypeptides or the active ingredient polypeptide(s) of the pharmaceutical composition comprise a T cell epitope that is restricted to at least three HLA class I molecules of the individual; and (ii) predicting that the individual will have a cytotoxic (CD8+) T cell response to administration of the panel of polypeptides or the pharmaceutical composition; and/or (B) (i) determining that the panel of polypeptides or the active ingredient polypeptide(s) of the pharmaceutical composition comprise a T cell epitope that is restricted to at least three, or in some cases at least four HLA class II molecules of the individual; and (ii) predicting that the individual will have a helper (CD4+) T cell response to administration of the panel of polypeptides or the pharmaceutical composition.
Further disclosed herein, in certain embodiments, are methods of determining a probability that a specific human individual will have a T cell response (cytotoxic/CD8+ or helper/CD4+) to administration of a panel of polypeptides or pharmaceutical composition described herein, wherein the method comprises identifying T cell epitopes in the polypeptides or active ingredient polypeptides that are restricted to at least three HLA class I or at least three or at least four HLA class II of the individual, and wherein (A) (a) a higher number T cell epitopes that are restricted to at least three HLA class I of the individual; and/or (b) a higher number of T cell epitopes that are both (I) restricted to at least three HLA class I of the individual; and (II) fragments of different SARS-CoV-2 structural proteins, corresponds to a higher probability of a cytotoxic/CD8+ T cell response in the individual; and/or (B) (a) a higher number T cell epitopes that are restricted to at least three or at least four HLA class II of the individual; and/or (b) a higher number of T cell epitopes that are both (I) restricted to at least three or at least four HLA class II of the individual; and (II) fragments of different SARS-CoV-2 structural proteins, corresponds to a higher probability of a helper/CD4+ T cell response in the individual.
In some embodiments, the individual is predicted to have a cytotoxic T cell response, or higher than a predetermined threshold probability of having a cytotoxic T cell response to administration of the panel of peptides or the pharmaceutical composition, and the method further comprises selecting or recommending administration of the pharmaceutical composition as a method of treating the individual, and optionally further comprises treating the individual by administering the panel of polypeptides or the pharmaceutical composition to the individual.
Additionally disclosed herein, in certain embodiments, are methods of treatment as described herein, wherein the individual receiving treatment has been predicted to have a cytotoxic or helper T cell response to administration of the panel of polypeptides or the pharmaceutical composition using a method described herein, or higher than a predetermined threshold probability of having a cytotoxic T or helper cell response to administration of the panel of polypeptides or the pharmaceutical composition using a method described herein.
The presence in a vaccine or immunotherapy composition of at least two T cell epitopes that (i) correspond to fragments of one or more target polypeptide antigens, and (ii) can bind to at least three HLA class I alleles of an individual is predictive for a clinical response. A “clinical response” or “clinical benefit” as used herein may be the prevention or a delay in the onset of a disease or condition, the amelioration of one or more symptoms, the induction or prolonging of remission, or the delay of a relapse or recurrence or deterioration, or any other improvement or stabilization in the disease status of an individual. A clinical response may be also the prevention of infections caused by different mutated variants of Coronavidiae viruses.
Accordingly, disclosed herein, in certain embodiments, are methods of predicting that a specific human individual will have a clinical response to a method of treatment as described herein or to administration of a panel of peptides or pharmaceutical composition as described herein, or of determining a probability of a clinical response. The method is similar to that described herein for predicting a T cell response, but a clinical response is predicted by determining that the panel of polypeptides or the active ingredient polypeptide(s) of the pharmaceutical composition comprise two different T cell epitopes that are each restricted to at least three HLA class I molecules of the individual.
Pharmaceutical Compositions, Methods of Treatment and Modes of Administration
Disclosed herein, in certain embodiments, are pharmaceutical compositions or vaccines comprising one or more of the peptides, polynucleic acids or vectors described herein. Such pharmaceutical compositions or vaccines are used in methods of inducing an immune response, treating, vaccinating or providing immunotherapy to an individual. The methods of treatment described herein comprise administering the pharmaceutical composition to the individual.
The pharmaceutical compositions or vaccines described herein comprise, in addition to one or more peptides, nucleic acids or vectors, a pharmaceutically acceptable excipient, carrier, diluent, buffer, stabilizer, preservative, adjuvant or other materials well known to those skilled in the art. Such materials are preferably non-toxic and preferably do not interfere with the pharmaceutical activity of the active ingredient(s). The pharmaceutical carrier or diluent may be, for example, water containing solutions. The precise nature of the carrier or other material may depend on the route of administration, e.g. oral, intravenous, cutaneous or subcutaneous, nasal, intramuscular, intradermal, and intraperitoneal routes.
In some embodiments, the pharmaceutical compositions of the disclosure comprise one or more “pharmaceutically acceptable carriers”. These are typically large, slowly metabolized macromolecules such as proteins, saccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, sucrose (Paoletti, 2001, Vaccine, 19:2118-2126), trehalose (WO 00/56365), lactose and lipid aggregates (such as oil droplets or liposomes). Such carriers are well known to those of ordinary skill in the art. In some embodiments, the pharmaceutical compositions contain diluents, such as water, saline, glycerol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present. Sterile pyrogen-free, phosphate buffered physiologic saline is a typical carrier (Gennaro, 2000, Remington: The Science and Practice of Pharmacy, 20th edition, ISBN:0683306472).
In some embodiments, the pharmaceutical compositions of the disclosure are lyophilized or in aqueous form, i.e. solutions or suspensions. Liquid formulations of this type allow the compositions to be administered direct from their packaged form, without the need for reconstitution in an aqueous medium, and are thus ideal for injection. In some embodiments, the pharmaceutical compositions are presented in vials, or they may be presented in ready filled syringes. The syringes may be supplied with or without needles. A syringe will include a single dose, whereas a vial may include a single dose or multiple doses.
Liquid formulations of the disclosure are also suitable for reconstituting other medicaments from a lyophilized form. Where a pharmaceutical composition is to be used for such extemporaneous reconstitution, the disclosure provides a kit, which may comprise two vials, or may comprise one ready-filled syringe and one vial, with the contents of the syringe being used to reconstitute the contents of the vial prior to injection.
In some embodiments, the pharmaceutical compositions of the disclosure include an antimicrobial, particularly when packaged in a multiple dose format. Antimicrobials may be used, such as 2-phenoxyethanol or parabens (methyl, ethyl, propyl parabens). Any preservative is preferably present at low levels. Preservative may be added exogenously and/or may be a component of the bulk antigens which are mixed to form the composition (e.g. present as a preservative in pertussis antigens).
In some embodiments, the pharmaceutical compositions of the disclosure comprise detergent e.g. Tween (polysorbate), DMSO (dimethyl sulfoxide), DMF (dimethylformamide). Detergents are generally present at low levels, e.g. <0.01%, but may also be used at higher levels, e.g. 0.01-50%.
In some embodiments, the pharmaceutical compositions of the disclosure include sodium salts (e.g. sodium chloride) and free phosphate ions in solution (e.g. by the use of a phosphate buffer).
In some embodiments, the pharmaceutical compositions are encapsulated in a suitable vehicle either to deliver the peptides into antigen presenting cells or to increase the stability. As will be appreciated by a skilled artisan, a variety of vehicles are suitable for delivering a pharmaceutical composition of the disclosure. Non-limiting examples of suitable structured fluid delivery systems may include nanoparticles, liposomes, microemulsions, micelles, dendrimers and other phospholipid-containing systems. Methods of incorporating pharmaceutical compositions into delivery vehicles are known in the art.
In order to increase the immunogenicity of the composition, in some embodiments, the pharmacological compositions comprise one or more adjuvants and/or cytokines.
Suitable adjuvants include an aluminum salt such as aluminum hydroxide or aluminum phosphate, but may also be a salt of calcium, iron or zinc, or may be an insoluble suspension of acylated tyrosine, or acylated sugars, or may be cationically or anionically derivatized saccharides, polyphosphazenes, biodegradable microspheres, monophosphoryl lipid A (MPL), lipid A derivatives (e.g. of reduced toxicity), 3-O-deacylated MPL [3D-MPL], quil A, Saponin, QS21, Freund's Incomplete Adjuvant (Difco Laboratories, Detroit, Mich.), Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.), AS-2 (Smith-Kline Beecham, Philadelphia, Pa.), CpG oligonucleotides, bioadhesives and mucoadhesives, microparticles, liposomes, polyoxyethylene ether formulations, polyoxyethylene ester formulations, muramyl peptides or imidazoquinolone compounds (e.g. imiquamod and its homologues). Human immunomodulators suitable for use as adjuvants in the disclosure include cytokines such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc), macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), granulocyte, macrophage colony stimulating factor (GM-CSF) may also be used as adjuvants.
In some embodiments, the compositions comprise an adjuvant selected from the group consisting of Montanide ISA-51 (Seppic, Inc., Fairfield, N.J., United States of America), QS-21 (Aquila Biopharmaceuticals, Inc., Lexington, Mass., United States of America), GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum, levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete and incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT). In some embodiments, the adjuvant is Montanide adjuvant.
By way of example, the cytokine may be selected from the group consisting of a transforming growth factor (TGF) such as but not limited to TGF-α and TGF-β; insulin-like growth factor-I and/or insulin-like growth factor-II; erythropoietin (EPO); an osteoinductive factor; an interferon such as but not limited to interferon-α, -β, and -γ; a colony stimulating factor (CSF) such as but not limited to macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF). In some embodiments, the cytokine is selected from the group consisting of nerve growth factors such as NGF-β; platelet-growth factor; a transforming growth factor (TGF) such as but not limited to TGF-α. and TGF-β; insulin-like growth factor-I and insulin-like growth factor-II; erythropoietin (EPO); an osteoinductive factor; an interferon (IFN) such as but not limited to IFN-α, IFN-β, and IFN-γ; a colony stimulating factor (CSF) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF); an interleukin (Il) such as but not limited to IL-1, IL-1.alpha., IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12; IL-13, IL-14, IL-15, IL-16, IL-17, IL-18; LIF; kit-ligand or FLT-3; angiostatin; thrombospondin; endostatin; a tumor necrosis factor (TNF); and LT.
It is expected that an adjuvant or cytokine can be added in an amount of about 0.01 mg to about 10 mg per dose, preferably in an amount of about 0.2 mg to about 5 mg per dose. Alternatively, the adjuvant or cytokine may be at a concentration of about 0.01 to 50%, preferably at a concentration of about 2% to 30%.
In certain aspects, the pharmaceutical compositions of the disclosure are prepared by physically mixing the adjuvant and/or cytokine with peptides described herein under appropriate sterile conditions in accordance with known techniques to produce the final product.
In some embodiments, the compositions disclosed herein are prepared as a (ribo)nucleic acid vaccine. In some embodiments, the nucleic acid vaccine is a DNA vaccine. In some embodiments, DNA vaccines, or gene vaccines, comprise a plasmid with a promoter and appropriate transcription and translation control elements and a nucleic acid sequence encoding one or more polypeptides of the disclosure. In some embodiments, the plasmids also include sequences to enhance, for example, expression levels, intracellular targeting, or proteasomal processing. In some embodiments, DNA vaccines comprise a viral vector containing a nucleic acid sequence encoding one or more polypeptides of the disclosure. In additional aspects, the compositions disclosed herein comprise one or more nucleic acids encoding peptides determined to have immunoreactivity with a biological sample. For example, in some embodiments, the compositions comprise one or more nucleotide sequences encoding 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more peptides comprising a fragment that is a T cell epitope capable of binding to at least three HLA class I molecules and/or at least three or four HLA class II molecules of a patient. In some embodiments, the DNA or gene vaccine also encodes immunomodulatory molecules to manipulate the resulting immune responses, such as enhancing the potency of the vaccine, stimulating the immune system or reducing immunosuppression. Strategies for enhancing the immunogenicity of DNA or gene vaccines include encoding of xenogeneic versions of antigens, fusion of antigens to molecules that activate T cells or trigger associative recognition, priming with DNA vectors followed by boosting with viral vector, and utilization of immunomodulatory molecules. In some embodiments, the DNA vaccine is introduced by a needle, a gene gun, an aerosol injector, with patches, via microneedles, by abrasion, among other forms. In some forms the DNA vaccine is incorporated into liposomes or other forms of nanobodies. In some embodiments, the DNA vaccine includes a delivery system selected from the group consisting of a transfection agent; protamine; a protamine liposome; a polysaccharide particle; a cationic nanoemulsion; a cationic polymer; a cationic polymer liposome; a cationic nanoparticle; a cationic lipid and cholesterol nanoparticle; a cationic lipid, cholesterol, and PEG nanoparticle; a dendrimer nanoparticle. In some embodiments, the DNA vaccines is administered by inhalation or ingestion. In some embodiments, the DNA vaccine is introduced into the blood, the thymus, the pancreas, the skin, the muscle, a tumor, or other sites.
In some embodiments, the compositions disclosed herein are prepared as an RNA vaccine. In some embodiments, the RNA is non-replicating mRNA or virally derived, self-amplifying RNA. In some embodiments, the non-replicating mRNA encodes the peptides disclosed herein and contains 5′ and 3′ untranslated regions (UTRs). In some embodiments, the virally derived, self-amplifying RNA encodes not only the peptides disclosed herein but also the viral replication machinery that enables intracellular RNA amplification and abundant protein expression. In some embodiments, the RNA is directly introduced into the individual. In some embodiments, the RNA is chemically synthesized or transcribed in vitro. In some embodiments, the mRNA is produced from a linear DNA template using a T7, a T3, or a Sp6 phage RNA polymerase, and the resulting product contains an open reading frame that encodes the peptides disclosed herein, flanking UTRs, a 5′ cap, and a poly(A) tail. In some embodiments, various versions of 5′ caps are added during or after the transcription reaction using a vaccinia virus capping enzyme or by incorporating synthetic cap or anti-reverse cap analogues. In some embodiments, an optimal length of the poly(A) tail is added to mRNA either directly from the encoding DNA template or by using poly(A) polymerase. The RNA may encode one or more peptides comprising a fragment that is a T cell epitope capable of binding to at least three HLA class I and/or at least three or four HLA class II molecules of a patient. In some embodiments, the fragments are derived from an antigen that is expressed in cancer. In some embodiments, the RNA includes signals to enhance stability and translation. In some embodiments, the RNA also includes unnatural nucleotides to increase the half-life or modified nucleosides to change the immunostimulatory profile.
In some embodiments, the RNAs is introduced by a needle, a gene gun, an aerosol injector, with patches, via microneedles, by abrasion, among other forms. In some forms the RNA vaccine is incorporated into liposomes or other forms of nanobodies that facilitate cellular uptake of RNA and protect it from degradation. In some embodiments, the RNA vaccine includes a delivery system selected from the group consisting of a transfection agent; protamine; a protamine liposome; a polysaccharide particle; a cationic nanoemulsion; a cationic polymer; a cationic polymer liposome; a cationic nanoparticle; a cationic lipid and cholesterol nanoparticle; a cationic lipid, cholesterol, and PEG nanoparticle; a dendrimer nanoparticle; and/or naked mRNA; naked mRNA with in vivo electroporation; protamine-complexed mRNA; mRNA associated with a positively charged oil-in-water cationic nanoemulsion; mRNA associated with a chemically modified dendrimer and complexed with polyethylene glycol (PEG)-lipid; protamine-complexed mRNA in a PEG-lipid nanoparticle; mRNA associated with a cationic polymer such as polyethylenimine (PEI); mRNA associated with a cationic polymer such as PEI and a lipid component; mRNA associated with a polysaccharide (for example, chitosan) particle or gel; mRNA in a cationic lipid nanoparticle (for example, 1,2 dioleoyloxy 3 trimethylammoniumpropane (DOTAP) or dioleoylphosphatidylethanolamine (DOPE) lipids); mRNA complexed with cationic lipids and cholesterol; or mRNA complexed with cationic lipids, cholesterol and PEG-lipid. In some embodiments, the RNA vaccine is administered by inhalation or ingestion. In some embodiments, the RNA is introduced into the blood, the thymus, the pancreas, the skin, the muscle, a tumor, or other sites, and/or by an intradermal, intramuscular, subcutaneous, intranasal, intranodal, intravenous, intrasplenic, intratumoral or other delivery route.
In some embodiments, the polynucleotide or oligonucleotide components are naked nucleotide sequences or be in combination with cationic lipids, polymers or targeting systems. They may be delivered by any available technique. For example, the polynucleotide or oligonucleotide may be introduced by needle injection, preferably intradermally, subcutaneously or intramuscularly. Alternatively, the polynucleotide or oligonucleotide may be delivered directly across the skin using a delivery device such as particle-mediated gene delivery. The polynucleotide or oligonucleotide may be administered topically to the skin, or to mucosal surfaces for example by intranasal, oral, or intrarectal administration.
Uptake of polynucleotide or oligonucleotide constructs may be enhanced by several known transfection techniques, for example those including the use of transfection agents. Examples of these agents include cationic agents, for example, calcium phosphate and DEAE-Dextran and lipofectants, for example, lipofectam and transfectam. The dosage of the polynucleotide or oligonucleotide to be administered can be altered.
The term “treatment” as used herein includes therapeutic and prophylactic treatment. Administration is typically in a “prophylactically effective amount” or a “therapeutically effective amount” (as the case may be, although prophylaxis may be considered therapy), this being sufficient to result in a clinical response or to show clinical benefit to the individual, e.g. an effective amount to prevent or delay onset of the disease or condition, to ameliorate one or more symptoms, to induce or prolong remission, or to delay relapse or recurrence.
The dose may be determined according to various parameters, especially according to the substance used; the age, weight and condition of the individual to be treated; the route of administration; and the required regimen. The amount of antigen in each dose is selected as an amount which induces an immune response. A physician will be able to determine the required route of administration and dosage for any particular individual. The dose may be provided as a single dose or may be provided as multiple doses, for example taken at regular intervals, for example 2, 3 or 4 doses administered hourly. Typically, peptides, polynucleotides or oligonucleotides are typically administered in the range of 1 pg to 1 mg, more typically 1 pg to 10 μg for particle mediated delivery and 1 μg to 1 mg, more typically 1-100 more typically 5-50 μg for other routes. Generally, it is expected that each dose will comprise 0.01-3 mg of antigen. An optimal amount for a particular vaccine can be ascertained by studies involving observation of immune responses in individuals.
In some embodiments, the method of treatment comprises administration to an individual of more than one peptide, polynucleic acid or vector. These may be administered together/simultaneously and/or at different times or sequentially. The use of combinations of different peptides, optionally targeting different antigens, may be important to overcome the challenges of viral heterogeneity and HLA heterogeneity of individuals. The use of peptides of the disclosure in combination expands the group of individuals who can experience clinical benefit from vaccination. Multiple pharmaceutical compositions, manufactured for use in one regimen, may define a drug product. In some cases, different peptides, polynucleic acids or vectors of a single treatment may be administered to the individual within a period of, for example, 1 year, or 6 months, or 3 months, or 60 or 50 or 40 or 30 days.
Routes of administration include but are not limited to intranasal, oral, subcutaneous, intradermal, and intramuscular. The subcutaneous administration is particularly preferred. Subcutaneous administration may for example be by injection into the abdomen, lateral and anterior aspects of upper arm or thigh, scapular area of back, or upper ventrodorsal gluteal area.
In some embodiments, the compositions of the disclosure are administered in one, or more doses, as well as, by other routes of administration. For example, such other routes include, intracutaneously, intravenously, intravascularly, intraarterially, intraperitnoeally, intrathecally, intratracheally, intracardially, intralobally, intramedullarly, intrapulmonarily, and intravaginally. Depending on the desired duration of the treatment, the compositions according to the disclosure may be administered once or several times, also intermittently, for instance on a monthly basis for several months or years and in different dosages.
Solid dosage forms for oral administration include capsules, tablets, caplets, pills, powders, pellets, and granules. In such solid dosage forms, the active ingredient is ordinarily combined with one or more pharmaceutically acceptable excipients, examples of which are detailed above. Oral preparations may also be administered as aqueous suspensions, elixirs, or syrups. For these, the active ingredient may be combined with various sweetening or flavoring agents, coloring agents, and, if so desired, emulsifying and/or suspending agents, as well as diluents such as water, ethanol, glycerin, and combinations thereof.
In some embodiments, the compositions of the disclosure are administered, or the methods and uses for treatment according to the disclosure are performed, alone or in combination with other pharmacological compositions or treatments, for example other immunotherapy, vaccine or anti-virals. In some embodiments, the other therapeutic compositions or treatments are administered either simultaneously or sequentially with (before or after) the composition(s) or treatment of the disclosure.
In some embodiments, the method of treatment is a method of vaccination or a method of providing immunotherapy. As used herein, “immunotherapy” is the treatment of a disease or condition by inducing or enhancing an immune response in an individual. In certain embodiments, immunotherapy refers to a therapy that comprises the administration of one or more drugs to an individual to elicit T cell responses. In a specific embodiment, immunotherapy refers to a therapy that comprises the administration or expression of polypeptides that contain one or more PEPIs to an individual to elicit a T cell response to recognize and kill cells that display the one or more PEPIs on their cell surface in conjunction with a class I HLA. In another embodiment, immunotherapy refers to a therapy that comprises the administration or expression of polypeptides that contain one or more PEPIs presented by class II HLAs to an individual to elicit a T helper response to provide co-stimulation to cytotoxic T cells that recognize and kill diseased cells that display the one or more PEPIs on their cell surface in conjunction with a class I HLAs. In still another specific embodiment, immunotherapy refers to a therapy that comprises administration of one or more drugs to an individual that re-activate existing T cells to kill target cells and/or virus.
The SARS-CoV genome has a size of ˜30 kilobases which, like other coronaviruses, encodes for multiple structural and non-structural proteins. The structural proteins include the spike (S) protein, the envelope (E) protein, the membrane (M) protein, and the nucleocapsid (N) protein.
The PolyPEPI-SCoV-2 vaccine disclosed herein is composed of one or more 30 amino acid long peptides capable of inducing positive, desirable T cell (both CD8 cytotoxic and CD4 helper) responses and B cell mediated antibody responses against one or more, and preferably all 4 of the structural viral antigens in a high proportion of individuals in the global population.
A total of 19 whole genome sequences of COVID-19 were downloaded on 28 Mar. 2020 from the NCBI database. (ncbi.nm.nih.gov/genome/genomes/86693)
The accession IDs are the following: NC_045512.2, MN938384.1, MN975262.1, MN985325.1, MN988713.1, MN994467.1, MN994468.1, MN997409.1, MN988668.1, MN988669.1, MN996527.1, MN996528.1, MN996529.1, MN996530.1, MN996531.1, MT135041.1, MT135043.1, MT027063.1, MT027062.1. The first ID represents the GenBank reference sequence. Four structural protein sequences (Surface glycoprotein, Envelope protein, Membrane glycoprotein, Nucleocapsid phosphoprotein) of translated coding sequences were aligned and compared with a multiple sequence alignment. Of the 19 sequences 15 were completely the same. However, we obtained single amino acid changes in 4 nucleocapsid proteins. These replacements are the following: MN988713.1: Nucleocapsid 194 S→X, MT135043.1: Nucleocapsid 343 D→V, MT027063.1: Nucleocapsid 194 S→L, MT027062.1: Nucleocapsid 194 S→L. None of these changes affected the epitopes that have been selected for targets in the present vaccine polypeptides.
Seventeen peptide fragments were selected from the conserved regions of the presently known viral antigen sequences for SARS-CoV-2 structural proteins. The fragments were selected to maximize multi-HLA class I-binding PEPI3+ and multi-HLA class II-binding PEPI4+, i.e. shared personal epitopes, in a model population. The peptides were also designed to incorporate linear B cell epitopes. Specifically, 9mer sequences in the conserved regions of the four target antigens that are PEPI2+ in the highest proportion of individuals in the model population were selected. These 9mers were extended to incorporate nearby linear B-cell epitopes in the conserved sequence of the target antigens. 30mer fragments of the target antigens that incorporate both the 9mer “bestEPIs” and linear B cell epitopes were then selected to maximize the proportion of individuals in the model population having a HLA class II-binding PEPI4+ in the 30mer fragment. The model population comprises ˜16,000 HLA-genotyped individuals obtained from a bone-marrow transplant biobank, with about 1,000 individuals from each of 16 different ethnic groups. The sequences of the selected 30 mer peptide fragments and HLA class I-binding epitopes that are PEPI3+ and HLA class II-binding epitopes that are PEPI4+ in the highest proportion of individuals in the model population are shown in Table 2A.
CFTNVYADSFVIRGDEVRQIAPGQTGKIAD
ALQIPFAMQMAYRFNGIGVTQNVLYENQKL
FAMQMAYRFNGIGVTQNVLYENQKLIANQF
LSYFIASFRLFARTR
SMWSFNPETNILLNV
As suggested in the article “Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies” (Ahmed et al), we modelled the possible efficacy (immunogenicity) of a vaccine based on the targets identified therein. The result was compared to a selection of PolyPEPI-SCov-2 vaccine peptides as described herein.
SF Ahmed et al identified 61 T-cell epitopes associated with 19 HLAI alleles to provide estimated accumulated population coverage of 96.29% based on global allele frequencies. (Ahmed et al. Viruses, 12(3). 2020) The following T-cell epitopes shown in Table 3 were suggested as potential targets for a vaccine (Table 3 of the article; 2 of 61 were only 8 mer epitopes, we excluded from the simulation).
Ahmed et al suggest that the estimated maximum population coverage might be achieved by selecting at least one epitope for each listed HLA allele (i.e. 19 sequences). Accordingly, we made a random selection from this T-cell epitope set, selecting one epitope for each HLA allele (exactly as suggested by the authors). Because these are promiscuous HLA-binding epitopes, therefore sometimes we selected the same epitope for more than one HLA allele. This was repeated 30 times and the selected epitopes were compared to 10 peptides selected for PolyPEPI-SCoV2 (SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, 17). The in-silico comparison was performed on our ˜16,000 HLA-genotyped individuals database obtained from a bone-marrow transplant biobank. Our database contains data from 16 ethnic groups (about 1,000 individuals per group). We computed the proportion of individuals with CD8+ immune response against at least one epitope. The worldwide (global) coverage of the PolyPEPI-SCoV2 is 99.8%, compared to the simulated vaccine (random epitope selection), where the average coverage was 61% (±9.9%), for some of the ethnic groups (e.g. Caucasians) achieving lower protection than for others (e.g. Japanese) (
A further special (not practical) situation was modelled, where all T-cell epitopes listed in Ahmed et al (n=59) were selected into the vaccine. In this case the worldwide coverage increased to up to 88% but still not reaching the level of PolyPEPI-SCoV2 (
We also modelled the ability of the PolyPEPI-SCoV2 vaccine (same 10 peptides selected) to induce HLA class II restricted CD4 responses (HLA class II PEPIs) in addition to CD8 response (
Based on the previous dataset derived from Ahmed et al, we computed the number of immunogenic epitopes in each individual in the model population. The distribution of this number shows the strengths of the vaccine against potential mutations.
For the vaccine containing all 59 epitopes the situation would be somewhat better: 69% of individuals can have immune response against 2 or more epitopes (
Modelling of COVID-19 infection and projections warn of rapid evolution which could undermine attempts to vaccinate against and treat infection. There is an urgent need to project how transmission of the novel Beta-coronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, the inventors measured how these factors affect transmission of human coronaviruses HCoV-OC43 and HCoV-HKU1. (Kissler et al. 2020 doi.org/10.1101/2020.03.04.20031112). The design of the vaccine peptides and compositions described herein are robust to rapid virus evolution and cover global population by the selection of multiple immunogenic but conserved sequences, preferably derived from multiple structural proteins.
It is anticipated that as the virus continues to evolve and as more data is collected, additional mutations will be observed. Such mutations will not affect the global coverage of the polypeptides and multi-peptide vaccine described herein, provided that mutations occur outside of the identified epitope regions. Even if mutations do occur within any of the epitope regions selected, then the remaining immunogenic epitopes still provide robust protection against the virus, since the majority of individuals will retain a broad repertoire of virus-specific memory T cell clones, For example, for the ten peptide vaccine comprising polypeptides of SEQ ID NOs: 2, 5, 7, 9, 12, 13, 14, 15, 16, and 17, 94% of patients are predicted to have immune responses against at least 3 vaccine peptides and 85% and 71% against 4 and 5 peptides, respectively.
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
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