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• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
  • A61P31/14—Antivirals for RNA viruses
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/12—Viral antigens
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/12—Viral antigens
  • A61K39/215—Coronaviridae, e.g. avian infectious bronchitis virus
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
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  • C12N15/86—Viral vectors
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  • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
  • C12N2770/00011—Details
  • C12N2770/20011—Coronaviridae
  • C12N2770/20022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
  • C12N2770/00011—Details
  • C12N2770/20011—Coronaviridae
  • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

• the present invention relates to proteins and nucleic acid sequences suitable for use in COVID-19 vaccines.
• Coronaviruses are a large family of single-stranded, enveloped RNA viruses that belong to the Coronaviridae family.
• the limited number of coronaviruses known to be able to infect humans were considered in the past as relatively harmless respiratory human pathogens, causing mild infections.
• SARS-CoV Severe Acute Respiratory Syndrome Coronavirus
• MERS-CoV Middle East Respiratory Syndrome Coronavirus
• SARS-CoV Severe Acute Respiratory Syndrome Coronavirus
• MERS-CoV Middle East Respiratory Syndrome Coronavirus
• ARDS acute respiratory distress syndrome
• sepsis sepsis
• septic shock cardiac disease
• thromboembolic events such as pulmonary embolism and multi-organ failure.
• COVID-19 vaccines and vaccine candidates act by inducing an immune response against virus protein antigens, making use of different strategies and technologies: traditional inactivated or live-attenuated virus vaccines, based on the introduction in the host of a number of different SARS-CoV-2 antigens, vaccines based on recombinantly produced SARS-CoV-2 proteins in association with adjuvants and gene-based vaccines, such as mRNA, DNA or vector vaccines, which deliver genes encoding the viral protein antigens for in vivo production in the cells of the host.
• traditional inactivated or live-attenuated virus vaccines based on the introduction in the host of a number of different SARS-CoV-2 antigens
• vaccines based on recombinantly produced SARS-CoV-2 proteins in association with adjuvants and gene-based vaccines, such as mRNA, DNA or vector vaccines, which deliver genes encoding the viral protein antigens for in vivo production in the cells of the host.
• SARS-COV-2 is characterised by four structural proteins, namely spike (S) protein, envelope (E) protein, membrane (M) protein and nucleocapsid (N) protein (Chen Y et al, J Med Virol 2020, 92: 418-423).
• the SARS-CoV-2 S protein has the 1273 aminoacid sequence of SEQ.ID. No: 1 and consists of a signal peptide located at the N-terminus (amino acids 1-13), the S1 subunit (14-685 residues) and the S2 subunit (686-1273 residues).
• the S1 subunit mediates receptor binding to ACE2 through the receptor binding domain (RBD) and the S2 subunit is responsible for the viral and host cell membrane fusion (Letko et al, Nat Microbiol 2020, 5: 562-569, Huang et al, Acta Pharmacologica Sinica 2020, 41 :1141-1149).
• the S2 subunit changes from a prefusion to a postfusion (hairpin) conformation.
• surface proteases cleave the S2 subunit (Silverira et al, Life Sci 2021 , 267:1128919).
• the vaccines approved so far by EMA are based on nucleic acids that induce the production in the host of the spike protein as protein antigen: the mRNA based Comirnaty vaccine developed by Pfizer and BioNTech, the mRNA based Moderna COVID-19 vaccine developed by Moderna and the DNA, viral vector delivered vaccines Vaxzevria developed by Oxford University and AstraZeneca and COVID-19 Vaccine Janssen developed by Janssen-Cilag International.
• Recent evidence has suggested a potential activity of the SARS-CoV-2 spike protein on cell signalling that is independent from facilitation of viral infection.
• the spike protein can induce pro-inflammatory responses in vitro in murine and human macrophages (Shirato et al, Heliyon 2021 , 7(2) e06187) and can activate cell signaling events in cultured human vascular cells (Suzuki et al, Vascular Pharmacology 2021 , 137: 106823).
• the spike protein is expressed mainly in myocites, fibroblasts, dendritic cells and lymphocytes but levels of expression have been detected with some of the vaccines also in other organs (information available at https://www.ema.europa.eu/).
• Nuclear hormone receptors are a family of ligand-regulated transcription factors that are activated by thyroid and steroid hormones and various other lipid-soluble signals, including retinoic acid and vitamin D.
• Steroid hormones in particular androgens and estrogens, have been shown to regulate a wide range of physiological functions such as development and maintenance of secondary sexual characteristics, metabolism, blood salt balance, immune and inflammatory responses, response to stress and/or neuronal function.
• estrogens have been implicated in the etiology of breast, endometrial, renal, and uterine cancer (Okamoto et al, Toxicology Letters 2020, 318: 99-103), while a pivotal role of androgens has been demonstrated in the pathogenesis of prostate cancer (Cold Spring Harb Perspect Med 2017;7:a030452).
• the activity of these molecules is mediated by nuclear receptors, the estrogen and the androgen receptor, that function as hormone-activated transcription factors. These receptors are involved in diverse activities but share a remarkable structural and functional similarity. In the absence of the ligand they exist within target cells in a transcriptionally inactive form.
• co-regulators Upon ligand activation, they bind to the promoters of target genes and form a transcriptional complex with a number of interacting proteins, collectively known as co-regulators, that can either activate (coactivators (CoA)) or inactivate (corepressors (CoR)) transcriptional activity, thereby triggering the activation or repression of target gene expression (Patel et al, Pharm Ther 2018, 186: 1-24; Zella et al, Arch Biochem Biophys 2007, 460(2): 206-212).
• coactivators Coactivators
• CoR corepressors
• the SARS-CoV-2 spike protein contains a number of LxxLL-like motifs homolog to those of the nuclear coactivator 1 (NCOA1), that are able to bind to the NCOA1 binding domain and activate the transcription activity of the estrogen and androgen receptors. Furthermore, the sequence homology of the NCOA1 binding domain throughout the different nuclear receptors supports a potential ability of the spike protein to also activate transcription induced by other nuclear receptors, such as the Vitamin D and thyroid hormone receptor.
• NCOA1 nuclear coactivator 1
• the spike protein produced or contained in vaccines can interfere with the activity of nuclear receptors, in particular the estrogen and androgen receptors, and create an unbalance between physiological and pathological activities mediated by these receptors, thus generating unwanted, serious side effects.
• the present inventors have identified mutations in the LxxLL motifs of SARS-CoV-2 spike protein that abolish the binding activity of the protein to the NCOA1 binding domain of the estrogen and androgen receptors.
• an object of the invention is a mutated SARS-CoV-2 spike protein or a variant thereof, wherein at least one of the aminoacids isoleucine or leucine at a position corresponding to aminoacid 818, 821 , 822, 841 , 844, 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (SEQ ID NO: 1) are replaced by alanine.
• a further object of the invention is a mutated SARS-CoV-2 spike protein according to the invention having the aminoacid sequence of SEQ ID NO: 2, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30 or SEQ ID NO: 31 .
• a further object of the invention is an immunogenic fragment of a mutated SARS-CoV-2 spike protein or of a variant according to the invention.
• a further object of the invention is an mRNA encoding for a mutated SARS-CoV-2 spike protein, a variant or an immunogenic fragment according to the invention.
• a further object of the invention is said mutated SARS-CoV-2 spike protein, variant, fragment, mRNA or DNA for use in the prevention of COVID-19 in a subject.
• a further object of the invention is a vaccine comprising said mutated SARS-CoV-2 spike protein, variant or fragment, mRNA or DNA.
• a further object of the invention is said vaccine for use in the prevention of COVID-19 in a subject.
• Figure 1 shows the Estrogen receptor (ER) complexed with nuclear receptor coactivator. The whole complex is reported in the cartoon; the ER monomers are in grey surface, while the NCOA segments are reported in black cartoon and lines.
• ER Estrogen receptor
• Figure 2 shows the network of the most significant interactions of ER1 and ER2.
• the Nuclear receptor COActivators directly bind the nuclear receptors and stimulate transcriptional activities.
• Figure 3 shows the sequence alignment among LDX region in spike and other LDX cofactor-receptor domains.
• Figure 4 shows the 3D best docking hypothesis for spike-ER blind docking.
• the proteins are reported in cartoon.
• the ER dimer is in white cartoon while the spike protein is reported in black surface.
• Figure 5 shows the 3D best docking hypothesis for spike-ER motif-oriented docking.
• the proteins are reported in cartoon.
• the ER dimer is in white cartoon while the spike protein is reported in black surface.
• Figure 6 shows cell proliferation, expressed as percentage of control, induced by treatment of MCF-7 breast cancer cells with vehicle (CTR), estradiol (ESTR), wild type spike protein (SPIKE) or combinations of the two, either alone or in the presence of Raloxifene, measured as described in Example 2.
• CTR vehicle
• ESTR estradiol
• SPIKE wild type spike protein
• Figure 7 shows cell proliferation, expressed as percentage of control, induced by treatment of MCF-7 breast cancer cells with vehicle (CTRL), peptide 2, 5 or 7, wild type spike protein, wild type spike protein plus raloxifene or raloxifene alone, measured as described in Example 2.
• CTRL vehicle
• peptide 2, 5 or 7 wild type spike protein, wild type spike protein plus raloxifene or raloxifene alone, measured as described in Example 2.
• Figure 8 shows cell proliferation, expressed as percentage of control, induced by treatment of LNCap prostate cancer cells with peptide 2, 5 or 7 or wild type spike protein, as described in Example 2.
• Figure 9 shows results of proteomic analysis carried with Proteome Profiler Human XL Cytokine Array Kit (THP1 cell line differentiated with TPA/LPS and treated for 24h), after treatment with control (CTR), estrogen (ESTR), wild type spike protein (SPIKE) or raloxifene and wild type spike protein (RAL+SPIKE), as described in Example 3.
• CTR control
• ESR estrogen
• SPIKE wild type spike protein
• RAL+SPIKE wild type spike protein
• FIG 10 shows the Tartrate Resistant Acid Phosphatase (TRAP) activity determination by Enzyme-linked immunosorbent assay (U/L) in Osteoclasts differentiated from RAW264.7 macrophages and treated with 1 nM estradiol and 10ng/mL of spike wt, or mutant SP5, SP7 or SP5+SP7, as described in Example 4b.
• TRIP Tartrate Resistant Acid Phosphatase
• the present invention is based on the surprising finding that the SARS-CoV-2 spike protein exposes three LxxLL-like motifs that are able to mediate the binding and activation of nuclear receptors, in particular of estrogen and androgen receptor. As will be shown in the Examples, each of these motifs is able to activate proliferation of cancer cells induced by the estrogen or androgen receptor.
• the use in new or commercially available spike based COVID-19 vaccines of a SARS-CoV-2 spike protein having a sequence carrying these mutations or an mRNA or DNA sequences encoding it allows to maintain an equally effective immune response with a higher safety profile compared to the use of wild type SARS-CoV-2 spike protein.
• the present invention is directed to a mutated SARS-CoV-2 spike protein, variants and fragments thereof as well as mRNA and DNA encoding for the same, suitable to be used as active ingredient in vaccines for the prevention of COVID-19.
• a first object of the invention is a mutated SARS-CoV-2 spike protein or a variant thereof, wherein at least one of the aminoacids isoleucine or leucine at a position corresponding to aminoacid 818, 821 , 822, 841 , 844, 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (UniProtKB - PODTC2, SEQ ID NO: 1) is replaced by alanine.
• At least one of the aminoacids isoleucine or leucine at a position corresponding to aminoacid 818, 821 , 822, 841 , 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (SEQ ID NO: 1) is replaced by alanine.
• At least the aminoacids 818, 821 and 822, or the aminoacid 841 or the aminoacids 861 , 864 and 865 of SEQ ID NO: 1 are replaced by alanine.
• At least the aminoacids 818, 821 and 822 or the aminoacid 841 and 844 or the aminoacids 861 , 864 and 865 of SEQ ID NO: 1 are replaced by alanine
• the isoleucine or leucine at positions corresponding to aminoacids 818, 821 , 822, 841 , 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (SEQ ID NO: 1) are replaced by alanine.
• the mutated SARS-CoV-2 spike protein has the aminoacid sequence of SEQ ID NO: 2.
• the aminoacids isoleucine or leucine at positions corresponding to aminoacids 841 and 844 of the wild type SARS-CoV-2 protein sequence are replaced by alanine.
• the mutated SARS-CoV-2 spike protein has the aminoacid sequence of SEQ ID NO: 28.
• the aminoacids isoleucine or leucine at positions corresponding to aminoacids 861 , 864 and 865 of the wild type SARS-CoV-2 protein sequence are replaced by alanine.
• the mutated SARS-CoV-2 spike protein has the aminoacid sequence of SEQ ID NO: 29.
• the aminoacids isoleucine or leucine at positions corresponding to aminoacids 841 , 844, 861 , 864 and 865 of the wild type SARS- Cov-2 protein sequence are replaced by alanine.
• the mutated SARS-CoV-2 spike protein has the aminoacid sequence of SEQ ID NO: 30.
• the aminoacids isoleucine or leucine at positions corresponding to aminoacids 818, 821 , 822, 841 , 844, 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (SEQ ID NO: 1 ) are replaced by alanine.
• the mutated SARS-CoV-2 spike protein has the aminoacid sequence of SEQ ID NO: 31 .
• the aminoacid replacements introduced in the above described mutated SARS-CoV-2 spike protein are able to inhibit the activity of the spike protein on the nuclear hormone receptors and, at the same time, do not modify the conformation and antigenic properties of the SARS- CoV-2 spike protein.
• the mutated SARS-CoV-2 spike protein according to the invention can be modified by introducing further substitutions, or deletions or insertions that improve the stability of the mutated protein or improve the immunogenic activity against variants of concern of the SARS-CoV-2 virus characterised by modifications in the aminoacid sequence of the spike protein.
• a further object of the invention is a variant of any of the mutated SARS- CoV-2 spike protein, as described above.
• At least one of the aminoacids isoleucine or leucine at a position corresponding to aminoacid 818, 821 , 822, 841 , 844, 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (SEQ ID NO: 1 ) is replaced by alanine.
• said variant has the same aminoacids of the corresponding mutated SARS- COV-2 protein at positions corresponding to aminoacid 818, 821 , 822, 841 , 844, 861 , 864 and 865 of the wild type SARS-Cov-2 protein sequence (SEQ ID NO: 1).
• said variant has the same aminoacid sequences of the corresponding mutated SARS-CoV-2 spike protein or variant in the following positions:
• the variant presents the aminoacid replacements at positions corresponding to aminoacid 818, 821 , 822, 841 , 844, 861 , 864 and 865 of SEQ ID NO: 1 described above.
• variant of the mutated SARS-CoV-2 spike protein it is meant a protein having an aminoacid sequence which differs from the sequence of the mutated SARS-CoV-2 spike protein as described above, in that it contains one or more substitutions, deletions or insertions of aminoacids.
• Said substitutions, deletions or insertions of aminoacids may be in any position except a position corresponding to aminoacid 818, 821 , 822, 841 , 844, 861 , 864 and 865 of SEQ ID NO: 1 .
• said substitutions, deletions or insertions do not interfere with the conformation and the antigenic properties of the mutated SARS-CoV-2 spike protein according to the present invention.
• the variant has a sequence with an aminoacid identity with the corresponding mutated SARS-CoV-2 spike protein as described above of at least 80%, 85%, 90%, 95%, 98%, 99%.
• said variant has a sequence with aminoacid replacements that stabilize the protein in the prefusion conformation.
• the use as an antigen of the spike protein in this conformation induces the production of antibodies that are able to respond and inactivate the virus in the early stages of the infection and before this enters into the cells, thus significantly increasing vaccine efficacy.
• S-2P mutant SARS-2-S spike protein
• V987P the mutant SARS-2-S spike protein
• BNT162b Pfizer/BioNTech
• Moderna mRNA-1273
• alternative variants of SARS-CoV-2 spike protein with a stable prefusion conformation and a higher yield of expression compared to S-2P have also been described in the literature. These are characterized by the replacements A892P and A942P or F817P and A899P.
• the most promising variant as regards stability and expression described in the literature is the HexaPro variant that includes all 6 aminoacid replacements described above.
• At least two of the following aminoacids of said mutated SARS-CoV-2 spike protein are replaced by proline:
• a first variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 2, wherein the aminoacid lysine at position 986 of SEQ ID NO: 2 and the valine at position 987 of SEQ ID NO: 2 are replaced by proline (SEQ ID NO: 3).
• a second variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 2, wherein the alanines at positions 892 and 942 of SEQ ID NO: 2 are replaced by proline
• a third variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 2, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 2 and alanine at position 899 of SEQ ID NO: 2 and are replaced by proline (SEQ ID NO: 5).
• a fourth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 2, wherein the aminoacid lysine at position 986 of SEQ ID NO: 2, valine at position 987 of SEQ ID NO: 2 and alanine at positions 892 and 942 of SEQ ID NO: 2 are replaced by proline (SEQ ID NO: 6).
• a fifth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 2, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 2, alanine at positions 892, 899 and 942 of SEQ ID NO: 2, lysine at position 986 of SEQ ID NO: 2 and valine at position 987 of SEQ ID NO: 2 are replaced by proline (SEQ ID NO: 7).
• a sixth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 2, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 2, alanine at positions 892, 899 and 942 of SEQ ID NO: 2 are replaced by proline (SEQ ID NO: 8).
• a seventh variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 28, wherein the aminoacid lysine at position 986 of SEQ ID NO: 28 and the valine at position 987 of SEQ ID NO: 28 are replaced by proline (SEQ ID NO: 32).
• An eighth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 28, wherein the alanines at positions 892 and 942 of SEQ ID NO: 28 are replaced by proline (SEQ ID NO: 33).
• a ninth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 28, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 28 and alanine at position 899 of SEQ ID NO: 28 and are replaced by proline (SEQ ID NO: 34)
• a tenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 28, wherein the aminoacid lysine at position 986 of SEQ ID NO: 28, valine at position 987 of SEQ ID NO: 28 and alanine at positions 892 and 942 of SEQ ID NO: 28 are replaced by proline (SEQ ID NO: 35)
• An eleventh variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 28, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 28, alanine at positions 892, 899 and 942 of SEQ ID NO: 28, lysine at position 986 of SEQ ID NO: 28 and valine at position 987 of SEQ ID NO: 28 are replaced by proline (SEQ ID NO: 36)
• a twelfth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 28, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 28, alanine at positions 892, 899 and 942 of SEQ ID NO: 28 are replaced by proline (SEQ ID NO: 37)
• a thirteenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 29, wherein the aminoacid lysine at position 986 of SEQ ID NO: 29 and the valine at position 987 of SEQ ID NO: 29 are replaced by proline (SEQ ID NO: 38).
• a fourteenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 29, wherein the alanines at positions 892 and 942 of SEQ ID NO: 29 are replaced by proline (SEQ ID NO: 39).
• a fifteenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 29, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 29 and alanine at position 899 of SEQ ID NO: 29 and are replaced by proline (SEQ ID NO: 40)
• a sixteenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 29, wherein the aminoacid lysine at position 986 of SEQ ID NO: 29, valine at position 987 of SEQ ID NO: 29 and alanine at positions 892 and 942 of SEQ ID NO: 29 are replaced by proline (SEQ ID NO: 41 ).
• a seventeenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 29, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 29, alanine at positions 892, 899 and 942 of SEQ ID NO: 29, lysine at position 986 of SEQ ID NO: 29 and valine at position 987 of SEQ ID NO: 29 are replaced by proline (SEQ ID NO: 42)
• An eighteenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 29, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 29, alanine at positions 892, 899 and 942 of SEQ ID NO: 29 are replaced by proline (SEQ ID NO: 43)
• a nineteenth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 30, wherein the aminoacid lysine at position 986 of SEQ ID NO: 30 and the valine at position 987 of SEQ ID NO: 30 are replaced by proline (SEQ ID NO: 44).
• a twentieth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 30, wherein the alanines at positions 892 and 942 of SEQ ID NO: 30 are replaced by proline (SEQ ID NO: 45).
• a twenty-first variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 30, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 30 and alanine at position 899 of SEQ ID NO: 30 are replaced by proline (SEQ ID NO: 46)
• a twenty-second variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 30, wherein the aminoacid lysine at position 986 of SEQ ID NO: 30, valine at position 987 of SEQ ID NO: 30 and alanine at positions 892 and 942 of SEQ ID NO: 30 are replaced by proline (SEQ ID NO: 47).
• a twenty-third variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 30, wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 30, alanine at positions 892, 899 and 942 of SEQ ID NO: 30, lysine at position 986 of SEQ ID NO: 30 and valine at position 987 of SEQ ID NO: 30 are replaced by proline (SEQ ID NO: 48)
• a twenty-fourth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO:
• a twenty-fifth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 31 , wherein the aminoacid lysine at position 986 of SEQ ID NO: 31 and the valine at position 987 of SEQ ID NO: 31 are replaced by proline (SEQ ID NO: 50).
• a twenty-sixth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 31 , wherein the alanines at positions 892 and 942 of SEQ ID NO: 31 are replaced by proline (SEQ ID NO: 51).
• a twenty-seventh variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO:
• a twenty-eigth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 31 , wherein the aminoacid lysine at position 986 of SEQ ID NO: 31 , valine at position 987 of SEQ ID NO: 31 and alanine at positions 892 and 942 of SEQ ID NO: 31 are replaced by proline (SEQ ID NO: 53).
• a twenty-ninth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 31 , wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 31 , alanine at positions 892, 899 and 942 of SEQ ID NO: 31 , lysine at position 986 of SEQ ID NO: 31 and valine at position 987 of SEQ ID NO: 31 are replaced by proline (SEQ ID NO: 54)
• a thirtieth variant is a variant of the mutated SARS-CoV-2 protein of SEQ ID NO: 31 , wherein the aminoacids phenylalanine at position 817 of SEQ ID NO: 31 , alanine at positions 892, 899 and 942 of SEQ ID NO: 31 are replaced by proline (SEQ ID NO: 55).
• proline SEQ ID NO: 55.
• the vaccine candidate NVX-CoV2373 contains as active ingredient a variant of the SARS-CoV-2 spike protein having the aminoacid replacements R682Q, R683Q, R685Q that does not interfere with antigenic properties of the protein and confers a significantly increased protease resistance.
• a further aminoacid replacement that prevents cleavage of the protein by the protease furine is the aminoacid replacement R685A.
• the aminoacids arginine at a position corresponding to aminoacid 682, 683 and 685 of SEQ ID NO: 1 is replaced by glutamine.
• Particularly preferred variants according to this embodiment are any of the variants as descrived above, further containing the replacement of the aminoacids arginine at a position corresponding to aminoacid 682, 683 and 685 of SEQ ID NO: 1 with glutamine.
• Particularly preferred variants of the mutated SARS-CoV-2 protein according to this embodiment are those having the aminoacid sequence of SEQ. ID. NO: 9 to SEQ. ID. NO: 15 (variants 31 to 37).
• the aminoacid arginine at a position corresponding to aminoacid 685 of SEQ ID NO: 1 is replaced by alanine.
• variants according to this embodiment are any of the variants as descrived above, further containing the replacement of the aminoacids arginine at a position corresponding to aminoacid 685 of SEQ ID NO: 1 with alanine.
• vaccines are under development based on SARS-COV-2 spike proteins sequences which incorporate such modifications.
• the variants of the mutated SARS-CoV-2 spike protein according to the invention comprise the aminoacid modifications found in the spike protein of Delta (B.1.617.2): and Omicron (BA.1) virus variant.
• the variant of the mutated SARS-CoV-2 spike protein contains the following amminoacid modification at positions corresponding to the aminoacids of SEQ ID NQ.1 listed below: - T19R, EF156/157del, R158G, L452R, T478K, D614G, P681 R and D950N, or
• variants according to this embodiment are any of the variants as described above, further containing the following amminoacid modification at positions corresponding to the aminoacids of SEQ ID N0.1 listed below:
• COVID-19 vaccine candidates are based on immunogenic fragments of the SARS-CoV-2 spike protein or mRNA or DNA encoding for them (Forni et al, Cell Death & Differentiation 2021 , 28: 626-639).
• the LxxLL motifs identified by the inventors in the wild type spike protein have the ability to activate nuclear receptors.
• a further object of the present invention is an immunogenic fragment of the mutated SARS-CoV-2 spike protein or of a variant thereof as described above, said fragment comprising at least one sequence of said mutated SARS-CoV-2 spike protein or variant selected from:
• a further object of the present invention is an immunogenic fragment of the mutated SARS-CoV-2 spike protein or of a variant thereof as described above, said fragment comprising at least one sequence of said mutated SARS-CoV-2 spike protein or variant selected from:
• a further object of the present invention is an immunogenic fragment of the mutated SARS-CoV-2 spike protein or a variant thereof as described above, said fragment comprising a sequence corresponding to the aminoacid sequences from aminoacid 818 to aminoacid 865 of SEQ ID NO: 2, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30 or SEQ ID NO: 31.
• a “fragment” of the mutated SARS-CoV-2 spike protein or a variant thereof according to the present invention refers to proteins having an aminoacid sequence which correspond to an N-terminally and/or C-terminally truncated sequence of a mutated SARS-CoV-2 spike protein or variant thereof according to the invention.
• the immunogenic fragments according to the invention contain epitopes able to trigger protective immune responses in the host.
• Epitopes of wild type SARS-CoV-2 spike protein that have a reduced risk of triggering autoimmune response and stimulate the production of protective antibodies have been identified, corresponding to sequences 232-246, 233-247, 471-503, 604-625, 817-833, 891 -907, 897-913, 1164-1191 , 1182-1209 of SEQ ID NO: 1 .
• the peptide 597-603 induces antibodies that enhance infection through an epitope sequence-dependent.
• the immunogenic fragments according to the invention further contain at least two, non-overlapping sequences selected from the following aminoacid sequences:
• the immunogenic fragment according to the invention comprises the aminoacid sequence from position 865 to position 1209 of SEQ ID NO: 2, SEQ ID NO: 29, SEQ ID NO: 30 or SEQ ID NO: 31 .
• the immunogenic fragment according to the invention comprises the aminoacid sequence from position 471 to position 817 of SEQ ID NO: 1 .
• the immunogenic fragment according to the invention comprises the aminoacid sequence from position 232 to position 470 of SEQ ID NO: 1 .
• the variants or fragments of the invention do not contain the aminoacid sequence from position 597 to position 603 of SEQ ID NO: 1 .
• a further object of the present invention are proteins comprising the aminoacid sequence of a mutated SARS-CoV-2 spike protein, variant or fragment thereof according to the present invention and one or more additional sequences.
• said additional sequences are not immunogenic and are used to confer the protein or fragment specific functional properties, for example as regards tissue distribution. According to another preferred embodiment, said additional sequences are able to stimulate the immune response towards epitopes of the mutated SARS-CoV-2 spike protein, variant or fragment thereof.
• a further object of the present invention is an mRNA encoding for the above described mutated SARS- CoV-2 spike protein, variant, peptide or protein.
• said mRNA is a nucleoside modified mRNA sequence.
• uridine residues are replaced with a modified nucleoside selected from pyridin-4-one ribonucleoside, 5-aza-uridine, 2-thio-5-azauridine,2-thiouridine, 4-thio-pseudouridine, 2- thio-pseudouridine, 5-hydroxyuridine, 3-methyluridine, 5- carboxymethyl-uridine, 1- carboxymethyl-pseudouridine, 5-propynyl-uridine, 1-propynyl-pseudouridine, 5- taurinomethyluridine, 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine, 1- taurinomethyl-4-thiouridine, 5-methyl-uridine, 1 -methyl-pseudouridine, 4-thio-1 -methyl- pseudouridine, 2-thio-1-methylpseudouridine, 1 -methyl-1 -
• the coding region of the mRNA according to the invention contain an increased G/C compared to the G/C content present in the corresponding coding region for the wild type SARS-CoV-2 spike protein. This is obtained by introducing into the sequence synonymous codon substitutions that allows an increase of G/C ratio.
• codon usage has been optimized for expression in human cells.
• a further object of the present invention is a DNA sequence encoding for the mutated SARS- CoV-2 spike protein, a variant or a peptide thereof as described above.
• said DNA is contained in a plasmid.
• said plasmid contains at least a promoter and a stop codon.
• said DNA is contained in a viral vector.
• Said viral vector may be non-replicating or replicating.
• Said viral vector is preferably selected from adeno or pox viruses. More preferably, said viral vector is selected from an adenovirus type 5 (Ad5) vector, adenovirus type 26 (Ad26) vector, replication-deficient simian adenovirus ChAdOxl vector.
• proteins, mRNA or DNA according to the present invention can be prepared by methods well known in the art.
• a further object of the present invention is a mutated SARS-CoV-2 spike protein, a variant or peptide thereof or an mRNA or DNA encoding them, as above described, for use in the prevention of COVID-19 in a subject.
• a further object of the present invention is a vaccine composition containing a mutated SARS-CoV-2 spike protein, a variant or fragment thereof or an mRNA or DNA encoding them, as above defined.
• the vaccine composition is preferably for use in prevention of COVID-19.
• the vaccine can be formulated in accordance with well-known techniques for the preparation of protein or nucleic acids-based vaccines, as for example described in Batty et al, AdvDrug Delivery Rev 2021 , 169: 168-189.
• said vaccine contains an adjuvant agent.
• an “adjuvant” according to the invention is a component that is able to enhance the immunostimulatory properties of the composition.
• Said adjuvant is selected from adjuvants well known to the skilled person and suitable for the specific antigen and formulation used.
• the vaccine according to the invention can be administered by parenteral administration, preferably intradermal, intramuscular or subcutaneous administration, oral administration or nasal administration.
• Spike 3D model was built based on PDB 6VYB returned to its wild-type form and fully glycosylated.
• An asymmetric glycosylation of the three protomers was derived by glycoanalyitic data for the N-glycans and O-glycans as published (Casalini L et al, ACS Cent. Sci. 2020, 6:1722-1734, https://doi.orq/10.1021/acscentsci.0c01056).
• the proteins were modeled using Amber14SB force field (Maier J A et al, J. Chem. Theory Comput.
• Topology files were generated with the pdb2gmx GROMACS tool, using the amber99sb forcefield (Lindorff-Larsen K et al, Proteins 2010,78:1950-1958, https://dx.doi.org/10.1002/prot.22711). Protein was inserted in a triclinic box, extending up to 15 A from the solute, and immersed in TIP3P water molecules (Jorgensen WL et al, J Chem Phys 1983, 79:926-935, https://dx.doi.Org/10.1063/1 .445869 ). Counter ions were added to neutralize the overall charge with the genion GROMACS tool.
• the XRAY PDB model with code 30LL was used, containing Estradiol and Nuclear receptor coactivator 1 (Mocklinghoff S et al, ChemBioChem 2010, 11 :2251 -2254, https://doi.Org/10.1002/cbic.201000532).
• the Spike protein and ER were used as receptor and ligand, respectively.
• the HDOCK tool performs docking to sample putative binding modes through an FFT-based search method, and then scoring the protein-protein interactions. Finally, the top 100 predicted complex structures were provided, and the best ten hypotheses were visually inspected to confirm the reliability of the calculation. The entire workflow is described (Yan Y et al, Nat Protoc 2020, 15:1829-1852, https://doi.org/10.1038/s41596-020-0312-x).
• the first check involved the identification of proteins known to interact with estrogen receptors. After identifying these ER interacting proteins, the second step involved the study of any sequence analogies between the spike protein and the ER effector proteins.
• LxxLL LxxLL
• Spike protein-ER motif-oriented docking The structural information that ER residues are recognized by NCOAs was used to guide the docking study of ER on spike by optimizing protein-protein interactions. With the protein structures and residue restraints as input, a suitable model was generated by the HDOCK server. Given that the structural information of interaction between ER and NCOA are known, a second docking study was carried out, that considered the ER residues that guarantee interaction with the NCOAs, thus guiding the molecular docking procedure. The best binding hypothesis obtained from the guided docking study is shown in Figure 5 that highlights the binding of the ER to the spike region containing the motifs homologous to the LxxLL pattern.
• Peptide 2 SKRSFIEDLLFNKVTL (SEQ ID NO: 16)
• Peptide 5 IKQYGDCLGDIAARDLI (SEQ ID NO: 17)
• Each of the peptides contains one of the LxxLL motifs found in the wild type spike protein.
• the peptides were synthesized by CASLO ApS (Technical University of Denmark, DTU- Science Park Vaccinvej 381 , DK-2800 Kongens Lyngby, Denmark), by using a Fmoc- based solid-phase peptide synthesis protocol. Each peptide was acetylated at N-terminus and amidated at C-terminus; they were stored as lyophilized hydrochloride salts.
• the purity of the peptides was assessed by analytical RP-HPLC (C18-250 mm c 4.6 mm I.D., flow rate of 1 mL/min; absorbance detected at 220 nm) and verified also by MALDI-TOF mass spectrometry.
• Spike protein was used at the final concentration of 10 ng/ml in medium.
• Raloxifene was used at 2 mM final concentration in medium.
• Estradiol stock solution was prepared in ethanol and used at the final concentration of 1 nM diluted in medium.
• Peptides were diluted in PBS at 4mg/ml concentration and then 10ug/ml was the concentration used for the assay (final concentration in medium).
• BrdU assay was performed (Abeam, UK). BrdU is incorporated into newly synthesized DNA of actively proliferating cells. 20 pl_ of the diluted 1X BrdU label were added to the appropriate wells and incubated 24 hours. BrdU was incorporated into the DNA of dividing cells. To enable antibody binding to the incorporated BrdU cells must be fixed, permeabilized, and the DNA denatured. This is all done in one step by treatment with Fixing Solution. Detector anti-BrdU monoclonal antibody is pipetted into the wells and allowed to incubate for one hour, during which time it binds to any incorporated BrdU.
• MCF-7 cell line is an invasive ductal/breast carcinoma cell hormone-dependent (both estrogen and progesterone receptor-positive).
• MCF-7 was obtained from ATCC and grown in DMEM (Dulbecco's Modified Eagle Medium), supplemented with 10% fetal bovine serum (FBS, Corning, USA), penicillin/streptomycin and glutamine (Sigma, USA) at 37 °C in a 5% C02 and 95% humidified incubator (Thermo, USA). Before treatments, to reduce estrogen levels in FBS the cells were cultured for 24h in phenol red-free medium containing 5% dextran-coated charcoal treated serum, followed by incubation in phenol-red free, serum-free medium, supplemented with 0.2% BSA for at least 24h.
• DMEM Dulbecco's Modified Eagle Medium
• FBS fetal bovine serum
• penicillin/streptomycin and glutamine Sigma, USA
• cells were treated with estradiol, wild type spike protein, raloxifene, estradiol and raloxifene, wild type spike protein and raloxifene, estradiol, spike protein and raloxifene for 24 hours and proliferation was measured.
• the peptides are all able to induce proliferation similar to that induced by spike.
• the data obtained demonstrated that each of the LxxL motifs in wild type spike protein are able to induce activation of the estrogen receptor.
• Established androgen-dependent cell line LNCap was used as a model for this study.
• Cells were cultured in DMEM, supplemented with 10% fetal bovine serum (FBS, Corning, USA), penicillin/streptomycin and glutamine (Sigma, USA) at 37 ⁇ in a 5% C02 and 95% humidified incubator (Thermo, USA).
• FBS fetal bovine serum
• glutamine Sigma, USA
• the cells were cultured for 24h in phenol red-free medium containing 5% dextran-coated charcoal treated serum, followed by incubation in phenol-red free, serum-free medium, supplemented with 0.2% BSA for at least 24h. Then cells were treated with peptides 2, 5 and 7 or wild type spike for 24h and proliferation was measured.
• THP-1 Human monocytes THP-1 were purchased from ATCC and cultured following manufacturer’s instructions. Then, THP-1 were differentiated using 20 ng/ml phorbol 12- myristate 13-acetate (PMA) for 72 hours, followed by LPS stimulation (100 ng/ml) for 24 hours and treated with estradiol, raloxifene and wild type spike, wild type spike + raloxifene, estradiol + wild type spike, estradiol + raloxifene + wild type spike, at the concentrations used in Example 2, for 24h. The media were then collected and the proteome profile assay was carried out.
• PMA phorbol 12- myristate 13-acetate
• conditioned media from THP-1 treated cells were centrifuged to remove particulates and assayed immediately. The sample amount was adjusted as suggested (500 pi).
• the reagents were prepared following manufacturer’s protocols (R&D, USA). Briefly, the membranes were incubated with Array Buffer 6 for 1 hour on a rocking platform shaker. The samples were prepared by adding 1 ml of Array Buffer 4 in two separated tubes and then 15 mI of reconstituted mouse cytokine detection antibody cocktail (> 40 mouse cytokines) to each prepared sample and incubated 1 hour. Then, the Array Buffer 6 was aspirated and replaced with the sample/antibody mixtures and incubated at 4 ° C overnight.
• IL-8 appears the most abundant, being up-regulated by both estradiol and wild type spike.
• Raloxifene was effective in counteracting the effect of spike.
• the non-enzymatic chitinase-3 like-protein-1 (CHI3L1) is up-regulated by both estradiol and wild type spike but raloxifene was able to counteract only the effects of spike alone.
• Osteopontin was upregulated by both estradiol and wild type spike and raloxifene was able to counteract the effects of spike alone
• the nucelotide sequences encoding for aminoacids from 16 to 1213 of the wild type spike protein (extracellular domain) and for the corresponsing SP5, SP7 and SP5 + SP7 mutants described below were generated and inserted into a plasmid DNA vector having the Human cytomegalovirus (CMV) immediate early enhancer and promoter, the murine Ig kappa chain leader sequence for protein secretion, the bovine growth hormone polyadenylation (bGH-PolyA) signal, a specialized termination sequence for protein expression in eukaryotic cells and the kanamycin resistance gene from Staphylococcus aureus for plasmid amplification in bacteria.
• CMV Human cytomegalovirus
• bGH-PolyA bovine growth hormone polyadenylation
• SP5 + SP7 mutations L841A, I844A, L861A, L864A, L865A with reference to SEQ. ID NO: 1 , each also containing the stabilising aminoacid replacements R685A, K986P and V987P, with reference to SEQ. ID NO: 1
• the spike protein and SP5, SP7 and SP5 + SP7 were produced by transient transfection of Expi293F high-density cells with the ExpiFectamine 293 (Thermo Fisher) lipid cationic transfection reagent according to the manufacturer's instructions.
• the supernatant containing the proteins was collected after 5 days of incubation from start of transfection and subjected to clarification by centrifugation and filtration for the subsequent purification steps.
• the proteins were batch purified using IMAC (Immobilized Metal Chelate Affinity Chromatography) using PureCube Ni-NTA Agarose resin slurry (Cube-Biotech).
• the resin slurry was centrifuged and incubated with equilibration buffer (50mM NaH2P04, 500mM NaCI, pH 7.4, 10mM imidazole).
• equilibration buffer 50mM NaH2P04, 500mM NaCI, pH 7.4, 10mM imidazole.
• the equilibrated resin was combined with the culture supernatant containing the recombinant proteins and incubated o/n, 4°C, on a rotating platform.
• the resin was subsequently collected by centrifugation, washed, and the protein was eluted by an elution buffer containing 300 mM Imidazole and subjected to dialysis in phosphate buffer (PBS) using slide-A-lyzers (Thermo Fisher) as indicated in the product datasheet.
• PBS phosphate buffer
• the proteins were quantified on a spectrophotometer measuring the absorbance at 280 nm. The purity of the proteins was assessed by SDS-PAGE and Western Blot analysis, conducted under both reduced and non-reducing conditions. Further characterization of their binding capacity to the hACE2 receptor and the related affinity was evaluated by BioLayer interferometry BLI as described in example 4a. hACE-2 receptor bindinq assav Binding studies were performed in order to verify the ability of produced spike proteins (wt and SP5, SP7 and SP5+SP7) to bind the hACE2 receptor by using the Octet Red (Forte Bio) system.
• the biosensors were immersed for 10 minutes in 1x buffer followed by a measurement of the basal signal for 60s, at this point the hACE2-hFc was loaded for 300s (until the biosensor was completely saturated).
• the biosensor tips conjugated with hACE2-hFc were immersed for 300s in wells containing different concentrations of antigen (spike wt protein and its mutants SP5, SP7 and SP5+SP7) to evaluate the association curves, followed by 900s of dissociation time in kinetic buffer.
• the binding curve data was collected and then analyzed using the data analysis software v11 .1 (FORTEBIO). The binding sensorgrams were aligned at the start of the antigen binding cycle and after the single reference subtraction. Kd values were calculated using a 1 :1 global Langmuir binding model.
• biosensor tips with the various antigens were also immersed in wells containing kinetic buffer to allow for single reference subtractions to compensate for the natural dissociations of the captured antigens.
• the tips of the biosensor were used without regeneration.
• TRIP Tartrate Resistant Acid Phosphatase
• RAW264.7 (murine macrophages ATCC, USA) were cultured as manufacturer’s protocol. Then 1.5x 10 5 cells/cm 2 in 24-well dishes were seeded and mouse receptor activator of nuclear factor kb ligand (RANKL, Miltenyi Biotec, Germany) was added at the final concentration of 35 ng/ml to initiate osteoclasts (OC) development (day 0) as previously described ( Collin-Osdoby and Osdoby 2012, PMID: 22130930). At day 3, cells were examined under the microscope and refed with fresh medium containing RANKL. At day 6, RAW-OC population was prevalent and ready for treatments and then biochemical studies.
• RANKL nuclear factor kb ligand
• Cells were treated with 1 nM Estradiol or with 10 ng/ml spike wt, SP5, SP7 or SP5+SP7 for 24h. After 24 h of treatment, cells were quickly collected by sterile tubes and resuspended using PBS (pH 7.4), to dilute cell suspension to the concentration of approximately 1 million/ml. Then, cells were subjected to repeated freeze-thaw cycles to let out the inside components. In the meantime, the reagents of the kit were brought to room temperature. The standard curve, reagents and samples were prepared following manufacturer’s protocol. Briefly, 50 pi of standard were added to “standard wells” and 40 mI of sample to “sample wells”.

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