WO2023043868A2 - Coronavirus vaccine, yeast strains, methods of detection, methods of treatment and uses thereof - Google Patents
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Classifications
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- C—CHEMISTRY; METALLURGY
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- 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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- A61P31/12—Antivirals
- A61P31/14—Antivirals for RNA viruses
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- 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
- C12N15/80—Vectors or expression systems specially adapted for eukaryotic hosts for fungi
- C12N15/81—Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts
- C12N15/815—Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts for yeasts other than Saccharomyces
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- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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- A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
- A61K2039/55505—Inorganic adjuvants
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- A—HUMAN NECESSITIES
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- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
- A61K2039/55511—Organic adjuvants
- A61K2039/55561—CpG containing adjuvants; Oligonucleotide containing adjuvants
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2740/00—Reverse transcribing RNA viruses
- C12N2740/00011—Details
- C12N2740/10011—Retroviridae
- C12N2740/16011—Human Immunodeficiency Virus, HIV
- C12N2740/16041—Use of virus, viral particle or viral elements as a vector
- C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- 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
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- 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 refers to a coronavirus vaccine, yeast strains, methods of detection and treatment and uses thereof. More specifically it refers to a coronavirus vaccine comprising the deglycosylated RBD domain of the coronavirus spike protein and one or more adjuvants, wherein the RBD domain is produced in the yeast Pichia pastoris (now classified as Komagataella phaffii).
- the amino acid sequence of the RBD domain may have the sequence set forth in SEQ ID NO.1 or SEQ ID NO.2.
- the vaccine may further comprise one or more adjuvants.
- Patent document US 2011/0230640 A1 describes methods for preparing a deglycosylated peptide by replacing an amino acid at the N-glycosylation site to generate a specific antibody for the deglycosylated form.
- Spike protein S from another virus (SARS-CoV) as well as polypeptides and peptide fragments of the S protein and conservative variants thereof are known. Use of the deglycosylated RBD domain in diagnostics is not contemplated.
- a coronavirus vaccine comprising the coronavirus spike protein deglycosylated RBD domain and one or more adjuvants is provided, wherein the RBD domain is produced in P. pastoris.
- the amino acid sequence of the RBD domain is shown in SEQ ID NO.1, but it may be any sequence having 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, or 85% sequence identity as compared to SEQ ID NO.1.
- the amino acid sequence of the RBD domain is shown in SEQ ID NO.2, but it may be any sequence having 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, or 85% sequence identity as compared to SEQ ID NO.2.
- the RBD domain may have an amino acid sequence corresponding to any of the coronavirus variants.
- the coronavirus is SARS- CoV-2.
- the vaccine may further comprise an adjuvant, for example CpG-ODN, aluminum hydroxide, alhydrogel, aluminum phosphate, calcium phosphate, STING agonists, TLR agonists, Poly(I:C), cholera toxin, heat labile enterotoxin, Saponins (QS-21), particulate adjuvants such as nanoparticles or VLP (virus-like particles), virosomes, AS04, ISCOMS, PLG, emulsions such as MF59, AS02, Montanide ISA-51, and ISA-720, MPL, AGP, DC_Chol, OM-174, endogenous human immunomodulators such as hGM-CSF, hIL-12 and Immudaptin, inert carriers such as gold particles, among others, or combinations thereof.
- an adjuvant for example CpG-ODN, aluminum hydroxide, alhydrogel, aluminum phosphate, calcium phosphate, STING agonists, TLR agonists,
- the vaccine comprises from 5 ⁇ g to 200 ⁇ g of deglycosylated RBD of the coronavirus spike protein per dose, from 10 ⁇ g to 100 ⁇ g/dose of CpG-ODN and from 10% v/v to 50% v/v / dose of aluminum hydroxide.
- a stably transformed yeast strain expressing a protein comprising the RBD domain amino acid sequence of the SARS-CoV-2 spike protein bound to a Sortase A recognition amino acid sequence linked to a His6 tag is provided.
- the yeast is P. pastoris.
- a method for detecting anti coronavirus antibodies comprising at least the following steps: a) contacting the deglycosylated RBD domain of the coronavirus spike protein with an amount of a biological sample, wherein the RBD domain is produced in P. pastoris; and b) incubation and development.
- the coronavirus may be SARS-CoV-2 or another coronavirus, for example Severe acute respiratory syndrome-associated coronavirus (SARS- CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV) or others belonging to the coronaviridae family.
- the biological sample used in the method may be any biological sample, for example serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood, cerebrospinal fluid, pericardial fluid, lymph, pus, wherein the method may be any method, for example, direct or indirect ELISA, lateral flow over proteins immobilized on a support, dot blot (point hybridization), radioimmunoassay.
- biological sample for example serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood, cerebrospinal fluid, pericardial
- the method comprises the following steps: a) contacting the deglycosylated RBD domain of the SARS-CoV-2 spike protein with a solid support and incubation; b) adding an amount of a biological sample, for example, serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood, cerebrospinal fluid, pericardial fluid, lymph, pus, and incubation; and c) adding a labelled antibody and developing.
- a biological sample for example, serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood
- an immunization method comprising administering to an animal an amount of a coronavirus vaccine comprising the deglycosylated RBD domain of the coronavirus spike protein and one or more adjuvants, wherein the RBD domain is produced in P. pastoris.
- the animal may be a mammal or a bird.
- the deglycosylated RBD domain of the SARS-CoV-2 spike protein for preparing a vaccine and/or for obtaining anti coronavirus antibodies, and/or for manufacturing a method for detecting anti coronavirus antibodies in a biological sample, wherein the SARS-CoV-2 spike protein RBD domain has been produced in P. pastoris and has then been deglycosylated.
- Figure 1 shows: A: Amino acid sequence of the mature protein containing sequences of the RBD domain (black) followed by a splice-site for sortase A (bold) and a 6 Histidine tag (underlined).
- B Scheme of an expression vector for producing RBD in Pichia pastoris. The expression vector is integrated into the Pichia pastoris genome.
- AOX1 alcohol oxidase promoter
- RBD-Sortase A RBD sequence followed by a Sortase A splice-site (grey). His6x indicates the sequence of 6 histidines for purification and recognition.
- Figure 2 shows a scheme for obtaining a yRBD producing strain.
- Vector pPICZ ⁇ A described in Figure 1 was digested with the enzyme SacI and used for transforming electrocompetent Pichia pastoris yeast strains X-33 or Y-7556 or Y- 1603. Clones with the highest zeocine resistance were isolated and verified by PCR (- negative control without DNA, + positive control with a plasmid used for integration in yeast; alpha, empty vector, 1, 7, 10, 20, 32, 36: tested colonies for integration of the plasmid in the genome). Clone 7 was induced and the yRBD protein was purified in a Ni-NTA affinity column. Elution profile with 300 mM imidazole is shown. Figure 3 shows the steps for obtaining yRBD in a bioreactor.
- Figure 4 shows the characterization of yRBD and a conformational comparison with RBD produced in HEK-293T mammalian cells.
- NTD N-terminal domain
- RBD Receptor binding domain
- S1/S2 furin cleavage site
- CH central helix
- CD Connector domain
- TM Transmembrane domain
- B Glycosylation analysis of RBD with endoglycanases. Purified RBD (3 ⁇ g) from mammalian or yeast cells was denatured for 10 min at 100°C and digested with PNGase F (500 mU) or EndoH (5 mU) for 2 hs at 37°C.
- FIG. 7 shows deglycosylation kinetics of yRBD with EndoH purified from P. pastoris.
- Five ⁇ g of pure yRBD protein were treated with EndoH at a RBD:EndoH molar ratio of 3000:1 for the indicated times (in hs).
- the resulting protein was resolved in 12% SDS-PAGE and stained with Coomassie blue, identifying protein isoforms with glycans (Gly) and after the treatment of glycans removal (Non-Gly).
- Figure 8 shows the characterization of yRBD (glycosylated) and yRBD- C101 (deglycosylated) proteins by HPLC.
- An analytical C18 reverse-phase HPLC chromatogram was performed. It was carried out in an ACN gradient and with a mobile phase of 0.05% TFA. The gradient was from 0 to 100% over 40 min (10- 50 min of the run). The integration of the main peak was 95.7%. The peaks visualized at retention times of less than 5 min were buffer components and salts. In the chromatogram, the mobile phase injection profile has been substracted. Twenty one 21 micrograms of protein were seeded.
- Figure 9 shows the results of mass spectrometry for glycosylated and deglycosylated yRBD (yRBD-C101).
- Figure 10 shows circular dichroism spectra in far UV (A) and near UV (B). The concentrations required for near UV were restricted to yRBD (dotted black line) and yRBD-C101 (solid black line), as proteins are needed at high concentrations.
- Figure 11 shows the aggregation state of glycosylated yRBD and deglycosylated yRBD (yRBD-C101).
- A UV absorption spectra. Absence of a significant slope between 340 and 310 nm is indicative of the presence of light scattering and thus of aggregation or presence of particulate matter.
- C Cellular response of splenocytes from mice immunized with yRBD or with yRBD-C100.
- Figure 14 shows the reaction of Sortase A for removing the His6-tag from yRBD-C101.
- the yRBD-C101 protein was treated (S+) or not treated (S-) with Sortase A at a 10:1 molar ratio for 16 hs at 25°C.
- Each sample was passed through a Ni-NTA column. T: total before seeding in the column, F: not retained by the column; E: eluted with 300 mM Imidazole.
- T total before seeding in the column
- F not retained by the column
- E eluted with 300 mM Imidazole.
- Also shown are elution positions of yRBD-C101 (RBD) and Sortase A (sortase).
- the terms “RBD domain” and “RBD protein” have the same meaning and are used interchangeably.
- the term “yRBD” corresponds to the RBD domain produced in P. pastoris.
- the terms yRBD-C101 and yRBD-C100 are equivalent and correspond to the deglycosylated form of yRBD.
- the present invention describes obtaining the SARS-CoV-2 RBD domain in a heterologous eukaryotic system different from mammals, which is less expensive, better scalable for mass production and GRAS (Generally Recognized as Safe), such as for example in an expression system in Pichia pastoris.
- This invention offers all the advantages of expressing RBD in a heterologous system such as one from yeasts, readily scalable to industrial levels, and very economic, but without the disadvantages of a specific glycosylation different from the one produced in a mammalian system because glycans are completely removed, maintaining the protein in its native conformation.
- the invention solves a long felt need, as it allows for obtaining an equally effective antigen as the one produced in mammalian cells, or other systems, but being produced in a much more affordable system. It also overcomes a prior technical prejudice: “a protein produced in a system different from that of mammals cannot be used as the glycans will be different.”
- the amino acid sequence of the yRBD domain SEQ ID No.
- Pichia pastoris culture was transformed with the vector and integration into the genome was verified by PCR.
- Four clones were selected to induce expression (Figure 2).
- the protein thus obtained was named yRBD.
- Yeasts (Pichia pastoris) transformed with the expression vector were grown in a bioreactor.
- Figure 3 shows the results of growth in a bioreactor. Increase of biomass throughout the process is shown on the left and the 4 steps are identified (numbered sections). On the right, the increase of the yRBD- specific band in the culture supernatant by SDS-PAGE stained with Coomassie blue is shown.
- Figure 4 shows a theoretical UV spectrum and yRBD spectrum compared to the RBD spectrum produced in HEK-293T mammalian cells. A comparative circular dichroism spectrum is also shown.
- the HPLC analysis of Figure 4 shows purity of production in both systems (HEK-293T mammalian cells and Pichia pastoris). Further shown are tryptophan fluorescence spectra of yRBD and RBD produced in HEK-293T indicating the existence of similarity of hydrophobicity of the tryptophan environment of the RBD protein grown in both systems.
- the protein produced in Pichia pastoris is structurally similar to the one produced in mammalian cells.
- the HPLC spectrum shows a wider peak due to size dispersion of the glycans, especially in yRBD, a fact that is also observed when using the SDS-PAGE technique.
- the molecular mass observed by SDS-PAGE (about 26 kDa) for both deglycosylated RBD proteins corresponds to that which may be obtained from the RBD amino acid sequence (residues 319 to 537 of the spike protein).
- the yRBD protein produced in yeasts shows high isoform heterogeneity.
- the yRBD proteins were treated under conditions that would allow to maintain their native conformational structure (as opposed to the previous technology as shown in Figure 5).
- homogeneity of the deglycosylated protein is significantly greater than that of yRBD (insert in Figure 8 and Figure 9A), wherein it may be observed that the peaks are wider and that there is a wide distribution of species with two significant means, one at 31403 Da and the other at 42169 Da.
- the secondary and tertiary structure of the yRBD protein was analyzed.
- the yRBD protein purified and obtained under native conditions was deglycosylated with endoH and its conformational similarity was evaluated with respect to other produced yRBD variants.
- Circular dichroism (CD) spectra in the far UV are indicative of the secondary structure content (chirality around the peptide bond), while in the near UV the spectra are indicative of the chiral environment of aromatic residues, and thus a fingerprint of the tertiary structure of the protein).
- Circular dichroism spectra of yRBD and yRBD-C101 were obtained ( Figure 10). After deglycosylating yRBD, the spectra were completely overlapping.
- the deglycosylated protein (yRBD-C101) prepared as described herein has circular dichroism spectral features in the far UV (190-240 nm) which are similar to those of yRBD ( Figure 10A), thus indicating that the secondary structure patterns of the protein are similar.
- the deglycosylated protein shows circular dichroism spectral features in the near-UV (240-340 nm) which are similar to those of yRBD ( Figure 10B), identified as a consequence of the asymmetric or chiral packing of aromatic residue side chains that absorb circularly polarized dextrorotatory and levorotatory light in a different manner, and ultimately are well associated with the tertiary structure of the antigen. That is, the tertiary structure of both proteins, yRBD and deglycosylated yRBD (yRBD-C101), is similar. In the near region, deglycosylation does not produce any modification of the characteristic signals of the protein.
- the yRBD and yRBD-C101 proteins were immobilized in multiwell plates and used for detecting anti SARS-CoV-2 antibodies in sera from patients that had been classified as patients with symptoms of disease (positive) and a serum bank obtained before the COVID-19 pandemic (negative).
- the results shown in Figure 12 clearly show how the yRBD- C101 protein is more efficient and precise for identifying negative and positive sera, since although the latter have a variable response depending on the degree of immunization of each patient, the cut-off line of negatives is clearly lower, strongly indicating that the yRBD-C101 protein does not produce false positives.
- yRBD and yRBD-C100 or C101 produce a humoral immune response, but is significantly higher (10-fold) when the deglycosylated variants, yRBD-C100 or C101, are used.
- the antibodies generated by the deglycosylated protein have a greater neutralizing power and generate a better cellular response. Therefore it is considered that yRBD-C101, or any deglycosylated variant, is an excellent candidate for preparing a vaccine.
- deglycosylated yRBD (yRBD-C101) is suitable for use in serological diagnostic assays, given that it allows for distinguishing positive patients from negative patients.
- Example 1 Method to obtain a SARS-CoV-2 RBD-producing Pichia pastoris strain and to purify yRBD. Design of sequences: The DNA sequence for expression of the yRBD protein was designed so as to contain: the peptide of the Saccharomyces cerevisiae factor for protein secretion into the extracellular medium, which is cleaved during secretion (SEQ ID NO. 3).
- the DNA sequence coding for the sequence comprised between amino acids 319 to 537 of the SARS-CoV-2 spike protein (SEQ ID NO.4).
- the recognition sequence of the Sortase A enzyme (SEQ ID NO.5).
- the sequence of 6 histidines (SEQ ID NO.6) followed by a translation termination signal.
- the DNA sequence was synthesized using codon optimization for Pichia pastoris and cloned into the expression vector pPICZalpha A between the restriction sites EcoRI and SacII ( Figure 1A).
- the purified mature protein contains the RBD sequence (residues 319-537) followed by a Sortase A recognition sequence, and a His6 tag (C-terminal) ( Figure 1 B) (SEQ ID NO.2).
- Example 3 Induction of yRBD protein synthesis.
- BMGY buffered glycerol complex medium
- BMMY buffered methanol complex medium
- yeast extract 1% yeast extract, (Difco) 2% peptone
- 100 mM potassium phosphate pH 6,0, 1.34% YNB 0.4 mg biotin L-1, 0.5% methanol, (Sintorgan) or buffered minimum methanol medium containing histidine (Sigma)
- BMMH 100 mM potassium phosphate pH 6.0, 1.34% YNB, 0.4 mg of biotin L-1, 4 mg of histidine L-1, 0,5% methanol
- the first step of the fermentation process consisted of a batch culture with low salt basal medium (LSM, Low Salt Medium) with glycerol (40 g/L) as only carbon source, in order to obtain a great amount of Pichia pastoris biomass, while the AOX1 promoter was repressed by a high concentration of glycerol.
- the second step consisted of a fed-batch culture, in which the culture was fed with a concentrated glycerol solution (600 g/L) supplemented with a solution of trace minerals (PTM1), to increase biomass, and generate a gradual de-repression of the AOX1 promoter. Said feeding was performed as a function of dissolved oxygen thereby avoiding glycerol accumulation in the culture.
- a transition step was carried out by applying a methanol pulse such that its concentration in the cultures was of 4 g/L, in order to adapt the yeasts to growth with methanol as sole carbon source.
- an expression induction phase of the recombinant protein was performed by feeding the culture with pure methanol, supplemented with trace minerals. Said feeding was also carried out as a function of dissolved oxygen thereby avoiding accumulation of methanol in the culture.
- Each fermentation started by inoculating the bioreactor with a pre- grown culture of Pichia pastoris cells in an Erlenmeyer flask at 10-fold the starting concentration in the bioreactor, which was of an OD600 from 0.8 to 1.5 with the same culture medium at 30°C and 250 rpm.
- Example 4 Purification and characterization of yRBD. The induction supernatant was thawed cold and brought to pH 7.4 with NaOH. It was centrifuged for 20 min at 10000 x g to remove debris and precipitates, and seeded in a column containing Ni-NTA pre-equilibrated in 20 mM Tris, 150 mM NaCl, Imidazole 20 mM Buffer at pH 7.4.
- the protein was passed at a flow rate of 1.5 ml/min, the column was washed with 250 volumes of 20 mM Tris, 150 mM NaCl, 20 mM Imidazole Buffer at pH 7.4 and eluted in the same buffer but with 300 mM Imidazole.
- Fractions containing the yRBD protein ( Figure 2) were collected, dialyzed against 20 mM Tris, NaCl 150 mM Buffer, pH 7.4.
- the yRBD concentration was determined by UV spectrophotometry using an absorption coefficient of 33850 M-1 cm-1. When produced in a bioreactor, a yield of 180 mg per liter of supernatant was obtained.
- Example 5 Analysis of the structure of RBD glycans produced in different expression systems. Analysis of RBD glycosylation with endoglycanases: Purified RBD (3 ⁇ g) from mammalian or yeast cells was denatured for 10 min at 100°C and digested with PNGase F (500 mU) or EndoH (5 mU) for 2 hs at 37°C. The proteins were separated by 14% SDS-PAGE gel.
- Example 6 Method to obtain deglycosylated RBD protein with a commercial Endo H enzyme (yRBD-C100): The yRBD protein (5 ⁇ g) produced in P.
- EndoH enzyme was purified following the protocol described in the reference (Wang et al., 2015).
- the yRBD protein was treated with EndoH at a 3000:1 molar ratio for 16 hs at 37°C in 50 mM TEA buffer, pH 5.5. Complete removal of glycans was determined by SDS-PAGE. The treatment for 19-20 hs was established as the optimal procedure.
- Example 7 Preparation of all tested vaccines, quali- and quantitative composition and method therefor. 1. The quality and degree of purity of the protein used in the tested vaccines were confirmed by HPLC and SDS-PAGE.
- LPS lipopolysaccharides
- yRBD (15.4 ⁇ g/mouse/dose) was prepared and combined with the HPLC-grade phosphorothioate oligonucleotide CpG-ODN 1826 (5′ TCC ATG ACG TTC CTG ACG TT 3′ SEQ ID NO.9) (20 ⁇ g/mouse/dose) (Oligos Etc. Inc., Integrated DNA Technologies, OR, USA) and aluminum hydroxide (Al(OH)3) (20% (v/v)/mouse/dose).
- Vaccine compositions comprising from 5 ⁇ g to 200 ⁇ g of the deglycosylated yRBD domain of the coronavirus spike protein, from 10 ⁇ g to 100 ⁇ g/dose of CpG-ODN and from 10% v/v to 50% v/v of aluminum hydroxide were assayed.
- Example 8 Detailed method of measuring antibody levels in immunized mice. Preimmune sera were collected before starting immunization.
- Blood samples were obtained 30 days after the first immunization (antigen priming) and 20 days after the second immunization (antigen boost) by venipuncture of the facial vein. After coagulation at room temperature for 1 to 2 h, the blood samples were centrifuged in a centrifuge at 3000 rpm / min for 10 min at 4 °C. The upper serum layer was collected and stored at -20 °C. Identification of serum antibodies produced against the yRBD and yRBD- C100/C101 and yRBD-C101-H proteins in mice was carried out by a standard ELISA assay. Both the RBD protein produced in P.
- HEK-293T mammalian cells as the one produced in HEK-293T mammalian cells (gold standard) were used to coat 96-well flat bottom plates (Thermo Scientific NUNC-MaxiSorp) at a final concentration of 1 ⁇ g / mL (100 ⁇ L / well) in coating buffer containing phosphate buffered saline (PBS) at a pH of 7.4 and then incubated at 4 °C overnight. After blocking with PBS containing 8% nonfat dry milk powder for 2 hours at 37 °C, plates were washed 5 times with PBS containing 0.05% Tween 20 (PBST). An IgG determination was performed to evaluate the content of total specific immunoglobulins.
- PBS phosphate buffered saline
- Mouse sera were serially diluted and RBD-sensitized plates were incubated at 37°C for 1.5 hs in PBS with 1% non-fat dry milk powder (blocking solution). Subsequently, plates were washed with PBST and the RBD- interacting mouse IgGs were detected using an anti-IgG antibody conjugated with the HRP enzyme (horseradish peroxidase, DAKO P0447) diluted 1/1000 in blocking solution and added to the wells. After incubating for 1 h at 37°C, plates were washed 5 times with PBST and developed with 3,3',5,5' tetramethyl- biphenyl-diamine (TMB) for 15 min.
- HRP enzyme horseradish peroxidase
- lentivirus were produced by co-transfection of HEK-293T cells with plasmids bearing a green fluorescent protein (GFP) reporter gene (pLB from Stephan Kissler, Addgene plasmid No. 11619; http://n2t.net/addgene:11619; RRID:Addgene_11619), a plasmid providing the genes for lentivirus structural proteins (VRC5602, NIH) and the coding sequence of the spike protein (VRC7475_2019-nCoV-S-WT, NIH).
- GFP green fluorescent protein
- HEK-293T cells (2 ⁇ 10 7 ) were seeded in a 150 mm tissue culture plate in DMEM media containing 10% fetal bovine serum. The next day, cells were transfected with 10 ⁇ g of VRC5602, 5 ⁇ g of pLB-GFP and 3 ⁇ g of VRC7475_2019-nCoV-S-WT in OptiMEM medium using PEI at a 1:3 DNA:PEI ratio. Twenty-four hours later, for transfection efficiency, indicated as GFP fluorescence, they were collected 48 h after transfection and stored at 4°C; fresh media (DMEM + 5% FBS) was added.
- DMEM + 5% FBS fresh media
- the combined supernatants were clarified by centrifugation during 10 min at 3000 rpm in order to sediment residual cells.
- the clarified supernatant was centrifuged for 5 hs at 10,000 rpm.
- the pellet was resuspended in a storage medium (OptiMEM + 6% sucrose) and the aliquots were frozen at -80 °C until required.
- Pseudotyped lentivirus titers were measured by pre-transduction of HEK- 293T cells seeded in 96-well plates (2x10 4 cells/well) and transiently transfected with 100 ng of ACE2 (NIH) and 10 ng of protease TMPRSS2 (NIH) by well.
- the pseudotyped virus stock (concentrated supernatant) was serially diluted in assay medium (DMEM + 2.5% FBS), incubated during 2 hs at 37°C and added to the transfected cells.
- Virus titers were calculated by counting GFP positive cells using an automated counting tool in ImageJ (NIH). For the assay, 200-225 GFP positive cells/field were used using a 100X magnification.
- Neutralization assays were performed with transiently transfected HEK- 293T cells (24 hs before transduction) with ACE2 receptor and TMPRSS2 protease genes. Finally, dilution mixtures of sera and pseudovirus (100 ⁇ l) were added to 96-well plates containing 2x10 4 cells/well.
- mice All experimental protocols were approved by the socuno y Uso de Animales de Laboratorio (CICUAL) [Institutional Commitee for care and use of laboratory animals] of the Instituto de Ciencia y Tecnolog ⁇ a Dr. César Milstein, Pablo Cassará Foundation (ICT MILSTEIN 001-20). All methods were performed according to the ISO9001 and CICUAL guidelines. Immunization of mice was carried out by experts from the High-Level Technological Service [Servicio Tecnológico de Alto Nivel] CONICET (STAN No. 4482).
- mice were obtained from the animal facility of the Faculty of Veterinary Sciences, University of La Plata [Facultad de Ciencias Veterinarias de la Universidad de La Plata] (Argentina). Mice were housed at the animal facilities of the Instituto de Ciencia y Tecnolog ⁇ a Dr. César Milstein, Pablo Cassará Foundation. Female mice (6 to 8 weeks of age) were intraperitoneally immunized with a protein mass comprising from 15.4 to 40 ⁇ g of yRBD or yRBD-C101 or yRBD- C101-H produced in P.
- Example 10 Determination of antibodies in patient sera by an ELISA assay. Protocol used to test antibodies specific to RBD protein in patient sera. It is a two-day protocol. On day one, a 96-well plate was sensitized with 125 ng/well of yRBD-C100 (or yRBD-C101 or yRBD-C101-H) diluted in 100 ul/well of carbonate/bicarbonate buffer pH 9.6. It was incubated at 4°C ON. On day 2, firstly the plate was blocked and the solution of the wells was discarded. It was blocked with 300 ul of PBS-T (0.1%) 5% milk. Then it was incubated for 1 h at room temperature.
- yRBD-C100 or yRBD-C101 or yRBD-C101-H
- Example 11 Removal of Histidine tags from yRBD-C101
- the yRBD-C101 protein was treated with Sortase A at a RBD:Sortase A molar ratio of 10:1 during 16 hs at 25°C in TBS buffer (20mM Tris, 150 mM NaCl pH 7.4) spiked with 10 mM CaCl2.
- the yRBD-C101 protein was purified by passing through a TBS-equilibrated Ni-NTA column, where the eluate that did not interact with the column was collected directly. This preparation is described as yRBD-C101-H.
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Abstract
The invention refers to a vaccine and a method to obtain coronavirus antibodies, yeast strains, methods of detection, methods of treatment and uses thereof. A coronavirus vaccine comprising the deglycosylated RBD domain of the coronavirus spike protein and one or more adjuvants, wherein the RBD domain is produced in P. pastoris. Among others, the amino acid sequence of the RBD domain may be the sequence set forth in SEQ ID NO. 1 or SEQ ID NO. 2, wherein the vaccine may further comprise one or more adjuvants.
Description
CORONAVIRUS VACCINE, YEAST STRAINS, METHODS OF DETECTION, METHODS OF TREATMENT AND USES THEREOF The present invention refers to a coronavirus vaccine, yeast strains, methods of detection and treatment and uses thereof. More specifically it refers to a coronavirus vaccine comprising the deglycosylated RBD domain of the coronavirus spike protein and one or more adjuvants, wherein the RBD domain is produced in the yeast Pichia pastoris (now classified as Komagataella phaffii). Among others, the amino acid sequence of the RBD domain may have the sequence set forth in SEQ ID NO.1 or SEQ ID NO.2. The vaccine may further comprise one or more adjuvants. BACKGROUND In some documents, hyperglycosylation of hepatitis B virus envelope proteins is removed to generate in vitro diagnostic systems and vaccines for both active and passive treatment or for preventing diseases and/or infections caused by a hepatitis virus. Patent document US 2011/0230640 A1 describes methods for preparing a deglycosylated peptide by replacing an amino acid at the N-glycosylation site to generate a specific antibody for the deglycosylated form. Spike protein S from another virus (SARS-CoV), as well as polypeptides and peptide fragments of the S protein and conservative variants thereof are known. Use of the deglycosylated RBD domain in diagnostics is not contemplated. Generally, all disclosures are directed to a coronavirus other than SARS-CoV-2. Patent EP1618127 refers to SARS coronavirus nucleic acids and proteins. These nucleic acids and proteins may be used for preparing and manufacturing
vaccine formulations, diagnostic reagents, kits, etc. The effect of deglycosylation on antibody binding was investigated in a section of the patent. It was demonstrated that deglycosylation did not affect binding of the anti-histidine Mab antibody to the treated S oligomer. However, reactivity with rabbit anti-sera produced against purified virus was compromised. BRIEF DESCRIPTION OF THE INVENTION A coronavirus vaccine comprising the coronavirus spike protein deglycosylated RBD domain and one or more adjuvants is provided, wherein the RBD domain is produced in P. pastoris. In a preferred embodiment, the amino acid sequence of the RBD domain is shown in SEQ ID NO.1, but it may be any sequence having 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, or 85% sequence identity as compared to SEQ ID NO.1. In a preferred embodiment, the amino acid sequence of the RBD domain is shown in SEQ ID NO.2, but it may be any sequence having 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, or 85% sequence identity as compared to SEQ ID NO.2. A person skilled in the art would know that the RBD domain may have an amino acid sequence corresponding to any of the coronavirus variants. In another preferred embodiment, the coronavirus is SARS- CoV-2. The vaccine may further comprise an adjuvant, for example CpG-ODN, aluminum hydroxide, alhydrogel, aluminum phosphate, calcium phosphate, STING agonists, TLR agonists, Poly(I:C), cholera toxin, heat labile enterotoxin, Saponins (QS-21), particulate adjuvants such as nanoparticles or VLP (virus-like particles), virosomes, AS04, ISCOMS, PLG, emulsions such as MF59, AS02, Montanide ISA-51, and ISA-720, MPL, AGP, DC_Chol, OM-174, endogenous human immunomodulators such as hGM-CSF, hIL-12 and Immudaptin, inert
carriers such as gold particles, among others, or combinations thereof. In a preferred embodiment the vaccine comprises from 5 µg to 200 µg of deglycosylated RBD of the coronavirus spike protein per dose, from 10 µg to 100 µg/dose of CpG-ODN and from 10% v/v to 50% v/v / dose of aluminum hydroxide. A stably transformed yeast strain expressing a protein comprising the RBD domain amino acid sequence of the SARS-CoV-2 spike protein bound to a Sortase A recognition amino acid sequence linked to a His6 tag is provided. In a preferred embodiment, the yeast is P. pastoris. Further provided is a method for detecting anti coronavirus antibodies comprising at least the following steps: a) contacting the deglycosylated RBD domain of the coronavirus spike protein with an amount of a biological sample, wherein the RBD domain is produced in P. pastoris; and b) incubation and development. The coronavirus may be SARS-CoV-2 or another coronavirus, for example Severe acute respiratory syndrome-associated coronavirus (SARS- CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV) or others belonging to the coronaviridae family. The biological sample used in the method may be any biological sample, for example serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood, cerebrospinal fluid, pericardial fluid, lymph, pus, wherein the method may be any method, for example, direct or indirect ELISA, lateral flow over proteins immobilized on a support, dot blot (point hybridization), radioimmunoassay. In a preferred embodiment, the method comprises the following steps: a) contacting the deglycosylated RBD domain of the SARS-CoV-2 spike protein with a solid
support and incubation; b) adding an amount of a biological sample, for example, serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood, cerebrospinal fluid, pericardial fluid, lymph, pus, and incubation; and c) adding a labelled antibody and developing. Also provided is an immunization method comprising administering to an animal an amount of a coronavirus vaccine comprising the deglycosylated RBD domain of the coronavirus spike protein and one or more adjuvants, wherein the RBD domain is produced in P. pastoris. The animal may be a mammal or a bird. Further provided is the use of the deglycosylated RBD domain of the SARS-CoV-2 spike protein for preparing a vaccine and/or for obtaining anti coronavirus antibodies, and/or for manufacturing a method for detecting anti coronavirus antibodies in a biological sample, wherein the SARS-CoV-2 spike protein RBD domain has been produced in P. pastoris and has then been deglycosylated. BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 shows: A: Amino acid sequence of the mature protein containing sequences of the RBD domain (black) followed by a splice-site for sortase A (bold) and a 6 Histidine tag (underlined). B: Scheme of an expression vector for producing RBD in Pichia pastoris. The expression vector is integrated into the Pichia pastoris genome. AOX1: alcohol oxidase promoter, RBD-Sortase A: RBD sequence followed by a Sortase A splice-site (grey). His6x indicates the sequence of 6 histidines for purification and recognition. Figure 2 shows a scheme for obtaining a yRBD producing strain. Vector
pPICZαA described in Figure 1 was digested with the enzyme SacI and used for transforming electrocompetent Pichia pastoris yeast strains X-33 or Y-7556 or Y- 1603. Clones with the highest zeocine resistance were isolated and verified by PCR (- negative control without DNA, + positive control with a plasmid used for integration in yeast; alpha, empty vector, 1, 7, 10, 20, 32, 36: tested colonies for integration of the plasmid in the genome). Clone 7 was induced and the yRBD protein was purified in a Ni-NTA affinity column. Elution profile with 300 mM imidazole is shown. Figure 3 shows the steps for obtaining yRBD in a bioreactor. A 5L bioreactor was inoculated with 500 mL of a Pichia pastoris culture at OD600 nm = 10. The inncrease of biomass throughout the process is shown on the left, indicating the 4 steps involved. On the right, the increase of the yRBD-specific band in the culture supernatant by SDS-PAGE stained with Coomassie blue is shown. The production in the supernatant is of 450 mg/L and after purification a yield of 180 mg/L was obtained. Figure 4 shows the characterization of yRBD and a conformational comparison with RBD produced in HEK-293T mammalian cells. Comparative spectra of yRBD (dashed black line) and RBD-HEK (grey line) are shown, suggesting the similarity of the secondary as well as tertiary structures of both proteins. Likewise, the HPLC elution profile, although very similar and indicating high purity, shows a wider peak in the case of yRBD due to its higher degree of glycosylation. Figure 5 shows a study of RBD glycosylation in HEK-293T cells and in P. pastoris by SDS-PAGE and reverse phase HPLC. (A) Schematic representation of SARSCoV-2 glycoprotein. It shows the N-terminal domain (NTD), Receptor
binding domain (RBD), furin cleavage site (S1/S2), central helix (CH), Connector domain (CD), and Transmembrane domain (TM). (B) Shows residues involved in glycosylation (the residues involved in O- and N- glycosylation are indicated by dashed and solid lines, respectively) (B) Glycosylation analysis of RBD with endoglycanases. Purified RBD (3 µg) from mammalian or yeast cells was denatured for 10 min at 100°C and digested with PNGase F (500 mU) or EndoH (5 mU) for 2 hs at 37°C. The proteins were separated by 14% SDS-PAGE gel, showing the position of glycosylated and non-glycosylated forms of each species. Bands corresponding to PNGaseF (36 KDa) and EndoH (29 KDa) are indicated with empty or solid arrowheads, respectively. Glycosylated forms are indicated as Gly, whereas non-glycosylated forms are indicated as Non Gly. Figure 6 shows yRBD deglycosylation under native conditions with commercial EndoH.1: untreated yRBD protein, 2: EndoH, 3: yRBD (5 µg) treated with 5 mU of EndoH for 16 hs at 37°C. Samples were resolved in 12% SDS- PAGE and stained with Coomassie blue, identifying protein isoforms with glycans (Gly) and after the treatment of removal of glycans (Non-Gly). Figure 7 shows deglycosylation kinetics of yRBD with EndoH purified from P. pastoris. Five µg of pure yRBD protein were treated with EndoH at a RBD:EndoH molar ratio of 3000:1 for the indicated times (in hs). The resulting protein was resolved in 12% SDS-PAGE and stained with Coomassie blue, identifying protein isoforms with glycans (Gly) and after the treatment of glycans removal (Non-Gly). Figure 8 shows the characterization of yRBD (glycosylated) and yRBD- C101 (deglycosylated) proteins by HPLC. An analytical C18 reverse-phase HPLC chromatogram was performed. It was carried out in an ACN gradient and with a
mobile phase of 0.05% TFA. The gradient was from 0 to 100% over 40 min (10- 50 min of the run). The integration of the main peak was 95.7%. The peaks visualized at retention times of less than 5 min were buffer components and salts. In the chromatogram, the mobile phase injection profile has been substracted. Twenty one 21 micrograms of protein were seeded. Figure 9 shows the results of mass spectrometry for glycosylated and deglycosylated yRBD (yRBD-C101). It may be noted that, in addition to reducing size, deglycosylation generates a greater homogeneity by eliminating the sugars. Figure 10 shows circular dichroism spectra in far UV (A) and near UV (B). The concentrations required for near UV were restricted to yRBD (dotted black line) and yRBD-C101 (solid black line), as proteins are needed at high concentrations. Figure 11 shows the aggregation state of glycosylated yRBD and deglycosylated yRBD (yRBD-C101). (A) UV absorption spectra. Absence of a significant slope between 340 and 310 nm is indicative of the presence of light scattering and thus of aggregation or presence of particulate matter. (B) Characterization of yRBD and yRBC-C101 (clone 101 in the figure) by molecular exclusion chromatography. A Superose 6 column and a JASCO HPLC-type system were used. The buffer comprised 20 mM Tris-HCl, 150 mM NaCl, pH 7.4. The black arrow shows low molecular weight species present in the digestion buffer with EndoH. Flow rate was 0.5 ml/min (an elution time of 20 min corresponds to 10 mL). Figure 12 shows the difference in detection signals of anti SARS-CoV-2 antibodies in sera from positive and negative patients. Figure 13 shows the advantages of using yRBD-C101 as a vaccine
candidate. (A) Comparison of antibody generation by injecting yRBD and yRBD- C101 antigens in mice. (B) In vitro neutralization assay using pseudotyped SARS- CoV-2 lentivirus. Sera from mice (n=5) immunized with yRBD or with yRBD-C101 were used. Whereas viral particles are capable of transducing GFP-encoding RNA into cells in the presence of pre-immune serum, in the presence of serum from immunized mice transduction is significantly prevented in a concentration- dependent fashion. (C) Cellular response of splenocytes from mice immunized with yRBD or with yRBD-C100. The ability of restimulated memory cells to secrete gamma Interferon was analyzed using the Elispot technique. Figure 14 shows the reaction of Sortase A for removing the His6-tag from yRBD-C101. The yRBD-C101 protein was treated (S+) or not treated (S-) with Sortase A at a 10:1 molar ratio for 16 hs at 25°C. Each sample was passed through a Ni-NTA column. T: total before seeding in the column, F: not retained by the column; E: eluted with 300 mM Imidazole. Also shown are elution positions of yRBD-C101 (RBD) and Sortase A (sortase). DESCRIPTION OF THE INVENTION Definitions: The terms “RBD domain” and “RBD protein” have the same meaning and are used interchangeably. The term “yRBD” corresponds to the RBD domain produced in P. pastoris. The terms yRBD-C101 and yRBD-C100 are equivalent and correspond to the deglycosylated form of yRBD. The present invention describes obtaining the SARS-CoV-2 RBD domain in a heterologous eukaryotic system different from mammals, which is less expensive, better scalable for mass production and GRAS (Generally
Recognized as Safe), such as for example in an expression system in Pichia pastoris. As glycans are involved in protein folding, initially the systems' own glycosylation is very useful for producing a properly folded functional protein, but may alter recognition by antibodies, receptors, the immune system, etc. The invention comprises producing the RBD domain of the SARS-CoV-2 spike protein in a heterologous system for a correct folding, followed by subsequent removal of N-glycans from the domain for use in diagnostics, treatment and prevention. For example, for a serological diagnosis by ELISA or lateral flow, generation of neutralizing antibodies and generation of a protective immune response for SARS-CoV-2. This invention offers all the advantages of expressing RBD in a heterologous system such as one from yeasts, readily scalable to industrial levels, and very economic, but without the disadvantages of a specific glycosylation different from the one produced in a mammalian system because glycans are completely removed, maintaining the protein in its native conformation. The invention solves a long felt need, as it allows for obtaining an equally effective antigen as the one produced in mammalian cells, or other systems, but being produced in a much more affordable system. It also overcomes a prior technical prejudice: “a protein produced in a system different from that of mammals cannot be used as the glycans will be different.” The amino acid sequence of the yRBD domain (SEQ ID No. 2) was designed and expressed by preparing a gene construct comprising: 1) The DNA sequence encoding the peptide of the Saccharomyces cerevisiae factor for secretion into the extracellular medium (SEQ ID NO. 3),
which is cleaved during secretion. 2) The DNA sequence encoding for the sequence comprised between amino acids 319 to 537 of the SARS-CoV-2 spike protein (RBD) (SEQ ID NO.4). 3) The DNA sequence of recognition of the Sortase A enzyme (SEQ ID NO.5). 4) The DNA sequence encoding 6 histidines followed by a translation termination signal (SEQ ID NO.6). The construct was introduced in an expression vector into Pichia pastoris, a scheme of which is shown in Figure 1B. A Pichia pastoris culture was transformed with the vector and integration into the genome was verified by PCR. Four clones were selected to induce expression (Figure 2). The protein thus obtained was named yRBD. Yeasts (Pichia pastoris) transformed with the expression vector were grown in a bioreactor. Figure 3 shows the results of growth in a bioreactor. Increase of biomass throughout the process is shown on the left and the 4 steps are identified (numbered sections). On the right, the increase of the yRBD- specific band in the culture supernatant by SDS-PAGE stained with Coomassie blue is shown. Quantification of the supernatant showed a production of 450 mg of yRBD/liter of culture supernatant, which after purification yielded 180 mg/liter Figure 4 shows a theoretical UV spectrum and yRBD spectrum compared to the RBD spectrum produced in HEK-293T mammalian cells. A comparative circular dichroism spectrum is also shown. The HPLC analysis of Figure 4 shows purity of production in both systems (HEK-293T mammalian cells and Pichia pastoris). Further shown are tryptophan fluorescence spectra of yRBD and RBD produced in HEK-293T indicating the existence of similarity of hydrophobicity of
the tryptophan environment of the RBD protein grown in both systems. In conclusion, the protein produced in Pichia pastoris is structurally similar to the one produced in mammalian cells. However, the HPLC spectrum shows a wider peak due to size dispersion of the glycans, especially in yRBD, a fact that is also observed when using the SDS-PAGE technique. To determine whether the RBD domain produced in different expression systems originates different sizes of RBD domains due to differences in the N- glycosylation specific for each expression system, the RBD produced in HEK- 293T cells and in Pichia pastoris cells was analyzed using generic high-mannose and complex glycan endoglycosidase enzymes (PNGaseF) or high-mannose glycan-specific enzymes (Endoglycosidase H). Figure 5A shows the N- glycosylation sites of the spike protein RBD domain. Figure 5B shows that the size of the RBD domain produced in HEK-293T cells was reduced from about 35 kDa to 26 kDa after treatment with PNGaseF but not with EndoH, whereas the size of the RBD domain produced in Pichia pastoris was reduced from several bands with an average distribution of from 42 kDa to 26 kDa with both enzymes. This indicates that the RBD protein produced in HEK-293T cells presents complex glycans whereas the RBD protein produced in Pichia pastoris presents high-mannose glycans, and that both reach the same size after deglycosylation. The molecular mass observed by SDS-PAGE (about 26 kDa) for both deglycosylated RBD proteins corresponds to that which may be obtained from the RBD amino acid sequence (residues 319 to 537 of the spike protein). As may be seen in Figure 6, the yRBD protein produced in yeasts shows high isoform heterogeneity. In order to obtain yRBD proteins with a native tertiary structure but with no glycans, having also a homogeneous size, the yRBD
proteins were treated under conditions that would allow to maintain their native conformational structure (as opposed to the previous technology as shown in Figure 5). The purified yRBD protein produced in P. pastoris was treated with endoglycosidase H (EndoH) (Roche) in sodium citrate buffer. The reactions were incubated and then analyzed by 12% SDS-PAGE. This preparation of deglycosylated yRBD with a commercial enzyme was designated yRBD-C100. Parallel control reactions were carried out under the same conditions but without addition of the endoglycosidase. Figure 6 shows deglycosylation of yRBD under native conditions with a commercial EndoH.1: untreated yRBD protein, 2: EndoH, 3: yRBD (5 µg) treated with 5 mU of EndoH for 16 hs at 37°C. Samples were resolved in 12% SDS- PAGE and stained with Coomassie blue. Protein isoforms with glycans (Gly) and after the removal of glycans (Non-Gly) are identified. Commercial EndoH is produced in bacteria, which may cause undesired reactions, the yRBD protein was treated with an EndoH enzyme produced in yeasts and complete removal of glycans was confirmed by SDS-PAGE (Figure 7). A treatment for 19-20 hs was established as the optimal procedure. This preparation of deglycosylated yRBD with an enzyme prepared in the laboratory was designated yRBD-C101. For the purpose of the present invention, yRBD- C100 and yRBD-C101 are structurally the same and interchangeable. All immunization and diagnostic assays were carried out with both domains (yRBD- C100 and yRBD-C101). Homogeneity and mass of the glycosylated and deglycosylated yRBD protein (yRBD-C101) were analyzed. The homogeneity due to absence of glycans in the deglycosylated yRBD protein (yRBD-C101), was also confirmed
by reverse phase HPLC (C18) (Figure 8) and by mass spectrometry (Figure 8), and a single majority species having a mass of 26632 Da. Of note is that homogeneity of the deglycosylated protein is significantly greater than that of yRBD (insert in Figure 8 and Figure 9A), wherein it may be observed that the peaks are wider and that there is a wide distribution of species with two significant means, one at 31403 Da and the other at 42169 Da. The secondary and tertiary structure of the yRBD protein was analyzed. The yRBD protein purified and obtained under native conditions was deglycosylated with endoH and its conformational similarity was evaluated with respect to other produced yRBD variants. Circular dichroism (CD) spectra in the far UV are indicative of the secondary structure content (chirality around the peptide bond), while in the near UV the spectra are indicative of the chiral environment of aromatic residues, and thus a fingerprint of the tertiary structure of the protein). Circular dichroism spectra of yRBD and yRBD-C101 were obtained (Figure 10). After deglycosylating yRBD, the spectra were completely overlapping. The deglycosylated protein (yRBD-C101) prepared as described herein has circular dichroism spectral features in the far UV (190-240 nm) which are similar to those of yRBD (Figure 10A), thus indicating that the secondary structure patterns of the protein are similar. The deglycosylated protein shows circular dichroism spectral features in the near-UV (240-340 nm) which are similar to those of yRBD (Figure 10B), identified as a consequence of the asymmetric or chiral packing of aromatic residue side chains that absorb circularly polarized dextrorotatory and levorotatory light in a different manner, and ultimately are well associated with the tertiary structure of the antigen. That is, the tertiary structure
of both proteins, yRBD and deglycosylated yRBD (yRBD-C101), is similar. In the near region, deglycosylation does not produce any modification of the characteristic signals of the protein. For these reasons it is considered that there are not significant conformational alterations as a consequence of the deglycosylation. The UV absorption spectrum allows for calculating protein concentration in a precise manner, and also for confirming the absence of oligomers and light- scattering aggregates that would be obvious as a slope in the 340-320 nm region (Figure 11A). This slope is absent in the preparations of the yRBD and yRBD- C101 proteins. The absence of aggregates in antigen preparation was also confirmed by analytical molecular exclusion on a Superose 6 column and a JASCO chromatographic system. Figure 11B shows the chromatographic profile thus obtained. Absence of high molecular weight aggregates is observed in both protein samples (yRBD and yRBD-C101), as well as a higher homogeneity of the sample of yRBD-C101 when compared to yRBD (the latter being heterogeneous from the point of view of glycosylations). There was no evidence of species with small elution volumes (0-25 min or 0-12.5 mL). Clearly, the two major species, as a product of a different glycosylation degree may be observed in the case of yRBD; and in a single homogeneous peak in the case of the deglycosylated yRBD-C101 protein. The ability of yRBD-C101 to distinguish sera from positive and negative patients is described below. The yRBD and yRBD-C101 proteins were immobilized in multiwell plates and used for detecting anti SARS-CoV-2 antibodies in sera from patients that had been classified as patients with
symptoms of disease (positive) and a serum bank obtained before the COVID-19 pandemic (negative). The results shown in Figure 12 clearly show how the yRBD- C101 protein is more efficient and precise for identifying negative and positive sera, since although the latter have a variable response depending on the degree of immunization of each patient, the cut-off line of negatives is clearly lower, strongly indicating that the yRBD-C101 protein does not produce false positives. In addition, the ability to detect anti SARS-CoV-2 antibodies in serum of positive patients using yRBD-C101 vs RBD produced in HEK-293T mammalian cells was compared. Table 1 shows the results of sera from 32 patients, 2 negative (labelled as Neg Cont.), the remaining patients were vaccinated or tested positive for COVID-19 by PCR. It is observed that known positive sera are better detected with yRBD-C101 than with RBD obtained in HEK-293T mammalian cells (indicated with shading). Table 1
25 26 27 28 29 30 31 32
Neg Pos The results indicate the following: % of negative sera testing negative with RBD-HEK: 100% % of negative sera testing negative with yRBD-C101: 100% % of positive sera detected with RBD-HEK: 9/32 = 28.1% % of positive sera detected with yRBD-C101: 25/32 = 78.13% That is, yRBD-C101 obtained in P. pastoris and subsequently deglycosylated showed superior results than the glycosylated RBD-HEK protein for detecting serum from positive patients. The advantages of yRBD-C101 as a COVID-19 vaccine are shown below. Immunization with the yRBD-C101 protein resulted in a significant increase of the immune response when compared to an immunization using yRBD, both immunizations performed under the same conditions. Titers of 0.9 x 106 were obtained with the first dose whereas with the second dose a titer of anti-RBD total IgG of 1.8 x 107 was obtained (Figure 13A). It is shown that the second dose of
yRBD-C101 generates an amount that is at least one order different with respect to the second dose of yRBD. The neutralizing responses observed with the antibodies generated by immunizing with yRBD was lower than that shown with yRBD-C101 (Figure 13B), being superior the immunization with yRBD-C101. Both yRBD and yRBD-C101 produced a cellular response evidenced by the production of IFN-gamma from spleen cells. However, the response obtained with yRBD-C100 was greater, nearly two-fold; and more homogeneous (Figure 13C). In conclusion, the yRBD protein produced in P. pastoris and deglycosylated (yRBD-C100 or yRBD-C101) was properly folded. The yRBD protein showed to be similar to the RBD protein produced in mammalian cells with respect to its properties as an antigen in ELISA methods, regarding purity and homogeneity. Both yRBD and yRBD-C100 or C101 produce a humoral immune response, but is significantly higher (10-fold) when the deglycosylated variants, yRBD-C100 or C101, are used. The antibodies generated by the deglycosylated protein have a greater neutralizing power and generate a better cellular response. Therefore it is considered that yRBD-C101, or any deglycosylated variant, is an excellent candidate for preparing a vaccine. In addition, deglycosylated yRBD (yRBD-C101) is suitable for use in serological diagnostic assays, given that it allows for distinguishing positive patients from negative patients. As the designed sequence has a Sortase A enzyme splice-site, a procedure was established for removing histidine tags and for purifying the protein from Sortase A enzyme residues (Figure 14). This preparation was
designated yRBD-C101-H. It should be noted that the last step of purification removes protein residues from which the tag were not removed, plus the Sortase A used for the procedure, which also has histidine tags. The procedure for obtaining the deglycosylated yRBD domains is highly efficient: an unexpected amount of about 505 mg of pure deglycosylated yRBD per kg of fresh weight is obtained. This invention is better illustrated in the following examples, which should not be construed as a limitation of the scope thereof. On the contrary, it should be clearly understood that other embodiments, modifications and equivalents thereof may be possible after reading the present description, which may be suggested to a person of skill without departing from the spirit of the present invention and/or the scope of the appended claims. EXAMPLES Example 1: Method to obtain a SARS-CoV-2 RBD-producing Pichia pastoris strain and to purify yRBD. Design of sequences: The DNA sequence for expression of the yRBD protein was designed so as to contain: the peptide of the Saccharomyces cerevisiae factor for protein secretion into the extracellular medium, which is cleaved during secretion (SEQ ID NO. 3). The DNA sequence coding for the sequence comprised between amino acids 319 to 537 of the SARS-CoV-2 spike protein (SEQ ID NO.4). The recognition sequence of the Sortase A enzyme (SEQ ID NO.5). The sequence of 6 histidines (SEQ ID NO.6) followed by a translation termination signal. The DNA sequence was synthesized using codon optimization for Pichia pastoris and cloned into the expression vector pPICZalpha A between the
restriction sites EcoRI and SacII (Figure 1A). The construct used in the transformation comprises the RBD coding sequence (residues 319-537) (SEQ ID NO.4) fused at the N terminal end with the secretion signal of Saccharomyces cerevisiae factor alpha (N-terminal) (SEQ ID NO.3), and at the C terminal end a recognition sequence of Sortase A followed by a His6 tag (C-terminal) (SEQ ID NO. 5) and (SEQ ID NO.6). As the alpha factor is removed by yeasts during the secretion process, the purified mature protein contains the RBD sequence (residues 319-537) followed by a Sortase A recognition sequence, and a His6 tag (C-terminal) (Figure 1 B) (SEQ ID NO.2). Example 2: Method to obtain a yRBD-producing Pichia pastoris strain. Pichia pastoris X-33 strain was grown in YPD medium to OD600nm = 1, centrifuged for 4 min at 2500 x g, resuspended sequentially in 1 initial volume, ½ volume, 1/25 volume and 1/500 volume of sterile water, each time centrifuging for 4 min at 2500 x g. Aliquots of 80 ul were electroporated at 2.5 kV, 25 µF, 200 Ohm with 8 µg of the vector linearized with the restriction enzyme SacI (NEB) and selected in YPDS medium supplemented with 100 µg/ml zeocin. The resulting colonies were grown in increasing concentrations of zeocin. Clones resistant to more than 500 µg/ml zeocin were selected. PCR method to demonstrate integration of the construct into the genome of P. pastoris: A PCR was performed with DNA colonies as follows: A tip from each colony isolated from Pichia pastoris was resuspended in 4 µl of 20mM NaOH in a 0.2 ml PCR tube and heated for 10 min at 95°C It was cooled to 4°C followed by addition to each tube of 21 µl of a mix containing
H2O: 13.5 µl Tris-HCl 100mM pH 9, KCl 500mM, Triton X-1001% Buffer: 2.5 µl 25 mM MgSO4: 2 µl 40 mM dNTP (dATP + dCTP + dGTP + dTTP) (10 mM of each): 0.5 µl AOX1 Fw Primer (10 µM): 1 µl RBD Rev Primer (10 µM): 1 µl Taq polymerase: 0.5 µl AOX1 Fw primer sequence: 5’-GACTGGTTCCAATTGACAAGC-3’ (SEQ ID NO.7) RBD Rv primer sequence: 5’ -GTTCCATGCAATGACGCATC-3’ (SEQ ID NO.8) Thirty cycles were performed comprising: 30 sec at 94°C 30 sec at 52°C 1 min 30 sec at 72°C A final cycle of 5 min at 72°C Five 5 µl of seeding buffer (30% glycerol, 0.25% OrangeG) were added to each tube They were analyzed in 1% agarose gel in TEA buffer and developed with ethidium bromide. Example 3: Induction of yRBD protein synthesis. Production of yRBD in batches: For the production of yRBD in batch mode, individual colonies inoculated in a buffered glycerol complex medium (BMGY) (1% yeast extract, 2% bactopeptone, 1.34% YNB, 400 µg biotin L-1, 0.1M potassium phosphate, pH 6.0 and 1% glycerol) were used and cultures were
grown at 28°C with stirring at 250 rpm until the culture reached an OD600nm = 4-6. Cells were collected, resuspended in buffered methanol complex medium (BMMY: 1% yeast extract, (Difco) 2% peptone, 100 mM potassium phosphate pH 6,0, 1.34% YNB, 0.4 mg biotin L-1, 0.5% methanol, (Sintorgan) or buffered minimum methanol medium containing histidine (Sigma) (BMMH: 100 mM potassium phosphate pH 6.0, 1.34% YNB, 0.4 mg of biotin L-1, 4 mg of histidine L-1, 0,5% methanol) until an initial OD600nm = 1.0 was reached and then incubated at 28°C with stirring at 250 rpm in volume flasks covered with microporous tape sheets for an enhanced oxygenation. Every 24 h methanol was added to a final concentration of 0,5% and pH was adjusted to 6. Induction was maintained for 72-90 hs at 28°C, then the cells were removed by centrifugation at 3000 × g for 10 min and the supernatant was frozen at -80°C until required. Production of yRBD in a bioreactor: Fermentations in a bioreactor were carried out using a procedure that included four steps (Figure 3), based on previous works (Noseda et al., 2013; Chen et al., 2014; Noseda et al., 2016; Chen et al., 2017). The first step of the fermentation process consisted of a batch culture with low salt basal medium (LSM, Low Salt Medium) with glycerol (40 g/L) as only carbon source, in order to obtain a great amount of Pichia pastoris biomass, while the AOX1 promoter was repressed by a high concentration of glycerol. The second step consisted of a fed-batch culture, in which the culture was fed with a concentrated glycerol solution (600 g/L) supplemented with a solution of trace minerals (PTM1), to increase biomass, and generate a gradual de-repression of the AOX1 promoter. Said feeding was performed as a function of dissolved oxygen thereby avoiding glycerol accumulation in the culture. Next, a transition step was carried out by applying a methanol pulse such that its
concentration in the cultures was of 4 g/L, in order to adapt the yeasts to growth with methanol as sole carbon source. Finally, an expression induction phase of the recombinant protein was performed by feeding the culture with pure methanol, supplemented with trace minerals. Said feeding was also carried out as a function of dissolved oxygen thereby avoiding accumulation of methanol in the culture. Each fermentation started by inoculating the bioreactor with a pre- grown culture of Pichia pastoris cells in an Erlenmeyer flask at 10-fold the starting concentration in the bioreactor, which was of an OD600 from 0.8 to 1.5 with the same culture medium at 30°C and 250 rpm. During the fermentation process in a bioreactor, temperature was kept constant at 30°C throughout the steps of batch, glycerol fed-batch and transition phase, and at 25°C during the step of induction with methanol. The pH was kept constant (pH:5) by addition of H3PO4 (42.5% v/v) and NH4OH (14% v/v). Also, said alkaline solution was the source of nitrogen throughout the fermentation. The required levels of dissolved oxygen were achieved by stirring (from 700rpm to 1200 rpm) and sterile air was supplied (1-2 LLM). pH was determined on-line using a pH electrode (Mettler-Toledo, GmbH) and dissolved oxygen concentration by means of a polarographic probe (Mettler-Toledo). Foaming was prevented by automatic addition of a 3% solution (v/v) of anti-foaming 289 (Sigma). Example 4: Purification and characterization of yRBD. The induction supernatant was thawed cold and brought to pH 7.4 with NaOH. It was centrifuged for 20 min at 10000 x g to remove debris and precipitates, and seeded in a column containing Ni-NTA pre-equilibrated in 20 mM Tris, 150 mM NaCl, Imidazole 20 mM Buffer at pH 7.4. The protein was passed at a flow rate of 1.5 ml/min, the column was washed with 250 volumes of
20 mM Tris, 150 mM NaCl, 20 mM Imidazole Buffer at pH 7.4 and eluted in the same buffer but with 300 mM Imidazole. Fractions containing the yRBD protein (Figure 2) were collected, dialyzed against 20 mM Tris, NaCl 150 mM Buffer, pH 7.4. The yRBD concentration was determined by UV spectrophotometry using an absorption coefficient of 33850 M-1 cm-1. When produced in a bioreactor, a yield of 180 mg per liter of supernatant was obtained. Example 5: Analysis of the structure of RBD glycans produced in different expression systems. Analysis of RBD glycosylation with endoglycanases: Purified RBD (3 µg) from mammalian or yeast cells was denatured for 10 min at 100°C and digested with PNGase F (500 mU) or EndoH (5 mU) for 2 hs at 37°C. The proteins were separated by 14% SDS-PAGE gel. Example 6: Method to obtain deglycosylated RBD protein with a commercial Endo H enzyme (yRBD-C100): The yRBD protein (5 µg) produced in P. pastoris and purified was treated with 5 mU of endoglycosidase H (EndoH) (Roche) in sodium citrate buffer 50 mM, pH 5.5. Reactions were incubated for 16 hs at 37°C and analyzed by 12% SDS- PAGE. Parallel control reactions were carried out under the same conditions but without addition of the endoglycosidase. Method to obtain native RBD protein deglycosylated with an Endo H enzyme produced in yeasts (yRBD-C101): As the commercial enzyme is expensive and produced in bacteria, which may cause undesired reactions, yRBD was treated with an EndoH enzyme produced in yeasts. The EndoH enzyme was purified following the protocol described in the reference (Wang et al., 2015). The yRBD protein was treated with EndoH at a 3000:1 molar ratio for
16 hs at 37°C in 50 mM TEA buffer, pH 5.5. Complete removal of glycans was determined by SDS-PAGE. The treatment for 19-20 hs was established as the optimal procedure. Example 7: Preparation of all tested vaccines, quali- and quantitative composition and method therefor. 1. The quality and degree of purity of the protein used in the tested vaccines were confirmed by HPLC and SDS-PAGE. Additionally, a protocol for removal of lipopolysaccharides (LPS) from protein preparations was performed by overnight incubation at 4ºC of the purified proteins with a polymyxin B matrix followed by a second incubation (2-3 hs) at room temperature. The matrix was pre-equilibrated in 20 mM Tris-HCl, 100 mM NaCl, buffer solution, pH 7.0. Endotoxin concentration in the protein samples was determined by the service of Laboratorios Fundación Cassará. All protein samples were adjusted to a final volume of 200 µL and LPS content was measured using a commercial kit from Charles River Endosafe (R160), based on the chromogenic method of the Limulus amebocyte lysate assay (LAL), with a sensitivity of 0.015 EU / mL. No LPS were detected in the yRBD preparation. Subsequently, proteins were filtered using a 0.22 micrometer filter under sterile conditions. Once sterile and free from endotoxin, for example, a mass of yRBD (15.4 µg/mouse/dose) was prepared and combined with the HPLC-grade phosphorothioate oligonucleotide CpG-ODN 1826 (5′ TCC ATG ACG TTC CTG ACG TT 3′ SEQ ID NO.9) (20 µg/mouse/dose) (Oligos Etc. Inc., Integrated DNA Technologies, OR, USA) and aluminum hydroxide (Al(OH)3) (20% (v/v)/mouse/dose). Vaccine compositions comprising from 5 µg to 200 µg of the deglycosylated yRBD domain of the coronavirus spike protein, from 10 µg to 100 µg/dose of CpG-ODN and from 10% v/v to 50% v/v of
aluminum hydroxide were assayed. The following yRBD: yRBD-C101 and yRBD-C101-H, were tested as vaccines, and the results thereof did not show significant differences. Example 8: Detailed method of measuring antibody levels in immunized mice. Preimmune sera were collected before starting immunization. Blood samples were obtained 30 days after the first immunization (antigen priming) and 20 days after the second immunization (antigen boost) by venipuncture of the facial vein. After coagulation at room temperature for 1 to 2 h, the blood samples were centrifuged in a centrifuge at 3000 rpm / min for 10 min at 4 °C. The upper serum layer was collected and stored at -20 °C. Identification of serum antibodies produced against the yRBD and yRBD- C100/C101 and yRBD-C101-H proteins in mice was carried out by a standard ELISA assay. Both the RBD protein produced in P. pastoris as the one produced in HEK-293T mammalian cells (gold standard) were used to coat 96-well flat bottom plates (Thermo Scientific NUNC-MaxiSorp) at a final concentration of 1 µg / mL (100 µL / well) in coating buffer containing phosphate buffered saline (PBS) at a pH of 7.4 and then incubated at 4 °C overnight. After blocking with PBS containing 8% nonfat dry milk powder for 2 hours at 37 °C, plates were washed 5 times with PBS containing 0.05% Tween 20 (PBST). An IgG determination was performed to evaluate the content of total specific immunoglobulins. Mouse sera were serially diluted and RBD-sensitized plates were incubated at 37°C for 1.5 hs in PBS with 1% non-fat dry milk powder (blocking solution). Subsequently, plates were washed with PBST and the RBD- interacting mouse IgGs were detected using an anti-IgG antibody conjugated with
the HRP enzyme (horseradish peroxidase, DAKO P0447) diluted 1/1000 in blocking solution and added to the wells. After incubating for 1 h at 37°C, plates were washed 5 times with PBST and developed with 3,3',5,5' tetramethyl- biphenyl-diamine (TMB) for 15 min. The reaction was stopped with 50 µL / well of 1,0 M H2SO4 (stopping solution). Absorbance was measured in a microplate reader (Thermo Multiscan FC ELISA) at 450 nm (A450). Antibody titer was determined as the inverse of the last dilution considered positive with a cut-off value defined as A450 = 0.20, which was twice than that of a group of sera from normal mice (from 30 non-immunized animals). Statistical significance was evaluated with Student’s t test, using a log-transformation value of the ELISA titers. The differences were considered significant if p <0.05. In addition, neutralizing antibodies were measured in a neutralization assay using pseudotyped SARS-CoV-2 S lentivirus. The lentivirus were produced by co-transfection of HEK-293T cells with plasmids bearing a green fluorescent protein (GFP) reporter gene (pLB from Stephan Kissler, Addgene plasmid No. 11619; http://n2t.net/addgene:11619; RRID:Addgene_11619), a plasmid providing the genes for lentivirus structural proteins (VRC5602, NIH) and the coding sequence of the spike protein (VRC7475_2019-nCoV-S-WT, NIH). HEK-293T cells (2×107) were seeded in a 150 mm tissue culture plate in DMEM media containing 10% fetal bovine serum. The next day, cells were transfected with 10 µg of VRC5602, 5 µg of pLB-GFP and 3 µg of VRC7475_2019-nCoV-S-WT in OptiMEM medium using PEI at a 1:3 DNA:PEI ratio. Twenty-four hours later, for transfection efficiency, indicated as GFP fluorescence, they were collected 48 h after transfection and stored at 4°C; fresh media (DMEM + 5% FBS) was added. After 48 hs, the combined supernatants
were clarified by centrifugation during 10 min at 3000 rpm in order to sediment residual cells. The clarified supernatant was centrifuged for 5 hs at 10,000 rpm. The pellet was resuspended in a storage medium (OptiMEM + 6% sucrose) and the aliquots were frozen at -80 °C until required. Pseudotyped lentivirus titers were measured by pre-transduction of HEK- 293T cells seeded in 96-well plates (2x104 cells/well) and transiently transfected with 100 ng of ACE2 (NIH) and 10 ng of protease TMPRSS2 (NIH) by well. The pseudotyped virus stock (concentrated supernatant) was serially diluted in assay medium (DMEM + 2.5% FBS), incubated during 2 hs at 37°C and added to the transfected cells. Virus titers were calculated by counting GFP positive cells using an automated counting tool in ImageJ (NIH). For the assay, 200-225 GFP positive cells/field were used using a 100X magnification. Neutralization assays were performed with transiently transfected HEK- 293T cells (24 hs before transduction) with ACE2 receptor and TMPRSS2 protease genes. Finally, dilution mixtures of sera and pseudovirus (100 µl) were added to 96-well plates containing 2x104 cells/well. Pseudovirus infectivity was determined 48 hs later and images were obtained using an inverted microscope (IX-71 OLYMPUS), and analyzed with the microscope Micro-Manager Open Source Software. Serum antibody neutralization titers were calculated by regression curve fitting using GraphPad Prism software Inc. (La Jolla, CA). The 50% inhibitory concentration (IC50), corresponding to the dilution of antibody in serum caused a 50% reduction of GFP positive cells compared to cells treated with control of "virus only". Example 9: Immunization method and vaccination protocols. Treatment of laboratory animals was similar to that of the US National
Institutes of Health. All experimental protocols were approved by the Comisión Institucional para el Cuidado y Uso de Animales de Laboratorio (CICUAL) [Institutional Commitee for care and use of laboratory animals] of the Instituto de Ciencia y Tecnología Dr. César Milstein, Pablo Cassará Foundation (ICT MILSTEIN 001-20). All methods were performed according to the ISO9001 and CICUAL guidelines. Immunization of mice was carried out by experts from the High-Level Technological Service [Servicio Tecnológico de Alto Nivel] CONICET (STAN No. 4482). BALB/c mice were obtained from the animal facility of the Faculty of Veterinary Sciences, University of La Plata [Facultad de Ciencias Veterinarias de la Universidad de La Plata] (Argentina). Mice were housed at the animal facilities of the Instituto de Ciencia y Tecnología Dr. César Milstein, Pablo Cassará Foundation. Female mice (6 to 8 weeks of age) were intraperitoneally immunized with a protein mass comprising from 15.4 to 40 µg of yRBD or yRBD-C101 or yRBD- C101-H produced in P. pastoris in the presence of the HPLC-grade phosphorothioate oligonucleotide CpG-ODN 1826 (5′ TCC ATG ACG TTC CTG ACG TT 3′ SEQ ID NO. 9) (about 20 µg/mouse/dose) (Oligos ETC. Inc., Integrated DNA Technologies, OR, USA) and aluminum hydroxide (Al (OH)3) (about 20% (v/v)/mouse/dose) and boosted on day 30 with the same dose. Additional control animals were injected with Al(OH)3 (20% (v/v)) plus CpG-ODN 1826 (20 µg) per mouse using the same immunization program. Example 10: Determination of antibodies in patient sera by an ELISA assay. Protocol used to test antibodies specific to RBD protein in patient sera. It is a two-day protocol. On day one, a 96-well plate was sensitized with 125 ng/well
of yRBD-C100 (or yRBD-C101 or yRBD-C101-H) diluted in 100 ul/well of carbonate/bicarbonate buffer pH 9.6. It was incubated at 4°C ON. On day 2, firstly the plate was blocked and the solution of the wells was discarded. It was blocked with 300 ul of PBS-T (0.1%) 5% milk. Then it was incubated for 1 h at room temperature. For preparing the samples, 1:200 dilutions of the sera to be tested were prepared in PBS-T (0.1%) 5% milk. The blocking solution was discarded and incubated with 100 ul/well of sera dilutions for 1 h at room temperature and with gentle stirring. The dilutions of the samples were discarded and washed 4 times with 250 ul/well of PBS-T (0.1%). It was incubated with a secondary antibody, by adding 100 ul of the secondary antibody (human α-IgG) conjugated to a 1/5000 HRP dilution in PBS-T 0.1% + 0.4% BSA. Then it was incubated for 1 h at room temperature with gentle stirring. For the development, the secondary antibody solution was discarded and the plate was washed 4 times with 250 ul/well of PBS-T (0.1%). Then 100 ul/well of TMB were added followed by incubation for 10 min. The reaction was stopped by adding 100 ul/well of 1% HCl. Finally, absorbance was measured at 450 nm. Example 11: Removal of Histidine tags from yRBD-C101 The yRBD-C101 protein was treated with Sortase A at a RBD:Sortase A molar ratio of 10:1 during 16 hs at 25°C in TBS buffer (20mM Tris, 150 mM NaCl pH 7.4) spiked with 10 mM CaCl2. The yRBD-C101 protein was purified by passing through a TBS-equilibrated Ni-NTA column, where the eluate that did not interact with the column was collected directly. This preparation is described as yRBD-C101-H.
Claims
1. A coronavirus vaccine, characterized by comprising the deglycosylated RBD domain of the coronavirus spike protein and one or more adjuvants, wherein the RDB domain is produced in yeasts.
2. The vaccine according to claim 1, characterized in that the amino acid sequence of the RBD domain comprises a sequence having at least 85% sequence identity to the sequence set forth in SEQ ID NO. 1.
3. The vaccine according to claim 1, characterized in that the amino acid sequence of the RBD domain comprises a sequence having at least 85% sequence identity to the sequence set forth in SEQ ID NO. 2.
4. The vaccine according to claim 1, characterized in that the amino acid sequence of the RBD domain comprises the sequence set forth in SEQ ID NO. 1.
5. The vaccine according to claim 1, characterized in that the amino acid sequence of the RBD domain comprises the sequence set forth in SEQ ID NO. 2.
6. The vaccine according to claim 1, characterized in that the coronavirus is SARS-CoV-2 or variants thereof.
7. The vaccine according to claim 1, characterized in that the RBD domain does not contain glycans.
8. The vaccine according to claim 1 , characterized in that the adjuvant is selected from the group consisting of CpG-ODN, aluminum hydroxide and
combinations thereof.
9. The vaccine according to claim 1 , characterized by comprising from 5 μg to 200 pg/dose of the deglycosylated RBD domain, from 10 μg to 100 μg/dose of CpG-ODN and from 10% v/v to 50% v/v of aluminum hydroxide.
10. A transformed yeast strain, characterized by expressing and releasing into the media a protein comprising the amino acid sequence of the RBD domain of the SARS-CoV-2 spike protein bound to a Sortase A recognition amino acid sequence linked to a His6 tag, wherein the expression is stable.
11 . The strain according to claim 10, characterized in that said strain is P. pastoris.
12. The yeast strain according to claim 10, characterized by comprising in its genome at least a DNA sequence encoding a signal peptide of Saccharomyces cerevisiae factor for its secretion into the extracellular medium bound to the DNA sequence coding for the sequence comprised between amino acids 319 to 537 of the SARS-CoV-2 spike protein bound to the recognition DNA sequence of the Sortase A enzyme bound to the DNA sequence encoding 6 histidines bound to a translation termination signal.
13. A method for detecting anti coronavirus antibodies, characterized by comprising at least the following steps: a. contacting the deglycosylated RBD domain of a coronavirus spike protein with an amount of a biological sample, wherein the RBD domain is produced in P. pastoris; and b. incubation and development.
14. The method according to claim 13, characterized in that the coronavirus is SARS-CoV-2 or variants thereof.
15. The method according to claim 13, characterized in that the biological sample is selected from the group consisting of serum, plasma, peripheral blood, saliva, breast milk, gastric secretions, mucous membranes, ascitic fluid, sweat, peritoneal fluids, faecal material, tears, vomit, vaginal secretions, sinusoidal cavity lavage or bronchoalveolar lavage, umbilical cord blood, cerebrospinal fluid, pericardial fluid, lymph and pus.
16. The method according to claim 13, characterized in that said method is selected from direct ELISA, indirect ELISA, lateral flow over protein immobilized on support, dot blot and radioimmunoassay.
17. The method according to claim 13, characterized by comprising the following steps: a. contacting the deglycosylated RBD domain of the SARS-CoV-2 spike protein or variants thereof with a solid support and incubating; b. adding an amount of a biological sample and incubating; and c. adding a labelled antibody and developing.
18. The method according to claim 13, characterized in that the deglycosylated RBD domain of the SARS-CoV-2 spike protein comprises an amino acid sequence selected from SEQ ID NO. 1, SEQ ID NO. 2, sequences having at least 85% identity to SEQ ID NO. 1, sequences having at least 85% identity to SEQ ID NO. 2, wherein said domain does not contain glycans.
19. An immunization method characterized by comprising applying to an animal an amount of the vaccine of claim 1.
20. The method according to claim 19, characterized by comprising applying at least one dose comprising from 5 μg to 200 μg of the deglycosylated
RBD domain, from 10 μg to 100 μg of CpG-ODN and from 10% v/v to 50% v/v of
aluminum hydroxide.
21. Use of the deglycosylated RBD domain of the SARS-CoV-2 spike protein or variants thereof for preparing a vaccine.
22. Use of the deglycosylated RBD domain of the SARS-CoV-2 spike protein or variants thereof in a method for detecting anti coronavirus antibodies in a biological sample.
23. A deglycosylated RBD domain of the SARS-CoV-2 spike protein, characterized in that it was obtained in P. pastoris and subsequently deglycosylated.
24. The deglycosylated RBD domain of the SARS-CoV-2 spike protein, characterized in that it is used for immunizing an animal or for diagnostics.
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ARP210102579A AR123532A1 (en) | 2021-09-16 | 2021-09-16 | CORONAVIRUS VACCINE, YEAST STRAINS, DETECTION METHODS, TREATMENT METHODS AND USES |
ARP20210102579 | 2021-09-16 |
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EP3728588A4 (en) * | 2017-12-22 | 2022-03-09 | The Broad Institute, Inc. | Cas12a systems, methods, and compositions for targeted rna base editing |
US11690907B2 (en) * | 2018-06-12 | 2023-07-04 | Kbio Holdings Limited | Vaccines formed by virus and antigen conjugation |
US20210206810A1 (en) * | 2019-11-20 | 2021-07-08 | Ingenza Ltd. | Detection of Optimal Recombinants Using Fluorescent Protein Fusions |
CN112300251B (en) * | 2020-02-24 | 2022-04-05 | 成都威斯克生物医药有限公司 | Protein and vaccine for anti SARS-CoV-2 infection |
US11376320B2 (en) * | 2020-03-05 | 2022-07-05 | Iowa State University Research Foundation, Inc. | Immunogenic and vaccine compositions against SARS-CoV-2 |
RU2720614C9 (en) * | 2020-04-23 | 2021-02-09 | федеральное государственное бюджетное учреждение «Национальный исследовательский центр эпидемиологии и микробиологии имени почетного академика Н.Ф. Гамалеи» Министерства здравоохранения Российской Федерации | Immunobiological agent and a method for use thereof for inducing specific immunity against the sars-cov-2 severe acute respiratory syndrome virus (versions) |
CN111920946B (en) * | 2020-08-07 | 2021-05-28 | 合肥诺为尔基因科技服务有限公司 | Cyclic dinucleotide modified aluminum nanoparticle vaccine adjuvant-delivery system and SARS-CoV-2 subunit vaccine based on the same |
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