Patent Application
20240189416
This application contains a sequence listing, which is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file name of “CRU6045WOPCT1_Sequence_Listing” creation date of Nov. 11, 2021 and having a size of 4.49 MB. The sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.
The present invention relates to the field of medicine. The invention in particular relates to stabilized recombinant pre-fusion Coronavirus spike (S) proteins, in particular to SARS-COV-2 S proteins, to nucleic acid molecules encoding said SARS-COV-2 S proteins, and uses thereof, e.g. in vaccines.
Corona viruses (CoVs) are viruses responsible for mild respiratory tract infections and atypical pneumonia in humans. CoVs are a large family of enveloped, single-stranded positive-sense RNA viruses belonging to the order Nidovirales, which can infect a broad range of mammalian species including cats, dogs, cows, bats, and humans, and avian species. Coronaviruses possess large, trimeric spike glycoproteins (S) that mediate binding to host cell receptors as well as fusion of viral and host cell membranes. The Coronavirus family contains the genera Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. These viruses cause a range of diseases including enteric and respiratory diseases. The host range is primarily determined by the viral spike protein (S protein), which mediates entry of the virus into host cells. Coronaviruses that can infect humans are found both in the genus Alphacoronavirus and the genus Betacoronavirus. Known coronaviruses of the genus Betacoronavirus that cause respiratory disease in humans include SARS-COV, MERS-COV, HCoV-OC43 and HCoV-HKU1, and the currently circulating SARS-COV-2.
SARS-COV-2 is a coronavirus that emerged in humans from an animal reservoir in 2019 and rapidly spread globally. SARS-COV-2 is a Betacoronavirus, like MERS-COV and SARS-COV, all of which have their origin in bats. The name of the disease caused by the virus is coronavirus disease 2019, abbreviated as COVID-19. Symptoms of COVID-19 range from mild symptoms to severe illness and death for confirmed COVID-19 cases.
It is well known that viruses constantly change through mutation, and new virus variants are expected to occur over time. Sometimes new variants emerge and disappear. Other times, new variants emerge and persist. Multiple variants of the virus that causes COVID-19 have already been identified globally during this pandemic. Scientists are continuously monitoring changes in the virus, including changes to the spike protein on the surface of the virus. In collaboration with a SARS-COV-2 Interagency Group (SIG), CDC established 3 classifications for the SARS-COV-2 variants being monitored: Variant of Interest (VOI), Variant of Concern (VOC), and Variant of High Consequence (VOHC). There are currently several VOCs identified, including:
B.1.1.7: This variant was initially detected in the UK.
B.1.351: This variant was initially detected in South Africa in December 2020.
P.1: This variant was initially identified in travelers from Brazil, who were tested during routine screening at an airport in Japan, in early January.
B.1.427 and B.1.429: These two variants were first identified in California in February 2021 and were classified as VOCs in March 2021.
The B.1.526, B.1.526.1, B.1.525, B.1.617, B. 1.617.1, B. 1.617.2, B. 1.617.3, and P.2 variants circulating in the United States are classified as variants of interest.”
The B.1.1.7, B. 1.351, P.1, B.1.427, and B. 1.429 variants circulating in the United States are classified as variants of concern.
In the case of SARS-COV-2 the S protein is the major surface protein. The S protein forms homotrimers and is composed of an N-terminal S1 subunit and a C-terminal S2 subunit, responsible for receptor binding and membrane fusion, respectively. Recent cryo-EM reconstructions of the CoV trimeric S structures of alpha-, beta-, and deltacoronaviruses revealed that the S1 subunit comprises two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD). SARS-COV-2 makes use of its S1 RBD to bind to human angiotensin-converting enzyme 2 (ACE2) (Hoffmann et. al. (2020): Wrapp et. al. (2020)).
Coronaviridae S proteins are classified as class I fusion proteins and are responsible for fusion. The S protein fuses the viral and host cell membranes by irreversible protein refolding from the labile pre-fusion conformation to the stable post-fusion conformation. Like many other class I fusion proteins, Coronavirus S protein requires receptor binding and cleavage for the induction of conformational change that is needed for fusion and entry (Belouzard et al. (2009): Follis et al. (2006); Bosch et al. (2008), Madu et al. (2009): Walls et al. (2016)). Priming of SARS-COV2 involves cleavage of the S protein by furin at a furin cleavage site at the boundary between the S1 and S2 subunits (S1/S2), and by TMPRSS2 at a conserved site upstream of the fusion peptide (S2′) (Bestle et al. (2020); Hoffmann et. al. (2020)).
In order to refold from the pre-fusion to the post-fusion conformation, there are two regions that need to refold, which are referred to as the refolding region 1 (RR1) and refolding region 2 (RR2) (
When viral fusion proteins, like the SARS-COV-2 S protein, are used as vaccine components, the fusogenic function of the proteins is not important. In fact, only the mimicry of the vaccine component to the virus is important to induce reactive antibodies that can bind the virus. Therefore, for development of robust efficacious vaccine components it is desirable that the meta-stable fusion proteins are maintained in their pre-fusion conformation. It is believed that a stabilized fusion protein, such as a SARS-COV-2 S protein, in the pre-fusion conformation can induce an efficacious immune response.
In recent years several attempts have been made to stabilize various class I fusion proteins, including Coronavirus S proteins. A particularly successful approach was shown to be the stabilization of the so-called hinge loop at the end of RR1 preceding the base helix (WO2017/037196, Krarup et al. (2015); Rutten et al. (2020), Hastie et al. (2017)). This approach has also proved successful for Coronavirus S proteins, as shown for SARS-COV, MERS-COV and SARS-COV2 (Pallesen et al. (2016): Wrapp et al. (2020)). Although the proline mutations in the hinge loop indeed increase the expression of the Coronavirus S protein, the S protein may still suffer from instability. Thus, for improved vaccine design or S proteins which can for example be used as tools, e.g. as a bait for monoclonal antibody isolation, further stabilization is desired.
Since the novel SARS-COV-2 virus was first observed in humans in late 2019, over 154 million people have been infected and more than 3 million have died as a result of COVID-19, in particular because SARS-COV-2, and corona viruses more generally, lack effective treatment. In addition, there is currently no vaccine available to prevent coronavirus induced disease (COVID-19), leading to a large unmet medical need. Since emerging infectious diseases, such as COVID-19, present a major threat to public health and economic systems, there is an urgent need for novel components that can be used e.g. in vaccines to prevent coronavirus induced respiratory disease.
The invention provides recombinant SARS-COV-2 S proteins that have improved trimer yields and/or improved (thermal) stability as compared to previously described SARS-CoV-2 S proteins.
The present invention also provides stabilized, recombinant, pre-fusion SARS-COV-2 S proteins, i.e. SARS-COV-2 S proteins that are stabilized in the pre-fusion conformation, and fragments thereof.
In certain embodiments, the pre-fusion SARS-COV-2 S proteins are soluble proteins, preferably trimeric soluble proteins.
The resulting stable pre-fusion SARS-COV-2 S protein trimers are useful for immunization (vaccination) purposes, e.g. to improve chances of inducing broadly neutralizing antibodies and reducing induction of non-neutralizing and weakly neutralizing antibodies upon administration of the recombinant stabilized SARS-COV-2 S protein trimers or nucleic acid encoding the stabilized SARS-COV-2 S protein trimers.
The invention also provides nucleic acid molecules encoding the pre-fusion SARS-CoV-2 S proteins and fragments thereof, as well as vectors, e.g. adenovectors, comprising such nucleic acid molecules.
The invention further provides methods of stabilizing SARS-COV2 S proteins in the pre-fusion conformation, and to the pre-fusion SARS-COV-2 S proteins obtainable by said methods.
The invention moreover provides compositions, preferably immunogenic compositions, comprising a SARS-COV-2 S protein, or a fragment thereof, a nucleic acid molecule and/or a vector, as described herein.
The invention also provides compositions for use in inducing an immune response against SARS-COV-2 S protein, and in particular to the use thereof as a vaccine against SARS-COV-2 associated disease, such as COVID-19.
The invention also relates to methods for inducing an immune response against SARS-COV-2 in a subject, comprising administering to the subject an effective amount of a pre-fusion SARS-COV-2 S protein or a fragment thereof, a nucleic acid molecule encoding said SARS-COV-2 S protein, and/or a vector comprising said nucleic acid molecule, as described herein. Preferably, the induced immune response is characterized by the induction of neutralizing antibodies to the SARS-COV-2 virus and/or protective immunity against the SARS-COV-2 virus.
In particular aspects, the invention relates to methods for inducing anti-SARS-COV-2 S protein antibodies in a subject, comprising administering to the subject an effective amount of an immunogenic composition comprising a pre-fusion SARS-COV-2 S protein, or a fragment thereof, a nucleic acid molecule encoding said SARS-COV-2 S protein, and/or a vector comprising said nucleic acid molecule, as described herein.
The invention also relates to the use of the SARS-COV-2 S proteins or fragments thereof, as described herein, for isolating monoclonal antibodies against a SARS-COV-2 S protein from infected humans.
Also provided is the use of the pre-fusion SARS-COV-2 S proteins of the invention in methods of screening for candidate SARS-COV-2 antiviral agents, including but not limited to antibodies against SARS-COV-2.
In another general aspect, the invention relates to an isolated nucleic acid molecule encoding a recombinant SARS-COV-2 S protein of the invention and vectors comprising the isolated nucleic acid molecule operably linked to a promoter. In one embodiment, the vector is a viral vector. In another embodiment, the vector is an expression vector. In one preferred embodiment, the viral vector is an adenovirus vector.
Another general aspect relates to a host cell comprising the isolated nucleic acid molecule or vector encoding the recombinant SARS-COV-2 S protein of the invention. Such host cells can be used for recombinant protein production, recombinant protein expression, or the production of viral particles.
Another general aspect relates to methods of producing a recombinant SARS-COV-2 S protein, comprising growing a host cell comprising an isolated nucleic acid molecule or vector encoding the recombinant SARS-COV-2 S protein of the invention under conditions suitable for production of the recombinant SARS-COV-2 S protein.
The foregoing summary, as well as the following detailed description of the invention, will be better understood when read in conjunction with the appended drawings. It should be understood that the invention is not limited to the precise embodiments shown in the drawings.
As explained above, the spike protein (S) of SARS-COV-2 and of other Corona viruses is involved in fusion of the viral membrane with a host cell membrane, which is required for infection. SARS-COV-2 S RNA is translated into a 1273 amino acid precursor protein, which contains a signal peptide sequence at the N-terminus (e.g. amino acid residues 1-13 of SEQ ID NO: 1) which is removed by a signal peptidase in the endoplasmic reticulum. Priming of the S protein typically involves cleavage by host proteases at the boundary between the S1 and S2 subunits (S1/S2) in a subset of coronaviruses (including SARS-COV-2), and at a conserved site upstream of the fusion peptide (S2′) in all known corona viruses. For SARS-COV-2, furin cleaves at S1/S2 between residues 685 and 686 and subsequently within S2 at the S2′ site between residues at position 815 and 816 by TMPRSS2. C-terminal to the S2′ site the proposed fusion peptide is located at the N-terminus of the refolding region 1 (
Several vaccines against SARS-COV-2 infection are currently available. Several different vaccine modalities are possible, such as RNA or vector-based vaccines, and/or subunit vaccines based on purified S protein. Since class I proteins are metastable proteins, increasing the stability of the pre-fusion conformation of fusion proteins increases the expression level of the protein because less protein will be misfolded and more protein will successfully transport through the secretory pathway. Therefore, if the stability of the pre-fusion conformation of the class I fusion protein, like SARS-COV-2 S protein is increased, the immunogenic properties of a vector-based vaccine will be improved since the expression of the S protein is higher and the conformation of the immunogen resembles the pre-fusion conformation that is recognized by potent neutralizing and protective antibodies. For subunit-based vaccines, stabilizing the pre-fusion S conformation is even more important. In addition, it is important that the stabilized S proteins have improved trimer yields as compared to previously described SARS-COV-2 S protein trimers. Besides the importance of high expression, which is needed to manufacture a vaccine successfully, maintenance of the trimeric pre-fusion conformation during the manufacturing process and during storage over time is critical for protein-based vaccines. In addition, for a soluble, subunit-based vaccine, the SARS-COV-2 S protein needs to be truncated by deletion of the transmembrane (TM) and the cytoplasmic region to create a soluble secreted S protein (sS). Because the TM region is responsible for membrane anchoring and increases stability, the anchorless soluble S protein is considerably more labile than the full-length protein and will even more readily refold into the post-fusion end-state. In order to obtain soluble trimeric S protein in the stable pre-fusion conformation that shows high expression levels and high stability, the pre-fusion conformation thus needs to be stabilized. Because also the full length (membrane-bound) SARS-COV-2 S protein is metastable, the stabilization of the pre-fusion conformation is also desirable for the full-length SARS-COV-2 S protein, i.e. including the TM and cytoplasmic region, e.g. for any DNA, RNA, live attenuated or vector-based vaccine approach.
The present invention provides recombinant SARS-COV-2 S proteins that have improved trimer yields and/or improved (thermal) stability as compared to previously described SARS-COV-2 S proteins.
The present invention thus provides stabilized, recombinant pre-fusion SARS-COV-2 S proteins, comprising an S1 and an S2 domain, and comprising at least one mutation selected from the group consisting of a mutation of at least one amino acid in the loop region corresponding to amino acid residues 941-945 into P, a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutation at position 572, a mutation at position 532, a disulfide bridge between residues 880 and 888, and a disulfide bridge between residues 884 and 893, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1, and fragments thereof. According to the invention it has been demonstrated that the presence of specific amino acids and/or a disulfide bridge at the indicated positions increase the stability of the proteins in the pre-fusion conformation. According to the invention, the specific amino acids or disulfide bridges are introduced by substitution (mutation) of the amino acid at that position into a specific amino acid according to the invention. According to the invention, the proteins thus comprise one or more mutations in their amino acid sequence, i.e. the naturally occurring amino acid at these positions has been substituted with another amino acid. In certain embodiments, the proteins comprise an amino acid sequences, wherein the amino acid at position 892 is not alanine (A), the amino acid at position 614 is not aspartic acid (D), the amino acid at position 532 is not Asparagine (N) and/or amino acid at position 572 is not threonine (T).
In certain embodiments, the proteins comprise at least two mutations comprising a mutation of at least one amino acid in the loop region corresponding to amino acid residues 941-945 into P, and a mutation selected from the group consisting of a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutation at position 572, a mutation at position 532, a disulfide bridge between residues 880 and 888 and a disulfide bridge between residues 884 and 893.
In certain embodiments, the proteins comprise at least two mutations comprising a mutation of at least one amino acid in the loop region corresponding to amino acid residues 941-945 into P, and a mutation selected from the group consisting of a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutations at position 572 and a mutations at position 532, a disulfide bridge between residues 880 and 888 and a disulfide bridge between residues 884 and 893, provided that the proteins do not comprise both the disulfide bridge between residues 880 and 888 and the disulfide bridge between residues 884 and 893.
In certain embodiments, the proteins thus comprise a mutation of at least one amino in the loop region corresponding to amino acid residues 941-945 into P, a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutation of the amino acid at position 572, and/or a mutation at position 532, and/or either a disulfide bridge between residues 880 and 888 or a disulfide bridge between residues 884 and 893.
In a preferred embodiment, the disulfide bridge is a disulfide bridge between residues 880 and 888. According to the invention it is to be understood that “a disulfide bridge between residues 880 and 880” means that the amino acids at the positions 880 and 888 have been mutated into C. Similarly, it is to be understood that “a disulfide bridge between residues 884 and 893” means that the amino acids at the positions 884 and 893 have been mutated into C
In certain embodiments, the at least one mutation in the loop region corresponding to amino acid residues 941-945 is a mutation of the amino acid at position 942 into P. Alternatively, or in addition, the at least one mutation in the loop region corresponding to amino acid residues 941-945 is a mutation of the amino acid at position 941 into P.
Alternatively, or in addition, the at least one mutation in the loop region corresponding to amino acid residues 941-945 is a mutation of the amino acid at position 944 into P.
Alternatively, or in addition, the mutation at position 892 is a mutation into P.
Alternatively, or in addition, the mutation at position 614 is a mutation into N or G.
Alternatively, or in addition, the mutation at position 532 is a mutation into P.
Alternatively, or in addition, the mutation at position 572 is a mutation into I.
The invention thus also provides stabilized, recombinant pre-fusion SARS-COV-2 S proteins, comprising an S1 and an S2 domain, wherein the amino acid at position 941, 942 or 944 is P, the amino acid at position 892 is P, the amino acid at position 614 is N or G, the amino acid at position 572 is I, and/or the amino acid at position 532 is P, and/or comprising a disulfide bridge between residues 880 and 888, and/or a disulfide bridge between residues 884 and 893, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In a preferred embodiment, the amino acid at position 892 is proline (P), the amino acid at position 614 is asparagine (N) or glycine (G), the amino acid at position 942 is proline (P) or the amino acid at position 944 is proline (P).
An amino acid according to the invention can be any of the twenty naturally occurring (or ‘standard’ amino acids) or variants thereof, such as e.g. D-amino acids (the D-enantiomers of amino acids with a chiral center), or any variants that are not naturally found in proteins, such as e.g. norleucine. Each known natural amino acid has a full name, an abbreviated one letter code, and an abbreviated three letter code, all of which are well known to those of ordinary skill in the art. For example, the three and one letter abbreviated codes used for the twenty naturally occurring amino acids are as follows: alanine (Ala: A), arginine (Arg: R), aspartic acid (Asp: D), asparagine (Asn: N), cysteine (Cys: C), glycine (Gly: G), glutamic acid (Glu: E), glutamine (Gln: Q), histidine (His: H), isoleucine (Ile: I), leucine (Leu: L), lysine (Lys: K), methionine (Met: M), phenylalanine (Phe: F), proline (Pro: P), serine (Ser; S), threonine (Thr: T), tryptophan (Trp: W), tyrosine (Tyr: Y) and valine (Val: V). Amino acids can be referred to by their full name, one letter abbreviated code, or three letter abbreviated code. The standard amino acids can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size and functional groups. These properties are important for protein structure and protein-protein interactions. Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds (or disulfide bridges) to other cysteine residues, proline that induces turns of the polypeptide backbone, and glycine that is more flexible than other amino acids. Table 1 shows the abbreviations and properties of the standard amino acids.
It will be appreciated by a skilled person that the mutations can be made to the protein by routine molecular biology procedures.
In certain embodiments, the present invention provides recombinant SARS-COV-2 S proteins, and fragments thereof, wherein the amino acid at position 942 is P, the amino acid at position 892 is P, the amino acid at position 614 is N or G, the amino acid at position 532 is P and/or the amino acid at position 572 is I, and/or which comprise a disulfide bridge between residues 880 and 888 or a disulfide bridge between residues 884 and 893, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In a preferred embodiment, the invention provides SARS-COV-2 proteins or fragments thereof, wherein the amino acid at position 942 is P, the amino acid at position 614 is N or G, and which comprise a disulfide bridge between residues 880 and 888, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In certain embodiments, the SARS-COV-2 S proteins further comprise a deletion of the furin cleavage site. A deletion of the furin cleavage, e.g. by mutation of one or more amino acids in the furin cleavage site (such that the protein is not cleaved by furin), renders the protein uncleaved, which further increases its stability. Deleting the furin cleavage site can be achieved in any suitable way that is known to the skilled person. In certain embodiments, the deletion of the furin cleavage site comprises a mutation of the amino acid at position 682 into S and/or a mutation of the amino acid at position 685 into G.
In certain embodiments, the proteins further comprise a mutation of the amino acids at position 986 and/or 987 into proline. In certain embodiments, the amino acid at position 986 is not proline. In certain embodiments, the amino acid at position 986 is K and the amino acid at position 987 is P.
In preferred embodiments, the present invention provides recombinant SARS-COV-2 S proteins, and fragments thereof, comprising a deletion of the furin cleavage site, and wherein the amino acid at position 942 is P, the amino acid at position 892 is P, the amino acid at position 987 is P, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In another preferred embodiment, the present invention provides recombinant SARS-CoV-2 S proteins, and fragments thereof, comprising a deletion of the furin cleavage site and wherein the amino acid at position 942 is P, the amino acid at position 892 is P, the amino acid at position 614 is N or G, the amino acid at position 987 is P, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In another preferred embodiment, the SARS-COV-2 S proteins comprise a deletion of the furin cleavage site and the amino acid at position 942 is P, the amino acid at position 892 is P, the amino acid at position 614 is N and the amino acid at position 987 is P.
In another preferred embodiment, the SARS-COV-2 S proteins comprise a deletion of the furin cleavage site and the amino acid at position 944 is P, the amino acid at position 614 is G, the amino acid at position 572 is I, the amino acid at position 532 is P, and comprises a disulfide bridge between residues 880 and 888, and wherein the amino acid at position 987 is P.
In certain embodiments, the invention provides SARS-COV 2 proteins comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 5-194 and SEQ ID NO: 197-418, SEQ ID NO: 420 and SEQ ID NO: 421, or fragments thereof. In a preferred embodiment, the SARS-COV 2 proteins comprise an amino acid sequence of SEQ ID NO: 417 or SEQ ID NO: 418. In certain embodiments, the proteins according to the invention do not comprise a signal peptide sequence or a tag sequence.
The term “fragment” as used herein refers to a peptide that has an amino-terminal and/or carboxy-terminal and/or internal deletion, but where the remaining amino acid sequence is identical to the corresponding positions in the sequence of a SARS-COV-2 S protein, for example, the full-length sequence of a SARS-COV-2 S protein. It will be appreciated that for inducing an immune response and in general for vaccination purposes, a protein needs not to be full length nor have all its wild type functions, and fragments of the protein are equally useful. A fragment according to the invention is an immunologically active fragment, and typically comprises at least 15 amino acids, or at least 30 amino acids, of the SARS-COV-2 S protein. In certain embodiments, it comprises at least 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, or 550 amino acids, of the SARS-COV-2 S protein. In certain documents, a fragment is the SARS-COV-2 S ectodomain.
In certain embodiments, the proteins according to the invention are soluble (trimeric) proteins, e.g. S protein ectodomains, and comprise a truncated S2 domain. As used herein a “truncated” S2 domain refers to a S2 domain that is not a full length S2 domain, i.e. wherein either N-terminally or C-terminally one or more amino acid residues have been deleted. According to the invention, at least the transmembrane domain and cytoplasmic domain are deleted (corresponding to the amino acids 1-1208 of SEQ ID NO: 1) to permit expression as a soluble ectodomain (corresponding to the amino acids 1-1208 of SEQ ID NO: 1). For the stabilization of such soluble trimeric SARS-COV-2 S protein in the pre-fusion conformation, a heterologous trimerization domain, such as a fibritin-based trimerization domain, may be fused to the C-terminus of the Corona virus S protein ectodomain. This fibritin domain or ‘Foldon’ is derived from T4 fibritin and was described earlier as an artificial natural trimerization domain (Letarov et al., (1993): S-Guthe et al., (2004)). Thus, in certain embodiments, the transmembrane region has been replaced by a heterologous trimerization domain. In a preferred embodiment, the heterologous trimerization domain is a foldon domain comprising the amino acid sequence of SEQ ID NO:4. However, it is to be understood that according to the invention other trimerization domains are also possible or no heterologous trimerization domain is added to the S ectodomain.
In a preferred embodiment, the soluble trimeric SARS-COV2 S proteins of the invention do not comprise a heterologous trimerization domain.
In preferred embodiments, the present invention provides recombinant SARS-COV-2 S proteins comprising a truncated S2 domain and comprising a deletion of the furin cleavage site and wherein the amino acid at position 942 is P, the amino acid at position 892 is P, the amino acid at position 987 is P, wherein the protein does not comprise a heterologous trimerization domain and wherein numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In preferred embodiments, the present invention provides recombinant SARS-COV-2 S proteins comprising a truncated S2 domain and comprising a deletion of the furin cleavage site and wherein the amino acid at position 942 is P, the amino acid at position 892 is P, the amino acid at position 614 is N or G, the amino acid at position 987 is P, wherein the protein does not comprise a heterologous trimerization domain and wherein numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
The recombinant prefusion SARS-COV-2 S proteins according to the invention preferably have improved trimer yields and/or improved (thermal) stability.
Alternatively, or in addition, the prefusion SARS-COV-2 S proteins according to the invention induce increased titers of neutralizing antibodies, as compared to SARS-COV-2 S proteins without the stabilizing mutations of the invention.
In certain embodiment, the pre-fusion SARS-COV-2 S proteins according to the invention are stable, i.e. do not readily change into the post-fusion conformation upon processing of the proteins, such as e.g. upon purification, freeze-thaw cycles, and/or storage etc. In certain embodiments, the pre-fusion SARS-COV-2 S proteins have an increased stability as compared to SARS-COV-2 S proteins without the mutations of the invention, e.g. as indicated by an increased melting temperature (measured by e.g. differential scanning fluorimetry).
The proteins according to the invention may comprise a signal peptide, also referred to as signal sequence or leader peptide, corresponding to amino acids 1-13 of SEQ ID NO: 1. Signal peptides are short (typically 5-30 amino acids long) peptides present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.
In certain embodiments, the proteins according to the invention do not comprise a signal peptide.
In certain embodiments, the proteins comprise a tag sequence, such as a HIS-Tag or C-Tag. A His-Tag (or polyhistidine-tag) is an amino acid motif in proteins that consists of at least five histidine (H) residues, preferably placed at the N- or C-terminus of the protein, which is generally used for purification purposes. Alternatively, other tags like a C-tag can be used for these purposes. In certain embodiments, the proteins according to the invention do not comprise a tag sequence.
The invention also provides methods for stabilizing a SARS-COV-2 S protein, said method comprising introducing in the amino acid sequence of a SARS-COV-2 S protein at least one mutation selected from the group consisting of a mutation of at least one amino acid in the loop region corresponding to amino acid residues 941-945 into P, a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutation at position 572, a mutation at position 532, a disulfide bridge between residues 880 and 888, and a disulfide bridge between residues 884 and 893, wherein the numbering of the amino acid positions is according to the numbering of the amino acid positions in SEQ ID NO: 1.
In certain embodiments, the methods comprise introducing at least two mutations comprising a mutation of at least one amino acid in the loop region corresponding to amino acid residues 941-945 into P, and a mutation selected from the group consisting of a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutation at position 572, a mutation at position 532, a disulfide bridge between residues 880 and 888 and a disulfide bridge between residues 884 and 893.
In certain embodiments, the methods comprise introducing at least two mutations comprising a mutation of at least one amino acid in the loop region corresponding to amino acid residues 941-945 into P, and a mutation selected from the group consisting of a mutation of the amino acid at position 892, a mutation of the amino acid at position 614, a mutation at position 572, a mutation at position 532, a disulfide bridge between residues 880 and 888 and a disulfide bridge between residues 884 and 893, provided that the proteins do not comprise both the disulfide bridge between residues 880 and 888 and the disulfide bridge between residues 884 and 893.
In certain embodiments, the at least one mutation in the loop region corresponding to amino acid residues 941-945 is a mutation of the amino acid at position 942 into P. Alternatively, or in addition, the at least one mutation in the loop region corresponding to amino acid residues 941-945 is a mutation of the amino acid at position 941 into P.
Alternatively, or in addition, the at least one mutation in the loop region corresponding to amino acid residues 941-945 is a mutation of the amino acid at position 944 into P.
Alternatively, or in addition, the mutation at position 892 is a mutation into P.
Alternatively, or in addition, the mutation at position 614 is a mutation into N or G.
Alternatively, or in addition, the mutation at position 532 is a mutation into P.
Alternatively, or in addition, the mutation at position 572 is a mutation into I.
Alternatively, or in addition, the methods further comprise deleting the furin cleavage site. Deleting the furin cleavage site may be achieved in any way known in the art.
In certain embodiments, the deletion of the furin cleavage site comprises introducing a mutation of the amino acid at position 682 into S and/or a mutation of the amino acid at position 685 into G.
Alternatively, or in addition, the methods further comprise introducing a mutation of the amino acids at position 986 and/or 987 into proline. In a preferred embodiment, the methods comprise introducing a mutation of the amino acid at position 987 into proline.
The present invention further provides nucleic acid molecules encoding the SARS-CoV-2 S proteins according to the invention. The term “nucleic acid molecule” as used in the present invention refers to a polymeric form of nucleotides (i.e. polynucleotides) and includes both DNA (e.g. cDNA, genomic DNA) and RNA, and synthetic forms and mixed polymers of the above.
In preferred embodiments, the nucleic acid molecules encoding the proteins according to the invention are codon-optimized for expression in mammalian cells, preferably human cells, or insect cells. Methods of codon-optimization are known and have been described previously (e.g. WO 96/09378 for mammalian cells). A sequence is considered codon-optimized if at least one non-preferred codon as compared to a wild type sequence is replaced by a codon that is more preferred. Herein, a non-preferred codon is a codon that is used less frequently in an organism than another codon coding for the same amino acid, and a codon that is more preferred is a codon that is used more frequently in an organism than a non-preferred codon. The frequency of codon usage for a specific organism can be found in codon frequency tables, such as in http://www.kazusa.or.jp/codon. Preferably more than one non-preferred codon, preferably most or all non-preferred codons, are replaced by codons that are more preferred. Preferably the most frequently used codons in an organism are used in a codon-optimized sequence. Replacement by preferred codons generally leads to higher expression.
It will be understood by a skilled person that numerous different polynucleotides and nucleic acid molecules can encode the same protein as a result of the degeneracy of the genetic code. It is also understood that skilled persons may, using routine techniques, make nucleotide substitutions that do not affect the protein sequence encoded by the nucleic acid molecules to reflect the codon usage of any particular host organism in which the proteins are to be expressed. Therefore, unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. Nucleotide sequences that encode proteins and RNA may or may not include introns.
Nucleic acid sequences can be cloned using routine molecular biology techniques, or generated de novo by DNA synthesis, which can be performed using routine procedures by service companies having business in the field of DNA synthesis and/or molecular cloning (e.g. GeneArt, GenScript, Invitrogen, Eurofins).
In certain embodiments, the nucleic acid sequences encode SARS-COV 2 proteins comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 5-194 and SEQ ID NO: 197-418, SEQ ID NO: 420 and SEQ ID NO: 421, or fragments thereof.
In a preferred embodiment, the nucleic acid sequence encodes a SARS-COV 2 protein comprising an amino acid sequence of SEQ ID NO: 417 or SEQ ID NO: 418.
The invention also provides vectors comprising a nucleic acid molecule as described above. In certain embodiments, a nucleic acid molecule according to the invention thus is part of a vector. Such vectors can easily be manipulated by methods well known to the person skilled in the art and can for instance be designed for being capable of replication in prokaryotic and/or eukaryotic cells. In addition, many vectors can be used for transformation of eukaryotic cells and will integrate in whole or in part into the genome of such cells, resulting in stable host cells comprising the desired nucleic acid in their genome. The vector used can be any vector that is suitable for cloning DNA and that can be used for transcription of a nucleic acid of interest.
In certain embodiments of the invention, the vector is an adenovirus vector. An adenovirus according to the invention belongs to the family of the Adenoviridae, and preferably is one that belongs to the genus Mastadenovirus. It can be a human adenovirus, but also an adenovirus that infects other species, including but not limited to a bovine adenovirus (e.g. bovine adenovirus 3, BAdV3), a canine adenovirus (e.g. CAdV2), a porcine adenovirus (e.g. PAdV3 or 5), or a simian adenovirus (which includes a monkey adenovirus and an ape adenovirus, such as a chimpanzee adenovirus or a gorilla adenovirus). Preferably, the adenovirus is a human adenovirus (HAdV, or AdHu), or a simian adenovirus such as chimpanzee or gorilla adenovirus (ChAd, AdCh, or SAdV), or a rhesus monkey adenovirus (RhAd). In the invention, a human adenovirus is meant if referred to as Ad without indication of species, e.g. the brief notation “Ad26” means the same as HAdV26, which is human adenovirus serotype 26. Also as used herein, the notation “rAd” means recombinant adenovirus, e.g., “rAd26” refers to recombinant human adenovirus 26.
Most advanced studies have been performed using human adenoviruses, and human adenoviruses are preferred according to certain aspects of the invention. In certain preferred embodiments, a recombinant adenovirus according to the invention is based upon a human adenovirus. In preferred embodiments, the recombinant adenovirus is based upon a human adenovirus serotype 5, 11, 26, 34, 35, 48, 49, 50, 52, etc. According to a particularly preferred embodiment of the invention, an adenovirus is a human adenovirus of serotype 26. Advantages of these serotypes include a low seroprevalence and/or low pre-existing neutralizing antibody titers in the human population, and experience with use in human subjects in clinical trials.
Simian adenoviruses generally also have a low seroprevalence and/or low pre-existing neutralizing antibody titers in the human population, and a significant amount of work has been reported using chimpanzee adenovirus vectors (e.g. U.S. Pat. No. 6,083,716; WO 2005/071093; WO 2010/086189; WO 2010085984; Farina et al, 2001, J Virol 75: 11603-13; Cohen et al, 2002, J Gen Virol 83: 151-55: Kobinger et al, 2006, Virology 346: 394-401: Tatsis et al., 2007, Molecular Therapy 15: 608-17: see also review by Bangari and Mittal, 2006, Vaccine 24: 849-62; and review by Lasaro and Ertl, 2009, Mol Ther 17: 1333-39). Hence, in other embodiments, the recombinant adenovirus according to the invention is based upon a simian adenovirus, e.g. a chimpanzee adenovirus. In certain embodiments, the recombinant adenovirus is based upon simian adenovirus type 1, 7, 8, 21, 22, 23, 24, 25, 26, 27.1, 28.1, 29, 30, 31.1, 32, 33, 34, 35.1, 36, 37.2, 39, 40.1, 41.1, 42.1, 43, 44, 45, 46, 48, 49, 50 or SA7P. In certain embodiments, the recombinant adenovirus is based upon a chimpanzee adenovirus such as ChAdOx 1 (see e.g. WO 2012/172277), or ChAdOx 2 (see e.g. WO 2018/215766). In certain embodiments, the recombinant adenovirus is based upon a chimpanzee adenovirus such as BZ28 (see e.g. WO 2019/086466). In certain embodiments, the recombinant adenovirus is based upon a gorilla adenovirus such as BLY6 (see e.g. WO 2019/086456), or BZ1 (see e.g. WO 2019/086466).
Preferably, the adenovirus vector is a replication deficient recombinant viral vector, such as rAd26, rAd35, rAd48, rAd5HVR48, etc.
In a preferred embodiment of the invention, the adenoviral vectors comprise capsid proteins from rare serotypes, e.g. including Ad26. In the typical embodiment, the vector is an rAd26 virus. An “adenovirus capsid protein” refers to a protein on the capsid of an adenovirus (e.g., Ad26, Ad35, rAd48, rAd5HVR48 vectors) that is involved in determining the serotype and/or tropism of a particular adenovirus. Adenoviral capsid proteins typically include the fiber, penton and/or hexon proteins. As used herein a “capsid protein” for a particular adenovirus, such as an “Ad26 capsid protein” can be, for example, a chimeric capsid protein that includes at least a part of an Ad26 capsid protein. In certain embodiments, the capsid protein is an entire capsid protein of Ad26. In certain embodiments, the hexon, penton and fiber are of Ad26.
One of ordinary skill in the art will recognize that elements derived from multiple serotypes can be combined in a single recombinant adenovirus vector. Thus, a chimeric adenovirus that combines desirable properties from different serotypes can be produced. Thus, in some embodiments, a chimeric adenovirus of the invention could combine the absence of pre-existing immunity of a first serotype with characteristics such as temperature stability, assembly, anchoring, production yield, redirected or improved infection, stability of the DNA in the target cell, and the like. See for example WO 2006/040330 for chimeric adenovirus Ad5HVR48, that includes an Ad5 backbone having partial capsids from Ad48, and also e.g. WO 2019/086461 for chimeric adenoviruses Ad26HVRPtr1, Ad26HVRPtr12, and Ad26HVRPtr13, that include an Ad26 virus backbone having partial capsid proteins of Ptr1, Ptr12, and Ptr13, respectively)
In certain embodiments the recombinant adenovirus vector useful in the invention is derived mainly or entirely from Ad26 (i.e., the vector is rAd26). In some embodiments, the adenovirus is replication deficient, e.g., because it contains a deletion in the E1 region of the genome. For adenoviruses being derived from non-group C adenovirus, such as Ad26 or Ad35, it is typical to exchange the E4-orf6 coding sequence of the adenovirus with the E4-orf6 of an adenovirus of human subgroup C such as Ad5. This allows propagation of such adenoviruses in well-known complementing cell lines that express the E1 genes of Ad5, such as for example 293 cells, PER.C6 cells, and the like (see, e.g. Havenga, et al., 2006, J Gen Virol 87: 2135-43: WO 03/104467). However, such adenoviruses will not be capable of replicating in non-complementing cells that do not express the E1 genes of Ad5.
The preparation of recombinant adenoviral vectors is well known in the art. Preparation of rAd26 vectors is described, for example, in WO 2007/104792 and in Abbink et al., (2007) Virol 81(9): 4654-63. Exemplary genome sequences of Ad26 are found in GenBank Accession EF 153474 and in SEQ ID NO: 1 of WO 2007/104792. Examples of vectors useful for the invention for instance include those described in WO2012/082918, the disclosure of which is incorporated herein by reference in its entirety.
Typically, a vector useful in the invention is produced using a nucleic acid comprising the entire recombinant adenoviral genome (e.g., a plasmid, cosmid, or baculovirus vector). Thus, the invention also provides isolated nucleic acid molecules that encode the adenoviral vectors of the invention. The nucleic acid molecules of the invention can be in the form of RNA or in the form of DNA obtained by cloning or produced synthetically. The DNA can be double-stranded or single-stranded.
The adenovirus vectors useful in the invention are typically replication deficient. In these embodiments, the virus is rendered replication deficient by deletion or inactivation of regions critical to replication of the virus, such as the E1 region. The regions can be substantially deleted or inactivated by, for example, inserting a gene of interest, such as a gene encoding a SARS-COV-2 S protein (usually linked to a promoter) within the region. In some embodiments, the vectors of the invention can contain deletions in other regions, such as the E2, E3 or E4 regions, or insertions of heterologous genes linked to a promoter within one or more of these regions. For E2- and/or E4-mutated adenoviruses, generally E2- and/or E4-complementing cell lines are used to generate recombinant adenoviruses. Mutations in the E3 region of the adenovirus need not be complemented by the cell line, since E3 is not required for replication.
A packaging cell line is typically used to produce sufficient amounts of adenovirus vectors for use in the invention. A packaging cell is a cell that comprises those genes that have been deleted or inactivated in a replication deficient vector, thus allowing the virus to replicate in the cell. Suitable packaging cell lines for adenoviruses with a deletion in the E1 region include, for example, PER. C6, 911, 293, and E1 A549.
In a preferred embodiment of the invention, the vector is an adenovirus vector, and more preferably a rAd26 vector, most preferably a rAd26 vector with at least a deletion in the E1 region of the adenoviral genome, e.g. such as that described in Abbink, J Virol, 2007. 81(9): p. 4654-63, which is incorporated herein by reference. Typically, the nucleic acid sequence encoding the SARS-COV-2 S protein is cloned into the E1 and/or the E3 region of the adenoviral genome.
Host cells comprising the nucleic acid molecules encoding the pre-fusion SARS-COV-2 S proteins also form part of the invention. The pre-fusion SARS-COV-2 S proteins may be produced through recombinant DNA technology involving expression of the molecules in host cells, e.g. Chinese hamster ovary (CHO) cells, tumor cell lines, BHK cells, human cell lines such as HEK293 cells, PER. C6 cells, or yeast, fungi, insect cells, and the like, or transgenic animals or plants. In certain embodiments, the cells are from a multicellular organism, in certain embodiments they are of vertebrate or invertebrate origin. In certain embodiments, the cells are mammalian cells, such as human cells, or insect cells. In general, the production of a recombinant proteins, such the pre-fusion SARS-COV-2 S proteins of the invention, in a host cell comprises the introduction of a heterologous nucleic acid molecule encoding the protein in expressible format into the host cell, culturing the cells under conditions conducive to expression of the nucleic acid molecule and allowing expression of the protein in said cell. The nucleic acid molecule encoding a protein in expressible format may be in the form of an expression cassette, and usually requires sequences capable of bringing about expression of the nucleic acid, such as enhancer(s), promoter, polyadenylation signal, and the like. The person skilled in the art is aware that various promoters can be used to obtain expression of a gene in host cells. Promoters can be constitutive or regulated, and can be obtained from various sources, including viruses, prokaryotic, or eukaryotic sources, or artificially designed.
Cell culture media are available from various vendors, and a suitable medium can be routinely chosen for a host cell to express the protein of interest, here the pre-fusion SARS-CoV-2 S proteins. The suitable medium may or may not contain serum.
A “heterologous nucleic acid molecule” (also referred to herein as ‘transgene’) is a nucleic acid molecule that is not naturally present in the host cell. It is introduced into for instance a vector by standard molecular biology techniques. A transgene is generally operably linked to expression control sequences. This can for instance be done by placing the nucleic acid encoding the transgene(s) under the control of a promoter. Further regulatory sequences may be added. Many promoters can be used for expression of a transgene(s), and are known to the skilled person, e.g. these may comprise viral, mammalian, synthetic promoters, and the like. A non-limiting example of a suitable promoter for obtaining expression in eukaryotic cells is a CMV-promoter (U.S. Pat. No. 5,385,839), e.g. the CMV immediate early promoter, for instance comprising nt. −735 to +95 from the CMV immediate early gene enhancer/promoter. A polyadenylation signal, for example the bovine growth hormone poly A signal (U.S. Pat. No. 5,122,458), may be present behind the transgene(s). Alternatively, several widely used expression vectors are available in the art and from commercial sources, e.g. the pcDNA and pEF vector series of Invitrogen, pMSCV and pTK-Hyg from BD Sciences, pCMV-Script from Stratagene, etc, which can be used to recombinantly express the protein of interest, or to obtain suitable promoters and/or transcription terminator sequences, polyA sequences, and the like.
The cell culture can be any type of cell culture, including adherent cell culture, e.g. cells attached to the surface of a culture vessel or to microcarriers, as well as suspension culture. Most large-scale suspension cultures are operated as batch or fed-batch processes because they are the most straightforward to operate and scale up. Nowadays, continuous processes based on perfusion principles are becoming more common and are also suitable. Suitable culture media are also well known to the skilled person and can generally be obtained from commercial sources in large quantities, or custom-made according to standard protocols. Culturing can be done for instance in dishes, roller bottles or in bioreactors, using batch, fed-batch, continuous systems and the like. Suitable conditions for culturing cells are known (see e.g. Tissue Culture, Academic Press, Kruse and Paterson, editors (1973), and R.I. Freshney, Culture of animal cells: A manual of basic technique, fourth edition (Wiley-Liss Inc., 2000, ISBN 0-471-34889-9)).
The invention further provides compositions comprising a pre-fusion SARS-COV-2 S protein and/or a nucleic acid molecule, and/or a vector, as described above. The invention also provides compositions comprising a nucleic acid molecule and/or a vector, encoding such pre-fusion SARS-COV-2 S protein. The invention further provides immunogenic compositions comprising a pre-fusion SARS-COV-2 S protein, and/or a nucleic acid molecule, and/or a vector, as described above. The invention also provides the use of a stabilized pre-fusion SARS-COV-2 S protein, a nucleic acid molecule, and/or a vector, according to the invention, for inducing an immune response against a SARS-COV-2 S protein in a subject. Further provided are methods for inducing an immune response against SARS-COV-2 S protein in a subject, comprising administering to the subject a pre-fusion SARS-COV-2 S protein, and/or a nucleic acid molecule, and/or a vector according to the invention. Also provided are pre-fusion SARS-COV-2 S proteins, nucleic acid molecules, and/or vectors, according to the invention for use in inducing an immune response against SARS-COV-2 S protein in a subject. Further provided is the use of the pre-fusion SARS-CoV-2 S proteins, and/or nucleic acid molecules, and/or vectors according to the invention for the manufacture of a medicament for use in inducing an immune response against SARS-CoV-2 S protein in a subject. In certain embodiments, the nucleic acid molecule is DNA and/or an RNA molecule.
The pre-fusion SARS-COV-2 S proteins, nucleic acid molecules, or vectors of the invention may be used for prevention (prophylaxis, including post-exposure prophylaxis) of SARS-COV-2 infections.
As used herein SARS-COV-2 may refer to the Wuhan-Hu-1 strain as originally identified in 2019 in Wuhan, or to variants thereof, e.g. variants comprising one or more mutations in the S protein, including but not limited to the B.1, B1.1.7, B.1.351, P1, B. 1.427, B.1.429, B.1.526, B.1.526.1, B.1.525, B.1.617, B.1.617.1, B. 1.617.2, B.1.617.3, and P.2 virus variants.
In certain embodiments, the prevention may be targeted at patient groups that are susceptible for and/or at risk of SARS-COV-2 infection or have been diagnosed with a SARS-CoV-2 infection. Such target groups include, but are not limited to e.g., the elderly (e.g. ≥50 years old, ≥60 years old, and preferably ≥65 years old), hospitalized patients and patients who have been treated with an antiviral compound but have shown an inadequate antiviral response. In certain embodiments, the target population comprises human subjects from 2 months of age.
The pre-fusion SARS-COV-2 S proteins, nucleic acid molecules and/or vectors according to the invention may be used e.g. in stand-alone treatment and/or prophylaxis of a disease or condition caused by SARS-COV-2, or in combination with other prophylactic and/or therapeutic treatments, such as (existing or future) vaccines, antiviral agents and/or monoclonal antibodies.
The invention further provides methods for preventing and/or treating SARS-COV-2 infection in a subject utilizing the pre-fusion SARS-COV-2 S proteins, nucleic acid molecules and/or vectors according to the invention. In a specific embodiment, a method for preventing and/or treating SARS-COV-2 infection in a subject comprises administering to a subject in need thereof an effective amount of a pre-fusion SARS-COV-2 S protein, nucleic acid molecule and/or a vector, as described above. A therapeutically effective amount refers to an amount of a protein, nucleic acid molecule or vector, that is effective for preventing, ameliorating and/or treating a disease or condition resulting from infection by SARS-COV-2. Prevention encompasses inhibiting or reducing the spread of SARS-COV-2 or inhibiting or reducing the onset, development or progression of one or more of the symptoms associated with infection by SARS-COV-2. Amelioration as used in herein may refer to the reduction of visible or perceptible disease symptoms, viremia, or any other measurable manifestation of SARS-COV-2 infection.
For administering to subjects, such as humans, the invention may employ pharmaceutical compositions comprising a pre-fusion SARS-COV-2 S protein, a nucleic acid molecule and/or a vector as described herein, and a pharmaceutically acceptable carrier or excipient. In the present context, the term “pharmaceutically acceptable” means that the carrier or excipient, at the dosages and concentrations employed, will not cause any unwanted or harmful effects in the subjects to which they are administered. Such pharmaceutically acceptable carriers and excipients are well known in the art (see Remington's Pharmaceutical Sciences, 18th edition, A. R. Gennaro, Ed., Mack Publishing Company [1990]: Pharmaceutical Formulation Development of Peptides and Proteins, S. Frokjaer and L. Hovgaard, Eds., Taylor & Francis [2000]; and Handbook of Pharmaceutical Excipients, 3rd edition, A. Kibbe, Ed., Pharmaceutical Press [2000]). The CoV S proteins, or nucleic acid molecules, preferably are formulated and administered as a sterile solution although it may also be possible to utilize lyophilized preparations. Sterile solutions are prepared by sterile filtration or by other methods known per se in the art. The solutions are then lyophilized or filled into pharmaceutical dosage containers. The pH of the solution generally is in the range of pH 3.0 to 9.5, e.g. pH 5.0 to 7.5. The CoV S proteins typically are in a solution having a suitable pharmaceutically acceptable buffer, and the composition may also contain a salt. Optionally stabilizing agent may be present, such as albumin. In certain embodiments, detergent is added. In certain embodiments, the CoV S proteins may be formulated into an injectable preparation.
In certain embodiments, a composition according to the invention further comprises one or more adjuvants. Adjuvants are known in the art to further increase the immune response to an applied antigenic determinant. The terms “adjuvant” and “immune stimulant” are used interchangeably herein and are defined as one or more substances that cause stimulation of the immune system. In this context, an adjuvant is used to enhance an immune response to the SARS-COV-2 S proteins of the invention. Examples of suitable adjuvants include aluminium salts such as aluminium hydroxide and/or aluminium phosphate: oil-emulsion compositions (or oil-in-water compositions), including squalene-water emulsions, such as MF59 (see e.g. WO 90/14837): saponin formulations, such as for example QS21 and Immunostimulating Complexes (ISCOMS) (see e.g. U.S. Pat. No. 5,057,540; WO 90/03184, WO 96/11711, WO 2004/004762, WO 2005/002620); bacterial or microbial derivatives, examples of which are monophosphoryl lipid A (MPL), 3-O-deacylated MPL (3dMPL), CpG-motif containing oligonucleotides, ADP-ribosylating bacterial toxins or mutants thereof, such as E. coli heat labile enterotoxin LT, cholera toxin CT, and the like: eukaryotic proteins (e.g. antibodies or fragments thereof (e.g. directed against the antigen itself or CD1a, CD3, CD7, CD80) and ligands to receptors (e.g. CD40L, GMCSF, GCSF, etc), which stimulate immune response upon interaction with recipient cells. In certain embodiments the compositions of the invention comprise aluminium as an adjuvant, e.g. in the form of aluminium hydroxide, aluminium phosphate, aluminium potassium phosphate, or combinations thereof, in concentrations of 0.05-5 mg, e.g. from 0.075-1.0 mg, of aluminium content per dose.
The pre-fusion SARS-COV-2 S proteins may also be administered in combination with or conjugated to nanoparticles, such as e.g. polymers, liposomes, virosomes, virus-like particles. The SARS-COV-2 S proteins may be combined with or encapsidated in or conjugated to the nanoparticles with or without adjuvant. Encapsulation within liposomes is described, e.g. in U.S. Pat. No. 4,235,877. Conjugation to macromolecules is disclosed, for example in U.S. Pat. No. 4,372,945 or U.S. Pat. No. 4,474,757.
In other embodiments, the compositions do not comprise adjuvants.
In certain embodiments, the invention provides methods for making a vaccine against a SARS-COV-2 virus, comprising providing a composition according to the invention and formulating it into a pharmaceutically acceptable composition. The term “vaccine” refers to an agent or composition containing an active component effective to induce a certain degree of immunity in a subject against a certain pathogen or disease, which will result in at least a decrease (up to complete absence) of the severity, duration or other manifestation of symptoms associated with infection by the pathogen or the disease. In the present invention, the vaccine comprises an effective amount of a pre-fusion SARS-COV-2 S protein and/or a nucleic acid molecule encoding a pre-fusion SARS-COV-2 S protein, and/or a vector comprising said nucleic acid molecule, which results in an immune response against the S protein of SARS-COV-2. This provides a method of preventing serious lower respiratory tract disease leading to hospitalization and the decrease in frequency of complications such as pneumonia and bronchiolitis due to SARS-COV-2 infection and replication in a subject. The term “vaccine” according to the invention implies that it is a pharmaceutical composition, and thus typically includes a pharmaceutically acceptable diluent, carrier or excipient. It may or may not comprise further active ingredients. In certain embodiments it may be a combination vaccine that further comprises additional components that induce an immune response against SARS-COV-2, e.g. against other antigenic proteins of SARS-COV-2, or may comprise different forms of the same antigenic component. A combination product may also comprise immunogenic components against other infectious agents, e.g. other respiratory viruses including but not limited to influenza virus or RSV. The administration of the additional active components may for instance be done by separate, e.g. concurrent administration, or in a prime-boost setting, or by administering combination products of the vaccines of the invention and the additional active components.
Compositions may be administered to a subject, e.g. a human subject. The total dose of the SARS-COV-2 S proteins in a composition for a single administration can for instance be about 0.01 μg to about 10 mg, e.g. 1 μg-1 mg, e.g. 10 μg-100 μg. Determining the recommended dose will be carried out by experimentation and is routine for those skilled in the art.
Administration of the compositions according to the invention can be performed using standard routes of administration. Non-limiting embodiments include parenteral administration, such as intradermal, intramuscular, subcutaneous, transcutaneous, or mucosal administration, e.g. intranasal, oral, and the like. In one embodiment a composition is administered by intramuscular injection. The skilled person knows the various possibilities to administer a composition, e.g. a vaccine in order to induce an immune response to the antigen(s) in the vaccine.
A subject as used herein preferably is a mammal, for instance a rodent, e.g. a mouse, a cotton rat, or a non-human-primate, or a human. Preferably, the subject is a human subject.
The proteins, nucleic acid molecules, vectors, and/or compositions may also be administered, either as prime, or as boost, in a homologous or heterologous prime-boost regimen. If a boosting vaccination is performed, typically, such a boosting vaccination will be administered to the same subject at a time between one week and one year, preferably between two weeks and four months, after administering the composition to the subject for the first time (which is in such cases referred to as ‘priming vaccination’). In certain embodiments, the administration comprises at least one prime and at least one booster administration.
The invention further provides a host cell comprising the isolated nucleic acid molecule or vector encoding the recombinant SARS-COV-2 S protein of the invention. Such host cells can be used for recombinant protein production, recombinant protein expression, or the production of viral particles.
In addition, the invention relates to methods of producing a recombinant SARS-COV-2 S protein, comprising growing a host cell comprising an isolated nucleic acid molecule or vector encoding the recombinant SARS-COV-2 S protein of the invention under conditions suitable for production of the recombinant SARS-COV-2 S protein.
The SARS-COV-2 S proteins of the invention may also be used to isolate monoclonal antibodies from a biological sample, e.g. a biological sample (such as blood, plasma, or cells) obtained from an immunized animal or infected human. The invention thus also relates to the use of the SARS-COV-2 protein as bait for isolating monoclonal antibodies.
Also provided is the use of the pre-fusion SARS-COV-2 S proteins of the invention in methods of screening for candidate SARS-COV-2 antiviral agents, including but not limited to antibodies against SARS-COV-2
In addition, the proteins of the invention may be used as diagnostic tool, for example to test the immune status of an individual by establishing whether there are antibodies in the serum of such individual capable of binding to the protein of the invention. The invention thus also relates to an in vitro diagnostic method for detecting the presence of an ongoing or past CoV infection in a subject said method comprising the steps of a) contacting a biological sample obtained from said subject with a protein according to the invention; and b) detecting the presence of antibody-protein complexes.
A plasmid corresponding to the semi-stabilized SARS-COV2 S protein described by (Wrapp et. al., Science 2020, FurinKO+PP according to SEQ ID NO: 3) was synthesized and codon-optimized at Gene Art (Life Technologies, Carlsbad, CA). A variant with a HIS tag (based on SEQ ID NO: 3) and a variant with a C-tag were purified. The constructs were cloned into pCDNA2004 or generated by standard methods widely known within the field involving site-directed mutagenesis and PCR and sequenced. The expression platform used was the Expi293F cells. The cells were transiently transfected using ExpiFectamine (Life Technologies) according to the manufacturer's instructions and cultured for 6 days at 37° C. and 10% CO2. The culture supernatant was harvested and spun for 5 minutes at 300 g to remove cells and cellular debris. The spun supernatant was subsequently sterile filtered using a 0.22 um vacuum filter and stored at 4ºC until use.
SARS-COV2 S trimers were purified using a two-step purification protocol including either CaptureSelect™ C-tag affinity column for C-tagged protein, or, for HIS-tagged protein, by complete His-tag 5 mL (Roche). Both proteins were further purified by size-exclusion chromatography using a HiLoad Superdex 200 16/600 column (GE Healthcare). The C-tagged and HIS tagged S trimer was unstable after repeated freeze/thaw cycles (
In order to stabilize the labile pre-fusion conformation of SARS-COV2 S protein, amino acid residues at position 614, 892 and 942 (numbering according to SEQ ID NO: 1) were mutated. Plasmids coding for the recombinant SARS-COV-2 S protein ectodomains which were C-terminally fused to a foldon (SEQ ID NO: 4) were expressed in Expi293Fcells, and 3 days after transfection the supernatants were tested for binding to ACE2-Fc using AlphaLISA (
For the AlphaLISA assay, SARS-COV2 S variants in the pcDNA2004 vector containing a linker followed by a sortase A tag followed by a Flag-tag followed by a flexible (G4S)7 linker and ending with a His-tag, were prepared (the sequence of the tag, which was placed at the C-terminus of the S protein, is provided in SEQ ID NO: 2). Three days after transfection, crude supernatants were diluted 300 times in AlphaLISA buffer (PBS+0.05% Tween-20+0.5 mg/mL BSA). Then, 10 μL of each dilution were transferred to a 96-well plate and mixed with 40 μL acceptor beads, donor beads and ACE2-Fc. The donor beads were conjugated to ProtA (Cat #: AS102M, Perkin Elmer), which binds to ACE2Fc. The acceptor beads were conjugated to an anti-His antibody (Cat #: AL128M, Perkin Elmer), which binds to the His-tag of the construct.
The mixture of the supernatant containing the expressed S protein, the ACE-2-Fc, donor beads, and acceptor beads was incubated at room temperature for 2 hours without shaking. Subsequently, the chemiluminescent signal was measured with an Ensight plate reader instrument (Perkin Elmer). The average background signal attributed to mock transfected cells was subtracted from the AlphaLISA counts measured for each of the SARS-CoV-2 S variants. Subsequently, the whole data set was divided by signal measured for the SARS-COV-2 S protein having the S backbone sequence signal to normalize the signal for each of the S variants tested to the backbone.
Compared with the soluble uncleaved S variant with a C-terminal foldon domain (SEQ ID NO: 2) or the variant with the additional PP (SEQ ID NO:3), the S variants with stabilizing substitutions D614N, A892P and A942P showed higher ACE2-Fc binding (
The cell culture supernatants of transfections with a semi-stable uncleaved SARS-CoV-2 S+PP design and with a labile uncleaved SARS-COV-2 S protein, and of variants with a single point mutation as described above (D614N, A892P and A942P) were analyzed using analytical SEC (
In order to stabilize the labile pre-fusion conformation of SARS-COV-2 S protein, disulfide bridges were introduced between residues 880 and 888 or between residues 884 and 893, and point mutations were introduced at position 532 and 572. Similar to EXAMPLE 2, plasmids coding for the uncleaved SARS-COV-2 S protein with or without the double proline in the hinge loop were expressed in Expi293Fcells, and 3 days after transfection the supernatants were tested for binding to ACE2-Fc using AlphaLISA as described in EXAMPLE 2 (
Compared with the soluble labile uncleaved S variant with a C-terminal foldon, the variants with stabilizing substitutions T572I, N532P and with the introduction of a disulfide between residues 880 and 888 showed higher ACE2-Fc binding (
In addition, compared with the soluble semi stable uncleaved S variant with a C-terminal foldon domain and the double proline, the variants with stabilizing substitutions T572I, N532P, with the introduction of a disulfide between residues 880 and 888 and with a disulfide between residues 884 and 893 showed higher ACE2-Fc binding (
The cell culture supernatants of transfections with a semi stable uncleaved SARS-CoV-2 S+PP design and with a labile uncleaved SARS-COV-2 S protein, and of variants with an introduced disulfide bridge or a single point mutation as described above (T572I, N532P, CYS880-CYS888 and CYS884-CYS893) were analyzed using analytical SEC (
In order to stabilize the labile pre-fusion conformation of SARS-COV-2 S protein, point mutations were introduced at position 941 and 944. Similar to EXAMPLE 2, plasmids coding for the labile uncleaved SARS-COV-2 S protein were expressed in Expi293Fcells, and 3 days after transfection the supernatants were tested for binding to ACE2-Fc using AlphaLISA as described in EXAMPLE 2 (
Compared with the soluble labile uncleaved S variant with a C-terminal foldon, the variants with additional stabilizing substitutions T941P and A944P showed higher ACE2-Fc binding (
The cell culture supernatants of transfections with a labile uncleaved SARS-COV-2 S protein, and of variants with a single point mutation as described above (T941P and A944P) were analyzed using analytical SEC (
Melting temperatures for S trimers were determined using MicroCal capillary DSC system. 400 μL of 0.5 mg/mL protein sample was used per measurement. The measurement was performed with a start temperature of 20° C. and a final temperature of 110° C. The scan rate 100° C./h and the feedback mode: Low (=signal amplification). The data were analyzed using the Origin J. Software (MicroCal VP-analysis tool). The purified uncleaved S trimer (SEQ ID NO: 2) showed a wide range of melting events with a major melting event (Tm2) at 64ºC (
A cell-cell fusion assay to mimic the entry pathway of SARS-COV-2 at the plasma membrane was developed by transiently co-expressing GFP, ACE2, TMPRSS2 and full-length S variants in HEK293 cells (see
In order to stabilize the labile pre-fusion conformation of SARS-COV-2 S protein, a combination of indicated stabilizing point mutations from previous examples were introduced in SEQ ID NO:2 (
In order to obtain soluble native S trimers, a C-terminal heterologous trimerization domain was added as described by Pallesen et al. (Pallesen, PNAS, 2017). To investigate whether the point mutations sufficiently stabilized the protein to trimerize without the addition of a trimerization domain, a variant was made with four stabilizing mutations without the foldon (DF) (A892P-A942P-D614N-V987P-DF). As shown in
Purified SARS-2 S trimers with indicated mutations (
RBD exposure was characterized by ACE2, by neutralizing antibody SAD-S35 and non-neutralizing antibody CR3022 (Yuan et al., (2020) that compete with ACE2. ACE2 and SAD-S35 can only bind RBD in the up configuration and CR3022 can only bind when 2 RBDs are in the up configuration (
Different full length (FL) S proteins were produced in Expi292F cells. COR200660 (660) has a furin knock out mutation, i.e a mutation of the amino acid at position 682 into S and/or a mutation of the amino acid at position 685 into G. COR200662 (662) is the same as 660, but with an additional A942P substitution. COR200007 (007) has furin knock out mutation and additional mutations K986P and V987P. COR200664 is the same as 007, but with an additional A942P substitution.
Higher amounts of spikes detected in the supernatant when A942P is present compared with when it is not present (as shown in
The antigenicity of the seven membrane bound S proteins encoded by the different DNA constructs was evaluated in cell-based ELISA (CBE) as described below. Binding was assessed to three neutralizing ligands, i.e. angiotensin-converting enzyme 2 (ACE2-Fc) (Liu et al. (2017)), and two monoclonal antibodies (mAbs), COVA1-22 and COVA2-15 (Brouwer et al., 2020) and two non-neutralizing mAbs, i.e. CR3015 (van den Brink et al., (2005)) and CR3046 (Bos et al., (2020)). The D614N (like D614G), A892P and T572I substitutions decrease the binding of CR3015 and CR3046 compared to the wild type spike in the membrane suggesting that these substitutions stabilize the spike. A892P and T572I decrease binding of CR3015 and CR3046 with or without D614G (
HEK293 cells were seeded at 2×105 cells/mL in appropriate medium in a flat-bottomed 96-well microtiter plate (Corning). The plate was incubated overnight at 37° C. in 10% CO2. After 24 h, transfection of the cells was performed with 300 ng DNA per well and the plate was incubated for 48 h at 37° C. in 5% CO2. Two days post transfection, cells were washed with 100 μl/well of blocking buffer containing 1% (w/v) BSA (Sigma), 1 mM MgCl2, 1.8 mM CaCl2, and 5 mM Tris pH 8.0 in 1×PBS (GIBCO). After washing, nonspecific binding was blocked, using 100 μl/well of blocking solution for 20 min at 4° C. Subsequently, cells were incubated in 50 μl/well blocking buffer containing 1 μg/ml primary antibodies ACE2-Fc, COVA1-22, COVA2-15, CR3015 and CR3046 for 1 hr at 4° C. The plate was washed three times with 100 μl/well of the blocking buffer, three times with 100 μl/well of washing buffer containing 1 mM MgCl2, 1.8 mM CaCl2 in 1×PBS and then incubated with 100 μl/well of the blocking buffer for 5 min at 4° C. After blocking, the cells were incubated with 50 μl/well of secondary antibodies HRP conjugated Mouse Anti-Human IgG (Jackson, 1:2500) or HRP Conjugated goat anti-mouse IgG (Jackson, 1:2500) then incubated 40 min at 4° C. The plate was washed three times with 100 μl/well of the blocking buffer, three times with 100 μl/well washing buffer. 30 μl/well of BM Chemiluminescence ELISA substrate (Roche, 1:50) was added to the plate, and the luminosity was immediately measured using the Ensight Plate Reader.
Antigenicity of COR200617, COR200619 and COR201225 was assessed with a panel of neutralizing antibodies against the N-terminal domain (NTD) (4A8 (Chi et. al., (2020) and several antibodies that bind either the RBD in the up and down or antibodies that only bind RBD in the up configuration. See Henderson et. al., (2020) for the definition of ‘up’ and ‘down’. The following antibodies are directed against the closed conformation of spike and recognize both the up and down state: COVA1-22 (Brouwers et. al., (2020)), against the RBD in the ‘up’ or ‘down’ position (S2M11 (Tortorice et. al., (2020)), C144 (Barnes et. al., (2020), 2-43 (Liu et al, (2020)) and COVA2-15 Brouwers et. al., (2020)). The following antibodies are directed against the RBD in the open conformation of spike and recognize the up state: (ACE2-Fc and SAD-S35 (AcroBiosystems), as described below. As shown in
Antibodies were immobilized on anti-hIgG (AHC) sensors (FortéBio, cat. #18-5060) in 1×kinetics buffer (FortéBio, cat. #18-1092) in 96-well black flat-bottom polypropylene microplates (FortéBio, cat. #3694). The experiment was performed on an Octet RED384 instrument (Pall-FortéBio) at 30° C. with a shaking speed of 1000 rpm. Activation was 600 s, immobilization of antibodies 900 s, followed by washing for 600 s, and then binding the S proteins for 300 s. The data analysis was performed using the FortéBio Data Analysis 12.0 software (FortéBio).
In this example the in vivo immunogenicity of recombinant SARS-COV-2 Spike proteins of the invention was assessed. SARS-COV-2 S proteins were generated that were stabilized in a predominantly closed conformation: COR201225 and COR200619. The immunogenicity was compared to a stabilized SARS-COV-2 spike protein with an open conformation (COR200627).
The Spike protein variants thus were presented from most closed (top) to the most open variant (bottom). All constructs had furin knockout mutations (R682S R685G). In addition, the constructs contained the stabilizing mutations that are shown in the table below:
Groups of 7 female BALB/c mice (age 8-10 weeks at the start of the study) were intramuscularly immunized with 5 or 0.5 μg S protein with 100 μg aluminium hydroxide adjuvant on day 0 and day 28. Mice were bled on day 27 and 41 to analyze neutralizing antibody responses against SARS-COV-2 B.1 (Wuhan-Hu-1+D614G) Spike protein by a pseudovirion neutralization assay (psVNA) or the SARS-COV-2 L-0008 isolate (lineage B.1) by wild-type VNA (wtVNA). See Solforosi et al., for details on the assays used.
Neutralizing antibody titers against the SARS-COV-2 isolate L-0008 (lineage B.1) were undetectable or close to the LLOD four weeks (day 27) after immunization with one dose of COR200627 (open conformation) as measured by a wild-type virus neutralization assay (wtVNA) (
According to the present invention, it thus has been shown that COR201225 and COR200619 (predominantly closed and containing stabilizing mutations according to the invention) are immunogenic in mice and induce higher neutralizing antibody levels against SARS-COV-2, compared to COR200627 (open conformation) 4 and 6 weeks after immunization.
As shown in the previous examples, the substitutions A942P, A944P, A892P and F880C-G888C increased the trimer yield of soluble S protein without the K986P and V987P substantially (
Four stabilizing mutations D614N, A892P, A942P and V987P were introduced in the Wuhan-Hu-01 sequence. The quadruple mutant was then imaged by cryo-EM. A 2-steps 3D classification illustrates that out of 833,000 classified particles, ˜80% was closed with all RBDs in the down state and 38% was categorized into a well-defined closed class while ˜20% showed 1 RBD-up (
SARS-COV-2 S protein samples were prepared in 20 mM Tris, 150 mM NaCl, pH7 buffer at a concentration of 0.15 mg/mL and applied to glow discharged Quantifoil R2/2 200 mesh grids before being double side blotted for 3 seconds in a Vitrobot Mark IV (Thermo Fisher Scientific and plunge frozen into liquid ethane cooled. Grids were loaded into a Titan Krios electron microscope (Thermo Fisher Scientific) operated at 300 kV, equipped with a Gatan K3 BioQuantum direct electron detector. A total of 9,760 movies were collected over two microscopy sessions at The Netherlands Centre for Electron Nanoscopy (NeCEN). Detailed data acquisition parameters are summarized in Table 1.
Collected movies were imported into RELION-3.1-beta (Zivanov, Nakane et al. 2018) and subjected to beam induced drift correction using MotionCor2 (Zheng, Palovcak et al. 2017) and CTF estimation by CTFFIND-4.1.18 (Rohou and Grigorieff 2015). Detailed steps of the image processing workflow are illustrated in
The SARS-COV-2 S PDBID 6VXX and 6VSB structures (Walls, Park et al. 2020, Wrapp, Wang et al. 2020) were used as starting models. PHENIX-1.18.261 (Liebschner, Afonine et al. 2019), Coot (Emsley, Lohkamp et al. 2010) and the Namdinator webserver (Kidmose, Juhl et al. 2019) were iteratively used to build atomic models. Geometry and statistics are given in Table 4 and 5. Final maps were displayed using UCSF ChimeraX (Goddard, Huang et al. 2018).
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWF
CMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWF
FLGRSLEVLFQGPGSLPETGGGSDYKDDDDKGGGGSGGGGGGGGSGGGGSGGGGSHHHHHH
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWF
FLGRSLEVLFQGPGSLPETGGGSDYKDDDDKGGGGSGGGGSGGGGSGGGGSGGGGSHHHHHH
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWF
Signal peptide
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWF
Signal peptide
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWF
Signal peptide
This application is a Section 371 of International Application No. PCT/EP2021/062461 filed May 11, 2021, which was published in the English language Nov. 18, 2021, under International Publication No. WO 2021/228842 A1, which claims priority under 35 U.S.C. § 119(b) to U.S. Patent Application No. 63/022,776, filed May 11, 2020, and to U.S. Patent Application No. 62/705,579, filed Jul. 6, 2020, the disclosures of each of which are incorporated herein by reference in their entireties.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/062461 | 5/11/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63022776 | May 2020 | US | |
| 62705579 | Jul 2020 | US |
