WO2006051091A1 - Compositions against sars-coronavirus and uses thereof - Google Patents
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Classifications
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
- C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
- C07K16/1002—Coronaviridae
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
- C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
- C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
- C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
- C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
- C07K2317/622—Single chain antibody (scFv)
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
- C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
Definitions
- the invention relates to medicine.
- the invention relates to compositions comprising binding molecules capable of specifically binding to and neutralizing SARS- coronavirus (SARS-CoV) .
- SARS-CoV SARS- coronavirus
- the compositions are useful in the diagnosis of SARS-CoV and the prophylaxis and/or treatment of a condition resulting from SARS-CoV.
- SARS-CoV severe acute respiratory syndrome
- Figure 1 shows results from an ELISA, wherein the binding of the single-chain phage antibodies called SC03-014 and SC03-022 to an immobilized UV-inactivated SARS-CoV preparation (left column) or immobilized FBS (right column) was measured.
- SC02-006 is also shown. On the y-axis the absorbance at 492 nm is shown.
- Figure 2 shows an ELISA binding of IgGs CR03-014, CR03-022, control IgG and no IgG to an inactivated SARS-CoV preparation. On the Y-axis the absorbance at 492 nm is shown.
- Figure 3 shows a FACS binding of the scFv phage antibodies SC03-014, SC03-022 and a control scFv phage antibody to the full length S protein expressed on HEK293T cells (left column) or mock transfected HEK293T cells (right column) .
- the mean fluorescense intensity is shown on the Y- axis.
- Figure 4 shows an ELISA binding of the antibodies CR03-014, CR03-022 and a control antibody to the S565 fragment (amino acids 1-565 of the S protein of SARS-CoV; left column) , S318- 510 fragment (amino acids 318-510 of the S protein of SARS- CoV; middle column) and an irrelevant control myc-tagged antigen (right column) .
- S565 fragment amino acids 1-565 of the S protein of SARS-CoV; left column
- S318- 510 fragment amino acids 318-510 of the S protein of SARS- CoV; middle column
- an irrelevant control myc-tagged antigen right column
- Figure 5 shows an ELISA binding of dilutions of antibodies
- CR03-014, CR03-022 and a control antibody to the S565 fragment of the S protein of SARS-CoV On the Y-axis the absorbance at 492 nm and on the X-axis the amount of antibody in ⁇ g/ml is shown.
- Figure 6 shows a competition ELISA for binding to the S565 fragment.
- Figure 6A shows competition between biotinylated antibody CR03-014 without competing antibody or with 1, 5 or 25 ⁇ g/ml competing antibody CR03-014, CR03-022 or control antibody.
- Figure 6B shows competition between biotinylated antibody CR03-022 with or without the competing antibodies as described above. On the Y-axis the % of maximal binding is shown and on the X-axis the amount of the competing antibody in ⁇ g/ml.
- Figure 7 shows a sandwich ELISA using anti-S protein antibodies. Immobilized antibodies CR03-014 and CR03-022 were used to capture S protein fragment S318-510. Bound fragment was detected using biotinylated antibody CR03-014, CR03-022 or control antibody. On the Y-axis the absorbance at 492 nm is shown.
- Figure 8 shows binding of the monoclonal anti-SARS-antibodies CR03-014 and CR03-022 to the amino acid region of 318-510 of the S protein of the SARS-CoV strain Frankfurt 1 (called WT S318-510) and naturally occuring variants of the WT S318-510 fragment (variant A, mutation K344R; variant B, mutation S353F; variant C, mutation R426G and N437D; variant D, mutation Y436H; variant E, mutation Y442S; variant F, mutation N479S; variant G, mutation K344R, F360S, N479K and T487S; variant H, mutation K344R, F360S, L472P, D480G, and T487S; variant I, mutation K344R and F501Y) .
- the control is an irrelevant myc-His tagged protein. On the Y-axis the absorbance at 492 nm is shown.
- Figure 9 shows the comparison of the nucleotide and amino acid sequences of the SARS-CoV wild-type strain (SARS-CoV strain HKU 39849) and escape viruses of antibody CR03-014. Virus- infected cells were harvested 2 days post-infection and total RNA was isolated. cDNA was generated and used for DNA sequencing. Regions containing mutations are shown and the mutations are indicated in bold. Numbers above amino acids indicate amino acids numbers from S protein including signal peptide. The sequences in Figure 9 are also represented by SEQ ID Nos:118-121.
- Figure 10 shows binding of the monoclonal anti-SARS-antibodies CR03-014 and CR03-022 to the amino acid region of 318-510 of the S protein of the SARS-CoV strain Frankfurt 1 (called FRAl S318-510) and an escape variant of antibody CR03-014 harboring a P462L substitution.
- FRAl S318-510 the amino acid region of 318-510 of the S protein of the SARS-CoV strain Frankfurt 1
- P462L substitution On the Y-axis the absorbance at 492 nm is shown.
- binding molecule refers to an intact immunoglobulin including monoclonal antibodies, such as chimeric, humanised or human monoclonal antibodies, or to an antigen-binding and/or variable domain comprising fragment of an immunoglobulin that competes with the intact immunoglobulin for specific binding to the binding partner of the immunoglobulin, e.g. the SARS-CoV. Regardless of structure, the antigen-binding fragment binds with the same antigen that is recognised by the intact immunoglobulin.
- An antigen-binding fragment can comprise a peptide or polypeptide comprising an amino acid sequence of at least 2 contiguous amino acid residues, at least 5 contiguous amino acid residues, at least 10 contiguous amino acid residues, at least 15 contiguous amino acid residues, at least 20 contiguous amino acid residues, at least 25 contiguous amino acid residues, at least 30 contiguous amino acid residues, at least 35 contiguous amino acid residues, at least 40 contiguous amino acid residues, at least 50 contiguous amino acid residues, at least 60 contiguous amino residues, at least 70 contiguous amino acid residues, at least contiguous 80 amino acid residues, at least contiguous 90 amino acid residues, at least contiguous 100 amino acid residues, at least contiguous 125 amino acid residues, at least 150 contiguous amino acid residues, at least contiguous 175 amino acid residues, at least 200 contiguous amino acid residues, or at least contiguous 250 amino acid residues of the amino acid sequence of the binding
- binding molecule includes all immunoglobulin classes and subclasses known in the art. Depending on the amino acid sequence of the constant domain of their heavy chains, binding molecules can be divided into the five major classes of intact antibodies: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes) , e.g., IgAl, IgA2, IgGl, IgG2, IgG3 and IgG4.
- Antigen-binding fragments include, inter alia, Fab, F(ab') f F(ab')2 f Fv, dAb, Fd, complementarity determining region (CDR) fragments, single-chain antibodies (scFv) , bivalent single-chain antibodies, single-chain phage antibodies, diabodies, triabodies, tetrabodies, (poly)peptides that contain at least a fragment of an immunoglobulin that is sufficient to confer specific antigen binding to the (poly)peptide, etc.
- the above fragments may be produced synthetically or by enzymatic or chemical cleavage of intact immunoglobulins or they may be genetically engineerd by recombinant DNA techniques .
- a binding molecule or antigen-binding fragment thereof may have one or more binding sites. If there is more than one binding site, the binding sites may be identical to one another or they may be different.
- the binding molecule can be a naked or unconjugated binding molecule but can also be part of an immunoconjugate.
- a naked or unconjugated binding molecule is intended to refer to a binding molecule that is not conjugated, operatively linked or otherwise physically or functionally associated with an effector moiety or tag, such as inter alia a toxic substance, a radioactive substance, a liposome, an enzyme. It will be understood that naked or unconjugated binding molecules do not exclude binding molecules that have been stabilized, multimerized, humanized or in any other way manipulated, other than by the attachment of an effector moiety or tag.
- naked and unconjugated binding molecules are included herewith, including where the modifications are made in the natural binding molecule-producing cell environment, by a recombinant binding molecule-producing cell, and are introduced by the hand of man after initial binding molecule preparation.
- naked or unconjugated binding molecule does not exclude the ability of the binding molecule to form functional associations with effector cells and/or molecules after administration to the body, as some of such interactions are necessary in order to exert a biological effect.
- biological sample encompasses a variety of sample types, including blood and other liquid samples of biological origin, solid tissue samples such as a biopsy specimen or tissue cultures, or cells derived therefrom and the progeny thereof.
- the term also includes samples that have been manipulated in any way after their procurement, such as by treatment with reagents, solubilization, or enrichment for certain components, such as proteins or polynucleotides.
- the term encompasses various kinds of clinical samples obtained from any species, and also includes cells in culture, cell supernatants and cell lysates .
- CDR Complementarity determining regions
- complementarity determining regions means sequences within the variable regions of binding molecules, such as immunoglobulins, that usually contribute to a large extent to the antigen binding site which is complementary in shape and charge distribution to the epitope recognised on the antigen.
- the CDR regions can be specific for linear epitopes, discontinuous epitopes, or conformational epitopes of proteins or protein fragments, either as present on the protein in its native conformation or, in some cases, as present on the proteins as denatured, e.g., by solubilization in SDS. Epitopes may also consist of posttranslational modifications of proteins.
- expression-regulating nucleic acid sequence refers to polynucleotide sequences necessary for and/or affecting the expression of an operably linked coding sequence in a particular host organism.
- the expression-regulating nucleic acid sequences such as inter alia appropriate transcription initiation, termination, promoter, enhancer sequences; repressor or activator sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (e.g., ribosome binding sites) ; sequences that enhance protein stability; and when desired, sequences that enhance protein secretion, can be any- nucleic acid sequence showing activity in the host organism of choice and can be derived from genes encoding proteins, which are either homologous or heterologous to the host organism.
- the identification and employment of expression-regulating sequences is routine to the person skilled in the art.
- the term "functional variant”, as used herein, refers to a binding molecule that comprises a nucleotide and/or amino acid sequence that is altered by one or more nucleotides and/or amino acids compared to the nucleotide and/or amino acid sequences of the parent binding molecule and that is still capable of competing for binding to the binding partner, e.g. SARS-CoV, with the parent binding molecule.
- the modifications in the amino acid and/or nucleotide sequence of the parent binding molecule do not significantly affect or alter the binding characteristics of the binding molecule encoded by the nucleotide sequence or containing the amino acid sequence, i.e. the binding molecule is still able to recognize and bind its target.
- the functional variant may have conservative sequence modifications including nucleotide and amino acid substitutions, additions and deletions. These modifications can be introduced by standard techniques known in the art, such as site-directed mutagenesis and random PCR- mediated mutagenesis, and may comprise natural as well as non- natural nucleotides and amino acids . Conservative amino acid substitutions include the ones in which the amino acid residue is replaced with an amino acid residue having similar structural or chemical properties. Families of amino acid residues having similar side chains have been defined in the art.
- amino acids with basic side chains e.g., lysine, arginine, histidine
- acidic side chains e.g., aspartic acid, glutamic acid
- uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cystine, tryptophan
- nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine
- beta-branched side chains e.g., threonine, valine, isoleucine
- aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
- a variant may have non-conservative amino acid substitutions, e.g., replacement of an amino acid with an amino acid residue having different structural or chemical properties. Similar minor variations may also include amino acid deletions or insertions, or both. Guidance in determining which amino acid residues may be substituted, inserted, or deleted without abolishing immunological activity may be found using computer programs well known in the art.
- a mutation in a nucleotide sequence can be a single alteration made at a locus (a point mutation) , such as transition or transversion mutations, or alternatively, multiple nucleotides may be inserted, deleted or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleotide sequence. The mutations may be performed by any suitable method known in the art. Host
- the term "host”, as used herein, is intended to refer to an organism or a cell into which a vector such as a cloning vector or an expression vector has been introduced.
- the organism or cell can be prokaryotic or eukaryotic. It should be understood that this term is intended to refer not only to the particular subject organism or cell, but to the progeny of such an organism or cell as well. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent organism or cell, but are still included within the scope of the term "host” as used herein.
- human when applied to binding molecules as defined herein, refers to molecules that are either directly derived from a human or based upon a human sequence. When a binding molecule is derived from or based on a human sequence and subsequently modified, it is still to be considered human as used throughout the specification. In other words, the term human, when applied to binding molecules is intended to include binding molecules having variable and constant regions derived from human germline immunoglobulin sequences based on variable or constant regions either or not occuring in a human or human lymphocyte or in modified form.
- the human binding molecules may include amino acid residues not encoded by human germline immunoglobulin sequences, comprise substitutions and/or deletions (e.g., mutations introduced by for instance random or site-specific mutagenesis in vitro or by somatic mutation in vivo) .
- substitutions and/or deletions e.g., mutations introduced by for instance random or site-specific mutagenesis in vitro or by somatic mutation in vivo.
- "Based on” as used herein refers to the situation that a nucleic acid sequence may be exactly copied from a template, or with minor mutations, such as by error-prone PCR methods, or synthetically made matching the template exactly or with minor modifications.
- Semisynthetic molecules based on human sequences are also considered to be human as used herein.
- binding molecules when applied to binding molecules as defined herein, refers to binding molecules that are substantially free of other proteins or polypeptides, particularly free of other binding molecules having different antigenic specificities, and are also substantially free of other cellular material and/or chemicals.
- the binding molecules when they are recombinantly produced, they are preferably substantially free of culture medium, and when the binding molecules are produced by chemical synthesis, they are preferably substantially free of chemical precursors or other chemicals, i.e., they are separated from chemical precursors or other chemicals which are involved in the synthesis of the protein.
- isolated when applied to nucleic acid molecules encoding binding molecules as defined herein, is intended to refer to nucleic acid molecules in which the nucleotide sequences encoding the binding molecules are free of other nucleotide sequences, particularly nucleotide sequences encoding binding molecules that bind binding partners other than SARS-CoV.
- isolated refers to nucleic acid molecules that are substantially separated from other cellular components that naturally accompany the native nucleic acid molecule in its natural host, e.g., ribosomes, polymerases, or genomic sequences with which it is naturally associated.
- isolated nucleic acid molecules such as a cDNA molecules, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
- monoclonal antibody refers to a preparation of antibody molecules of single molecular composition.
- a monoclonal antibody displays a single binding specificity and affinity for a particular epitope.
- human monoclonal antibody refers to an antibody displaying a single binding specificity which have variable and constant regions derived from or based on human germline immunoglobulin sequences or derived from completely synthetic sequences . The method of preparing the monoclonal antibody is not relevant.
- nuclei c acid molecule refers to a polymeric form of nucleotides and includes both sense and antisense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above.
- a nucleotide refers to a ribonucleotide, deoxynucleotide or a modified form of either type of nucleotide. The term also includes single- and double-stranded forms of DNA.
- a polynucleotide may include either or both naturally-occurring and modified nucleotides linked together by naturally-occurring and/or non-naturally occurring nucleotide linkages .
- the nucleic acid molecules may be modified chemically or biochemically or may contain non- natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as uncharged linkages ⁇ e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, etc.) .
- uncharged linkages ⁇ e.g., methyl phosphonates, phosphotriesters,
- the above term is also intended to include any topological conformation, including single-stranded, double-stranded, partially duplexed, triplex, hairpinned, circular and padlocked conformations.
- synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions . Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of the molecule.
- a reference to a nucleic acid sequence encompasses its complement unless otherwise specified.
- a reference to a nucleic acid molecule having a particular sequence should be understood to encompass its complementary strand, with its complementary sequence.
- the complementary strand is also useful, e.g., for antisense therapy, hybridization probes and PCR primers.
- operably linked refers to two or more nucleic acid sequence elements that are usually physically linked and are in a functional relationship with each other.
- a promoter is operably linked to a coding sequence if the promoter is able to initiate or regulate the transcription or expression of a coding sequence, in which case the coding sequence should be understood as being "under the control of” the promoter.
- pharmaceutically acceptable excipient any inert substance that is combined with an active molecule such as a drug, agent, or binding molecule for preparing an agreeable or convenient dosage form.
- pharmaceutically acceptable excipient is an excipient that is non-toxic to recipients at the dosages and concentrations employed and is compatible with other ingredients of the formulation comprising the drug, agent or binding molecule.
- binding in reference to the interaction of a binding molecule, e.g. an antibody, and its binding partner, e.g. an antigen, means that the interaction is dependent upon the presence of a particular structure, e.g. an antigenic determinant or epitope, on the binding partner.
- the antibody preferentially binds or recognizes the binding partner even when the binding partner is present in a mixture of other molecules or organisms.
- the binding may be mediated by covalent or non- covalent interactions or a combination of both.
- specifically binding means immunospecifically binding to an antigen or a fragment thereof and not immunospecifically binding to other antigens.
- a binding molecule that immunospecifically binds to an antigen may bind to other peptides or polypeptides with lower affinity as determined by, e.g., radioimmunoassays (RIA), enzyme-linked immunosorbent assays (ELISA) , BIACORE, or other assays known in the art. Binding molecules or fragments thereof that immunospecifically bind to an antigen may be cross-reactive with related antigens . Preferably, binding molecules or fragments thereof that immunospecifically bind to an antigen do not cross-react with other antigens.
- terapéuticaally effective amount refers to an amount of the binding molecule as defined herein that is effective for preventing, ameliorating and/or treating a condition resulting from infection with SARS-CoV.
- treatment refers to therapeutic treatment as well as prophylactic or preventative measures to cure or halt or at least retard disease progress.
- Those in need of treatment include those already inflicted with a condition resulting from infection with SARS-CoV as well as those in which infection with SARS-CoV is to be prevented.
- Subjects partially or totally recovered form infection with SARS-CoV might also be in need of treatment.
- Prevention encompasses inhibiting or reducing the spread of SARS-CoV or inhibiting or reducing the onset, development or progression of one or more of the symptoms associated with infection with SARS-CoV.
- vector denotes a nucleic acid molecule into which a second nucleic acid molecule can be inserted for introduction into a host where it will be replicated, and in some cases expressed.
- a vector is capable of transporting a nucleic acid molecule to which it has been linked.
- vectors include, but are not limited to, plasmids, cosmids, bacterial artificial chromosomes (BAC) and yeast artificial chromosomes (YAC) and vectors derived from bacteriophages or plant or animal (including human) viruses.
- Vectors comprise an origin of replication recognised by the proposed host and in case of expression vectors, promoter and other regulatory regions recognised by the host.
- a vector containing a second nucleic acid molecule is introduced into a cell by transformation, transfection, or by making use of viral entry mechanisms.
- Certain vectors are capable of autonomous replication in a host into which they are introduced (e.g., vectors having a bacterial origin of replication can replicate in bacteria) .
- Other vectors can be integrated into the genome of a host upon introduction into the host, and thereby are replicated along with the host genome.
- the invention provides compositions of binding molecules capable of specifically binding to SARS-CoV and having SARS- CoV neutralizing activity.
- said binding molecules are human binding molecules .
- the invention further provides for the use of the compositions of the invention in the prophylaxis and/or treatment of a subject having, or at risk of developing, a condition resulting from SARS-CoV. Besides that, the invention pertains to the use of the compositions of the invention in the diagnosis/detection of SARS-CoV.
- the present invention encompasses compositions comprising at least two binding molecules.
- the binding molecules are immunoglobulins . Fragments of immunoglobulins still having the desired functionality and/or activity of the complete immunoglobulin are also considered immunoglobulins according to the invention.
- the at least two binding molecules, i.e. immunoglobulins are capable of specifically binding to a coronavirus .
- Coronaviruses include, but not limited to, avian infectious bronchitis virus, avian infectious laryngotracheitis virus, enteric coronavirus, equine coronavirus, coronavirus Group 1 species such as for instance human coronavirus 229E or human coronavirus NL63, coronavirus Group 2 species such as human coronavirus OC43 or chicken enteric coronavirus, coronavirus Group 3 species, human enteric coronavirus 4408, and SARS-CoV.
- the compositions can be administered to a mammal to treat, prevent or ameliorate one or more symptoms associated with a coronavirus infection.
- the invention relates to synergistic compositions, i.e.
- compositions exhibiting synergistic coronavirus neutralizing activity.
- the compositions comprise at least two binding molecules, i.e. immunoglobulins, that are capable of specifically binding to a coronavirus and that have coronavirus neutralizing activity, characterized in that the binding molecules act synergistically in neutralizing coronavirus.
- binding molecules i.e. immunoglobulins
- the term "synergistic" means that the combined effect of the binding molecules when used in combination is greater than their additive effects when used individually.
- the neutralizing activity of the composition is greater than the sum of the neutralizing activity of each immunoglobulin alone.
- immunoglobulins present in the synergistic coronavirus neutralizing activity exhibiting compositions may have coronavirus neutralizing activity when used as an individual binding molecule.
- one binding molecule of the at least two binding molecules in the compositions exhibiting synergistic coronavirus neutralizing activity may have coronavirus neutralizing activity when used individually.
- both of the at least two binding molecules, i.e. immunoglobulins have coronavirus neutralizing activity when used individually.
- one of the at least two binding molecules in the synergistic coronavirus neutralizing activity exhibiting compositions may bind to a coronavirus and the other binding molecule may bind to a cell associated receptor of the coronavirus.
- both binding molecules may bind to either the coronavirus or cell associated receptor.
- the coronavirus is a SARS-CoV including animal or human SARS-CoV.
- the SARS-CoV is a human SARS-CoV.
- the invention thus provides compositions comprising at least two binding molecules, i.e. immunoglobulins, capable of specifically binding to SARS-CoV and preferably having SARS- CoV neutralizing activity.
- the compositions preferably exhibit synergistic SARS-CoV neutralizing activity.
- the compositions comprise at least two binding molecules, i.e. immunoglobulins, having SARS-CoV neutralizing activity, characterized in that the binding molecules act synergistically in neutralizing SARS-CoV.
- the SARS-CoV neutralizing activity of the composition is greater than the sum of the neutralizing activity of each immunoglobulin alone.
- the binding molecules in the compositions act synergistically in neutralizing a plurality of SARS-CoV strains (see Table 1 for a list of several known SARS-CoV genome sequences and S protein genes) .
- each of the immunoglobulins in the composition is capable of neutralizing a plurality of (different) SARS-CoV strains, preferably human SARS-CoV strains .
- at least one of the binding molecules, i.e. immunoglobulins, of the compositions of the invention is capable of neutralizing an animal SARS- CoV.
- the binding molecules in the compositions of the invention may neutralize coronavirus infectivity, such as
- SARS-CoV infectivity by several modes of action including, but not limited to, preventing the attachment of the coronavirus to possible receptors on host cells, inhibition of the release of RNA into the cytoplasm of the cell, prevention of RNA transcription or translation, or inhibition or downregulation of coronavirus replication.
- the binding molecules may act by fixing complement or be capable of assisting in the lysis of enveloped coronavirus. They might also act as opsonins and augment phagocytosis of coronavirus either by promoting its uptake via Fc or C3b receptors or by agglutinating the coronavirus to make it more easily phagocytosed.
- the binding molecules in the compositions may have similar modes of action or may have different modes of action.
- the compositions neutralize coronavirus, such as SARS-CoV, infectivity by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% relative to infection of host cells by the coronavirus in the absence of said compositions.
- Assays for measuring virus neutralizing activity are known to the skilled person. Examples of such assays are described below.
- the binding molecules, i.e. immunoglobulins, in the compositions of the invention may be capable of specifically binding to a coronavirus, such as SARS-CoV, in activated or inactivated/attenuated form.
- the binding molecules may also be capable of specifically binding to one or more fragments of the coronavirus including inter alia a preparation of one or more proteins and/or (poly)peptides derived from the coronavirus.
- the fragment at least comprises an antigenic determinant recognised by the binding molecules of the invention.
- An "antigenic determinant" as used herein is a moiety, such as a coronavirus (such as SARS-CoV) ,
- binding molecules i.e. immunoglobulins
- SAA-CoV spike (S) protein, the membrane (matrix) protein, the (small) envelope protein, Orf 3, Orf 4, Orf 7, Orf 8, Orf 9, Orf 10 and Orf 14.
- the amino acid sequence of proteins and potential proteins of various known strains of coronaviruses can be found in the EMBL- database and/or other databases .
- SARS coronavirus Urbani can be found in the EMBL-database under accession number AY278741
- the complete genome of the SARS coronavirus HSR 1 can be found under accession number AY323977
- the complete genome of the SARS coronavirus Frankfurt 1 can be found under accession number AY291315
- the complete genome of the SARS coronavirus TOR2 can be found under accession number AY274119.
- At least one of the binding molecules, i.e. immunoglobulins, in the compositions of the invention is capable of specifically binding to the S protein of SARS-CoV.
- the other binding molecule may bind to a receptor of SARS-CoV present on or associated with target cells.
- An example of such a receptor is the ACE-2 receptor (see Li et al. , 2003) .
- all binding molecules in the compositions of the invention are capable of specifically binding to the S protein of SARS-CoV.
- At least one of the binding molecules in the compositions of the invention is capable of specifically binding to the extracellular domain of the S protein of SARS-CoV. This domain consists of amino acids 15- 1195 of the S protein.
- at least one binding molecule in the compositions of the invention is capable of specifically binding to amino acids 318-510 of the S protein of SARS-CoV.
- the neutralizing binding molecules, i.e. immunoglogulins, in the compositions of the invention may react with overlapping, competing epitopes, but preferably they react with different/distinct, non-competing epitopes of the coronavirus, such as SARS-CoV.
- compositions comprising at least two binding molecules capable of specifically binding to a coronavirus, such as SARS-CoV, wherein the binding molecules are capable of reacting with different, non-competing epitopes of the coronavirus.
- the coronavirus is a human coronavirus, more preferably the coronavirus is SARS-CoV.
- Compositions comprising at least two binding molecules wherein each binding molecule binds to a different epitope or site on a virus are more suitable for preventing the escape of resistant variants of the virus compared to compositions comprising at least two binding molecules wherein each binding molecule binds to an overlapping epitope or site on the virus.
- the different, non-competing epitopes recognised by the binding molecules, i.e. immunoglobulins, in the compositions of the invention are located on the S protein of SARS-CoV, particularly the extracellular domain of the S protein, more particularly within amino acids 318-510 of the S protein.
- at least one of the binding molecues, i.e. immunoglobulins, of the compositions of the invention is capable of reacting with amino acids 318-510 of the S protein of a human and an animal SARS-CoV.
- immunoglobulins of the compositions of the invention reacts with an epitope comprising the amino acid sequence of SEQ ID NO: 128.
- the epitope may consist of 11, 11 to 15, 11 to 20, 11 to 25, 11 to 30, 11 to 35, 11 to 40, 11 to 45 or even more amino acids.
- at least one of the binding molecules, i.e. immunoglobulins, in the compositions of the invention is capable of reacting with amino acids 318-510 of the S protein of a SARS-CoV, wherein the amino acid at position 479 is an amino acid other than asparagine, to a similar extent as with amino acids 318-510 of the S protein of a SARS-CoV, wherein the amino acid at position 479 is an asparagine.
- substitution of the amino acid at position 479 does not dramatically influence the binding of at least one of the immunoglobulins in the compositions of the invention to amino acids 318-510 of the S protein of SARS-CoV.
- "To a similar extent" as defined above means that the binding molecule binds to amino acids 318-510 of the S protein of a SARS-CoV, wherein the amino acid at position 479 is an amino acid other than asparagines, in an amount of at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, preferably at least 100%, compared to the binding of the binding molecule to amino acids 318-510 of the S protein of a SARS-CoV, wherein the amino acid at position 479 is an asparagine. Binding can be measured by methods well known to a person skilled in the art such as for instance ELISA.
- the binding molecules in the compositions according to the invention are preferably human binding molecules, i.e. immunoglobulins . They can be intact immunoglobulin molecules such as polyclonal or monoclonal antibodies, in particular human monoclonal antibodies, or the binding molecules can be antigen-binding fragments including, but not limited to, Fab, F(ab') f F(ab')2 f Fv, dAb, Fd, complementarity determining region (CDR) fragments, single-chain antibodies (scFv) , bivalent single-chain antibodies, single-chain phage antibodies, diabodies, triabodies, tetrabodies, and (poly)peptides that contain at least a fragment of an immunoglobulin that is sufficient to confer specific antigen binding to the SARS-CoV or fragment thereof.
- immunoglobulins can be intact immunoglobulin molecules such as polyclonal or monoclonal antibodies, in particular human monoclonal antibodies, or the binding molecules can be antigen-bind
- the human binding molecules are preferably human monoclonal antibodies .
- the binding molecules in the compositions can be in non-isolated or isolated form.
- the compositions may further comprise at least one other therapeutic agent.
- the therapeutic agent is useful in the prophylaxis and/or treatment of a condition resulting from a coronavirus such as for instance SARS-CoV.
- binding molecules can bind to their binding partners, i.e.
- affinity constant K d -value
- the affinity constants can vary for antibody isotypes.
- affinity binding for an IgM isotype refers to a binding affinity of at least about 1.0*10 ⁇ 7 M.
- Affinity constants can for instance be measured using surface plasmon resonance, i.e. an optical phenomenon that allows for the analysis of real ⁇ time biospecific interactions by detection of alterations in protein concentrations within a biosensor matrix, for example using the BIACORE system (Pharmacia Biosensor AB, Uppsala, Sweden) .
- the binding molecules may bind to a coronavirus in soluble form such as for instance in a sample or may bind to a coronavirus bound or attached to a carrier or substrate, e.g., microtiter plates, membranes and beads, etc.
- Carriers or substrates may be made of glass, plastic (e.g., polystyrene), polysaccharides, nylon, nitrocellulose, or teflon, etc.
- the surface of such supports may be solid or porous and of any- convenient shape.
- the binding molecules may bind to a coronavirus in purified/isolated or non-purified/non- isolated form.
- the binding molecules, i.e. immunoglobulins, of the compositions according to the invention comprise at least a CDR3 region, preferably a heavy chain CDR3 region, comprising the amino acid sequence of SEQ ID N0:l or SEQ ID NO:2.
- the binding molecules comprising the heavy chain CDR3 region of SEQ ID NO: 1 further comprise a light chain CDR3 region comprising the amino acid sequence of SEQ ID NO: 129.
- the binding molecules comprising the heavy chain CDR3 region of SEQ ID NO: 1 further comprise a heavy chain CDRl, heavy chain CDR2, light chain CDRl and light chain CDR2 region comprising the amino acid sequence of SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, and SEQ ID NO: 133, respectively.
- the binding molecules comprising the heavy chain CDR3 region of SEQ ID NO:2 further comprise a light chain CDR3 region comprising the amino acid sequence of SEQ ID NO: 134.
- the binding molecules comprising the heavy chain CDR3 region of SEQ ID NO:2 further comprise a heavy chain CDRl, heavy chain CDR2, light chain CDRl and light chain CDR2 region comprising the amino acid sequence of SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, and SEQ ID NO: 138, respectively.
- the binding molecules according to the invention comprise a heavy- chain variable region comprising the amino acid sequence of SEQ ID NO: 4 or SEQ ID NO: 6.
- the binding molecules i.e.
- immunoglobulins in the compositions of the invention comprise at least one CDR region of a binding molecule comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 4 or SEQ ID NO: 6. In another embodiment they comprise two, three, four, five or even all six CDR regions.
- the binding molecules according to the invention comprise a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 4 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 8, or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 6 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 10.
- the binding molecules having coronavirus, such as SARS-CoV, neutralizing activity are administered in IgGl or IgA format.
- compositions may comprise at least one functional variant of a binding molecule as defined herein.
- the compositions may also consist of only functional variants of binding molecules as herein described. Molecules are considered to be functional variants of a binding molecule, if the variants are capable of competing for specifically binding to a coronavirus, such as SARS-CoV, or a fragment thereof with the parent binding molecules . In other words, when the functional variants are still capable of binding to the coronavirus, such as SARS-CoV, or a fragment thereof.
- the functional variants are capable of neutralizing coronavirus, such as SARS-CoV, infectivity and should together with the other binding molecule (or other functional variant) or other binding molecules (or other functional variants) form a composition exhibiting synergistic coronavirus, such as SARS-CoV, neutralizing activity.
- the neutralizing activity of a functional variant may either be higher or be lower compared to the parent binding molecules .
- Functional variants include, but are not limited to, derivatives that are substantially similar in primary structural sequence, but which contain e.g. in vitro or in vivo modifications, chemical and/or biochemical, that are not found in the parent binding molecule.
- modifications are well known to the skilled artisan and include inter alia acetylation, acylation, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, glycosylation, methylation, pegylation, proteolytic processing, phosphorylation, and the like.
- functional variants can be binding molecules as defined in the present invention comprising an amino acid sequence containing substitutions, insertions, deletions or combinations thereof of one or more amino acids compared to the amino acid sequences of the parent binding molecules.
- functional variants can comprise truncations of the amino acid sequence at either or both the amino or carboxy termini.
- Functional variants may have the same or different, either higher or lower, binding affinities compared to the parent binding molecule but are still capable of binding to a coronavirus, such as SARS-CoV, or a fragment thereof and preferably still capable of neutralizing coronavirus, such as SARS-CoV, infectivity.
- functional variants may have increased or decreased binding affinities for a coronavirus, such as SARS-CoV, or a fragment thereof compared to the parent binding molecules .
- a coronavirus such as SARS-CoV
- the amino acid sequences of the variable regions including, but not limited to, framework regions, hypervariable regions, in particular the CDR3 regions, are modified.
- the light chain and the heavy chain variable regions comprise three hypervariable regions, comprising three CDRs, and more conserved regions, the so-called framework regions (FRs) .
- the hypervariable regions comprise amino acid residues from CDRs and amino acid residues from hypervariable loops.
- Functional variants intended to fall within the scope of the present invention have at least about 50% to about 99%, preferably at least about 60% to about 99%, more preferably at least about 70% to about 99%, even more preferably at least about 80% to about 99%, most preferably at least about 90% to about 99%, in particular at least about 95% to about 99%, and in particluar at least about 97% to about 99% amino acid sequence homology with the parent binding molecules as defined herein.
- Computer algorithms such as inter alia Gap or Bestfit known to a person skilled in the art can be used to optimally align amino acid sequences to be compared and to define similar or identical amino acid residues.
- Functional variants can be obtained by altering the parent binding molecules or parts thereof by general molecular biology methods known in the art including, but not limited to, error-prone PCR, oligonucleotide-directed mutagenesis and site-directed mutagenesis.
- the invention includes compositions comprising at least one immunoconjugate, i.e. a molecule comprising at least one binding molecule or functional variant thereof as defined herein and further comprising at least one tag.
- compositions consisting of immunoconjugates .
- the compositions may further comprise another molecule, such as a therapeutic agent or immunoconjugate having a different specificity.
- the immunoconjugates of the invention may comprise more than one tag. These tags can be the same or distinct from each other and can be joined/conjugated non-covalently to the binding molecules.
- the tag(s) can also be joined/conjugated directly to the binding molecules through covalent bonding. Alternatively, the tag(s) can be joined/conjugated to the binding molecules by means of one or more linking compounds. Techniques for conjugating tags to binding molecules are well known to the skilled artisan.
- the tags of the immunoconjugates of the present invention may be therapeutic agents, but preferably they are detectable moieties/agents.
- Compositions comprising immunoconjugates comprising a detectable agent can be used diagnostically to, for example, assess if a subject has been infected with a coronavirus, such as SARS-CoV, or monitor the development or progression of a coronavirus, such as SARS-CoV, infection as part of a clinical testing procedure to, e.g., determine the efficacy of a given treatment regimen. However, they may also be used for other detection and/or analytical and/or diagnostic purposes.
- Detectable moieties/agents include, but are not limited to, enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive materials, positron emitting metals, and nonradioactive paramagnetic metal ions .
- the tags used to label the binding molecules for detection and/or analytical and/or diagnostic purposes depend on the specific detection/analysis/diagnosis techniques and/or methods used such as inter alia immunohistochemical staining of (tissue) samples, flow cytometric detection, scanning laser cytometric detection, fluorescent immunoassays, enzyme-linked immunosorbent assays (ELISA' s), radioimmunoassays (RIA' s), bioassays (e.g., neutralisation assays), Western blotting applications, etc.
- immunohistochemical staining of tissue samples preferred labels are enzymes that catalyze production and local deposition of a detectable product.
- compositions of the invention can also be attached to solid supports, which are particularly useful for in vitro immunoassays or purification of a coronavirus or a fragment thereof.
- solid supports might be porous or nonporous, planar or nonplanar.
- the binding molecules of the present invention or functional fragments thereof can be fused to marker sequences, such as a peptide to facilitate purification.
- an antibody can be conjugated to a second antibody to form an antibody heteroconjugate.
- the binding molecules of the invention may be conjugated/attached to one or more antigens.
- these antigens are antigens which are recognised by the immune system of a subject to which the binding molecule-antigen conjugate is administered.
- the immunoconjugates can be produced as fusion proteins comprising the binding molecules of the invention and a suitable tag. Fusion proteins can be produced by methods known in the art such as, e.g., recombinantly by constructing nucleic acid molecules comprising nucleotide sequences encoding the binding molecules in frame with nucleotide sequences encoding the suitable tag(s) and then expressing the nucleic acid molecules .
- nucleic acid molecules encoding at least a binding molecule or functional fragment thereof present in the compositions according to the invention.
- Such nucleic acid molecules can be used as intermediates for cloning purposes, e.g. in the process of affinity maturation described above.
- the nucleic acid molecules are isolated or purified.
- nucleic acid molecules are also intended to be a part of the present invention.
- Functional variants are nucleic acid sequences that can be directly translated, using the standard genetic code, to provide an amino acid sequence identical to that translated from the parent nucleic acid molecules.
- the nucleic acid molecules encode binding molecules comprising a CDR3 region, preferably a heavy chain CDR3 region, comprising the amino acid sequence of SEQ ID N0:l or SEQ ID NO:2.
- the nucleic acid molecules of the invention encode binding molecules comprising a light chain CDR3 region comprising the amino acid sequence of SEQ ID NO: 129 or SEQ ID NO: 134.
- nucleic acid molecules of the invention encode binding molecules comprising a heavy chain CDRl region comprising the amino acid sequence of SEQ ID NO: 130 or SEQ ID NO: 135; a heavy chain CDR2 region comprising the amino acid sequence of SEQ ID NO: 131 or SEQ ID NO: 136; a light chain CDRl region comprising the amino acid sequence of SEQ ID NO: 132 or SEQ ID NO: 137; and/or a light chain CDR2 region comprising the amino acid sequence of SEQ ID NO: 133 or SEQ ID NO: 138.
- the nucleic acid molecules encode binding molecules comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 4 or SEQ ID NO: 6.
- the nucleic acid molecules encode binding molecules comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 4 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 8 or they encode a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 6 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 10.
- nucleic acid molecules encoding the heavy chain variable region of the binding molecules of the invention comprise the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:5.
- the nucleic acid molecules encoding the light chain variable region of the binding molecules of the invention comprise the nucleotide sequence of SEQ ID NO: 7 or SEQ ID NO: 9.
- the nucleic acid molecules of the invention may even contain the nucleotide sequences or parts thereof of the at least two binding molecules present in the compostions of the invention.
- vectors i.e. nucleic acid constructs, comprising one or more nucleic acid molecules according to the present invention.
- Vectors can be derived from plasmids such as inter alia F, Rl, RPl, Col, pBR322, TOL, Ti, etc; cosmids; phages such as lambda, lambdoid, M13, Mu, Pl, P22, Q ⁇ , T-even, T-odd, T2, T4, T7, etc; plant viruses; or animal viruses.
- Vectors can be used for cloning and/or for expression of the binding molecules of the invention and might even be used for gene therapy purposes .
- Vectors comprising one or more nucleic acid molecules according to the invention operably linked to one or more expression-regulating nucleic acid molecules are also covered by the present invention.
- the binding molecules present in the compositions of the invention may be expressed on separate vectors but may also be expressed on the same vector.
- the choice of the vector (s) is dependent on the recombinant procedures followed and the host used. Introduction of vectors in host cells can be effected by inter alia calcium phosphate transfection, virus infection, DEAE-dextran mediated transfection, lipofectamin transfection or electroporation.
- Vectors may be autonomously replicating or may replicate together with the chromosome into which they have been integrated.
- the vectors contain one or more selection markers .
- markers may depend on the host cells of choice, although this is not critical to the invention as is well known to persons skilled in the art. They include, but are not limited to, kanamycin, neomycin, puromycin, hygromycin, zeocin, thymidine kinase gene from
- HSV-TK Herpes simplex virus
- dhfr dihydrofolate reductase gene from mouse
- Vectors comprising one or more nucleic acid molecules encoding the binding molecules as described above operably linked to one or more nucleic acid molecules encoding proteins or peptides that can be used to isolate the binding molecules are also covered by the invention. These proteins or peptides include, but are not limited to, glutathione-S- transferase, maltose binding protein, metal-binding polyhistidine, green fluorescent protein, luciferase and beta- galactosidase.
- Hosts containing one or more copies of the vectors mentioned above are an additional subject of the present invention.
- the hosts are host cells.
- Host cells include, but are not limited to, cells of mammalian, plant, insect, fungal or bacterial origin.
- Bacterial cells include, but are not limited to, cells from Gram positive bacteria such as several species of the genera Bacillus, Streptomyces and Staphylococcus or cells of Gram negative bacteria such as several species of the genera Escherichia, such as E. coli, and Pseudomonas.
- yeast cells are used in the group of fungal cells.
- yeast strains such as inter alia Pichia pastoris, Saccharomyces cerevisiae and Hansenula polymorpha.
- insect cells such as cells from Drosophila and Sf9 can be used as host cells.
- the host cells can be plant cells expression systems using mammalian cells such as Chinese Hamster Ovary (CHO) cells, COS cells, BHK cells or Bowes melanoma cells are preferred in the present invention.
- mammalian cells provide expressed proteins with posttranslational modifications that are most similar to natural molecules of mammalian origin. Since the present invention deals with molecules that may have to be administered to humans, a completely human expression system would be particularly preferred. Therefore, even more preferably, the host cells are human cells.
- human cells are inter alia HeLa, 911, AT1080, A549, 293 and HEK293T cells.
- Preferred mammalian cells are human retina cells such as 911 cells or the cell line deposited at the European Collection of Cell Cultures (ECACC) , CAMR, Salisbury,
- PER.C6 refers to cells deposited under number 96022940 or ancestors, passages up ⁇ stream or downstream as well as descendants from ancestors of deposited cells, as well as derivatives of any of the foregoing.
- the human producer cells comprise at least a functional part of a nucleic acid sequence encoding an adenovirus El region in expressible format.
- said host cells are derived from a human retina and immortalised with nucleic acids comprising adenoviral El sequences, such as the cell line deposited at the European Collection of Cell Cultures (ECACC) , CAMR, Salisbury, Wiltshire SP4 OJG, Great Britain on 29
- ECACC European Collection of Cell Cultures
- binding molecules or functional variants are well known to the skilled artisan.
- One method comprises the steps of a) culturing a host as defined above under conditions conducive to the expression of the binding molecules or functional variants, and b) optionally, recovering the expressed binding molecules or functional variants.
- the expressed binding molecules or functional variants thereof can be recovered from the cell free extract, but preferably they are recovered from the culture medium. Methods to recover proteins, such as binding molecules, from cell free extracts or culture medium are well known to the man skilled in the art. Binding molecules or functional variants thereof as obtainable by the above described method are also a part of the present invention.
- binding molecules or functional variants thereof can be produced synthetically by conventional peptide synthesizers or in cell-free translation systems using RNA nucleic acid derived from DNA molecules according to the invention. Binding molecule or functional variants thereof as obtainable by the above described synthetic production methods or cell-free translation systems are also a part of the present invention.
- binding molecules according to the present invention preferably human binding molecules specifically binding to a coronavirus, such as SARS- CoV, or a fragment thereof, may be generated by transgenic non-human mammals, such as for instance transgenic mice or rabbits, that express human immunoglobulin genes.
- the transgenic non-human mammals have a genome comprising a human heavy chain transgene and a human light chain transgene encoding all or a portion of the human binding molecules as described above.
- the transgenic non-human mammals can be immunized with a purified or enriched preparation of a coronavirus, such as SARS-CoV, or a fragment thereof.
- Protocols for immunizing non-human mammals are well established in the art. See Using Antibodies: A Laboratory Manual, Edited by: E. Harlow, D. Lane (1998), Cold Spring Harbor Laboratory, Cold Spring Harbor, New York and Current Protocols in Immunology, Edited by: J.E. Coligan, A.M. Kruisbeek, D.H. Margulies, E.M.
- the human binding molecules are produced by B cells or plasma cells derived from the transgenic animals or human subjects that have been exposed to SARS-CoV.
- the human binding molecules are produced by hybridomas which are prepared by fusion of B cells obtained from the above described transgenic non-human mammals or human subjects to immortalized cells. B cells, plasma cells and hybridomas as obtainable from the above described transgenic non-human mammals or human subjects and human binding molecules as obtainable from the above described transgenic non-human mammals or human subjects are also a part of the present invention.
- Methods of identifying binding molecules, preferably human binding molecules such as human monoclonal antibodies or fragments thereof, or nucleic acid molecules encoding the binding molecules may comprise the steps of a) contacting a phage library of binding molecules, preferably human binding molecules, with a coronavirus, such as SARS-CoV, or a fragment thereof, b) selecting at least once for a phage binding to the coronavirus or the fragment thereof, and c) separating and recovering the phage binding to the coronavirus or the fragment thereof.
- the selection step may be performed by contacting a phage library with a coronavirus which is inactivated.
- the coronavirus may be isolated or non-isolated, e.g.
- the selection step may be performed in the presence of a fragment of a coronavirus such as an extracellular part of the coronavirus (such as SARS-CoV) , one or more proteins or (poly)peptides derived from a coronavirus, fusion proteins comprising these proteins or (poly)peptides, and the like.
- a coronavirus such as an extracellular part of the coronavirus (such as SARS-CoV)
- proteins or (poly)peptides derived from a coronavirus such as SARS-CoV
- fusion proteins comprising these proteins or (poly)peptides, and the like.
- phage display libraries collections of human monoclonal antibody heavy and light chain variable region genes are expressed on the surface of bacteriophage, preferably filamentous bacteriophage, particles, in for example single-chain Fv (scFv) or in Fab format (see de Kruif et al. , 1995b) .
- bacteriophage preferably filamentous bacteriophage, particles, in for example single-chain Fv (scFv) or in Fab format (see de Kruif et al. , 1995b) .
- phage library of binding molecules preferably scFv phage library
- RNA can be isolated from inter alia bone marrow or peripheral blood, preferably peripheral blood lymphocytes.
- the subject can be an animal vaccinated or exposed to a coronavirus, but is preferably a human subject which has been vaccinated or has been exposed to a coronavirus.
- the human subject has recovered from the coronavirus .
- phage display libraries may be constructed from immunoglobulin variable regions that have been partially assembled in vitro to introduce additional antibody diversity in the library (semi-synthetic libraries) .
- in vitro assembled variable regions contain stretches of synthetically produced, randomized or partially randomized DNA in those regions of the molecules that are important for antibody specificity, e.g. CDR regions.
- Coronavirus specific phage antibodies can be selected from libraries by immobilising a coronavirus (in inactivated or active form) or target antigens such as antigens from a coronavirus on a solid phase and subsequently exposing the coronavirus (in inactivated or active form) or target antigens to a phage library to allow binding of phages expressing antibody fragments specific for the solid phase-bound antigen (s) .
- Non- bound phages are removed by washing and bound phages eluted from the solid phase for infection of Escherichia coli (E.coli) bacteria and subsequent propagation.
- phage library can first be subtracted by exposing the phage library to non-target antigens bound to a solid phase. Phages may also be selected for binding to complex antigens such as complex mixtures of coronavirus proteins or (poly)peptides or host cells expressing one or more proteins or (poly)peptides of a coronavirus .
- Antigen specific phage antibodies can be selected from the library by incubating a solid phase with bound thereon a preparation of an inactivated coronavirus with the phage antibody library to let for example the scFv or Fab part of the phage bind to the proteins/polypeptides of the coronavirus preparation. After incubation and several washes to remove unbound and loosely attached phages, the phages that have bound with their scFv or Fab part to the preparation are eluted and used to infect Escherichia coli to allow amplification of the new specificity. Generally, one or more selection rounds are required to separate the phages of interest from the large excess of non-binding phages.
- known proteins or (poly)peptides of the coronavirus can be expressed in host cells and these cells can be used for selection of phage antibodies specific for the proteins or (poly)peptides .
- a phage display method using these host cells can be extended and improved by subtracting non-relevant binders during screening by addition of an excess of host cells comprising no target molecules or non-target molecules that are similar, but not identical, to the target, and thereby strongly enhance the chance of finding relevant binding molecules (This process is referred to as the MabstractTM process. MabstractTM is a pending trademark application of Crucell Holland B.V., see also US Patent Number 6,265,150 which is incorporated herein by reference) .
- a method of obtaining a binding molecule, preferably a human binding molecule or a nucleic acid molecule encoding such a binding molecule may comprise the steps of a) performing the above described method of identifying binding molecules, preferably human binding molecules such as human monoclonal antibodies or fragments thereof, or nucleic acid molecules encoding the binding molecules, and b) isolating from the recovered phage the human binding molecule and/or the nucleic acid encoding the human binding molecule.
- the DNA encoding the scFv or Fab can be isolated from the bacteria or phages and combined with standard molecular biological techniques to make constructs encoding bivalent scFvs or complete human immunoglobulins of a desired specificity (e.g. IgG, IgA or IgM) .
- constructs can be transfected into suitable cell lines and complete human monoclonal antibodies can be produced (see HuIs et al. , 1999; Boel et al. , 2000) .
- compositions of the invention may comprise inter alia stabilising molecules, such as albumin or polyethylene glycol, or salts .
- stabilising molecules such as albumin or polyethylene glycol
- salts used are salts that retain the desired biological activity of the binding molecules and do not impart any undesired toxicological effects. Examples of such salts include, but are not limited to, acid addition salts and base addition salts.
- Acid addition salts include, but are not limited to, those derived from nontoxic inorganic acids, such as hydrochloric, nitric, phosphoric, sulfuric, hydrobromic, hydroiodic, phosphorous and the like, as well as from nontoxic organic acids such as aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like.
- nontoxic inorganic acids such as hydrochloric, nitric, phosphoric, sulfuric, hydrobromic, hydroiodic, phosphorous and the like
- nontoxic organic acids such as aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like.
- Base addition salts include, but are not limited to, those derived from alkaline earth metals, such as sodium, potassium, magnesium, calcium and the like, as well as from nontoxic organic amines, such as N,N'- dibenzylethylenediamine, N-methylglucamine, chloroprocaine, choline, diethanolamine, ethylenediamine, procaine and the like.
- the binding molecules of the invention may be coated in or on a material to protect them from the action of acids or other natural or non-natural conditions that may inactivate the binding molecules .
- the invention provides compositions comprising at least two nucleic acid molecule encoding binding molecules as defined in the present invention.
- the compositions may comprise aqueous solutions such as aqueous solutions containing salts (e.g., NaCl or salsts as described above), detergents (e.g., SDS) and/or other suitable components .
- the present invention pertains to pharmaceutical compositions comprising a composition according to the invention.
- the pharmaceutical composition of the invention further comprises at least one pharmaceutically acceptable excipient.
- a pharmaceutical composition according to the invention can further comprise at least one other therapeutic, prophylactic and/or diagnostic agent.
- said further therapeutic and/or prophylactic agents are agents capable of preventing and/or treating an infection and/or a condition resulting from a coronavirus, such as SARS-CoV.
- Therapeutic and/or prophylactic agents include, but are not limited to, anti-viral agents. Such agents can be binding molecules, small molecules, organic or inorganic compounds, enzymes, polynucleotide sequences etc. Examples of anti-viral agents are well known to the skilled artisan. Agents that are currently used to treat patients infected with for instance SARS-CoV are interferon- alpha, steroids and potential replicase inhibitors.
- compositions of the invention can be tested in suitable animal model systems prior to use in humans.
- animal model systems include, but are not limited to, ferrets, mice, rats, chicken, cows, monkeys, pigs, dogs, rabbits, etc.
- compositions must be sterile and stable under the conditions of manufacture and storage.
- the compositions of the present invention can be in powder form for reconstitution in the appropriate pharmaceutically acceptable excipient before or at the time of delivery.
- the preferred methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
- the compositions of the present invention can be in solution and the appropriate pharmaceutically acceptable excipient can be added and/or mixed before or at the time of delivery to provide a unit dosage injectable form.
- the pharmaceutically acceptable excipient used in the present invention is suitable to high drug concentration, can maintain proper fluidity and, if necessary, can delay absorption.
- compositions of the invention can be prepared with carriers that will protect them against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems.
- a controlled release formulation including implants, transdermal patches, and microencapsulated delivery systems.
- Biodegradable, biocompatible polymers can inter alia be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid.
- compositions may be necessary to coat the compositions with, or co-administer the compositions with, a material or compound that prevents the inactivation of the binding molecules in the compositions.
- the binding molecules of the compositions may be administered to a subject in an appropriate carrier, for example, liposomes, or a diluent.
- the routes of administration can be divided into two main categories, oral and parenteral administration. These two categories include several routes of administration well known to the skilled person.
- the preferred administration route is intravenous, particularly preferred is intramuscular.
- Oral dosage forms can be formulated in several formulations and may contain pharmaceutically acceptable excipients including, but not limited to, inert diluents, granulating and disintegrating agents, binding agents, lubricating agents, preservatives, colouring, flavouring or sweetening agents, vegetable oils, mineral oils, wetting agents, and thickening agents.
- compositions of the present invention can also be formulated for parenteral administration.
- Formulations for parenteral administration can be inter alia in the form of aqueous or non-aqueous isotonic sterile non ⁇ toxic injection or infusion solutions or suspensions.
- the solutions or suspensions may comprise agents that are non ⁇ toxic to recipients at the dosages and concentrations employed.
- agents are well known to the skilled artisan and include 1, 3-butanediol, Ringer's solution, Hank's solution, isotonic sodium chloride solution, oils or fatty acids, local anaesthetic agents, preservatives, buffers, viscosity or solubility increasing agents, water-soluble antioxidants, oil-soluble antioxidants, and metal chelating agents .
- the pharmaceutical compositions of the invention can be used as a medicament. So, a method of treatment and/or prevention of a coronavirus infection using the pharmaceutical compositions of the invention is another part of the present invention.
- the (pharmaceutical) compositions of the invention can inter alia be used in the diagnosis, prophylaxis, treatment, or combination thereof, of one or more conditions resulting from a coronavirus . They are suitable for treatment of yet untreated patients suffering from a condition resulting from a coronavirus and patients who have been or are treated from a condition resulting from a coronavirus . They protect against further infection by a coronavirus and/or will retard the onset or progress of the symptoms associated with a coronavirus.
- the (pharmaceutical) compositions can be used in a method to detect, prevent, and/or treat a human coronavirus, such as SARS-CoV, infection.
- a human coronavirus such as SARS-CoV
- the above mentioned compositions and pharmaceutical compositions may be employed in conjunction with other molecules useful in diagnosis, prophylaxis and/or treatment of a coronavirus infection. They can be used in vitro, ex vivo or in vivo.
- the pharmaceutical compositions of the invention can be co-administered with a vaccine against a coronavirus, such as SARS-CoV.
- the vaccine may also be administered before or after administration of the pharmaceutical compositions of the invention.
- Administration of the pharmaceutical compositions of the invention with a vaccine might be suitable for postexposure prophylaxis and might also decrease possible side effects of a live-attenuated vaccine in immunocompromised recipients.
- binding molecules are typically formulated in the compositions and pharmaceutical compositions of the invention in a therapeutically or diagnostically effective amount.
- Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic response) .
- a suitable dosage range may for instance be 0.05-100 mg/kg body weight, preferably 0.1-15 mg/kg body weight.
- the molar ratio of the two binding molecules in the compositions and pharmaceutical compositions of the invention may vary from 1:100 to 100:1, preferably from 1:50 to 50:1, more preferably from 1:25 to 25:1, particularly 1:10 to 10:1, and more particularly 1:5 to 5:1.
- a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation.
- the molecules and compositions according to the present invention are preferably sterile.
- the other molecules useful in diagnosis, prophylaxis and/or treatment can be administered in a similar dosage regimen as proposed for the binding molecules of the invention. If the other molecules are administered separately, they may be adminstered to a patient prior to (e.g., 2 minutes, 5 minutes, 10 minutes, 15 minutes, 30 minutes, 45 minutes, 60 minutes, 2 hours, 4 hours, 6 hours, 8 hours, 10 hours, 12 hours, 14 hours, 16 hours, 18 hours, 20 hours, 22 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 7 days, 2 weeks, 4 weeks or 6 weeks before) , concomitantly with, or subsequent to (e.g., 2 minutes, 5 minutes, 10 minutes, 15 minutes, 30 minutes, 45 minutes, 60 minutes, 2 hours, 4 hours, 6 hours, 8 hours, 10 hours, 12 hours, 14 hours, 16 hours, 18 hours, 20 hours, 22 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 7 days, 2 weeks, 4 weeks or 6 weeks before) , concomitantly with, or subsequent
- Human binding molecules and pharmaceutical compositions comprising the human binding molecules are particularly useful, and often preferred, when to be administered to human beings as in vivo therapeutic agents, since recipient immune response to the administered antibody will often be substantially less than that occasioned by administration of a monoclonal murine, chimeric or humanised binding molecule.
- the invention concerns the use of (pharmaceutical) compositions according to the invention in the preparation of a medicament for the diagnosis, prophylaxis, treatment, or combination thereof, of a condition resulting from a coronavirus .
- the coronavirus is a human coronavirus such as SARS-CoV.
- kits comprising at least one composition according to the invention or at least one pharmaceutical composition according to the invention are also a part of the present invention.
- the above described components of the kits of the invention are packed in suitable containers and labeled for diagnosis, prophylaxis and/or treatment of the indicated conditions .
- compositions may be packaged individually.
- the above-mentioned components may be stored in unit or multi- dose containers, for example, sealed ampules, vials, bottles, syringes, and test tubes, as an aqueous, preferably sterile, solution or as a lyophilized, preferably sterile, formulation for reconstitution.
- the containers may be formed from a variety of materials and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle) .
- the kit may further comprise more containers comprising a pharmaceutically acceptable buffer.
- kits can be instructions customarily included in commercial packages of therapeutic, prophylactic or diagnostic products, that contain information about for example the indications, usage, dosage, manufacture, administration, contraindications and/or warnings concerning the use of such therapeutic, prophylactic or diagnostic products .
- the invention further pertains to a method of detecting a SARS-CoV in a sample, wherein the method comprises the steps of a) contacting a sample with a diagnostically effective amount of compositions or pharmaceutical compositions according to the invention, and b) determining whether the compositions or pharmaceutical compositions specifically bind to a molecule of the sample.
- the sample may be a biological sample including, but not limited to blood, serum, urine, tissue or other biological material from (potentially) infected subjects, or a nonbiological sample such as water, drink, etc.
- the (potentially) infected subjects may be human subjects, but also animals that are suspected as carriers of a coronavirus, such as SARS-CoV, might be tested for the presence of the coronavirus using the compositions or pharmaceutical compositions.
- the sample may first be manipulated to make it more suitable for the method of detection. Manipulation mean inter alia treating the sample suspected to contain and/or containing the coronavirus in such a way that the coronavirus will disintigrate into antigenic components such as proteins, (poly)peptides or other antigenic fragments.
- compositions or pharmaceutical compositions are contacted with the sample under conditions which allow the formation of an immunological complex between the binding molecules in the compositions or pharmaceutical compositions and the coronavirus or antigenic components thereof that may be present in the sample.
- the formation of an immunological complex if any, indicating the presence of the coronavirus in the sample, is then detected and measured by suitable means.
- suitable means include, inter alia, homogeneous and heterogeneous binding immunoassays, such as radioimmunoassays (RIA) , ELISA, immunofluorescence, immunohistochemistry, FACS, BIACORE and Western blot analyses.
- the invention provides a method of screening a binding molecule or a functional variant of a binding molecule for specific binding to a different, non- overlapping epitope of a coronavirus such as SARS-CoV as the epitope bound by a binding molecule or functional variant of the invention, wherein the method comprises the steps of a) contacting a binding molecule or a functional variant to be screened, a binding molecule or functional variant of the invention and a coronavirus or fragment thereof, b) measure if the binding molecule or functional variant to be screened is capable of competing for specifically binding to the coronavirus or fragment thereof with the binding molecule or functional variant of the invention.
- a coronavirus such as SARS-CoV
- the binding molecule or functional variant to be screened is not capable of competing for specifically binding to the coronavirus or fragment thereof with the binding molecule or functional variant of the invention, it most likely binds to a different, non-overlapping epitope.
- Assays to screen for non-competing binding molecules and measure (synergistic) neutralizing activity are well known to the skilled person.
- Example 1 Construction of a scFv phage display library using peripheral blood lymphocytes of a patient having been exposed to SARS-CoV
- Lymphocytes were obtained from a patient recovered from SARS-CoV (see Rickerts et al. 2003) and frozen in liquid nitrogen. The lymphocytes were quickly thawed in a 37 0 C water bath and transferred to wet-ice. The lymphocytes were diluted with cold DMEM culture medium to a final volume of 50 ml in a 50 ml tube and centrifuged for 5 minutes at 350xg. The obtained cell pellet was suspended in 5 ml DMEM and cell density was determined microscopically using trypan-blue exclusion to visualize dead cells. All cells ( ⁇ 5xlO 6 ) were spun again for 5 minutes at 350xg, decanted and suspended in residual fluid (DMEM) .
- DMEM residual fluid
- RNA was prepared from these cells using organic phase separation (TRIZOLTM) and subsequent ethanol precipitation. The obtained RNA was dissolved in DEPC treated ultrapure water and the concentration was determined by OD 260 nm measurement. Thereafter, the RNA was diluted to a concentration of 100 ng/ ⁇ l. Next, 1 ⁇ g of RNA was converted into cDNA as follows: To 10 ⁇ l total RNA, 13 ⁇ l DEPC treated ultrapure water and 1 ⁇ l random hexamers (500 ng/ ⁇ l) were added and the obtained mixture was heated at 65 0 C for 5 minutes and quickly cooled on wet-ice.
- TRIZOLTM organic phase separation
- the obtained cDNA products were diluted to a final volume of 200 ⁇ l with DEPC treated ultrapure water.
- the OD 260 nm of a 50 times diluted solution (in 10 rtiM Tris buffer) of the dilution of the obtained cDNA products gave a value of 0.1.
- PCR reaction mixtures contained, besides the diluted cDNA products, 25 pmol sense primer and 25 pmol anti-sense primer in a final volume of 50 ⁇ l of 20 rtiM Tris-HCl (pH 8.4), 50 rtiM KCl, 2.5 rtiM MgCl 2 , 250 ⁇ M dNTPs and 1.25 units Taq polymerase.
- the DNA obtained was dissolved in 50 ⁇ l ultrapure water and per ligation mix two times 2.5 ⁇ l aliquots were electroporated into 40 ⁇ l of TGl competent E. coli bacteria according to the manufacturer' s protocol (Stratagene) . Transformants were grown overnight at 37 0 C in a total of 27 dishes (three dishes per pooled fraction; dimension of dish: 240 mm x 240 mm) containing 2TY agar supplemented with 50 ⁇ g/ml ampicillin and 4.5% glucose. A (sub) library of variable heavy chain regions was obtained by scraping the transformants from the agar plates. This
- (sub) library was directly used for plasmid DNA preparation using a QiagenTM kit.
- the light chain immunoglobulin sequences were amplified from the same cDNA preparation in a similar three round PCR procedure and identical reaction parameters as described above for the heavy chain regions with the proviso that the primers depicted in Tables 5-9 were used.
- the first amplification was performed using a set of seventeen light chain variable region sense primers (eleven for the lambda light chain (see Table 5) and six for the kappa light chain (see Table 6) ) each combined with an anti-sense primer recognizing the C-kappa called HuCk 5'-ACACTCTCCCCTGTTGAAGCTCTT-S' (see SEQ ID NO: 89) or C-lambda constant region HuC ⁇ 2 5'-TGAACATTCTGTAGGGGCCACTG-S' (see SEQ ID NO: 90) or HuC ⁇ 7 5'-AGAGCATTCTGCAGGGGCCACTG-S' (see SEQ ID NO: 91) (the HuC ⁇ 2 and HuC ⁇ 7 anti-sense primers were
- the fractions were digested with Sail and Notl and ligated in the heavy chain (sub) library vector, which was cut with the same restriction enzymes, using the same ligation procedure and volumes as described above for the heavy chain (sub) library. Ligation purification and subsequent transformation of the resulting definitive library was also performed as described above for the heavy chain (sub) library.
- the transformants were grown in 30 dishes (three dishes per pooled fraction; dimension of dish: 240 mm x 240 mm) containing 2TY agar supplemented with 50 ⁇ g/ml ampicillin and 4.5% glucose. All bacteria were harvested in 2TY culture medium containing 50 ⁇ g/ml ampicillin and 4.5% glucose, mixed with glycerol to 15% (v/v) and frozen in 1.5 ml aliquots at - 8O 0 C.
- Antibody fragments were selected using antibody phage display libraries and technology, essentially as described in US patent 6,265,150 and in WO 98/15833, both of which are incorporated herein in their entirety. All procedures were performed at room temperature unless stated otherwise.
- An inactivated SARS-CoV preparation (Frankfurt 1 strain) was prepared as follows. Medium from Vero cells which were infected with SARS-CoV strain Frankfurt 1 was harvested as soon as cyotopathic effect (CPE) was observed. Cell debris was removed by centrifugation of the harvested medium for 15 minutes at 3000 rpm. The obtained supernatant was collected, spun again for 15 minutes at 3000 rpm and transferred to a clean tube.
- CPE cyotopathic effect
- ultracentrifuge tubes were filled with 10 ml sterile 25% glycerol in PBS. 20 ml of the cleared supernatant was gently applied on the glycerol cushion and the tubes were spun for 2 hours at 20,000 rpm at 4 0 C. The supernatant was discarded and the virus pellets were resuspended in 1 ml TNE buffer (10 rtiM Tris-HCl pH 7.4, I mM EDTA, 200 rtiM NaCl) and stored at -8O 0 C. Next, the resuspended virus pellets were gamma-irradiated at 45kGy on dry ice. Subsequently, they were tested for the absence of infectivity in cell culture. If absence of infectivity was established, the thus obtained inactivated SARS-CoV preparation was used for selection of single-chain phage antibodies specifically binding to SARS-CoV.
- the inactivated virus preparation and heat-inactivated fetal bovine serum (FBS) were coated overnight at 4°C onto the surface of separate MaxisorpTM plastic tubes (Nunc) .
- the tubes were blocked for two hours in 3 ml PBS containing 2% FBS and 2% fat free milk powder (2% PBS-FM) . After two hours the FBS- coated tube was emptied and washed three times with PBS.
- 500 ⁇ l (approximately 10 13 cfu) of a phage display library expressing single-chain Fv fragments (scFvs) essentially prepared as described by De Kruif et al.
- scraped bacteria were used to inoculate 2TY medium containing ampicillin, tetracycline and glucose and grown at a temperature of 37°C to an OD 600 nm of -0.3.
- CT or VCSM13 helper phages were added and allowed to infect the bacteria after which the medium was changed to 2TY containing ampicillin, tetracycline and kanamycin. Incubation was continued overnight at 30°C. The next day, the bacteria were removed from the 2TY medium by centrifugation after which the phages in the obtained supernatant were precipitated using polyethylene glycol 6000/NaCl.
- the phages were dissolved in a small volume of PBS containing 1% BSA, filter- sterilized and used for a next round of selection.
- the selection/re-infection procedure was performed two or three times.
- individual E.coli colonies were used to prepare monoclonal phage antibodies .
- individual colonies were grown to log-phase and infected with VCSM13 helper phages after which phage antibody production was allowed to proceed overnight.
- Phage antibody containing supernatants were tested in ELISA for binding activity to the SARS-CoV preparation which was coated to 96- well plates. In the above-described selection, the phage antibody called SC03-014 was obtained.
- ScFvs of the phage antibody SC03-014 were produced as described before in De Kruif et al. (1995a and 1995b) and references therein (which are incorporated herein in their entirety) .
- the buffer of the scFvs was adjusted to 1 x PBS.
- UV-inactivated SARS-CoV Single chain Fv fragments
- SARS-CoV Single chain Fv fragments
- scFvs single chain Fv fragments
- UV-inactivated SARS-CoV (Frankfurt 1 strain) was prepared as follows. Medium from Vero cells which were infected with 0.1. moi (multiplicity of infection) SARS-CoV strain Frankfurt 1 was harvested as soon as cyotopathic effect (CPE) was observed. Cells were once frozen at -20°C and thawed. Cell debris was removed by centrifugation of the harvested medium for 15 minutes at 3000 rpm.
- the obtained supernatant was collected, spun again for 15 minutes at 3000 rpm and transferred to a clean tube. Subsequently, ultracentrifuge tubes were filled with 10 ml sterile 25% v/v glycerol in PBS. 20 ml of the cleared supernatant was gently applied on the glycerol cushion and the tubes were spun for 2 hours at 20,000 rpm at 4 0 C in a Beckman SW28 rotor. The supernatant was discarded and the virus pellets were resuspended in 1 ml TNE buffer (10 rtiM Tris-HCl pH 7.4, I mM EDTA, 200 rtiM NaCl) and stored at -8O 0 C.
- TNE buffer 10 rtiM Tris-HCl pH 7.4, I mM EDTA, 200 rtiM NaCl
- the resuspended virus pellets were UV-irradiated at 4 0 C for 15 minutes (UV-B radiation 280-350 nm; ⁇ max 306 nm) . Subsequently, they were tested for the absence of infectivity in cell culture. If absence of infectivity was established, the thus obtained inactivated SARS-CoV preparations were used for further experiments .
- Selected single-chain phage antibodies that were obtained in the screens described above were validated in ELISA for specificity, i.e. binding to the UV-inactivated SARS-CoV preparation prepared as described supra. Additionally, the single-chain phage antibodies were also tested for binding to 10% FBS. For this purpose, the UV-inactivated SARS-CoV preparation or 10% FBS preparation was coated to MaxisorpTM ELISA plates. After coating, the plates were blocked in 2% PBS-FM. The selected single-chain phage antibodies were incubated in an equal volume of 4% PBS-FM to obtain blocked phage antibodies . The plates were emptied, washed three times with PBS, after which the blocked phage antibodies were added.
- V L gene of scFv SC03-014 was amplified using oligonucleotides 5K-I acctgtctcgagttttccatggctgacatccagat gacccagtctccatcctcc (SEQ ID NO: 98) and sy3K-C gctgggggcggccac ggtccgtttgatctccaccttggtcccc (SEQ ID NO: 99) and the PCR product cloned into vector pSyn-C05-C ⁇ .
- V L gene of scFv SC03-022 was amplified using oligonucleotides 5K-J acctgtctcgagt tttccatggctgacatcgtgatgacccagtctccag (SEQ ID NO: 100) and sy3K- F gctgggggcggccacggtccgcttgatctccaccttggtccc (SEQ ID NO: 101) and the PCR product cloned into vector pSyn-C05-C ⁇ . Nucleotide sequences for all constructs were verified according to standard techniques known to the skilled artisan.
- V H genes of scFv SC03-014 were amplified using oligonucleotides 5H-B acctgtcttgaattctccatggccgaggtgcagctggtggagtctg (SEQ ID NO: 102) and sy3H-A gcccttggtgctagcgctggagacggtcaccagggtgccctggcccccc (SEQ ID NO:103) .
- V H genes of scFv SC03-022 were amplified using oligonucleotide set 5H-H acctgtcttgaattctccatggccgaggtgcag ctggtgcagtctgg (SEQ ID NO: 104) and sy3H-C gcccttggtgctagcgct ggagacggtcacggtggtgccctggccccccc (SEQ ID NO: 105) . Thereafter, the PCR products were cloned into vector pSyn-C03-HC ⁇ l and nucleotide sequences were verified according to standard techniques known to the skilled person in the art.
- pgG103-014C03 and pgG103-022C03 encoding the anti-SARS-CoV human IgGl heavy chains were transiently expressed in combination with the pSyn-C05-VkI (V L SC03-014) and pgG103-022C05 (V L SC03-022), respectively in HEK293T or PER.C6 ® cells and supernatants containing IgGl antibodies were obtained.
- the nucleotide sequences of the heavy chains of the antibodies called CR03-
- 014 and CR03-022 are shown in SEQ ID NO: 106 and SEQ ID NO: 108, respectively.
- the amino acid sequences of the heavy chains of the antibodies CR03-014 and CR03-022 are shown in SEQ ID NO: 107 and SEQ ID NO: 109, respectively.
- the nucleotide sequences of the light chain of antibodies CR03-014 and CR03-022 is shown in SEQ ID NO: 110 and SEQ ID NO: 112, respectively.
- the amino acid sequences of the light chain of antibodies CR03-014 and CR03-022 is shown in SEQ ID NO: 111 and SEQ ID NO: 113.
- the recombinant human monoclonal antibodies were purified over protein-A columns and size-exclusion columns using standard purification methods used generally for immunoglobulins (see for instance WO 00/63403 which is incorporated by reference herein) .
- Example 6 Screening assay for SARS-CoV neutralizing activi ty of recombinant human anti -SARS-CoV antibodies
- the SARS-CoV neutralization assay was performed on Vero cells (ATCC CCL 81) .
- the SARS-CoV strains used in the neutralization assay were the Frankfurt 1 strain (for the complete genome of this strain see EMBL-database accession # AY291315) (Rickerts et al. 2003) .
- Virus stocks of the strains were used in a titer of 4xlO 3 TCID 50 /ml (50% tissue culture infective dose per ml) , with the titer calculated according to the method of Spearman and Kaerber which is known to the average skilled person.
- Recombinant human anti-SARS-CoV antibodies produced as described above were screened by serially 2-fold-dilution of the undiluted material (2.5 mg/ml) in PBS starting from 1:4 (dilution range 1:4 - 1:512) .
- a neutralization titer of ⁇ 1:4 was regarded as specific evidence of reactivity of the antibodies against SARS-CoV in the screening assay.
- Convalescent serum from a SARS-patient was used as a positive control for the neutralization assay.
- CPE cytopathic effect
- the highest antibody/serum dilution giving protection in 66% percent of wells was defined as the neutralizing antibody titer.
- the experiment was performed three times in triplicate (see Tables 12A, B and C) .
- the IgGs CR03-014, CR03-022, a negative control IgGl and a positive control serum from a SARS-patient were tested for SARS-CoV neutralizing activity.
- both neutralizing antibodies may be suitable in the prophylaxis and/or treatment of a condition resulting from a SARS-CoV infection.
- SARS-CoV strains were used to evaluate the potency and breadth of protection of the anti- SARS-CoV antibodies.
- HKU-66, HKU-61567, GZ43 and GZ50 were passaged on FRhK-4 cells for two or three times before testing (see Table 13) .
- Strain HKU-61644 was passaged on Vero cells and tested after passage 1 and 15.
- the SARS-CoV neutralization assay was performed on FRhK-4 cells as follows. A 500 ⁇ l stock solution (100 ⁇ g/ml) of antibody was prepared in maintenance medium (MM, MEM supplemented with 1% w/v FCS) . From this stock solution 2- fold-serially dilutions were prepared.
- antibody concentrations varied from 0.1 to 50 ⁇ g/ml in the presence of 1000 TCID 50 /ml SARS-CoV.
- the 96-well plate containing the antibody/virus mixtures was preincubated for 1-2 hours at 37 0 C.
- 100 ⁇ l of the antibody/virus mixtures were added in quadruplicate to wells from a second 96-well tissue culture plate containing confluent FRhK-4 cells in 100 ⁇ l MM and incubated at 37 0 C.
- 100 TCID 50 of SARS-CoV was present in the presence of antibody concentrations varying from 0.05 to 25 ⁇ g/ml.
- the cells were cultured at 37°C and observed for the development of CPE at 72 and 96 hours.
- CPE was compared to a positive control (SARS-CoV inoculated cells) and a negative control (cells incubated with MM only) .
- the antibody neutralization titer was determined as the concentration of antibody which gave 100% protection of the quadruplicate cell cultures .
- the monoclonal anti-SARS-CoV antibody CR03-014 completely neutralized 100 TCID 50 of all tested SARS-CoV isolates at a concentration of 12.5 ⁇ g/ml (see Table 13) . This indicates that antibody CR03-014 is able to neutralize a variety of SARS-CoV isolates.
- SARS-CoV neutralization assay was performed as described for the Frankfurt 1 strain supra to determine synergy between SARS-CoV neutralizing antibodies CR03-014 and CR03-022.
- Stock solutions of antibody CR03-014 and CR03-022 of approximately similar potency were mixed in different ratios.
- the CR03-014 antibody stock solution of 2.5 mg/ml was diluted 4- fold to 625 ⁇ g/ml.
- antibody CR03-014 and CR03- 022 were mixed in the following ratios (mixture A: CR03-014 0%, CR03-022 100%; mixture B: CR03-014 10%, CR03-022 90%; mixture C: CR03-014 50%, CR03-022 50%; mixture D: CR03-014 90%, CR03-022 10%; and mixture E: CR03-014 100%, CR03-022 0%) .
- the mixtures should neutralize SARS-CoV at the same titer as the individual antibodies present in the mixtures .
- the mixtures should neutralize SARS-CoV at a higher titer as the individual antibodies present in the mixtures .
- the neutralization assay was performed twice in triplicate wells as described above. The results of both assays were combined. Protection of at least 66% percent of the wells (4 of the 6 wells tested) was defined as the neutralizing antibody titer.
- the neutralization titers of the separate mixtures are shown in Table 14. From Table 14 can be deducted that the mixtures had the following titers: mixture A, 64; mixture B, 256; mixture C, >1024; mixture D, 256; and mixture E, 16.
- the SARS-CoV neutralization assay showing synergy between the anti-SARS-CoV antibodies was performed on FRhK-4 cells (ATCC CRL-1688) as follows.
- the SARS-CoV strain called HK-39849 (GenBank accession number AY278491) was used in a titer of 2xlO 3 TCID 50 /ml as calculated according to the method of Reed and Muench known to the average skilled person.
- the human anti-SARS-CoV antibodies were screened by serially 1.46-fold-dilution in maintenance medium (MM) (1% w/v FCS in MEM with antibiotic) starting at a concentration of 200 ⁇ g/ml (dilution range 200 - 6.7 ⁇ g/ml) in duplo.
- MM maintenance medium
- FCS 1% w/v FCS in MEM with antibiotic
- concentration 200 ⁇ g/ml concentration of 200 ⁇ g/ml (dilution range 200 - 6.7 ⁇ g/ml) in duplo.
- Four different compositions were tested: antibody CR03- 014 individually, antibody CR03-022 individually, control IgGl antibody, and antibodies CR03-014 and CR03-022 in combination (start concentration 200 ⁇ g/ml of each antibody) .
- 110 ⁇ l of virus suspension was mixed with 110 ⁇ l of the respective recombinant human anti-SARS-CoV antibody dilution and incubated for one hour at 37°C.
- Clmixt is the concentration of the first component in the mixture which leads to a certain level of inhibition (f)
- cleffect is that concentration of the first component which alone (in the absence of the second component) will result in the same inhibitory effect as the mixture of the two components
- c2mixt and c2effect are the corresponding concentrations for the second component.
- Example 7 Binding of anti -SARS antibodies to SARS-CoV, SARS-CoV spike protein and fragments thereof.
- An ELISA to detect binding of anti-SARS antibodies to SARS-CoV was performed as follows. Wells of ELISA plates were coated overnight with UV-inactivated SARS-CoV preparation in 50 rtiM bicarbonate buffer pH 9.6. The wells of the plates were washed three times with PBS containing 0.05% Tween and blocked for 2 hours at 37 0 C with PBS containing 1% BSA. Next, the antibodies diluted in PBS containing 1% BSA were incubated for 1 hour at room temperature.
- Single chain phage antibodies SC03-014 and SC03-022 were analyzed for their ability to bind HEK293T cells that recombinantly express proteins of SARS-CoV.
- HEK293T cells were transfected with a plasmid carrying a cDNA sequence encoding the spike (S) protein from SARS-CoV strain Frankfurt 1 or with control vector.
- S spike
- single-chain phage antibodies were first blocked in an equal volume of 4% PBS-M for 15 minutes at 4°C prior to the staining of the transfected HEK293T cells.
- the blocked phage antibodies were added to mock transfected HEK293T cells and HEK293T cells transfected with the SARS-CoV S protein.
- the binding of the single chain phage antibodies to the cells was visualized using a biotinylated anti-Ml3 antibody (Santa Cruz Biotechnology) followed by streptavidin-phycoerythrin (Caltag) .
- the single chain phage antibodies SC03-014 and SC03-022 were capable of binding spike transfected HEK293T cells, whereas no binding to mock transfected HEK293T cells was observed.
- a control single chain phage antibody did neither recognize the spike transfected HEK293T cells nor the mock transfected HEK293T cells.
- S318-510 A fragment corresponding to amino acid residues 318-510 of the S protein (portion called S318-510) was amplified on S gene cDNA using the oligonucleotide primers: EcoRIspikeFor318 5'- cctggaattctccatggccaacatcaccaacc-3' (SEQ ID NO: 116) and XfoaIspikeRev510 5' -gaagggccctctagacacggtggcagg-3' (SEQ ID NO: 117) .
- the resulting fragment was digested with EcoRl-Xbal and cloned into pHAVT20/myc His A to yield pHAVT20/myc-His A S318-510.
- This vector expression of fragment S318-510 fused to the HAVT20 leader sequence was under control of the human, full-length, immediate-early CMV promoter.
- DNA transfections were performed in HEK293T cells for transient expression using standard techniques .
- the S protein derived fragments were used directly from culture supernatant or were purified from culture supernatant using Ni-NTA (Qiagen) .
- An ELISA to evaluate binding of antibodies to the S protein derived fragments was performed as follows.
- Wells of ELISA plates were coated overnight with 5 ⁇ g/ml anti-myc antibody in 50 rtiM bicarbonate buffer pH 9.6. The wells of the plates were washed three times with PBS containing 0.05% Tween and blocked for 2 hours at 37 0 C with PBS containing 1% BSA. The wells coated with anti-myc antibody were incubated with the myc-tagged fragments S565 or S318-510 diluted in PBS containing 1% BSA for 1 hour at room temperature. The wells were washed three times with PBS containing 0.05% Tween. Next, the antibodies CR03-014, CR03-022 or control antibody diluted in PBS containing 1% BSA were incubated for 1 hour at room temperature.
- CM5 sensorchips and running buffer HBS-EP were from Biacore AB (Uppsala Sweden) .
- Recombinant S318-510 fragment was immobilized to CM5 chips using an amine coupling procedure resulting in a response level of approximately 1,000 resonance units (RU) .
- the sensor chip surface was regenerated with a pulse of 5 ⁇ l 5 nM NaOH.
- Biacore evaluation software (BIAevalution, July 2001) was used to fit the association and dissociation curves of all concentrations injected.
- the individual K D for CR03-014 and CR03-022 was determined as 16.3 nM and 0.125 nM, respectively, the K D for the antibodies binding simultaneously as 5.71 nM and for binding of CR03-014 to CR03-022 saturated S318-510 as 14.8 nM.
- the dose reduction indices of 3 and 20 for CR03-014 and CR03-022 respectively, neither simultaneous nor sequential binding of the monoclonal antibodies resulted in changes of K D which could explain their synergistic neutralizing action through cooperative binding.
- Figure 6B shows that binding of antibody CR03-022 was unaffected in the presence of excess unlabeled monoclonal antibody control or antibody CR03-014. As expected, binding of both biotinylated CR03-014 and CR03-022 was effectively reduced by their unlabeled counterparts (see Figures 6A and B) . These results demonstrate that the antibodies CR03-014 and CR03-022 do not compete with each other for binding to the S318-510 fragment and recognize different/distinct, non- competing epitopes .
- the diversity within the region 318-510 of the S protein was determined as follows. A list containing more than 146 genomes or genes encoding complete human SARS-CoV or fragments thereof was compiled. In 114 cases, an open reading frame encoding for full-length spike (S) protein was identified.
- a 318-510 fragment (variant G) corresponding to the sequence of four animal SARS-like CoVs (Genbank accession numbers AY304486 - AY304489; see also Table 1, SARS-CoV SZ3, SZ13, SZ16 and SZl, respectively) was generated.
- the four SARS-like CoVs which were isolated from raccoon dogs and palm civet cats, contain the amino acid substitutions K344R, F360S, N479K and T487S (see Guan et al. 2003) .
- CR03-014 was capable of binding to variants A-E and variants H and I to a similar extent as to the wild-type fragment. Binding of CR03-014 to variant F (N479S substitution) was substantially lower than binding to the other fragments. No binding of CR03-014 to fragment G (K344R, F360S, N479K and T487S substitutions) was observed.
- Antibody CR03-022 was capable of binding all variant S318-510 fragments to a similar extent as the wild-type (non-mutated) S318-510 fragment. Together this indicates that residue N479 is involved in binding of CR03-014, either directly by being part of the binding site of CR03-014 or indirectly by being important for the correct conformation of the binding site of CR03-014 within the S protein. Since, antibody CR03-022 is capable of binding to recombinant fragments composed of amino acid residues 318-510 of all human SARS-CoV isolates (as described in Table 15) and in addition is also capable of binding to animal SARS-like CoV, CR03-022 is suitable for treatment and/or protection against SARS-CoV isolates in general.
- a combination/cocktail comprising both antibodies, CR03-014 and CR03-022, as both antibodies are capable of specifically binding to human SARS- CoV and the antibodies act synergistically in neutralizing human SARS-CoV.
- the combination/cocktail of CR03-014 and CR03-022 comprises synergistic human SARS-CoV neutralizing activity.
- An additional advantage of such a combination/cocktail is its capability of neutralizing human SARS-CoV as well as animal SARS-like CoV.
- escape viruses of CR03-014 and CR03-022 were generated.
- the process for generating escape viruses of CR03-014 is given infra.
- the process for generating escape viruses of CR03-022 was identical with the proviso that 60 ⁇ g/ml antibody instead of 20 ⁇ g/ml was used in all respective steps.
- Serial dilutions (0.5 ml) of SARS-CoV strain HKU 39849 were incubated with a constant amount (20 ⁇ g/ml giving a ⁇ 3 log reduction of TCID 50 /ml) of antibody CR03-014 (0.5 ml) for 1 hour at 37°C/5% CO2 before addition to wells containing FRhK-4 cells.
- the virus was allowed to attach to the cells for 1 hour at 37°C/5% CO 2 , then removed and cells were washed twice with medium. Finally, cells were incubated for 2 days in the presence of selecting antibody CR03-014 at 20 ⁇ g/ml in 0.5 ml medium.
- the nucleotide sequence of the SARS-CoV spike open reading frame was determined.
- Viral RNA of each of the escape viruses and wild- type SARS-CoV virus was isolated and converted into cDNA by standard RT-PCR.
- the cDNA was used for nucleotide sequencing of the SARS-CoV spike ORF in order to identify mutations.
- Figure 9 shows the results of the sequencing data for the five E014 escape viruses obtained. All escape viruses contained a nucleotide mutation at position 1385 (C to T) , which resulted in an amino acid mutation P to L at position 462 in the spike protein.
- the neutralization index (NI) was determined for each of the E014 and E022 escape viruses.
- a virus was defined as an escape variant, if the neutralization index was ⁇ 2.5 logs.
- the process of determining the NI is given below for E014 escape viruses.
- the process was identical for E022 escape viruses with the proviso that 60 ⁇ g/ml instead of 20 ⁇ g/ml monoclonal antibody was used in all respective steps .
- the neutralization index was determined by subtracting the number of infectious virus particles (in TCIDso/ml) produced in FRhK-4 cell cultures infected with virus plus monoclonal antibody (20 ⁇ g/ml) from the number of infectious virus particles (in TCID 50 /ml) produced in FRhK-4 cell cultures infected with virus alone ( [log TCID50/ml virus in absence of monoclonal antibody minus log TCID50/ml virus in presence of monoclonal antibody]) . An index lower than 2.5 logs was considered as evidence of escape.
- each escape virus and wild-type SARS-CoV 100 TCID 50 was incubated for 1 hour at 37°C/5% CO 2 with 20 ⁇ g/ml of CR03-014 before addition to FRhK-4 cells.
- the virus was allowed to attach to the cells for 1 hour at 37°C/5% CO2 after which the inoculum was removed and cells were washed twice with medium before being replenished with medium containing 20 ⁇ g/ml of CR03-014. After a 2 day incubation at 37°C/5% CO 2 the medium was harvested and the TCID 50 /ml of each virus was determined.
- the concentration of antibody used to determine the NI resulted in a ⁇ 3 log reduction of virus titer when performed on the wild-type SARS- CoV virus.
- wild type SARS-CoV was neutralized by CR03- 014 as judged by the NI of 3.3.
- the NI for each escape virus was ⁇ 2.5 and thus each of the escape viruses was no longer neutralized by CR03-014.
- wild-type SARS-CoV virus was also neutralized by CR03-022 (see Table 17) .
- the NI for each E022 escape virus was >2.5 and thus it was concluded that each of the escape viruses was still neutralized by CR03-022.
- the amino acid substitution in four of the five E022 escape viruses apparently does not play a role in neutralization of SARS-CoV by CR03-022. It might have been induced non-specifically during the course of the experiment. This agrees with finding by Poon et al. (2005) who observed the mutation at position 863 (T to I) when SARS-CoV was passaged multiple times in FRhK-4 cells.
- the neutralizing epitope of CR03-022 could not be determined by means of generating escape viruses. This may be caused by the functional constraints of the binding region on the S protein. A mutation occurring in this region may be detrimental to the stability of the virus and could therefore not be isolated in the experiments described above.
- a recombinant S318-510 fragment harbouring the P to L substitution at position 462 was constructed essentially as described supra. DNA transfection of the resulting plasmid was performed in HEK293T cells for transient expression and the fragments were directly used from culture supernatant. The ELISA was performed as described supra. Briefly, the fragments were captured on anti-myc coated microtiter wells. Subsequently, antibodies CR03-014 and CR03- 022 were added and binding of the antibodies was detected using an anti-human IgG HRP-conjugate.
- antibody CR03-014 was not able to bind the S318-510 fragment carrying a P to L substitution at position 462. Binding of CR03-022 was not affected by this amino acid substitution. This further indicates that antibody CR03-022 is capable of binding to a different/distinct, non-competing epitope on the S protein and suggests that CR03-022 might be used to compensate potential lack of neutralization of SARS-CoV variants by CR03-014.
- ADE occurred when macrophages were infected with SARS-CoV in the presence of the neutralizing anti-SARS-CoV monoclonal antibody CR03-014, the non-neutralizing anti-SARS-CoV monoclonal antibody CR-03-015, the monoclonal antibody called CR-JA (an monoclonal antibody against rabies which is used herein as a control antibody) , convalescent serum from an individual exposed to SARS-CoV and serum from a healthy individual.
- CR-JA an monoclonal antibody against rabies which is used herein as a control antibody
- PBMCs Human peripheral blood mononuclear cells
- PBMCs Hong Kong
- the PBMCs were separated by Ficoll-Paque gradient centrifugation (Pharmacia Biotech, Uppsala, Sweden) .
- To isolate monocytes 2 x 10 7 PBMCs were allowed to adhere onto petridishes (Greiner, Frickenhausen, Germany) for 1 hour in RPMI 1640 medium supplemented with 20 rtiM HEPES, 2 rtiM glutamine, 0.6 ⁇ g/ml penicillin, and 60 ⁇ g/ml streptomycin and 5% heat-inactivated autologous plasma. After washing with medium, the adherent monocytes were detached by pipeting and re-seeded into 24 well plates at a density of 2*10 5 cells per well in supplemented RPMI 1640 medium.
- monocytes were also seeded and allowed to adhere onto glass coverslips.
- the purity of the monocytes on the glass coverslips was confirmed by staining with a CD14 R- phycoerythrin (R-PE) -conjugated mouse anti-human monoclonal antibody (BD Biosciences, San Diego, U.S.A.) .
- R-PE R- phycoerythrin
- Medium in the monocyte cultures was replaced every 2-3 days and the cells were allowed to differentiate for 14 days in vitro. Differentiation of monocytes into macrophages was confirmed by the typical morphology of macrophages .
- the obtained primary human monocyte-derived macrophages were used in further experiments. Two days prior to the ADE experiments, the supplemented RPMI 1640 medium was exchanged into Macrophage Serum Free medium (SFM) (Invitrogen, Carlsbad, CA, U.S.A.) .
- SFM Macrophage Serum Free medium
- MM medium MEM including 1% FCS and 0.6 ⁇ g/ml penicillin, and 60 ⁇ g/ml streptomycin
- convalescent serum from a SARS-CoV exposed individual and serum from a healthy individual was mixed with 300 ⁇ l of SARS-CoV.
- MM medium mixed with SARS-CoV served as the virus control.
- the virus/monoclonal antibody mixtures and virus/serum mixtures were incubated for one hour at 37 0 C.
- RNA was generated with 10 ⁇ l of RNA, and reverse-transcribed by 200 U of Superscript II reverse transcriptase (Invitrogen) in a 20 ⁇ l reaction containing 25 ng oligo-dTi2-i8 primer, 10 rtiM dithiothreitol, and 0.5 rtiM deoxynucleotide triphosphates . Reactions were incubated at 42 0 C for 50 minutes, followed by a heat inactivation step
- reaction mix (72 0 C for 15 minutes) .
- the reaction mix was diluted 10 times by the addition of 180 ⁇ l buffer AE (Qiagen) and stored at - 2O 0 C.
- Reactions were performed in a LightCycler (Roche) with the following conditions: 10 minutes at 95 0 C, followed by 40 cycles of 95 0 C for 0 seconds, 66 0 C for 5 seconds, and 72 0 C for 9 seconds . Plasmids containing the target sequence were used as positive controls. Fluorescence signals from these reactions were captured at the end of the extension step in each cycle (87 0 C) . To determine the specificity of the assay, PCR products were subjected to melting curve analysis at the end of the assay (65 to 95 0 C; 2°C/second) .
- Reverse transcription with sense (negative strand detection) or anti- sense (positive strand detection) primers to the polymerase gene of SARS-CoV was achieved by using Superscript II reverse transcriptase (Invitrogen) according to manufacturer's instructions .
- Complementary DNA was generated with 5 ⁇ L of RNA, and reverse-transcribed by 200 U of Superscript II reverse transcriptase (Invitrogen) in a 20 ⁇ l reaction containing 0.1 ⁇ M gene specific primer, 10 rtiM dithiothreitol, and 0.5 rtiM deoxynucleotide triphosphates. Reactions were incubated at 42 0 C for 50 minutes, followed by a heat inactivation step (72 0 C for 15 minutes) .
- reaction was diluted 10 times by the addition of 180 ⁇ L buffer AE (Qiagen) and stored at -2O 0 C.
- 2 ⁇ l of diluted complementary DNA was amplified in 20 ⁇ l containing 3.5 rtiM of MgCl2, 0.25 ⁇ M of forward primer (coro3: 5'-TACACACCTCAGCGTTG-3' (SEQ ID NO:124)), and 0.25 ⁇ M of reverse primer (coro4: 5'- CACGAACGTGACGAAT-3' (SEQ ID NO:125)) .
- Reactions were performed in a LightCycler (Roche) with the following conditions: 10 min at 95 0 C, followed by 50 cycles of 95 0 C for 10 seconds, 6O 0 C for 5 seconds, and 72 0 C for 9 seconds. Plasmids containing the target sequence were used as positive controls. Fluorescence signals from these reactions were captured at the end of the extension step in each cycle. To determine the specificity of the assay, PCR products were subjected to melting curve analysis at the end of the assay (65 to 95 0 C; 0. l°C/seconds) . Data for viral RNA were normalised for RNA levels of ⁇ -actin housekeeping gene.
- results show that positive strand SARS-CoV RNA was detected in all macrophage cultures that were incubated with SARS-CoV, which confirms the abortive infection of macrophages by SARS- CoV.
- the levels of positive strand RNA observed in macrophage cultures infected with SARS-CoV in the presence of anti-SARS- CoV monoclonal antibodies CR03-014 or CR03-015 or convalescent serum were not significantly higher than in macrophage cultures infected with SARS-CoV in the presence of control monoclonal antibody CR-JA or serum from a healthy individual or in the absence of monoclonal antibody or serum (data not shown) .
- 15-mer linear and looped/cyclic peptides were synthesized from proteins of SARS-CoV and screened using credit-card format mini-PEPSCAN cards (455 peptide formats/card) as described previously (see inter alia WO 84/03564, WO 93/09872, Slootstra et al. 1996) . All peptides were acetylated at the amino terminus.
- the antigenic peptides found in the analysis method may not only be used for detection of the SARS-CoV strain Urbani and the prevention and/or treatment of a condition resulting from the SARS-CoV strain Urbani, but may also be useful in detecting SARS-CoV in general and preventing and/or treating a condition resulting from SARS-CoV in general.
- the protein-id of the surface spike glycoprotein of for instance the SARS-CoV strains T0R2, Frankfurt 1 and HSR 1 in the EMBL- database is AAP41037, AAP33697 and AAP72986.
- accession number in the EMBL-database of the complete genome of the strains T0R2, Frankfurt 1 and HSR 1 is AY274119, AY291315 and AY323977, respectively. Under these accession numbers the amino acid sequence of the other (potential) proteins of these strains can be found.
- the deprotected peptides were reacted on the cards with an 0.5 rtiM solution of 1, 3-bis (bromomethyl)benzene in ammonium bicarbonate (20 rtiM, pH 7.9/acetonitril (1:1 (v/v) ) .
- the cards were gently shaken in the solution for 30-60 minutes, while completely covered in the solution.
- the cards were washed extensively with excess of H20 and sonicated in disrupt-buffer containing 1% SDS/0.1% beta-mercaptoethanol in PBS (pH 7.2) at 70°C for 30 minutes, followed by sonication in H20 for another 45 minutes.
- Recombinant human anti-SARS-CoV antibodies CR03-014 and CR03-022 were tested for binding to each linear and looped peptide in a PEPSCAN-based enzyme-linked immuno assay (ELISA) .
- ELISA enzyme-linked immuno assay
- the 455-well creditcard-format polypropylene cards, containing the covalently linked peptides, were incubated with the antibodies (1-10 ⁇ g/ml; diluted in blocking solution which contains 5% horse-serum (v/v) and 5% ovalbumin (w/v) ) (4°C, overnight) .
- the peptides were incubated with anti-human antibody peroxidase (dilution 1/1000) (1 hour, 25°C) , and subsequently, after washing the peroxidase substrate 2, 2 '-azino-di-3-ethylbenzthiazoline sulfonate (ABTS) and 2 ⁇ l/ml 3% H2O2 were added. Controls (for linear and looped) were incubated with anti-human antibody peroxidase only. After 1 hour the colour development was measured. The colour development of the ELISA was quantified with a CCD- camera and an image processing system.
- the set-up consisted of a CCD-camera and a 55 mm lens (Sony CCD Video Camera XC-77RR, Nikon micro-nikkor 55 mm f/2.8 lens), a camera adaptor (Sony Camera adaptor DC-77RR) and the Image Processing Software package Optimas, version 6.5 (Media Cybernetics, Silver Spring, MD 20910, U.S.A.) .
- Optimas runs on a pentium II computer system.
- the recombinant human anti-SARS-CoV-antibodies CR03-014 and CR03-022 were tested for binding to the 15-mer linear and looped/cyclic peptides synthesized as described supra.
- Relevant binding of a peptide to a recombinant human anti- SARS-CoV antibody was calculated as follows .
- the average OD- value for each antibody was calculated for the respective proteins (sum of OD-values of all peptides/total number of peptides) .
- the standard deviation of this average was calculated.
- the standard deviation was multiplied by 2 and the obtained value was added to the average value to obtain the correction factor.
- the OD-value of each peptide was then divided by this correction factor. If a value of 0.9 or higher was found, then relevant binding was considered to be present between the specific peptide and the respective antibody.
- Particularly interesting appear to be domains comprising several reactive peptides, i.e. domains comprising consecutive peptides, wherein at least most of the peptides in the domains are reactive with the antibody.
- Monoclonal antibody CR03-014 did not appear to react specifically with a peptide or domains comprising several peptides within the SARS-CoV spike protein indicating that CR03-014 may recognize a discontinuous non-linear epitope.
- Monoclonal antibody CR03-022 reacted with a series of looped peptides in two domains (data not shown) .
- the domains are comprised of amino acid residues 430-449 and 484-503 of the SARS-CoV spike protein and have the amino acid sequences ATSTGNYNYKYRYLRHGKLR (SEQ ID NO: 126) and YTTTGIGYQPYRVWLSFEL (SEQ ID NO:127), respectively.
- both domains have the motif TXTGXXXXXYR (SEQ ID NO: 128) in common, indicating that this motif may be crucial for the binding of antibody CR03-022 to the SARS-CoV spike protein.
- Table 1 List of currently known SARS-CoV genome sequence and spike genes .
- Table 2 Human IgG heavy chain variable region primers (sense) .
- Table 3 Human IgG heavy chain J-region primers (anti-sense) .
- Table 4 Human IgG heavy chain variable region primers extended with Sfil/Ncol restriction sites (sense) and human IgG heavy chain J-region primers extended with XhoI/BstEII restriction sites (anti-sense) .
- Table 6 Human kappa chain variable region primers (sense) .
- Table 7 Human lambda chain J-region primers (anti-sense) .
- Table 8 Human lambda chain J-region primers (anti-sense) .
- Table 9 Human kappa chain variable region primers extended with Sail restriction sites (sense) , human kappa chain J- region primers extended with Notl restriction sites (anti- sense) , human lambda chain variable region primers extended with Sail restriction sites (sense) and human lambda chain J- region primers extended with Notl restriction sites (anti- sense) .
- Table 10 Distribution of the different light chain products over the 10 fractions.
- Table 11 Data of the single-chain Fvs capable of binding SARS-CoV.
- Table 12B SARS-CoV neutralization experiment II.
- Table 13 Concentrations of the monoclonal anti-SARS-CoV antibody CR03-014 giving complete protection against 100 TCID 50 of the different SARS-CoV isolates indicated in an in vitro neutralization assay.
- Table 14 SARS-CoV neutralization experiment of several mixtures of CR03-014 and CR03-022.
- Table 15 List of SARS-CoV strains having a region 318-510 of the S protein not identical to the region 318-510 of the S protein of SARS-CoV Frankfurt 1 strain.
- GIy Ser GIy lie Ser Thr Pro Met Asp VaI 1 5 10
- GIy GIu Ser Leu Lys lie Ser Cys Lys GIy Ser GIy Tyr GIy Phe lie 20 25 30
- Trp Met GIy lie lie Tyr Pro GIy Asp Ser GIu Thr Arg Tyr Ser Pro 50 55 60
- GIy GIn GIy Thr Lys VaI GIu lie Lys Arg 100 105
- Lys VaI GIu lie Lys Arg Ala Ala Ala 245
- GIu Trp VaI GIy Arg lie Arg Ser Lys Ala Asn Ser Tyr Ala Thr Ala
- Phe Thr Leu Thr lie Ser Ser Leu GIn Pro GIu Asp Phe Ala Thr Tyr 210 215 220
- Lys VaI GIu lie Lys Arg Ala Ala Ala
- GIu Trp Met GIy lie lie Tyr Pro GIy Asp Ser GIu Thr Arg Tyr Ser 50 55 60
- Ser GIy Ser GIy Thr Asp Phe Thr Leu Thr lie Ser Ser Leu GIn Ala 210 215 220
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AT05817101T ATE550037T1 (en) | 2004-11-11 | 2005-11-10 | COMPOSITIONS AGAINST THE SARS CORONAVIRUS AND THEIR USES |
NZ553701A NZ553701A (en) | 2004-11-11 | 2005-11-10 | Composition comprising SC03-014 and SC03-022 antibodies against SARS-CoV |
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KR1020077009194A KR101255861B1 (en) | 2004-11-11 | 2005-11-10 | Compositions against sars-coronavirus and use thereof |
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ATE550037T1 (en) | 2012-04-15 |
SG159542A1 (en) | 2010-03-30 |
KR20070083768A (en) | 2007-08-24 |
AU2005303758A1 (en) | 2006-05-18 |
CA2582057A1 (en) | 2006-05-18 |
KR101255861B1 (en) | 2013-04-17 |
US8106170B2 (en) | 2012-01-31 |
CA2582057C (en) | 2015-08-11 |
US20080014204A1 (en) | 2008-01-17 |
EP1812067B1 (en) | 2012-03-21 |
EP1812067A1 (en) | 2007-08-01 |
NZ553701A (en) | 2009-12-24 |
AU2005303758B2 (en) | 2011-04-28 |
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