WO2006095180A2 - Anticorps monoclonaux humanises contre le coronavirus associe a sras et traitement des patients atteints du syndrome respiratoire aigu severe (sras) - Google Patents

Anticorps monoclonaux humanises contre le coronavirus associe a sras et traitement des patients atteints du syndrome respiratoire aigu severe (sras) Download PDF

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Publication number
WO2006095180A2
WO2006095180A2 PCT/GB2006/000848 GB2006000848W WO2006095180A2 WO 2006095180 A2 WO2006095180 A2 WO 2006095180A2 GB 2006000848 W GB2006000848 W GB 2006000848W WO 2006095180 A2 WO2006095180 A2 WO 2006095180A2
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seq
antibody
sars
chain
group
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PCT/GB2006/000848
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WO2006095180A3 (fr
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Ka Man Leung
Dong Xiao Feng
Shiu Fun Pang
Yuet Wai Kan
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Ultra Biotech Limited
The Regents Of The University Of California
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Publication of WO2006095180A2 publication Critical patent/WO2006095180A2/fr
Publication of WO2006095180A3 publication Critical patent/WO2006095180A3/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • 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
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • 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
    • C07K2317/60—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)

Definitions

  • This invention relates to therapeutic antibodies. More specifically, it relates to humanized single chain variable fragment antibodies and whole antibodies against SARS- associated coronavirus and method of treating patient suffering from SARS (severe acute respiratory syndrome).
  • SARS-Co V SARS-associated coronavirus
  • phage display library As described in [20], a particular phage library, constructed by James Marks (Department of Anesthesia and Pharmaceutical Chemistry, University of California, San Francisco General Hospital), contains millions of independent clones of single-chain variable fragment (scFv) antibodies[9] appears to be a suitable tool to develop specific antibodies against SARS-CoV. Like other coronaviruses, the SARS-CoV also utilizes a surface glycoprotein named as spike protein to infect host cells [I]. The spike protein of SARS-CoV consists of 1255 amino acid residues and can be divided into two sub-domains, Sl and S2 domains.
  • the Sl domain mediates the binding of the virus to its receptor angiotensin-converting enzyme 2 mainly distributing on the surface of human lung cells [18].
  • the S2 domain mediates membrane fusion between the virus and the host cell. Two strategies can be employed to block the infection of SARS-CoV, either to block the binding of the Sl domain to the receptor or to block the fusion of the virus mediated by the S2 domain.
  • humanized antibodies against SARS-CoV are provided.
  • Such humanized antibodies either in the form of scFv or as a whole antibody, bind specifically to the S2 domain of the spike protein of SARS-CoV.
  • a preferred epitope in the S2 domain is the region of Leu803-Ala828, although other epitopes may also provide satisfactory results.
  • An antibody of the present invention preferably has one or more peptide segments defined by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, or SEQ ID NO: 7 in its V H chain, and/or has one or more segments defined by SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, or SEQ ID NO: 14 in its V L chain.
  • a particular antibody of the present invention comprises seven peptide segments in the V H chain defined by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, and SEQ ID NO: 7, respectively, and seven peptide segments in the V L chain defined by SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14, respectively.
  • a preferred antibody comprises a V H chain containing a sequence defined by SEQ ID NO: 24 and a V L chain containing a sequence defined by SEQ ID NO: 25.
  • a method of identifying scFv gene fragment that confers the above antibody the binding specificity to the S2 domain of the spike protein of the SARS-CoV comprises the steps of (a) obtaining a conjugated or recombinant protein containing a peptide segment of the S2 domain of the spike protein; (b) obtaining a phage display library; and (c) selecting from the phage display library specific phage- displayed scFvs using the conjugated or recombinant protein as the binding agent to identify the scFv gene fragment that confer binding specificity to the S2 domain of the spike protein.
  • preparations of the antibody can be made by subcloning the scFv gene fragment into a proper vector, for example, pET28 vector from Novagen, transforming the reconstructed vector into E. Colt strain BL21, and inducing its expression by IPTG.
  • the scFv gene fragment can be subcloned into the gene encoding a whole human antibody so that a whole humanized antibody with the same binding specificity can be expressed.
  • the above preparation of humanized antibody can be further processed using known methods in the pharmaceutical industry into a pharmaceutical formulation with a proper carrier.
  • a method of treating, preventing, or ameliorating a pathological condition in a patient, wherein said pathological condition is associated with coronavirus SARS-CoV comprising a step of administering to said patient a therapeutically effective amount of a humanized antibody that has a binding specificity to an epitope in the S2 domain of the spike protein of SARS-CoV.
  • FIG. 1 shows the results of phage clones from each round of panning in the polyclonal ELISA assay.
  • FIG. 2 shows the results of individual S2-a-specific antibody clones in the monoclonal ELISA assay.
  • FIG. 3 shows the results of individual S2-b-specific antibody clones in the monoclonal
  • FIG. 4 illustrates DNA fingerprinting of clones to determine diversity by BstNI restriction enzyme analysis.
  • FIG. 5 shows results of sequencing analysis of V H and V L chain genes of S2-a and S2-b- specif ⁇ c human mAbs.
  • FIG. 6 shows results of immunofluorescence staining of SARS-CoV infected Vero cells.
  • Synthetic peptide S2a (NFSQILPDPLKPTKRS - SEQ ID NO: 15) was obtained from UCSF (University of California, San Francisco) and was supplied at >95% pure as assessed by
  • S2a corresponds to the S783-798 region in the S2 domain of SARS-CoVs spike protein.
  • S2b is a peptide segment corresponding to the 803 - 828 region of the S2 domain. Pure synthetic S2a peptide was conjugated to BSA and OVA carrier protein to increase the coating efficiency on the Immunotube for screening.
  • BSA carrier protein bovine serum albumin
  • OVA ovalbumin
  • S2b is relatively hydrophobic and is not soluble in the common buffer.
  • S2b was expressed as a purified thioredoxin (Trx) fusion protein in E. coli and as panning bait for selection. Prior to selection, the library was depleted of the Trx fusion protein binders.
  • the amino acid sequence of the SARS-CoV spike protein was used to design a codon- optimized version of the gene encoding the spike protein, as described elsewhere [12].
  • 2Sb an oligonucleotide based on the DNA sequence encoding the residues 803 to 828 (LLFNKVTLADAGFMKQYGECLGDINA - SEQ ID NO: 16) of spike protein, was synthesized.
  • the sequence of the oligonucleotide is 5'AATTCGCTGTTATTTA ATAAGGTGACCCTGGCAGACGCGGGGTTCATGAAACAGTATGGTGAATGCTTGGGC GATATTAACGCCA-3' (SEQ ID NO: 23).
  • the synthetic gene was cloned into the bacterial expression vector pET32b (Novagen) fused with the 3 'terminal of the thioredoxin (Trx) gene.
  • the cloned gene was confirmed by DNA sequencing.
  • the ligated vector was transformed into Escherichia coli BL21 (Novagen).
  • the S2b Trx fusion proteins were induced to express by isopropyl-b-D-thiogalactopyranoside (IPTG) and were purified according to the manufacturer's protocols for Ni-nitrilotriacetic acid (Ni-NTA) resin (QIAGEN).
  • the library can be constructed according to the detailed description provided in the publications by Hoogenboon, et al [Nucleic Acids Research Vol. 19, No. 15, pp 4133-4137] and O'Connell D, et al., [Phage versus phagemid libraries for generation of human monoclonal antibodies. J MoI Biol. 2002 Aug 2;321(l):49-56].
  • a scFv phage antibody library was constructed in fd phage.
  • the fd phage display library was derived from a phagemid library [16] by subcloning the sfil/Notl scFv insert from pHENl into fd-Sfil/Notl [17].
  • Ligation mixtures were used to transform Escherichia coli TGl and the transformation mixture plated on TYE plates containing 15 ug/ml tetracycline.
  • Library size was calculated by counting the number of tetracycline-resistant colonies.
  • Library quality was verified by determining the percentage of clones with inserts of appropriate size for an scFv gene, performed by colony PCR screening using the primer fdseq [15] and fd2 [15].
  • Library diversity was confirmed by BstNl fingerprinting the amplified scFv genes [15].
  • the library was stored in 2xYT containing 15 ug/ml tetracycline and 15% glycerol at -8O 0 C.
  • Phase library selection scFvs were selected by using antibody phage display library and technology. Specific phage-displayed scFvs were affinity-selected by using proteins absorbed to Immunotubes (Nunc). For selections with S2a conjugated protein, Immunotubes (Nunc, Maxisorb) were coated with 10 ug/ml of BSA conjugated S2a overnight at 4 0 C. For the subsequent round of panning, selection was alternated between OVA conjugated and BSA conjugated S2a protein to prevent selection against carrier protein.
  • phages were depleted against recombinant control protein before selection by pre-incubating the phage library with 10 ug/ml recombinant control protein in a total volume of 1 ml for 60 minutes at room temperature.
  • the coated immunotubes were blocked with 2% (w/v) skimmed milk powder in PBS for one hour at room temperature.
  • the phage library was first adsorbed in phosphate-buffered saline (PBS) containing 2% skimmed milk powder.
  • plaque-forming units (9 x 10 11 ) of phage-scFvs prepared from phage library was mixed and introduced for panning into immunotubes. Unbound phages were removed by 6 washes with PBS containing 0.02% Tween 20, followed by 10 washes with PBS.
  • Bound phages were eluted with 1 ml of 10OmM Triethylamine (Sigma), neutralized with 0.5 ml of IM Tris-HCl (pH7.4) and then used to infect 20 ml of exponentially growing E. coli TGl.
  • E. coli was grown at 37 0 C for 30 minutes after which time the culture was plated on TYE plates containing 15 ug/ml tetracycline. After overnight growth, colonies were scraped from the plates and used to generate phage for second round of selection as described in ref 15.
  • Antigen-binding phage antibodies were identified by phage ELISA. Individual colonies were picked into 96-well microtiter plates containing 2 xYT with 15 ug/ml tetracycline. Bacteria were grown overnight at 3O 0 C, the bacteria pelleted, and supernatant, containing phage particles used for ELISA. The spike protein fragments, either carrier protein conjugated (BSA or OVA conjugated S2a, 10 ug/ml) or recombinant antigens (S2b-Trx, 10 ug/ml) were coated onto 96-well plates in bicarbonate buffer (pH 9.6) overnight at 4 0 C.
  • BSA carrier protein conjugated
  • S2b-Trx recombinant antigens
  • the number of unique phage antibodies were estimated by PCR fingerprinting of the scFv genes with the restriction enzyme BstNI (New England Biolab) as described in ref 5 and confirmed by DNA sequencing. Sequencing runs were performed in both directions for each clone using fd2 primer 5'-TTTTTGGAGATTTTCAAC-S' and fdseql primer 5'- GAATTTTCTGTATGAGG-3', referenced to as SEQ ID NO: 17 and SEQ ID NO: 18, respectively.
  • BIOCHIPS slides (Euroimmun, Luebeck, Germany), coated with SARS-Co V-infected cells and non-infected cells were utilized. 25 ul of diluted scFv was added to a well of the slide and incubated for overnight at 4 0 C. The slide was washed with PBST and air dried. 20 ul of the diluted fluorescein labeled mouse anti-c-myc secondary antibodies (1:100) were added and incubated at room temperature for 30 minutes. The slide was washed with PBST with diluted Evan Blue (1:400), air dried, and mounted. The mounted slide was observed under fluorescence microscope (Leica DML).
  • the scFv gene fragments were subcloned into pSynl vector and transformed into E. coli BL21 (DE3) (Novagen).
  • the scFv expression was induced by growth in 2xYT medium supplemented with 100 ug/ml ampicillin and 1 mM isopropyl-D-thiogalactoside for 4 hours at
  • Soluble periplasmic extracts were obtained by osmotic shock at 4 0 C using lysis buffer containing 20% sucrose, ImM EDTA, 30OmM Tris-
  • scFvs contain a His-6 tag that allows purification by Ni-NTA agarose column (Qiagen).
  • the scFvs purified from the periplasmic extracts were dialyzed with PBS for immunofluorescence and neutralization assays.
  • VH genes of Al 1 single-chain fragment variable were amplified using PCR from the phage DNA with the primer pairs: CTACGCGTGTCTTGTCCCAGGTGGAGCTGGTGGA (SEQ ID NO: 19) and GTGCTAGCTGAGGAGACGGTGACCAGG (SEQ ID NO: 20)
  • the amplified DNA was digested with Mlul and Nhel, ligated into N5KGlVal-Lark( IDEC Pharmaceuticals, San Diego) and clones containing the correct V H were identified by DNA sequencing.
  • Y n genes of Al 1 scFv were amplified from the PHAGE DNA with the primer pairs: TGCACGATGTGAGTCTGTGTTGACGCAGG (SEQ ID NO: 21) and GTAAGCTTGGTCCCTCCGCCGAA (SEQ ID NO: 22).
  • the resulting DNA was subcloned into pGEM-T easy vector (Promega) and clones containing the correct Vr* identified by DNA sequencing.
  • V « genes were excised from pGEM-T easy vector with Dralll and Hindlll and ligated into Dralll- and HiddiiI-digestedN5KGl Val-Lark DNA containing the appropriate V H gene.
  • Clones containing the correct V H and Y ⁇ gene were identified by DNA sequencing, and vector DNA was used to transfect CHO DG44 cells by electroporation.
  • Stable cell lines were established by selection in 400ug/ml G418 and expanded into IL spinner flasks. Supernatant containing IgG was collected, concentrated by ultrafiltration, and purified on Protein G (GE healthcare). Panning against purified SARS-CoV spike protein fragment
  • the above human non-immune phage display antibody library was then screened to select the scFv antibodies specific to the above selected antigenic determinant region (S2-a or S2-b) of the spike protein.
  • Each round of panning selection comprised a cycle of scFv-phage binding to the immobilized antigen, washing away of unbound and non-specifically bound scFv-phage, elution of the specifically bound scFv-phage, and propagation of enriched scFv-phage for entry into next round of panning.
  • the titer of the recovered phage was 7.3 x 10 6 and 3.6 x 10 6 cfu/ml after four round of selection on carrier protein conjugated S2a and S2b-Trx fusion protein. It is believed that an increase in the number of eluted phages after several rounds of panning manifested the specific binding.
  • Table 1 Results obtained after panning a human phage display scFv library (9 x 10 11 cfu diversity) against spike protein fragments S2-a and S2-b.
  • polyclonal phage were prepared after the fourth round of selection and analyzed for its binding to two target fragments (S2a and S2b) by ELISA. After each round of panning, the output phages were amplified and applied to microtiter wells coated with different antigens. Each microtiter well was coated with 10 ug/ml of the antigen. Bound phages were detected by horseradish peroxidase (HRP)-conjugated anti- Mi 3 antibody. Phage ELISA, shown in FIG. 1, demonstrated the enrichment of S2a and S2b- specific phages during panning cycles.
  • HRP horseradish peroxidase
  • phages were prepared from individual colonies from the fourth round of selection.
  • the binding specificity of the scFv was determined by phage ELISA using the target antigen and other control proteins as substrates. Referring to the results in Table 2, forty eight and ninety six individual clones were picked for the ELISA analysis against S2-a and S2-b spike protein fragments, respectively.
  • FIG. 2a of the 48 random clones analyzed, 16 clones specifically recognized S2-a protein, but not control peptide CETA, OVA and BSA control protein.
  • FIG. 2b shows that six specific clones were found to bind S2-a in a dose-dependent manner.
  • the scFv gene was amplified by PCR and the PCR product was digested with the frequently cutting restriction enzyme BstNI (PCR fingerprinting). From the sixteen S2-a binding scFvs, unique fingerprints were observed, indicating the presence of unique antibody (see Figure 4a). DNA sequence of representative scFv clones 6 and 13 was shown in Figure 5.
  • Table 2 Monoclonal ELISA. Single clones obtained after 4th rounds of panning were tested for binding to the target antigen and control antigen in ELISA. Binding phages were detected with an HRP-conjugated anti-M13 antibody. Signal to noise ratio over 2 are regarded as ELISA positive. Number of ELISA positive clones/ Target antigen Control antigen , « . . , . ,. ,
  • Synthetic S2a Carrier protein (BSA, OVA), 16 / 48

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Abstract

L'invention porte sur un anticorps humanisé ayant une spécificité de liaison à un épitope dans le domaine S2 d'une protéine en forme de spicule du CoV associé à SRAS, en particulier un épitope dans la région de Leu803-Ala828. L'anticorps reconnaît spécifiquement les cellules infectées par le CoV associé à SRAS et est utile pour traiter des patients souffrants du CoV associé à SRAS.
PCT/GB2006/000848 2005-03-10 2006-03-10 Anticorps monoclonaux humanises contre le coronavirus associe a sras et traitement des patients atteints du syndrome respiratoire aigu severe (sras) WO2006095180A2 (fr)

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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111471103A (zh) * 2020-03-20 2020-07-31 唐山怡安生物工程有限公司 一种新冠病毒（2019-nCOV）的异源抗体及其制备方法
CN111778218A (zh) * 2020-06-04 2020-10-16 山东宽和正生物医药有限公司 噬菌体展示抗体库及基于其淘筛获得的针对新冠病毒SARS-CoV-2的单克隆抗体
WO2021186190A1 (fr) * 2020-03-19 2021-09-23 Imperial College Innovations Limited Anticorps anti-coronavirus
WO2021238910A1 (fr) * 2020-05-25 2021-12-02 Guo Bingshi Anticorps dirigés contre la protéine spike du coronavirus et leurs utilisations
WO2022010353A1 (fr) * 2020-07-10 2022-01-13 Leyden Laboratories B.V. Procédés d'identification d'anticorps à réaction croisée contre les coronavirus
WO2022161346A1 (fr) * 2021-01-27 2022-08-04 Bioduro (Jiangsu) Co., Ltd. Anticorps dirigé contre le sars-cov-2

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Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021186190A1 (fr) * 2020-03-19 2021-09-23 Imperial College Innovations Limited Anticorps anti-coronavirus
CN111471103A (zh) * 2020-03-20 2020-07-31 唐山怡安生物工程有限公司 一种新冠病毒（2019-nCOV）的异源抗体及其制备方法
WO2021238910A1 (fr) * 2020-05-25 2021-12-02 Guo Bingshi Anticorps dirigés contre la protéine spike du coronavirus et leurs utilisations
CN111778218A (zh) * 2020-06-04 2020-10-16 山东宽和正生物医药有限公司 噬菌体展示抗体库及基于其淘筛获得的针对新冠病毒SARS-CoV-2的单克隆抗体
CN113336846A (zh) * 2020-06-04 2021-09-03 山东宽和正生物医药有限公司 针对新冠病毒SARS-CoV-2的单克隆抗体E11
CN113336846B (zh) * 2020-06-04 2023-11-10 山东宽和正生物医药有限公司 针对新冠病毒SARS-CoV-2的单克隆抗体E11
WO2022010353A1 (fr) * 2020-07-10 2022-01-13 Leyden Laboratories B.V. Procédés d'identification d'anticorps à réaction croisée contre les coronavirus
NL2026043B1 (en) * 2020-07-10 2022-03-15 Leyden Laboratories B V Methods for identifying coronavirus cross-reacting antibodies
WO2022161346A1 (fr) * 2021-01-27 2022-08-04 Bioduro (Jiangsu) Co., Ltd. Anticorps dirigé contre le sars-cov-2
CN115427441A (zh) * 2021-01-27 2022-12-02 保诺生物科技(江苏)有限公司 针对sars-cov-2的抗体
CN115427441B (zh) * 2021-01-27 2023-09-05 保诺生物科技(江苏)有限公司 针对sars-cov-2的抗体

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