US20110020323A1 - Gram-positive bacteria specific binding compounds - Google Patents

Gram-positive bacteria specific binding compounds Download PDF

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Publication number
US20110020323A1
US20110020323A1 US12/837,358 US83735810A US2011020323A1 US 20110020323 A1 US20110020323 A1 US 20110020323A1 US 83735810 A US83735810 A US 83735810A US 2011020323 A1 US2011020323 A1 US 2011020323A1
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Prior art keywords
sequence
antibody
seq
functional
functional equivalent
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Inventor
Tim Beaumont
Mark J. Kwakkenbos
Eric J. Brown
John H. Morisaki
Wouter L.W. Hazenbos
Sanjeev Mariathasan
Kimberly Kajihara
Yi Xia
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AIMM Therapeutics BV
Genentech Inc
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AIMM Therapeutics BV
Genentech Inc
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Priority to US12/837,358 priority Critical patent/US20110020323A1/en
Application filed by AIMM Therapeutics BV, Genentech Inc filed Critical AIMM Therapeutics BV
Assigned to AIMM THERAPEUTICS B.V. reassignment AIMM THERAPEUTICS B.V. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BEAUMONT, TIM, KWAKKENBOS, Mark Jeroen
Assigned to GENENTECH, INC. reassignment GENENTECH, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BROWN, ERIC J., HAZENBOS, WOUTER L.W., KAJIHARA, KIMBERLY, MARIATHASAN, SANJEEV, MORISAKI, JOHN HIROSHI, XIA, YI
Publication of US20110020323A1 publication Critical patent/US20110020323A1/en
Priority to US13/305,659 priority patent/US8617556B2/en
Priority to US13/786,206 priority patent/US9399673B2/en
Priority to US13/786,215 priority patent/US9090677B2/en
Priority to US14/103,715 priority patent/US9266943B2/en
Priority to US14/728,826 priority patent/US9458228B2/en
Priority to US14/981,643 priority patent/US9688745B2/en
Priority to US15/246,301 priority patent/US9927428B2/en
Priority to US15/900,589 priority patent/US20180292391A1/en
Abandoned legal-status Critical Current

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    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
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    • C07K14/475—Growth factors; Growth regulators
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    • C07K16/1271—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria from Micrococcaceae (F), e.g. Staphylococcus
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    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
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    • C07K2317/565—Complementarity determining region [CDR]
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    • G01N2800/26—Infectious diseases, e.g. generalised sepsis

Definitions

  • the invention relates to the fields of biology, immunology and medicine.
  • Gram-positive microorganisms cause the majority of systemic infections.
  • Staphylococcus aureus S. aureus .
  • About 20% of the population is a long-term carrier of S. aureus.
  • S. aureus can cause a range of illnesses from minor skin infections, such as pimples, impetigo (may also be caused by Streptococcus pyogenes ), boils, cellulitis folliculitis, furuncles, carbuncles, scalded skin syndrome and abscesses, to life-threatening diseases such as pneumonia, meningitis, osteomyelitis, endocarditis, Toxic shock syndrome (TSS), and septicemia.
  • TSS Toxic shock syndrome
  • aureus is capable of infecting all kinds of organs and tissues. S. aureus infections occur in immunocompetent as well as immune compromised people. About 50% of the infections in US intensive care units are caused by this pathogen. Three hundred thousand S. aureus infections per year, resulting in 12,000 deaths, are reported in the US (see also Moran et al. NEMJ 355, 666-674 (2006)).
  • MRSA Methicillin-resistant S. aureus
  • LTA lipoteichoic acid
  • antibodies or functional parts thereof or immunoglobulin chains or functional equivalents thereof which comprise: (a) a heavy chain CDR1 sequence comprising a sequence which has at least 70% sequence identity to the sequence RFAMS (SEQ ID NO:1), and/or (b) a heavy chain CDR2 sequence comprising a sequence which has at least 70% sequence identity to the sequence SINNGNNPYYARSVQY (SEQ ID NO:2), and/or (c) a heavy chain CDR3 sequence comprising a sequence which has at least 70% sequence identity to the sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or (d) a light chain CDR1 sequence comprising a sequence which has at least 70% sequence identity to the sequence RASENVGDWLA (SEQ ID NO:4), and/or, (e) a light chain CDR2 sequence comprising a sequence which has at least 70% sequence identity to the sequence KTSILES (SEQ ID NO:5), and/or (f) a light chain CDR3 sequence comprising
  • the antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof which comprises: (a) a heavy chain CDR1 sequence comprising a sequence which has the sequence RFAMS (SEQ ID NO:1), and/or (b) a heavy chain CDR2 sequence comprising a sequence which has the sequence SINNGNNPYYARSVQY (SEQ ID NO:2), and/or (c) a heavy chain CDR3 sequence comprising a sequence which has the sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or (d) a light chain CDR1 sequence comprising a sequence which has the sequence RASENVGDWLA (SEQ ID NO:4), and/or, (e) a light chain CDR2 sequence comprising a sequence which has the sequence KTSILES (SEQ ID NO:5), and/or (f) a light chain CDR3 sequence comprising a sequence which has the sequence QHYXRFPYT, wherein X is I or M (SEQ ID NO:6).
  • the antibody or functional part or immunoglobulin chain or functional equivalent has a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:7) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILESGVPSRFSGS GSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRTV, wherein X is I of M (SEQ ID NO:8).
  • the antibody or functional part or immunoglobulin chain or functional equivalent has a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:7) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILESGVPSRFSGS GSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRA, wherein X is I of M (SEQ ID NO:10).
  • the antibody or functional part or immunoglobulin chain or functional equivalent has a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:7) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILESGVPSRFSGS GSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKVEIKRTV, wherein X is I of M (SEQ ID NO:11).
  • the antibody or functional part or immunoglobulin chain or functional equivalent has a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLVESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARS VQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:9) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILESGVPSRFSGS GSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRTV, wherein X is I of M (SEQ ID NO:8).
  • the antibody or functional part or immunoglobulin chain or functional equivalent has a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLVESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARS VQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:9) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILESGVPSRFSGS GSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRA, wherein X is I of M (SEQ ID NO:10).
  • the antibody or functional part or immunoglobulin chain or functional equivalent has a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLVESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARS VQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:9) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILESGVPSRFSGS GSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKVEIKRTV, wherein X is I of M (SEQ ID NO:11).
  • an asparagine has been replaced by another amino acid.
  • the asparagine is an asparagine at position 53 of the heavy chain, whereby the amino acid numbering is according to Kabat (1991).
  • the other amino acid is serine.
  • At least one amino acid other than cysteine has been replaced with cysteine.
  • the at least one amino acid other than cysteine is valine at light chain position 205 and/or valine at light chain position 110, and/or alanine at heavy chain position 114, whereby the amino acid numbering is according to Kabat (1991).
  • the invention provides isolated antibodies that bind to in vivo-grown S. aureus .
  • the antibody is human.
  • the invention also provides antibodies or functional parts or immunoglobulin chains or functional equivalents capable of binding an SD-repeat dependent epitope.
  • antibodies or functional parts or immunoglobulin chains or functional equivalents capable of binding to S. aureus ClfA, ClfB, SdrC, SdrD and SdrE.
  • antibodies or functional parts or immunoglobulin chains or functional equivalents which are capable of competing with any antibody or functional part or immunoglobulin chain or functional equivalent described herein for binding to a Staphylococcus species.
  • the antibody or functional part or immunoglobulin chain or functional equivalent is a human antibody.
  • nucleic acid sequences with a length of at least 15 nucleotides, or functional equivalents thereof, encoding at least one CDR sequence of any of the antibodies or functional parts or immunoglobulin chains or functional equivalents described herein.
  • the invention provides isolated, synthetic or recombinant nucleic acid sequences, or functional equivalents thereof, comprising a sequence which has at least 70% sequence identity to a sequence selected from the group consisting of cgctttgccatgagc (SEQ ID NO:12), tcgatcaataatgggaataacccatactacgcacggtcggtacaatac (SEQ ID NO:13), gatcaccctagtggctggcccacctttgactcc (SEQ ID NO:14), cgggccagtgaaaacgttggtgactggttggcc (SEQ ID NO:15), aagacatctattctagaaagt (SEQ ID NO:16) and caacactatatacgtttcccgtacact (SEQ ID NO:17).
  • the nucleic acid sequence or functional equivalent comprises a sequence which has at least 70% sequence identity to at least part of a nucleotide sequence as depicted in FIG. 1 , said part having at least 15 nucleotides and encoding at least one CDR region.
  • nucleic acid sequences comprising a sequence encoding an amino acid sequence which has at least 70% sequence identity to the sequence RFAMS (SEQ ID NO:1), and/or at least 70% sequence identity to the sequence SINNGNNPYYARSVQY (SEQ ID NO:2), and/or at least 70% sequence identity to the sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or at least 70% sequence identity to the sequence RASENVGDWLA (SEQ ID NO:4), and/or at least 70% sequence identity to the sequence KTSILES (SEQ ID NO:5), and/or at least 70% sequence identity to the sequence QHYXRFPYT, wherein X is I or M (SEQ ID NO:6), and/or at least 70% sequence identity to the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQN
  • any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein for use as a medicament and/or prophylactic agent for at least in part treating and/or preventing a Gram-positive bacterium-related disorder.
  • Methods of treating and/or preventing a Gram-positive bacterium-related disorder comprising administering an effective amount of any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein are further provided herein.
  • any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein for the preparation of a medicament and/or prophylactic agent for at least in part treating and/or preventing a Gram-positive bacterium-related disorder.
  • compositions comprising any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein and a pharmaceutical acceptable carrier, diluent or excipient.
  • isolated or recombinant antibodies producing cell capable of producing any antibodies or functional parts or immunoglobulin chains or functional equivalents described herein.
  • methods for producing any antibodies or functional parts or immunoglobulin chains or functional equivalents described herein comprising providing a cell with any nucleic acid sequences or functional equivalents described herein and allowing said cell to translate the nucleic acid sequences or functional equivalents described herein, thereby producing any of the antibodies or functional parts or immunoglobulin chains or functional equivalents described herein.
  • the method further comprises harvesting, purifying and/or isolating any of the antibodies or functional parts or immunoglobulin chains or functional equivalents described herein.
  • any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein for diagnosis of a Staphylococcus infection.
  • Methods for diagnosing a Staphylococcus infection comprising contacting a sample with any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein are also provided.
  • antibodies or functional parts thereof or an immunoglobulin chains or functional equivalents thereof described herein for use in the diagnosis of a Staphylococcus infection.
  • the invention also provides use of any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein for detecting S. aureus and/or S. epidermidis .
  • Methods for detecting S. aureus and/or S. epidermidis comprising contacting a sample with any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof or any nucleic acid sequences or functional equivalents thereof described herein are also provided.
  • a sample e.g. solution
  • any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof described herein comprising contacting a sample (e.g. solution) with any antibodies or functional parts or an immunoglobulin chains or functional equivalents thereof described herein.
  • FIG. 1 Heavy chain and light chain sequences of antibody F1.
  • FIG. 2 F1 antibody binds to LTA preparations from several Gram-positive bacteria.
  • LTA preparations were derived from Sigma and tested in a capture ELISA with a mouse polyclonal anti-LTA or
  • FIG. 3 Recombinant F1 antibody binds to S. aureus but not to S. pneumoniae .
  • Bacteria were incubated with F1 antibody, or a control IgG (D25, a human anti-RSV antibody) or without first antibody (IgG-PE only). After washing the secondary antibody was added (IgG-PE).
  • 6 clinical isolates were tested in two separate experiments for the binding of F1. Tested were a PVL+strain (SA-1), 3 regular (SA-2 SA-3 and SA-4), and 2 MRSA strains (SA-5 and SA-6).
  • FIG. 4 (a) Binding of rF1 antibody to 14 S. aureus strains. (b) rF1 antibody binds to S. epidermidis but not to Bacillus subtilis, Enterococcus faecalis, Listeria monocytogenes and Streptococcus pyogenes.
  • FIG. 5 (a) rF1 antibody binds to MRSA in different growth stages, Iso C: isotype control, Med: media control (b) rF1 antibody binds to MRSA isolated from infected tissue.
  • FIG. 6 rF1 antibody binds to SDR proteins.
  • IP Immunoprecipitation
  • IP Immunoprecipitation
  • FIG. 7 Binding of rF1 to SDR proteins expressed in S. aureus and E. coli .
  • FIG. 8 rF1 binds to SDR domains expressed by S. aureus .
  • Constructs expressed by S. aureus and tested for binding to rF1 left
  • Western blots of S. aureus lysates containing the expressed constructs with anti-MBP (maltose binding protein), anti-His and rF1 antibody right.
  • FIG. 9 Sequences of heavy chain A114C (a) and light chain V205C (b) variants of antibody rF1. Numbering according to Kabat (1991), boxes: CDRs.
  • the present invention provides antibodies, functional parts thereof or immunoglobulin chains or functional equivalents thereof capable of specifically binding Staphylococcus species in their natural context. Therefore, they are useful for counteracting and/or preventing and/or diagnosing disorders related to the presence of Staphylococcus species.
  • Staphylococcus species Preferably, S. aureus is counteracted.
  • MRSA is counteracted.
  • Staphylococcus epidermidis Another preferred Staphylococcus species which is counteracted.
  • Staphylococcus epidermidis is usually non-pathogenic, but patients with a compromised immune system are often at risk for developing an infection. Infections can be both hospital and community acquired, but they are more of a threat to hospital patients. Most susceptible to infection with S. epidermidis are intravenous drug users, newborns, elderly, and those using catheters or other artificial appliances. Infections are associated with intravascular devices (prosthetic heart valves, shunts, etc.) but also commonly occur in prosthetic joints, catheters, and large wounds. Symptoms include fever, headache, fatigue, anorexia and dyspnea.
  • the present invention provides isolated or recombinant human antibodies, functional parts thereof or immunoglobulin chains or functional equivalents thereof capable of specifically binding Staphylococcus species.
  • Human antibodies and functional parts according to the invention are capable of binding Staphylococcus species in its natural context, so that various Staphylococcus species are counteracted upon administration of said antibodies, functional parts thereof or immunoglobulin chains or functional equivalents thereof.
  • Said human antibodies, functional parts thereof or immunoglobulin chains or functional equivalents thereof are therefore particularly suitable for treatment or prevention of infection by such Staphylococcus species.
  • Said human antibodies, functional parts thereof or immunoglobulin chains or functional equivalents thereof according to the invention are more suitable for therapeutic and/or prophylactic use for human individuals, as compared to chimeric antibodies, because of the absence of non-human sequences. This significantly reduces the risk of adverse side effects.
  • One particularly preferred antibody according to the present invention is the antibody designated “F1”, which has heavy chain and light chain variable domain sequences as depicted in FIG. 1 .
  • the term “F1” as used herein encompasses all F1 antibodies, for instance isolated or recombinantly produced F1. Recombinantly produced F1 is herein also called “rFl”.
  • the CDR sequences of F1, which in particular contribute to the antigen-binding properties of F1, are also depicted in FIG. 1 .
  • Antibody F1 is fully human, is capable of specifically binding Staphylococcus species such as S. aureus and S. epidermidis and is therefore preferred for therapeutic use for human individuals.
  • antibody F1 is capable of binding whole bacteria in vivo as well as in vitro. Further provided is therefore an isolated or recombinant human antibody or a functional part thereof, which is capable of specifically binding S. aureus and/or S. epidermidis . Furthermore, antibody F1 is capable of binding to bacteria that have been grown in infected tissue of, for example, an animal. Provided is therefore an isolated antibody that binds to in vivo-grown S. aureus , wherein “in vivo-grown” is defined as grown in infected tissue of an animal during infection with S. aureus . Also provided is an isolated, recombinant or synthetic immunoglobulin chain or functional equivalent thereof comprising at least one CDR sequence of a human immunoglobulin variable region which is specific for S. aureus and/or S. epidermidis.
  • a functional part of an antibody is defined as a part which has at least one shared property as said antibody in kind, not necessarily in amount. Said functional part is capable of binding the same antigen as said antibody, albeit not necessarily to the same extent.
  • a functional part of an antibody preferably comprises a single domain antibody, a single chain antibody, a nanobody, an unibody, a single chain variable fragment (scFv), a Fab fragment or a F(ab′) 2 fragment.
  • a functional part of an antibody is also produced by altering an antibody such that at least one property—preferably an antigen-binding property—of the resulting compound is essentially the same in kind, not necessarily in amount. This is done in many ways, for instance through conservative amino acid substitution, whereby an amino acid residue is substituted by another residue with generally similar properties (size, hydrophobicity, etc), such that the overall functioning is likely not to be seriously affected.
  • a heavy chain of an antibody is the larger of the two types of chains making up an immunoglobulin molecule.
  • a heavy chain comprises constant domains and a variable domain, which variable domain is involved in antigen binding.
  • a light chain of an antibody is the smaller of the two types of chains making up an immunoglobulin molecule.
  • a light chain comprises a constant domain and a variable domain. The variable domain is, together with the variable domain of the heavy chain, involved in antigen binding.
  • Complementary-determining regions are the hypervariable regions present in heavy chain variable domains and light chain variable domains.
  • the CDRs of a heavy chain and the connected light chain of an antibody together form the antigen-binding site.
  • a functional equivalent of an immunoglobulin chain is defined herein as an artificial binding compound, comprising at least one CDR sequence of an immunoglobulin chain.
  • the present invention provides the insight that the CDR sequences depicted in FIG. 1 provide desired binding characteristics
  • a skilled person is well capable of generating variants comprising at least one altered CDR sequence. For instance, conservative amino acid substitution is applied. It is also possible to alter at least one CDR sequence depicted in FIG. 1 in order to generate a variant antibody, or a functional part thereof, with at least one altered property as compared to F1.
  • an antibody or functional part is provided comprising a CDR sequence which is at least 70% identical to a CDR sequence as depicted in FIG. 1 , so that the favorable binding characteristics of F1 are at least in part maintained or even improved.
  • the resulting antibody or functional part comprises at least one improved property, such as for instance an improved binding affinity, selectivity and/or stability, as compared to F1.
  • Variant antibodies or functional parts thereof comprising an amino acid sequence which is at least 70% identical to a CDR sequence as depicted in FIG. 1 are therefore also within the scope of the present invention.
  • Various methods are available in the art for altering an amino acid sequence. For instance, a heavy chain or light chain sequence with a desired CDR sequence is artificially synthesized.
  • a nucleic acid sequence encoding a CDR sequence is mutated, for instance using random—or site-directed—mutagenesis.
  • the invention therefore provides an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof, which comprises:
  • a heavy chain CDR1 sequence comprising a sequence which has at least 70% sequence identity to the sequence RFAMS (SEQ ID NO:1), and/or
  • a heavy chain CDR2 sequence comprising a sequence which has at least 70% sequence identity to the sequence SINNGNNPYYARSVQY (SEQ ID NO:2), and/or
  • a heavy chain CDR3 sequence comprising a sequence which has at least 70% sequence identity to the sequence DHPSSGWPTFDS (SEQ ID NO:3).
  • an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof which comprises:
  • a light chain CDR1 sequence comprising a sequence which has at least 70% sequence identity to the sequence RASENVGDWLA (SEQ ID NO:4), and/or
  • a light chain CDR2 sequence comprising a sequence which has at least 70% sequence identity to the sequence KTSILES (SEQ ID NO:5), and/or
  • a light chain CDR3 sequence comprising a sequence which has at least 70% sequence identity to the sequence QHYXRFPYT, wherein X is I or M (SEQ ID NO:6).
  • CDR sequences are the CDR sequences of antibody F1; VH IgHV3-23 and VL IgKV1-5, and variants thereof. Binding compounds comprising CDR sequences with at least 70% sequence identity to F1 CDRs are particularly suitable for counteracting and/or preventing (the effects of) infections by S. aureus and/or S. epidermidis . It was found that a variant of F1, comprising VH IgHV3-23 and VL IgKV1-5, in which the isoleucine in light chain CDR3 of the light chain was altered to a methionine, was still capable of specifically binding Staphylococcus species such as S. aureus and S. epidermidis.
  • a binding compound according to the invention comprises a CDR sequence which is at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 86%, more preferably at least 87%, more preferably at least 88%, more preferably at least 89%, more preferably at least 90% identical to at least one of the CDR sequences depicted in FIG. 1 .
  • a binding compound according to the invention comprises a CDR sequence which is at least 91%, more preferably at least 92%, more preferably at least 93%, more preferably at least 94%, more preferably at least 95% identical to at least one of the CDR sequences depicted in FIG. 1 .
  • the particularly preferred antibody F1 comprises CDR sequences which consist of the CDR sequences depicted in FIG. 1 .
  • a particularly preferred embodiment according to the invention thus provides an isolated, synthetic or recombinant antibody or a functional equivalent thereof which is capable of specifically binding S. aureus and/or S. epidermidis and which comprises:
  • a heavy chain CDR1 sequence comprising the sequence RFAMS (SEQ ID NO:1), and/or
  • a heavy chain CDR2 sequence comprising the sequence SINNGNNPYYARSVQY (SEQ ID NO:2), and/or
  • a heavy chain CDR3 sequence comprising the sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or
  • a light chain CDR1 sequence comprising the sequence RASENVGDWLA (SEQ ID NO:4), and/or
  • a light chain CDR2 sequence comprising the sequence KTSILES (SEQ ID NO:5), and/or
  • a light chain CDR3 sequence comprising the sequence QHYXRFPYT, wherein X is I or M (SEQ ID NO:6).
  • a binding compound which comprises the heavy chain CDR1 and CDR2 sequences and the light chain CDR1 and CDR2 sequences as depicted in FIG. 1 , or sequences that are at least 70%, preferably at least 75%, more preferably at least 80%, more preferably at least 81%, more preferably at least 82%, more preferably at least 83%, more preferably at least 84%, more preferably at least 85% identical thereto.
  • an isolated, synthetic or recombinant antibody or a functional part thereof or an immunoglobulin chain or a functional equivalent thereof which comprises a heavy chain CDR1 sequence comprising a sequence which is at least 70% identical to the sequence RFAMS (SEQ ID NO:1) and a heavy chain CDR2 sequence comprising a sequence which is at least 70% identical to the sequence SINNGNNPYYARSVQY (SEQ ID NO:2) and a light chain CDR1 sequence comprising a sequence which is at least 70% identical to the sequence RASENVGDWLA (SEQ ID NO:4) and a light chain CDR2 sequence comprising a sequence which is at least 70% identical to the sequence KTSILES (SEQ ID NO:5).
  • Said binding compound preferably comprises CDR sequences which are at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 86%, more preferably at least 87%, more preferably at least 88%, more preferably at least 89%, more preferably at least 90%, more preferably at least 91%, more preferably at least 92%, more preferably at least 93%, more preferably at least 94%, most preferably at least 95% identical to the above mentioned heavy chain CDR sequences and light chain CDR sequences.
  • said binding compound also comprises a heavy chain CDR3 sequence comprising a sequence which is at least 70% identical to the sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or a light chain CDR3 sequence comprising a sequence which is at least 70% identical to the sequence QHYXRFPYT, wherein X is I or M (SEQ ID NO:6).
  • a binding compound comprising the above mentioned heavy chain CDR1, CDR2 and CDR3 sequences as well as the above mentioned light chain CDR1, CDR2 and CDR3 sequences is also provided.
  • a human antibody capable of specifically binding Staphylococcus species it has become possible to produce an immunoglobulin chain or functional equivalent thereof comprising at least one CDR sequence of a human immunoglobulin variable domain which is specific for Staphylococcus species. Further provided is thus an isolated, recombinant or synthetic immunoglobulin chain or functional equivalent thereof comprising at least one CDR sequence of a human immunoglobulin variable region which is specific for Staphylococcus species.
  • a human antibody is provided.
  • said at least one human CDR sequence or at least one sequence in at least one of the framework regions is optimized, preferably in order to improve binding efficacy or stability. This is for instance done by mutagenesis experiments where after the stability and/or binding efficacy of the resulting compounds are preferably tested and an improved binding compound is selected.
  • framework sequences are for instance optimized by mutating a nucleic acid molecule encoding such framework sequence where after the characteristics of the resulting antibody—or functional part—are preferably tested. This way, it is possible to obtain improved antibodies or functional parts.
  • human germline sequences are used for framework regions in antibodies or functional parts thereof or immunoglobulin chains or functional equivalents according to the invention.
  • germline sequences preferably minimizes the risk of immunogenicity of said antibodies, immunoglobulin chains or functional equivalents or parts, because these sequences are less likely to contain somatic alterations which are unique to individuals from which the framework regions are derived, and may cause an immunogenic response when applied to another human individual.
  • Antibodies or functional parts thereof or immunoglobulin chains or functional equivalents thereof comprising a heavy chain amino acid sequence which has at least 70% sequence identity to the heavy chain sequence as depicted in FIG. 1 are also provided. Such heavy chain sequence provides desired binding properties, as evidenced by antibody F1.
  • light chain amino acid sequences which have at least 70% sequence identity to the light chain sequence as depicted in FIG. 1 and a light chain sequence in which an isoleucine in CDR3 is altered to methionine, also provide desired binding properties, as evidenced by antibody F1, and a variant of antibody F1 comprising said alteration.
  • an antibody or functional part or immunoglobulin chain or functional equivalent having a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:7) and/or having a light chain sequence which has at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKT SILESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRTV, wherein in X is I or M (SEQ ID NO:8).
  • variants of the F1 antibody have been developed, besides the variant indicated herein above in which an isoleucine in light chain CDR3 is altered to methionine. These variants are capable of binding to Staphylococcus species.
  • antibody variants include antibodies or functional parts or immunoglobulin chains or functional equivalents according to the invention, having a heavy chain sequence comprising the sequence EVQLVESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARS VQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:9), and/or the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:7)
  • An antibody or functional part or immunoglobulin chain or functional equivalent thereof according to the invention specifically binds to proteins comprising a serine-aspartate (SD) repeat.
  • SD repeat (Sdr) proteins are cell-surface-associated proteins that are present in several bacteria such as Staphylococcus species. Sdr proteins in general comprise an amino-terminal signal sequence, a functional domain called the A region, an SD repeat region, a cell wall-spanning region, a LPXTG motif, a hydrophobic membrane-spanning domain, and a series of positively charged residues.
  • the LPXTG motif is the target of a transpeptidase that cleaves the motif between threonine and glycine residues and anchors the protein to the peptidoglycan of the cell wall of gram-positive bacteria.
  • Sdr proteins are thought to interact with host molecules. Known Sdr proteins include ClfA (SdrA), ClfB (SdrB), SdrC, SdrD and SdrE of S. aureus , SdrF, SdrG and SdrH of S. epidermidis , SdrI of S. saprophyticus , SdrX of S. capitis , and SdrY and SdrZ of S. caprae.
  • a preferred antibody or functional part thereof or immunoglobulin chain or functional equivalent according to the invention specifically binds S. aureus, S. epidermidis, S. saprophyticus, S. capitis , and S. caprae . It is preferred that said antibody, immunoglobulin chain or functional equivalent or part thereof binds to ClfA (SdrA), ClfB (SdrB), SdrC, SdrD and SdrE of S. aureus , SdrF, SdrG and SdrH of S. epidermidis , SdrI of S. saprophyticus , SdrX of S. capitis , and SdrY and SdrZ of S. caprae .
  • the epitope of the antibody, immunoglobulin chain or functional equivalent or part thereof according to the invention comprises an SD repeat-dependent epitope in Sdr proteins, for instance SD repeat-dependent epitopes as present in S. aureus ClfA, ClfB, SdrC, SdrD and SdrE.
  • An SD repeat-dependent epitope is herein defined as an epitope recognized by antibody F1, which epitope require the presence of at least part of an SD repeat region as present in, but not limited to, S. aureus ClfA, ClfB, SdrC, SdrD and SdrE and S. epidermidis SdrF, SdrG and SdrH.
  • said epitope may comprise at least part of a molecule that binds to, or is associated with an Sdr protein.
  • examples of such molecules include, but are not limited to, amino acids, peptides, proteins, sugars and sugar residues.
  • said epitope comprises modifications of the SD repeat region. Said modifications comprise, for example, but are not limited to, glycosylation, amidation and/or phosphorylation. It will be clear to a skilled person that combination of these two embodiments is also possible.
  • the invention provides an antibody or functional part or immunoglobulin chain or functional equivalent according to the invention capable of binding an SD repeat-dependent epitope. Also provided is an antibody or functional part or immunoglobulin chain or functional equivalent capable of binding to S. aureus ClfA, ClfB, SdrC, SdrD and SdrE. Further provided is an antibody or functional part or immunoglobulin chain or functional equivalent which is capable of competing with an antibody or functional part or immunoglobulin chain or functional equivalent according to the present invention for binding to a Staphylococcus species, preferably S. aureus and/or S. epidermidis and/or S. saprophyticus and/or S. capitis and/or S. caprae , more preferably MRSA.
  • Staphylococcus species preferably S. aureus and/or S. epidermidis and/or S. saprophyticus and/or S. capitis and/or S. caprae , more preferably MRSA.
  • a disadvantage of antibodies is that their stability may be reduced, for example under harsh conditions. For instance deamidation, the removal of a functional amide group, may occur. Deamidation is a protein degradation pathway that may affect the biological functions of proteins, and which occurs mainly at asparagine residues, and to a lower extent at glutamine residues. In one embodiment, therefore, deamidation of an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is prevented by replacing an asparagine or glutamine by another amino acid.
  • An asparagine is preferably replaced by an amino acid other than glutamine, because deamidation may also occur at a glutamine residue. Replacement of an asparagine preferably does not substantially affect binding affinity of an antibody according to the invention to an antigen.
  • deamidation of an asparagine at position 53 of the heavy chain is prevented by replacing said asparagine by another amino acid.
  • the stability of an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is preferably increased.
  • replacing an asparagine at said position does not substantially affect the binding affinity for an antigen of an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention.
  • an asparagine at position 53 of the heavy chain is preferably replaced by an amino acid other than glutamine, more preferably an asparagine at said position is replaced by serine. Therefore, also provided by the invention is therefore an antibody or functional part or immunoglobulin chain or functional equivalent according to the invention, wherein an asparagine, preferably an asparagine at position 53 of the heavy chain, is replaced by another amino acid, preferably serine.
  • an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is coupled to another moiety to form antibody-drug conjugates.
  • An antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is for instance coupled to a cytotoxic agent, such as an antibiotic.
  • cytotoxic agent refers to a substance that reduces or blocks the function, or growth, of bacteria and/or causes destruction of bacteria.
  • Said other moiety for example a cytotoxic agent, is preferably coupled to said antibody or functional part thereof through a thiol group. Therefore, preferably one or more cysteines are incorporated into said antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof.
  • Cysteines contain a thiol group and therefore, incorporation of one or more cysteines into, or replacement of one or more amino acids by one or more cysteines of an antibody or functional part thereof according to the invention enable coupling thereof to another moiety.
  • Said one or more cysteines are preferably introduced into an antibody of functional equivalent thereof according to the invention at a position where it does not influence folding of said antibody or functional equivalent, and does not alter antigen binding or effector function.
  • the invention therefore provides an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention wherein at least one amino acid other than cysteine has been replaced by a cysteine.
  • at least two amino acids other than cysteine have been replaced by cysteine.
  • said at least one amino acid other than cysteine is valine at light chain position 15, and/or alanine at light chain position 144, and/or serine at light chain position 168, and/or valine at light chain position 205 and/or valine at light chain position 110, and/or alanine at heavy chain position 84, and/or alanine at heavy chain position 114, and/or alanine at heavy chain position 168, and/or serine at heavy chain position 172, more preferably valine at light chain position 205 and/or valine at light chain position 110, and/or alanine at heavy chain position 114 (numbering according to Kabat, 1991).
  • one or more other amino acids of the heavy and/or light chain can be replaced by cysteine if the replacement does not influence folding of said antibody or functional equivalent, and does not alter antigen binding or effector function.
  • An antibody or functional part or immunoglobulin chain or functional equivalent according to the invention preferably comprises a variable heavy chain sequence and/or a variable light chain sequence which is at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 90%, most preferably at least 95% identical to a heavy chain sequence and/or the light chain sequence as depicted in FIG. 1 , or a light chain sequence as depicted in FIG. 1 in which the isoleucine in CDR3 is altered to a methionine.
  • An antibody or functional part or immunoglobulin chain or functional equivalent according to the invention preferably comprises a heavy chain as well as a light chain which resemble the heavy and light chain of F1. Further provided is therefore an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof comprising a heavy chain sequence and a light chain sequence which are at least 70%, more preferably at least 80%, more preferably at least 85%, more preferably at least 90%, most preferably at least 95% identical to the heavy chain sequence and the light chain sequence as depicted in FIG. 1 , or a light chain sequence as depicted in FIG. 1 in which the isoleucine in CDR3 is altered to a methionine.
  • an antibody or functional part which has a heavy chain sequence as depicted in FIG. 1 and a light chain sequence as depicted in FIG. 1 or a light chain sequence as depicted in FIG. 1 in which the isoleucine in CDR3 is altered to a methionine.
  • One embodiment provides an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof comprising a heavy chain sequence consisting of the heavy chain sequence as depicted in FIG. 1 , and/or comprising a light chain sequence consisting of the light chain sequence as depicted in FIG. 1 or a light chain sequence as depicted in FIG. 1 in which the isoleucine in CDR3 is altered to a methionine.
  • a shortened heavy chain or light chain sequence while maintaining a binding property of interest.
  • such a shortened heavy chain or light chain is generated which has a shorter constant region, as compared to the original heavy or light chain.
  • the variable domain is preferably maintained.
  • a Fab fragment or F(ab′) 2 fragment or a single domain antibody or a single chain antibody or a nanobody or an unibody or a scFv fragment based on a heavy chain sequence or light chain sequence depicted in FIG. 1 is produced.
  • a functional part of an antibody comprising at least a functional part of a sequence as depicted in FIG. 1 , or a light chain sequence as depicted in FIG. 1 in which the isoleucine in CDR3 is altered to a methionine, is therefore also provided.
  • Said functional part has a length of at least 20 amino acids and comprises at least one sequence selected from the group consisting of a sequence which is at least 70% identical to the heavy chain CDR1 sequence depicted in FIG.
  • the invention further provides an isolated, synthetic or recombinant nucleic acid sequence or a functional equivalent thereof with a length of at least 15 nucleotides, preferably at least 30 nucleotides, more preferably at least 50 nucleotides, more preferably at least 75 nucleotides, encoding a binding compound according to the invention.
  • nucleic acid is for instance isolated from a B-cell which is capable of producing an antibody according to the invention.
  • a preferred embodiment provides a nucleic acid sequence comprising a sequence which has at least 70% sequence identity to at least 15 nucleotides of a nucleic acid sequence as depicted in FIG. 1 .
  • a nucleic acid sequence according to the invention preferably comprises a sequence which has at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 90%, most preferably at least 95% sequence identity to at least 15 nucleotides of a nucleic acid sequence as depicted in FIG. 1 .
  • said nucleic acid sequence as depicted in FIG. 1 comprises at least one CDR encoding sequence.
  • One preferred embodiment provides an isolated, synthetic or recombinant nucleic acid sequence with a length of at least 15 nucleotides, or a functional equivalent thereof, encoding at least one CDR sequence of an antibody or immunoglobulin chain according to the invention.
  • Said nucleic acid sequence preferably encodes at least one CDR sequence which has at least 70% sequence identity to a CDR region of antibody F1.
  • Nucleic acid sequences encoding F1 CDR regions are depicted in FIG. 1 .
  • nucleic acid sequence comprising a sequence which has at least 70% sequence identity to a sequence selected from the group consisting of cgctttgccatgagc (SEQ ID NO:12), tcgatcaataatgggaataacccatactacgcacggtcggtacaatac (SEQ ID NO:13), gatcaccctagtagtggctggcccacctttgactcc (SEQ ID NO:14), cgggccagtgaaaacgttggtgactggttggcc (SEQ ID NO:15), aagacatctattctagaaagt (SEQ ID NO:16) and caacactatatacgtttcccgtacact (SEQ ID NO:17).
  • Said nucleic acid sequence or functional equivalent preferably comprises a sequence which has at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 90% sequence identity to any of the above mentioned sequences. Further provided is a nucleic acid sequence or functional equivalent thereof comprising a sequence which has at least 70% sequence identity to at least part of a nucleotide sequence as depicted in FIG. 1 , said part having at least 15 nucleotides and encoding at least one CDR region.
  • a nucleic acid sequence or functional equivalent thereof preferably encodes a region which has at least 70% sequence identity to an F1 CDR region, an F1 heavy chain and/or an F1 light chain.
  • One embodiment thus provides an isolated, synthetic or recombinant nucleic acid sequence, or a functional equivalent thereof, comprising a sequence encoding an amino acid sequence which has at least 70% sequence identity to the sequence RFAMS (SEQ ID NO:1), and/or at least 70% sequence identity to the sequence SINNGNNPYYARSVQY (SEQ ID NO:2), and/or at least 70% sequence identity to the sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or at least 70% sequence identity to the sequence RASENVGDWLA (SEQ ID NO:4), and/or at least 70% sequence identity to the sequence KTSILES (SEQ ID NO:5), and/or at least 70% sequence identity to the sequence QHYXRFPYT, wherein X is I or M (SEQ ID NO:6), and/or at least 70% sequence identity
  • nucleic acid sequences or functional equivalents thereof encoding variants of the F1 antibody according to the invention.
  • nucleic acid sequences encoding a heavy chain sequence comprising the sequence EVQLVESGGGLVQPGGSLR LSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSVQYRFTVSRDVSQNTVSLQ MNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:9), and/or the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGNNPYYARSV QYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDSWGPGTLVTVSS (SEQ ID NO:7), and encoding a light chain sequence comprising the sequence DIQLTQSPSALPASVGDRVSI TCRASENVGDWLAWYRQKPG
  • an asparagine at position 53 of the heavy chain (numbering according to Kabat, 1991) is replaced by another amino acid other than glutamine, in order to prevent deamidation of the asparagine at said position.
  • said asparagine is replaced by a serine.
  • % sequence identity is defined herein as the percentage of residues in a candidate amino acid of nucleic acid sequence that is identical with the residues in a reference sequence after aligning the two sequences and introducing gaps, if necessary, to achieve the maximum percent identity. Methods and computer programs for the alignment are well known in the art.
  • a nucleic acid molecule or nucleic acid sequence of the invention preferably comprises a chain of nucleotides, more preferably DNA and/or RNA.
  • a nucleic acid molecule or nucleic acid sequence of the invention comprises other kinds of nucleic acid structures such as for instance a DNA/RNA helix, peptide nucleic acid (PNA), locked nucleic acid (LNA) and/or a ribozyme.
  • PNA peptide nucleic acid
  • LNA locked nucleic acid
  • ribozyme a nucleic acid sequence
  • nucleic acid sequence also encompasses a chain comprising non-natural nucleotides, modified nucleotides and/or non-nucleotide building blocks which exhibit the same function as natural nucleotides.
  • a nucleic acid sequence according to the present invention is particularly useful for generating binding compounds which are specific for S. aureus and/or S. epidermidis . This is for instance done by introducing such nucleic acid sequence into a cell so that the cell's nucleic acid translation machinery will produce the encoded binding compound.
  • genes encoding a heavy and/or light chain according to the invention are expressed in so called producer cells, such as for instance cells of a Chinese hamster ovary (CHO), NSO (a mouse myeloma) or 293(T) cell line, some of which are adapted to commercial antibody production. Proliferation of said producer cells results in a producer cell line capable of producing antibodies or functional parts thereof according to the present invention.
  • said producer cell line is suitable for producing compounds for use in humans.
  • said producer cell line is preferably free of pathogenic agents such as pathogenic micro-organisms.
  • binding compounds consisting of human sequences are generated using a nucleic acid sequence according to the invention.
  • An isolated or recombinant antibody producing cell capable of producing an antibody or functional part or immunoglobulin chain or functional equivalent according to the invention is therefore also provided, as well as a method for producing an antibody or functional part or immunoglobulin chain or functional equivalent according to the invention, comprising providing a cell with a nucleic acid sequence or functional equivalent according to the invention and allowing said cell to translate said nucleic acid sequence or functional equivalent according to the invention, thereby producing said antibody or functional part or immunoglobulin chain or functional equivalent according to the invention.
  • An antibody producing cell is defined herein as a cell which is capable of producing and/or secreting an antibody or a functional part thereof, and/or which is capable of developing into a cell which is capable of producing and/or secreting antibody or a functional part thereof.
  • An antibody producing cell according to the invention is preferably a producer cell which is adapted to commercial antibody production.
  • said producer cell is suitable for producing compounds for use in humans.
  • a method according to the invention preferably further comprises a step of harvesting, purifying and/or isolating said antibody or functional part or immunoglobulin chain or functional equivalent according to the invention.
  • the thus obtained binding compounds according to the invention are preferably used in diagnosis of Staphylococcus infection, isolation or detection of Staphylococcus bacteria, distinguishing between Staphylococcus species and other gram-positive bacteria and human therapy, optionally after additional purification, isolation and/or other processing steps.
  • an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the present invention is particularly suitable for diagnostic uses.
  • a sample such as a tissue or blood sample
  • a Staphylococcus bacteria preferably S. aureus and/or S. epidermidis , more preferably MRSA.
  • said sample can be mixed with an antibody or immunoglobulin chain or functional equivalent or part thereof according to the invention.
  • Said antibody, immunoglobulin chain or functional equivalent or part will specifically bind to Staphylococcus bacteria, preferably S. aureus and/or S. epidermidis .
  • Bacteria bound to an antibody, immunoglobulin chain or functional equivalent or part can be isolated from the sample using any method known in the art, for example, but not limited to, isolation using magnetic beads, streptavidin-coated beads, or isolation through the use of secondary antibodies immobilized on a column. After washing of the bound bacteria and antibody, immunoglobulin chain or functional equivalent or part thereof, bacteria can be eluted from said antibody, immunoglobulin chain or functional equivalent or part by any method known in the art. For instance, binding between bacteria and antibody, immunoglobulin chain or functional equivalent or part can be disrupted by increasing the concentration of salts and/or reducing or increasing pH, and/or by addition of excess epitope.
  • Staphylococcus bacteria preferably S. aureus and/or S. epidermidis
  • Staphylococcus bacteria may be used for various applications. For instance, infection with several different gram-positive bacteria may result in overlapping symptoms in an individual. In such cases, it can be difficult to discriminate between S. aureus and/or S. epidermidis and other gram-positive bacteria.
  • An antibody, immunoglobulin chain or functional equivalent or part thereof according to the present invention can then be used to detect the presence of S. aureus and/or S. epidermidis , or for distinguishing between S. aureus and/or S. epidermidis and other bacteria.
  • Isolation of bacteria from a sample of an individual suspected of suffering from an infection with S. aureus and/or S. epidermidis or from any other source, such as a bacterial culture can facilitate detection of said Staphylococcus bacteria, because isolation results in an increased concentration and/or a higher purity of said Staphylococcus bacteria.
  • Isolation of Staphylococcus species preferably S. aureus and/or S. epidermidis , more preferably MRSA
  • S. aureus and/or S. epidermidis can for instance further be used to identify the specific S. aureus and/or S. epidermidis strain, preferably the MRSA strain in a sample. Identification of said strain can for instance be performed by determining the sequence of the bacterial DNA. In such case it is preferred to first obtain an isolated S. aureus and/or S. epidermidis.
  • an antibody, immunoglobulin chain or functional equivalent or part thereof according to the present invention is labeled in order to be able to detect said antibody, immunoglobulin chain, or functional equivalent or part, for instance, but not limited to, fluorescently labeled, or radioactively labeled.
  • an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is detected using a labeled secondary antibody which is directed against said antibody, immunoglobulin chain or functional equivalent or part thereof according to the invention. If binding of said antibody, immunoglobulin chain or functional equivalent or part thereof is detected, S. aureus and/or S. epidermidis is present.
  • an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof for diagnosis of a Staphylococcus infection, preferably S. aureus infection, more preferably MRSA infection, for detecting S. aureus and/or S. epidermidis , preferably MRSA, and for distinguishing between S. aureus and/or S. epidermidis , preferably MRSA and other gram-positive bacteria.
  • an antibody or functional part thereof or an immunoglobulin chain or functional equivalent thereof according to the invention for use in the diagnosis of a Staphylococcus infection, preferably S. aureus infection, more preferably MRSA infection.
  • Said method preferably comprises providing a sample of an individual suspected of suffering from an infection with S. aureus and/or S. epidermidis , preferably MRSA, or from any other source, such as a bacterial culture, adding an antibody or functional part or an immunoglobulin chain or functional equivalent thereof according to the invention to said sample, allowing binding of said antibody or functional part or an immunoglobulin chain or functional equivalent thereof according to the invention to S. aureus and/or S. epidermidis bacteria, when present, and isolating S. aureus and/or S. epidermidis bacteria bound to an antibody or functional part or an immunoglobulin chain or functional equivalent thereof according to the invention from said sample.
  • Gram-positive bacteria-specific binding compounds according to the invention and nucleic acid sequences coding therefore have been provided, including human binding compounds, improved therapeutic applications have become available.
  • Gram-positive bacteria such as S. aureus and/or S. epidermidis are counteracted by binding compounds according to the invention.
  • a binding compound according to the invention is therefore particularly suitable for use as a medicine or prophylactic agent.
  • binding compounds are used which consist of human sequences, or which have at most 5% of non-human sequences, in order to reduce the chance of adverse side effects when human individuals are treated.
  • An antibody or functional part or an immunoglobulin chain or functional equivalent thereof or a nucleic acid sequence or functional equivalent thereof according to the invention for use as a medicament and/or prophylactic agent is therefore also herewith provided.
  • nucleic acid or functional equivalent according to the invention When a nucleic acid or functional equivalent according to the invention is administered, it will be translated in situ into a binding compound according to the invention.
  • said antibody comprises antibody F1, or a functional part thereof.
  • Said medicament or prophylactic agent is preferably used for counteracting or at least in part preventing an infection by S. aureus and/or S. epidermidis or for counteracting or at least in part preventing adverse effects of an infection by S. aureus and/or S. epidermidis .
  • an antibody or functional part or an immunoglobulin chain or functional equivalent thereof or a nucleic acid sequence or functional equivalent thereof according to the invention for use as a medicament and/or prophylactic agent for at least in part treating and/or preventing a condition related to S. aureus and/or S. epidermidis .
  • Non-limiting examples of such conditions are skin infections, pimples, impetigo, boils, cellulitis folliculitis, furuncles, carbuncles, scalded skin syndrome, abscesses, pneumonia, meningitis, osteomyelitis, endocarditis, toxic shock syndrome and septicemia.
  • S. aureus infection is counteracted or at least in part prevented.
  • an MRSA-related condition is counteracted, diminished and/or at least in part prevented.
  • a use of an antibody or functional part or an immunoglobulin chain or functional equivalent thereof or a nucleic acid sequence or functional equivalent thereof according to the invention for the preparation of a medicament and/or prophylactic agent for at least in part treating and/or preventing S. aureus and/or S. epidermidis is therefore also provided, as well as a method for at least in part treating or preventing a condition related to S. aureus and/or S.
  • S. aureus and/or S. epidermidis the method comprising administering to an individual in need thereof a therapeutically effective amount of an antibody or functional part or an immunoglobulin chain or functional equivalent according to the invention, preferably after said individual has been diagnosed to be infected by S. aureus and/or S. epidermidis .
  • Said condition preferably comprises at least one of the S. aureus - related conditions listed above, most preferably an MRSA-related condition.
  • Said antibody preferably comprises antibody F1, or a functional part thereof.
  • a binding compound according to the invention is preferably administered to an individual before an infection has taken place.
  • a binding compound according to the invention is administered when an individual is already infected.
  • Said binding compound is preferably administered to individuals with an increased risk of complications, such as for instance hospitalized individuals and/or individuals with compromised immunity. Also elderly people have an increased risk of bacterial conditions.
  • Binding compounds according to the invention are preferably administered via one or more injections. Dose ranges of binding compounds according to the invention to be used in the therapeutic applications as described herein before are designed on the basis of rising dose studies in the clinic in clinical trials for which rigorous protocol requirements exist. Typical doses are between 0.1 and 10 mg per kg body weight.
  • binding compounds according to the invention are typically combined with a pharmaceutically acceptable carrier, diluent and/or excipient.
  • suitable carriers for instance comprise keyhole limpet haemocyanin (KLH), serum albumin (e.g. BSA or RSA) and ovalbumin.
  • KLH keyhole limpet haemocyanin
  • BSA serum albumin
  • ovalbumin ovalbumin.
  • said suitable carrier comprises a solution like for example saline
  • nucleic acid encoding a binding compound according to the invention is used.
  • binding compounds upon administration of such nucleic acid, binding compounds are produced by the host's machinery. Produced binding compounds are capable of preventing and/or counteracting Gram-positive bacterial infection and/or the adverse effects of such infection.
  • a nucleic acid sequence or functional equivalent according to the invention for use as a medicament and/or prophylactic agent is therefore also herewith provided.
  • Said nucleic acid is preferably used for counteracting S. aureus and/or S. epidermidis , more preferably S. aureus , most preferably MRSA.
  • Said Gram-positive bacterium-related condition preferably comprises an infection by S. aureus or S. epidermidis , more preferably an S. aureus infection, most preferably an MRSA infection.
  • composition comprising an antibody or functional part or an immunoglobulin chain or functional equivalent thereof or a nucleic acid sequence or functional equivalent thereof according to the invention and a pharmaceutical acceptable carrier, diluent or excipient.
  • Said pharmaceutical composition is preferably suitable for human use.
  • B-cells were obtained from fresh blood of adults by Ficoll separation and CD4/CD8 negative selection with MACS microbeads as described by the manufacturer (Miltenyi Biotech). To obtain memory B cells, cells were sorted for CD19 + CD3 ⁇ CD27 + IgD ⁇ IgA ⁇ on a FACSaria (Becton Dickinson). The use of these tissues was approved by the medical ethical committees of the institution and was contingent on informed consent. Donors were selected based on carrying hospital acquired MRSA strains with genotype cluster 109 and 16.
  • B-cells maintained in standard culture medium containing IMDM (Gibco), 8% FBS (HyClone) and penicillin/streptomycin (Roche) were co-cultured on ⁇ -irradiated (50Gy) mouse L cell fibroblasts stably expressing CD40L (CD40L-L cells, 10 5 cells/ml) and recombinant mouse IL-21 (25 ng/ml, R&D systems).
  • rhIL-4 (R&D) was used at 50 ng/ml. Cells were routinely tested by PCR and were found negative for the presence of mycoplasma and EBV (data not shown).
  • the BCL6 retroviral construct has been described before (Shvarts A. et al. Genes Dev 16, 681-686 (2002)).
  • cDNA encoding human Bcl-xL was kindly provided by Dr. Stanley Korsmeyer.
  • BCL6 and Bcl-xL were separately cloned into a BCL6-NGFR and a BclxL-GFP construct.
  • These constructs were transfected into the LZRS retroviral packaging cells, phoenix is described before (Jaleco A. C. et al. Blood 94, 2637-2646 (1999); Scheeren F. A. et al. Nat Immunol 6, 303-313 (2005)).
  • Memory B-cells were double transduced by the BCL6 and Bcl-xL containing retroviruses after activation on CD40L-L cells in the presence of rmIL-21 for 36 hrs as described before (Diehl S. A. et al. J Immunol 180, 4805-4815 (2008); Kwakkenbos M. et al. Nat Med in press (2009)). Transduced cells were maintained on CD40L-L cells with rmIL-21.
  • ELISA plates were coated with anti-human IgG (Jackson ImmunoResearch Laboratories) at 5 ⁇ g/ml in PBS for 1 hr at 37° C. or o/n at 4° C. and washed in ELISA wash buffer (PBS, 0.5% Tween-20). 4% milk in PBS was used as blocking agent, before serial dilution of cell culture supernatants and an enzyme-conjugated detection antibody was added (dilution 1:2500 for HRP-conjugated anti-IgG (Jackson)). TMB substrate/stop solution (Biosource) was used for development of the ELISAs.
  • lysates from the Newman and SH1000 strains Both were made in PBS and directly coated at 5 to 10 ⁇ g ml ⁇ 1 before B cell culture supernatants were tested un- or 1:2 diluted.
  • an LTA detection ELISA was developed. Purified LTA preparations from S. aureus, B. subtilis, S. faecalis and S. pyogenes (Sigma) was added to ELISA plates coated with polyclonal IgG purified mouse anti-LTA (1/200 stock 1 mg ml ⁇ 1 , QED Bioscience), before secondary antibodies were added.
  • LTA preparations were coated at 1 ⁇ g ml ⁇ 1 before rF1 (10 ⁇ g ml ⁇ 1 ) or control antibodies (1:5 dilution of hybridoma supernatant) were added and further detected with conjugated anti-human or mouse antibodies.
  • the panel of purified LTA preparations included: B. subtilis, S. aureus, L. lactic, L. garvieae, B. bifidum, M. luteus, L. casei, L. mesenteroides, B. licheniformis, L. welshimeri, E. hirae, L. raffinolactis, S. mutans, S. pneumoniae .
  • Several variants contain or lack alanine residues and/or lipid anchors (not depicted here).
  • the Newman S. aureus and the S. pneumoniae strain were used. Newman was cultured in TSH 50 ml 0/N, then 1 ml was resuspendend in 100 ml for 2 to 2.5 hrs till OD:1 and bacteria were collected. S. pneumoniae was cultured in Todd Hewitt medium mixed with yeast medium. Before, bacteria were incubated with F1 antibody, a control IgG (D25, a human anti-RSV antibody) or only with the secondary antibody (IgG-PE only), cells were pretreated with 100% total mouse serum to prevent background staining. After washing the secondary antibody was added (IgG-PE). Antibody incubations were performed for 20 min on ice.
  • B-cells from several B-cell populations were double transduced with retroviruses containing BCL6-NGFR and Bch xL-GFP (Diehl et al and Kwakkenbos et al).
  • B-cell cultures were started in 96 wells plate with a cell density of 500 cells/well. Supernatant of these mini-cultures was collected and used in ELISAs to screen for the presence of S.
  • aureus -specific IgG antibodies in these ELISAs the coating was cell lysates of two S. aureus strains, SH1000 and Newman). Mini-cultures that were screened positive in both the SH1000 as well as the Newman S. aureus were seeded in new mini-cultures at a density of 10 cells/well. Again, supernatant of these mini-cultures was collected and screened in the SH1000 and Newman ELISAs. Clones that were screened positive in both ELISAs were seeded into monoclonal cultures (i.e. 1 cell/well). After testing the supernatant of these monoclonal cultures, one clone (named F1) was found to produce S. aureus specific monoclonal IgG antibodies.
  • the rF1 antibody was tested on purified LTA preparations from several bacteria. As shown in FIG. 2A , the rF1 antibody binds well to commercial LTA samples obtained from S. aureus and B. subtilis , and a bit less profoundly to LTA samples from S. faecalis and S. pyogenes . The rF1 antibody did not bind to an LTA sample from S. pneumoniae (data not shown). In addition rF1 recognized highly purified LTA samples from B. subtilis, B. licheniformis and two isolates of S. aureus ( FIG. 2 b ).
  • rF1 did not bind to LTA preparations from S. mutans ( FIG. 2 b ) or from L. lactic, L. garvieae, B. bifidum, M. luteus, L. casei, L. mesenteroides, L. welshimeri, E. hirae, L. raffinolactis, S. mutans and S. pneumoniae (results not shown).
  • rF1 antibody In order to study whether the rF1 antibody would also recognize living Gram-positive bacteria, binding of the rF1 antibody to S. aureus and S. pneumoniae was tested by using flow cytometry. As shown in FIG. 3A , the rF1 antibody binds to living S. aureus bacteria (Newman strain), but not to S. pneumoniae . In addition we show that rF1 recognized 6 clinical S. aureus isolates; one is a pathogenic strain which is PVL positive, 3 regular strains and 2 MRSA strain ( FIG. 3 b ).
  • TSA tryptic soy agar
  • TSB tryptic soy broth
  • bacteria were harvested from TSA plates or TSB cultures, and washed with Hanks Buffered Salt Solution (HBSS) without phenol red supplemented with 0.1% BSA (IgG free; Sigma) and 10 mM Hepes, pH 7.4 (HB buffer), by centrifugation at 1700 ⁇ g for 20 min. Bacterial concentrations were estimated by reading optical density at 630 nm. Bacterial suspensions of 20 ⁇ 10 8 CFU/mL in HB buffer were mixed with equal volumes of 300 ⁇ g/mL of rabbit IgG (Sigma), and incubated for 1 h at room temperature (RT) to block nonspecific IgG binding.
  • HBSS Hanks Buffered Salt Solution
  • rabbit IgG anti- S. aureus (Abcam) was added to a concentration of 20 ⁇ g/mL. After incubation for 15 min at RT, cells were washed twice with HB buffer, and resuspended in a mixture of anti-human IgG and anti-rabbit IgG secondary antibodies, each labeled with a different fluorochrome (Jackson Immunoresearch). After two washes with PBS, cells were resuspended in PBS with 2% paraformaldehyde and analyzed by flow cytometry. After selecting bacteria from double fluorescence plots by gating for positive staining with rabbit IgG anti- S. aureus , overlay histogram plots of fluorescence intensities of rF1 and isotype control were generated.
  • MRSA Methicillin-resistant S. aureus
  • MSSA methicillin-sensitive S. aureus
  • VISA vancomycin intermediate sensitive S. aureus
  • S. epidermidis S. epidermidis and several other gram-positive species were tested for binding to rF1 antibody.
  • rF1 strongly binds to all 14 S. aureus strains ( FIG. 4A ) and to S. epidermidis ( FIG. 4B ), but not to the other tested gram-positive species ( FIG. 4B ).
  • rF1 strongly binds to all growth stages tested ( FIG. 5A ).
  • a cell wall preparation of a 20 ml overnight culture of USA300 S. aureus strain was prepared by treatment of the culture (40 mg cell pellet/ml) with 100 mg/ml of lysostaphin in 30% raffinose buffer at 37° C. for 30 minutes. The entire cell wall prep was filtered, diluted up to 10 ml with NP40 Lysis buffer and incubated twice with anti-Flag M2 Agarose (Sigma) to deplete as much protein-A from the cell wall prep as possible. Final cell wall preparation was split into two parts and immunoprecipitated with 1 ug/ml of rF1 or isotype control human antibody. Antibodies were captured with Protein A/G Ultralink Resin (Pierce). The samples were then treated with 50 mM dithiothreitol, 10 mM 2-Iodoacetamide and run on an 8% Tris-glycine gel and subsequently silver stained or Western blotted with rF1.
  • Lysates from a 20 ml overnight culture of Staphylococcus epidermidis was prepared by bead beating in NP40 Lysis Buffer.
  • the resulting lysate preparation was diluted to 10 ml with NP40 Lysis Buffer, split into two parts and immunoprecipitated with 1 ug/ml of rF1 or control antibody.
  • Antibodies were captured with Protein A/G Ultralink Resin (Pierce).
  • the samples were then treated with 50 mM dithiothreitol, 10 mM 2-Iodoacetamide and run on an 8% Tris-glycine gel and subsequently silver stained or Western blotted with rF1.
  • Clumping factor-A (ClfA) gene was PCR amplified from the sequence encoding the signal sequence to the sequence encoding the glycine in the LPXTG motif from USA300 genomic DNA.
  • a c-terminal His Tag was engineered at the end of the LPXTG motif and ligated into the pTet S. aureus expression vector (pSAS10 from Genentech). The resulting construct was then electroporated into S. aureus WT RN4220.
  • a 20 ml culture of either the electroporated RN4220 or RN4220 empty (not carrying a pTet expression vector) was inoculated from an overnight culture (starting OD 600 of 0.15), grown for 1 hr in trypticase soy broth (TSB) and then induced protein expression for 2 hrs with anhydrotetracycline (200 ng/ml). At the end of the induction period, the S.
  • aureus culture was pre-lysed with lysostaphin (50 ug/ml) and then further lysed by bead beating in lysis buffer (150 mM NaCl, 20 mM Tris pH 7.5, 1% triton-X, and Roche protease inhibitor EDTA-free tablets). Cleared lysates were then incubated with NiNta resin (Qiagen) in the presence of 10 mM Imidazole for 1 hr at 4° C. to pull-down the recombinant ClfA protein.
  • lysis buffer 150 mM NaCl, 20 mM Tris pH 7.5, 1% triton-X, and Roche protease inhibitor EDTA-free tablets.
  • Cleared lysates were then incubated with NiNta resin (Qiagen) in the presence of 10 mM Imidazole for 1 hr at 4° C. to pull-down the recombinant ClfA protein.
  • E. coli expression of His-tagged Clfa The Clumping factor-A (ClfA) gene was PCR amplified from the sequence encoding the N-term signal sequence (with the start methionine) to the sequence encoding the glycine in the C-term LPXTG motif from USA300 genomic DNA. The amplified PCR product was then ligated in frame with a c-terminal His tag into the pET 21b(+) E. coli expression vector (Novagen). The resulting construct was transformed into E. coli BL21-gold (DE3) Competent Cells (Stratagene) and induced for protein expression for 3.5 hrs with IPTG according to the manufacturer's instructions. The induced E.
  • coli culture was lysed by bead beating in Lysis Buffer (150 mM NaCl, 20 mM Tris pH 7.5, 1% triton-X, and Roche protease inhibitor EDTA-free tablets). Cleared lysates were then incubated with NiNta resin (Qiagen) in the presence of 10 mM Imidazole for 1 hr at 4° C. to pull-down the recombinant ClfA protein.
  • Lysis Buffer 150 mM NaCl, 20 mM Tris pH 7.5, 1% triton-X, and Roche protease inhibitor EDTA-free tablets. Cleared lysates were then incubated with NiNta resin (Qiagen) in the presence of 10 mM Imidazole for 1 hr at 4° C. to pull-down the recombinant ClfA protein.
  • S. aureus cell surface SDR proteins ClfA, CUB, SdrC, SdrD, SdrE in E. coli The ClfA, ClfB, SdrC, SdrD and SdrE genes were PCR amplified from the sequence encoding the mature start of the protein to the sequence encoding the glycine in the LPXTG motif from USA300 genomic DNA and ligated in-frame with an N-terminal Unizyme tag into the ST239 Vector (Genentech). The constructs were transformed into E. coli 58F3 (Genentech), induced for protein expression and subsequently purified.
  • NiNta capture of NT Unizyme tagged SDR proteins 500 ug of purified N-terminal Unizyme tagged SDR proteins (ClfA, ClfB, SdrC, SdrD, SdrE) were diluted in PBS containing protease inhibitors (EDTA-free) and incubated with NiNta resin (Qiagen) for 1.5 hr at 4° C. NiNta resin with the captured Unizyme tagged SDR protein was then washed once with wash buffer (50 mM NaH 2 PO 4 , 300 mM NaCl; pH 8.0).
  • wash buffer 50 mM NaH 2 PO 4 , 300 mM NaCl; pH 8.0.
  • E. coli produced SDR proteins by S. aureus lysate A 25 ml culture was started from an overnight culture of ⁇ Pan Sdr mutant (ClfA-ClfB-SdrCDE-null; gift of Tim Foster, Trinity College Dublin) Newman S. aureus (starting OD 600 of 0.15) and grown in TSB for 3 hrs (exponential phase) 37° C., 200 rpm. The exponential phase culture was then resuspended in 1 ml of PBS and lysed with 200 ug/ml lysostaphin in the presence of 250 units of Benzonase Nuclease (Novagen) at 37° C. for 30 minutes.
  • the lysates were cleared of debris by spinning down at maximum speed in a micro-centrifuge for 10 minutes at 4° C. Modification of NiNta captured E. coli SDR protein was carried out by incubation with cleared ⁇ Pan Sdr mutant S. aureus lysates for 1 hr at 37° C.
  • MBP-SD Constructs The maltose binding protein (MBP) gene was PCR amplified from the pMAL-c5x vector (New England BioLabs [NEB], Ipswich, Mass., USA) from the sequence encoding the start of the mature protein until the sequence encoding the end of the Factor Xa cleavage site.
  • the varying lengths of c-terminal His tagged SD (SD, SDS, DSD, SDSD, SDSDS, SDSDSD) were synthesized as single stranded oligonucleotides and annealed together to make double stranded dna.
  • the Sdr region of the ClfA gene was PCR amplified from the sequence encoding the beginning (560D) of the Sdr region and included up to either the sequence encoding 618A or 709S of the SD region followed by the dna sequence coding for a His Tag from the respective plasmids pTet.ClfA.SD618A or pTet.ClfA.SD709S (Genentech).
  • the sequence encoding the A domain of the ClfA gene from the beginning of the mature protein until the sequence encoding the end of the A domain (538G) followed by the sequence coding for a His Tag was PCR amplified from the plasmid pTet.ClfA.Adom.538G (Genentech).
  • the MBP insert along with one of the various SD inserts or ClfA A domain were ligated into the pTet S. aureus expression vector (pSAS10 from Genentech).
  • the resulting constructs were then electroporated into the S. aureus RN4220 A sortase (sortase deletion mutant strain in the RN4220 background).
  • a 20 ml culture of either the electroporated RN4220 A sortase or RN4220 A sortase empty (not carrying a pTet expression vector) was inoculated from an overnight culture (starting OD 600 of 0.15), grown for 1 hr in trypticase soy broth (TSB) supplemented with glucose (2 g/L) and then induced for protein expression for 2 hrs with anhydrotetracycline (200 ng/ml). At the end of the induction period, the S.
  • TTB trypticase soy broth
  • aureus culture was resuspended in Column Buffer (150 mM NaCl, 20 mM Tris pH 7.5 and Roche protease inhibitor EDTA-free tablets) and lysed with 200 ug/ml lysostaphin in the presence of 250 units of Benzonase Nuclease (Novagen) at 37° C. for 30 minutes.
  • the lysates were cleared of debris by spinning down at maximum speed in a micro-centrifuge for 10 minutes at 4° C.
  • the cleared lysates were then incubated with amylose resin (NEB) along with a final EDTA concentration of 1 mM for 1.5 hrs at 4° C. to capture the expressed MBP-SD proteins.
  • NEB amylose resin
  • rF1 Reacts to a Unique Family of SDR (Ser-Asp-repeat) Proteins in S. aureus and S. epidermidis
  • rF1 binds to several components of the commercial teichoic acid preparation ( FIG. 6A , left panel) and of the cell wall lysate of S. aureus ( FIG. 6B , left panel). Using mass spectrometry these components of the WTA preparation and cell wall lysate were identified as ClfA (SdrA), ClfB (SdrB), SdrC, SdrD and SdrE ( FIG. 6A , right panel and FIG. 6B , right panel)
  • FIG. 6C shows binding of rF1 to several components of a cell wall lysate of S. epidermidis . These components were not identified with a control antibody. Using mass spectrometry these cell wall components were identified as SdrF, SdrG and SdrH ( FIG. 6C right panel).
  • rF1 antibody binds to ClfA Sdr regions consisting of the ClfA 560D-618S and ClfA 560D-709S ( FIG. 8 ) expressed in S. aureus . rF1 does not bind to the A-domain of ClfA or to small peptide sequences consisting of up to three SD repeats.
  • Phusion DNA polymerase, restriction enzymes EcoRV, KpnI, PvuII, ApaI, Agel, and AhdI, T4 DNA ligase were purchased from New England BioLabs, Ipswich, Mass., USA.
  • Pfu DNA polymerase, Quick change II Site-Directed Mutagenesis Kit were purchased from Stratagene/Agilent Technologies, Santa Clara, Calif., USA.
  • 2% agarose gel was purchased from Invitrogen, Carlsbad, Calif., USA.
  • pRK vectors pRK.LPG3.HuKappa and pRK.LPG4.HumanHC were obtained from Genentech/Roche, South San Francisco, Calif., USA.
  • variable domains of heavy and light chains of rF1 Mab from the pCPEO vectors were placed into the pRK mammalian expression vectors.
  • Polymerase chain reaction (PCR) was performed in a total volume of 50 ml using Pfu DNA polymerase according to standard PCR procedures.
  • V H was amplified with the primers YiHCF) 5′-ATG GCT GAG GTG CAG CTG GTG GAG TCT G-3′ (SEQ ID NO:18) and YiHCR25′-GAA CAC GCT GGG GCC C TT GGT GCT GGC ACT CGA GAC TGT GAC CAG GGT GCC AGG T*CC CCA G-3′ (SEQ ID NO:19) (the restriction sites of PvuII and ApaI are underlined and the * indicates the single nucleotide G to T change to eliminate the internal ApaI site) and V L was amplified with the primers YiLCF 5′-CGG CTC GAC C GA TAT C CA GCT GAC CCA GAG-3′ (SEQ ID NO:20) and YiLCR 5′-GAT TTC CAG CTT GGT ACC CTG GCC G-3′ (SEQ ID NO:21) (the EcoRV and KpnI are underlined).
  • V H and V L were individually digested by PvuII and ApaI for V H , EcoRV and KpnI for V L , followed by Gel purification (Invitrogen, Catalog# K2100-12).
  • V H and V L were individually ligated into pRK vector fragments of pRK/PvuII, ApaI for Heavy chain and pRK/EcoRV, KpnI for light chain using T4 DNA ligase.
  • the DNA plasmids were confirmed by restriction enzyme digestion patterns, i.e. rF1V H released ⁇ 300 by and 5.8 kb bands by Agel, whereas rF1V L shown 2.3 and 3.1 kb bands by AhdI on 2% agarose gel.
  • the rF1 pRK plasmids underwent a series of site-directed mutagenesis to stabilize the rFl Mab by N (AAC) 53S (AGC) in heavy chain CDR2 with using FHV 5′-GGT GGC CAG CAT CAA C AG C GG CAA CAA CCC CTA CTA CG-3′ (SEQ ID NO:22) and RHV 5′-CGT AGT AGG GGT TGT TGC C GC T GT TGA TGC TGG CCA CC-3′ (SEQ ID NO:23) (mutagenesis site is underlined) via Quik change II Site-Directed Kit.
  • the mutagenesis variant was sequenced.
  • the primary sequence of antibody rF1 contained one potential asparagine deamidation site in light chain CDR2: N NG NN (SEQ ID NO:24). Stress testing revealed an increase of deamidation in stressed samples at N53 (numbering according to Kabat, 1991). Site-directed mutagenesis was performed to stabilize the rF1 Mab by N (AAC, (SEQ ID NO:25)) to 53S (AGC, (SEQ ID NO:26)) substitution in heavy chain CDR2. Sequencing of the mutagenesis variant confirmed an N53S mutation.
  • the rF1 pRK plasmids underwent a series of site-directed mutagenesis with oligos of rF1pRK.LC(205/210)VCF (468075) 5′-GGG CCT GAG CTC GCC C TG C AC AAA GAG CTT CAA CAG-3′ (SEQ ID NO:27) and rF1pRK.LC(205/210)VCR (468076) 5′-CTG TTG AAG CTC TTT G TG C AG GGC GAG CTC AGG CCC-3′ (SEQ ID NO:28) (Cys mutant is underlined) to generate the light chain linkers of rF1 thioMab, and rF1pRK.HCN53S.A121CF (468-464) 5′-CTG GTC ACA GTC TCG AGT TGC AGC ACC AAG GGC CCA TC-3′ (SEQ ID NO:29) and rF1pRK.HCN53S.A

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