Antibodies that bind to a serine-aspartate (sd) repeat (sdr) protein, pharmaceutical compositions comprising them and their use

1 238074/2

Title: Antibodies that binds to a serine-aspartate (SD) repeat (sdr) protein, pharmaceutical compositions comprising them and their uses

The present application is a divisional application divided out of Israel Patent Application No. 217497 filed January 12, 2012 and antedated as of July 15, 2010.

The invention relates to the fields of biology, immunology and medicine.

Gram-positive microorganisms cause the majority of systemic infections. One important member of these Gram-positive pathogens is 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. S. 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)). A major problem is the increasing antibiotic resistance of S. aureus.

Methicillin-resistant S. aureus (MRSA) emerged in the 1960s. It was initially identified in health care settings. However, MRSA appears to be present among persons in the community which have not been hospitalized. Treatment of MRSA is difficult and expensive, due to the limited sensitivity of MRSA to antibiotics.

However, very few alternatives of antibiotics are available. Vancomycin is often used to treat penicillin-resistant MRSA. US patent 6,939,543 describes a murine antibody against lipoteichoic acid (LTA) which is capable of binding S. aureus. Based on this murine antibody, a recombinant chimeric mouse/human antibody was produced which contains human heavy and light chain constant domains. However, such chimeric mouse/human antibody has the disadvantage that murine sequences are present, which involves the risk of serious side effects when administered to humans.

It is an object of the present invention to provide means and methods for counteracting and/or preventing Gram-positive bacteria-related diseases. It is a further object of the invention to provide alternative and/or improved binding compounds against various Gram-positive bacteria, preferably Staphylococcus species, 2 238074/2 more preferably MRSA. It is a further object of the invention to provide human binding compounds against various Gram-positive bacteria, preferably Staphylococcus species, more preferably MRSA.

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. Preferably, S. aureus is counteracted. In a particularly preferred embodiment, MRSA is counteracted. Another preferred Staphylococcus species which is counteracted is Staphylococcus epidermidis.

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.

In a preferred embodiment, 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 3 238074/2 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 "Fl", which has heavy chain and light chain variable domain sequences as depicted in Figure 1. The term "Fl" as used herein encompasses all Fl antibodies, for instance isolated or recombinantly produced Fl. Recombinantly produced Fl is herein also called "rFl". The CDR sequences of Fl, which in particular contribute to the antigen-binding properties of Fl, are also depicted in Figure 1. Antibody Fl 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.

Importantly, antibody Fl 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 Fl 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 4 238074/2 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.

As is well known by the skilled person, 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 (CDRs) 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.

Now that the present invention provides the insight that the CDR sequences depicted in Figure 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 Figure 1 in order to generate a variant antibody, or a functional part thereof, with at least one altered property as compared to Fl.

Preferably, an antibody or functional part is provided comprising a CDR sequence which is at least 70% identical to a CDR sequence as depicted in Figure 1, so that the favorable binding characteristics of Fl are at least in part maintained or even improved. A CDR sequence as depicted in Figure 1 is preferably altered such that 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 Fl. Variant antibodies or functional parts thereof comprising an amino acid 5 238074/2 sequence which is at least 70% identical to a CDR sequence as depicted in Figure 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. Preferably, a nucleic acid sequence encoding a CDR sequence is mutated, for instance using random - or site-directed - mutagenesis.

In one embodiment the invention therefore provides an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof, which comprises: - a heavy chain CDRl 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).

Further provided is an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof, which comprises: - a light chain CDRl sequence comprising a sequence which has at least 70% sequence identity to the sequence RASENVGD WLA (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).

The above mentioned CDR sequences are the CDR sequences of antibody Fl; VH IgHV3-23 and VL IgKVl-5, and variants thereof. Binding compounds comprising CDR sequences with at least 70% sequence identity to Fl 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 Fl, comprising VH IgHV3-23 and VL IgKVl-5, in which the isoleucine in light chain CDR3 of the light chain was 6 238074/2 altered to a methionine, was still capable of specifically binding Staphylococcus species such as S. aureus and S. epidermidis.

Preferably, 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 Figure 1. Most preferably, 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 Figure 1. The particularly preferred antibody Fl, described above, comprises CDR sequences which consist of the CDR sequences depicted in Figure 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 CDRl 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 CDRl 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).

In one embodiment a binding compound is provided which comprises the heavy chain CDRl and CDR2 sequences and the light chain CDRl and CDR2 sequences as depicted in Figure 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 7 238074/2 85% identical thereto. Further provided is therefore 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 CDRl 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 CDRl 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. Preferably, 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 CDRl, CDR2 and CDR3 sequences as well as the above mentioned light chain CDRl, CDR2 and CDR3 sequences is also provided.

Now that a human antibody capable of specifically binding Staphylococcus species has been provided by the present invention, 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. In a preferred embodiment, a human antibody is provided.

Optionally, 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 8 238074/2 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.

Besides optimizing CDR sequences in order to improve binding efficacy or stability, it is often advantageous to optimize at least one sequence in at least one of the framework regions. This is preferably done in order to improve binding efficacy or stability. 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. In a preferred embodiment, human germline sequences are used for framework regions in antibodies or functional parts thereof or immunoglobulin chains or functional equivalents according to the invention. The use of 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 Figure 1 are also provided. Such heavy chain sequence provides desired binding properties, as evidenced by antibody Fl. Moreover, light chain amino acid sequences which have at least 70% sequence identity to the light chain sequence as depicted in Figure 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 Fl, and a variant of antibody Fl comprising said alteration. Further provided is therefore an antibody or functional part or immunoglobulin chain or functional equivalent according to the invention, having a heavy chain sequence comprising a sequence which has at least 70% sequence identity to the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINN GNNPYYARSVQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWP TFDS WGPGTLVTVSS (SEQ ID NO:7) and/or having a light chain sequence which 9 238074/2 has at least 70% sequence identity to the sequence

DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSIL

ESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRT V, wherein in X is I or M (SEQ ID NO:8).

Several variants of the Fl 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.

Examples of such 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 EVQLVESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNG NNPYYARSVQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTF DS WGPGTLVTVSS (SEQ ID NO:9), and/or the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINNGN NPYYARSVQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWPTFDS WGPGTLVTVSS (SEQ ID NO:7), and a light chain sequence comprising the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILES G VPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRA, wherein X is I of M (SEQ ID NO:10), and/or the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILES GVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKVEIKRTV, wherein X is I of M (SEQ ID NO:11), and/or the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSILES GVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRTV, wherein X is I of M (SEQ ID NO:8).

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-rerroinal signal sequence, a functional domain caiied Hio A region, an Sl) rops-ar region, a cell wall- spanning region, a LPXTG morif, a hydrophobic meinbrane-spjnnmg domain, and a series of positively charged 10 238074/2 residues. The LFXTG mutif is the target of a transpeptidase that cleaves the mutif between threonine and glycine residues and anchors the protein Lo the peptidoglycan of the ceil wail of gram- posi rive bacteria. Sdr proteins are thought to interact with host molecules. Known Sdr proteins include CIfA (SdrA), CIfB (SdrB),

SdrC, SdrD and SdrE of S . aureus, SdrF, SdrG and SdrH of S. epidermidis, Sdrl of S. saprophytics, SdrX of S. capitis, and SdrY and SdrZ of S. caprae.

Therefore, a preferred antibody or functional part thereof or immunoglobulin chain or functional equivalent according to the invention specifically binds S. aureus, S. epidermidis, S. sapropkyiicus, S. capitis, and S. caprae. It is preferred that said antibody, immunoglobulin chain or functional equivalent or part thereof binds to CIfA (SdrA), CIfB (SdrB), SdrC, SdrD and SdrE of S . aureus, SdrF, SdrG and SdrH of S. epidermidis, Sdrl of S. βaprophyiicus, 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 CIfA, CIfB, SdrC, SdrD and SdrE. An SD repeat- dependent epitope is herein defined as an epitope recognized by antibody Fl, which epitope require the presence of at least part of an SD repeat region as present in, but not limited to, S. aureus CIfA, CIfB, SdrC, SdrD and SdrE and S. epidermidis SdrF, SdrG and SdrH. In one embodiment 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. In another embodiment, 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.

Therefore, 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 CIfA, CIfB, 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 11 238074/2 according to the present invention for binding to a Staphylococcus species, preferably S. aureus and/or S. epidermidis and/or >S. saprcφhyiicus 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. In one embodiment deamidation of an asparagine at position 53 of the heavy chain (numbering according to Kabat, 1991) is prevented by replacing said asparagine by another amino acid. By preventing deamidation of an asparagine at position 53 the stability of an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is preferably increased. As is shown in the examples, despite the fact that said asparagine is located in a CDR, 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.

In one embodiment, an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention is coupled to another 12 238074/2 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. The term "cytotoxic agent" as used herein 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. Preferably at least two amino acids other than cysteine have been replaced by cysteine. In a preferred embodiment, 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). A skilled person will understand that, as an alternative or in addition, 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.

In international patent applications WO2006/034488, WO2008/141044, WO2009/052249, WO2009/012256, WO2009/012268 and WO2009/099728 methods for 13 238074/2 engineering antibodies with reactive cysteine residues are described as well as amino acid positions suitable for cysteine engineering.

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 Figure 1, or a light chain sequence as depicted in Figure 1 in which the isoleucine in CDR3 is altered to a methionine. The higher the identity, the more closely said binding compound resembles antibody Fl. 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 Fl. 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 Figure 1, or a light chain sequence as depicted in Figure 1 in which the isoleucine in CDR3 is altered to a methionine. In one embodiment an antibody or functional part is provided which has a heavy chain sequence as depicted in Figure 1 and a light chain sequence as depicted in Figure 1 or a light chain sequence as depicted in Figure 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 Figure 1, and/or comprising a light chain sequence consisting of the light chain sequence as depicted in Figure 1 or a light chain sequence as depicted in Figure 1 in which the isoleucine inCDR3 is altered to a methionine. Alternatively, as is well known by the skilled person, it is possible to generate a shortened heavy chain or light chain sequence while maintaining a binding property of interest. Preferably, such a shortened heavy chain 14 238074/2 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. For instance, 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 Figure 1 is produced. A functional part of an antibody comprising at least a functional part of a sequence as depicted in Figure 1, or a light chain sequence as depicted in Figure 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 CDRl sequence depicted in Figure 1 and a sequence which is at least 70% identical to the heavy chain CDR2 sequence depicted in Figure 1 and a sequence which is at least 70% identical to the heavy chain CDR3 sequence depicted in Figure 1 and a sequence which is at least 70% identical to the light chain CDRl sequence depicted in Figure 1 and a sequence which is at least 70% identical to the light chain CDR2 sequence depicted in Figure 1 and a sequence which is at least 70% identical to the light chain CDR3 sequence depicted in Figure 1, or a light chain CDR3 sequence as depicted in Figure 1 in which the isoleucine is altered to a methionine.

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. Such 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 Figure 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 15 238074/2

Figure 1. Preferably, said nucleic acid sequence as depicted in Figure 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 Fl. Nucleic acid sequences encoding Fl CDR regions are depicted in Figure 1. Further provided is therefore an isolated, synthetic or recombinant nucleic acid sequence, or a functional equivalent 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), 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 Figure 1, said part having at least 15 nucleotides and encoding at least one CDR region. A nucleic acid sequence or functional equivalent thereof according to the present invention preferably encodes a region which has at least 70% sequence identity to an Fl CDR region, an Fl heavy chain and/or an Fl 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 16 238074/2 sequence DHPSSGWPTFDS (SEQ ID NO:3), and/or at least 70% sequence identity to the sequence RASENVGD WLA (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 EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINN GNNPYYARSVQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWP TFDS WGPGTLVTVSS (SEQ ID NO:7), and/or at least 70% sequence identity to the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSIL ESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRT V, wherein X is I or M (SEQ ID NO:8). Also provided are nucleic acid sequences or functional equivalents thereof encoding variants of the Fl antibody according to the invention. Provided by the invention are, for example, nucleic acid sequences encoding a heavy chain sequence comprising the sequence EVQLVESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINN GNNPYYARSVQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWP TFDS WGPGTLVTVSS (SEQ ID NO:9), and/or the sequence EVQLLESGGGLVQPGGSLRLSCAASGFTLSRFAMSWVRQAPGRGLEWVASINN GNNPYYARSVQYRFTVSRDVSQNTVSLQMNNLRAEDSATYFCAKDHPSSGWP TFDS WGPGTLVTVSS (SEQ ID NO:7), and encoding a light chain sequence comprising the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSIL ESG VPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRA, wherein X is I of M (SEQ ID NO: 10), and/or the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSIL ESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKVEIKRT V, wherein X is I of M (SEQ ID NO:11), and/or the sequence DIQLTQSPSALPASVGDRVSITCRASENVGDWLAWYRQKPGKAPNLLIYKTSIL ESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYXRFPYTFGQGTKLEIKRT V, wherein X is I of M (SEQ ID NO:8).

In one embodiment an asparagine at position 53 of the heavy chain (numbering according to Kabat, 1991) is replaced by another amino acid other than 17 238074/2 glutamine, in order to prevent deamidation of the asparagine at said position. Preferably said asparagine is replaced by a serine.

The term "% 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.

As used herein, a nucleic acid molecule or nucleic acid sequence of the invention preferably comprises a chain of nucleotides, more preferably DNA and/or RNA. In other embodiments 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. Such other nucleic acid structures are referred to as functional equivalents of a nucleic acid sequence. The term "functional equivalent of a 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. In one embodiment, 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. Preferably, said producer cell line is suitable for producing compounds for use in humans. Hence, said producer cell line is preferably free of pathogenic agents such as pathogenic micro-organisms.

Most preferably, binding compounds consisting of human sequences are generated using a nucleic acid sequence according to the invention. 18 238074/2

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. Preferably, 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. For instance, a sample, such as a tissue or blood sample, can be obtained from an individual or from any other source suspected to be infected with a Staphylococcus bacteria, preferably S. aureus and/or S. epidermidis, more preferably MRSA. Subsequently, said sample can be mixed with an antibody or immunoglobulin 19 238074/2 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.

Isolation of Staphylococcus bacteria, preferably S. aureus and/or S. epidermidis, 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, 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.

In one embodiment of the invention, an antibody, immunoglobulin chain or functional equivalent or part thereof according to the present invention is labeled in 20 238074/2 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.

Alternatively, 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.

Provided by the invention is therefore a use of an antibody or functional part thereof or immunoglobulin chain or functional equivalent thereof according to the invention 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. Also provided is 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.

Further provided is a method for isolating S. aureus and/or S. epidermidis bacteria from a solution using an antibody or functional part or an immunoglobulin chain or functional equivalent thereof according to the invention. 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.

Now that 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. 21 238074/2

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.

Preferably, 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. 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. In a particularly preferred embodiment said antibody comprises antibody Fl, 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. Further provided is therefore 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. Preferably, S. aureus infection is counteracted or at least in part prevented. Most preferably, 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. epidermidis, the method comprising administering to an individual in need thereof a therapeutically effective amount of an antibody or functional part or an 22 238074/2 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 Fl, or a functional part thereof.

In order to counteract Gram-positive bacteria, a binding compound according to the invention is preferably administered to an individual before an infection has taken place. Alternatively, 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. For therapeutic application binding compounds according to the invention are typically combined with a pharmaceutically acceptable carrier, diluent and/or excipient.

Examples of suitable carriers for instance comprise keyhole limpet haemocyanin (KLH), serum albumin (e.g. BSA or RSA) and ovalbumin. In one preferred embodiment said suitable carrier comprises a solution like for example saline.

In yet another embodiment a nucleic acid encoding a binding compound according to the invention is used. As already described, 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. Further provided is therefore a use of a nucleic acid sequence 23 238074/2 or functional equivalent according to the invention for the preparation of a medicament and/or prophylactic agent for at least in part treating and/or preventing a Gram-positive bacterium-related condition. Said Gram-positive bacterium-related condition preferably comprises an infection by S. aureus or S. epidermidis, more preferably an S. aureus 5 infection, most preferably an MRSA infection.

Further provided is a pharmaceutical 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 10 composition is preferably suitable for human use.

The invention is further explained in the following examples. These examples do not limit the scope of the invention, but merely serve to clarify the invention.

All patent documents and other publications that are referred to in the detailed description are incorporated herein by reference for all purposes. 15 24 238074/2

Examples

Example 1

METHODS B cell isolation 5 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 10 informed consent. Donors were selected based on carrying hospital acquired MRSA strains with genotype cluster 109 and 16.

Cell culture B-cells maintained in standard culture medium containing IMDM (Gibco), 8% 15 FBS (HyClone) and penicillin/streptomycin (Roche) were co-cultured on γ-irradiated (50Gy) mouse L cell fibroblasts stably expressing CD40L (CD40L-L cells, 105 cells/ml) and recombinant mouse IL-21 (25ng/ml, R&D systems). rhIL-4 (R&D) was used at 50ng/ml. Cells were routinely tested by PCR and were found negative for the presence of mycoplasma and EBV (data not shown).

20 Bulk transduced human memory B cells double positive for NGFR and GFP were purified by FACS cell sorting and cultured in 96 well plates at a cell density of 500 cell per well. Culture supernatants were tested in ELISAs using bacterial lysates of the Newman and SHlOOO strains. Positive cultures were subcloned at 10 cell/well cell density in 96 well plates and again tested by ELISA. Subsequently positive cultures 25 were seeded at 1 cell per well and tested again by ELISA for reactivity against S. aureus strains Newman and SH1000. 25 238074/2

Retroviral transduction

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 BcIxL-GFP construct. These constructs were transfected into the LZRS retroviral packaging cells, phoenix as 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

To determine antibody content ELISA plates were coated with anti-human IgG

(Jackson ImmunoResearch Laboratories) at 5 μg/ml in PBS for lhr 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.

For screening purposes we used lysates from the Newman and SHlOOO strains.

Both were made in PBS and directly coated at 5 to 10 μg ml λ before B cell culture supernatants were tested un- or 1:2 diluted.

To explore the antigen specificity of the human IgGl clone Fl, 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 \ QED Bioscience), before secondary antibodies were added.

In addition, we tested several LTA preparations derived from a library developed by W. Fischer (Institut fur Biochemie, Univ of Erlangen, Germany) and kindly provided by B. Appelmelk (VU, Amsterdam, Netherlands) (see for more details (Keller R. et al. Infect Immun 60, 3664-3672 (1992), Polotsky V. Y. et al. Infection and Immunity 64, 380-383 (1996) and Greenberg J. W. et al. Infection and Immunity 64, 26 238074/2 3318-3325 (1996)) and reviewed in (Weidenmaier C. et al. Nat Rev Microbiol 6, 276287 (2008)) in direct ELISA's. LTA preparations were coated at 1 μg ml x before rFl (10 μg ml x) 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. lactis, L. gawieae, 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).

Binding of the Fl antibody to bacterial cultures

The Newman S. aureus and the S. pneumoniae strain (serotype 3) were used.

Newman was cultured in TSH 50 ml O/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 Fl 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.

Fl sequence determination and expression cloning

We isolated total RNA using Trizol (Invitrogen), generated cDNA by using superscript RT, performed PCR and cloned the heavy and light chain variable regions into the pCR2.1 TA cloning vector (Invitrogen). To rule out reverse transcriptase or DNA polymerase induced mutations, we performed several independent cloning experiments. To produce recombinant Fl mAb we cloned Fl heavy and light variable regions in frame with human IgGl and Kappa constant regions into a pcDNA3.1 (Invitrogen) based vector and transiently transfected 293T cells. We purified recombinant Fl from the culture supernatant with Protein A.

RESULTS

Generation of the Fl clone 27 238074/2

From three subjects who were tested positive for MRSA but were not sick, 50-60ml of heparin blood was collected and peripheral B-cells were isolated after a ficoll purification step. B-cells from several B-cell populations were double transduced with retroviruses containing BCL6-NGFR and Bcl-xL-GFP (Diehl et al and Kwakkenbos et 5 al). From the IgG, CD27 positive population, polyclonal mini-cultures 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, SHlOOO and Newman). Mini-cultures that were screened positive in both the 10 SHlOOO 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 SHlOOO 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 Fl) was found to produce S. 15 aureus specific monoclonal IgG antibodies.

Antibodies in the supernatant of the Fl clone bind to LTA preparations from S. aureus

Generating the Fl clone, we already found that supernatant of Fl bound to the bacterial 20 cell lysates of two S. aureus strains, SHlOOO and Newman. The major cell wall

compound of Gram-positive bacteria is LTA, and therefore we decided to test binding of Fl supernatant to S. aureus LTA preparations in an ELISA. As shown in Table 1, supernatant of the Fl clone binds to bacterial cell lysates of the SHlOOO and Newman S. aureus strain but also to commercially purchased purified S. aureus LTA 25 preparations. We noted, however, that the binding to the LTA preparations was significantly lower than that observed with whole bacteria. 28 238074/2

Table 1: Supernatant of the Fl clone binds to S. aureus LTA preparations. As a negative control an anti-mouse-HRP conjugated secondary antibody was used.

Another control was an anti-influenza virus antibody that only detected influenza H3 protein. 5 F1 clone Mouse anti-LTA Anti-flu control SH1000 1,004 -0,010 -0,007 Newman 0,753 -0,007 0,007 SA LTA (sig m 0.176 -0,005 -0,009 Flu H3 0.003 -0,002 1,523 No coat -0,013 -0,014 -0,015 10

The recombinant produced Fl antibody binds to LTA preparations from multiple sources

After cloning the antibody genes into expression vectors and producing recombinant Fl (rFl) antibody in an expression system, the rFl antibody was tested on purified LTA 15 preparations from several bacteria. As shown in Figure 2A, the rFl 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 rFl antibody did not bind to an LTA sample from S. pneumoniae (data not shown). In addition rFl recognized highly purified LTA samples from B. subtilis, B. licheniformis and two 20 isolates of S. aureus (Figure 2b). rFl did not bind to LTA preparations from S. mutans (Fig. 2b) or from L. lactis, L. garuieae, B. bifidum, M. luteus, L. casei, L. mesenteroides, L. welshimeri, E. hirae, L. raffinolactis, S. mutans and S. pneumoniae (results not shown). 25 Recombinant Fl antibody binds to living S. aureus bacteria

In order to study whether the rFl antibody would also recognize living Gram-positive bacteria, binding of the rFl antibody to S. aureus and S. pneumoniae was tested by using flow cytometry. As shown in figure 3A, the rFl antibody binds to living S. 29 238074/2 aureus bacteria (Newman strain), but not to S. pneumoniae. In addition we show that

rFl recognized 6 clinical S. aureus isolates; one is a pathogenic strain which is PVL positive, 3 regular strains and 2 MRSA strain (Figure 3b).

Example 2

METHODS

Bacterial strains and culture.

Methicillin-resistant S. aureus (MRSA) strains USA300 (1114), USA400, N315, USAlOO, USAlOOO, COL, MRSA252, as well as methicillin- sensitive S. aureus (MSSA) strains Reynolds, Becker, Smith Diffuse, MN8, and vancomycin intermediate sensitive (VISA) strain Mu50, were all obtained from the Network on Antibiotic Resistance in Staphylococcus aureus (NARSA); MSSA strains Newman and Rosenbach were from ATCC. Staphylococcus epidermidis, Bacillus subtilis, Enterococcus faecalis, and Streptococcus pyogenes were obtained from Ward's Natural Science; Listeria monocytogenes was from ATCC. Bacteria were grown on tryptic soy agar (TSA) plates supplemented with 5% sheep blood for 18 h at 37 0C. For liquid cultures, single colonies from TSA plates were inoculated into tryptic soy broth (TSB) and incubated at 37 0C while shaking at 200 rpm for 18 h. Fresh 100-fold dilutions of these cultures in fresh TSB were further subcultured for various times. FACS analysis of rFl binding to whole bacteria grown in vitro.

For antibody staining of whole cells, bacteria were harvested from TSA plates or TSB cultures, and washed with Hank's 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 x g for 20 min. Bacterial concentrations were estimated by reading optical density at 630 nm. Bacterial suspensions of 2OxIO8 CFU/mL in HB buffer were mixed with equal volumes of 300 μg/mL of rabbit IgG (Sigma), and incubated for 1 h at room temperature (RT) to block nonspecific IgG binding. Primary antibodies, including rFl and a human IgGl isotype control, were added to a final concentration of 2 μg/mL, and these mixtures were incubated for 15 30 238074/2 min at RT. After two washes with HB, bacterial pellets were resuspended in a solution of fluorescent anti-human IgG secondary antibodies (Jackson

Immunoresearch) and incubated for 15 min at RT. The bacteria were washed twice with PBS, resuspended in PBS with 1% paraformaldehyde, and analyzed by flow cytomery. FACS analysis of rFl binding to whole bacteria from infected tissues.

For analysis of antibody binding to bacteria from infected tissue, 4 h subcultures of USA300 in TSB were washed with PBS. Mice were injected intravenously with a 100 μL of a suspension of USA300 in PBS with an estimated concentration of 10x108 CFU/mL. Three days later, kidneys, livers, and lungs were harvested and homogenized using conical tissue grinder tubes (VWR). When indicated, organs were harvested at different time points of infection. To lyse mouse cells, the homogenates were incubated for 10 min at RT in PBS containing 0.1% Triton-X100 (Thermo), 10 μg/mL of DNAsel (Roche) and Complete Mini protease inhibitor cocktail (Roche), and passed through a 40 μιη filter (Falcon). The cell suspensions were washed twice with PBS and resuspended in HB buffer, mixed with equal volumes of 600 μg/mL of human IgG (Sigma), and incubated for 1 h at RT. Primary Abs, including rFl and a human IgGl isotype control, were added to a final concentration of 2 μg/mL. To differentiate bacteria from mouse organ debris, rabbit IgG anti-S. aureus (Abeam) was added to a concentration of 20 μg/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 rFl and isotype control were generated.

RESULTS rFl binds strongly to 14 S. aureus strains and S. epidermidis 31 238074/2

Seven Methicillin-resistant S. aureus (MRSA) strains, six methicillin-sensitive S. aureus (MSSA) strains, one vancomycin intermediate sensitive S. aureus (VISA) strain, S. epidermidis and several other gram-positive species were tested for binding to rFl antibody. As shown in figure 4, rFl strongly binds to all 14 S. aureus strains (figure 5 4A) and to S. epidermidis (figure 4B), but not to the other tested gram-positive species (figure 4B). rFl binds to MRSA from different growth stages and from in vivo infection

We tested the ability of mAb rFl to bind to bacteria both in different tissues and 10 over the course of infection. We found that rFl bound to bacteria isolated from murine kidney, liver and lung tissue two days after infection and that the binding to bacteria isolated from infected kidneys was stable, binding bacteria 2, 3 and 8 days after infection.

Binding of rFl antibody to different growth stages of MRSA (strain USA300), 15 namely early logarithmical growth (2 hours) and post exponential growth (8 hours) in TSB cultures, and growth of solid colonies on TSA plates was tested. rFl strongly binds to all growth stages tested (figure 5A).

Binding of rFl antibody to MRSA (strain USA300) to whole bacteria from infected tissue was tested in homogenized kidneys from mice three day after the mice 20 were systemically infected with MRSA. As shown in figure 5B rFl binds to MRSA obtained from infected tissue.

Example 3 25 Further experiments were performed to identify the epitope bound by antibody rFl. Although binding to LTA preparations had been observed (see, e.g.,

Example 1), that binding was not as robust as binding to whole bacteria suggesting that another epitope may be involved in rFl binding. 32 238074/2

METHODS

Immunoprecipitation, Western blotting and mass spectrometry of cell wall lysates of S. aureus and S. epidermidis and commercial WTA preparation 40 micrograms of a commercial wall teichoic acid (WTA) preparation from

Wood46 S. aureus strain (Biodesign/ Meridian Life Sciences, Maine) was split into two parts and immunoprecipitated with 1 ug/ml of rFl or isotype control human antibody.

Antibodies were captured with Protein A/G Ultralink Resin (Pierce). The samples were then treated with 5OmM dithiothreitol, 1OmM 2-Iodoacetamide and run on an 8% Trisglycine gel and subsequently Western blotted with rFl. 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 100mg/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 antiFlag 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 rFl or isotype control human antibody.

Antibodies were captured with Protein A/G Ultralink Resin (Pierce). The samples were then treated with 5OmM dithiothreitol, 1OmM 2-Iodoacetamide and run on an 8% Trisglycine gel and subsequently silver stained or Western blotted with rFl.

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 rFl or control antibody. Antibodies were captured with Protein A/G Ultralink Resin (Pierce). The samples were then treated with 5OmM dithiothreitol, 1OmM 2-Iodoacetamide and run on an 8% Tris-glycine gel and subsequently silver stained or Western blotted with rFl.

For proteomic analysis, samples were applied to a precast SDS PAGE mini gel and the resolved proteins stained with Coomassie Blue. Gel slices from the region of the gel corresponding to bands visualized by rFl western blot were excised and 33 238074/2 reduced, alkylated with iodoacetamide, and digested in situ with trypsin. Resulting tryptic peptides were analyzed by microcapillary reverse-phase liquid chromatography- nano electrospray tandem mass spectrometry on a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (LTQ-FT; Thermo Fisher) in a data- dependent experiment. Tandem mass spectral results were submitted for database searching using Mascot software (Matrix Science).

Expression of exogenous CIfA expressed in S. aureus and E. coli S.aureus expression of His -tagged CIfA: The Clumping factor- A (CIfA) 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 (pSASlO 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 ODeoo 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 CIfA protein. E. coli expression of His -tagged CIf a: The Clumping factor- A (CIfA) 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 34 238074/2 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 CIfA protein.

Expression of exogenous CIfA expressed in E. coli and incubation with S. aureus lysate_

Expression and Purification of S. aureus cell surface SDR proteins CIfA, CIfB, SdrC, SdrD, SdrE in E.coli: The CIfA, CIfB, 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 inframe 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: 500ug of purified N-terminal Unizyme tagged SDR proteins (CIfA, CIfB, 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 NaEbPCU, 30OmM NaCl; pH 8.0).

Modification of E.coli produced SDR proteins by S. aureus lysate: A 25 ml culture was started from an overnight culture of ΔΡαη Sdr mutant (ClfA-CIfB-SdrCDE-null; gift of Tim Foster, Trinity College Dublin) Newman S. aureus (starting ODeoo 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 ΔPan Sdr mutant S. aureus lysates for 1 hr at 37°C. 35 238074/2

Western Blotting of modified E.coli SDR protein: Non- modified or modified

NiNta captured E.coli SDR protein samples were then washed 3x with wash buffer (50 mM NaH2PO4, 30OmM NaCl, 10 mM Imidazole; pH 8.0), prepared for Western

Blotting and run on an 8% Tris Glycine Gel (Invitrogen). Western blots were blotted with either the rFl antibody or an anti-Unizyme antibody (Genentech).

Identification of SDR domain as antigen for rFl S. aureus expression of MBP-SD Constructs: The maltose binding protein (MBP) gene was PCR amplified from the pMAL-c5x vector (New England BioLabs [NEB], Ipswich, MA, 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 CIfA 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). As a control, the sequence encoding the A domain of the CIfA 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 CIfA A domain were ligated into the pTet S. aureus expression vector (pSASlO from Genentech). The resulting constructs were then electroporated into the S. aureus RN4220 Δ sortase (sortase deletion mutant strain in the RN4220 background). A 20 ml culture of either the electroporated RN4220 Δ sortase or RN4220 Δ sortase empty (not carrying a pTet expression vector) was inoculated from an overnight culture (starting OD600 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. aureus culture was resuspended in Column Buffer (150 mM NaCl, 20mM Tris pH 7.5 and Roche protease inhibitor EDTA-free tablets) and lysed with 200 ug/ml lysostaphin 36 238074/2 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 microcentrifuge for 10 minutes at 4°C. The cleared lysates were then incubated with

amylose resin (NEB) along with a final EDTA concentration of ImM for 1.5 hrs at 4°C to capture the expressed MBP-SD proteins.

Western Blotting of S. aureus expressed MBP-SD Constructs: Amylose resin with the captured MBP-SD proteins were washed three times with Column Buffer, further prepared for Western blotting analysis and run on an 8% Tris-glycine gel. Western blots were blotted with either the rFl antibody, an anti-penta His antibody (Qiagen) or an anti-MBP antibody (NEB).

RESULTS rFl reacts to a unique family of SDR (Ser-Asp-repeat) proteins in S. aureus and S. epidermidis A commercial teichoic acid preparation and cell wall lysate (WTA) of S. aureus (USA300 strain) was tested for binding to rFl after immunoprecipitation. rFl binds to several components of the commercial teichoic acid preparation (figure 6A, left panel) and of the cell wall lysate of S. aureus (figure 6B, left panel). Using mass spectrometry these components of the WTA preparation and cell wall lysate were identified as CIfA (SdrA), CIfB (SdrB), SdrC, SdrD and SdrE (figure 6A, right panel and figure 6B, right panel) A cell wall lysate of S. epidermidis was tested for binding to rFl after immunoprecipitation. Figure 6C (left panel) shows binding of rFl 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 (figure 6C right panel).

Exogenous CIfA expression in S. aureus and E.coli

Exogenous CIfA expressed in S. aureus is reactive to rFl, whereas CIfA expressed in E. coli was not (figure 7A). However, incubation of E. coli expressed Sdr 37 238074/2 proteins CIfA (SdrA), CIfB (SdrB), SdrC, SdrD and SdrE with S. aureus lysate regained rFl reactivity (figure 7B). rFl binds to SDR domains expressed in S. aureus rFl antibody binds to CIfA Sdr regions consisting of the CIfA 560D-618S and CIfA 560D-709S (figure 8) expressed in S. aureus. rFl does not bind to the A-domain of CIfA or to small peptide sequences consisting of up to three SD repeats.

Example 4

METHODS

Cloning of the variable regions of rFl into pRK vector

Phusion DNA polymerase, restriction enzymes EcoRV, Kpnl, PvuII, Apal,

Agel, and Ahdl, T4 DNA ligase were purchased from New England BioLabs, Ipswich, MA, USA. Pfu DNA polymerase, Quick change II Site-Directed Mutagenesis Kit were purchased from Stratagene/Agilent Technologies, Santa Clara, California, USA. 2% agarose gel was purchased from Invitrogen, Carlsbad, California, USA. pRK vectors pRK.LPG3.HuKappa and pRK.LPG4.HumanHC were obtained from

Genentech/Roche, South San Francisco, California, USA.

The variable domains of heavy and light chains of rFl 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 μl using Pfu DNA polymerase according to standard PCR procedures. VH was amplified with the primers YiHCF) 5'-ATG GCT GAG GTG CAG CTG GTG GAG TCT G-3' (SEQ ID NO:18) and YiH CR2 5'-GAA CAC GCT GGGGCCCTT 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 Apal are underlined and the * indicates the single nucleotide G to T change to eliminate the internal Apal site) and VL was amplified with the primers YiLCF 5'-CGG CTC GAC CGA TAT CCA 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 Kpnl are underlined). Unique PCR products with 393 (VH) and 328 (VL) bp, respectively, were 38 238074/2 directly digested by PvuII and Apal for VH, ECORV and Kpnl for VL, followed by Gel purification (Invitrogen, Catalog# K2100-12). VH and VL were individually ligated into pRK vector fragments of pRK/Pvull, Apal for Heavy chain and pRK/EcoRV, Kpnl for light chain using T 4 DNA ligase. The DNA plasmids were confirmed by restriction enzyme digestion patterns, i.e. rFIVH released ~300 bp and 5.8 kb bands by Agel, whereas rFIVL shown 2.3 and 3.1 kb bands by Ahdl on 2% agarose gel.

Chemical stress testing

By comparing antibody primary sequence data to experimentally observed degradation events, it has become clear that certain sequence motifs may be prone to degradation (i.e, aspartate isomerization at DD, DG, and DS sequences and asparagine deamidation at NG sequences). If such a degradation "hot spot" appears in the CDR of an antibody, binding and potency may be negatively impacted. For molecules containing hot spots, chemical stress testing provides a way to assess the susceptibility of these motifs to degradation by putting the antibody into a platform formulation buffer and comparing a control sample to one stressed at 4O0C for two weeks. If degradation is observed the primary sequence can be re-engineered to remove the hot spot.

After the sample is stressed for two weeks at 4O0C, a variety of analytical assays are performed to assess where and how much degradation occurred. An imaged capillary isoelectric focusing (icIEF) analysis was performed to examine charge variants and the intact and reduced antibody mass was verified using mass spectrometry, and an LC-MS/MS peptide map was performed to obtain site-specific degradation information.

Mutagenesis

The rFl 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 CAG CGG CAA CAA CCC CTA CTA CG-3' (SEQ ID NO:22) and RHV 5'-CGT AGT AGG GGT TGT TGC CGCTGT 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. 39 238074/2

RESULTS

The primary sequence of antibody rFl contained one potential asparagine deamidation site in light chain CDR2: NNGNN (SEQ ID NO:24). Stress testing revealed an increase of deamidation in stressed samples at N53 (numbering according to 5 Kabat, 1991). Site-directed mutagenesis was performed to stabilize the rFl 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. 10 Example 5

Development of Cys variants for antibody-drug conjugate (ADC) applications

The rFl pRK plasmids underwent a series of site-directed mutagenesis with 15 oligos of rFlpRK.LC(205/210)VCF (468075) 5'-GGG CCT GAG CTC GCC CTG CAC AAA GAG CTT CAA CAG-3' (SEQ ID NO:27) and rFlpRK.LC(205/210)VCR (468076) 5'-CTG TTG AAG CTC TTT GTG CAG GGC GAG CTC AGG CCC-3'

(SEQ ID NO:28) (Cys mutant is underlined) to generate the light chain linkers of rFl thioMab, and rFlpRK.HCN53S.Al2lCF (468464) 5'-CTG GTC ACA GTC TCG AGT 20 TGC AGC ACC AAG GGC CCA TC-3' (SEQ ID NO:29) and rFlpRK.HCN53S.Al2lCR (468465) 5'-GAT GGG CCC TTG GTG CTG CAA CTC GAG ACT GTG ACC AG-3' (SEQ ID NO:30) (Cys mutant is underlined) to make the heavy chain linkers of rFl thioMab via the Stratagene's Site-Directed method. Light chain V205C and heavy chain A114C were confirmed by sequencing of the variants 25 (figure 9). 40 238074/2

Brief description of the drawings

Figure 1: Heavy chain and light chain sequences of antibody Fl

Figure 2: Fl antibody binds to LTA preparations from several Gram-positive bacteria, (a) LTA preparations were derived from Sigma and tested in a capture ELISA with a mouse polyclonal anti-LTA or (b) a highly purified set of LTA preparations derived from W. Fischer. D25, a human anti-RSV antibody was used as non-specific negative control and a mouse monoclonal anti-LTA antibody as a positive control.

Figure 3: Recombinant Fl antibody binds to S. aureus but not to S. pneumoniae, (a) Bacteria were incubated with Fl 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). (b) 6 clinical isolates were tested in two separate experiments for the binding of Fl. Tested were a PVL+ strain (SA-I), 3 regular (SA-2 SA-3 and SA-4), and 2 MRSA strains (SA-5 and SA-6).

Figure 4: (a) Binding of rFl antibody to 14 S. aureus strains, (b) rFl antibody binds to S. epidermidis but not to Bacillus subtilis, Enterococcus faecalis, Listeria monocytogenes and Streptococcus pyogenes.

Figure 5: (a) rFl antibody binds to MRSA in different growth stages, Iso C: isotype control, Med: media control (b) rFl antibody binds to MRSA isolated from infected tissue.

Figure 6: rFl antibody binds to SDR proteins, (a) Immunoprecipitation (IP) of a commercial teichoic acid preparation of S. aureus (Wood 46 strain) with rFl or isotype control antibody, followed by Western blotting with rFl antibody (left) and mass spectrometry analysis of fragments from the WTA preparation bound by rFl antibody (right), (b) Immunoprecipitation (IP) of cell wall lysate of S. aureus (USA300 strain) with rFl or control antibody, followed by Western blotting (WB) with rFl antibody (left) and mass spectrometry analysis of cell wall fragments (USA300 strain) bound by 41 238074/2 rFl antibody (right) (c) Immunoprecipitation of cell wall lysate of S. epidermidis with rFl or isotype control antibody, followed by Western blotting with rFl antibody (left), mass spectrometry analysis of cell wall fragments bound by rFl antibody (right). 5 Figure 7: Binding of rFl to SDR proteins expressed in S. aureus and E. coli. (a)

Western blotting of S. aureus and E. coli lysates containing overexpressed His- tagged CIfA using anti-His (left) and rFl (right) antibody, (b) Western Bloting of E. coli cell lysates containing his-tagged CIfA, CIfB, SdrC, SdrD and SdrE following incubation with S. aureus lysate with rFl (top) or anti-His (bottom) antibody. 10

Figure 8: rFl binds to SDR domains expressed by S. aureus. Constructs expressed by S. aureus and tested for binding to rFl (left), Western blots of S. aureus lysates containing the expressed constructs with anti-MBP (maltose binding protein), anti-His and rFl antibody (right). 15

Figure 9: Sequences of heavy chain A114C (a) and light chain V205C (b) variants of antibody rFl. Numbering according to Kabat (1991), boxes: CDRs. 42 238074/2

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