Title of Invention


Abstract A composition for preventing or treating non-aureus or non-epidermidis staph infection and other bacterial infection in a subject, comprising: 1 -95% a RAP polypeptide effective to elicit an antibody response in the subject to prevent or treat a bacterial non-aureus or non-epidermidis staph infection and other infection caused by bacterial species in v/hich a RAP polypeptide plays a role in pathogenesis, and remaining amount of pharmaceutically acceptable carrier such as herein described
This application is a continuatioa-in-part of U.S. application serial no, 09/839,695, which is a continuation-in-part of serial no. 09/054,331, filed April 2, 1998 and now issued as U.S. PatentNo. 6,291,431, which application claims the benefit of U.S. provisional application serial no/60/068,094, filed December 19, 1997, now abandoned, each of which applications is incorporated by reference in its entirety herein for all purposes.
The present invention relates to methods and compositions for treatment or prevention of bacterial biofilm, infection, diseases or symptoms caused by bacteria, including those associated with infection by Staphylococcus spp.
Drug resistant Staphylococci are a major medical problem
Staphylococci (especially S. aureus and S. epidermidis) are major human pathogens and are the most common cause of nosoconu'al infections reported in the U.S. Each year approximately two million hospitalizations result in nosocomial infections, increasing hospital death rate in the U.S. by 35%. S. aureus and S. epidermidis infections are the leading cause of nosocomial pneumonia, surgical site and bloodstream infections, medical device associated infections, as well as community-acquired infections such as osteomyelitis and septic arthritis, skin infections, endocarditis, and meningitis (Rubin RJ et al., Emerg Infect Dis. 1999; 5:9-17 [ I ]). Currently, more than 95% of patients with slaphylococcal infections

worldwide do not respond to first-line antibiotics such as penicillin or ampicillin. Drug-resistant staphylococcus was once largely confined to hospitals and nursing homes but is now spreading to communities as well (Lowy FD. N. Engl. J. Med, 1998; 339:520-532 [2]). The emergence and spread of drug-resistant bacteria underscores the need to find new modes of prevention and alternative antibiotic treatment to bacterial infections, including S. aureus, S. epidermldis and others. The instant invention addresses this need and others.
S. aureus cause diseases by producing virulence factors
S. aureus are part of the normal flora of the human skin, but can cause fatal diseases due to the formation of biofilms and/or the production of toxic exomolecules. The toxins include toxic-shock syndrome toxin-1 (TSST-1), a pyrogenic toxin that causes toxic shock syndrome; Stapliylococcal enterotoxins, a major cause of food poisoning; Proteases that allow the bacteria to exploit its environment of metabolites and enable its spread within the host; Hemolysins, leukocidin and other virulence factors that are expressed, secreted or sequestered by staphylococci and have been shown to affect the outcome of the infective process [2],
A novel approach for therapy development is to interfere with staphylococcal virulence (biofilm formation and toxin production). Eliminating the production of virulence factors does not only make the bacteria far less pathogenic, but may also make the bacteria more susceptible to host immune defenses and to conventional antibiotics (Balaban N, et al,, Science 1998; 280:438-440 [3]).
Regulation of Staphylococcal virulence bv quorum sensing
Biofilm formation and toxin production is regulated by a quorum sensing mechanism, where molecules produced and secreted by the bacteria (autoinducers) reach a threshold concentration and activate signal transduction pathways, leading to activation of the genes

that encode for virulence factors [2].
S. aureus express surface molecules such as fibronectin binding-proteins, fibrinogen binding-protein and protein A, in the early exponential phase of growth, when the bacteria are in lower density [2]. Expression of adhesion molecules allows the bacteria to adhere to and colonize host cells and implanted medical devices. When in higher densities, the bacteria produce toxic exomolecules such as Toxic Shock Syndrome Toxin-1 (TSST-1), enterotoxins, proteases and hemolysins that allow the bacteria to survive, disseminate and establish the infection [2].
The ability of the bacteria to express adhesion molecules and colonize when in lower densities and to express toxic exomolecules and cause disease when in higher densities, is due to a complex regulatory process, which involves quorum sensing (QS) mechanisms (Kleerebezem M, et al., Mol. Microbiol. 1997; 24: 895-904 [4]) and activation of genetic loci such as traP (Balaban N et al., J Biol Chem 2001; 276:2658-2667 [5]) agr (Lina G, et al., Mol Microbiol 1998; 28:655-662 [6], sar (Heyer G, et al, Infect. Immun. 2002; 70:127-133 [7]), sae (Giraudo AT et al., FEMS Microbiol. Lett. 1999; 177:15-22 [8]). These processes act in parallel or in concert to regulate virulence [5].
To date, two staphylococcal quorum-sensing systems (SQS) have been described. SQS 1 consists of the autoinducer RNAIII-activating protein (RAP) and its target molecule TRAP [3,5]. RAP is a protein of about 33kDa [3] that is an ortholog of the ribosomal protein L2 (coded by the rplB gene) and usually consists of 277 amino acids. RplB is highly conserved among eubacteria ((see detailed description below). TRAP is a ~21kDa protein that is phosphorylated in the presence of RAP [5]. The sequence of TRAP is highly conserved among staphylococcal strains and species and its secondary structure is highly conserved among gram positive bacteria. TRAP usually consists of 167 amino acids (see detailed description below).

SQS 2 is composed of the products of the gene regulatory system agr. agr encodes two divergently transcribed transcripts, RNAII and RNAIII (Novick RP, et al, Mol. Gen. Genet. 1995; 248: 446-458 [9], and Novick RP et al, EMBO J 1.993; 12:3967-3975 [10]). RNAII is a polycistronic transcript that encodes AgrA, AgrC; AgrD and AgrB, where AgrD is a pro-peptide that yields an autoinducing peptide (AIP) that is processed and secreted with the aid of AgrB (Otto M. Peptides 2001; 22:1603-1608 [11] and Saenz HL et al., Arch Microbiol 2000; 174:452-455 [12]). Once agr is activated and AIP is secreted, it induces the phosphorylation of AgrC [6] and AgrA, leading to the production of the regulatory RNA molecule termed RNAIII [10]. RNAIEI upregulates the production of numerous secreted toxins [10].
Interaction beftveen SQS1 and SQS 2
RAP induces the phosphorylation of its target molecule TRAP, leading in a yet unknown manner both to increased cell adhesion and to the activation of agr. Once agr is activated and RNAII is produced (in the midexponential phase of growth), the octapeptide (AEP) and its receptor AgrC are made. AIP downregulates TRAP phosphorylation [5] (leading to reduced adhesion properties) and independently to upregulation of the phosphorylation of its receptor, AgrC [6]. This leads to the phosphorylation of AgrA, resulting in the production of RNAIII. RNAIII leads to the expression of many toxic exomolecules [10].
Inhibition of SQS 1: A novel mode of therapy and prevention of bacterial infections
Mice that were vaccinated with RAP (native or recombinant) were protected from a challenge of S. aureus [3]. This confirms the important role of RAP in S. aureus pathogenesis

and opens an opportunity for the development of a new vaccine.
Staphylococcal infections can be inhibited by RNAEQ inhibiting peptide (RIP). RIP inhibits Staphylococci from adhering and from producing toxins by interfering with the known function of SQS 1. RIP competes with RAP on inducing TRAP phosphorylation, thus leading to inhibition of the phosphorylation of TRAP [5]. This leads to a decrease in cell adhesion and biofilm formation, to inhibition of RNAIII synthesis and to suppression of the virulence phenotype [3]. The peptide RIP was first isolated from culture supernatants of coagulase negative Staphylococci that were identified with 99% certainty to be S. xylosus. The sequence of RIP was identified as YSPXTNF, where X can be a Cys, a Trp, or a modified amino acid, as well as peptide derivatives like YKPITN (Qov Y, et al., Peptides, 2001; 22:1609-1920 [13]. Synthetic RIP analogues were designed in their amide form as YSPWTNF(-NH2) and shown to be extremely effective in inhibiting RNAIII in vitro and in suppressing S. aureus infections in vivo, including: cellulitis (tested in mice against S. aureus Smith Diffuse), septic arthritis (tested in mice against S. aureus LS-1), keratitis (tested in rabbits against'S. aureus 8325-4), osteomyelitis (tested in rabbits against S. aureus MS), and mastitis (tested in cows against S. aureus Newbould 305, AE-1, and environmental infections) (Balaban N, et al, Peptides 2000; 21:1301-1311 [14], These findings indicate that RIP can serve as a useful therapeutic molecule to prevent and suppress Staphylococcal infections,
Biofilm-related infections
Bacteria that attach to surfaces aggregate in a hydrated polymeric matrix of their own synthesis to form biofilms. Formation of these sessile communities and their inherent resisknce to antimicrobial agents are at the root of many persistent and chronic bacterial infections (Costerton JW, et al., Science. 1999; 21:284:1318-1322 [15]). Biofilms develop preferentially on inert surfaces, or on dead tissue, and occur commonly on medical devices and
fragments of dead tissue such as sequestra of dead bone; they can also form on living tissues, as in the case of endocarditis. Biofilms grow slowly, in one or more locations, and biofilm infections are often slow to produce overt symptoms. Sessile bacterial cells release antigens and stimulate the production of antibodies, but the antibodies are not effective in killing bacteria within biofilms and may cause immune complex damage to surrounding tissues. Even in individuals with excellent cellular and humoral immune reactions, biofilm infections are rarely resolved by the host defense mechanisms. Antibiotic therapy typically reverses the symptoms caused by planktonic cells released from the biofilm, but fails to kill the biofilm. For this reason biofilm infections typically show recurring symptoms, after cycles of antibiotic therapy, until the sessile population is surgically removed from the body. It is therefore important to prevent biofilm formation rather than to try to eradicate biofilms once they have formed.
As shown in Table 1, many of biofilm-related nocosomial infections are caused by staphylococci [15],
Table 1. Partial list of human nosocomial infections involving biofilms.
(Table Removed)

RIP reduces bacterial adhesion
RIP decreased bacterial adhesion to eukaryotic cells (tested on HEp2 cells) and to plastic (tested on polystyrene, silicone and polyurethane (Balaban N, et al., Kidney Int. 2003; 63:340-345 [16]). RIP could be used to coat medical devices to prevent staphylococcal infections.
RIP deviates from AIP
RIP deviates from AIP in that RIP is a linear peptide [13] while AIP must contain a thiolactone structure to be active [11], the sensor of RIP is TRAP [5] while the sensor of AIP is AgrC [6], RIP inhibits both cell adhesion and toxin production [16] while inhibitory AIPs inhibit toxin production but activate cell adhesion (Vuong C, Saenz HL, Gotz F, Otto M. Impact of the agr quorum-sensing system on adherence to polystyrene in Staphylococcus aureus. J Infect Dis 2000; 182:1688-1693 [17].
Molecular mechanisms of RIP
While the specific molecular mechanisms are not fully understood, ilt is known that RIP inhibits agr expression (RNAII and RNAIII [13]) and therefore inhibits the production of toxins (Vieira-da-Motta 0, et al., Peptides, 2001; 22:1621-1628 [18]). It is known that RIP regulates cell adhesion in an agr-independent mechanism, because adhesion of agr null cells are equally inhibited in the presence of RIP as the wild type [16]. Because RIP inhibits TRAP phosphorylation [5] and TRAP has been demonstrated to be essential for cell adhesion, agr expression and pathogenesis (see detailed description below), RIP regulates S. aureus pathogenesis via TRAP, and perhaps via additional targets.
The mechanism through which RIP inhibits quorum sensing mechanisms, discussed above, involves inhibition of the phosphorylation of TRAP. There is evidence of the presence of TRAP and TRAP phosphorylation in S. epldermidis (see detailed description below), indicating that there is a similar quorum sensing mechanisms both in S. aureus and in S. epidermidis and the potential for RIP to interfere with biofilm formation and infections caused by both species. In addition, there is evidence that TRAP is conserved among all staphylococcal strains and species, and thus that other Staphyloccoal species have a similar quorum sensing mechanism as described above. As a result, RIP should be effective against any type of staphylococcus.
RAP and TRAP are target sites for therapy in many types of bacteria
Other infection-causing bacteria appear to have proteins with sequence similarity to TRAP. These bacteria include Bacillus subtilus, Bacillus anthracis, Bacillus cereus, Listeria innocua, Listeria monoctogenes (see detailed description of invention).
Still farther, RAP is an ortholog of the ribosomal protein L2, encoded by the rplB
gene. L2 is highly conserved among bacteria, including specifically Streptococcus ssp, Listeria spp, Lactococcus-spp, Enterococcus spp, Escherichia coli, Clostridium acetobtylicwn, and Bacillus spp. This finding indicates that treatment aimed at disturbing the function of RAP in S. aureus will also be effective in treating L2-synthesizing bacteria as well (see detailed description).
The invention features methods and compositions for treatment and/or prevention of infection by, or disease caused by infection with bacteria expressing RAP or TRAP or RAP-like or TRAP-like molecules (for example Staphylococcus spp., including S. aureus and S. epidermidis, Bacillus spp., including B. subtilus, B. cereus, B. anthracis, Listeria spp., including L. innocua and L monoctogenes, Streptococcus pyogenes, Lactococcus lactis, Enterococcusfaecalis, Escherichia coli, and Clostridium acetobtylicwn).
The invention features treatment methods including coating devices, injecting systemically (IV IP IM or SQ), applying topically, or taking orally.
One aspect of the invention is a composition containing a polypeptide containing an amino acid sequence comprising all or parts of the general formula Y(K or S) PXTNF (SEQ ID NOS: 1 and 2 in Serial No. 09/839,695), where any of the amino acids can be modified and where X can be C, W, or I. Pharmaceutical compositions are also provided in some embodiments.
A further aspect of the invention is a composition wherein the polypeptide comprises an amino acid sequence containing the general formula IKKY(K or S)PXTN, where X is C, W, I, or modified amino acids. Pharmaceutical compositions are also provided in some embodiments.
A further aspect of the invention is a method for treating a host for certain bacterial infections, wherein an antagonist of the RAP receptor is administered to the host. In some embodiments the host is a human patient. In further embodiments the host is an animal, such as but not limited to an experimental animal. In some embodiments the antagonist is a polypeptide, a peptidomimetic, or an antibody.
A further aspect of the invention is a nucleic acid molecule encoding a polypeptide of the invention. The nucleic acid molecule can be RNA or DNA or an antisense nucleic acid molecule. In an embodiment, the nucleic acid molecule comprises the nucleotide sequence of RIP, RAP or TRAP or their homologues.
In another aspect, the invention features an isolated native or recombinant RAP polypeptide, as well as nucleic acid encoding such RAP polypeptides.
In another aspect, the invention features an isolated native or synthetic RIP peptide, as well as nucleic acid encoding such RIP peptides.
In another aspect, the invention features an isolated TRAP polypeptide (native or recombinant, TRAP or TRAP homologues), as well as nucleic acid encoding such TRAP polypeptides.
Figure 1 is a multi sequence alignment analysis (ClustalW) of deduced RAP (RplB) amino acid sequences from the following bacteria: S. aureus RN6390B (AF205220), S. epidermidis RP62A (TIGR database), Streptococcuspyogenes Ml GAS (AE014137), Listeria monocytogenes EGD (AL591983), Lactococcus lactis (AE006438), Enterococcusfaecalis (TIGR database), Escherichia coll K12 (AE000408), Clostridium acetobutylicum (AE007808) and Bacillus subtilis (Z99104).

Figure 2 is a photograph of a gel showing rRAP (2Dg) (lanes 1,3) and culture supematants of S. aureits KN6390B containing native RAP (30 Dl of 30-fold concentration of postexponential supernatant proteins) (lanes 2,4) were applied to SDS 12.5% PAGE. Gel was western blotted, membrane stained in ponceau to visualize proteins (lanes 1,2), blocked in milk, and incubated with monoclonal anti-rRAP antibodies (ascites, diluted 1:1000). Bound antibodies were d'&scted by peroxidase-conjugated anti-mouse antibodies, visualized by chemiluminescence, and membrane autoradiographed (lanes 3,4).
Figure 3A is a graph showing that. S. aureus cells containing the rnaiii::blaZ fusion construct (2xl07 early exponential) were grown for 45min with increasing amounts of rRAP (0-lOODg). D-lactamase activity was determined and expressed as OD at 490/650nm. As a positive control, partially purified RAP (native, postexponential supematants of S. aureus RN6390B >10kDa that were applied to a lOlcD cutoff membrane).
Figure 3B is a photograph of a gel showing that cells (108 early exponential) were grown with (Lane 1) or without (lane 2) Img rRAP for 30min, cells were collected, Northern blotted, and the presence of RNA1II was detected using RNAIII-specific radiolabeled DNA. Membrane was autoradiographed and density of bands determined.
Figure 4 is a graph showing'the percent mortality of Balb/c native mice (control) or mice vaccinated with rL2, and challenged with 2 x 109 S. aureus.
Figure 5 is a graph showing the development of lesions in r.L2 vaccinated animals that survived a challenge of 2 x iOy S. aureiis.
Figure 6A is a grosvtli curve for cells grown from the early exponential phase for several Jus and their density determined (OD fiOOmn) at lime intervals. Circle: TRAP*. Square: TRAF.
Figure 6B is a photograph of a gell showing cell samples from each, growth phase (equivalent to ~3x H)1* cells) reflected in Figure 6A.. Cells were collected. Northern blotted, and ihc presence of RNAlll was detected using RNAHI-speeific radiolabeled DNA. Membrane was aulo radio graphed. S.

aureus TRAP+ (laues 1,2,3) a0d S. aureus TRAP" (laaes 4,5,6). Laues 1,4: Early exponential. Lanes 2,5: Midexponential. Lanes 3,6: Postexponential.
Figure 7A is a photograph that shows cells grown on a sheep blood agar plate to test for hemolysis. Hemolysis by TRAP+ is represented on the portion portion of the figure and TRAP" is represented on the bottom.
Figure 7B is a graph depicting adherence of early exponential S. aureus TRAP+ ajul TRAP" strains that were grown at 37°C for 4 hrs in polystyrene microtiter plates. Adherent bacteria were stained with safYanin and absorbance determined at 490tim.
Figure 8 is a graph depicting lesion size vs.-£ aureus 8325-4 parent strain (TRAP+) (left panel) and the S. aureus 8325-4 (TRAP") mutant strain (right panel).
Figure 9 is a multi-sequence alignment analysis (CluslalW) of deduced TRAP nmino acid sequences from staphylococcal strains aud species.
Figure 10 shows iiecondary structures predictions of TRAP and its homologues. Alignment of deduced arnino acid sequences of S. aureus TRAP (GenBank AF202641), L moiiocytogenes LMO22I3 (GenBank AL59I982) and B. sublilis YhgC (GenBank Z.99109) supplemented with their putative secondary structures predicted by use of the PCIPRED v.2.4 coils shown as solid lines, helices as horizontal cylinders and strands as arrows.
Figure 1. I shows gene region maps that were designed on the basis of DNA sequences obtained from the GenBank and corresponding genome project databases. The S. aweus imP (AF202641 and this study) and its hornologues in S. epidennidis (T1GR database and this study), Listcria monocytogenes (AL591982), L. innocua (AL596171), Bacillwt xnbtilis (Z991.09) and B. aiilhracis (TIGR database) are shown as gray arrows; inverted black triangles indicate a putative transcriptions) terminator. A distance (in IcB) between flanking liemE and arxB genes is shown within an interrupted two-head arrow. htiinE gene encodes an enzyme of the late step of the protohcme IX biosynthelic pathway, ecsBC genes encode
components of Hie protein secretion apparatus as well as secretory protein genes transcription in a coordinated fashion (B, subtilts); cadD gene is strongly similar to that of the 5. aureus plasraiid pRWOO I; pbpF gene codes for a penicillin-binding protein involved in the B. sublilis germination process; gsn&syhgB, yhfA and v/iaA encode hypothetical proteins of unknown functions.
Figure 12 is a photograph of a gel showing in vivo phosphorylation ofListeria iiioiioaylogenes strain .1001 (lane I), L. monocyiogenes strain ScotlA (lane 2, and.L ivanovii st;ain 3009, by growing early exponential cells with P32 for 1 hr. Total cell homogenate was separated by SDS PAGE and the gel autoradiographed.
Figure 13 is a photograph of a gel showing that RIP inhibits TRAP phosphorylation both in S. aiirewi and in 8. e.pidennidix. S. awe.ua (right panel) and S, Kpidermidis (left panel) were in vivo phosphorylated for llir in the presence or absence of RIP. Total cell homogenatc was separated by SDS PAGE and the gel autoradiographed.
Figure 14 A. is a graph depicting adherence in the presence of RIP (RJP-) and in the absence of RIP (RJP-I-). FITC-labeled bacterial cells (106 CPU) were applied to microtiter plates containing confluent 104 HaCat cells, in the presence or absence of 5ug RIP (RIP +/-). Cells were incubated for 30min at 37°C, washed in PBS and fluorescence at 485/530nm was determined.
Figure 1.4B is a graph depicting adherence in the presence of RIP (RIP-) and in the absence of RIP (RIP+), S. epidermidis were grown in polystyrene plates for 3 hrs, adherent bacteria were stained by safranin and absorbance at 490nrn was determined.
Table .1. Prevention of S. epidermic/Is infection using KIP-coated Dacron grafts in the presence or absence of local (A) or parcnteral (B) antibiotic prophylaxis.
Table 2. RIP prevents Dacron-graft associate S. epidermidit (A) and S. aureus (B) infections.
Diagram 1. Proposed .mechanism of .V. aureus path.ogenesi.is.
Before the present proteins, formulations and methods are described, it is to be understood that this invention is not limited to the particular compounds, characteristics and steps described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.
All publications and patents mentioned herein are incorporated herein by reference to disclose and describe the specific methods and/or materials in connection with which the publications and patents are cited. The publications and patents discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication or patent by virtue of prior invention. Further, the dates of publication or issuance provided may be different from the actual dates which may need to be independently confumed.
Generally, the nomenclature used hereafter, and the laboratory procedures in cell culture and protein biochemistry are those well known and commonly employed in the art. Generally, enzymatic reactions and column chromatography are performed according the manufacturer's specifications. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which mis invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described. For the purposes of the present invention, the foregoing terms are defined below. The terms "pharmaceutically acceptable" or "therapeutically acceptable" refer to a substance which does not interfere with the
effectiveness or the biological activity of the active ingredients and which is not toxic to the host or the patient.
The terms "encoding" or "encodes" refer generally to the sequence information being present in a translatable form, usually operably linked to a promoter. A sequence is operably linked to a promoter when the functional promoter enhances transcription or expression of that sequence. An anti-sense strand is considered to also encode the sequence, since the same informational content is present in a readily accessible form, especially when linked to a sequence which promotes expression of the sense strand. The information is convertible using the standard, or a modified, genetic code. See, e.g. Watson et sJ., (1987) The Molecular Biology of the Gene. (4th Edition), Vols. 1 & 2, Benjamin, Menlo Park, California
As used to refer to nucleic acid sequences, the term "homologous" indicates that two or more nucleotide sequences share a majority of their sequence. Generally, this will be at least about 70% of their sequence and preferably at least 95% of their sequence.
Another indication that sequences are substantially identical is if they hybridize to the same nucleotide sequence under stringent conditions (see, e.g., Sambrook etal, Molecular Cloning - A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1985). Stringent conditions are sequence-dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (TA for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically, stringent conditions will be those in which the salt concentration is at least about 0.2 molar at pH 7 and the temperature is at least about 60°C.
As used to refer to proteins, polypeptides, or peptides, which terms are used interchangeably here, the term "homologous" is meant to indicate two proteins orpolypeptides share a majority of their amino acid sequences. Generally, this will be at least 90% and usually more than about 95%. Homology for polypeptides or proteins is typically measured using sequence analysis software, see e.g. Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison Wisconsin 53705. Protein analysis software matches similar sequences using measure of homology assigned to various substitutions, deletions, and other modifications. Conservative substitutions typically include substitutions within the following groups glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
As used herein the term "isolated" is meant to describe a compound of interest (e.g., either a polynucleotide or a polypeptide) that is in an environment different from that in which the compound naturally occurs. "Isolated" is meant to include compounds that are within samples that are substantially enriched for the compound of interest and/or in which the compound of interest is partially or substantially purified.
The term "isolated" as applied to, for example, nucleic acids, means a nucleic acid subst'.atially separated from other macromolecules, cellular components, or DNA sequences which naturally accompany a native nucleic acid, e.g. ribosomes, polymerases, other nucleic acid sequences, and the like. The term includes a nucleic acid or polypeptide that has been removed from its naturally occurring environment, and includes recombinant or cloned DNA isolates and chemically synthesized analogues, and analogues biologically synthesized by heterologous systems. A substantially pure or biologically pure nucleic acid includes isolated forms of the nucleic acid.
The phrase "biologically pure" or "substantially pure" refers to material that is substantially or essentially free from components which normally accompany it as found in its native state, e.g., at least 60% free, preferably 75% free, and most preferably 90% freefrom other components with which it is naturally associated.
The term "recombinant" refers to a nucleic acid sequence which is not naturally occurnug, or is made by the artificial combination of two otherwise separated segments of sequence, i,e. by chemical synthesis, genetic engineering, and the like.
The term "treatment" or "treating" means any therapeutic intervention in a mammal, preferably a human or bovine, or any other animal capable of suffering from a bacterial infection of a type that could be prevented and/or treated as described herein. The range of such animals is considered to be quite broad, and includes species as disparate as humans and birds.
(i) prevention, that is, causing the clinical symptoms not to develop, e.g., preventing infection from occurring and/or developing to a harmful state;
(ii) inhibition, that is, arresting the development of clinical symptoms, e.g., stopping an ongoing infection so mat the infection is eliminated completely or to the degree that it is no longer harmful;
(iii) relief, that is, causing the regression of clinical symptoms, e.g., causing a relief of fever and/or inflammation caused by an infection; and
(iv) in prevention of biofilm formation (or microbiological evidence of bacteria (prior to actual symptoms)).
Treatment is generally applied to any mammal susceptible to of having a[n] bacterial infection caused by any of the species described herein (e.g., mammals, birds, etc.), generally a mammal, for example a human or bovine where the treatment can be applied for prevention of bacterial infection of for amelioration of active bacterial infection, where the bacteria is a Staphylococcus spp bacteria
The terms "effective amount" and/or "therapeutic amount" means a dosge sufficient to provide prevention and/or treatment for the disease state being treated. This will vary
depending on the patient, the disease and the treatment being effected. In the case of a bacterial infection, an "effective amount" is that amount necessary to substantially improve the likelihood of treating the infection, in particular that amount which improves the likelihood of successfully preventing infection or eliminating infection when it has occurred.
The term "protein" "polypeptidc" or "peptlde" as used herein is intended to encompass any amino acid sequence and include modified sequences (e.g., glycosylated, PEGylated, containing conservative amino acid substitutions, containing protective groups including for example 5-oxo-prolyl. amidation, etc.). The term includes naturally occurring (e.g.. non-recombinant) proteins, polypeptides, peptides, and oligopeptides, as well as those which are recombinantly or synthetically synthesized according to methods well known in the art. As used in connection with the present invention the term "protein" "polypepiide" or "peptide is specifically intended to cover naturally occurring molecules which occur in Staphylocaccus spp. and useful in treating infection or in generating antibodies useful in treating infection. Where "polypeptide" "protein" or "peptide" are recited herein to refer to an amino acid sequence of a naturally-occurring protein molecule, "polypeptide," "protein," or "peptide", and like terms are not meant to limit the amino acid sequence to the complete, native amino acid sequence associated with the recited protein molecule. In addition, the polypeptides and proteins of the invention, or fragments thereof, can be generated in synthetic form having D-amino acids rather than the naturally occurring L-amino acids.
"Polynucleotide" as used herein refers to an oligonucleotide, nucleotide, and fragments or portions thereof, as well as to peptide nucleic acids (PNA), fragments, portions or antisense molecules thereof, and to DNA or RNA of genomic or synthetic origin which can be single- or double-stranded, and represent the sense or antisense strand. Where "polynucleotide" is used to refer to a specific polynucleotide sequence (e.g. a RIP, TRAP or RAP protein-encoding polynucleotide or n RIP derivative, TRAP-like or RAP-like protein-encoding polynueleotide)), "polynucleotide" is meant to encompass polynucleotides that encode a protein that is functionally equivalent to the recited protein, e.g., polynucleotides that are degenerate variants (i. e., variants in nucleic acid sequence that encode the same amino acid sequence and exist due to the degeneracy of the genetic code), or polynucleotides that encode biologically active variants or fragments of the recited protein.
By "antisense polynucleotide" is meant a polynucleotide having a nucleotide sequence complementary to a given polynucleotide sequence including polynucleotide sequences associated with the transcription or translation of the given polynucleotide sequence (e.g, a promoter) and/or to a coding sequence of the given polynucleotide sequence, where the antisense polynucleotide is capable of hybridizing to a polynucleotide sequence. Of particular intere;t are antisense polynucleotides capable of inhibiting transcription and/or translation, either in vitro or in vivo.
"Peptide nucleic acid" as used herein refers to a molecule which comprises an oligomer to which an amino acid residue, such as lysine, and an amino group have been added. These small molecules, also designated anti-gene agents, stop transcript elongation by binding to their complementary (template) strand of nucleic acid (Nielsen et al 1993 Anticancer Drug Des 8:53-63).
The term "antibody" is meant to refer to an immunoglobulin protein which is capable of binding an antigen. Antibody as used herein is meant to include the entire antibody as well as any antibody fragments (e.g., F(ab)', Fab, Fv) capable of binding the epitope, antigen or antigenic fragment of interest. Preferred antibodies for assays and vaccines of the invention are immunoreactive or immunospecific for and therefore specifically and selectively bind to a protein of interest, e.g., an anti-RAP or TRAP antibody. The term "antibody" encompasses all types of antibodies, e.g., polyclonal, monoclonal, humanized, chimeric, and those produced by the phage display methodology. Particularly preferred antibodies of the invention areantibodies which have a relatively high degree of affinity for RAP or TRAP, An antibody of the invention is preferably imrnunoreactive with and immunospecific for a specific species, e.g., P .\P or TRAP obtained from Staphylococcus aureus.
"Antigenic fragment" of a protein is meant a portion of such a protein which is capable of binding an antibody.
By "binds specifically" is meant high avidity and/or high affinity binding of an antibody to a specific polypeptide, e.g., epitope of a protein, e.g., RAP protein. Antibody binding to its epitope on this specific polypeptide is preferably stronger than binding of the same antibody to any other epitope, particularly those which may be present in molecules in association with, or in the same sample, as the specific polypeptide of interest, e.g., binds more strongly to epitope fragments of a protein such as RAP so that by adjusting binding conditions the antibody binds almost exclusively to an epitope site or fragments of a desired protein.
By "detectably labeled antibody" is meant an antibody (or antibody fragment which retains binding specificity), having an attached detectable label. The detectable label is normally attached by chemical conjugation, but where the label is a polypeptide, it could alternatively be attached by genetic engineering techniques. Methods for production of detectably labeled proteins are well known in the art. Detectable labels known in the art include radioisotopes, fluorophores, paramagnetic labels, enzymes (e.g., horseradish peroxidase), or other moieties or compounds which either emit a detectable signal (e.g., radioactivity, fluorescence, color) or emit a detectable signal after exposure of the label to its substrate. Various detectable label/substrate pairs (e.g., horseradish peroxidase/diaminobenzidine, avidin/streptavidin, luciferase/luciferin), methods for labeling antibodies, and methods for using labeled antibodies are well known in the art (see, for example, Harlow and Lane, eds. (Antibodies: A Laboratory Manual (1988) Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, Ni;j.
The instant invention provides polypeptides for the prevention and treatment of infections caused by Staphylococcus spp. and other bacteria. These polypeptides contain the general formula Y(K or S)PXTNF (SEQ ID NOS: 1 and 2, in Serial No. 09/839,695), where X is C, W, or I. Amirto acids can be modified find can include D-amino acids. In a further . embodiment, the polypeptides may contain the general formula KKY(K or S) PXTN, where X is C, W, or I, or modified amino acids.
The use of nucleic acids encoding the polypeptides of the invention are also included in the scope of the invention. Such nucleic acids may be DNA, UNA, or antisense nucleic acids. The nucleic acid molecules of the invention may be provided as synthetic or purified, isolated molecules, including but not limited to "naked DNA"; in vectors such as but not limite,1 to plasmids or viruses, including expression vectors, or complexed to other compounds for administration. Such techniques are well known in the art. The polypeptides of the invention are preferably synthesized de novo by any technique commonly known in the art or may be encodeed by nucleic acid, such as RNA or DNA, delivered to the host.
The polypeptides of the invention are typically administered to hosts having or at risk of having a staphylococcal infection such as an S. aureus or S. epidermidis infection. The hosts are typically human patients. Animals may also be treated with the compositions of the invention, including but not limited to animals of commercial or veterinary importance such as cows, sheep, goats, rabbits and pigs, and experimental animals such as rats, mice, rabhils or guinea pigs.
As used herein, "therapeutic dose" is a dose that prevents, alleviates, abates, or otherwise reduces the severity of symptoms in a patient. The compositions of the invention may be used prophylactically to prevent staphylococcal infections or may be therapeutically used after the onset of symptoms. In some embodiments, induction of the fonnation of antibodies to the administered compound is desirable. In such instances, standard immunization protocols used in the art are preferred. The compositions administered for
immunization may optionally include adjuvants.
In some embodiments of the invention, antagonists of RAP or TRAP or RAT' receptor are provided. Without being limited to any one theory, RIP may function by competing with RAP for binding to the RAP receptor, thus acting as an antagonist of the RAP, TRAP and/or RAP receptor. Such antagonists include but are not limited to antibodies which specifically bind to RAP or TRAP; antibodies which specifically bind to a RAP or TRAP ligand; ligands for RAP TRAP or RIP; antisense nucleic acids; aid peptide, non-peptide, and peptidomimetic analogs of RAP, RIP, and their ligands.
Antibodies can be synthetic, monoclonal, or polyclonal and can be made by techniques well known in the art. For therapeutic applications, "human" monoclonal antibodies having human constant and variable regions are often preferred so as to minimize the immune response of a patient against the antibody. Such antibodies can be generated by immunizing transgenic animals which .contain human immunoglobulin genes. See Jakobovits et al. Ann NYAcad Sci 764:525-535 (1995). In connection with synthetic and semi-synthetic antibodies, such terms are intended to cover but are not limited to antibody fragments, isotype switched antibodies, humanized antibodies (e.g., mouse-human, human-mouse, and the like), hybrids, antibodies having plural specificities, fully synthetic antibody-like molecules, and the like.
As discussed below, antibodies can be screened for the ability to block the binding of a ligand to RAP, TRAP or RIP and/or for other properties, such as the ability to protect in vivo against bacterial infection.
In some embodiments of the invention, antisense nucleic acid molecules are used as antagonists of RAP pi1 TRAP. Antisense nucleic acid molecules are complementary
oligonucleotide strands of nucleic acids designed to bind to a specific sequence of nucleotides to inhibit production of a targeted protein. These agents may be used alone or in combination with other antagonists.
The antisense antagonist may be provided as an antisense oligonucleotide such as RNA (see, for example, Murayama et al. Antisense Nucleic Acid Drug Dev. 7:109-114 (1997)). Antisense sequences may also be provided in a viral vector, such as, for example, in hepatitis B virus (see, for example, Ji et al., J. Viral Hepat. 4:167-173 (1997)); in adeno-associated virus (see, for example, Xiao et al. Brain Res. 756:76-83 (1997)); or in other systems including but not limited to an HVJ(Sendai virus)-liposome gene delivery system ( see, for example, Kaneda et alAnn. N. Y. Acad. Sci. 811:299-308 (1997)); a "peptide vector" (see, for example, Vidal et al. CR Acad. 5rc//C/32):279-287 (1997)); as a gene in an episomal or plasmid vector (see, for example, Cooper et al Proc. Natl. Acad. Sci. U.S.A. 94:6450-6455 (1997), Yew etal. Hum Gene TJier. 8:575-584 (1997)); as a gene in a peptide-DNA aggregate (see, for example, Niidome et al. J. Biol Chan. 272:1530.7-15312 (1997)); as "naked DNA" (see, for example, U.S. 5,580,859 and U.S. 5,589,466); and inlipidic vector systems (see, for example, Lee et al. Crit Rev Ther Drug Carrier Syst. 14:173-206 (1997)).
'Candidate antagonists of the RAP, TRAP or RAP receptor can be screened for function by a variety of techniques known in the art and/or disclosed within the instant application, such as protection against S. aureus infection in a mouse model. A multitude of appropriate formulations of the antagonists of the invention can be found in the formulary blown to all pharmaceutical chemists; Remington's Pharmaceutical Sciences, (15th Edition, Mack Publishing Company, Easton, Pennsylvania (1975)), particularly Chapter 87, by Biaug, Seymour, therein. These formulations include for example, powders, pastes, ointments, jelly, waxes, oils, lipids, anhydrous absorption bases, oil-in-water or vvater-in-oil emulsions, emulsions carbowax (polyethylene glycols of a variety of molecular weights), semi-solid gels,and semi-solid mixtures containing carbowax.
The quantities of active ingredient necessary for effective therapy will depend on many different factors, including means of administration, target site, physiological state of the patient, and other medicaments administered. Thus, treatment dosages should be titrated to optimize safety and efficacy. Typically, dosages used in vitro may provide useful guidance in the amounts useful for in situ administration of the active ingredients. Animal testing of effective doses for treatment of particular disorders will provide further predictive indication of human dosage. Various considerations are described, for example, in Goodman and Oilman's The Plumnacological Basis of Therapeutics, 7th Edition (1985), MacMillan Publishing Company, New York, and Remington's Pharmaceutical Sciences 18th Edition, (1990) Mack Publishing Co. Easton Perm. Methods for administration are discussed therein, including oral, intravenous, intraperitoneal, intramuscular, transdermal, nasal, iontophoretic administration, and the like.
The compositions of the invention may be administered in a variety of unit dosage forms depending on the method of administration. For example, unit dosage forms suitable for oral administration include solid dosage forms such as powder, tablets, pills, and capsules, and liquid dosage forms, such as elixirs, syrups, and suspensions. The active ingredients may also be administered parenterally in sterile liquid dosage forms. Gelatin capsules contain the active ingredient and as inactive ingredients powdered carriers, such as glucose, lactose, sucrose, mannitol, starch, cellulose or cellulose derivatives, magnesium stearate, stearic acid, sodium saccharin, talcum, magnesium carbonate and the like.
Examples of additional inactive ingredients that may be added to provide desirable color, taste, stability, buffering capacity, dispersion or other known desirable features are red iron oxide, silica gel, sodium lauryl sulfate, titanium dioxide, edible white ink and the like. Similar diluents can be used to make compressed tablets. Both tablets and capsules can bemanufactured as sustained release products to provide for continuous release of medication over a period of hours. Compressed tablets can be sugar coated or film coated to mask any unpleasant taste and protect the tablet from the atmosphere, or enteric-coated for selective disintegration in the gastrointestinal tract. Liquid dosage forms for oral administration can contain coloring and flavoring to increase patient acceptance.
The concentration of the compositions of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected
The compositions of the invention may also be administered via liposomes. Lirosomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations the composition of the invention to be delivered is incorporated as .part of a liposome, alone or in conjunction with a molecule which binds to a desired target, such as antibody, or with other therapeutic or imraunogenic compositions. Thus, liposomes either filled or decorated with a desired composition of the invention of the invention can delivered systemically, or can be directed to a tissue of interest, where the liposomes then deliver die selected therapeutic/immunogenic polypeptide compositions.
Liposomes for use in the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, tcid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szokaet al. Ann. Rev. Biophys. Bioang. 9:467 (1980), U.S. Patent Nos. 4,235,871,4,501,728,4,837,028, and 5,019,369, incorporated herein by reference.A liposome suspension containing a composition of the invention may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the composition of the invention being delivered, and the stage of the disease being treated.
For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more compositions of the invention of the invention, and more preferably at a concentration of 25%-75%.
For aerosol administration, the compositions of the invention are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of compositions of the invention are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.
The constructs of the invention can additionally be delivered in a depot-type system, an encapsulated form, or an implant by techniques well-known in the art. Similarly, the constructs can be delivered via a pump to a tissue of interest.
Any of the foregoing formulations may be appropriate in treatments and therapies inaccordance with the present invention, provided that the active agent in the formulation is not inactivated by the formulation and the formulation is physiologically compatible.. PolydojuU and/or monoclonal antibodies to the polypeptides of the present invention may be prepared. The polypeplides of the invention thereof may be prepared as described herein, and coupled to a carrier molecule, for example keyhole limpet hemocyanin, and injected into rabbits at selected limes over several months. The rabbit sera may be tested for immunoreactivity to the polypeptides thereof, Monoclonal antibodies may be made by injecting mice with the polypeptides. Monoclonal antibodies maybe screened by methods known in the art, as are described, for example, in Harlow and Lane (1988) Antibodies: A laboratory manual. Cold Spring Harbor Press, New York, and Coding (1986) Monoclonal antibodies: Principles and Practice (2d ed.) Academic Press, New York. The antibodies will be tested for specific immunoreactivity with an epilope of the polypeptides. These antibodies will find use in diagnostic assays or as an active ingredient in a pharmaceutical composition.
For production of polyclonal antibodies, an appropriate target immune system is selected, typically a mouse or rabbit, although other species such as goats, sheep, cows, guinea pigs, and rats may be used. The substantially purified antigen is presented to the immune system according to methods known in the art. The immunological response is typically assayed by an immunoassay. Suitable examples include ELISA, RIA, fluorescent assay, or the like. These antibodies will find use in diagnostic assays or as an active ingredient in a pharmaceutical composition.
The present invention also provides a protein (RAP) isolated and purified from a non-pathogenic Staphylococclts spp.. The RAP protein has a molecular weight of about 33 kDa. In one embodiment, RAP is the protein encoded by a polynucleotide comprising the sequence of SEQ ID NO: 12 in Serial No. 09/839,695 and comprising an amino acid sequence of SEQ ID
NO: 13 in Serial No. 09/839,695. These sequences are provided in the Sequence Listing
ffi below.
RAP Nucleic Acid
The term "RAP gene" is used genetically to designate RAP genes and their alternate forms. "RAP gene" is also intended to mean the open reading frame encoding specific RAP proteins, and adjacent 5' and 3' non-coding nucleotide sequences involved in the regulation of expression (e.g., promoter region). The gene may be introduced into an appropriate vector for extrachromosomal maintenance or for integration into the host, in one embodiment the RAP gene comprises the sequence of SEQ ID NO: 12 in Serial No. 09/839,695.
,RAP regulatory sequences may be used to identify cis acting sequences required for transcriptional or translational regulation of RAP expression, especially at different stages of grow£'(e.g., early, mid, and late log phase), and to identify cis acting sequences and trans acting factors that regulate or mediate RAP expression. Such transcriptional or translational control regions may be operably linked to a RAP coding sequence or other coding sequence.
The nucleic acid compositions used in the subject invention may encode all or a part of the RAP protein as appropriate. Fragments may be obtained of the DNA sequence by chemically synthesizing oligonucleotides in accordance with conventional methods, by restriction enzyme digestion, by PCR amplification, etc. For the most part, DNA fragments will be of at least about ten contiguous nucleotides, usually at least about 15 nt, more usually at least about 18 nt to about 20 nt, more usually at least about 25 nt to about 50 nt. Such small DNA fragments are useful as primers for PCR, hybridization screening, etc. Larger DNA fragments, i.e. greater than 100 nt ore useful for production of the encoded polypeptide. For use in amplification reactions, such as PCR, a pair of primers will be used.
The exact composition of the primer sequences is not critical to the invention, but for most applications the primers will hybridize to the subject sequence under stringent conditions, as known in the art. It is preferable to choose a pair of primers that will generate an amplification product of at least about 50 nt, preferably at least about 100 nt. Algorithms for the selection of primer sequences are generally known, and are available in commercial software packages. Amplification primers hybridize to complementary strands of DNA, and will prime towards each other.
The RAP gene and RAP coding sequence are isolated and obtained in substantial purity, generally as other than an intact bacterial chromosome. Usually, the DNA will be obtained substantially free of other nucleic acid sequences that do not include a RAP sequence or fragment thereof, generally being at least about 50%, usually at least about 90% pure a;n.d are typically "recombinant", i.e. flanked by one or more nucleotides with which it is not normally associated on a naturally occurring chromosome.
The DNA sequences are used in a variety of ways. They may be used as probes for identifying RAP coding sequences of other strains of Staphylococcus or of other bacteria. Homologues isolated from other stains, species, or genera generally have substantial sequence similarity to one another, i.e. at least 75%, usually at least 90%, more usually at least 95% sequence identity. In general, RAP-encoding sequences of the invention (including hcmologoues, variants, etc.) are characterized by having a sequence identity greater than at least about 65%, preferably at least about 75%, more preferably at least about 85%, and can be greater than at least about 90% or more as determined by the Smith-Waterman homology search algorithm as implemented in MPSRCH program (Oxford Molecular). For the purposes of this invention, a sequence identity is calculated using the Smith-Waterman algorithm as follows: Global DNA sequence identity must be greater than 65% as determined by the Smith-Waterman homology search algorithm as implemented in MPSRCH program (OxfordMolecular) using an affine gap search with the following search parameters: gap open penalty, 12; and gap extension penalty, 1.
Nucleic acids having sequence similarity can also be detected by hybridization under low stringency conditions, for example, at 50°C and 6XSSC (0.9 M saline/0,09 M sodium citrate) and remain bound when subjected to washing at 55°C in 1XSSC (0.15 M sodium chloride/0.015 M sodium citrate). In addition, sequence identity may also be determined by hybridization under high stringency conditions, for example, at 50°C or higher and 0.1XSSC (15 inM salme/0.15 mM sodium citrate). By using probes, particularly labeled probes of DNA sequences, one can isolate homologous or related genes. It may also be possible to identify homologs of RAP from mammalian sources.
The RAP-encoding DNA may also be used to detect expression of the gene in a biological specimen. Methods and materials for probing a sample for the presence of particular nucleotide sequences are well established in the literature and do not require elaboration here. mRNA is isolated from a cell sample. mRNA may be amplified by RT-PCR, using reverse transcriptase to form a complementary DNA strand, followed by polymerase chain reaction amplification using primers specific for the subject DNA sequences. Alternatively, rnRNA sample is separated by gel electrophoresis, transferred to a suitable support, e.g. nitrocellulose, nylon, etc., and then probed with a fragment of the subject DNA as a probe. Other techniques, such as oligonucleotide ligation assays, in situ hybridizations, and hybridization to DNA probes arrayed on a solid chip may also find use. Detection of mRNA hybridizing to an RAP sequence is indicative of RAP gene expression in the sample.
The RAP nucleic acid sequence may be modified for a number of purposes, particularly where they will be used intracellularly, for example, by being joined to a nucleic acid cleaving agent, e.g. a chelated metal ion, such as iron or chromium for cleavage of the gene; or the like.The RAP coding sequence and/or promoter sequence may be mutated in various ways knowi. in the art to generate targeted changes in promoter strength, sequence of the encoded protein, etc. The DNA sequence or product of such a mutation will be substantially similar to the sequences provided herein, i.e. will differ by at least one nucleotide or amino acid, respectively, and may differ by at least two but not more than about ten nucleotides or amino acids. The sequence changes may be substitutions, insertions or deletions. Deletions may further include larger changes, such as deletions of a domain. Other modifications of interest include production of fusion proteins (e.g., with green fluorescent proteins (GFP), luciferase, and the like).
Techniques for in vitro mutagenesis of cloned genes are known. Examples of protocols for scanning mutations may be found in Gustin et al., 1993 Biotechniques 14:22; Barany, 1985 Gene 37:111-23; Colicelli et al., 1985 Mol Gen Genet 199:537-9; and Prentki et al., 1984 Gene 29:303-13. Methods for site specific mutagenesis can be found in Sambrook et al., 1989 Molecular Cloning: A Laboratory Manual, CSH Press, pp. 15.3-15.108; Weiner et al., 1993 Gene 126:35-41; Sayers etal., 1992 Biotechniques 13:592-6; Jones and Winistorfer, 1992 Biotechniques 12:528-30; Barton et al., 1990 Nucleic Acids Res 18:7349-55; Marotti and Tomich, 1989 Gene Anal Tech 6:67-70; and Zhu 1989 Anal Biochem 177:120-4.
RAP Protein
RAP protein can be produced by any suitable means, e.g., by isolated from a bacteria that naturally expresses RAP, by recombinant means (e.g., by expression of a polynucleotide having a sequence of SEQ ID NO: 12 in Serial No. 09/839,695), by synthetic means, and the like.
In one embodiment, RAP is isolated directly from a strain of Staphyhcoccus producing RAP, e.g., S. aureus. Typically, wild type cells are collected from postexponential
culture-broth. Cells are then centriruged and the supernatant subjected to purification by, for example, filtration followed by lyophilizaetion, resuspension in water, and further purification.
The staphylococci bacterium from which RAP may be isolated may include, but is not necessarily limited to, S. aureus, S, capitus, S. warneri, S. capitis, S. caprae, S. carnosus, S. saprophyticus, S. chronii, S. simulans, S. caseolyticus, S. epidermidis, S. haemolyticus, S. hom'mis, S. hyicus, S. kloosii, S. lentus, S. lugdunensis, S. scruri, S. simulans, and S. xylosus. Preferably RAP is isolated from S. aureus.
In another embodiment, RAP-encoding nucleic acid is employed to synthesize full-length RAP protein or fragments thereof, particularly fragments corresponding to functional domains (e.g., phosphorylation sites that interact with RAP, etc.}; and including fusions of the subject polypeptides to other proteins or parts thereof. For expression, an expression cassette may be employed, providing for a transcriptional and translational initiation region, which may be inducible or constitutive, where the coding region is operably linked under the transcriptional control of the transcriptional initiation region, and a transcriptional and translational termination region. Various transcriptional initiation regions may be employed that are functional in the expression host.
The polypeptides may be expressed in prokaryotes or eukaryotes in accordance with conventional ways, depending upon the purpose for expression. For large scale production of the protein, a unicellular organism, such as E. coli, B. subtilis, S. cerevisiae, or cells of a higher organism such as vertebrates, particularly mammals, e.g. COS 7 cells, may be used as the expression host cells. Alternatively, RAP fragments can be synthesized.
With the availability of the polypeptides in large amounts, by employing an expression host, RAP protein can be isolated and purified in accordance with conventional ways, e.g., using HPLC, exclusion chiomatography, gel electrophoresis, affinity
chroraatography, or other purification technique. The purified protein will generally be at least about 80% pure, preferably at least about 90% pure, and may be up to and including 100% pure.
The RAP proteins (native., recombinant or synthetic) can be used for the production of antibodies, where short fragments provide for antibodies specific for the particular polypeptide, and larger fragments or the entire protein allow for the production of antibodies over the surface of the polypeptide. Antibodies may be raised to the wild-type or variant forms of RAP. Antibodies may be raised to isolated peptides corresponding to these domains, or to the native protein, e.g. by immunization with cells expressing RAP, immunization with liposomes having RAP protein inserted in the membrane, etc.
Anti-RAP antibodies
The present invention also provides an antibody that specifically binds and is irnmunoreactive with RAP. The antibody may be monoclonal, polyclonal or humanized, and is prepared using methods well known in the art. In general, antibodies are prepared in accordance with conventional ways, where the protein or an antigenic portion thereof is used as an immunogen, by itself or conjugated to known immunogenic carriers, e.g. KLH, pre-S HBsAg, other viral or eukaryotic proteins, or the like. Various adjuvants may be employed, with a series of injections, as appropriate. For monoclonal antibodies, after one or more booster injections, the spleen is isolated, the lymphocytes immortalized by cell fusion, and then screened for high affinity antibody binding. In a preferred embodiment, the spleen or lymph node cells and myeloma cells are mixed in about 20:1 to about 1:1 ratio, but preferably in about 2:1 ratio. It is preferred that the same species of animal serve as the source of somatic and myeloma cells used in the fusion procedure, where the animal is chosen from rat, mouse, rabbit, cow, chicken, turkey, or man. The fusion of the somatic and myeloma cells
produces a hybridoma, which is grown in culture to produce the desired monoclonal antibody by standard procedures. For further description, see, for example, Monoclonal Antibodies: A Laboratory Manual. Harlow and Lane eds., Cold Spring Harbor Laboratories, Cold Spring Harbor, New York, 1988. If desired, the mRNA encoding the heavy and light chains may be isolated and mutagenized by cloning in E. coli, and the heavy and light chains mixed to further enhance the affinity of the antibody. Alternatives to in vivo immunization as a method of raising antibodies include binding to phage "display" libraries, usually in conjunction with in vitro affinity maturation.
The polyclonal antibodies of the present invention may be produced by injecting a rat, a mouse, a rabbit, a cow, a chicken, or a turkey with RAP to initiate an immunogenic response. They can be polyclonal or monoclonal, and can be engineered or synthesized. RAP may be coupled to a protein carrier such as deyhole limpet hefflocyanin (KLH) or bovine serurii albumin (BSA). An adjuvant may also be used. After a suitable amount of time to establish a high-titer of anti-RAP antibodies, the serum or eggs are collected. The presence of antibody in the serum or eggs may be tested by radioimmunoassay (RIA), by enzyme-linked immunosorbent assay (ELISA), or by immunoprecipitation. The immunoglobulins may be isolated by the sequential precipitation methods, by conventional methods of "salting out" the protein fractions from a salt solution, or by chromalographical methods well known to those skilled in the art.
RAP (Rplff) sequences in bacteria
RAP was purified from culture supernatants of S. aureus RN6390B, and the NHj-terminal sequence of RAP was determined to be IKKYKPITN (Balaban N, et al. Science 2000,287: 39la [ 18]. This sequence was compared (TblastN algorithm) to
several S. aureus databases where only one ORF was found to match strongly to the above peptide sequence. This ORF' encodes a putative 277 amino acid protein, which is an ortholog of L2 (or RplB) sequences (Ban N, et al., Science 2000, 289: 905-920 [19],..
The corresponding gene in S. aureus RN6390B was amplified by PCR and sequenced (OenBank accession number AF205220). S. aureus putative RplB is highly homologous to RplB in other bacteria (Fig. 1). Furthermore, its sequence was compared to that of other S. aureus genome sequences available, and it was found to be totally conserved among strains (data not shown).
Production of recombinant RAP (termed either rRAP or rL2) To produce rRAP, forward and reverse primers corresponding to the 5' and 3' ends of rap (rplB) gene with added restriction sites were designed. These primers were used to amplify the complete rplB gene by PCR, using S. aureus RN6390B chromosomal DNA as a template. Amplified DNA was digested and ligated into the corresponding sites of pET14b vector (Novagen, WI) that possess a six histidine tag at the 5' end of the inserted gene. Plasmid containing rap (pET2-5) was used to transform E. coli BL-21(DE3)/pLysS. Cells were induced and harvested, and recombinant His-rRAP protein was isolated using a nickel column and his tag removed by thrombin.
Specifically, to produce rL2, forward and reverse primers corresponding to the 5' and 3' ends of rap gene with added 5' Ndel and 3' BamHI restriction sites were designed based on the sequence of rap (underlined). These primers, 5' GAA TTC CAT ATG GCT ATT AAA AAG TAT AAG 3' (nucleotides 1-21 (SEQ ID NO: 14 in Serial No. 09/839,695)) and 5' CGC GCG GAT CCT TAT TTT TTC.TTA CGT CCACG 3' (complement of nucleotides 840-819 (SEQ ID NO: 15 in Serial No. 09/839,695)), were used amplify the complete rap gene by
PCR, using S. aureus chromosomal DNA as a template. Amplified DNA was digested by Ndel and BamHI and ligated into the corresponding sites of pET14b vector (Novagen, WI) that possess a six histidine tag at the 5' end of the inserted gene. Plasmid containing rap (pET2-5) was used to transform E. coli BL-21(DE3)pLysS (SBpET2-5). Induction of synthesis of recombinant protein was carried out by addition of ImM IPTG to the culture and incubation for 3 hours. Cells were harvested and washed once with 50mM Tris buffer pH 7.9. Recombinant His-rRAP protein was isolated using a nickel column according to the manufacturer's instructions with some modifications (Xpress Systems Protein Purification, Invitrogen, CA). Cell pellet of 50ml was resuspended in 10ml binding buffer (20mM sodium phosphate pH 7.8+Q.5M NaCl) and sonicated (for 2 cycles of 15 sec pulses at the maximal level with 30 sec intervals) and then spun in a microcentrifuge. The supernatant was loaded onto the pre - equilibrated nickel column.
Prior to loading, the column containing chelated Sepharose beads was loaded with a charging buffer containing 50 mM NiCl, and equilibrated with binding buffer. The column was washed three times with five volumes of binding buffer, followed by three washes with five volumes of 20mM sodium phosphate+0.5M NaCl pH 7.8, then with buffer adjusted to pH 6. Recombinant protein was sequentially eluted from the column using 0-5M imidazole. His tag was removed by thrombin.
Monoclonal anti-rRAP antibodies recognize native RAP Monoclonal antibodies were produced from mice that were primed by rRAP. Hybridoma supernatants were tested by ELISA for the presence of specific antibodies against injected antigen. Positive hybridomas were cloned and used to raise ascites. To test if antibodies to recombinant protein recognize the native molecule, rRAP and partially purified native RAP (postexponential supernatants of wild type S. aureus RN6390 >10kDa) were
applied to SDS 12.5% PAGE, western blotted, and membrane stained in ponceau (Fig. 2 lanes 1,2). The membrane was blocked, and incubated with ascites made of a positive anti rRAP hybridoma (diluted 1:1000). Bound antibody was detected using peroxidase-conjugated anti mouse IgG, and visualized by chemilunu'nescence (Fig. 2 lanes 3,4). As shown in Fig. 2, monr"lonal antibodies raised against rRAP specifically recognize the native molecule that is secreted to the supernatant (Fig. 2 lane 4).
Recombinant RAP is active and induces RNAIII synthesis
To test if rRAP is active and can induce RNAIII synthesis, S. aureus cells containing rnaiii::blaZ fusion construct were incubated with increasing amounts of rRAP. As controls, cells were incubated only with growth medium (negative control). RNAIH (as D-lactamase activity) was detected by the addition of nitrocefin, a yellow substrate that turns pink in the presence of D-lactamase. This method is useful when the difference between experimental and control groups is at least twice, and one group turns pink while the other remains yellow. As shown in Fig. 3A, rRAP activates RNAIII synthesis in a concentration dependent manner, reaching threshold levels at 2.25nmole/107 bacteria, Activation of RNAIII by recombinant RAP was similar to that of partially purified RAP. The increase in RNAIII synthesis (D lactamase activity) in the presence of 2.25nmole rRAP is significant (P TRAP
TRAP is necessary for S, aureus pathogenesis
RAP has been shown to induce and RIP has been shown to inhibit TRAP phospuorylation [5]. To show that TRAP is important for S. aureus pathogenesis, the traP gene was disrupted in S. aureus 8325-4 and the parent strain (TRAP+) and the mutant strain (TRAP") were tested for growth, RNAIII synthesis, toxin production and pathogenesis. To test for cell growth and RNAIII synthesis, cells were grown from the early to the post exponential phase of growth. At time intervals cell density was determined and cell samples from each growth phase were collected, Northern blotted, and the presence of RNAIII was detected using RNAIII-specific radiolabeled DNA. As shown in Fig. 6A, no difference in cell growth was observed between TRAP+ and TRAP" strains. The synthesis of RNAIII in the TRAP-*- strain was observed from the midexponential phase but was absent in the TRAP" strain (Fig. 6B), confirming that TRAP is an important factor in the induction of RNAIII synthesis'.
RNAIII is known to upregulate the production of many of the toxins produced by S. aureus, some of which are hemolysins [2J. To test for the production of hemolysins, the TRAP+ and TRAP" strains were grown on a sheep blood agar plate overnight at 37°C and then at 4°C (to test for both D and 0 hemolysins). As shown in Fig. 7A, no hemolysis was observed in the TRAP" strain, confirming that TRAP is an important factor in toxin production.
To test whether TRAP is important for biofilm formation, the TRAP+ and TRAP" strains were grown in polystyrene wells and adherent bacteria was stained by safranin. As shown in Fig. 7B, safranin staining was greatly reduced in the TRAP" strain, suggesting that TRAP is an important factor in cell adhesion and biofilm formation.
To test the importance of TRAP in S. aureus pathogenesis in vivo, the TRAP+ and TRAP" strains were injected subcutaneously into mice and animals followed for mortality,

the development of lesion and overall health. As shown in Fig. 8, all animals (n=10) that were injected with 4xl08 CPU (of TRAP+ that were grown on a plate) developed a lesion with aa average size of 1.74 cm2. All animals (n=5) that were injected with 6xl09 CPU (of TRAP+ that were grown on a plate) developed a lesion with an average size of 9.4 cm2. Of 8 animals (n=8) that were injected with 1.3xl09 CPU (TRAP+ that were grown in culture (*)), 4 died within the first 24 hrs and the rest developed a large lesion, with an average size of 8.63 cm2. On the other hand, all animals that were injected with the TRAP" strain seemed perfectly healthy, including the few that developed a very small lesion. Specifically, none of the animals (n=10) that were injected with 3xl08 CPU of TRAP" that were grown on a plate, developed a lesion. All animals (n=5) that were injected with 2.6xl09 CPU of TRAP" that were grown on a plate developed a small lesion with an average size of 0.62 cm2. Of the animals (n=8) that were injected with l.SxlO9 CPU of TRAP" that were grown in culture (*), 7 animals developed no lesion at all and^one animal developed a small lesion of 0.4 cm2 (average size of 0.05 cm2). The differences in lesion size between the animals that were injected with the TRAP+ or TRAP" strains is significant (p Amino acid sequence analysis of TRAP
The traP gene in various clinical isolates of S. aureus and S. epidermidis was amplified by PCR, and its sequence determined. Comparison of these sequences to BLAST searches in different databases (including the NCBI Microbial Genomes Databases [http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome,html]) indicates that TRAP is unique to staphylococci. Comparison of the deduced amino acid sequences of the S. aureus and S, epidermidis TRAP proteins shows that they are highly conserved among
staphylococci. Multi sequence alignment analysis (ClustalW) of S. aureus TRAP protein sequence's from the various strains indicates that its sequence is divided into two sub-groups (Fig. 9). Group I includes TRAP in 8325, which is identical to TRAP in COL, MSSA476, Mu50/ATCC700699 and N315 (16) and our clinical nare-isolates # 7 and 11. Group II includes TRAP in our clinical nare-isolates 12 and 15 and MRSA252 (Sanger Centre Database). TRAP of Group I is ~97% identical to that of Group II (an £-value determined with the blast? algorithm is 2e-84). Similarity of both group I TRAP and Group II TRAP sequences to that of 5. epidermidis is approximately 86% (an £-value is 9e-65).
S, aureus clinical isolate #12 has an insertion of IS1181 exactly in front of the TRAP stop codon (GenBank accession number AJ489447). Insertion of IS1811 shifted the native traP stop codon but introduced another stop codon 27 bp downstream, that elongated TRAP from 167 to 176 AA (TRAP-t-GSSSFMVGR) (Fig. 9), Like other clinical or lab strains, TRAP -s phosphorylated and RNAIII is expressed in strain isolate # 12, suggesting that the insertion element does not disrupt its function (not shown).
Secondary structure predictions of TRAP
TRAP is highly unique to staphylococci, but has some sequence similarity to the hypothetical protein YhgC protein in Bacillus subtilis (GenBank Accession Number Z99109) (an £-value is 9e-15). Interestingly, in addition to Bacillus subtilis, among more than 160 eubacterial genomes, only in Bacillus anthracis which is 97% identical to that of B. cereus (TIGR database), Listeria innocua and L monocytogenes ORFs could be identified which have some sequence similarity to TRAP (an E'-values are 0.005, 0.035 and 0.1, respectively). Like TRAP, all ORFs are of exactly 167 AA except for YhgC, which is 166 AA (Fig. 10).
The secondary structure of these proteins was predicted using the protein structure prediction server The PCIPRED v.2.4 [http://bioinf.cs.ucl.ac.uk/psiform.html/]. Interestingly,
I although the sequence similarity of these QRFs is very low, their predicted secondary
structures are very similar to that of TRAP (Fig. 10).
Chromosomal organization of the S. aureus TRAP gene region and comparison with other pram-positive eubacteria.
The same organization of the TRAP gene region is found in all Staphylococcus spp (in both S. aureus and S. epidermidis) genomes (Fig. 11). The TRAP gene is flanked by two polycistronic operons; one of them (upstream oftraP) encodes enzymes of the late step of the protoheme IX biosynthetic pathway (hemEHY genes), the second (downstream oftraP) codes for a putative multi protein transporting system (ecsAB(C) genes). The direction of the traP gene transcription is opposite to both hem and ecs operons. The same organization is found also in yhgC region in B. subtilis, B. anthracis and in the TRAP-like ORFs in Listeria (Fig. 11). These results suggest that TRAP represents a class of signal transducers in bacteria and that it can be a target site for therapy in many bacterial species in addition to staphylococci.
Phosphorylation of TRAP and TRAP like molecules and inhibition of TRAP phosphorylation by RIP
Because TRAP-like molecules are found in other bacterial species in addition to staphylocopcci, we tested whether they can undergo phosphorylation. We grew various strains of Listeria (L. monocytogenes andL. ivanovii) and various strains of Bacillus anthracis, B. subtilis and B. cereus) with P32, and tested for phosphorylation of TRAP (21kDa) by SDS PAGE followed by autoradiography. As shown in Fig. 12 for Listeria spp, a 21kDa protein was in vivo phosphorylated, as expected. Similar results were obtained for Bacillus spp. (not shown). These results suggest that pathogenesis may also be regulated via TRAP piiosphorylation in bacteria expression TRAP-like proteins.
To test for TRAP phosphorylation in S. epidermidis, in vivo phosphorylation assays were carried out as described for S. aureus [5]. Briefly, early exponential S. epidermidis were grown in the presence of phosphate-free buffer supplemented with radiolabeled orthophosphate with or without RIP (10Qg/107 cells). After a Ihr incubation period, the cells were collected by centrifugation, treated with lysostaphin followed by the addition of sample buffer, and total cell homogenate was applied without boiling to 15% SDS PAGE and the gel autoradiographed. The same experiment was carried out on 6390B S. aureus cells as a positive control. Results (Fig. 13) show that TRAP phosphorylation can be inhibited by RIP also hi S. epidermidis. These results are not surprising in view of the fact that TRAP is found also in S. epidermidis, and they show that TRAP phosphorylation and expression is important for staphylococcal pathogenesis. Because its sequence is highly conserved among staphylococcal strains and species and because its secondary structure is similar to many TRAP-like molecules in other bacteria, TRAP can be a target site for therapy in many bacterial species in addition to staphylococci.
RIP (native or synthetic, YSPWTNF or derivatives) has been shown not only to inhibits RNAII and RNAIII synthesis and thus to inhibit toxin production [13,18] but have also been shown to inhibits S. aureus adherence to human cells and to inhibits the formation of biofilm on plastic [16]. Virulence of S. epidermidis is also often associated with their ability to adhere to host cells and to form biofilm on medical devices. To test whether RIP can prevent S. epidermidis from colonizing host cells and therefore be a candidate for therapy and prevention, FITC-labeled S. epidermidis were incubated in the presence or absence of RJP with a confluent layer of keratinocytes (HaCat cells) for 30min. As shown in Fig. 14A, RIP significantly (pO.05) reduced S. epidermidis adherence to HaCat cells.
To test whether RIP reduces adherence and biofilm formation of S. epidermidis to plastic, early exponential S. epidermidis were grown for 3 hrs in rrticrotiter plates made of polystyrene, and adherent cells were stained with safranin. These experimental conditions allow for biofilm to be formed (as observed by atomic force microscopy, not shown). As shown in Fig. 14B, RIP significantly reduced the number of cells that adhered to the plastic. These results clearly demonstrate that RIP inhibits the adhesion of S. epidermidis to host cells and to plastic in vitro.
RIP can protect from a graft-associated infections and is svnerzistic to antibiotics
To test if RIP can prevent graft-associated infections, rat-graft model was used.
Induction of graft-associated infection
Rats (Wistar adult males (300-350g), n=15/experimental group) were anaesthetized, hair on their back shaved and the skin cleansed with 10% povidone-iodine solution. A subcutaneous pocket was made on the side of the median line by a 1.5 cm incision. Aseptically, 1 cm2 sterile collagen-sealed Dacron graft (AlbograftTM, Sorin Biomedica Cardio, S.p.A., Saluggi VC, Italy) was implanted into the pocket. Immediately prior to implantation, the Dacron grafts were soaked for 20 min in sterile solutions of 10 mg/1 RIP in saline or saline only or inactive RIP peptide analogue (YKPETNF) as controls, with or without antibiotics (mupirocin lOOmg/1, quinupristin-dalfopristin 50 mg/1, levofloxacin 30mg/l, rifampin 5mg/l). Pockets were closed by skin clips and 1ml sterile saline solution with or without 2xl07 bacteria was inoculated onto the graft surface using a tuberculin syringe to create a subcutaneous fluid-filled pocket. Some of the animals that had grafts soaked only with RIP or saline were injected intraperitoneally with antibiotics (oefazolin 30mg/kg, imipenem 30mg/kg, teicoplanin lOmg/kg, levofloxacin lOmg/kg), Grafts were explanted 7
days following implantation. Estimated RIP that adhered to the graft was 10-260g.
Assessment of graft infection
The explanted grafts were placed in sterile tubes, washed in sterile saline solution, placed in tubes containing 10 ml of phosphate-buffered saline solution and sonicated for 5 min to remove the adherent bacteria from the grafts. Quantitation of viable bacteria was performed by culturing serial 10-fold dilutions (0.1 ml) of the bacterial suspension on blood agar plates. All plates were incubated at 37°C for 48 h and evaluated for the presence of the strain. Bacteria were quantitated by counting the number of colony forming unites (CPU) per plate. To determine if bacteria were efficiently removed from the graft, washed and sonicated grafts were observed under a Nikon Eclipse E 600 optical microscope (Nikon Y-THS, Japan).
Statistical analysis
Quantitative culture results of the in vivo experiments were presented as mean D SD of the mean. Comparisons of the results were performed by the analysis of variance (ANOVA) on the log-transformed data. Statistical analysis was performed for in vitro adhesion assays using Student's t-Test by Microsoft Excel (Microsoft, WA). Significance was accepted when the P value was D 0.05.
To test if RIP can prevent graft-associated infections, Dacron grafts were coated with or without RIP, and with or without various types of antibiotics (for local prophylaxis experiments). Coated grafts were implanted in rats, bacteria injected into the implants, implants removed after a week, and bacterial load determined. Alternatively, Dacron grafts were first coated with RIP, bacteria injected, and antibiotics were administered by the intraperitoneal route (for parenteral prophylaxis experiments). As a negative control, grafts
were implanted without local or pareuteral RIP/antibiotics prophylaxis and no bacteria were injected. As a positive control, grafts were implanted, bacteria were injected, but no RIP/antibiotics prophylaxis was given. As a negative control to RIP, an inactive form of RIP analogue (YKPETNF) was used instead of RIP.
The results (table 1) clearly indicate that RIP reduces bacterial load of all strains tested by log 3, and that when it is applied together with some antibiotics, it can eliminate bacterhl load by 100%. Specifically,
1) None of the animals included in the uncontaminated negative control group had
microbiological evidence of graft infection.
2) All 15 rats included in the contaminated untreated positive control group
demonstrated evidence of graft infection, with quantitative culture results showing 6.8 D 10^
1.9 D 106 CPU/ml, 8,1 D 106 +/- 2.2 D 106 CPU/ml, 7.3 D 10fi +/- 6.4 D 105 CFU/ml for the
inoculated OISE strain, MRSE strain and MSSE strain, respectively. Grafts coated with the
inactive RIP peptide analogue demonstrated evidence of graft infection similarly to untreated
controls, with quantitative culture results showing 6.52 D 106 +/- 3 D 106 CFU/ml, 7.08 0
106 +/- 2.1 D 106 CFU/ml, 5.4 D 106 +/- 8 D 105 CFU/ml for the inoculated GISE strain,
MRSE strain and MSSE strain, respectively.
3) All groups with 10 mg/1 RIP-soaked Dacron grafts showed evidence of
decreased intensity of staphylococcal infection compared to the untreated control group, with.
6.2 D 104 + 2.0 D 104CFU/mL (p 103 + 2.3 D 103 CFU/mL (pO.OOl), for inoculated GISE strain, MRSE strain and MSSE
strain, respectively.
4) In the rats inoculated with GISE, RIP graft treatment was inhibiting bacteria
better than the parenteral antibiotics prophylaxis (>10 to 100 folds), (see table IB) and was
still more effective than levofloxacin and rifampicin local prophylaxis, but not as effective as

mupirocin and quinopristin-dalfopristin local prophylaxis (see table 1 A). In the rats inoculated with MRSE or MSSE, RIP treatment was equally or more effective than most antibiotics, with the exception of Teicoplanin in the parental prophylaxis experiments (see table IB) and mupirocin, quinupristin-dalfopristin in the local prophylaxis (see table 1A).
5) When RIP graft treatment was associated with antibiotic prophylaxis, the level of inhibition of bacterial load was greater (if compared to the single agents alone), and in some cases it reached 100%, as in the case of RIP with teicoplanin given parenterally for the MRSE and MSSE strains (p Similar results were obtained with S, aureus MRSA, MSSA and GISA, and with vancomycin resistant S, aureus and S. epidermidis strains VISA and VISE (not shown).
RIP can protect from graft associated infections in vivo
Animals (15/group) received a Dacron-graft implanted in a subcutaneous pocket. Graft -vas subsequently infected with either S. epidermidis (tested on MSSE, MRSE and GISE) or with S.aureus (tested on MSSA, MRSA and GISA). The Dacron-graft prior to implantation was soaked in saline with or without 20 mg/1 of RIP and some animal received 10 mg/1 of RIP i.p. as a prophylaxis treatment. Results are summarized in table 2A and 2B.
These results clearly show that RIP can be used to coat medical devices to prevent any type of staphylococcal infections and that RIP is synergistic to antibiotics.

Identifying Agents Suitable for Preventing and/or Treating Staphvlococcal infections
Of particular interest in the present invention is the identification of agents that have activity in affecting the expression and/or function of RAP and/or TRAP. In general agents of interest are those that inhibit RAP or TRAP activity, e.g., by inhibiting the ability of RAP to effect activation of RNAIII synthesis. Such agents are candidates for development of treatments for infection of pathogenic Staphylococcus. Of particular interest are screening assays for agents that have a low toxicity for human cells and/or high specificity for Staphylococcus, preferably with substantially no or little pressure for selection of strains resistant to the action of the agent, and without substantially affecting normal flora of the host (e.g., as distinguished from wide-spectrum antibiotics).
The term "agent" as used herein describes any molecule, e.g. protein or pharmaceutical, with the capability of altering RAP or TRAP activity, or mimicking or enhancing RIP activity, as described above. Generally a plurality of assay mixtures are run in parallel with different agent concentrations to detect differential responses to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e. at zero concentration or below the level of detection.
Candidate agents encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typical:/ include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules
including, but not limited to: peptides, saccharides, fatty acids, steroids, pheromones, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial (e.g., non-pathogenic Staphylococcus), fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs, can contain protective groups e.g. prolyl, or can contain D amino acids.
Screening of Candidate Agents
A wide variety of in vitro assays may be used to screen candidate agents, including labeled in vitro binding assays, e.g., protein-protein binding, protein-DNA binding assays, electrophoretic mobility shift assays, immunoassays for protein binding, and the like. Purified naturally-occurring or recombinant or synthestic RAP, TRAP and/or RIP polypeptides, and/or synthetically produced peptides or fragments of RAP TRAP and/or RIP, can be used in various screening assays to identify ligands or substrates that bind to, modulate (e.g., increase or inhibit), or mimic the action of the native proteins. The purified proteins may also be used for determination of three-dimensional crystal structure, which can be used for modeling intermolecular interactions, transcriptional regulation, etc.
The screening assay can be a binding assay, wherein one or more of the molecules
may be joined to a label, and the label directly or indirectly provide a detectable signal. Various labels include radioisotopes, fluorescers, chemiluminescers, enzymes, specific binding molecules, particles, e.g. magnetic particles, and the like. Specific binding molecules include pairs, such as biotin and streptavidin, digoxin and antidigoxin etc. For the specific binding members, the complementary member would normally be labeled with a molecule that provides for detection, in accordance with known procedures. In general, the particular type of screening assay employed will preferably one amenable to parallel, simultaneous screening of a large number of candidate agents.
Screening assays of the present invention encompass assays that examine the effect of candidate agents on the roles of RAP, TRAP and RIP in RNAUI production and/or virulence factor production. For example, the candidate agent may be contacted with pathogenic Staphylococcus and the levels of rnaiii transcription in the presence of the agent compared to rnaiii transcription levels in the presence of RJP, RAP, TRAP and/or a combination of RIP RAP rnd TRAP. Such screening assays can utilize recombinant host cells containing reporter gene systems such as CAT (chloramphenicol acetyltransferase), p-galactosidase, and the like operably associated with maiii or virulence factor genes to facilitate detection of rnaiii or virulence gene transcription or to facilitate detection of RNAIII or virulence factor production. Alternatively, the screening assay can detect rnaiii or virulence factor transcription using hybridization techniques (e.g., Northern blot, PCR, etc.) well known in the art.
A variety of other reagents may be included in the screening assays described herein. Where the assay is a binding assay, these include reagents like salts, neutral proteins, e.g. alburrin, detergents, etc, that are used to facilitate optimal protein-protein binding, protein-DNA binding, and/or reduce non-specific or background interactions. Reagents that improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, antimicrobial
agents, etc. may be used. The mixture of components are added in any order that provides for the requisite binding. Incubations are performed at any suitable temperature, typically between 4°C and 40°C. Incubation periods are selected for optimum activity, but may also be optimized to facilitate rapid high-throughput screening. Typically between 0.1 and 1 hours will be sufficient.
Screening of Candidate Agents In An Animal Model
Agents having a desired activity as determined in the assays described above can be further screened for their ability to affect Staphylococcus virulence factor production, and to affect Staphylococcus infection, in a non-human animal model. The animal model selected will vaiy with a number of factors including, but not limited to, the particular pathogenic strain of Staphylococcus against which candidate agents are to be screened, the ultimate host for which the candidate agents are to serve as therapeutics, etc. Animals suitable for use in screening assays include any animal susceptible to infection by the selected Staphylococcus species. For example, where the Staphylococcus species is S. aureus or S. epidermidis, the animal model can be a rodent model, preferably a rat or a mouse model.
In general, the candidate agent is administered to a non-human animal susceptible to Staphylococcus infection, where the animal has been infected with Staphylococcus or receives an infectious does of Staphylococcus in conjunction with the candidate agent. The candidate agent can be administered in any manner desired and/or appropriate for delivery of the agent in order to effect a desired result. For example, the candidate agent can be administered by injection (e.g., by injection intravenously, intramuscularly, subcutaneously, or directly into the tissue in which the desired affect is to be achieved), topically, orally, or by any other desirable means. Normally, this screen will involve a number of animals receiving varying amounts and concentrations of the candidate agent (from no agent to an amount of agent hat
approaches an upper limit of the amount that can be delivered successfully to the animal), and may include delivery of the agent in different formulations. The agent? can be administered singly or can be combined in combinations of two or more, especially where administration of a combination of agents may result in a synergistic effect, The agent can be used to coal: a device thai will then, be implanted into the animal.
The effect of agent administration upon (the animal model can be monitored by any suitable method, such as assessing the number and size of Staphylococcus-associated lesions, microbiological evidence of infection, overall health, etc. Where the candidate agent affects Staphylococcus infection in a desirable manner (e.g., by reducing infectious load, facilitating lesion regression, etc.), the candidate agent is identified as an agent suitable for use in treatment of Staphylococcus infection.
The invention provides a method for preventing or treating a human or an animal susceptible to infection by certain bacterial infections (e.g., S. aureus in humans) by administering an agent that inhibits RAP or TRAP activity in facilitating virulence factor production, e.g., by inhibition RAP-mediated activiation of RNAIH and subsequent virulence factor production.
The compounds having the desired pharmacological activity may beadministered in a physiologically acceptable carrier to a host for treatment or prevention of pathogenic Staphylococcus infection. The therapeutic agents may be administered in a variety of ways, orally, topically, parenterally e.g. subcutaneousJy, intraperitoneally, intravascularly, intrapuimonary (inhalation), etc. Depending upon the manner of introduction, the compounds may be formulated in a variety of ways. The concentration of therapeutically active compound in the formulation may vary from about 0.1-100 wt.%.
The pharmaceutical compositions can be prepared in various forms, such as granules, tablets, pills, suppositories, capsules, suspensions, salves, lotions and the like. Pharmaceutical grade organic or inorganic carriers and/or diluents suitable for oral and topical use can be used to make up compositions containing the therapeutically active compounds. Diluents known to the art include aqueous media, vegetable and animal oils and fats. Stabilizing agents, wetting and emulsifying agents, salts for varying the osmotic pressure or buffers for securing an adequate pH value, and skin penetration enhancers can be used as auxiliary agents.
in one embodiment, the host is treated by administration of RIP or with a RAP or TRAP inhibitors, such as an anti-RAP antibody, or both. In one embodiment the RAP inhibitor is co-administered with other RAP or TRAP inhibitors and/or co-administered with other inhibitors of-staphyhcoccal virulence, e.g., co-administered with RIP and/or with conventional antibiotics. In another embodiment a RAP or TRAP inhibitor, RIP, and a RAP or TRAP inhibitor (e.g., an anti-RAP or TRAP antibody) are administered. Such combination therapies (e.g., administration of multiple RAP inhibitory agents; administration of RAP and RIP; and/or administration of RAP or TARP inhibitor, RIP, and/or TARP or RAP inhibitor) may involve co-administration or sequential administration of the active components. The dosage regimen may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the therapeutic situation. The active compounds may be administered in any convenient manner, such as by oral, intravenous, intramuscular, subcutaneous, buccal, transdermal, or inhalation routes.
Formulations composed of RIP, RAP inhibitor, TRAP inhibitor, or combination of, are administered at a therapeutically effective dosage, e.g., a dosage sufficient to improve the chance of successful prevention or treatment of infection. Administration of such a
formulation can be via any of the accepted modes of administration ror agents tnat serve similar utilities, preferably by systemic administration. Administration can include above combinations with other inhibitors, for example conventional antibiotics.
Human dosage levels for treating infections are known and generally include a daily dose from about 0.1 to 500.0 mg/kg of body weight per day, preferably about 6.0 to 200.0 mg/kg, and most preferably about 12.0 to 100.0 mg/kg. Generally, it is sought to obtain a serum concentration of such a formulation approximating or greater than circulating levels needed to reduce or eliminate any infection in less than 10 days. For administration to a 70 kg person, the dosage range would be about 50 mg to 3.5 g per day, preferably about 100 mg to 2 g per day, and most preferably about 200 mg to 1 g per day. The amount of formulation administered will, of course, be dependent on the subject and the severity of the affliction, the manner and schedule of administration and the judgment of the prescribing physician.
In employing formulation for treatment of infections, any pharmaceutically acceptable mode of administration can be used. The formulations can be administered either alone or in combination with other pharmaceutically acceptable excipients, including solid, semi-solid, liquid or aerosol dosage forms, such as, for example, tablets, capsules, powders, liquids, gels, suspensions, suppositories, aerosols or the like. The formulations can also be administered in sustained or controlled release dosage forms (e.g., employing a slow release bioerodable delivery system), including depot injections, osmotic pumps, pills, transdermal and transcutaneous (including electrotransport) patches, and the like, for prolonged administration of a predetermined rate, preferably in unit dosage forms suitable for single administration of precise dosages or, as discussed below, the coating of a device that is to be inserted into a body.
The compositions will typically include a conventional pharmaceutical carrier or excipient and a formulation of the invention. In addition, these compositions may include
other active agents, carriers, adjuvants, etc. Generally^ depending on the intended mode of administration, the phannaceutically acceptable composition will contain about 0.1% to 90%, preferably about 0.5% to 50%, by weight of active compound, the remainder being suitable pharmaceutical excipients, carriers, etc. Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art. For example, see Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pennsylvania, 15th Edition, 1975.
Parental administration is generally characterized by injection, either subcutaneously, intradermally, intramuscularly, or intravenously, preferably subcutaneously. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol or the like. In addition, if desired, the pharmaceutical compositions to be administered may also contain minor amounts of non-toxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, solubility enhancers, and the like, such as for example, sodium acetate, sorbitan monolaurate, triethanolamine oleate, cyclodextrins, and the like.
The percentage of active ingredient contained in such parental compositions is highly dependent on the specific nature thereof, as well as the needs of the subject. However, percentages of active ingredient of 0.01% to 10% in solution are employable, and will be higher if the composition is a solid which will be subsequently diluted to the above percentages. Preferably, the composition will comprise 0.2-2% of the active ingredient in solution.
A more recently devised approach for parental administration employs the implantation of a slow-release or sustained-release system, such that a constant level of dosage is maintained. Various matrices (e.g., polymers, hydrophilic gels, and the like) for
controlling the sustained release, and for progressively diminishing the rate of release of active agents are known in the art. See U.S. Patent Nos. 3,845,770 (describing elementary osmotic pumps); 3,995,651,4,034,756 and 4,111,202 (describing miniature osmotic pumps); 4.320,759 and 4,449,983 (describing multichamber osmotic systems referred to as push-pull and push-melt osmotic pumps); and 5,023,088 (describing osmotic pumps patterned for the sequentially timed dispensing of various dosage units).
Formulations of active components may also be administered to the respiratory tract as a nasal or pulmonary inhalation aerosol or solution for a nebulizer, or as a micro fine powder for inhalation, alone or in combination with an inert carrier such as lactose, or with other pharmaceutically acceptable excipients. In such a case, the particles of the formulation may advantageously have diameters of less than 50 microns, preferably less than 10 microns. See, e.g., U.S. Patent No. 5,364,838, which discloses a method of administration for insulin that can be adapted for the administration of formulations of the present invention.
The invention provides a vaccine for inoculating a human or a animal susceptible to infection by certain bacterial.infections (e.g., S. aureus and S. epidermidis) by administering RAP, TRAP, or an antigenically effective portion of RAP or TRAP, in a pharmaceutically acceptable carrier, which may optionally comprise an adjuvant. Formulations appropriate for elicitauon of the immune response are well known in the art. In general, the host is exposed to the antigen, such as RAP or TRAP, which perturbs the host's immune system and results in an immune response towards the antigen. An adjuvant can be added with the antigen to increase the immune response to the antigen. The amount of polypeptide administered is an amount sufficient to elicit a protective immune response in the host. Methods for determining such appropriate amounts are routine and well known in the art. For example, RAP, TRAP
and/oi antigenically effective portion(s) thereof can be used to vaccinate an animal model of Staphylococcus infection. The amounts effective in such animal models can be extrapolated to other hosts (e.g., livestock, humans, etc.) in order to provide for an amount effective for vaccination.
Vaccination of animals with recombinant RAP (rL2)
4 week old female Balb/C mice (ten mice/group) were injected subcutaneously on days 0, 7, 21 with 50ug rL2 (50ug/50ul PBS) together with 50ul complete Freund's adjuvant on first injection and incomplete Freund's adjuvant on second and third injections. Control animal ? were injected with adjuvant/PBS only. Animals were challenged on day 35 with 2xl09 Smith Diffuse S. aureus (SD) prepared as described below. Animals were observed daily for mortality, overall health and development of lesion. The size of the lesion was measured (area=0.5 n (length) (width).
Preparation of bacteria for challenge: Smith Diffuse S. aureus was grown overnight at 37°C on blood agar plates. Bacteria was suspended in PBS at 2xl010 cells/ml. 2xl09 (ICOul) cells were injected to vaccinated and control animals subcutaneously, together with Img cytodex beads, to induce a local infection.
Antibody level as determined by ELISA. A drop of blood was collected from the tip of the tail before the first vaccination and 10 days after the third vaccination. ELISA plates were coated overnight with 50ul of 25ug/ml antigen or with 3% BSA as a control. Wells were then blocked with 3% BSA for 3hrs at room temperature, and 50ul sera (diluted 1:1000 in PBS) was applied for 2.5 hrs at room temperature. Unbound antibody was removed and welh were washed 5x 2min with PBS with 0,05% Tween 20. 50ul peroxidase-conjugated anti-mouse antibody (Sigma) diluted 1:2000 with PBS/Tween was applied for Ihr 37°C.
unoound antibody was removed, and wells were washed as above, and bound antibody was detected by ABTS (Sigma) according to the manufacturer's instructions.
Results of vaccination experiments
Development of antibody to the antigen: All vaccinated animals developed an antibody liter (>1000) to the injected antigen. None of the control animals had a detectable antibody level to the injected antigen.
Mortality post challenge: As shown in Fig. 4, of 10 control animals vaccinated with adjuvant only, 3 animals died within the first day post challenge, and another mouse died on the second day. Of 10 animals vaccinated with rL2, none died within the first day, one died on the second day and another died on the third day.
Lesion: All surviving animals developed a lesion and its size was determined on the fifth day post challenge. As shown in Fig. 5, the average lesion size of control animals was 7cm2, while the average lesion size of animals vaccinated with rL2 was only 2.5 cm2. Conclusions:
Animals vaccinated with rL2 had delayed mortality and a 50% reduction in mortality rate, and a 65% reduction in lesion size. These results suggest that rL2 can confer protection to a S. aureus infection. Of note is the fact that the number of bacteria used for challenge was exceptionally high and it is expected that if a lower number of bacteria were present, protection level from infection could be higher.
CONCLUSION: RAP (native or recombinant) inhibits RNAIII synthesis in vitro and protects animals from S. aureus infection in vivo. Because RAP is a homo log of L2, which is found in all bacteria, RAP can serve as a target site for therapy to various bacterial infections in addition to S. aureus.
The invention provides for a device, the surface of which is coated with a composition having an amount of a RAP inhibitory agent (e.g., an anti-RAP or anti-TRAP antibody, inhibitory peptides, RIP peptide or RIP derivative peptides) effective to inhibit biofilrn formation by Stapliyloeocci or by oilier bacteria expression RAP, TRAP or RAP-like or TRAP-like molecules. The coated device may be any device which may be associated with a risk of Staphylococcus or other bacterial infection or exposure of a host (e.g., surgery patient, menstruating female, etc.) to Staphylococcus virulence factors.
Coated devices encompassed by the present invention include, but are not limited to, catheters, needles, surgical instruments (e.g., scalpels, sponges, retractors, etc.), bandages and bandage materials (e.g., gauze, dressings, etc.), artificial joints, heart valves, and tampons, or any other medical device. Such devices have a tendency to bring Staphylococci or other bacteria into contact with the host, or to attract colonizations by staph bacteria (e.g., tampon), in such situations, the coated devices may prevent or reduce Slaphylococcus or other bacterial infection, or prevent or reduce the development of serious symptoms associated e.g. with exposure to Slaphylococcus virulence factors.

While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

We Claim:
1. A composition for preventing or treating non-aureus or non-epidermidis
staph infection and other bacterial infection in a subject, comprising:
1 -95% a RAP polypeptide effective to elicit an antibody response in the subject to prevent or treat a bacterial non-aureus or non-epidermidis staph infection and other infection caused by bacterial species in which a RAP polypeptide plays a role in pathogenesis,
and remaining amount pharmaceutically acceptable carrier such as herein described
2. A composition as claimed in claim 1, wherein said species is a
Stappylococcus species selected from the group consisting of S. capitus,
S. wameri, S. capitis, S. caprae, S. carnosus, S. saproptiyticus, S.
chronii, S. simulans, S, caseolyticus, S. haemolyticus, S. hominis, S.
hyicus, S. kloosii, S. lentus, S. lugdunensis, S. scruri, S, simulans, and S.
xylosus; Streptococcus pyogenes; a Listeria species selected from the
group consisting of L innocua and L. monoctogenes; Lactococcus lactis;
Enterococcus faecalis; Escherichia coli; Clostridium acetobutylicum; or a
Bacillus species selected from the group consisting of 6. subtilis, B.
cereus, and B. anthracis.












3906-delnp-2005-description (complete)-21-05-2008.pdf

3906-delnp-2005-description (complete).pdf
















Patent Number 236215
Indian Patent Application Number 3906/DELNP/2005
PG Journal Number 42/2009
Publication Date 16-Oct-2009
Grant Date 08-Oct-2009
Date of Filing 01-Sep-2005
Name of Patentee BALABAN NAOMI
Applicant Address 813 LAKE TERRACE CIRCLE, DAVIS, CA 95616, U.S.A.
# Inventor's Name Inventor's Address
PCT International Classification Number A61K
PCT International Application Number PCT/US2004/002679
PCT International Filing date 2004-01-30
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 10/358,448 2003-02-03 U.S.A.