# Patent

## Title
Transport peptides such as C-terminal Erns peptide and analogues thereof

## Abstract

The invention relates to peptides derived from or similar to the Erns protein of pestiviruses for type-specific diagnosis of infection, for eliciting antibiotic activity, and for transport of substances into a cell. For these purposes, the invention provides, among other things, an isolated, synthetic or recombinant protein or peptide module or functional equivalent thereof comprising an amino acid sequence having significant homology to, for example, an amino acid sequence of a peptide located from about amino acid position (a) 194 to about 220 in a pestiviral Erns protein (b) 59 to about 88 in an L3 loop of a cytotoxic RNase of a ribosome-inactivating protein, or (c) 187 to about 223 in a respiratory syncytial virus G-protein.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part of application Ser. No. 10/335,057, filed Dec. 30, 2002 now U.S. Pat. No. 7,067,487, which is a continuation of International Application No. PCT/NL01/00484, filed Jun. 28, 2001, designating the United States of America, and published in English as WO 02/00882 A2 on Jan. 3, 2002, the contents of the entirety of which is incorporated herein by this reference.


TECHNICAL FIELD
The various embodiments of the present invention generally relate to biotechnology. More specifically, embodiments of the invention relate to transport peptides, for example, derived from the Erns protein of pestiviruses for type-specific diagnosis of infection, for eliciting antibiotic activity and for transport of substances into a cell.
BACKGROUND
Hog cholera virus or classical swine fever virus (CSFV), bovine viral diarrhea virus (BVDV), and border disease virus (BDV) belong to the genus Pestivirus of the Flaviviridae family. CSFV is restricted to swine, while BVDV and BDV have been isolated from several species such as cattle, swine, sheep, deer, and giraffes. Although pigs can be infected by all of these pestiviruses, only CSFV induces severe, often fatal, disease. The disease is characterized by fever and, for instance, leukopenia and can run an acute, chronic, or subclinical course. Although effective live-attenuated vaccines are available, pigs are not vaccinated against CSFV in the European Union (EU) because vaccinated and infected pigs are serologically indistinguishable. Outbreaks of CSF in the EU are controlled by eradication of all pigs from infected farms and farms in the vicinity. Because of this strategy, more than 10 million pigs had to be killed and destroyed during the 1997-1998 CSF epizootic in The Netherlands, costing more than $2 billion. It is for this reason that a great demand exists for a marker vaccine that provides protective immunity and induces an antibody response in the vaccinated pigs that can be distinguished from the antibody response caused by a natural CSFV infection.
Like other members of the family, pestiviruses are plus-stranded RNA viruses whose genome comprises one long open reading frame. Translation into a hypothetical polyprotein is accompanied by processing into mature proteins. The structural proteins include a nucleocapsid protein C and three envelope glycoproteins Erns, E1 and E2. The envelope proteins Erns and E2 are able to induce neutralizing antibodies. Glycoprotein E2 is the most immunogenic protein of pestiviruses and elicits high titers of neutralizing antibodies after infection. Vaccination of target animals with E2 has shown to give complete protection against a lethal homologous challenge. When E2 is used for vaccination, serological diagnosis of a natural pestivirus infection has to be performed with an immunogenic/antigenic protein other than E2 that is present in the infectious pestivirus. For this purpose, the Erns glycoprotein can be used as an antigen in a diagnostic test. A population that is vaccinated with the E2 glycoprotein can still be tested serologically for pestivirus infection with a diagnostic test based on the Erns antigen. A serological test based on Erns can distinguish Erns antibody-positive sera from animals infected with the virus and Erns antibody-negative sera from uninfected animals. This is called the marker vaccine approach. Of course, these marker vaccines depend on sensitive tests and, in the case of CSFV, the test also has to be very specific because pigs can be infected with the other pestiviruses BVDV and BDV. Because BVDV and BDV do not cause (severe) clinical symptoms in pigs and the animals are not vaccinated for these viruses, the diagnostic test for a CSFV marker vaccine should only detect CSFV antibodies and no other pestivirus antibodies.
Serological tests based on the complete Erns protein have been developed previously but are not always satisfactory in that they are not specific enough in that they cannot discriminate sufficiently between infections with different pestivirus species or are not sensitive enough to detect early infections with a pestivirus. 
In one embodiment, the invention provides a so-called transport peptide module, herein also called “movin.” In principle, we found that most linear peptides of 10 to 18 residues long which have >40% arginines (R) or lysines (K) are capable of functioning as such a transport peptide module to which cargo can be attached. Such a transport peptide module preferably should not, or only to a small extent, contain negatively charged amino acids such as aspartic acid (D) or glutamic acid (E). Preferred peptide modules are identified herein with full sequence, such as, for example, in Tables 4, 5, and 9 to 11, or retro-inverso variants thereof.
Variations in amino acid sequence are well tolerated, at least from the viewpoint of translocation as activity. As a rule of thumb, it can be said that related sequences have at least 30-50% homology, preferably at least 70% homology, and most preferably at least 85% homology, to those displayed in these tables, which allows identifying further relevant sequences present in nature or capable of being synthesized.
Substitutions in the amino acid sequence of a transport peptide module can be applied to increase the translocation (transport) activity. An optimized transport peptide module can, for example, be synthesized according to retro-inverso peptide chemistry, in which the sequence is reversed and D-amino acids are used instead of L-amino acids. Transport peptides derived from the herein-indicated positions of the Erns peptide, L3 loop peptides or human respiratory syncytial virus protein G (HRSV-G) peptides, and peptide mimics or peptoides derived thereof were able to bind surface glycosaminoglycans like heparin. Therefore, finding that a peptide belongs to the group of linear heparin-binding peptides or is capable of binding related glycosaminoglycans can be used as a prediction that they likely also can function as transport peptides. However, heparin binding is not a prerequisite for a peptide being a transport peptide.
To check if the presence of heparin on the surface of the cell influenced the efficiency of translocation, it was tested whether heparin-binding peptides also translocated into mutant cells which were glycosaminoglycan deficient (cell lines pgsA-745 and pgsD-677). Titrations of all heparin-binding peptides on the different cells showed that peptides translocated with the same efficiency/activity into heparin-containing cells and in the mutant cells without heparin (data not shown). Thus, heparin-binding peptides have translocation activity, and binding of the peptides to heparin obviously does not block the peptide from penetrating the plasma membrane. Likely, the peptides have a high on/off rate for heparin, and the high affinity for phospholipids directs the peptides to the membrane and ultimately into the cell. On the other hand, heparin binding, albeit being predictive, does not seem to be a prerequisite for efficient translocation of the peptides.
The invention further provides a method for translocating a compound over a membrane of a cell, an epithelial layer, mucus layer, blood-brain barrier or skin comprising providing the compound with a transport peptide module according to the invention and contacting it with a cell. Such compounds, herein also called cargo, can be large; successful translocation of compounds up to 600 kD has been demonstrated and it is expected that even larger compounds may be translocated. From the perspective of speed of translocation in relation to the usefulness of the compound, compounds of preferred molecular weight are those of 60 to 500 kD and even more preferred are those of 120 to 300 kD. Compounds can also be of a varied nature. For example, it is possible to link macromolecules such as nucleotides, polypeptides, drugs such as antiviral, antimicrobial or anti-inflammatory drugs, and the like to a module as provided herein for successful translocation of such a compound. Topical application of such a compound, e.g., as a pharmaceutical composition, is specifically provided. A module as provided herein has excellent capacity to penetrate to the upper layers of the skin. Typical applications include further use of a labile linker such as a thioester or a O(C═O) CH2NRC (═O) CH2NHCH2 (C═O) SCys linker. For use of a transport peptide module according to the invention, drugs or macromolecules are typically covalently coupled to the peptide, examples of which are cyclosporine A, acyclovir, and terbenafine coupled with a module according to the invention.
This invention also provides, among others, peptide-based diagnostics in connection with diseases caused by pestivirus infections. Antigenic peptides as provided herein and useful for diagnostics can surprisingly also be used otherwise, such as antibacterial or transport peptides. Because in one embodiment the transport peptide module is a fragment derived of the Erns protein, it can be used for diagnosis of pestivirus infections when a marker vaccine is used that is based on E2, another pestivirus surface protein. Due to its unique biochemical character, a peptide as provided herein has the ability to permeate and kill microorganisms and has the ability to translocate itself and a coupled cargo across a cell membrane and epithelium barrier.
In a preferred embodiment, the invention provides a thus far unidentified small, independently folding protein (peptide) module related to modules present at the C-terminal end of pestivirus Erns, at the L3 loop of secreted cytotoxic Rnases that preferably belong to the group of type II ribotoxins such as alpha-sarcin, restrictocin, mitogillin, toxin Asp fi, clavin or gigantin, in a heparin-binding peptide, in a DNA/RNA-binding peptide, in HRSV-G protein, and its use as a transport peptide. Previously, the region responsible for translocation of alpha-sarcin was thought to be located in a hydrophobic stretch, located away from the L3 loop (Mancheno et al., Biophys. J. 68, 2387-2395, 1995). In a preferred embodiment, the invention provides an isolated, synthetic or recombinant protein module or functional equivalent thereof comprising an amino acid sequence that is at least 85% identical to any of the sequences shown in Tables 1-4 and 9-11, e.g., to an amino acid sequence of a peptide located from about amino acid position 194 to 220 in a pestiviral Erns protein and/or that is at least 70% identical to an L3 loop sequence such as shown in Table 5.
Such transport peptide modules can be prepared synthetically with normal peptide synthesis or coupling techniques as described herein, starting from individual amino acids or by coupling or linking smaller peptides of relevant sequence to another or by cleaving off from larger peptides. When desired, nonconventional amino acids can be used, such as D-amino acids or others that normally do not occur in natural proteins. Peptides can also be prepared via recombinant DNA techniques via transcription and translation from recombinant nucleic acid encoding such a peptide or protein module, be it linked to, for example, a fusion protein or specific target molecule such as a desired binding molecule derived from an antibody or protein ligand or receptor-binding molecule, and so on. For example, we have successfully expressed a fusion protein of a transport peptide and Green Fluorescent protein in A72 cells. The Green Fluorescent protein showed the same cellular localization as the biotinylated transport peptide in the nucleoli and around the nucleus. This is in contrast to normally expressed Green Fluorescent protein, which was distributed evenly over the cell (data not shown).
In a preferred embodiment, the invention provides a transport peptide module or functional part thereof wherein at least the functional part of the peptide comprises a reversed amino acid sequence to one of a sequence given in claims 1 to 6 and wherein D-amino acids are used instead of L-amino acids. Reversing the sequence and using the D-amino acids instead enhances translocation activity, allowing improved use for, for example, transport of macromolecules or drugs through cell membrane barriers into cells.
In a preferred embodiment as explained herein, the invention provides a module which is functional as a transport peptide module, also when cargo is attached, wherein the peptide is located from about amino acid position 191 to 222, or from about 194 to 227, or from about 191 to 227, or from about amino acid position 176 to about 220, 222, or 227 in the case of the pestiviral Erns protein or residues 51-91 or 59-88 or from 62-88 or from 62-74, in the case of the L3 loop protein, or from about amino acid position 187 to 223 in a respiratory syncytial virus G-protein. Also, in HRSV type B, a similar region was detected from position 149 to 160 in protein G. These amino acid positions and their numbering are, of course, relative to known sequences as, for example, shown in the figures herein wherein alignments of various pestiviral sequences are shown, which, of course, allows, for example, for alignment with yet unknown pestiviral sequences and allows alignment with ribotoxin L3 loop sequences. As a rule of thumb, it can be said that related sequences have at least 30-50% homology, preferably at least 70% homology, most preferably at least 85% homology, which allows identifying further relevant sequences present in nature or capable of being synthesized. As examples herein, modules are described wherein the peptide comprises the amino acid sequence RQGAARVTSWLGRQLRIAGKRLEGRSK (SEQ ID NO:1); RQGTAKLTTWLGKQLGILGKKLENKSK (SEQ ID NO:2); RVGTAKLTTWLGKQLGILGKKLENKTK (SEQ ID NO:3); RQGAAKLTSWLGKQLGIMGKKLEHKSK (SEQ ID NO:4); GNGKLIKGRTPIKFGKADCDRPPKHSQNGMGK (SEQ ID NO:5); GDGKLIPGRTPIKFGKSDCDRPPKHSKDGNGK (SEQ ID NO:6); GEGKILKGRTPIKFGKSDCDRPPKHSKDGNGK (SEQ ID NO:7); GDGKILKGRTPIKWGNSDCDRPPKHSKNGDGK (SEQ ID NO:8); KRIPNKKPGKK (SEQ ID NO:9); KTIPSNKPKKK (SEQ ID NO:10); KPRSKNPPKKPK (SEQ ID NO:11); or a functional part thereof. However, variations can be introduced, for example, by increasing the positive charge of the peptide, preferably at positions that optimize the amphipathic nature of the peptide, but not necessarily. Another example is changing several or all L-amino acids to D-amino acids to reduce possible protease sensitivity. The translocation activity of the Erns peptide was further improved by substitution of the 2 lysines and the glutaminic acid by arginines. In a preferred embodiment, a retro-inverso variant of an above-identified peptide module is provided; such a retro-inverso peptide with an inversed sequence and D-amino acids replacing L-amino acids comprises even higher translocation activity.
Of course, the invention also provides a recombinant nucleic acid encoding a module according to the invention, for example, to provide for a proteinaceous substance provided with a module according to the invention, for example, provided with a targeting means.
The invention in one aspect also relates to the design of an antigenic substance, preferably peptide-based, corresponding to the protein module in the Erns protein of Pestiviruses or a L3 loop of ribotoxin II can be used as a basis for, e.g., diagnostics tests, antibacterial or transporter peptides. For example, in one embodiment, the invention provides a method for inducing an antibody comprising administering a module or a substance according to the invention to a host capable of forming antibodies. Antibodies can be induced classically by, for example, immunizing an animal with the antigenic substance, or via more modern techniques, such as phage display, whereby so-called synthetic antibodies are produced. Be it synthetic or classical (mono- or polyclonal), the invention provides an antibody specifically directed against a module according to the invention.
With the pestivirus-derived module and/or the antibody as provided herein, the invention provides a method for detecting the presence or absence of an antibody directed against a pestivirus in a sample comprising contacting the sample with a module or a substance according to the invention, the method preferably further comprising detecting the presence or absence of an antibody bound to the module or substance. Also provided is a method further comprising contacting the sample with the module or substance in the presence of a competing antibody directed against the module and detecting the presence or absence of competing antibody bound to the module or substance. Herewith, the invention provides use of a method according to the invention for differentiating at least one animal from at least another animal. The invention thus provides a test which is based on a small fragment of the Erns protein. Sequence analysis and homology modeling was used for pestivirus Erns to identify a region that can be used for the design of antigenic substances and resulted in the identification of a small independently folding protein module which, in its native state, is exposed on the protein surface of the complete Erns protein and can be used to design antigenic substances which are comparable or superior to the complete protein.
In a further embodiment, the invention not only provides a peptide that behaves as a superior antigen in the Erns peptide-ELISA but one that has additional characteristics that are very interesting and useful. Due to its unique biochemical nature, a peptide as provided herein, for example, corresponding to the Erns C-terminal domain or to a L3 loop in a ribotoxin, is able to interact with a cell membrane and destabilize the membrane.
The invention further provides a method for translocating a compound over a membrane of a cell, an epithelial layer, mucus layer, blood-brain barrier or skin comprising providing the compound with a module or substance or transport peptide module according to the invention and contacting it with a cell, and, furthermore, it provides a method for eliciting antibiotic activity to a microorganism comprising contacting the microorganism with the module or substance.
Herein, it is shown that such an Erns peptide or protein module as provided herein has antibacterial activity for, for example, gram-negative bacteria (E. Coli) and an L3 loop or Erns peptide and it has translocation activity for, for example, eukaryotic cell membranes. A biological membrane is a very efficient barrier that protects the micromilieu of cells or intracellular compartments from the outside milieu. In order to interfere directly with biological processes inside the cell, it is necessary that pharmaceuticals cross the lipid bilayer to block/bind their targets. Many promising, potential therapeutics (hydrophilic organic molecules, peptides, proteins or genes) are ineffective because the cell membrane forms an insurmountable barrier. However, several peptides have been discovered recently that can solve this problem because they are able to translocate over the lipid bilayer and are also able to transport a diverse set of cargos inside the cell.
Interactions of pore-forming peptides with model and artificial membranes have been studied extensively the last three decades. Several families of membrane destabilizing peptides with antitumor, haemolytic, antibacterial activity or a combination have been found. Many of these peptides form amphipathic helices with a hydrophobic face and a positive charged face that organize and aggregate on the membrane surface and destabilize the membrane. Their mode of action has some resemblance with the recently discovered transport peptides (Matsuzaki et al., Biochem. Biophys. Acta. 1376: 391-400, 1998; Lindgren et al., Trends Pharmacol. SCI 21: 99-103, 2000). The invention now provides a pharmaceutical composition comprising a module or substance according to the invention useful for several purposes. For example, the invention provides use of a module or a substance according to the invention for the preparation of a pharmaceutical composition capable of membrane translocation (a transport peptide), for the preparation of a pharmaceutical composition capable of eliciting antibiotic activity (an antibiotic), or for the preparation of a pharmaceutical composition capable of inducing antibodies (a vaccine) upon administration to a host.
The invention is further explained in the detailed description described herein without limiting it thereto.



BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
FIG. 1. Schematic representation of alignment of pestivirus Erns with RNase Rh which indicates the modular organization of Erns. Erns consists of an RNase domain (dotted) and a C-terminal membrane-active domain (filled black). The C-terminal domain (residues 191-227) which shows resemblance to the L3 loop of cytotoxic RNases is described in this invention. RNase-active site domains are shown as checkered boxes. Potential glycosylation sites are shown as ellipses.
FIG. 2. Helical wheel representation of residues 194-220 of CSFV Erns.
FIG. 3. Sequence alignment of pestivirus Erns C-terminal domains with magainin and the L3 loop of restrictocin. Residues within one distance unit from magainin are boxed. Units are defined in structural distance table in the magalign package of DNASTAR, Inc. The Structural table scores for residues that are chemically and spatially similar. All identities score a value of 6. Mismatches score less than identities. The Structural table is designed for use with the Jotun-Hein method.
FIG. 4. Crystal structure of RNAse Rh.
FIGS. 5A and 5B. Reactivity (optical density, OD) in CSFV 1p-peptide ELISA of dilutions of BVDV-specific swine sera (4b-9b) and CSFV-specific swine sera (9c to 13c) and CSFV-specific hyperimmune serum.
FIGS. 5C and 5D Reactivity in CSFV 1p-peptide ELISA of dilutions of BVDV-specific bovine sera (1-6, r4590-51, r4590-52, 841) and BVDV-specific hyperimmune serum.
FIGS. 6A and 6B. Reactivity of several panels of sera in the CSFV 1p-peptide ELISA as described in the test procedure. Negative field serum samples (n=96) were randomly obtained from slaughtered adult pigs and were all tested negative in standard pestivirus ELISA. Pestivirus-positive but CSFV-negative serum samples (n=96) were randomly obtained from slaughtered adult pigs. CSFV-positive field serum samples were obtained (n=95) from an infected farm (VR) that was infected during the CSF epizootic in the Netherlands in 1997-1998.
FIG. 7. Reactivity of successive serum samples collected during a vaccination/challenge experiment in the CSFV 1p-peptide ELISA. Twelve pigs were vaccinated with E2, 14 days before challenge.
FIGS. 8A-8C. Distribution of biotinylated CSFV Erns peptide (8A, 8C) and biotinylated control peptide (8B) (25 μM) after 30 minutes of incubation with subconfluent EBTr cells grown on a 10-well microscope slide. Cells were fixed with cold methanol and biotinylated peptide was visualized by staining with avidin-FITC for 30 minutes. Fluorescent micrograph (250×) (8A, 8B) or fluorescent micrograph using confocal microscope (600×) (8C).
FIGS. 9A and 9B. Distribution of biotinylated L3 peptide (9A) and magainin-1 peptide (9B) (6 μM) after 30 minutes of incubation with subconfluent EBTr cells grown on a 10-well microscope slide. Cells were fixed with cold methanol and biotinylated peptide was visualized by staining with avidin-FITC for 30 minutes. Fluorescent micrograph (250×).
FIGS. 10A-10H. Transport of avidin and streptavidin. Equimolar amounts of avidin-Texas Red (66 kD) (10A) or streptavidin-FITC (60 kD) (10C) were mixed with the biotinylated Erns peptide or unbiotinylated peptide (10B, 10D) (residues 194-220) (3 μM) and incubated with EBTr cells for 30 minutes. Transport of a complex of streptavidin-FITC with optimized Erns peptide biotin-GRQLRIAGRRLRGRSR (SEQ ID NO:39) (10E), optimized Erns peptide biotin-GRQLRRAGRRLRRRSR (SEQ ID NO:40) (10F), HRSV-G type A peptide biotin-KRIPNKKPGKKTTTPTKKPTIKTTKKDLKPQTTKPK (SEQ ID NO:41) (10G) and HRSV-G type A biotin-KRIPNKKPGKKT (SEQ ID NO:42) (10H).
FIGS. 11A and 11B. Distribution of FITC-labeled oligonucleotide (32 nt) (11A) and FITC-labeled oligo coupled to optimized Erns peptide (11B) at 56 μg oligo/ml after 30 minutes incubation with cells.
FIG. 12. Passage of HRP through epithelial cell sheet incubated with 0, 0.5, 5 and 50 μg/ml BVDV Erns peptide.



DETAILED DESCRIPTION OF THE INVENTION
For diagnostics, the invention provides a peptide comprising an amino acid sequence derived from Erns of a pestivirus, wherein the amino acid sequence has, for example, a length of 37 amino acid residues corresponding to the C-terminus of Erns, which is located C-terminal to the RNase domain. Preferably, the amino acid sequence comprises at least the amino acid residues 191-227 of Pestivirus Erns and has at most 4 amino acid differences therewith. Preferably, the pestivirus Erns peptide is selected from the group consisting of Classical Swine Fever Virus (CSFV), strain Alfort 187, BVDV-1 strain M96751, BVDV-2, or BDV, strain X818. The amino acid sequence preferably comprises a member selected from the group consisting of:











TABLE 1









CSFV
ENARQGAARVTSWLGRQLRIAGKRLEGRSKTW





(SEQ ID NO:12)



 



BVDV-1
EGARQGTAKLTTWLGKQLGILGKKLENKSKTW




(SEQ ID NO:13)



 



BVDV-2
EGARVGTAKLTTWLGKQLGILGKKLENKTKAW




(SEQ ID NO:14)



 



BDV
ENARQGAAKLTSWLGKQLGIMGKKLEHKSKTW




(SEQ ID NO:15).










More preferably, a member selected from the group consisting of:











TABLE 2









CSFV
ENARQGAARVTSWLGRQLRIAGKRLEGRSKTWFGAYA





(SEQ ID NO:16)



 



BVDV-1
EGARQGTAKLTTWLGKQLGILGKKLENKSKTWFGAYA




(SEQ ID NO:17)



 



BVDV-2
EGARVGTAKLTTWLGKQLGILGKKLENKTKAWFGAHA




(SEQ ID NO:18)



 



BDV
ENARQGAAKLTSWLGKQLGIMGKKLEHKSKTWFGANA




(SEQ ID NO:19).










Such as a member selected from the group consisting of:










TABLE 3







CSFV
DTALYLVDGMTNTIENARQGAARVTSWLG
(SEQ ID NO:20)




RQLRIAGKRLEGRSKTWFGAYA


 


BVDV-1
DTTLYLVDGLTNSLEGARQGTAKLTTWLG
(SEQ ID NO:21)



KQLGILGKKLENKSKTWFGAYA


 


BVDV-2
ETAIQLLDGATNTIEGARVGTAKLTTWL
(SEQ ID NO:22)



GKQLGILGKKLENKTKAWFGAHA


 


BDV
DTALYVVDGVTNTVENARQGAAKLTSWLG
(SEQ ID NO:23)



KQLGIMGKKLEHKSKTWFGANA.









It is preferable that the peptide is capable of adopting the tertiary structure of its counterpart in the corresponding Erns protein when it relates to an antigenic substance, or a precursor thereof, which allows discrimination between or identification of different pestivirus types or subtypes, or allows discrimination between or identification of antibodies against different pestivirus types or subtypes, which antigenic substance or precursor thereof comprises a peptide as defined herein.
A peptide, antigenic substance or precursor thereof as defined herein may be used in diagnosis of Pestivirus infections. This invention also provides a diagnostic test kit for the detection of Pestivirus, or antibodies against Pestivirus types or subtypes, which test kit comprises a peptide, antigenic substance or precursor thereof as defined herein, together with suitable means for detection. The test kit preferably provides for an enzyme-linked immunosorbent assay.
The invention also provides a method for the detection of (antibodies against) Pestivirus comprising contacting a sample of a body fluid with a peptide, antigenic substance or precursor thereof as defined herein, in a manner such that a complex comprising the peptide, antigenic substance or precursor, and an antibody directed against the peptide, substance or precursor can be formed, followed by detection of the complex.
Furthermore, the invention provides a pharmaceutical composition or vaccine for the prophylaxis of Pestivirus infections comprising a peptide, antigenic substance or precursor thereof as defined herein, together with a suitable adjuvant or excipient for administration to a mammal. The invention also provides a method for the prophylaxis of Pestivirus infections comprising administering to a mammal a composition as defined above, in an amount sufficient to elicit an immune response against Pestivirus. 
Furthermore, the invention provides a peptidomimeticum that mimics a peptide as defined herein.
Another aspect of this invention is a method for inducing antibodies against Pestivirus types or subtypes comprising administering to a mammalian host an antigenic substance or precursor thereof as defined herein, together with a suitable adjuvant, and harvesting resulting antibodies or antibody-producing cells from the mammalian host.
An antibody directed against a type or subtype of Pestivirus obtainable by the above method is also part of the invention. Preferably, the antibody is a monoclonal antibody.
In another aspect, the invention provides a diagnostic test kit for the detection of or the discrimination between (antibodies against) subtypes or types of Pestivirus comprising the above antibody and suitable means for detection.
For antibacterial and transport activity, the invention provides a similar amino acid sequence as listed in Tables 1 and 2. Systematic analysis showed that shorter peptides comprising Erns amino acids 194-220 had higher transport activity and lower hemolytic activity. This amino acid sequence preferably comprises a member selected from the group consisting of:










TABLE 4







CSFV
RQGAARVTSWLGRQLRIAGKRLEGRSK
(SEQ ID NO:1)



 


BVDV-1
RQGTAKLTTWLGKQLGILGKKLENKSK
(SEQ ID NO:2)


 


BVDV-2
RVGTAKLTTWLGKQLGILGKKLENKTK
(SEQ ID NO:3)


 


BDV
RQGAAKLTSWLGKQLGIMGKKLEHKSK
(SEQ ID NO:4)









or those presented in Table 5 relating to the L3 loop of ribosome-inactivating proteins.

Most peptides that have been used in serology represent continuous epitopes. It is impossible to detect antibodies against complex discontinuous epitopes using small linear peptides and it is difficult to predict discontinuous epitopes based on the amino acid sequence of a protein. In addition, the antigenic surface of large globular proteins cannot be mimicked accurately with a small linear peptide. We solved this problem by predicting an independently folding region in the Erns protein of pestiviruses that adopts a stable tertiary structure while retaining its antigenicity. This prediction is crucial for the correct design of a useful antigen. Two stretches of Pestivirus Erns show sequence homology with ribonuclease Rh (RNase Rh), a new class of microbial ribonuclease of Rhizopus niveus, a member of the T2/S RNase superfamily. A typical feature for this type of RNase is the low base specificity and the large molecular weight. The crystal structure of RNase Rh has been determined (Kurihara et al., J. Mol. Biol. 255: 310-320, 1996) and the three-dimensional (3D) structure confirmed that both stretches with sequence homology to Erns constitute the active site of the RNase. Apart from the two stretches of sequence homology, further homology in the rest of the protein was not apparent.
Despite a low sequence homology, we were able to construct an alignment using different types of scoring matrices and multiple sequence alignment of a large set of RNase sequences. A satisfactory alignment was not possible using alignment software with any parameter setting. Therefore, a part of the alignment was edited manually. For parts with low sequence homology, the alignment was guided by secondary structure prediction of the PHD software (Rost, B. and Sander, C., 1992, Nature, 360:540).
After inspection of the multiple sequence alignment, some major dissimilarities between the sequences of pestivirus Erns and the other RNases can be observed. Compared with sequences of the other RNases, the pestivirus sequences have a truncation at the N-terminus, large insertions after residues 83 and 135 and an elongated and very dissimilar C-terminus. The 37 C-terminal residues could not be aligned with the other RNases. Other characteristics of the C-terminus are the high number of positive charges and a high score for amphipathic helicity. A helical wheel representation of residues 191-221 shows an amphipathic helix with a hydrophobic face and a positively charged face (FIG. 2). The only three residues that may not correspond with the perfect amphipaticity are Ile210, Arg214 and Arg218. Although no obvious domains were found with software like SMART (Schultz et al., PNAS 95: 5857-5864, 1998), this C-terminal region, which is separate from the RNase domain according to the alignment, with its typical secondary structure can now be considered as a separate domain or module. Such a positively charged domain in an RNase molecule is not unique for Erns but has also been observed in type II ribotoxins, another class of RNases. This class of RNases comprises extracellular cytotoxins that hydrolyze the large ribosomal RNA (22) and are able to translocate across phospholipid bilayers (23). Although ribotoxins are known to enter cells, it is not known which region of the protein is responsible for translocation. The type II ribotoxins like alpha-sarcin and restrictocin contain a large inserted L3 loop (residues 53-91) compared with other RNases of the T1 superfamily (24, 25). This loop has structural similarity (but no sequence similarity) to loops found in lectin sugar-binding domains and may be responsible for the ribotoxin's ability to bind to the cell surface (24). The C-terminal domain of Erns has approximately the same length and contains similar sequence motifs as the ribotoxin II L3 loop (FIG. 3). Although the sequence similarity between the ribotoxin L3 loop and the C-terminus of Erns is low (FIG. 3), it is higher than the sequence similarity between L3 and the structurally similar lectin-binding domains (24). Although the ribotoxin L3 loop is also positively charged, it has no apparent amphipathic character. Another interesting homology of the E's C-terminal region is with the membrane interacting peptide magainin. The center of the E's peptide has high sequence homology with the N-terminal half of magainin (FIG. 3). This homology is even higher compared to the homology of magainin with other pore-forming peptides that have been described (26)
The (overall) 3D structure of Erns is similar to RNase Rh except for the C-terminal region, which is surprisingly similar to loop L3 of restrictocin or other ribotoxin II proteins. (This protein module likely folds independently, is metastable and can change to an alpha helical structure when it binds to the cell membrane.) The 3D structure of the C-terminal domain is not very important because of its spatial independence from the RNase domain.
With the aid of a modular structure, it is possible to define antigenic regions on the surface of the protein which can be mimicked by single linear peptides. The domain corresponding to the C-terminal 37 residues (191-227) is the best candidate because of its location on the outer rim on the surface of the Erns dimer; it forms a small functional domain which folds independently from the rest of the protein and it is not masked by any potential carbohydrate.
Development ELISA
The invention provides an antigenic and, in essence, proteinaceous substance for discrimination of infected animals with different types of pestiviruses from animals vaccinated with a subunit vaccine that does not contain the Erns peptide and infected animals. The antigenic substance is a peptide that corresponds to a C-terminal amino acid sequence of Pestivirus Erns which does not align with RNase Rh but with an L3 loop of a ribotoxin and folds independently from the rest of the protein.
An antigenic substance according to this invention is to be interpreted as any peptide-like or peptide-based substance (e.g., a protein module as provided herein optionally linked to another group such as a peptide or protein) capable of inducing an immune response against pestivirus or being recognized by serum-containing antibodies against a pestivirus. Precursors of such antigenic substances are, for example, comparable peptide-like or peptide-based substances which are not immunogenic themselves but need, for instance, to be coupled to a carrier to be able to induce an immune response or to be recognized. Peptide-based or peptide-like substances are intended to include anything with the function of the peptides according to the present invention. This means that these substances may be peptides themselves in which a number of amino acid residues have been replaced or modified. It also means that they may be fusion proteins, for instance, designed to present the amino acid sequence of the peptides of the invention on their surface. The definition also includes peptidomimetics and anti-idiotype antibodies derived from the peptides according to the invention.
In a preferred embodiment, the invention provides peptides that can be used in diagnostic assays for detection of antibodies directed against specific pestivirus types (CSFV, BDV, BVDV-I, BVDV-II).
The provision of the protein module, the independently folding region of Erns, relates to all types of pestiviruses and beyond. As a consequence, the invention is not limited to the peptides specifically disclosed herein, but extends to analogous peptides and their derivatives in all types of pestiviruses and all subtypes of these viruses and to homologues of the L3 loop of (ribosome inactivating) ribotoxin II proteins. Preferred peptides to be used according to the invention comprise at least antigenic parts of the peptides given in Table 2 or derivatives thereof, their length being from about 27 residues up to about 51 residues or transport peptides according to any one of Tables 1-5.
We have evaluated the applicability of the peptides in diagnostics by the development of different diagnostic assays: indirect ELISAs in which the antigen is recognized in solid phase and an indirect ELISA in which the antigen is recognized in liquid phase. Other diagnostic assays can, of course, be easily designed by the man skilled in the art. These may, of course, be provided in any suitable format.
Assays can be performed in solution and on solid phases. They can be performed using any kind of label, such as enzymes, solid particles, such as metal sols, or other sols, latex particles, dyes, fluorescent substances or radioactive materials. They even may be performed without labels, as can be done by agglutination assays. The peptides can be used to detect antibodies in, for instance, a fluid from a mammal, such as blood, serum, urine, and milk. Usually, the antibody is bound by a peptide, module or substance according to the invention, which may be present on a solid phase or in a liquid phase. Afterwards, the complex of peptide and antibody may be detected by a labeled reagent, which can be a labeled antibody directed against the host's (such as swine, bovine or sheep) antibodies.
According to the invention, the peptides can also be used to obtain antibodies which are specific for Pestivirus types and/or subtypes. The peptides are administered to a mammal, usually a rodent, in an immunogenic form, and after one or more booster administrations, the serum from the animal is harvested and antibodies can be purified therefrom.
Alternatively, the spleen of such animals may be removed to obtain antibody-producing cells. These can be changed, by fusion or transformation, into cell lines producing monoclonal antibodies. Assays based on (monoclonal) antibody-directed Pestivirus and induced by the peptides according to the invention are, therefore, also a part of the invention.
The peptides according to the invention can, of course, also be used in vaccines to prevent infection with Pestivirus. They may be used in conjunction with other antigens to elicit an immune response against Pestivirus. Usually, the peptide has to be coupled to a carrier to be presented in an immunogenic form before administration to a host. Other ways of rendering a peptide sufficiently immunogenic are known to the person skilled in the art. Adjuvants are usually added to vaccines to boost the immune response in a more aspecific manner.
Antibacterial and Transport Peptide
The invention further provides a membrane-active peptide or module or substance which can be used as an antibiotic and can be used as a transport peptide which is, for example, capable to carry cargos across the cell membrane. For coupling of cargo such as macromolecules, such as drugs, use is preferably made of a free hydroxyl group when available on the compound to be bound.
To use transport peptides as a drug-delivery system, these peptides can be linked to drugs via linkers. From the side of the drug or compound, for instance, cyclosporine A, acyclovir, or terbenafine, a functional group like the hydroxyl group can be used to couple a linking group via an ester bond. In the linking group, a function like a secondary amine (—NH—) can be inserted, which, by its orientation, catalyzes the cleavage of the ester bond with the drug and subsequently releases the original drug. An example of such a linker is: (drug) —O—CO—CH2—NR—CO—CH2—NH—CH2—CO-link2-(transport peptide).
The transport peptide can be coupled to this linker by a second linker (link2) using different chemistries. For instance, ethylenediamine can be coupled to the free carboxylic acid of the first linker. Subsequently, the resulting amino group can be coupled to a bromoacetic acid and this bromoacetyl group can react in high yield with, for instance, the free —SH group of a cysteine in the transporter peptide. Alternatively, the transport peptide can also be coupled directly to the labile linker via, for instance, a free amino group from the transport peptide.
Substituents in the linker on the different groups, like the group R on the tertiary amine, can help to regulate further the stability of the ester. Alternatively, thioesters can also be used as an even more labile linking group.
Alternative strategies can be used for the coupling of the transporter peptide to compounds that have no easily accessible hydroxyl group available. In the case of terbenafine, an ethynyletheen function can, for example, be used for the addition of the free —SH group in the linker to form for instance: (drug)—S—(CH2) n —NR—CO—CH2—NH—CH2—CO-link2-(transport peptide). This conjugate can easily be cleaved under basic conditions (internal base is present as secondary NH-group), releasing the original drug, here, in the example, terbenafine. The membrane-active peptide is similar to the described antigenic peptide which corresponds to a C-terminal amino acid sequence of Pestivirus Erns which does not align with RNase Rh but does align with magainin and, to some extent, with the L3 loop of ribotoxins and folds independently from the rest of the protein. The L3 loop peptides are specifically membrane-active peptides according to the invention as well. A membrane-active substance according to this invention comprises, for example, a peptide-like or peptide-based substance capable of inducing leakage of a bacterial membrane or disturbance of a eukaryotic cell membrane without leakage. Peptide-based or peptide-like substances are intended to include anything with the function of the peptides according to the present invention. This means that these substances may be peptides themselves in which a number of amino acid residues have been replaced or modified. It also means that they may be fusion proteins, for instance, designed to modify the cell specificity of the peptide. Preferred peptides to be used according to the invention comprise at least the membrane-active part of the peptides given in Tables 4, 5 and 10. Derivatives with a higher translocation activity are listed in Table 9.
The invention relates to a set of pestivirus diagnostic assays, antibacterial peptide and transport peptide based on peptides corresponding to the C-terminal domain of pestivirus Erns or the L3 loop of ribotoxin type II proteins. Preferred regions used for peptide-based diagnostics are listed in Table 2 and preferred membrane-active peptides used for antibiotics or transport peptides are listed in Tables 4 or 5, and 9 to 11. However, they can, of course, be used interchangeably for their various uses. The length of the peptide to be used in a diagnostic assay or vaccine is conveniently the exact length of the domain (residues 191 to 227, 37 residues) but can, of course, be shorter or longer, as long as it does not essentially change in antigenic or immunogenic character. The maximum length of a suitable peptide (residues 177 to 227, 51 residues) can incorporate a 14-residue linker region between the RNase domain and the C-terminal domain. This linker region may be exposed in case of uncertainty of the exact spatial position of the C-terminal domain relative to the RNase domain and because of the conformational change of the C-terminal domain. For that reason, the linker region may be part of a large C-terminal antigenic site. The preferred minimum length of a suitable peptide to be used in a diagnostic assay or vaccine is the part of the C-terminal domain that forms an amphipathic helix. This is the part of the C-terminal domain without the 5 C-terminal hydrophobic residues (191 to 222, 32 residues).
The diagnostic assays based on the peptides can be used to determine antibody levels in blood, serum, milk or other body fluids.
The materials according to the invention can be used for incorporation in vaccines, for example, to provide for a carrier of the desired antigen-to-antigen presenting cells, or to present an antigen within the context of MHC (I or II) peptide presentation, or to provide for mucosal vaccination by providing translocation of a desired antigen over an epithelial (gut) layer. The peptide can also be used to transport various cargos in eukaryotic cells, as far as into the Golgi system or in the nucleus of cells. Such cargos can comprise protein or peptide material, PNA, RNA or DNA, drugs, secondary metabolites, and so on. Peptide mixtures could be used as well to provide for synergy in antibacterial activity, transportation or translocation.
EXAMPLES
Structure Analysis of Pestivirus Erns 
A detailed analysis of the primary structure and homology modeling of pestivirus Erns allowed the definition of antigenic regions on the surface of the protein which can be mimicked by single linear peptides. The C-terminal 37 residues (191-227) are the best candidates because of their location on the outer rim on the surface of Erns and because they fold independently from the rest of the protein as a subdomain and are not masked by any potential carbohydrate. The independent character of the C-terminus is also illustrated by the functional analysis of Erns. Erns mutants have been made which are truncated from residue 168. In these mutants, the whole C-terminal part from residues 169 to 227 is missing. This mutant is still able to fold natively because the discontinuous active site is still intact and the mutant has wild-type RNase activity. Furthermore, the C-terminal 37 residues don't align with the other RNases but they do align with an L3 loop in ribotoxin type II proteins and with membrane-active peptides like magainins. These membrane-active peptides have a well-defined function, and for the magainins, it has been shown that they adopt helical conformations if they contact the cell membrane. We have demonstrated the membrane-active property of the Erns and/or L3. The membrane-active properties of the Erns peptide agree with the functionally independent nature of the subdomain. The location of this subdomain, the possibly independent folding of the sequence, the lack of potential glycosylation sites and its biological function make a peptide representing this region a suitable candidate to be used as an antigen/immunogen for immunoassays and vaccines. Furthermore, the biological activity of the Erns or the L3 peptide makes these peptides suitable candidates to be used as an antibacterial agent and/or a transport peptide.
ELISA Development
Peptide Synthesis
Peptides were selected from the C-terminal region (residues 191-227) of CSFV Erns, strain Alfort 187, BVDV Erns, strain M96751 and BDV Erns, strain X818 and the L3 loop of restrictocin (residues 59-88; Lamy and Davies, NAR 19: 1001-1006, 1991) and magainin (Zasloff, PNAS 84: 5449-5453, 1987):










CSFV:
acetyl-ENARQGAARV TSWLGRQLRI AGKRLEGRSK TWFGAYA-COOH
(SEQ ID NO:16)



 


CSFV:
biotin-ENARQGAARV TSWLGRQLRI AGKRLEGRSK TWFGAYA-COOH
(SEQ ID NO:16)


 


BVDV:
acetyl-EGARQGTAKL TTWLGKQLGI LGKKLENKSK TWFGAYA-COOH
(SEQ ID NO:17)


 


BVDV:
biotin-EGARQGTAKL TTWLGKQLGI LGKKLENKSK TWFGAYA-COOH
(SEQ ID NO:17)


 


BDV:
biotin-ENARQGAAKL TSWLGKQLGI MGKKLEHKSK TWFGANA-COOH
(SEQ ID NO:19)


 


restrictocin:
biotin-GNGKLIKGRTPIKFGKADCDRPPKHSQNGMGK-NH2
(SEQ ID NO:5)


 


magainin:
biotin-GIGKFLHSAGKFGKAFVGEIMKS-NH2
(SEQ ID NO:24)






Peptides were synthesized according to standard procedures on an Applied Biosystems 430A synthesizer using Fastmoc chemistry (Fields et al., Pept. Res. 4: 95-101, 1991). An extra CSFV and BVDV peptide were synthesized which were N-terminally biotinylated instead of acetylated.
Serum Samples
The following swine serum samples were incorporated in the study to evaluate the peptide ELISAs.

    
    
        Negative field serum samples (n=96) were randomly obtained from slaughtered adult pigs. Sera were all tested negative in the CSFV-E2 and pan-pestivirus antibody-specific Ceditest ELISAs.
        Pestivirus serum antibody-positive but CSFV-negative serum samples (n=96) were randomly obtained from slaughtered adult pigs. Swine sera were tested negative in Ceditest CSFV-E2-specific ELISA (Colijn et al., Vet. Micro. Biol. 59: 15-25, 1997) and positive in the pan-pesti ELISA (Paton et al., J. Virol. Meth. 31: 315-324, 1991; Kramps et al., Vet. Micro. Biol. 64: 135-144, 1999).
        CSFV antibody-positive field serum samples tested by virus neutralization test were obtained (n=95) from an infected pig farm (VR) that was infected during the CSF epizootic in the Netherlands in 1997-1998.
        Sequential serum samples were collected during a vaccination/challenge experiment of 12 pigs that were vaccinated with E2 and infected with CSFV, strain Brescia. Specific Pathogen-Free (SPF) animals were challenged with the virulent CSFV strain Brescia two weeks after a single vaccination with the E2 subunit vaccine.
        Panel of swine sera that were experimentally infected with BVDV (n=5, numbers 4-8).
        Panel of swine sera that were experimentally infected with CSFV strain Paderbom (n=5, numbers 9-13).
        Panel of bovine sera that were experimentally infected with BVDV (n=9, numbers 1-6, r4590-51, r4590-52, 841).
        Reference panel obtained from the European reference laboratory for CSFV: sera from swine that were experimentally infected with CSFV (n=14), BVD (n=1) or BVDV (n=12). Three sera were obtained from swine with experimental mixed infections of BVDV/BDV (n=1) and CSFV/BVDV (n=2).
        Pool of hyperimmune sera against CSFV (HIS CSFV).
        Pool of hyperimmune sera against BVDV (HIS BVDV).
    
    


Solid Phase Peptide ELISA (sp-ELISA)
Test Procedure
For the sp-ELISA, a similar format was chosen as for a previously developed RSV G-peptide ELISA (Langedijk et al., J. Imm. Meth. 193: 153-166, 1996). One microgram of N-terminally acetylated pestivirus peptide was coated per well of a high binding capacity flat bottom microplate (Greiner) in 50 μl of carbonate buffer, pH 9.0, at 37° C. and dried overnight. The optimal dilution of the peptide to coat ELISA plates was chosen in such a manner that maximum binding was obtained as determined in a checkerboard titration. Test sera were titrated. Mouse-anti-swine IgG (23.3.1b) conjugated to horseradish peroxidase (HRP) was diluted 1:1000. Rabbit anti-bovine IgG-HRP (P0159, Dako, Denmark) was diluted 1:1000. Conjugates and test sera were incubated for one hour at 37° C. in ELISA buffer (8.1 mM Na2HPO4, 2.79 mM KH2PO4, 0.5 M NaCl, 2.68 mM KCl, 1 mM Na2EDTA, 0.05% v/v Tween 80, pH 7.2) containing 4% horse serum. The substrate chromogen consisted of ABTS/H2O2. Incubation was performed during 30 minutes at 22° C. OD was measured at 405 nm (Titertek multiscan).
Results
The reactivity of BVDV-positive swine sera (4-8) and CSFV-positive swine sera (9-13) were tested for reactivity in the CSFV sp-ELISA and the BVDV sp-ELISA.
The reactivity of bovine sera (numbers 1-6, r4590-51, r4590-52, 841) were tested for reactivity in the CSFV sp-ELISA and the BVDV sp-ELISA.
Reactivity of the sera with the peptides was excellent, which shows that the peptides indeed correspond to an immunodominant region of Erns. This agrees with the prediction of the immunodominant character of the subdomain. However, the CSFV and BVDV sera are cross-reactive for both peptides. Although the panel of CSFV-specific swine sera reacted better than the panel of BVDV-specific swine sera in the CSFV ELISA, the reactivities of both panels of sera are similar in the BVDV ELISA. Similarly, the panel of BVDV-specific bovine sera shows high reactivity in the BVDV peptide ELISA (FIG. 5D), but the sera also cross-react considerably in the CSFV ELISA (FIG. 5C).
Liquid Phase Peptide ELISA (1p-ELISA).
Because of the high cross-reactivity in the solid phase peptide ELISA, an ELISA was developed in which the antigen was recognized in liquid phase (1p-ELISA). Moreover, by labeling the homologous peptide of the pestivirus of interest (CSFV peptide), unlabeled heterologous peptide of the cross-reactive pestivirus (BVDV peptide) could be used to block unspecific cross-reactivity.
In the liquid phase peptide ELISA for detection of antibodies against CSFV, the test serum was incubated with a mixture of biotinylated CSFV peptide and acetylated BVDV peptide (without biotin). CSFV-specific antibodies will preferably bind the biotinylated CSFV peptide and BVDV-specific antibodies will preferably bind the nonbiotinylated BVDV peptide. Subsequently, the mixture is transferred to an avidin-coated microtiter plate and the antibodies complexed to the biotinylated CSFV peptide will be caught by avidin and can be detected with an anti-swine peroxidase conjugate and subsequent incubation with substrate.
Test Procedure:
Avidin-coated microtiter plates: 400 ng of ImmunoPure avidine (No. 21121, Pierce, Rockfort, Ill., USA) in 100 μl of carbonate buffer (pH 9) in each well of a high binding capacity flat bottom microplate (Greiner). Plates were covered and incubated overnight at 37° C. After coating, the plates were kept frozen until use.
Before use, the avidin-coated plates were incubated with 100 μl of phosphate-buffered saline (PBS, pH 7) with 10% horse serum per well for two hours at 37° C. on a shaker.
Meanwhile, test serum (1:50) was incubated with a mixture of 10 ng biotinylated CSFV peptide and 30 ng of BVDV peptide in 100 μl of ELISA buffer with 4% of horse serum for one hour at 37° C.
Avidin-coated plates were washed and 100 μl of test serum and peptide mixture was transferred in the wells and incubated for 45 minutes at 37° C. Subsequently, plates were washed and incubated with 100 μl mouse-anti-swine IgG (23.3.1b) conjugated to horseradish peroxidase (HRP) (Van Zaane et al., 1987) diluted 1:1000 or with rabbit anti-bovine IgG-HRP (P0159, Dako, Denmark) diluted 1:1000. The substrate chromogen consisted of ABTS/H2O2. Incubation was performed during 30 minutes at 22° C. OD was measured at 405 nm (Titertek, multiscan). Cutoff value was chosen at OD>0.5, which is approximately 3 times the average background of known negative sera.
Results
The reactivity of BVDV-positive swine sera (4-8) and CSFV-positive swine sera (9-13) were tested for reactivity in the CSFV 1p-ELISA (FIGS. 5A-5D). This test format showed much better specificity than the sp-peptide ELISA.
To determine the specificity of the 1p-peptide-ELISA, 96 negative field serum samples were tested in the 1p-peptide-ELISA for CSFV Erns-Ab. Only 2 of 96 samples showed a positive response (cutoff was chosen at OD>0.5). Based on these data, the specificity of the 1p-peptide ELISA for CSFV Erns-Ab amounts to 98% (=94/96×100%) (FIGS. 6A-6B).
To determine the specificity of the 1p-peptide-ELISA, 96 field sera that contain antibodies directed against other pestiviruses than CSFV (BVDV and BDV) were tested in the 1p-peptide-ELISA. Only 2 of 96 samples showed a positive response (OD>0.5). Based on these data, the specificity of the 1p-peptide ELISA for CSFV Erns-Ab for non-CSFV-pestivirus-positive sera amounts to 98%(=94/96×100%) (FIGS. 6A-6B).
To determine the sensitivity of the 1p-peptide-ELISA, 95 field serum samples from a CSFV-infected farm (VR) obtained during the CSF epizootic in the Netherlands in 1997-1998 were tested in the 1p-peptide-ELISA. Not a single serum sample showed a positive response (OD>0.5). Based on these data, the sensitivity of the 1p-peptide ELISA for CSFV antibodies amounts to 100% (FIGS. 6A-6B).
An interesting application of the 1p-peptide ELISA is a diagnostic test that can be used to detect CSFV infection of E2-vaccinated pigs. Therefore, sera of E2-vaccinated pigs should be unreactive in the 1p-peptide ELISA and should be positive after CSFV challenge of the pigs. Successive serum samples, which were collected during a challenge experiment of 12 E2-vaccinated pigs that were infected with CSFV, were tested in the 1p-peptide ELISA (FIG. 7). The results show that all sera but one from E2-vaccinated pigs were negative prior to CSFV challenge. All animals (except one) seroconverted 14 to 28 days after challenge. Finally, the performance of the 1p-peptide ELISA was compared with the E2-based Ceditest ELISA and two other Erns-based ELISAs. The reactivity of a panel of European reference sera (see methods) was tested in all four ELISAs (Table 6). Although the E2-based ELISA was superior (one false-negative), the 1p-peptide ELISA performed better (three false-negative) than the other ELISAs based on epitope blocking using complete Erns (5 false-negative, one false-positive, one false-negative and six false-positive). It is very likely that the 1p-peptide ELISA can even be optimized when it is changed into an antibody-blocking format, like the other three ELISAs in Table 6.
To illustrate the compatibility of the peptide ELISA with other pestiviruses, the CSFV-specific peptide ELISA was changed into a BVDV and a BDV ELISA by exchanging the biotinylated CSFV peptide for a biotinylated BVDV peptide or a biotinylated BDV peptide and the acetylated BVDV peptide for the acetylated CSFV. The same amount of peptide was used as in the 1p-CSFV peptide ELISA and all assay conditions were kept similar. The panel of swine sera that were experimentally infected with BVDV (n=5, numbers 4-8) or CSFV (n=5, numbers 9-13) were tested in the three different 1p-peptide ELISAs for the three different pestivirus types. Table 7 shows that BVDV-positive sera react best in the BVDV-specific peptide ELISA and that the CSFV-positive sera react best in the CSFV ELISA, although the CSFV sera cross-react to some extent with the BVDV peptide. As expected, on the basis of the sequence homology, the BVDV and BDV ELISAs show less differentiation. The BVDV and BDV ELISAs both contained acetylated CSFV peptide as competing antigen. Some improvement may be possible when also acetylated BDV and BVDV peptide would be used as competing antigen in the BVDV and BDV ELISAs, respectively.
The acetylated CSFV peptide (Table 2) was further used to test the immunogenicity of the peptide in pigs and to examine whether vaccination with the peptide could protect the pigs after CSFV challenge. Pigs were vaccinated with the various amounts of the peptide, formulated in Freund's Complete Adjuvant (FCA). Four weeks later, the pigs were vaccinated again with 1.3 mg peptide, formulated in Freund's Incomplete Adjuvant (FIA). Five control pigs were vaccinated similarly with just FCA and FIA. Three weeks after the second vaccination, the pigs were challenged nasally with 100 LD50 CSFV, strain Brescia 456610. Antibody reactivity against the peptide was monitored during the experiment. Before and after challenge, virus isolations were performed on white blood cells. After death or euthanasia, organs (tonsil, spleen, kidney and ileum) were tested for the presence of viral antigen using an immunofluorescence test.
Monoclonal Antibody Production
Production of Erns peptide-specific monoclonal antibodies (Mabs) was performed as described (Wensvoort et al., 1986). Two BALB/c mice were immunized intraperitoneally with 400 μg CSFV or BVDV peptide (residues 191-227), mixed with Freund's complete adjuvant (FCA). After four weeks, the mice were boostered with 400 μg of peptide mixed in incomplete FCA, and three weeks later, the mice were boostered with 400 μg of peptide in phosphate-buffered saline. Three days later, the spleen cells were fused with sp20 cells and hybridomas were grown in selective medium. The Erns specificity of the produced Mabs (Mab 906-2-1 (BVDV) and Mab 907-35-1-1 (CSFV)) was determined using an Erns antigen detection ELISA. Additionally, the Mabs reacted in the Erns peptide-based ELISAs.
Transport Activity of Erns Peptide
Test Procedure.
Binding of Erns peptide. Monolayers or cytospins of cell suspensions of several cell types (Ebtr, SK6, sf-21, Caco-2 and HT-29) were fixed with acetone or 4%-paraformaldehyde. Glass slides or coverslips with fixed cells were incubated with biotinylated CSFV peptide (100 or 10 μg/ml PBS) for one hour at 37° C. After washing with PBS, the slips were incubated with avidin-HIRP (1:100, Zymed) or avidin-FITC (1:70, Zymed) for 30 minutes at 37° C. Cells were inspected for specific binding of the peptide by light microscopy (HRP) or fluorescence microscopy (FITC).
Translocation of Erns peptide. Translocation of the peptide across the plasma membrane was studied by incubation of live cells in suspension or subconfluent monolayers on coverslips with biotinylated peptide (200 to 0.4 μg/ml culture medium) for 1, 10, 30, 45 or 180 minutes. After the time period, cells were fixed with 4% paraformaldehyde or cold methanol and labeled with avidin-FITC as described above. Fixed cells were inspected with fluorescence microscopy. Internalization was established with confocal microscopy. The following cell lines were used: A72, canine fibroblast tumor cells; MDCK, canine kidney epithelial cells; CCO, sheat-fish ovaria cells; EK-1, eel kidney cells; CHS-E, salmon embryonal cells; BUEC, bovine umbilical endothelial cells; BFDL, bovine fetal diploid lung cells (fibroblast); PUEC, porcine umbilical endothelial cells; HT 29, colorectal adenocarcinoma, colon epithelial cells; CaCo-2, colorectal adenocarcinoma, colon epithelial cells; Hela, adenocarcinoma, cervix; Vero, normal monkey kidney epithelial cells; SK6, swine kidney cells; NPTh, newborn pig thyroid cells; ECTC, embryonal calf thyroid cells; MDBK, normal bovine kidney epithelial cells; EBTr, epithelial bovine trachea cells; Bovine sperm cells; Sp20 mouse myeloma B-cells.
Transepithelial transport. The potential of Erns peptide to permeabilize epithelium and assist transport of molecules across epithelium was tested in USSING chambers of the snapwell type with CaCo-2 or HT29 cells that closely mimic epithelial cell sheets.
The potential of Erns peptide to carry nonlinked molecules across epithelium was tested by mixing HRP (0.08 μg/ml culture medium) with several concentrations of Erns peptide (50, 5 and 0.5 μg/ml ringers medium) in the upper chamber. Samples were drawn from the lower chamber after 15, 30, 45, 60, 120 and 240 minutes, which were tested for HRP concentration.
Transdermal transport. The potential of the an Erns peptide to penetrate the skin was tested by applying 150 μl 0.3-4 mM of biotinylated peptide in a chamber containing an isolated piece of “fresh” human breast skin or in a chamber which was glued on the skin of a live pig, or applying 50 μl of peptide solution on the skin with a cotton wool tip, or applying 50 μl of a peptide solution mixed with 50 μl of contact gel on the skin for 30 minutes to 120 minutes. After the incubation time, the pig was killed, the skin was cleaned and biopsied, and a biopsy was frozen in liquid nitrogen. Cryosections of the skin samples were fixed on microscopic slides with acetone and incubated with streptavidin-FITC ( 1/100) for 30 minutes.
Hemolytic assay. Hemolytic activity of various peptide concentrations was determined by incubation with human, guinea pig or sheep erythrocyte suspensions (final erythrocyte concentration, 1% v/v) for one hour at 37° C. After cooling and centrifugation, the optical density of the supernatants were measured at 540 nm. Peptide concentrations causing 50% hemolysis (EC50) were derived from the dose-response curves.
Clonogenicity of mammalian cells. HeLa or EBTr cells were cultured in DMEM, supplemented with 20% fetal bovine serum and antibiotics in a humidified atmosphere supplied with 5% CO2 at 37° C. Exponentially growing cells were treated with trypsin and transferred to wells of a 96-well microtiter plate, resulting in approximately 300 cells for each 30 μl of growth medium containing various concentrations of peptide. After incubation for 75 minutes (the plates were incubated upside down to avoid anchorage), the cells were transferred and plated in wells of tissue culture plates, which contained 100 μl of growth medium. Cell growth was checked after 3 to 6 days.
Antimicrobial assay. Two bacterial strains (Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 29212) were inoculated on heart infusion agar with 5% sheep blood and incubated aerobically overnight at 37° C. From the pure cultures, suspensions were made in saline to a density of 0.5 McFarland. These suspensions were diluted ten-fold in Mueller Hinton II broth, resulting in a final inoculum of approximately 107 cfu/ml.
Standard 96-well microtiter trays were filled with 100 ill of two-fold dilutions of peptide in physiologic salt solution in each well, resulting in the following concentration range: 4000, 2000, 1000, 500, 250, 125, 62.25, 31.63, 15.82, 7.96 and 0 μg/ml. The trays in column 12 were filled with 200 μl MH II broth (negative control).
Columns 1-11 of the microtiter trays were filled with 100 μl of the final inoculum of the bacterial suspensions, thus diluting the concentrations of the peptide two fold, resulting in the following peptide concentration range in the wells: 2000, 1000, 500, 250, 125, 62.25, 31.63, 15.82, 7.96, 3.98 and 0 μg/ml. In rows B, C and D, 100 μl of the final inoculum of E. coli and, in rows E, F and G, 100 μl of the final inoculum of E. faecalis was pipetted. The final bacterial concentration was approximately 5×105 cfu/well. All trays were sealed and incubated overnight at 37° C. After incubation, the microtiter trays were inspected visually for bacterial growth and the absorbance of the cultures at 630 nm (A630) was determined with an ELISA-reader. The peptide concentrations in the wells with the lowest concentrations that showed no visible growth or increase in absorbance compared with the negative control wells were considered to be the Minimum Inhibitory Concentrations (MICs). The experiment was performed independently in triplicate. The test was repeated again in triplicate after two days with the final peptide concentration range in the wells: 5000, 2500, 1250, 625, 312.5, 156.25, 78.12, 39.06, 19.58, 9.79, 4.88, 2.44 and 1.22 μg/ml.
Peptide synthesis. A panel of truncated Erns peptides was synthesized to elucidate the minimal membrane-active region. A panel of truncated restrictocin L3 peptides was synthesized to elucidate the minimal membrane-active region. Substitutions in the amino acid sequence of the transport peptide module can be applied to increase the translocation activity. An optimized transport peptide can, for example, be synthesized according to retro-inverso peptide chemistry, in which the sequence is reversed and D-amino acids are used instead of L-amino acids. Synthesis is performed as described above.
Coupling of peptide to oligonucleotide. The optimized Erns peptide contains a Broom-acetic acid at its N-terminus (Broom-GRQLRIAGKRLEGRSK) (SEQ ID NO:25) coupled to two sulfhydryl groups at the 5′- and the 3′-end of an FITC-labeled 32 residue long oligonucleotide (Thiol-GTFITCCCACCGAGGCTAGCTACAACGACCCTTATAT-thiol) (SEQ ID NO:26).
Results
To determine the binding of the Erns peptide, biotinylated CSFV peptide was incubated with various fixed cells. Binding was determined after incubation with avidin-HRP or avidin-FITC. Biotinylated CSFV peptide was able to bind to all tested cell types. There was a marked difference between the binding to paraformaldehyde versus acetone-fixed cells. In contrast to the paraformaldehyde-fixed cells, the acetone-fixed cells showed less binding with the peptide. Because much of the membrane fraction gets washed away after acetone-fixation, this suggests that the peptide may bind to the membrane.
Next, cell suspensions (mouse myeloma and bovine sperm) and subconfluent monolayers of various cell types (see test procedure) were incubated with biotinylated CSFV peptide and fixed after different time intervals. Inspection with fluorescent microscopy and confocal microscopy showed that the peptide had penetrated inside all cell types. The peptide entered the cell within one minute, and optimal fluorescence was established after 30 minutes (FIG. 8). Peptide was translocated to specific regions inside the nucleus, which may be the nucleoli. Peptide was also distributed around the nucleus in membranous parts in the cytosol. The colocalization in the nucleoli was established by double staining with acridinorange (Merck, Darmstadt, Germany) and streptavidin—Texas red. Yellow fluorescence was observed which indicates colocalization of peptide and nucleoli stain. Next, the membrane-active region of the peptide was precisely defined by testing the translocation activity of a panel of truncations of the Erns peptide and some peptides with N-terminal additions and C-terminal deletions (Table 8). Translocation to the nucleus was more effective with the CSFV, strain Alfort, Erns peptide compared to the BVDV or BDV Erns peptide. The CSFV, strain Alfort, Erns peptide translocated also more effectively than the CSFV peptide corresponding to strains in which positions 209, 210 and 217 were substituted. Furthermore, deletion of the seven most C-terminal residues and the three N-terminal residues increased the nuclear translocation activity of the peptide. To reduce the length of the transport peptide further, the region responsible for translocation (residues 194-220) was truncated while arginines were introduced to maintain or enhance the translocation activity. N-terminal deletions were made of 4 and 5 residues and one extra arginine was introduced at the same face of the presumed helix. These shorter peptides retained translocation activity (Table 9). Next, 11 N-terminal residues were deleted and the glutamic acid was substituted by arginine. This substitution enhanced the translocation activity by a factor of 33. Replacing the two lysine residues by arginine residues enhanced the translocation activity by an additional factor of three. Introducing more arginines in the sequence did not improve the translocation activity of the biotinylated peptide (Table 9). Next, the optimized peptide (MDK-20) was synthesized with D-amino acids according to the retro-inverso approach with an additional lysine-MTT (peptide A941: biotin-rsrgrlrrgairlqrgK (SEQ ID NO:27) (MTT)-BrHAc). This peptide retained its translocation activity and showed even a higher translocation activity compared with the original MDK-20, showing the advantages of the retro-inverso approach.
Because of the homology between the Erns peptide, magainin and the L3 loop peptide, the biotinylated magainin and L3 loop peptide were also tested for translocation activity. L3 showed translocation activity, magainin did not (FIG. 9). Next, the membrane-active region of the peptide responsible for translocation was precisely defined by testing the translocation activity of a panel of truncations of the L3 peptide (Table 10). To elucidate general rules for peptide translocation, we searched for new transport peptides and tested them for translocation across the plasma membrane.
HIV-1 tat peptide, which is a transcription factor that binds DNA, the AntP peptide, which is a homeobox protein, and transportan, which is a hybrid peptide of a bee venom, and galparan. The only similarity between the known transport peptides is the content of basic residues. See also Wender, P. A. et al., 2000, Proc. Natl. Acad. Sci. USA, 97:13003-8, who, however, require high >50% arginine content.
To search for more transport peptides, we tested the translocation of basic peptides which were derived from linear DNA-binding motifs; RNA-binding motifs; heparin-binding motifs, basic enzymatic cleavage sites and nuclear localization signals. For nuclear localization signals (NLS), it is already known that they are able to translocate the nuclear membrane, although it is thought that they need to be recognized by a receptor in order to translocate. We tested whether peptides corresponding to nuclear localization sites could also be used as general transport peptides that cross the plasma membrane.
Several types of short transport peptides were found:
Monopartite: PKKKRKV (SEQ ID NO:28). Binds the import receptor Imp alpha/imp beta complex.
This sequence is identical to the NLS of simian virus 40 large T antigen.
Bipartite: KRPAAIKKAGQAKKKK (SEQ ID NO:29) (lysine-rich signals).
NLS of HIV-1 Rev RQARRNRRRRWR (SEQ ID NO:30).
HIV-1 rev is a viral RNA export factor and shuttles RNA outside the nucleus. The sequence motif binds RNA.
A synthetic peptide has been developed (RSG-1.2) that binds the Rev binding site RNA with 10 times higher affinity











DRRRRGSRPSGAERRRRR
(SEQ ID NO:31)







NLS of human herpesvirus-8 K8 protein TRRSKRRSHRKF (SEQ ID NO:32).
K8 protein is homologous to EB1 protein of Epstein-Barr virus (EBV), which is a transcriptional activator which directly binds specific sites on the DNA.
Another class of basic peptides that may in some cases also be NLS peptides are RNA/DNA-binding peptides. For instance, the HIV-1 Rev peptide also binds directly to RNA.
Other examples of peptides that bind DNA or RNA:
RNA-binding element of flockhouse virus (FHV)











NRTRRNRRRVR.
(SEQ ID NO:33)







RNA-binding element of bacteriophage lambda-N











QTRRRERRAEKQAQW.
(SEQ ID NO:34)







Another class of basic peptides are basic enzymatic cleavage sites.
An example of a viral enzymatic cleavage site is in the surface proteins of alpha viruses. The cleavage site between E3 and E2 is highly basic. After cleavage, it is the C-terminal region of E3 which is located at the distal end of the viral spike, interacting primarily with E2.
Western equine encephalitis virus E3: KCPSRRPKR (SEQ ID NO:35).
Other examples of basic peptides are linear heparin-binding sites. The transport peptide corresponding to the Erns C-terminal domain also binds heparin. Examples are peptides found in HRSV-G, type A: KRIPNKKPGKKTTTKPTKKPTIKTTKKDLKPQTTKPK (SEQ ID NO:36) and HRSV-G, type B: KSICKTIPSNKPKKK (SEQ ID NO:37).
These peptides showed translocation activity (Table 11). In the case of the heparin-binding sites of HRSV-G, the region responsible for translocation was mapped (Table 11). One of the most active HRSV-G peptides (Biotin-KRIPNKKPKK) (SEQ ID NO:38) was further optimized by changing all lysine residues into arginine residues to check whether the peptide showed higher translocation activity when residues were introduced which were more basic. Changing the four lysines to arginines improved the translocation activity by a factor of three (Table 11).
According to Table 9, the most active biotinylated peptide (residues 194-220) was still (faintly) detectable at 125 nM. As a result, the elucidation of the minimal essential part of the translocation peptide also proves that a C-terminal cargo of at least 6 residues can be transported and an N-terminal cargo of at least 13 residues plus a biotin can be transported. Because the peptide is probably also able to transport the RNase domain of Erns inside the cell, it is also expected that large proteins can be transported by the peptide. After mixing equimolar amounts of streptavidin-FITC (60 kD, nonglycosylated, neutral) with the most active Erns peptide (residues 194-220) and with an optimized Erns peptide (biotin-GRQLRIAGKRLEGRSK) (SEQ ID NO:25), it was possible to transport streptavidin-FITC inside the cell and the nucleus (FIG. 10). The peptides were also able to carry avidin-Texas Red (66 kD, glycosylated, positively charged) inside the cells. Also, the optimized Erns peptides and the long and short HRSV-G type A peptides (MDN-12 and MDP-32 according to Table 11) were tested for their ability to transport streptavidin-FITC into the cell (FIGS. 10F-10H). The translocation activity of the peptide complexed to the streptavidin cargo was different from the translocation of the biotinylated peptide alone. The optimized Erns peptide MDM-27, which has two additional positive charges compared to the optimized Erns peptide MDK-20, transports streptavidin-FITC much better than MDK-20. In contrast, in the case of the uncomplexed biotinylated peptide, the translocation activity was similar. This effect was even more pronounced when the longer HRSV-G peptide (MDN-12) was compared to the shorter HRSV-G peptide (MDP-32), which has less positive charge but higher translocation activity as a single, uncomplexed molecule without cargo (FIGS. 10G and 10H).
To check whether the transport peptide was also able to transport proteins that retain biological activity, the peptide was complexed with streptavidin conjugated to the enzyme β-galactosidase (600 kD). The complex was transported efficiently into the cells and retained its ability to release nonreducing terminal galactose. To check whether the peptides could transport oligonucleotides, the optimized Erns peptide was activated by a Broomacetic acid. Transport module Broom-GRQLRIAGRRLRGRSR (SEQ ID NO:39) was coupled to an FITC-labeled 32 oligonucleotide at the 5′- and the 3′-end. The complex was tested for translocation inside the cell and the nucleus. Titration of the uncoupled oligonucleotide and the complex of peptide and oligo showed that the intracellular accumulation of the oligonucleotide was 75 times higher when it was coupled to the transport peptide. To check whether the membrane destabilizing activity had a general toxic effect on cells, leakage of the cell was tested for tryphan blue after peptide incubation of 30 minutes. Only at high concentrations of peptide (>35 μM), some tryphan blue could be determined inside the cell, especially in isolated areas in the nucleus.
Hemolysis of erythrocytes can also be indicative for lytic effect of the peptides on eukaryotic cell membranes. Hemolysis of erythrocytes from several species was tested with the panel of Erns peptides (Table 8). The different peptides show a broad range of hemolytic activities on guinea pig erythrocytes. The peptide with the highest translocation activity (residues 194-220) has a low hemolytic activity. No significant hemolysis was observed with sheep and human erythrocytes. The effect of the Erns peptide on cell growth of HeLa cells and EBTr cells was determined in a clonogenicity assay as shown in Table 12. These data correspond to the other toxicity assays and indicate that the translocation activity is much higher than the cytotoxic activity.
Transdermal Transport
Next, it was tested whether the optimized Erns peptide (MDK-20) was able to penetrate an epithelial layer. Because of the stratum corneum layer, the skin seems to be the most difficult epithelial barrier to take. To test the penetration by the biotinylated peptide, a sample of human breast skin was contacted with the biotinylated peptide in vitro during two hours. In fixed cryosections of the skin, the biotinylated peptide could be visualized with streptavidin-FITC in the epidermis and the dermis (FIG. 13). The same results were obtained when the peptide was contacted with the skin of a pig in vivo. As soon as 30 minutes after application, penetration of the peptide into the epidermis was observed. Because of the high amount of proteolytic enzymes in the skin, transdermal transport was also tested with the stable retro-inverso peptide containing D-amino acids. Much more accumulation in the skin was observed for the peptide with D-amino acids (A941) compared with the original peptide containing L-amino acids (MDK-20)
Trans epithelial transport. Next, the peptide was tested for the ability to assist leakage of proteins through an epithelial cell sheet. Horseradish Peroxidase, which was mixed with the peptide, could be transferred through the cell sheet.
Antibacterial activity. Because of the membrane activity and the homology with antibacterial peptides, the antibacterial activities of the peptides were determined as described above. The peptides indeed showed antibacterial activity against the gram-negative E. coli (Table 13) but not against E. faecalis. The MICs against E. coli correlate with the translocation activity of the peptide. The restrictocin L3 peptide showed no antibacterial activity.










TABLE 5







Restrictocin
GNGKLIKGRTPIKFGKADCDRPPKHSQNGMGK
(SEQ ID NO:5)



 


Mitogillin
--------------------------------
(SEQ ID NO:5)


 


Toxin AspfI
--------------------------------
(SEQ ID NO:5)


 


Alpha-sarcin
-D---P----------S---------KD-N--
(SEQ ID NO:6)


 


Gigantin
-E--IL----------S---------KD-N--
(SEQ ID NO:7)


 


Clavin
-D--IL-------W-NS---------K--D--
(SEQ ID NO:8)
















TABLE 6







Comparison of reactivity of reference sera with different CSFV


diagnostic tests.
















E2-ELISA
ERNS ELISA




No.
DPI1
Inoculum
Cedi-E22
Cedi-Erns3
Bommelie4
Peptide
















1
43
CSFV Visbek/Han 95
+
+
+
0.171


2
16
CSFV Visbek/Han 95
+
+
+
0.477


3
20
CSFV Visbek/Han 95
+
+
+
1.796


4
20
CSFV Visbek/Han 95
+
−
+
3.165


5
14
CSFV Visbek/Han 95
+
+
+
0.7


6
21
CSFV Alfort 187
+
−
−
0.186


7
29
CSFV Diepholz1/Han 94
+
+
+
2.25


8
29
CSFV Diepholz1/Han 94
+
−
+
2.619


9
29
CSFV Diepholz1/Han 94
+
−
+
1.857


10
34
CSFV Visbek/Han 95
+
−
+
3.87


11
55
CSFV Visbek/Han 95
+
+
+
1.122


12
93
CSFV C-strain
+
+
+
0.543


13
69
CSFV Diepholz1/Han 94
+
+
+
2.146


14
28
CSFV Diepholz1/Han 94
−
+
+
1.103


15

BVDV NADL
−
−
−
0.103


16

BDV
−
−
−
0.45


17

BVDV 2214
−
+
+
0.161


18

BVDV NADL
−
−
−
0.118


19

BVDV NADL + BDV
−
−
+
0.136


20

BVDV + CSFV
+
+
+
3.208




Alfort 187


21

BVDV Osloss
−
−
−
0.146


22

BVDV Osloss
−
−
−
0.151


23

BVDV Osloss
−
−
−
0.151


24

BVDV Osloss
−
−
−
0.162


25

BVDV Osloss
−
−
−
0.172


26

BVDV Osloss
−
−
+
0.164


27

BVDV Osloss
−
−
+
0.149


28

BVDV Osloss
−
−
+
0.163


29

BVDV Osloss
−
−
+
0.215


30

CSFV Alfort 187 + BVDV
+
+
+
0.567




Osloss





1Days post infection. Serum numbers 21-29 obtained from same animal


2Cedi-E2 assay registration no.: BFAV/KSP/D10/98


3Cedi-Erns assay


4Bommelie AG/Intervet assay













TABLE 7







Comparison of reactivity (OD 405) in different Pestivirus peptide ELISAs.












Serum Number
CSFV
BVDV
BDV







 4 BVDV
0.236
1.346
0.781



 5 BVDV
0.129
0.724
0.388



 6 BVDV
0.106
3.211
0.824



 7 BVDV
0.250
4.000
4.000



 8 BVDV
0.104
4.000
2.325



 9 CSFV
0.487
0.367
0.349



10 CSFV
2.090
1.612
0.343



11 CSFV
2.555
0.610
0.246



12 CSFV
1.133
0.453
0.412



13 CSFV
1.253
0.573
0.436



HIS CSFV 1:500
2.263
0.471
0.624



HIS CSFV 1:1000
1.419
0.267
0.356



HIS CSFV 1:2000
0.871
0.166
0.180



Negative serum
0.152
0.150
0.153







All sera were diluted 1:50 except for the HIS sera













TABLE 8







Determination of minimal membrane-active sequence of Erns.












Residue

Cellular
Nuclear
Hemolysis



number
Sequence1
fluorescence
fluorescence
(mg/ml)
















191-227
$ENARQGAARVTSWLGRQLRIAGKRLEGRSKTWFGAYA#
(SEQ ID NO:16)
++++
++
0.07




—COOH


 


 191-2272
$ENARQGAARVTSWLGRQLSTAGKRLE*RSKTWFGAYA#
(SEQ ID NO:43)
+++
+
0.08



—COOH


 


191-227
$ENARQGAAKLTSWLGKQLGIMGKKLEHHSKTWFGANA
(SEQ ID NO:44)
++++
+
0.25


(BDV)
—COOH


 


 194-2303
$EGARQGTAKLTTWLGKQLGTAGKKLENKSKTWFGAYA#
(SEQ ID NO:45)
++++
+
0.25


 


184-223
$DGMTNTIENARQGAARVTSWLGRQLRIAGKRLEGRSKTWF#
(SEQ ID NO:46)
++++
++
0.15


 


181-220
$YLLDGMTNTIENARQGAARVTSWLGRQLRIAGKRLEGRSK#
(SEQ ID NO:47)
++++
+++
0.09


 


177-216
$DTALYLLDGMTNTIENARQGAARVTSWLGRQLRIAGKRLE#
(SEQ ID NO:48)
++
−
0.23


 


172-211
$GSLLQDTALYLLDGMTNTIENARQGAARVTSWLGRQLRIA#
(SEQ ID NO:49)
+
−
>0.33 
























Residue

Cellular
Nuclear
Hemolysis



number
Sequence1
fluorescence
fluorescence
(mg/ml)



















191-223
$ENARQGAARVTSWLGRQLRIAGKRLEGRSKTWF#
+++
+++
0.15



(SEQ ID NO:50)


 


191-220
$ENARQGAARVTSWLGRQLRIAGKRLEGRSK#
+++
+++
0.31



(SEQ ID NO:51)


 


191-216
$ENARQGAARVTSWLGRQLRIAGKRLE#
++
+
>0.33 



(SEQ ID NO:52)


 


191-211
$ENARQGAARVTSWLGRQLRIA#
+
−
>0.33 



(SEQ ID NO:53)


 


 194-2204
$RQGAARVTSWLGRQLRIAGKRLEGRSK#
++++
++++
0.26



(SEQ ID NO:1)


 


196-220
$GAARVTSWLGRQLRIAGKRLEGRSK#
+++
++
0.16



(SEQ ID NO:54)


 


199-220
$RVTSWLGRQLRIAGKRLEGRSK#
++
+
0.18



(SEQ ID NO:55)


 


202-220
$SWLGRQLRIAGKRLEGRSK#
+
+
>0.33 



(SEQ ID NO:56)


 


205-220
$GRQLRIAGKRLEGRSK#
+
−
>0.33 



(SEQ ID NO:25)


 


MAGAININ
$GIGKFLHSAGKFGKAFVGEIMKS#
−
−
?



(SEQ ID NO:24)


 


L3 loop
$GNGKLIKGRTPIKFGKADCDRPPKHSQNGMGK#
++++
++++
?


59-88
(SEQ ID NO:5)





1$ = biotin, #= amide, *= mixture of G and R at that position of the peptide, bold italic residues differ from Ems of CSFV, strain Alfort.


2sequence corresponds to distinct CSFV strains present in sequence database.


3sequence corresponds to BVDV, strain M96751.


4sequence of peptide showed highest activity.













TABLE 9







Optimization of Erns peptide.














Concentration



Peptide
Code
Sequence
(μM)













Translocation domain Erns
MDB-17
Biotin-RQGAARVTSWLGRQLRIAGKRLEGRSK-NH2
1.0


according to Table 8

(SEQ ID NO:1)


 



MDL-8
Biotin-RRVTSWLGRQLRIAGKRLEGRSK-NH2
1.0




(SEQ ID NO:57)


 



MDL-9
Biotin-RVRSWLGRQLRIAGKRLEGRSK-NH2
1.0




(SEQ ID NO:58)


 



MDA-19
Biotin-GRQLRIAGKRLEGRSK-NH2
1.0




(SEQ ID NO:25)


 



MDR-25
Biotin-GRQLRIAGKRLRGRSK-NH2
0.3




(SEQ ID NO:59)


 


Optimized transport peptide
MDK-20
Biotin-GRQLRIAGRRLRGRSR-NH2
0.1


(movin)

(SEQ ID NO:39)


 


Rhodamine labeled
A931
Rhodamine-GRQLRIAGRRLRGRSR-NH2
3.0




(SEQ ID NO:39)


 


Mutations in movin
MDM-25
Biotin-GRQLRRAGRRLRGRSR-NH2
0.1




(SEQ ID NO:60)


 



MDM-26
Biotin-GRQLRIAGRRLRRRSR-NH2
0.1




(SEQ ID NO:61)


 



MDM-27
Biotin-GRQLRRAGRRLRRRSR-NH2
0.1




(SEQ ID NO:40)


 


Shorter version of movin
MDM-28
Biotin-RQLRIAGRRLRGRSR-NH2
0.1




(SEQ ID NO:62)


 


Movin + bromoacetic acid
A941
Biotin-RSRGRLRRGAIRLQRG
0.03


biotine with D-aminozuren

-Lysine (MTT)- broomacetic acid


(retro-inverso)

(SEQ ID NO:63)
















TABLE 10







Mapping of restrictocin L3 loop.












Concentration



Peptide
Sequence
(μM)













Restrictocin
Biotin-GNGKLIKGRTPIKFGKADCDRPPKHSQNGMGK-NH2
1.0



L3
(SEQ ID NO:5)


 



Biotin-GNGKLIKGRTPIKFGKADCDRPPKHSQNGM-NH2
3.0



(SEQ ID NO:64)


 



Biotin-KLIKGRTPIKFGKADCDRPPKHSQNGMGK-NH2
0.3



(SEQ ID NO:65)


 



Biotin-KLIKGRTPIKFGKADCDRPPKHSQNGK-NH2
0.3



(SEQ ID NO:66)


 



Biotin-KGRTPIKFGKADCDRPPKHSQNGMGK-NH2
3.0



(SEQ ID NO:67)


 



Biotin-KLIKGRTPIKFGKADCDRPPKHSGK-NH2
0.3



(SEQ ID NO:68)


 



Biotin-KLIKGRTPIKFGKARCRRPPKHSGK-NH2
0.3



(SEQ ID NO:69)


 



Biotin-KLIKGRTPIKFGK-NH2



(SEQ ID NO:70)
















TABLE 11







Translocation activity of transport peptides.














Concentration



Name
Code
Sequence
(μM)













HRSV-G, type A
MDN-12
Biotin-KRIPNKKPGKKTTTKPTKKPTIKTTKKDLKPQTTKPK-NH2
1.0




(SEQ ID NO:36)


 



MDN-13
Biotin-KRIPNKKPGKKTTTKPTKKPTIKTTKKDLK-NH2
1.0




(SEQ ID NO:71)


 



MDP-04
Bioton-KRIPNKKPGKKTTTKPTKKPTIKTTKK-NH2
0.3




(SEQ ID NO:72)


 



MDP-08
Biotin-KRIPNKKPGKKTTTKPTKKPTIK-NH2
0.3




(SEQ ID NO:73)


 



MDP-19
Biotin-KRIPNKKPGKKTTTKPTKK-NH2
0.3




(SEQ ID NO:74)


 



MDP-32
Biotin-KRIPNKKPGKKT-NH2
 0.03




(SEQ ID NO:42)


 



MDS-34
Biotin-KRIPNKKPGKK-NH2
 0.03




(SEQ ID NO:9)


 



MDS-36
Biotin-KRIPNKKPKK
 0.03




(SEQ ID NO:38)


 



MDS-09
Biotin-KKPGKKTTTKPTKKPTIKTTKK-NH2
0.3




(SEQ ID NO:75)


 



MDS-23
Biotin-KKPGKKTTTKPTKK-NH2
0.3




(SEQ ID NO:76)


 




Biotin-KKTTTKPTKK-NH2




(SEQ ID NO:77)


 



MDS-37
Biotin-KKPTIKTTKK-NH2
0.3




(SEQ ID NO:78)


 


HRSV-G, type B,
MDP-21
Biotin-KSICKTIPSNKPKKK-NH2
1.0


region 1

(SEQ ID NO:37)


 



MDS-35
Biotin-KTIPSNKPKKK-NH2
0.1




(SEQ ID NO:10)


 


HRSV-G, type B,

Biotin-KPRSKNPPKKPK


region 2

(SEQ ID NO:11)
























Concentration



Name
Sequence
(μM)















NLS and DNA/RNA-binding peptides











HIV-1 Rev
Biotin-DTRQARRNRRRRWRERQRAAAAR-NH2
(SEQ ID NO:79)
0.1



 



Biotin-RQARRNRRRRWR-NH2
(SEQ ID NO:30)
0.3/0.1


 


RSG-1.2
Biotin-DRRRRGSRPSGAERRRRRAAAA-NH2
(SEQ ID NO:80)
0.1


 



Biotin-RRRRGSRPSGAERRRRR-NH2
(SEQ ID NO:81)
1.0/0.3


 


HIV-1 tat/tar
Biotin-RPRGTRGKGRRIRR-NH2
(SEQ ID NO:82)
0.3


 


Bacteriophage lambda N
Biotin-QTRRRERRAEKQAQW-NH2
(SEQ ID NO:34)
1.0


peptide


 



Biotin-RRRERRAEK-NH2
(SEQ ID NO:83)
1.0


 


Flockhouse virus peptide
Biotin-NRTRRNRRRVR-NH2
(SEQ ID NO:33)
 0.03


 


Monopartite, NLS simian
Biotin-PKKKRKV-NH2
(SEQ ID NO:28)
0.1


virus 40 large T antigen


 


Bipartite
Biotin-KRPAAIKKAGQAKKKK-NH2
(SEQ ID NO:29)
0.1


 


Herpes virus 8 k8 protein
Biotin-TRRSKRRSHRKF-NH2
(SEQ ID NO:32)
0.1


(res 124-135)







Proteolytic cleavage site of viral surface protein











Alpha virus E3
Biotin-KCPSRRPKR-NH2
(SEQ ID NO:35)
3.0








Antibacterial peptide











Antibacterial peptide
Biotin-RAGLQFPVGRVHRLLRK-NH2
(SEQ ID NO:84)
3.0



Buforin
















TABLE 12







Peptide concentration that inhibits cell growth.












Erns peptide
Erns peptide



Cell type
(191-227) (μM)
(194-220) (μM)







—





HeLa
50
40



EBTr
50
60

















TABLE 13







Antibacterial effect of Erns or L3 peptides.










Peptide1
MIC (μg/ml)2














191-227
47



191-227
91



194-230
93



184-223
46



181-220
51



177-216
224



172-211
>500



191-223
41



191-220
47



191-216
95



191-211
395



194-220
50



194-218
25



196-220
25



199-220
23



202-220
179



205-220
>500



L3
>500







1Same peptides as in Table 8.



2Minimal inhibitory concentration needed to inhibit bacterial growth.

## Claims

1. An isolated peptide domain of 10 to 18 residues long, said isolated peptide domain having greater than 40% arginines or lysines and said isolated peptide domain being at least 70% identical to an amino acid sequence of 10 to 18 residues long located within:
about amino acid position 194 to about amino acid position 220 in a pestiviral Erns protein RNase.

2. The isolated peptide domain of claim 1, wherein said peptide domain is at least 85% identical to said selected amino acid sequence.

3. An isolated peptide domain of 10 to 18 residues long having greater than 40% arginines or lysines and being a reversed amino acid sequence to an amino acid sequence of 10 to 18 residues long located within:
from about amino acid position 194 to about amino acid position 220 in a pestiviral Erns protein RNase wherein, further, D-amino acids are used instead of L-amino acids.

4. In combination, the isolated peptide domain of claim 1 together with a compound for delivery.

5. The combination of claim 4, further comprising means for targeting said combination to a specific site.

6. A pharmaceutical composition comprising:
an isolated peptide domain of 10 to 18 residues long having greater than 40% arginines or lysines and said isolated peptide domain being at least 70% identical to an amino acid sequence of 10 to 18 residues long located within:
about amino acid position 194 to about amino acid position 220 in a pestiviral Erns protein RNase; and

a compound for delivery.

7. A method for translocating a compound through a cell's membrane, said method comprising:
providing said compound with an isolated peptide domain of 10 to 18 residues long having greater than 40% arginines or lysines and said isolated peptide domain being at least 70% identical to an amino acid sequence of 10 to 18 residues long located within about amino acid position 194 to about amino acid position 220 in a pestiviral Erns protein RNase; and
contacting said compound and isolated peptide domain with the cell.

8. The method according to claim 7, wherein said compound has a molecular weight of less than about 600 kD.