WO2015192223A1

WO2015192223A1 - Peptide inhibitors of respiratory syncytial virus replication

Info

Publication number: WO2015192223A1
Application number: PCT/CA2015/050294
Authority: WO
Inventors: James B. MAHONY
Original assignee: Mahony James B
Priority date: 2014-05-14
Filing date: 2015-04-10
Publication date: 2015-12-23

Abstract

The present disclosure relates to peptides that inhibit Respiratory Syncytial Virus (RSV) replication, associated compositions, methods and uses thereof. The peptides target the interactive domain of the phosphoprotein of the RNA-dependent RNA polymerase complex of RSV and disrupt the polymerase complex thereby inhibiting RNA-dependent RNA polymerase activity. The peptides represent specific antiviral agents useful for treating RSV infections.

Description

PEPTIDE INHIBITORS OF RESPIRATORY SYNCYTIAL VIRUS REPLICATION

RELATED APPLICATIONS

[0001] This application claims priority to United States Provisional Patent Application No. 61/992,942 filed on May 14^th, 2014, the contents of which are hereby incorporated by reference in their entirety.

FIELD OF INVENTION

[0002] The present application relates to novel peptide inhibitors of RNA- dependent RNA polymerase activity and more specifically to peptide inhibitors of RNA-dependent RNA polymerase activity, methods and uses thereof for the treatment or prevention of respiratory syncytial virus (RSV).

BACKGROUND OF INVENTION

[0003] Respiratory syncytial virus (RSV) causes respiratory tract infections in humans and belongs to a large group of viruses that they are responsible for a number of human and animal diseases. Human RSV is a negative-sense, single- stranded RNA virus that belongs within the order Mononegavirales, the Paramyxoviridae family, the Pneumovirinae subfamily. Human and bovine RSV belong in the genus Pneumovirus while another respiratory virus human Metapneumovirus and Avian pneumovirus belong within a second genus Metapneumovirus. The second subfamily Paramyxovirinae includes a number of viruses that cause disease in humans and animals including the following: Measles virus (Morbillivirus genus), Mumps virus and Parainfluenza virus types 2 and 4 (Rubulavirus genus), Parainfluenza virus types 1 and 3 (Respirovirus genus), Hendravirus and Nipahvirus (Henipavirus genus), all of which cause disease in humans and Newcastle disease virus (Avulavirus genus) that causes disease in chickens. Other important viruses in this subfamily include Rinderpest virus (Morbillivirus genus) that causes disease in sheep and ruminants, Canine distemper virus (Morbillivirus genus) causes disease in dogs, and Sendai virus (Respirovirus genus) that infects rodents and pigs. Cows are susceptible to an RSV called bovine RSV. Paramyxoviruses are also responsible for a range of diseases in other animal species, for example canine distemper virus (dogs), phocine distemper virus (seals), cetacean morbillivirus (dolphins and porpoises) Newcastle disease virus (birds) and rinderpest virus (cattle). Some paramyxoviruses such as the henipaviruses are zoonotic pathogens, occurring naturally in an animal host, but also able to infect humans.

[0004] Virions are enveloped and can be spherical, filamentous or pleomorphic. Fusion proteins and attachment proteins appear as spikes on the virion surface. Matrix proteins inside the envelope stabilize virus structure. The nucleocapsid core is composed of the genomic RNA, nucleocapsid proteins, phosphoproteins and polymerase proteins.

[0005] The genome consists of a single segment of RNA, 15-19 kilobases in length and containing 6-10 genes. Non-coding regions include: a 3' leader sequence, 50 nucleotides in length which acts as a transcriptional promoter, and a 5' trailer sequence, 50-161 nucleotides long. Intergenomic regions between each gene are three nucleotides long for morbillivirus, respirovirus and henipavirus, and variable length (1 -56 nucleotides) for rubulavirus and pneumovirinae. Gene sequence within the genome are conserved across the family due to a phenomenon known as transcriptional polarity in which genes closest to the 3' end of the genome are transcribed in greater abundance than those towards the 5' end. This mechanism acts as a form of transcriptional regulation. The sequence of the six genes is Nucleocapsid - Phosphoprotein - Matrix - Fusion - Attachment - Large (polymerase). A description of the various genes follows:

N - the nucleocapsid protein associates with genomic RNA and protects the RNA from nuclease digestion;

P - the phosphoprotein binds to the N and L proteins and forms part of the RNA polymerase complex;

M - the matrix protein assembles between the envelope and the nucleocapsid core helping to organize and maintain virion structure;

F - the fusion protein projects from the envelope surface as a trimer and mediates cell entry by inducing fusion between the viral envelope and the cell membrane; H/HN/G - the cell attachment proteins span the viral envelope and project from the surface as spikes. They bind to sialic acid on the cell surface and facilitate cell entry. Note that the receptor for measles virus is unknown. Proteins are designated H for morbilliviruses and henipaviruses as they possess haemagglutination activity, observed as an ability to cause red blood cells to clump. HN attachment proteins occur in respiroviruses and rubulaviruses. These possess both haemagglutination and neuraminidase activity which cleaves sialic acid on the cell surface, preventing viral particles from reattaching to previously infected cells;

L - the large protein is the catalytic subunit of RNA dependent RNA polymerase (RDRP);

Accessory proteins - a mechanism known as RNA editing allows multiple proteins to be produced from the P gene. These are not essential for replication but may aid in survival in vitro or may be involved in regulating the switch from mRNA synthesis to antigenome synthesis.

Replication of the genome and expression of genes

[0006] Negative-sense ssRNA viruses (Group V) must have their genome copied by an RNA polymerase to form positive-sense RNA. This means that the virus must bring along with it the RNA-dependent RNA polymerase enzyme. The positive-sense RNA molecule then acts as viral mRNA, which is translated into proteins by the host ribosomes. The resultant protein goes on to direct the synthesis of new virions, such as capsid proteins and RNA replicase, which is used to produce new negative-sense RNA molecules.

[0007] RNA viruses are classified according to the sense or polarity of their RNA into negative-sense and positive-sense. Positive-sense viral RNA is similar to mRNA and thus can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation. As such, purified RNA of a positive-sense virus can directly cause infection though it may be less infectious than the whole virus particle. Purified RNA of a negative-sense virus is not infectious by itself as it needs to be transcribed into positive-sense RNA, however each virion can be transcribed to several positive-sense RNAs. [0008] After a virus enters the cell through receptor-mediated endocytosis the RNA is uncoated. From there, the RNA is able to act as a template for complementary RNA synthesis by the RNA-dependent RNA polymerase (RdRP) or RNA replicase. The complementary strand is then, itself, able to act as a template for the production of new viral genomes which are further packaged and released from the cell ready to infect more host cells. The RNA replicase is the enzyme that catalyzes the replication of genomic RNA using an RNA template. This is in contrast to a typical RNA polymerase, which catalyzes the transcription of RNA from a DNA template. The RNA Replicase has three subunits L, N, and P which come together to form a h ete roth m eric complex which is required for enzymatic activity.

Epidemiology

[0009] In temperate climates there is an annual epidemic during the winter months. In tropical climates, infection is most common during the rainy season. RSV is a leading cause of respiratory tract infection in children, especially those under the age of two years. In the United States, 60% of infants are infected during their first RSV season, and nearly all children will have been infected with the virus by 2-3 years of age. RSV is the major cause of lower respiratory tract infection and a leading cause of hospitalization in children under the age of five years. RSV is the most important pediatric viral infection worldwide with an estimated 64 million infections and 160,000 deaths annually. RSV is responsible for up to 75,000 hospitalizations and 2,400 deaths in infants <3 years of age annually in USA (CDC 2004). Natural infection with RSV does not induce protective immunity, and thus people can be infected multiple times. Sometimes an infant can become symptomatically infected more than once even within a single RSV season. Severe RSV infections have increasingly been found among elderly patients. There are no antiviral agents currently available for RSV only prophylactic humanized monoclonal antibody (Palivizumab) that reduces the hospitalization rate in children if given in a timely fashion. There is no vaccine against RSV and the only treatment available is oxygen therapy. RSV can be more prevalent in immunocompromised individuals such as children without maternal antibody or previous immunity or due to underlying genetic deficits such as hypogammaglobulinemia or T-cell defects.

[0010] There remains a need for new inhibitors of RNA-dependent RNA polymerase and for compositions suitable for the treatment for RSV. SUMMARY OF THE DISCLOSURE

[001 1] In one aspect, the present disclosure describes peptides that inhibit Respiratory Syncytial Virus (RSV) RNA-dependent RNA polymerase activity. In one embodiment, the peptides inhibit RNA replication, transcription, progeny virus production and therefore reduce cell infection. In one embodiment, the peptides described herein prevent intracellular virus replication and thus halt virus replication and the spread of RSV to adjacent cells.

[0012] The inventor has identified peptide inhibitors that disrupt the polymerase complex by targeting the Phosphoprotein of RSV. Three exemplary cognate peptides were synthesized that included specific regions of the Phosphoprotein, specifically the C-terminal 21 amino acids representing the Nucleocapsid binding domain (SEQ ID NO: 2; also described herein as peptide 8006) and two 21 amino acid sequences representing parts of the L subunit binding domain P-100-120 (SEQ ID NO: 3; also described herein as peptide 8120) and Pi₄o-i6o (SEQ I D NO: 4; also described herein as peptide 8121 . Each peptide also included an 1 1 amino acid nuclear localization sequence (Tyr-Gly-Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg; SEQ ID NO: 1 ) to allow the peptides to cross the cytoplasmic membrane and enter cells. The peptides were specifically selected to mimic the interactive domains of the phosphoprotein in order to bind to the nucelocapsid (N) and large polymerase subunits (L) and prevent the formation of the polymerase complex.

[0013] As shown in Example 1 , the peptides described herein act as dominant- negative competitive inhibitors to block the interaction or RNA polymerase and prevent virus replication. Peptides corresponding to a portion of the N and the L subunits were demonstrated to prevent RSV replication in both LLC-MK2 cells and R-Mix cells. As shown in Figure 9, peptides that target the interactive domains of the RSV phosphoprotein appear to inhibit RSV in a dose-dependent fashion. Furthermore, cytotoxicity testing of one of the peptides (peptide 8006) using an enzyme release assay did not indicate any cytotoxic effects, suggesting that the peptides will be well tolerated in clinical use.

[0014] As shown in Example 2, the C-terminal peptide corresponding to the nucleocapsid domain (SEQ ID NO: 2) was also demonstrated using an immunoprecipitation assay to block the interaction between RSV P and RSV N proteins. Furthermore, the effect of the peptide appears to be specific towards RSV, as the peptide does not appear to inhibit parainfluenza virus infection as shown in Figure 16.

[0015] Accordingly, in one embodiment there are provided isolated peptide inhibitors of RNA-dependent RNA polymerase activity. In one embodiment, the peptide comprises all or part of one of the interactive domains of the proteins in the RNA polymerase complex of RSV. In one embodiment, the peptide comprises a fragment or variant thereof of the phosphoprotein of the RNA polymerase complex of RSV, wherein the fragment inhibits RNA-dependent RNA polymerase activity. In one embodiment peptide inhibitor is a peptide mimetic of all or part of the C-terminal nucelocapsid binding domain or the L subunit binding domain of phosphoprotein.

[0016] In one embodiment, the peptide comprises all or part of an interactive domain of the phosphoprotein of RSV, wherein the peptide inhibits RNA-dependent RNA polymerase activity in Respiratory Syncytial Virus (RSV). In some embodiments, the phosphoprotein of RSV comprises an amino acid sequence with at least 80% sequence identity to a phosphoprotein sequence selected from SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 1 1 , SEQ ID NO: 12 and SEQ ID NO: 13.

[0017] In one embodiment, wherein the interactive domain comprises the nucleocapsid binding domain of the phosphoprotein or a portion adjacent to the nucleocapsid binding domain. For example in one embodiment, the nucleocapsid binding domain is the nucleocapsid binding domain set forth in amino acids 220 to 241 of SEQ ID NO: 9. Corresponding nucleocapsid binding domains in other phosphoprotein sequences may readily be identified by aligning the sequences with an exemplary nucleocapsid binding domain described herein, optionally as shown in Figure 12A.

[0018] As shown in the Examples, a peptide corresponding to the C-terminal nucleocapsid binding domain of phosphoprotein (peptide 8006; SEQ ID NO: 2) inhibits RSV replication. Accordingly, in one embodiment, the peptide comprises, consists essentially of, or consists of all or part of SEQ ID NO: 2, or a variant thereof. In one embodiment, the peptide comprises, consists essentially of, or consists of an amino acid sequence with at least 80%, at least 90% or at least 95% sequence identity to SEQ ID NO: 2. In one embodiment, the peptide comprises, consists essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18, at least 20 amino acids of SEQ ID NO: 2. In some embodiments, the peptide inhibits RNA dependent RNA polymerase activity.

[0019] In another embodiment, the interactive domain comprises the L subunit binding domain of the phosphoprotein or portions adjacent to the L subunit binding domain. For example in one embodiment, the L subunit binding domain is the L subunit binding domain set forth in amino acids 120 to 160 of SEQ ID NO: 9. Corresponding L subunit binding domains in other phosphoprotein sequences may readily be identified by aligning the sequences with an exemplary L subunit binding domain described herein, optionally as shown in Figures 12B and 12C. Peptides corresponding to the L subunit binding domain of phosphoprotein have also been demonstrated to inhibit RSV replication. Accordingly, in one embodiment, the peptide comprises , consists essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18 or at least 20 amino acids of amino acids 100 to 160 of SEQ ID NO: 9.

[0020] As shown in the Examples, peptides corresponding to different portions of the L subunit binding domain of phosphoprotein and/or portions adjacent to the L- subunit binding domain (peptides 8020 and 8021 ; SEQ ID NO: 3 and 4) inhibit RSV replication. Accordingly, in one embodiment the peptide comprises, consists essentially of, or consists of all or part of SEQ ID NO: 3 or SEQ ID NO: 4 or a variant thereof. In one embodiment, the peptide comprises, consists essentially of, or consists of an amino acid sequence with at least 80%, at least 90% or at least 95% sequence identity to SEQ I D NO: 3 or SEQ ID NO: 4. In one embodiment, the peptide comprises, consists essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18 or at least 20 amino acids of SEQ ID NO: 3 or SEQ ID NO: 4. In some embodiments, the peptide inhibits RNA dependent RNA polymerase activity.

[0021] In one embodiment, the peptide comprises a fragment of a phosphoprotein of RSV, or a variant thereof, wherein the peptide inhibits RNA dependent RNA polymerase activity. In one embodiment, the peptide is a fragment, or variant thereof, of the phosphoprotein sequence: MEKFAPEFHGEDANNRATKFLESIKGKFTSPKDPKKKDSIISVNSIDIEVTKESPITSNSTI INPTNE DD AGNKPNYQRKPLVS FKEDP PSDNPFSKLYKE IE FDNNEEESSYSYEEIN DQTNDNITARLDRIDEKLSEILGMLHTLWASAGPTSARDGIRDAMVGLREEMIEKIRTEAL MTNDRLEAMARLRNEESEKMAKDTSDEVSLNPTSEKLNNLLEGNDSDNDLSLEDF (SEQ I D

NO: 5), or

MEKFAPEFHGEDANNRATKFLESIKGKFTSPKDPKKKDSIISVNSIDIEVTKESPITSNSTI INPTNE DD VGNKPNYQRKPLVS FKEDP PSDNPFSKLYKE IE FDNNEEESSYSYEEIN DQTNDNITARLDRIDEKLSEILGMLHTLWASAGPTSARDGIRDAMVGLREDMIEKIRTEAL MTNDRLEAMARLRNEESEKMAKDTSDEVSLNPTSEKLNNLLEGNDSDNDLSLDDF (SEQ

ID NO: 9)

wherein the fragment, or variant thereof, inhibits RNA-dependent RNA polymerase activity.

[0022] The peptides described herein may optionally include a nuclear localization sequence and/or a cell-penetrating peptide. In one embodiment, the nuclear localization sequence and/or a cell-penetrating peptide helps the peptides n cross the cytoplasmic membrane and come into contact with the nucleocapsid and/or L subunits of the RSV polymerase complex. In one embodiment, the nuclear localization sequence is the amino acid sequence Tyr-Gly-Arg-Lys-Lys-Arg-Arg-Gln- Arg-Arg-Arg (SEQ ID NO: 1 ). Optionally, the peptides described herein include the nuclear localization sequence of SEQ ID NO: 1 and comprise, consist essentially of, or consist of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8, or a variant thereof.

[0023] In one embodiment, the peptides described herein may be conjugated to a carrier peptide or molecule. For example, in one embodiment, peptide is conjugated to a carrier peptide, optionally maltose-binding protein, transferrin or immunoglobulin lambda light chain.

[0024] Also provided are compositions comprising one or more of the peptides described herein and a pharmaceutically acceptable carrier or diluent.

[0025] In another embodiment, there is provided a kit comprising the peptides or compositions described herein, optionally in a container and/or with instructions for the use of the peptides of compositions for inhibiting RNA-dependent RNA polymerase or for the treatment or prevention of RSV in a subject in need thereof. [0026] Another aspect of the present application is a method of inhibiting or preventing RNA-dependent RNA polymerase activity of RSV comprising administering an effective amount of one or more of the peptides described herein or the compositions comprising one or more of the peptides described herein to a cell or subject in need thereof. The present disclosure also includes the use of one or more of the peptides described herein or a composition comprising one or more of the peptides described herein to inhibit or prevent RNA-dependent RNA polymerase activity of RSV in a cell or subject in need thereof.

[0027] An additional aspect of the present application is a method of inhibiting infection from RSV comprising administering an effective amount of one or more of the peptides described herein or the compositions comprising one or more of the peptides described herein to a cell or subject in need thereof. The present disclosure also includes the use of one or more of the peptides described herein or a composition comprising one or more of the peptides described herein to inhibit infection from RSV in a cell or subject in need thereof.

[0028] Another aspect of the present application is a method of inhibiting cell invasion of RSV comprising administering an effective amount of one or more of the peptides described herein or the compositions comprising one or more of the peptides described herein to a cell or subject in need thereof. The present disclosure also includes the use of one or more of the peptides described herein or a composition comprising one or more of the peptides described herein to inhibit cell invasion of RSV in a cell or subject in need thereof.

[0029] Another aspect of the present invention is a method comprising conjugating a peptide described herein to a carrier protein. In one embodiment, conjugating the peptide to a carrier protein such as ferritin, albumin or immunoglobulin domains increases the ½ life of the peptide by decreasing the amount of degradation by peptidases.

[0030] An additional aspect of the present invention is a method of treating or preventing infection from RSV comprising administering an effective amount of one or more of the peptides described herein or the compositions comprising one or more of the peptide inhibitors described herein to a cell or subject in need thereof. The present disclosure also includes uses of one or more of the peptides described herein or a composition comprising one or more of the peptide inhibitors disclosed herein for the treatment or prevention of infection from RSV in a cell or subject in need thereof. Also provided is a peptide as described herein for the treatment or prevention of RSV in a cell or in a subject in need thereof.

[0031] In one embodiment, the RSV is human RSV, bovine RSV or murine RSV. Optionally, the RSV is multi-drug resistant RSV. In one embodiment, the subject is immunocompromised. For example, in some embodiments the subject has chronic obstructive pulmonary disease (COPD), a lung infection or is infected with HIV. In one embodiment, the subject is a mammal, optionally a human.

[0032] Other features and advantages of the present application will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating preferred embodiments of the invention are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0033] Figure 1 is a diagram indicating that RSV phosphoprotein has binding domains for L and N subunits (adapted from Tran et al. , (2007) J. Gen. Virol. 88: 196)

[0034] Figure 2 is a micrograph demonstrating that Peptide 8006 inhibits RSV replication in LLC-MK2 cells.

[0035] Figure 3 is a micrograph demonstrating that Peptide 8006 inhibits RSV replication in R- Mix cells.

[0036] Figure 4 is a micrograph demonstrating that Peptide 8121 inhibits RSV replication in LLC-MK2 cells.

[0037] Figure 5 is a micrograph demonstrating that Peptide 8121 inhibits RSV replication in R-Mix cells.

[0038] Figure 6 is a micrograph demonstrating that Peptide 8120 blocks RSV replication in LLC-MK2 cells. [0039] Figure 7 is a micrograph demonstrating that Peptide 8120 inhibits RSV replication in R-Mix cells.

[0040] Figure 8 is a diagram showing the location of peptides 8006, 8121 , and 8120 within the Phosphoprotein gene of RSV (SED ID NO: 9)

[0041] Figure 9 is a diagram showing a dose response inhibition of RSV by peptide 8006.

[0042] Figure 10 is a diagram showing the lack of cytotoxicity of peptide 8006.

[0043] Figure 1 1 is a diagram showing the alignment of two RSV phoshoprotein genes and conserved peptides (SEQ ID NO: 9).

[0044] Figure 12 A, 12 B and 12 C are diagrams showing the alignment of two human RSV (SEQ ID NOS: 10 and 1 1 ), one ovine RSV (SEQ ID NO: 13, and one hMPV phosphoprotein genes (SEQ ID NO: 12).

[0045] Figure 13 is a diagram showing that peptides 8006, 8121 , and 8120 of RSV are greater than 50% helical based on the amino acid sequence of SEQ ID NO: 9.

[0046] Figure 14 is a micrograph showing that RSV peptide can be conjugated to a carrier protein for large scale production without loss of activity.

[0047] Figure 15 shows that a RSV P220-241 peptide mimetic blocks the interaction between RSV P and RSV N protein. Immunprecipitation with a-RSV N antibody pulls down both RSV N (A) and RSV P protein (B), supporting their interaction in vivo. In the presence of the RSV P220-241 peptide mimetic (SEQ ID NO: 2), full length RSV P and RSV N protein do not co-purify (C), suggesting that the peptide mimetic prevents this interaction.

[0048] Figure 16 shows that the RSV P220-241 peptide (SEQ I D NO: 2) does not inhibit parainfluenza virus infection. The "No Virus" control shows uninfected cells, the "Virus Only" shows a cell monolayer infected with parainfluenza virus, and the Virus + P220-241 shows that the RSV P peptide mimetic does not affect the infection. Based on these results, the RSV P220-241 mimetic is specific to RSV. DETAILED DESCRIPTION

[0049] In one aspect, the present description provides peptide inhibitors of Respiratory Syncytial Virus (RSV) replication. In one embodiment, the peptides described herein inhibit the activity of the RNA-dependent RNA polymerase complex of RSV.

[0050] The present inventor investigated the phoshoprotein of RSV for inhibition using peptide mimetics to disrupt the polymerase complex. Specifically, three exemplary cognate peptides were investigated that include specific regions of the phosphoprotein, namely, the C-terminal 21 amino acids representing the Nucelocapsid binding domain (SEQ ID NO. 2) and two 21 amino acid sequences representing parts of the L subunit binding domain P100-120 and P140-160 (SEQ ID NO. 3 and SEQ ID NO. 4, respectively). Each peptide also included an 1 1 amino acid nuclear localization sequence (SEQ ID NO. 1 ) to allow the peptides to cross the cytoplasmic membrane and enter cells.

[0051] In one embodiment, the description provides isolated peptide inhibitors of RNA-dependent RNA polymerase activity. The present disclosure includes peptide inhibitors of RNA-dependent RNA polymerase activity developed using the amino acid sequence data from the interactive domains of the polymerase complex. The present disclosure also demonstrates that the peptides inhibit RNA-dependent RNA polymerase activity of RSV, inhibit subsequent infection of cells as shown in Figures 2-7, and are not cytotoxic (Figure 10).

[0052] The peptides described herein may be used to inhibit and prevent RNA- dependent RNA polymerase activity, to inhibit infection from RSV, to inhibit cell invasion of RSV, and to treat or prevent infection from RSV.

[0053] Investigations into the activity of the RSV P220-241 C-terminal peptide (SEQ ID NO: 2) using immunoprecipitation as shown in Figure 15 confirmed that the peptide blocks the interaction between RSV P and RSV N proteins. Furthermore, the RSV P220-241 C-terminal peptide does not inhibit parainfluenza virus infection as shown in Figure 16, and therefore appears specific to inhibiting RSV.

Peptide Inhibitors of RNA-Dependent RNA Polymerase

[0054] In one embodiment, the present application includes novel isolated peptides that inhibit RNA-dependent RNA polymerase activity of RSV. [0055] Using an overlapping peptide library, binding regions or interactive domains on the Phosphoprotein and the Nucleocapsid binding protein and the L subunit binding domain were mapped and an exemplary set of peptide inhibitors were developed, termed Peptide 8006, Peptide 8120 and Peptide 8121 . Each of these peptides also included a nuclear localization sequence (SEQ ID NO: 1 ) to facilitate the peptides crossing the cytoplasmic membrane. Peptide 8006 comprises the amino acid sequence: Tyr-Gly-Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg-Glu-Lys- Leu-Asn-Asn-Leu-Leu-Glu-Gly-Asn-Asp-Ser-Asp-Asn-Asp-Leu-Ser-Leu-Asp-Asp- Phe (SEQ ID NO: 6) and Peptide 8120 comprises the amino acid sequence: Tyr-Gly- Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg-Lys-Leu-Tyr-Lys-Glu-Thr-lle-Glu-Thr-Phe-Asp- Asn-Asn-Glu-Glu-Glu-Ser-Ser-Tyr-Ser-Tyr (SEQ ID NO: 7) and Peptide 8121 comprises the amino acid sequence: Tyr-Gly-Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg- Glu-Lys-Leu-Ser-Glu-lle-Leu-Gly-Met-Leu-His-Thr-Leu-Val-Val-Ala-Ser-Ala-Gly-Pro- Thr (SEQ ID NO: 8).

[0056] In one embodiment, the peptides described herein have sequence identity to all or part of the amino acid sequences of Peptide 8006, Peptide 8120 and Peptide 8121 . In one embodiment, the peptides comprise, consist essentially of, or consist of EKLNNLLEGNDSDNDLSLDDF (SEQ ID NO: 2), KLYKETIETFDNNEEESSYSY (SEQ ID NO: 3) or EKLSEILGMLHTLVVASAGPT (SEQ ID NO: 4), or variants thereof.

[0057] Another embodiment of the present application is an isolated peptide inhibitor of RNA-dependent RNA polymerase activity, wherein the peptide inhibitor comprises interactive domains of the phosphoprotein of RSV and domains of the L and N proteins. In one embodiment, the interactive domains of the phosphoprotein of RSV are shown in Figure 1 . In one embodiment, the N protein binding domain of phosphoprotein corresponds to amino acids 220 to 241 of SEQ ID NO: 9. In one embodiment, the L binding domain of phosphoprotein corresponds to amino acids 120 to 160 of SEQ ID NO: 9. Optionally, the peptides described herein comprises all or part of the N protein binding domain or L protein binding domain or other RSV phosphoproteins, such as those shown in Figure 12, wherein the peptides inhibit RNA dependent RNA polymerase activity. In one embodiment, the peptides described herein overlap with all or part or the N protein binding domain of phosphoprotein or the L protein binding domain. In one embodiment, the peptides described herein comprise an amino acid sequence that is adjacent to the N protein binding domain of phosphoprotein or the L protein binding domain of phosphoprotein, wherein the peptide inhibits RSV RNA-dependent RNA polymerase activity and/or RSV replication.

[0058] As used herein the term "peptide" refers to a sequence of amino acids. The term is used interchangeably with "oligopeptide", "polypeptide" and "protein'. The peptide inhibitor described herein may comprise a sequence of approximately 10 to 300 amino acids in length. The term "amino acid" includes all of the naturally occurring amino acids as well as modified amino acids. The term "peptide inhibitor" or "peptide inhibitors" includes those produced from chemical synthesis and also includes peptide inhibitors produced synthetically to have the same primary structure or composition and the same function and/or activity of the peptide inhibitors disclosed herein. The term "produced synthetically" includes for example, peptide inhibitors produced from recombinant DNA technology.

[0059] The term "isolated" as used herein means a macromolecule such as a peptide that has been identified, separated, recovered from its natural environment, and/or has been produced synthetically. The term "isolated" includes a peptide inhibitor, which is substantially free of chemical precursors, or other chemicals when produced synthetically from chemical synthesis, and also includes a peptide inhibitor, which is substantially free of cellular material or culture media when produced synthetically from recombinant techniques.

[0060] The term "RNA-dependent RNA polymerase activity" refers to a function or activity that is part of the RNA-dependent RNA polymerase (RdRP), or RNA replicase, which is an enzyme that catalyzes the replication of RNA from an RNA template. This is in contrast to a typical RNA polymerase, which catalyzes the transcription of RNA from a DNA template. RNA-dependent RNA polymerase activity can, for example, be determined in vitro by an RNA transcription assay.

[0061] The term "Respiratory Syncytial Virus" (RSV) as used herein includes all types of RSV, including, without limitation, the negative-sense, single-stranded RNA virus of the family Paramyxoviridae, and the Order Mononegavirales and Group V ((- )ssRNA). Example of RSV include, but are not limited to, human RSV, ovine RSV, bovine RSV, murine RSV and human metapneumovirus. [0062] The term "interactive domains" as used herein refers to binding regions of amino acid sequences in proteins of the RNA-dependent RNA polymerase present in RSV that bind to and/or interact with each other to form a polymerase complex for RNA replication. The term "interactive domain" includes sequences adjacent to binding domains, such as a nucleocapsid binding domain or an L subunit binding domain.

[0063] The term "polymerase complex" as used herein refers to proteins of the RNA-dependent RNA polymerase present in RSV which interact with each other via interactive domains to form a polymerase complex for replication of RNA.

[0064] Another embodiment of the present disclosure is an isolated peptide that inhibits RNA-dependent RNA polymerase activity of RSV, wherein the peptide comprises interactive domains of the RNA-dependent RNA polymerase complex and the proteins are the phosphoprotein, and the nucleocapsid binding protein and the L subunit binding domain.

[0065] In one embodiment, the peptide comprises a fragment of the phosphoprotein sequence:

MEKFAPEFHGEDANNRATKFLESIKGKFTSPKDPKKKDSIISVNSIDIEVTKESPITSNSTI INPTNE DD AGNKPNYQRKPLVS FKEDP PSDNPFSKLYKE IE FDNNEEESSYSYEEIN DQTNDNITARLDRIDEKLSEILGMLHTLWASAGPTSARDGIRDAMVGLREEMIEKIRTEAL MTNDRLEAMARLRNEESEKMAKDTSDEVSLNPTSEKLNNLLEGNDSDNDLSLEDF (SEQ I D

NO: 5) or a variant thereof, wherein the fragment inhibits RNA-dependent RNA polymerase activity. Optionally, the peptide comprises a fragment, of the phosphoprotein sequences set forth in SEQ ID NOS: 9-13 or variant thereof.

[0066] In one embodiment, the peptides described herein have sequence identity to SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8 and inhibit RSV replication and/or RNA dependent RNA polymerase activity. In one embodiment, the peptides comprise, consist essentially of or consists of variants of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ I D NO: 7, or SEQ ID NO: 8 and inhibit RSV replication and/or RNA dependent RNA polymerase activity.

[0067] The term "variant" as used herein includes modifications, substitutions, additions, derivatives, analogs, fragments or chemical equivalents of the amino acid sequences disclosed herein that perform substantially the same function as the peptide inhibitors disclosed herein in substantially the same way. For instance, the variants have the same function of being useful to inhibit RNA-dependent RNA polymerase activity of RSV, to prevent RNA-dependent RNA polymerase activity of RSV and/or to treat or prevent infection from RSV.

[0068] Variants of the peptide inhibitors disclosed herein also include, without limitation, conservative amino acid substitutions. A "conservative amino acid substitution" as used herein, is one in which one amino acid residue is replaced with another amino acid residue without abolishing the desired function or activity of the peptide inhibitors disclosed herein. Conservative substitutions typically include substitutions within the following groups: glycine, alanine, valine, isoleucine, leucine, aspartic acid, glutamic acid, asparagine, glutamine, serine, threonine, lysine, arginine; and phenylalanine, tyrosine. Conserved amino acid substitutions involve replacing one or more amino acids of the polypeptides of the disclosure with amino acids of similar charge, size, and/or hydrophobicity characteristics. When only conserved substitutions are made the resulting variant should be functionally equivalent. Changes which result in production of a chemically equivalent or chemically similar amino acid sequence are included within the scope of the disclosure. If the peptide inhibitors of the present disclosure are made using recombinant DNA technology, variants of the peptide inhibitors may be made by using polypeptide engineering techniques such as site directed mutagenesis, which are well known in the art for substitution of amino acids. For example a hydrophobic residue, such as glycine can be substituted for another hydrophobic residue such as alanine. An alanine residue may be substituted with a more hydrophobic residue such as leucine, valine or isoleucine. A negatively charged amino acid such as aspartic acid may be substituted for glutamic acid. A positively charged amino acid such as lysine may be substituted for another positively charged amino acid such as arginine. The phrase "conservative substitution" also includes the use of a chemically derived residue in place of a non-derivatized residue provided that such polypeptide displays the requisite activity. In one embodiment, the peptides described herein comprise, consist essentially of, or consist of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8 and have 1 , 2, 3, 4, 5 or 6 conservative amino acid substitutions. [0069] Variants of the peptide inhibitors of the present disclosure also include additions and deletions to the amino acid sequences disclosed herein.

[0070] Variants of the peptide inhibitors of the present disclosure also include analogues thereof. The term "analog" as used herein includes any active agent capable of performing the function of the peptide inhibitors disclosed herein, and may include peptide mimetics and the like. The term "active" refers to molecules in a conformation suitable for performing substantially the same functions as the peptide inhibitors disclosed herein in substantially the same way. Peptide mimetics include synthetic structures that may serve as substitutes for peptides in interactions between molecules (see Morgan and Gainor, (1989) Ann. Reports Med. Chem. 24:243-252 for a review). Peptide mimetics include synthetic structures which may or may not contain amino acids and/or peptide bonds but are designed to retain the desired structural and functional features and thus may be suitable substitutes of the peptide inhibitor analog disclosed in the present disclosure.

[0071] Peptide mimetics also include molecules incorporating peptides into larger molecules with other functional elements (e.g. as described in WO99/25044). Peptide mimetics also include peptoids, oligopeptoids (Simon et al., (1972) Proc.Natl. Acad. Sci. USA 89:9367), and peptide libraries containing peptides of a designed length representing all possible sequences of amino acids corresponding to an isolated peptide of the disclosure. Peptide mimetics may be designed based on information obtained by systematic replacement of L-amino acids by D-amino acids, replacement of side chains with groups having different electronic properties, and by systematic replacement of peptide bonds with amide bond replacements. Local conformational constraints can also be introduced to determine conformational requirements for activity of a candidate peptide mimetic. The mimetics may include isosteric amide bonds, or D-amino acids to stabilize or promote reverse turn conformations and to help stabilize the molecule. Cyclic amino acid analogues may be used to constrain amino acid residues to particular conformational states. The mimetics can also include mimics of inhibitor peptide secondary structures. These structures can model the 3-dimensional orientation of amino acid residues into the known secondary conformations of proteins. Peptoids may also be used which are oligomers of N-substituted amino acids and can be used as motifs for the generation of chemically diverse libraries of novel molecules. [0072] The peptides of the present disclosure also include derivatives of the peptides and/or derivatives of the variant peptides. In one embodiment, the derivatives inhibit RSV replication and/or inhibit RNA-dependent RNA polymerase activity. The term "derivative" refers to a peptide having one or more residues chemically derivatized by reaction of a functional side group. Such derivatized molecules include for example, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, t-butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or O-alkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-im-benzylhistidine. Also included as derivatives are those peptides which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acids. For examples: 4-hydroxyproline may be substituted for proline; 5-hydroxylysine may be substituted for lysine; 3methylhistidine may be substituted for histidine; homoserine may be substituted for serine; and ornithine may be substituted for lysine. A derivative of a polypeptide also optionally includes polypeptides comprising forms of amino acids that are oxidized.

[0073] Variant peptide inhibitors of the present disclosure also include fragments thereof. The term "fragment" as used herein means a portion of a polypeptide that contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more of the entire length of the reference polypeptide.

[0074] In one embodiment, the peptides described include peptides with sequence identity to one or more of the peptides described herein that inhibit RNA- dependent RNA polymerase activity of RSV and/or inhibit RSV replication.

[0075] In one embodiment, the peptides comprise, consist essentially of, or consist of an amino acid sequence that, when optimally aligned, for example using the methods described herein, share at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with a second amino acid sequence. For example, in one embodiment, there is provided a peptide comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ I D NO: 7, or SEQ I D NO: 8 wherein the peptide inhibits RNA-dependent RNA polymerase activity of RSV and/or inhibits RSV replication.

[0076] The term "sequence identity" as used herein refers to the percentage of sequence identity between two polypeptide and/or nucleotide sequences.

[0077] To determine the percent identity of two amino acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues at corresponding amino acid positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=number of identical overlapping positions/total number of positions.times.100%). In one embodiment, the two sequences are the same length. The determination of percent identity between two sequences can also be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, (1990), Proc. Natl. Acad. Sci. U.S.A. 87:2264-2268, modified as in Karlin and Altschul, (1993), Proc. Natl. Acad. Sci. U.S.A. 90:5873-5877. Such an algorithm is incorporated into the N BLAST and XBLAST programs of Altschul et al., (1990), J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the N BLAST nucleotide program parameters set, e.g., for score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the present disclosure. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score-50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule of the present disclosure. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997), Nucleic Acids Res. 25:33893402. Alternatively, PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g. , of XBLAST and NBLAST) can be used (see, e.g., the NCBI website). Another preferred non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, (1988), CABIOS 4: 1 1 -17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.

[0078] The percentage of identity between two polypeptide sequences, the amino acid sequences of such two sequences are aligned, for example using the Clustal W algorithm (Thompson, JO, Higgins OG, Gibson TJ, 1994, Nucleic Acids Res. 22(22): 4673-4680.), together with BLOSUM 62 scoring matrix (Henikoff S. and Henikoff J.G., (1992), Proc. Natl. Acad. Sci. USA 89: 10915-10919.) and a gap opening penalty of 10 and gap extension penalty of 0.1 , so that the highest order match is obtained between two sequences wherein at least 50% of the total length of one of the sequences is involved in the alignment.

[0079] Other methods that may be used to align sequences are the alignment method of Needleman and Wunsch (Needleman and Wunsch. J. Mol. Bioi., (1970), 48:443), as revised by Smith and Waterman (Smith and Waterman. Adv. Appl. Math. (1981 ), 2:482) so that the highest order match is obtained between the two sequences and the number of identical amino acids is determined between the two sequences. Other methods to calculate the percentage identity between two amino acid sequences are generally art recognized and include, for example, those described by Carillo and Lipton (Carillo and Lipton SIAM J. Applied Math. (1988), 48: 1073) and those described in Computational Molecular Biology (Computational Molecular Biology, Lesk, e.d. Oxford University Press, New York, (1988), Biocomputing: Informatics and Genomics Projects). Generally, computer programs will be employed for such calculations.

[0080] The inventor has compared the sequence of Peptide 8006, Peptide 8120, and Peptide 8120 (SEQ ID NOS: 2-4) to that of the Phosophoprotein sequence of RSV (SEQ ID NO: 5). In particular, the sequence similarity between the peptides 8006 and phosphoprotein was determined and is shown in Figure 12A. The sequence similarity of Peptides 8121 and 8120 with phosphoprotein is presented in Figures 12B and C, respectively. The data indicates that these sequences are highly conserved. These conserved areas are greater than 90% coiled and greater than 50% helical. It is therefore expected that the exemplary peptides described herein will have activity against a broad range of different RSV including human RSV, ovine RSV, bovine RSV, murine RSV and human metapneumovirus.

[0081] In one embodiment there is provided a peptide comprising a fragment of a sequence shown in Figures 8 and 12 or a variant thereof, wherein the peptide inhibits of RNA-dependent RNA polymerase activity or RSV replication.

[0082] In one embodiment, the peptides described herein comprise, consist essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18, at least 20 amino acids of SEQ ID NO: 2, SEQ I D NO: 3 or SEQ ID NO: 4, wherein the peptide inhibits RSV RNA-dependent polymerase activity and/or RSV replication. In one embodiment, the peptide is a fragment of amino acids 100- 160 of SEQ ID NO: 5 or SEQ ID NO: 9, or a fragment of amino acids 220-241 of SEQ ID NO: 5 or SEQ ID NO: 9, wherein the peptide inhibits RSV RNA-dependent polymerase activity and/or RSV replication. In some embodiments, the peptide comprises, consists essentially of, or consists of a contiguous fragment of between 12 and 60, between 14 and 50, between 15 and 30 or between 20 and 40 amino acids of amino acids 100-160 of SEQ ID NO: 5 or SEQ ID NO: 9, or of an interactive domain of a RSV phosphoprotein shown in Figure 12. In one embodiment, the peptide is a fragment of comprising, consisting essentially of, or consisting of a contiguous fragment or between 12 and 21 , between 14 and 21 , between 16 and 21 or between 18 and 21 amino acids of SEQ ID NO: 5 or SEQ ID NO: 9, or of another nucleocapsid binding domain of an RSV phosphoprotein shown in Figure 12.

[0083] Another aspect of the present disclosure is an isolated nucleotide encoding a peptide inhibitor and/or variant disclosed herein. A nucleotide sequence that encodes a peptide inhibitor and/or variant of the present disclosure may be deduced by a person skilled in the art using computer nucleic acid prediction programs and/or mRNA codon- amino acid tables that are readily available in the art.

[0084] The term "isolated nucleotide" as used herein refers to a nucleotide or nucleic acid substantially free of cellular material or culture medium when produced by recombinant DNA techniques, or chemical precursors, or other chemicals when chemically synthesized. An "isolated nucleic acid" is also substantially free of sequences which naturally flank the nucleic acid (i.e. sequences located at the 5' and 3' ends of the nucleic acid) from which the nucleic acid is derived. The term "nucleic acid" is intended to include DNA and RNA and can be either double stranded or single stranded. The nucleic acid sequences contemplated by the present disclosure include isolated nucleotide sequences encoding a peptide inhibitor and/or variant disclosed herein.

[0085] To explore whether the RSV peptide inhibitors described herein could be conjugated to a carrier protein for large scale production, the RSV-P peptide was conjugated to the C-terminus of the carrier protein, Maltose binding protein (MBP), cloned into the peri His-MBP Gateway cloning vector and the fusion protein expressed in E. coli. MBP alone lacking the RSV-P or MBP containing a control peptide, FliJ, were also expressed as recombinant proteins and used as controls in the RSV inhibition assay. The MBP-RSV-P fusion protein inhibited RSV replication where the controls, MBP alone or MBP-FliJ did not inhibit RSV (Figure 14). The proof of principle experiment shows that the RSV-P peptide can be attached to carrier proteins without loss of activity and that human carrier proteins such as transferrin or immunoglobulin (IgG) lambda light chain could be used in humans.

Nuclear Localization Sequences and Cell-penetrating peptides

[0086] In an embodiment the peptides described herein optionally comprise a nuclear localization sequence and/or a cell-penetrating peptide. For example, in one embodiment, there is provided a fusion protein comprising a peptide that inhibits RNA-dependent RNA polymerase and a nuclear localization sequence or a cell- penetrating peptide. In one embodiment, the nuclear localization sequence is a TAT gene NLS, such as the sequence set forth in SEQ I D NO: 1 .

[0087] In an embodiment, the cell-penetrating peptide is a trans-activating transcriptional activator (TAT) peptide from Human Immunodeficiency Virus 1 (HIV- 1 ). In an embodiment, the TAT peptide comprises all or part of the amino acid sequence GGGYGRKKRRQRRR (SEQ ID NO: 14). In an embodiment, the peptides described herein include cell-penetrating peptides such as myristoylated peptides. Optionally, the cell-penetrating peptide and the peptide that inhibits RNA-dependent RNA polymerase are attached through a linker, such as another polypeptide sequence.

Methods of identifying inhibitors

[0088] In addition to the peptide inhibitors described above, other peptide inhibitors may be developed and identified using the methods described herein. For example, peptide inhibitors may be developed by mapping binding regions or interactive domains of polymerase complex subunit proteins, identifying candidate peptide inhibitors, and producing candidate peptide inhibitors. In one embodiment, the interactive domains of polymerase complex subunit proteins are mapped using an overlapping peptide library map. In another embodiment, the interactive domains of polymerase complex subunit proteins are mapped using Pepscan analysis. In another embodiment, candidate peptide inhibitors are identified or selected by evaluating the degree of binding or interaction of various amino acid regions within the interactive binding domains on polymerase complex subunit proteins. In another embodiment, the amino acid sequence of candidate peptide inhibitors is extended to include an approximate length of 30 to 35 amino acids to improve binding affinity. In another embodiment, for candidate proteins, any proteins that are known to interact to form bi- or trimolecular complexes that are functionally important either as an holoenzyme or scaffolding complex would be candidate proteins for the development of peptide inhibitors. In one embodiment, candidate peptide inhibitors may be produced synthetically. In another embodiment, candidate peptide inhibitors may be produced synthetically using solid-phase chemistry or solid phase chemical synthesis. In another embodiment, candidate peptide inhibitors may be produced synthetically using recombinant protein molecules to act as a carrier molecule for the peptide inhibitor. In one embodiment, a "fusion protein" (carrier molecule plus peptide inhibitor at one end) may be produced as a recombinant protein in, for example, without limitation, yeast or bacteria. In another embodiment, the yeast or bacteria may be produced in large fermenters. In another embodiment, the peptide inhibitor may be produced as a GST (glutathione S-transferase) peptide construct. In another embodiment, the peptide inhibitor may be produced by TEV cleavage from a recombinant GST protein or other protein construct with purification of the cleaved peptide. [0089] Accordingly, another embodiment of the present disclosure is a peptide inhibitor obtained by: mapping interactive domains of polymerase complex subunit proteins, identifying a candidate peptide inhibitor and producing the candidate peptide inhibitor.

[0090] The term "identifying" or "identified" means candidate peptide inhibitors that are selected on the basis of the degree of binding or interaction of amino acid regions on polymerase complex subunit proteins. The term "candidate" as used herein in reference to a peptide inhibitor includes peptide inhibitors that comprise interactive domains of polymerase complex subunit proteins of the RNA-dependent RNA polymerase of RSV or another respiratory virus.

Compositions

[0091] Another aspect of the present disclosure includes the peptides described herein suitably formulated into pharmaceutical compositions for administration to mammals in a biologically compatible form suitable for administration in vivo. The term "biologically compatible form suitable for administration in vivo" means a form of the substance to be administered in which any toxic effects are outweighed by the therapeutic effects.

[0092] Accordingly, another embodiment of the present disclosure includes a composition comprising one or more peptide inhibitors and a pharmaceutically acceptable carrier or diluent, or mixtures thereof. In one embodiment, the composition comprises a peptide comprising or consisting of SEQ ID NO: 2 or SEQ ID NO:6 (Peptide 8006), or a variant thereof, and a pharmaceutically acceptable carrier or diluent, or mixtures thereof. In another embodiment, the composition comprises a peptide comprising or consisting of SEQ ID NO: 3 or SEQ ID NO: 7 or (Peptide 8120), or a variant thereof, and a pharmaceutically acceptable carrier or diluent, or mixtures thereof. In another embodiment, the composition comprises a peptide comprising of consisting of SEQ I D NO: 4 of SEQ ID NO: 8 (Peptide 8121 ), or a variant thereof, and a pharmaceutically acceptable carrier or diluent, or mixtures thereof. In another embodiment, the composition comprises a peptide inhibitor comprising a fragment of the amino acid sequence of SEQ ID NO: 5, SEQ ID NO: 9 or a variant thereof and a pharmaceutically acceptable carrier or diluent, or mixtures thereof. In another embodiment, the composition comprises any combination of: Peptide 8006 and/or Peptide 8120 and/or Peptide8121 and/or a pharmaceutically acceptable carrier or diluent, or mixtures thereof. In another embodiment, the composition comprises: Peptide 8006, Peptide 8120, Peptide 8121 , a peptide inhibitor comprising a fragment of the amino acid sequence of SEQ ID NO: 5, SEQ ID NO: 9 or a variant thereof and a pharmaceutically acceptable carrier or diluent, or mixtures thereof.

[0093] The compositions containing the peptide inhibitors described herein can be prepared by known methods for the preparation of pharmaceutically acceptable compositions which can be administered to subjects, such that an effective quantity of the active substance is combined in a mixture with a pharmaceutically acceptable vehicle, including for example, a carrier or diluent. Suitable vehicles are described, for example, in Remington's Pharmaceutical Sciences (2003 - 20th edition) and in The United States Pharmacopeia: The National Formulary (USP 24 NF19) published in 1999. On this basis, the compositions include, albeit not exclusively, solutions of the substances in association with one or more pharmaceutically acceptable vehicles, carriers or diluents, and contained in buffered solutions with a suitable pH and iso-osmotic with the physiological fluids.

[0094] Pharmaceutical compositions include, without limitation, lyophilized powders or aqueous or non-aqueous sterile injectable solutions or suspensions, which may further contain antioxidants, buffers, bacteriostats and solutes that render the compositions substantially compatible with the tissues or the blood of an intended recipient. Other components that may be present in such compositions include water, surfactants (such as Tween), alcohols, polyols, glycerin and vegetable oils, for example. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules, tablets, or concentrated solutions or suspensions. The pharmaceutical composition may be supplied, for example but not by way of limitation, as a lyophilized powder which is reconstituted with sterile water or saline prior to administration to the subject.

[0095] Compositions of the present disclosure may comprise a pharmaceutically acceptable carrier. Suitable pharmaceutically acceptable carriers include essentially chemically inert and nontoxic compositions that do not interfere with the effectiveness of the biological activity of the pharmaceutical composition. Examples of suitable pharmaceutical carriers include, but are not limited to, water, saline solutions, glycerol solutions, ethanol, N-(1 (2,3-dioleyloxy)propyl)N,N,N- trimethylammonium chloride (DOTMA), diolesylphosphotidyl-ethanolamine (DOPE), and liposomes. Such compositions should contain a therapeutically effective amount of the compound, together with a suitable amount of carrier so as to provide the form for direct administration to the subject.

[0096] The composition may be in the form of a pharmaceutically acceptable salt which includes, without limitation, those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2- ethylarnino ethanol, histidine, procaine, etc.

[0097] In accordance with the methods and uses of the present disclosure, the peptide inhibitors or compositions comprising one or more of the peptide inhibitors, may be administered to a subject in a variety of forms depending on the selected route of administration, as will be understood by those skilled in the art. The peptide inhibitors or compositions comprising one or more of the peptide inhibitors disclosed in the present disclosure may be administered for example, by parenteral, intravenous, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intracisternal, intraperitoneal, intranasal, transepithelial, intrapulmonary, aerosol, topical, transdermal, buccal, nasal, rectal, intrathecal, sublingual, or oral administration, and the pharmaceutical compositions may be formulated accordingly. Parenteral administration may occur by continuous infusion over a selected period of time.

Kits

[0098] Another aspect of the present disclosure is a kit comprising one or more of the peptide inhibitors disclosed herein or the compositions comprising one or more of the peptide inhibitors disclosed herein and instructions for use thereof.

[0099] The kit can also include ancillary agents. For example, the kit can include an instrument for injecting the peptide inhibitors or compositions of the present disclosure into a subject, such as a syringe; a vessel for storing or transporting the peptide inhibitors or compositions; and/or pharmaceutically acceptable carriers or diluents, or mixtures thereof. Methods and uses

[00100] Another aspect of the present disclosure is a method of inhibiting RNA- dependent RNA polymerase activity of RSV or another respiratory virus comprising administering an effective amount of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein to a cell or subject in need thereof.

[00101 ] The present disclosure also includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein to inhibit RNA-dependent RNA polymerase activity of RSV in a cell or subject in need thereof. Another aspect of the disclosure includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for the manufacture of a medicament to inhibit RNA-dependent RNA polymerase activity of RSV in a cell or subject in need thereof. A further aspect of the present disclosure includes one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for use in inhibiting RNA-dependent RNA polymerase activity of RSV in a cell or subject in need thereof.

[00102] As used herein, "inhibit" or "inhibiting" a function or activity, such as RNA- dependent RNA polymerase activity of RSV, infection from RSV, or cell invasion from RSV, is to reduce the function or activity when compared to otherwise same conditions except for a condition or parameter of interest. The terms "inhibitor" and "inhibition", in the context of the present disclosure, are intended to have a broad meaning and include peptide inhibitors which directly or indirectly act on RNA- dependent RNA polymerase activity of RSV and/or the polymerase complex of RSV, infection from RSV or cell invasion from RSV and/or reduce function or activity of the polymerase and/or polymerase complex of RSV, or infection from RSV or cell invasion from RSV. The phrase "inhibiting RNA-dependent RNA polymerase activity" or "inhibit RNA-dependent RNA polymerase activity" means reducing RNA- dependent RNA polymerase activity as compared to otherwise same conditions, and includes reduction accomplished by directly or indirectly acting on the RNA- dependent RNA polymerase activity of RSV. [00103] The term "subject" as used herein refers to any member of the animal kingdom, preferably a mammalian one embodiment, the mammal is a cow, sheep, horse, pig, dog, or chicken susceptible to infections with RSV. In another embodiment, the mammal is a human. In one embodiment, the human is a subject that is immunocompromised. The term "immunocompromised" means a subject who has an immunodeficiency, and thus has an immune system that is impaired by disease or treatment of a disease as compared to a subject who is not immunocompromised. In another embodiment, an immunocompromised subject includes a subject having chronic obstructive pulmonary disease (COPD), a lung infection, or is infected with HIV.

[00104] The terms "therapeutically effective amount", "effective amount" or "sufficient amount" mean a quantity sufficient to, when administered to the subject, including a mammal, for example a human, achieve a desired result, for example an amount effect to inhibit RNA-dependent RNA polymerase activity of RSV in a subject. Effective amounts of therapeutic may vary according to factors such as the disease state, age, sex, weight of the subject. Dosage or treatment regime may be adjusted to provide the optimum therapeutic response. In addition, a "treatment" regime of a subject with a therapeutically effective amount may consist of a single administration, or alternatively comprise a series of applications. The length of the treatment period depends on a variety of factors, such as the severity of the infection or disease, the age of the subject, the concentration and the activity of the peptide inhibitors, or a combination thereof. It will also be appreciated that the effective dosage of the peptide inhibitors used for the treatment or prevention may increase or decrease over the course of a particular treatment or prevention regime. Changes in dosage may result and become apparent by standard diagnostic assays known in the art. The peptide inhibitors of the present disclosure may be administered before, during or after exposure to the virus.

[00105] A further aspect of the present disclosure is a method of preventing RNA- dependent RNA polymerase activity of RSV comprising administering an effective amount of one or more of the peptide inhibitors disclosed herein or the compositions comprising one or more of the peptide inhibitors disclosed herein to a cell or subject in need thereof. [00106] The present disclosure also includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein to prevent RNA-dependent RNA polymerase activity of RSV in a cell or subject in need thereof. Another aspect of the disclosure includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for the manufacture of a medicament to prevent RNA-dependent RNA polymerase activity of RSV in a cell or subject in need thereof. A further aspect of the present disclosure includes one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for use in preventing RNA- dependent RNA polymerase activity of RSV in a cell or subject in need thereof.

[00107] The term "preventing RNA-dependent RNA polymerase activity", "prevent RNA-dependent RNA polymerase activity, "inhibit RNA-dependent RNA polymerase activity" or "inhibiting RNA-dependent RNA polymerase activity" as used herein means blocking virulence of virions via blockage and/or interference of the RNA- dependent RNA polymerase system in RS as compared to otherwise same conditions.

[00108] An additional aspect of the present disclosure is a method of inhibiting infection from RSV comprising administering an effective amount of one or more of the peptide inhibitors disclosed herein or the compositions comprising one or more of the peptide inhibitors disclosed herein to a cell or subject in need thereof.

[00109] The present disclosure also includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein to inhibit infection from RSV in a cell or subject in need thereof. Another aspect of the disclosure includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for the manufacture of a medicament to inhibit infection from RSV in a cell or subject in need thereof. A further aspect of the present disclosure includes one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for use in inhibiting infection from RSV in a cell or subject in need thereof. [001 10] The term "inhibiting infection" or "inhibit infection" as used herein means reducing infection from RSV of cells as compared to otherwise same conditions. The inhibition of infection may be assessed using assays known to those skilled in the art. For example, inhibition of infection may be assessed by measuring viral counts, colonization, and replication of viral particles and comparing to otherwise same conditions. Inhibition of infection may also be assessed for example, by evaluating symptoms of infection, including for example, inflammation, redness, heat and/or pain as compared to otherwise same conditions.

[001 1 1 ] Another aspect of the present disclosure is a method of inhibiting virus replication including RNA transcription and genomic RNA replication of RSV or another respiratory virus comprising administering an effective amount of one or more of the peptide inhibitors disclosed herein or the compositions comprising one or more of the peptide inhibitors disclosed herein to a cell or subject in need thereof.

[001 12] The present disclosure also includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein to inhibit virus replication including RNA transcription and genomic RNA replication of RSV or another respiratory virus in a cell or subject in need thereof. Another aspect of the disclosure includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for the manufacture of a medicament to inhibit virus replication including RNA transcription and genomic RNA replication of RSV or another respiratory virus in a cell or subject in need thereof. A further aspect of the present disclosure includes one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for use in inhibiting virus replication including RNA transcription and genomic RNA replication of RSV or another respiratory virus in a cell or subject in need thereof.

[001 13] The term "inhibiting virus replication" or "inhibit virus replication" as used herein means reducing RNA transcription and genomic RNA replication of RSV or another respiratory virus as compared to otherwise same conditions. Inhibition of cell invasion may be assessed using assays known to those skilled in the art including, but not limited to, in vitro invasion assays. [001 14] An additional aspect of the present disclosure is a method of treating or preventing infection from RSV comprising administering an effective amount of one or more of the peptide inhibitors disclosed herein or the compositions comprising one or more of the peptide inhibitors disclosed herein to a cell or subject in need thereof.

[001 15] The present disclosure also includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein to treat or prevent infection from RSV in a cell or subject in need thereof. Another aspect of the disclosure includes uses of one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for the manufacture of a medicament to treat or prevent infection from RSV in a cell or subject in need thereof. A further aspect of the present disclosure includes one or more of the peptide inhibitors disclosed herein or a composition comprising one or more of the peptide inhibitors disclosed herein for use in treating or preventing infection from RSV in a cell or subject in need thereof.

[001 16] As used herein, and as well understood in the art, "treatment" or "prevention" are approaches for obtaining beneficial or desired results, including clinical results. Beneficial or desired clinical results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of extent of disease, stabilized (i.e. not worsening) state of disease, preventing spread of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. "Treatment" can also mean prolonging survival as compared to expected survival if not receiving treatment. "Palliating" a disease or disorder means that the extent and/or undesirable clinical manifestations of a disorder or a disease state are lessened and/or time course of the progression is slowed or lengthened, as compared to not treating the disorder.

[001 17] The phrase "treating or preventing infection from RSV" includes treating infection from RSV, preventing infection from RSV, decreasing the severity of infection from RSV, inhibiting RSV colonization, reducing shedding of RSV, and preventing RSV colonization or improving signs and symptoms related to infection from RSV. The present disclosure also includes the treatment or prevention of any disease that is associated with an infection from RSV. [001 18] In understanding the scope of the present disclosure, the term "comprising" and its derivatives, as used herein, are intended to be open ended terms that specify the presence of the stated features, elements, components, groups, integers, and/or steps, but do not exclude the presence of other unstated features, elements, components, groups, integers and/or steps. The foregoing also applies to words having similar meanings such as the terms, "including", "having" and their derivatives. Finally, terms of degree such as "substantially", "about" and "approximately" as used herein mean a reasonable amount of deviation of the modified term such that the end result is not significantly changed. These terms of degree should be construed as including a deviation of at least ±5% of the modified term if this deviation would not negate the meaning of the word it modifies.

[001 19] The above generally describes the present disclosure. A more complete understanding can be obtained by reference to the following specific examples. These examples are described solely for the purpose of illustration and are not intended to limit the scope of the disclosure. Changes in form and substitution of equivalents are contemplated as circumstances might suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitation.

[00120] The following non-limiting examples are illustrative of the present disclosure:

EXAMPLES

Example 1

[00121 ] The RSV phosphoprotein contains binding domains for the N protein (peptide 8006) and L protein (peptides 8121 and 8120). The addition of a nuclear localization sequence to these peptides allows the peptides to enter cells and act as dominant-negative, competitive inhibitors to block the interaction of the RNA polymerase subunits and prevent virus replication. Peptides 8006 (Figure 2 and 3), 8121 (Figure 4 and 5) and 8120 (Figure 6 and 7) when added with infectious RSV prevent RSV replication in both LLC-MK2 cells and R-Mix cells. Inhibition of replication is measured by a decrease in fluorescent staining of viral protein at 48 hours after infection using an RSV-specific monoclonal antibody and FITC- conjugated anti-lgG antibody (Figures 2 - 7).

[00122] Inhibition of RSV in LLC-MK2 cells by peptide 8006 is illustrated in Figure 2. LLC-MK2 cells were treated with peptide at a concentration of 1 mM and infected with RSV. Virus was detected at 48 hours by immunofluorescent staining with a monoclonal antibody. The data in the figure is representative of three independent experiments.

[00123] Inhibition of RSV in R-Mix cells by peptide 8006 is illustrated in Figure 3. R-Mix cells were treated with peptide at a concentration of 1 mM and infected with RSV. Virus was detected at 48 hours by immunofluorescent staining with a monoclonal antibody. The data in the figure is representative of three independent experiments.

[00124] Inhibition of RSV in LLC-MK2 cells by peptide 8121 is illustrated in Figure 4. LLC-MK2 cells were treated with peptide at a concentration of 1 mM and infected with RSV. Virus was detected at 48 hours by immunofluorescent staining with a monoclonal antibody. The data in the figure is representative of three independent experiments.

[00125] Inhibition of RSV in R-Mix cells by peptide 8121 is illustrated in Figure 5. R-Mix cells were treated with peptide at a concentration of 1 mM and infected with RSV. Virus was detected at 48 hours by immunofluorescent staining with a monoclonal antibody. The data in the figure is representative of three independent experiments.

[00126] Inhibition of RSV in LLC-MK2 cells by peptide 8120 is illustrated in Figure 6. LLC-MK2 cells were treated with peptide at a concentration of 1 mM and infected with RSV. Virus was detected at 48 hours by immunofluorescent staining with a monoclonal antibody. The data in the figure is representative of three independent experiments.

[00127] Inhibition of RSV in R-Mix cells by peptide 8120 is illustrated in Figure 7. R-Mix cells were treated with peptide at a concentration of 1 mM and infected with RSV. Virus was detected at 48 hours by immunofluorescent staining with a monoclonal antibody. The data in the figure is representative of three independent experiments. [00128] Location of peptide sequences within RSV phosphoprotein is illustrated in Figure 8. The location of peptides 8006, 8020 and 8021 are indicated and are underlined within the consensus sequence.

[00129] Peptide 8006 inhibits RSV in a dose-dependent fashion. At a concentration of 0.2 mM peptide 8006 inhibits RSV replication by 30%. The inhibition increases to 90% at a peptide concentration of 1 mM and increases to 100% at a peptide concentration of 1.5 mM (Figure 9). Various concentrations of peptide 8006 were used to treat LLC-MK2 cells for 30 minutes prior to infection with RSV. Virus was detected at 48 hours by immunofluorescent staining with a commercial monoclonal antibody specific for RSV. Data are expressed as mean ±SEM. The data in the figure is representative of three independent experiments.

[00130] Peptide 8006 was tested for cytotoxicity using an enzyme release assay. Peptide 8006 is not cytotoxic to HeLa cells. HeLa cells were treated with various concentrations of peptide for 30 minutes and culture supernatants (0.05 ml_) were collected and tested for adenylate kinase activity measured as relative light units (RLU) using the ToxiLight™ assay (Lonza) according to the manufacturer's instructions. Control samples were lysed with detergent to indicate maximum enzyme activity when cells are completely lysed. At a peptide concentration of 1 .5 mM the amount of adenylate kinase acitivity in the supernatants of HeLa cell cultures was not increased above the level of adenylate kinase activity in the supernatants of HeLa cell cultures not exposed to the peptide (Figure 10). Assays were performed in triplicate and the mean ± SEM values indicated in the error bars.

[00131 ] The alignment of two different RSV P sequences showing conservation is illustrated in Figure 1 1. The two phosphoprotein sequences are identical (SEQ ID NO: 9).

[00132] The alignment of two human RSV, an ovine RSV, and two hMPV showing conserved areas and location of peptide 8006 is illustrated in Figure 12A, wherein the location of peptide 8006 is indicated by bold and underlining.

[00133] The alignment of two human RSV, an ovine RSV, and two hMPV showing conserved areas and location of peptide 8121 is illustrated in Figure 12 B, wherein the location of peptide 8121 is indicated by bold and underlining. [00134] The alignment of two human RSV, an ovine RSV, and two hMPV showing conserved areas and location of peptide 8120 is illustrated in Figure 12 C, wherein the location of peptide 8120 is indicated by bold and underlining.

[00135] RSV Phosphoprotein secondary structure prediction is illustrated in Figure 13 showing a high proportion of alpha helical structure indicating a specific function.

[00136] Inhibition of RSV with various peptide mimetics is illustrated in Figure 14. R-Mix cells were pre-treated for 30 minutes with MBP-RSV-P peptide (panel A), MBP alone (panel B), or MBP-FNJ peptide (panel C) at the indicated concentrations, then infected with RSV. After 48 hours RSV was detected by immunofluorescent staining using a monoclonal antibody to RSV.

Summary

[00137] The RNA genome of the virus is encapsulated by the nucleocapsid (N) protein forming an RNase-resistant nucleocapsid core of the virus. The RNA-N complex acts as a template for replication and transcription by the polymerase complex of the virus which is made up of three subunits that includes the phosphoprotein (P), the large polymerase subunit (L), and the M2-1 and M2-2 cofactors. The P, N and L proteins constitute the minimal components required for viral RNA replication and transcription. The inventor determined that the polymerase complex therefore represents a potential target for disruption by a peptide mimetic, and targeted the Phosphoprotein of RSV for inhibition using peptide mimetics to disrupt the polymerases complex. Three exemplary cognate peptides were synthesized that included specific regions of the Phosphoprotein, that is, the C- terminal 21 amino acid representing the Nucelocapsid binding domain (peptide 8006) or two 21 amino acid sequences representing parts of the L subunit binding domain P100-120 and P140-160 (peptides 8120 and 8121 respectively). Each peptide also included of an 1 1 amino acid nuclear localization sequence (Tyr-Gly- Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg) to allow the peptides to cross the cytoplasmic membrane and enter cells.

Materials

[00138] HeLa cells, LLC-MK2 cells and RSV used in this study are obtained commercially from the American Type Culture Collection (ATCC). Antibody for staining RSV and R-Mix cells were obtained from Diagnostic Hybrids Inc. (Athens, OH). Peptides were synthesized by the APTC Peptide Synthesis Facility at The Hospital for Sick Children in Toronto, ON. All other common reagents were purchased from Sigma Chemicals in St. Louis, MO.

Methods

[00139] Infection and Immunofluorescent staining: LLC-MK2 cells were grown to confluency on glass coverslips in shell vials. Cell monolayers were pre-treated for 30 minutes with peptide inhibitors and then infected with RSV by adding 0.2 mL virus seed onto monolayers and centrifuging the monolayers for 30 minutes at 2,800 rpm. The virus inoculum was removed and fresh medium containing peptide was added. The cells were incubated at 37°C for 48 hours. Virus was detected by IF staining using a commercially available RSV-specific monoclonal antibody (Diagnostic Hybrids Inc, Athens OH) and a second FITC-conjugated anti-mouse Ig antibody. Infected cells were photographed using a Zeiss Fluromat fluorescent microscope.

[00140] Plaque assay: A confluent monolayer of MDCK cells in 6-well tissue culture plates is infected with RSV for 30 minutes at room temperature to allow infection to occur. The monolayer is overlaid with MEM medium, 0.65% agarose and 1 ug/mL of trypsin. The agarose containing medium is allowed to solidify at room temperature and the plates are incubated for 2-3 days at 37° C until visible plaques appear. The cells are fixed with 95% methanol/5% acetic acid for 20 minutes and stained with Giemsa stain. The plaques are counted visually, each plaque representing one infectious virus particle. The plaque assay can also be used to measure the inhibitory effect of peptides by incubating the monolayers with virus +/- peptide inhibitor and comparing the number of plaques with peptide to virus alone. Measuring infectious virus can be performed by plaque assay, counting virus particles by electron microscopy or quantitative polymerase chain reaction to measure viral load. Inhibition of infection may also be assessed in animal models of infection or in humans by evaluating symptoms of infection, including inflammation, pathology, and viral genome copy number in the lungs.

[00141 ] Adenylate kinase activity assay: HeLa cells were treated with various concentrations of peptide 8006, 8120, and 8121 for 30 minutes and culture supernatants (0.05 mL) were collected and tested for adenylate kinase activity measured as relative light units (RLU) using the ToxiLight™ assay (Lonza) according to the manufacturer's instructions. The detergent lysis aliquot shows maximum enzyme activity when cells are completely lysed by detergent.

[00142] Solid phase synthesis of peptides: Solid phase peptide synthesis (SSPS) using F-moc blocking groups is commonly used by commercial suppliers of synthetic peptides (Carpino L.A. "1 -Hydroxy-7-azabenxotriazole. An efficient peptide coupling additive". J. Am. Chem. Soc. 1993, 1 15(10): 4397-4398). The C-terminal amino acid was attached to a cross-linked polystyrene resin via an acid labile bond with a linker molecule. This resin was insoluble in the solvents used for synthesis, making it relatively simple and fast to wash away excess reagents and by-products. The N- terminus was protected with the Fmoc group, which is stable in acid, but removable by base. Any side chain functional groups were protected with base stable, acid labile groups.

Results

[00143] Peptide 8006 inhibited RSV replication in a dose response fashion with inhibition seen at concentrations as low as 0.2 mM and inhibition of greater than 90% at a concentration of 1 mM (Figure 2 and 3) in LLC-MK2 cells and R-Mix cells. Peptide 8121 inhibited RSV replication by greater than 95% at 1 mM (Figure 4 and 5) while peptide 8120 inhibited RSV by 90% at a concentration of 1 mM (Figure 6 and 7).

[00144] In order to evaluate the cytotoxicity of peptide 8006, HeLa cells were treated with increasing concentrations of peptide and cell lysis was evaluated using an adenylate kinase assay. Peptide concentrations of up to 1.5 mM were not toxic. (Figure 10).

[00145] To explore whether the RSV peptide could be conjugated to a carrier protein for large scale production, the RSV-P peptide was conjugated to the C- terminus of the carrier protein, Maltose binding protein (MBP), cloned into the peri His-MBP Gateway cloning vector and the fusion protein expressed in E. coli. MBP alone lacking the RSV-P or MBP containing a control peptide, FliJ, were also expressed as recombinant proteins and used as controls in the RSV inhibition assay. The MBP-RSV-P fusion protein inhibited RSV replication where the controls, MBP alone or MBP-FNJ did not inhibit RSV (Figure 14).

Discussion [00146] The present disclosure describes the discovery of peptide inhibitors, such as peptide 8006 and peptide 8121 , which inhibit RSV replication. Peptides 8006 and 8121 inhibit RSV replication in LLC-MK2 and R-Mix cells in vitro. RSV is a leading cause of respiratory tract infection in children under the age of two years and a leading cause of hospitalization. The inventor has shown that RSV replication can be inhibited by peptide mimetics that either prevent or disrupt RNA-dependent RNA polymerase activity. These in vitro experiments are being corroborated with an animal model of RSV infection. There is presently only one prophylactic for RSV viz. a humanized monoclonal antibody (Palivizumab) which decreases hospitalization rates by about 50% if infections are treated early enough. There are currently no specific antivirals available for RSV infections. The current peptides represent the first RSV-specific antivirals that could be used for the treatment of RSV infections. The peptides and compositions described herein may therefore be used for the treatment of pediatric RSV infections in hospitalized children given the limited benefit of Palivizumab. Optionally, the peptide inhibitors can be given by intranasal inhalation using either web nebulizers or dry powder inhalers. The advantage of the membrane transport sequence or nuclear localization sequence (NLS) is that the peptides will enter cells and inhibit RNA replication within minutes minimizing the possibility of degradation by peptidases that are present on mucosal surfaces of the respiratory tract.

[00147] The approach employed in the present disclosure is aimed at treating RSV and other Pneumovirus infections in children, adults and animals has several apparent advantages. The peptides represent the first and only specific antiviral drugs that are useful for inhibiting both RSV and other Pneumoviruses, such as human metapneumovirus (hMPV). Furthermore, the peptide should not induce or select for resistant viruses as commonly occurs with other antiviral drugs that are small molecules because the peptide interacts with a long stretch of amino acid residues within the interactive domain of the target protein. Finally, peptides are not cytotoxic. Without wishing to be bound by any particular theory, the peptide inhibitors described herein may inhibit virus replication by blocking the interaction of RNA polymerase subunits or disrupting an already formed polymerase complex via competitive inhibition. [00148] There is some sequence similarity of the phosphoprotein of human RSV strains A and B. These results indicate that this sequence is conserved and functionally important. These conserved areas are 100% helical further suggesting a conserved role in protein interaction. Since the sequence of phosphoproteins of human RSV, ovine RSV and human metapneumovirus (hMPV) and other Pneumoviruses are similar, peptide 8006 and 8121 will likely also inhibit ovine RSV, human metapneumovirus (hMPV) and other Pneumoviruses.

[00149] It was also shown that the RSV-P peptide can be attached to carrier proteins without loss of activity suggesting that human carrier proteins such as transferrin or immunoglobulin (IgG) lambda light chain could be conjugated to the peptides described herein and used in humans.

Example 2

Co-lmmunoprecipitations

[00150] Experiments were performed to investigate whether the P220-241 peptide (SEQ ID NO: 2) could block the interaction between RSV N and P protein in vitro. To accomplish this, LLC-MK2 cells were seeded in T25 flasks and grown until confluent. RSV was then added to the cells (MOI of 1 ) in Refeed medium and allowed to incubate for 4 days. When performing anti-His immunoprecipitations, purified P220-241 was added to cells at a concentration of 20 μΜ and incubated for 2 hours prior to scraping the cells. Following centrifugation, the cells were resuspended in 500 μΙ_ of ice cold lysis buffer (50 mM Tris-HCI pH 7.2, 100 mM KCI, 0.1 % SDS, 1 % Triton X- 100, 1 EDTA-free protease inhibitor) and allowed to nutate for 3 hours at 4°C. Primary anti-His (Sigma), anti-RSV N (Abeam), or anti-RSV P (Abeam) primary antibodies were then added to make a final dilution of 1 :500, and the solution was nutated overnight at 4°C. To bind the primary antibodies, 30 μΙ_ of protein A/G beads was for an additional hour at 4°C. The beads were resuspended in 30 μΙ_ of Laemmli buffer and boiled for 20 minutes. The samples were then analyzed by SDS-PAGE and Western blot using the appropriate primary antibody.

[00151 ] In the absence of P220-241 , RSV N and P co-immunoprecipitated, suggestive of an interaction in vivo (Figures 15A and B). However, the P220-241 peptide prevented this interaction (Figure 15C), suggesting that the peptide mimetic successfully disrupts the RSV P/N interaction. Viral Inhibition Assays

[00152] Further experiments were performed to confirm that the P220-241 peptide did not negatively affect other viruses to support its specificity towards RSV. To accomplish this, LLC-MK2 cells were seeded at a concentration of 1 .5x10⁵ cells (in DMEM+10% FBS) per shell vial containing microscope cover slips. The cells were allowed to grow overnight at 37°C and 5% C0₂ until fully confluent. Shell vials were washed with sterile PBS before being incubated with purified recombinant proteins in DMEM for 1 hour at 37°C and 5% C0₂. Cells were treated with P220-241 3 varying concentrations from 20 μΜ to 2.5 μΜ, while control peptides were used at a concentration of 20 μΜ. The media was then removed and the cells were infected with HPIV-2 (MOI of 1 ). Shell vials were centrifuged at 2,800 RPM for 30 minutes and then incubated at 37°C and 5% C0₂ for an additional 30 minutes. The viral media was removed, the cells were washed with sterile PBS, and were then treated with an additional round of recombinant protein in DMEM. Following a 48 hour incubation period at 37°C and 5% C0₂, the cells were washed with sterile PBS, fixed with ice cold acetone for 30 minutes, and then stained (in the dark) with D-Ultra Respiratory Virus Screening DFA Reagent (Diagnostic Hybrids) for 45 minutes at 37°C and 5% C0₂. The cover slips were mounted face down on glass slides and visualized by fluorescent microscopy using the EVOS Fluorescent Microscope (Life Technologies) at 10X magnification.

[00153] It was observed that the RSVP220-241 peptide had no effect on HPIV-2 infection (Figure 16), suggesting that the peptide mimetic is specific for RSV.

[00154] While the present disclosure has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the disclosure is not limited to the disclosed examples. To the contrary, the disclosure is intended to cover various modifications and equivalent arrangements within the spirit and scope of the appended claims.

[00155] All publications, patents and patent applications and sequence accession numbers are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application or sequence accession number was specifically and individually indicated to be incorporated by reference to its entirety.

Claims

WHAT IS CLAIMED IS:

1 . A peptide comprising all or part of an interactive domain of the phosphoprotein of RSV, wherein the peptide inhibits RNA-dependent RNA polymerase activity in Respiratory Syncytial Virus (RSV).

2. The peptide of claim 1 , wherein the phosphoprotein of RSV comprises an amino acid sequence with at least 80% sequence identity to a phosphoprotein sequence selected from SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 1 1 , SEQ ID NO: 12 and SEQ ID NO: 13.

3. The peptide of claim 1 or 2, wherein the interactive domain comprises the nucleocapsid binding domain of the phosphoprotein, optionally the nucleocapsid binding domain set forth in amino acids 220 to 241 of SEQ ID NO: 9.

4. The peptide of claim 3, wherein the peptide comprises, consists essentially of, or consists of all or part of SEQ ID NO: 2 or a variant thereof.

5. The peptide of claim 4, wherein the peptide comprises, consists essentially of, or consists of an amino acid sequence with at least 80%, at least 90% or at least 95% sequence identity to SEQ I D NO: 2.

6. The peptide of claim 4 or 5, wherein the peptide comprises, consists essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18, at least 20 amino acids of SEQ ID NO: 2.

7. The peptide of claim 1 or 2, wherein the interactive domain comprises the L subunit binding domain of the phosphoprotein, optionally all or part of the L subunit binding domain set forth in amino acids 120 to 160 of SEQ ID NO: 9.

8. The peptide of claim 7, wherein the peptide comprises, consists essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18 or at least 20 amino acids of amino acids 100 to 160 of SEQ I D NO: 9.

9. The peptide of claim 7 or 8, wherein the peptide comprises, consists essentially of, or consists of all or part of SEQ I D NO: 3 or SEQ I D NO: 4 or a variant thereof.

10. The peptide of any one of claims 7 to 9, wherein the peptide comprises, consists essentially of, or consists of an amino acid sequence with at least 80%, at least 90% or at least 95% sequence identity to SEQ ID NO: 3 or SEQ ID NO: 4.

1 1 . The peptide of any one of claims 7 to 10, wherein the peptide comprises, consists essentially of, or consists of a contiguous fragment of at least 12, at least 14, at least 16, at least 18 or at least 20 amino acids of SEQ ID NO: 3 or SEQ ID NO: 4.

12. The peptide of any one of claims 1 to 1 1 , wherein the peptide further comprises a nuclear localization sequence or a cell-penetrating peptide.

13. The peptide of claim 12, wherein the nuclear localization sequence is the amino acid sequence of SEQ ID NO: 1 .

14. The peptide of claims 12 or 13, wherein the peptide comprises, consists essential of, or consists of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8, or a variant thereof.

15. The peptide of any one of claims 1 to 14, wherein the peptide is conjugated to a carrier peptide, optionally maltose-binding protein, transferrin or immunoglobulin lambda light chain.

16. A composition comprising the peptide of any one of claims 1 to 15 and a pharmaceutically acceptable carrier or diluent.

17. Use of the peptide of any one of claims 1 to 15 or the composition of claim 16 to inhibit RNA-dependent RNA polymerase activity of a Respiratory Syncytial Virus (RSV) in a cell or in a subject in need thereof.

18. The use of claim 17, wherein the peptide inhibits infection from RSV in the cell or in the subject.

19. The use of claim 17, wherein the peptide inhibits cell invasion of RSV in the cell or in the subject.

20. The use of any one of claims 17 to 19, wherein the RSV is human RSV, bovine RSV or murine RSV.

21 . The use of any one of claims 17 to 20, wherein the cell in in vivo or in vitro.

22. Use of the peptide of any one of claims 1 to 15 or the composition of claim 16 for the treatment or prevention of Respiratory Syncytial Virus (RSV) in a subject in need thereof.

23. The use of claim 22, wherein the RSV is human RSV, bovine RSV or murine RSV.

24. The use of claim 22 or 23, wherein the RSV is multi-drug resistant RSV.

25. The use of any one of claims 22 to 24 wherein the subject is immunocompromised.

26. The use of claim 25, wherein the subject has chronic obstructive pulmonary disease (COPD), a lung infection or is infected with HIV.

27. The use of any one of claims 22 to 26, wherein the subject is a mammal.

28. The use of claim 27, wherein the mammal is a human.

29. A method for inhibiting RNA dependent RNA polymerase activity of a Respiratory Syncytial Virus (RSV) in a cell, the method comprising contacting the cell with the peptide of any one of claims 1 to 15 or the composition of claim 16.

30. The method of claim 29, wherein the cell in in vivo or in vitro.

31 . A method for the for treatment or prevention of Respiratory Syncytial Virus (RSV) in a subject in need thereof, the method comphsing administering to the subject the peptide of any one of claims 1 to 15 or the composition of claim 16.

32. The method of claim 31 , wherein the RSV is human RSV, bovine RSV or murine RSV.

33. The method of claim 31 or 32, wherein the RSV is multi-drug resistant RSV.

34. The method of any one of claims 31 to 33 wherein the subject is immunocompromised.

35. The method of claim 34, wherein the subject has chronic obstructive pulmonary disease (COPD), a lung infection or is infected with HIV.

36. The method of any one of claims 31 to 35, wherein the subject is a mammal.

7. The method of claim 36, wherein the mammal is a human.