Broad specturm anti-viral therapeutics and prophylaxis

Abstract

Provided are new compositions and methods for preventing and treating pathogen infection. In particular, provided are compounds having an anchoring domain that anchors the compound to the surface of a target cell, and a therapeutic domain that can act extracellularly to prevent infection of the target cell by a pathogen, such as a virus. Preferred target cells are epithelial cells. Also provided are compositions and methods for preventing viral diseases, such as influenza, using compounds having anchoring domains that can bind target cells linked to enzymatic activities that can act extracellularly to interfere with viral infection of target cells. Also provided are compositions and methods for preventing viral diseases such as influenza using compounds having anchoring domains that can bind target cells linked to protease inhibitors that can act extracellularly to interfere with viral infection of target cells.

1 . A pharmaceutical formulation comprising a sialidase or an active portion thereof, wherein the active portion retains enzymatic activity and does not comprise the full length enzyme.  
     
     
         2 . The pharmaceutical formulation of  claim 1  that is formulated as a spray.  
     
     
         3 . The pharmaceutical formulation of  claim 1  that is formulated as an inhalant.  
     
     
         4 . The pharmaceutical formulation of  claim 1  that is formulated as a suspension, a solution for injection or a solution for oral administration.  
     
     
         5 . The pharmaceutical formulation of  claim 1  that is formulated as a solution for eye drops.  
     
     
         6 . The pharmaceutical formulation of  claim 1  that is formulated as a cream, salve, gel, or ointment.  
     
     
         7 . The pharmaceutical formulation of  claim 1  that is formulated as a tablet, capsule or lozenge.  
     
     
         8 . The pharmaceutical formulation of  claim 1 , wherein the sialidase is a eukaryotic sialidase, a bacterial sialidase or a viral sialidase, or is substantially homologous thereto.  
     
     
         9 . The pharmaceutical formulation of  claim 8 , wherein the sialidase is a eukaryotic sialidase or is substantially homologous to a eukaryotic sialidase.  
     
     
         10 . The pharmaceutical formulation of  claim 9 , wherein the sialidase is a human sialidase or is substantially homologous to a human sialidase.  
     
     
         11 . The pharmaceutical formulation of  claim 10 , wherein the sialidase is substantially homologous to the NEU2 or NEU4 genes and comprises a sequence of amino acids that is substantially homologous to the sequence of amino acids set forth in SEQ ID NO:8 or SEQ ID NO:9.  
     
     
         12 . The pharmaceutical formulation of  claim 8 , wherein the sialidase is a bacterial sialidase or is substantially homologous to a bacterial sialidase.  
     
     
         13 . The pharmaceutical formulation of  claim 12 , wherein the bacterial sialidase is selected from the group consisting of  Vibrio cholerae  sialidase,  Clostridium perfringens  sialidase,  Actinomyces viscosus  sialidase and  Micromonospora viridifaciens  sialidase.  
     
     
         14 . The pharmaceutical formulation of  claim 13 , wherein the bacterial sialidase is  Actinomyces viscosus  sialidase.  
     
     
         15 . A method for the prophylaxis, prevention or treatment of infection by a pathogen, comprising: 
 administering a therapeutically effective amount of the formulation of  claim 1  to target cells of a subject.    
     
     
         16 . The method of  claim 15 , wherein the cells are endothelial cells.  
     
     
         17 . The method of  claim 15 , wherein the cells are epithelial cells.  
     
     
         18 . The method of  claim 17 , wherein the epithelial cells are respiratory epithelial cells, adenoid epithelial cells or bronchial epithelial cells.  
     
     
         19 . The method of  claim 15 , wherein the administering is by use of a nasal spray.  
     
     
         20 . The method of  claim 15 , wherein the administering is by use of an inhaler.  
     
     
         21 . The method of  claim 15 , wherein the administering is by oral administration.  
     
     
         22 . The method of  claim 15 , wherein the administering is performed from once to four times a day.  
     
     
         23 . The method of  claim 15 , wherein the pathogen is a bacterium.  
     
     
         24 . The method of  claim 15 , wherein the pathogen is a virus.  
     
     
         25 . The method of  claim 24 , wherein the virus is selected from among influenza, parainfluenza, adenovirus, retrovirus and respiratory syncytial virus.  
     
     
         26 . The method of  claim 25 , wherein the virus is influenza virus.  
     
     
         27 . A delivery system, comprising the pharmaceutical formulation of  claim 1 .  
     
     
         28 . The delivery system of  claim 27  that is a nebulizer, an atomizer or a dropper bottle.  
     
     
         29 . A method of using a sialidase for the prevention, prophylaxis or treatment of infection by a pathogen, comprising: 
 administering, to target cells of a subject, a therapeutically effective amount of at least one sialidase or an active portion thereof, wherein the active portion retains enzymatic activity and does not comprise a full length enzyme.    
     
     
         30 . The method of  claim 29 , wherein the cells are endothelial cells.  
     
     
         31 . The method of  claim 29 , wherein the cells are epithelial cells.  
     
     
         32 . The method of  claim 31 , wherein the epithelial cells are respiratory epithelial cells, adenoid epithelial cells or bronchial epithelial cells.  
     
     
         33 . The method of  claim 29 , wherein the sialidase is a viral sialidase, a bacterial sialidase, or a eukaryotic sialidase, or is substantially homologous thereto.  
     
     
         34 . The method of  claim 33 , wherein the sialidase is a eukaryotic sialidase or is substantially homologous to a eukaryotic sialidase.  
     
     
         35 . The method of  claim 34 , wherein the sialidase is a human sialidase or is substantially homologous to a human sialidase.  
     
     
         36 . The method of  claim 35 , wherein the sialidase is NEU2 (SEQ ID NO:8), or NEU4 (SEQ ID NO:9), or is substantially homologous thereto.  
     
     
         37 . The method of  claim 29 , wherein the sialidase is a bacterial sialidase or is substantially homologous to a bacterial sialidase.  
     
     
         38 . The method of  claim 37 , wherein the bacterial sialidase is selected from the group consisting of  Vibrio cholerae  sialidase,  Clostridium perfringens  sialidase,  Actinomyces viscosus  sialidase and  Micromonospora viridifaciens  sialidase.  
     
     
         39 . The method of  claim 38 , wherein the bacterial sialidase is  Actinomyces viscosus  sialidase.  
     
     
         40 . The method of  claim 29 , wherein the administering is by use of a nasal spray.  
     
     
         41 . The method of  claim 29 , wherein the administering is by use of an inhaler.  
     
     
         42 . The method of  claim 29 , wherein the administering is by oral administration.  
     
     
         43 . The method of  claim 29 , wherein the administering is performed from once to four times a day.  
     
     
         44 . The method of  claim 29 , wherein the pathogen is a bacterium.  
     
     
         45 . The method of  claim 29 , wherein the pathogen is a virus.  
     
     
         46 . The method of  claim 45 , wherein the virus is selected from among influenza, parainfluenza, adenovirus, retrovirus and respiratory syncytial virus.  
     
     
         47 . The method of  claim 46 , wherein the virus is influenza virus.  
     
     
         48 . The method of  claim 15  or  claim 29 , wherein the subject is a human subject.  
     
     
         49 . The method of  claim 15  or  claim 29 , wherein the subject is an animal subject.  
     
     
         50 . A compound, comprising: 
 an anchoring domain, wherein the anchoring domain comprises a peptide or protein that can bind to heparin or heparan sulfate at the surface of a target cell; and    a therapeutic chemical entity; wherein    the potency of the compound in the prevention, prophylaxis or treatment of a disease afflicting a target cell is greater than the potency of the therapeutic chemical entity in the absence of the anchoring domain.    
     
     
         51 . The compound of  claim 50 , wherein retention of the compound at or near the surface of the target cell is greater than retention of the therapeutic chemical entity in the absence of the anchoring domain.  
     
     
         52 . The compound of  claim 50  or  claim 51 , wherein the target cell is an epithelial cell.  
     
     
         53 . The compound of  claim 52 , wherein the epithelial cell is a respiratory epithelial cell.  
     
     
         54 . The compound of  claim 50  or  claim 51 , wherein the target cell is an endothelial cell.  
     
     
         55 . The compound of  claim 50 , wherein the therapeutic chemical entity is a protein, polypeptide, peptide, nucleic acid, peptide nucleic acid, nucleic acid analogue, nucleotide, nucleotide analogue, small organic molecule, polymer, lipid, steroid, fatty acid or carbohydrate.  
     
     
         56 . The compound of  claim 55 , wherein the therapeutic chemical entity is a protein or a polypeptide.  
     
     
         57 . The compound of  claim 56 , wherein the protein or polypeptide is an enzyme or a catalytically active portion thereof.  
     
     
         58 . The compound of  claim 57 , wherein the enzyme is a sialidase.  
     
     
         59 . The compound of  claim 58 , wherein the sialidase is a eukaryotic sialidase, a bacterial sialidase or a viral sialidase, or is substantially homologous thereto.  
     
     
         60 . The compound of  claim 59 , wherein the sialidase is a eukaryotic sialidase or is substantially homologous to a eukaryotic sialidase.  
     
     
         61 . The compound of  claim 60 , wherein the sialidase is a human sialidase or is substantially homologous to a human sialidase.  
     
     
         62 . The compound of  claim 61 , wherein the sialidase is substantially homologous to the NEU2 or NEU4 genes and comprises a sequence of amino acids that is substantially homologous to the sequence of amino acids set forth in SEQ ID NO:8 or SEQ ID NO:9.  
     
     
         63 . The compound of  claim 59 , wherein the sialidase is a bacterial sialidase or is substantially homologous to a bacterial sialidase.  
     
     
         64 . The compound of  claim 63 , wherein the bacterial sialidase is selected from among  Vibrio cholerae  sialidase,  Clostridium perfringens  sialidase,  Actinomyces viscosus  sialidase and  Micromonospora viridifaciens  sialidase.  
     
     
         65 . The compound of  claim 64 , wherein the bacterial sialidase is  Actinomyces viscosus  sialidase.  
     
     
         66 . The compound of  claim 50 , further comprising at least one peptide linker that links the anchoring domain to the therapeutic chemical entity.  
     
     
         67 . The compound of  claim 66 , wherein the peptide linker comprises at least one glycine residue.  
     
     
         68 . The compound of  claim 67 , wherein the peptide linker comprises the sequence (GGGGS)n, where n is a whole number from 1 to 20.  
     
     
         69 . The compound of  claim 50 , wherein the anchoring domain comprises a GAG-binding amino acid sequence of a naturally-occurring protein, or a sequence that is substantially homologous to the GAG-binding sequence of a naturally-occurring protein.  
     
     
         70 . The compound of  claim 69 , wherein the GAG-binding amino acid sequence is from a mammalian protein.  
     
     
         71 . The compound of  claim 70 , wherein the mammalian protein is a human protein.  
     
     
         72 . The compound of  claim 71 , wherein the GAG-binding amino acid sequence comprises the GAG-binding amino acid sequence of human platelet factor 4 (SEQ ID NO:2), human interleukin 8 (SEQ ID NO:3), human antithrombin III (SEQ ID NO:4), human apoprotein E (SEQ ID NO:5), human angio-associated migratory protein (SEQ ID NO:6), or human amphiregulin (SEQ ID NO:7), or a sequence substantially homologous thereto.  
     
     
         73 . A pharmaceutical formulation, comprising the compound of  claim 50 .  
     
     
         74 . The pharmaceutical formulation of  claim 73  that is formulated as a spray.  
     
     
         75 . The pharmaceutical formulation of  claim 73  that is formulated as an inhalant.  
     
     
         76 . The pharmaceutical formulation of  claim 73  that is formulated as a suspension, a solution for injection or a solution for oral administration.  
     
     
         77 . The pharmaceutical formulation of  claim 73  that is formulated as a solution for eye drops.  
     
     
         78 . The pharmaceutical formulation of  claim 73  that is formulated as a cream, salve, gel, or ointment.  
     
     
         79 . The pharmaceutical formulation of  claim 73  that is formulated as a tablet, capsule or lozenge.  
     
     
         80 . A delivery system, comprising the pharmaceutical formulation of any of claims  74 - 77 .  
     
     
         81 . The delivery system of  claim 80  that is a nebulizer, an atomizer or a dropper bottle.  
     
     
         82 . A method of increasing the potency of a therapeutic chemical entity in the prevention, prophylaxis or treatment of a disease, comprising: 
 linking the therapeutic chemical entity to an anchoring domain, wherein the anchoring domain comprises a peptide or protein that can bind to heparin or heparan sulfate at the surface of a target cell; whereby the potency of the therapeutic chemical entity is increased relative to its potency in the absence of the anchoring domain.    
     
     
         83 . The method of  claim 82 , wherein the linking is by a linker, wherein the linker is a chemical linker or a peptide linker.  
     
     
         84 . The method of  claim 82 , wherein the therapeutic chemical entity is a protein, polypeptide, peptide, nucleic acid, peptide nucleic acid, nucleic acid analogue, nucleotide, nucleotide analogue, small organic molecule, polymer, lipid, steroid, fatty acid or carbohydrate.  
     
     
         85 . The method of  claim 84 , wherein the therapeutic chemical entity is a protein or a polypeptide.  
     
     
         86 . The method of  claim 85 , wherein the protein or polypeptide is an enzyme or a catalytically active portion thereof.  
     
     
         87 . The method of  claim 86 , wherein the enzyme is a sialidase.  
     
     
         88 . The method of  claim 87 , wherein the sialidase is a eukaryotic sialidase, a bacterial sialidase or a viral sialidase, or is substantially homologous thereto.  
     
     
         89 . The method of  claim 88 , wherein the sialidase is a eukaryotic sialidase or is substantially homologous to a eukaryotic sialidase.  
     
     
         90 . The method of  claim 89 , wherein the sialidase is a human sialidase or is substantially homologous to a human sialidase.  
     
     
         91 . The method of  claim 90 , wherein the sialidase is substantially homologous to the NEU2 or NEU4 genes and comprises a sequence of amino acids that is substantially homologous to the sequence of amino acids set forth in SEQ ID NO:8 or SEQ ID NO:9.  
     
     
         92 . The method of  claim 88 , wherein the sialidase is a bacterial sialidase or is substantially homologous to a bacterial sialidase.  
     
     
         93 . The method of  claim 92 , wherein the bacterial sialidase is selected from among  Vibrio cholerae  sialidase,  Clostridium perfringens  sialidase,  Actinomyces viscosus  sialidase and  Micromonospora viridifaciens  sialidase.  
     
     
         94 . The method of  claim 93 , wherein the bacterial sialidase is  Actinomyces viscosus  sialidase.  
     
     
         95 . The method of any of claims  85 - 94 , wherein linkage of the anchoring domain to the therapeutic chemical entity is by fusion.  
     
     
         96 . The method of  claim 82 , wherein the anchoring domain comprises a GAG-binding amino acid sequence of a naturally-occurring protein, or a sequence that is substantially homologous to the GAG-binding sequence of a naturally-occurring protein.  
     
     
         97 . The method of  claim 96 , wherein the GAG-binding amino acid sequence is from a mammalian protein.  
     
     
         98 . The method of  claim 97 , wherein the mammalian protein is a human protein.  
     
     
         99 . The method of  claim 98 , wherein the GAG-binding amino acid sequence comprises the GAG-binding amino acid sequence of human platelet factor 4 (SEQ ID NO:2), human interleukin 8 (SEQ ID NO:3), human antithrombin III (SEQ ID NO:4), human apoprotein E (SEQ ID NO:5), human angio-associated migratory protein (SEQ ID NO:6), or human amphiregulin (SEQ ID NO:7), or a sequence substantially homologous thereto.  
     
     
         100 . A method for the prophylaxis, prevention or treatment of infection by a pathogen, comprising: 
 administering a therapeutically effective amount of the formulation of  claim 73  to target cells of a subject.    
     
     
         101 . The method of  claim 100 , wherein the cells are endothelial cells.  
     
     
         102 . The method of  claim 100 , wherein the cells are epithelial cells.  
     
     
         103 . The method of  claim 102 , wherein the epithelial cells are respiratory epithelial cells, adenoid epithelial cells or bronchial epithelial cells.  
     
     
         104 . The method of  claim 100 , wherein the administering is by use of a nasal spray.  
     
     
         105 . The method of  claim 100 , wherein the administering is by use of an inhaler.  
     
     
         106 . The method of  claim 100 , wherein the administering is by oral administration.  
     
     
         107 . The method of  claim 100 , wherein the administering is performed from once to four times a day.  
     
     
         108 . The method of  claim 100 , wherein the pathogen is a bacterium.  
     
     
         109 . The method of  claim 100 , wherein the pathogen is a virus.  
     
     
         110 . The method of  claim 109 , wherein the virus is selected from among influenza, parainfluenza, adenovirus, retrovirus and respiratory syncytial virus.  
     
     
         111 . The method of  claim 100 , wherein the subject is a human subject.  
     
     
         112 . The method of  claim 100 , wherein the subject is an animal subject.  
     
     
         113 . The method of  claim 25 , wherein the virus is parainfluenza virus.  
     
     
         114 . The method of  claim 46 , wherein the virus is parainfluenza virus.  
     
     
         115 . The method of  claim 110 , wherein the virus is parainfluenza virus.