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Full text of "USPTO Patents Application 09848616"

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WHAT IS CLAIMED IS: 

1 . A composition comprising a bacterial pilus to which an antigen or 
antigenic determinant has been attached by a covalent bond. 

2. The composition of c laim 1, ^herein said covalent bond is not a 
peptide bond. 

3 . The composition of claim f, wherein said bacterial pilus is a Type- 1 
pilus of Escherichia coli. 

4. The composition of clAim 1, wherein pilin subunits of said Type-1 
pilus comprises the amino acid sequence shown in SEQ ID NO: 146 or a sequence 
having at least 65, 70, 75, 80, 8^5, 90 or 95% sequence identity to SEQ ID 
NO: 146. 

5. The compositiad of claim 1, wherein said bacterial pilus and said 
antigen or antigen determinant are attached via a non-naturally occurring 
attachment. 

6. The composition of claim 1 , wherein said attachment comprises an 
organizer comprising at least one first attachment site, arid wherein said organizer 
is connected to said pilus by at least one covalent bond. 

7. The composition of claim 6, wherein said organizer is a 
polypeptide or a residue thereof, and ^vKerein said second attachment site is a 
polypeptide or a residue thereof 

8. The composition of claim 6, wherein said first and/or a second 
attachment sites/comprise: 




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or 



(a) an antigen and an antibody o/ antibody fragment thereto, 

(b) biotin and avidin; 

(c) strepavidin and biotin; 

(d) a receptor and its ligand; 

(e) a ligand-binding proteinyand its ligand; 

(f) interacting leucine zipper polypeptides; 

(g) an amino group and a/chemical group reactive thereto; 

(h) a carboxyl group and a chemical group reactive thereto; 

(i) a sulfhydryl group and a chemical group reactive thereto; 

(j) a combination thereof. 



9. The composition of claim 1, wherein said bacterial pilus and said 
antigen or antigentic derminant are attached by an attachment comprising 
interacting leucine zipper polypeptides. 

10. The composition of claim 5, wherein interacting leucine zipper 
polypeptides are JUN and/or FOS leucTTTfe zipper polypeptides. 



11. A composition comprising a bacterial pilin polypeptide to which 
an antigen or antigenic determinant has been attached by a covalent bond. 



/ 



12. The composition of claim 1 1, wherein said covalent bond is not a 
peptide bond. 



13. Theycomposition of claim 1 1 , wherein said polypeptide is from a 
Type-1 pilus of Escherichia coli. 



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14. The composition of claim 11, wherein said bacterial pilin 



polypeptide comprises the amino acid sequence shown in SEQ ID NO: 146 or a 
sequence having at least 65, 70, 75, 80, 85, 90 or/95% sequence identity to SEQ 
ID NO: 146. 



15. The composition of claim ^1, wherein said bacterial pilin 
polypeptide and said antigen or antigenic determinant are attached by a non- 



naturally occurring attachment. 



16. The composition of claim l/l, wherein said attachment comprises 
an organizer comprising at least orre~first attachment site, and wherein said 
organizer is connected to said pilus by a/least one covalent bond. 

17. The composition of claim 16, wherein said organizer is a 
polypeptide or a residue thereof, ancj' wherein said second attachment site is a 
polypeptide or a residue thereof. 



or 



an antigen and an antibody or antibody fragment thereto; 
biotin^nd avidin, 
strepavidin and biotin; 



18. The composition of claim 1 1, wherein said first and/or a second 
attachment sites comprise: / 
(a) 
(b) 
(c) 

a receptor and its ligand; 
a tfgand-binding protein and its ligand; 
interacting leucine zipper polypeptides; 
fan amino group and a chemical group reactive thereto; 
a carboxyl group and a chemical group reactive thereto; 
a sulfhydryl group and a chemical group reactive thereto; 



a combination thereof 



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19. The composition of claim 15, wherein said attachment comprises 
interacting leucine zipper polypeptides. 

20. The composition of claim 13, Wherein said interacting leucine 
zipper polypeptides are JUN and/or FOS leucine zipper polypeptides. 



21. A composition comprising: 

(a) a non-natural molecular scaffold comprising: 

(i) a core particle selected from the group consisting 



of: 



pilin protein; and 



site, 



(1) a bacterial pilus or pilin protein; and 

(2) a recombinant form of a bacterial pilus or 

(ii) an organizer comprising at least one first attachment 



wherein said organizer is cj&nnected to said core particle by at least one 
covalent bond; and 

(b) an antigei/ or antigenic determinant with at least one second 
attachment site, said second ^attachment site being selected from the group 
consisting of: 

(i) / an attachment site not naturally occurring with said 
antigen or antigenic determinant; and 

(iiy an attachment site naturally occurring with said 
antigen or antigenic determinant, 

wherein said second attachment site is capable of association through at 
least one non-peptide/bond to said first attachment site; and 

wherein said/antigen or antigenic determinant and said scaffold interact 
through said association to form an ordered and repetitive antigen array. 



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22. The composition of claim 21, wherein said organizer is a 
polypeptide or residue thereof; and wherein said second attachment site is a 
polypeptide or residue thereof. 

23 . The composition of claim 2 1 , wherein said first and/or said second 
attachment sites comprise: 

(a) an antigen and an antibo/iy or antibody fragment thereto; 

(b) biotin and avidin; 

(c) strepavidin and biotin;/ 

(d) a receptor and its ligand, 

(e) a ligand-binding prolan and its ligand; 

(f) interacting leucine y/ipper polypeptides; 

(g) an amino group and a chemical group reactive thereto; 

(h) a carboxyl group/and a chemical group reactive thereto; 

(i) a sulfhydryl group and a chemical group reactive thereto; 



or 



(j) a combination thereof 



24. The composition Gt claim 2 1 , wherein said first and/or said second 
attachment sites comprise interacting leucine zipper polypeptides. 

25 . The composit/on of claim 2 1 , wherein said bacterial pilus is a Type- 
1 pilus of Eschericia coli. 

26. The composition of claim 21, wherein pilus subunits of said type-1 
pilus comprise the amino acid sequence of SEQ ID No. 146 or a sequence having 
at least 65, 70, 75, 80/ 85, 90 or 95% sequence identity to SEQ ID NO: 146. 

27. The/composition of claim 26, wherein said interacting leucine 
zipper polypeptides are the JUN and/or FOS leucine zipper polypeptides. 



# 



* 



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28. A composit: on comprising: 

(a) a noi-natural molecular scaffold comprising: 

(i) a virus-like particle that is a dimer or a multimer of 
a polypeptide comprising ai nino acids 1-147 of SEQ ID NO: 1 58 as core particle 
or a sequence having at least 65, 70, 75, 80, 85, 90 or 95% sequence identity to 



SEQ ID NO: 158; and 



00 



site, 



wherein said organiz 
covalent bond; and 

(b) an an 
attachment site, said secor 
consisting of: 

(i) 



an organizer comprising at least one first attachment 

er is connected to said core particle by at least one 

igen or antigenic determinant with at least one second 
d attachment site being selected from the group 

an attachment site not naturally occurring with said 



antigen or antigenic determi lant; and 

an attachment site naturally occurring with said 
antigen or antigenic d^termiri^ 

wherein sai</ second^ttacfrment site is capable of association through at 
least one non-pept/de bondfta said first attachtp^nt site; and 

wherein said antispi i>r antigenip^determinant and said scaffold interact 
through said association/ToVfQ] n^arfordered and repetitive antigen array. 



29. The compositiDn of claim 28, wherein said organizer is a 
polypeptide or residue thereo 
polypeptide or residue thereof. 



; and wherein said second attachment site is a 



30. The composition 
attachment sites comprise: 

(a) an antigdn 

(b) biotin an 



of claim 28, wherein said first and/or said second 



and an antibody or antibody fragment thereto; 
avidin: 



V 



# 



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or 



(c) strepavidin and biotin; 

(d) a receptor and its ligand; 

(e) a ligand-biiiding protein and its ligand; 

(f) interactingfleucine zipper polypeptides; 

(g) an amino group and a chemical group reactive thereto; 

(h) a carboxyll group and a chemical group reactive thereto; 

(i) a sulfhydryTgroup and a chemical group reactive thereto, 

(j) ar comh/njation thereof^ 



3 1 . The composition of claim 30, wherein said first attachment site is 



an amino group and said second attachment site is a sulfhydryl group. 

32. The composition of claim 30, wherein^am virus-like particle and 
said antigen or antigenic determinant are attacjiea by an attachment comprising 
interacting leucine zipper polypeptides^ 



33. The composition of claim 32, wherein said interacting leucine 
zipper polypeptides are JUN and/or FOS FOS polypeptides. 



34. A composition comprising: 

(a) a non-natural molecular scaffold comprising: 

(i) Hepatitis B virus capsid protein comprising an 
amino acid sequence selected from the gimqxconsisting of: 

( 1 ) Jthi amino acichsequence of SEQ ID NO : 89 

(2) / theWmino acid sequence of SEQ ID NO: 90 

(3) / the Ifn/ino acid sequenge-tff^EQ ID NO: 93 

(4) [ the^qinoagid^^ 

(5) "^—tffe arfiino acid sequence of SEQ ID NO: 99 



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(6) the amino ac 



102: 



NO: 105; 
NO: 106; 
NO: 119; 
NO: 120; 
NO: 123; 
NO:125; 
NO:131; 
NO: 132; 
NO: 134; 
NO: 157; and 
NO: 158; and 
site, 



d sequence of SEQ ID NO: 



(7) the amino acid sequence of SEQ ID NO: 
104; 

(8) the amino Acid sequence of SEQ ID 

(9) the amino acid sequence of SEQ ID 

(10) the amino (acid sequence of SEQ ID 

(11) the amino/ acid sequence of SEQ ID 

(12) the amino acid sequence of SEQ ID 

(13) the amino acid sequence of SEQ ID 

(14) the amino acid sequence of SEQ ID 

^sequence of SEQ ID 

fuence of SEQ ID 

(17) the amino acid sequence of SEQ ID 

(18) the aminD acid sequence of SEQ ID 
(ii) an organizer comp irising at least one first attachment 




wherein said organizer is connected to said core particle by at least one 
covalent bond; and 



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(b) an antigen or antigenic determinant with at least one second 
attachment site, said second attachment site peing selected from the group 
consisting of: 

(i) an attachment sit£ not naturally occurring with said 
antigen or antigenic determinant; and 

(ii) an attachjrfeflt £ite naturally occurrijig-with said 
antigen or antigenic determinant, 

wherein said second attachr((entj§ite jfs caa^Ble of association through at 
least one non-peptide bond to said first attachment site; and 

wherein said antigen or antigenic determinant and said scaffold interact 
through said association to form an ordered and repetitive antigen array. 



35. The composition of (paim 34, wherein said organizer is a 
polypeptide or residue thereof, 

wherein said second attachment site is a polypeptide or residue thereof, 

and 

wherein said first attachment site is a lysine residue and said second 
attachment site is a cysteine residue, i 

36. The composition of! claim 34, wherein one or more cysteine 
residues of said Hepatitis B virus capsid protein have been either deleted or 
substituted with another amino acidl-Fesidue. 



37, The compo/itioif of ilaim 34, wl)£rein said first and/or said second 
attachment sites comprise 

(a) anf antigen and arf antibody or antibody fragment thereto; 

(b) biotin/and-aridin; 

(c) strepavidin ind biotin; 

(d) a receptor a id its ligand; 

(e) a ligand-biniling protein and its ligand; 



V 



/ 

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or 



(f) interacting leucine zipper polypeptides; 

(g) an amino group and a chemical group reactive thereto; 

(h) a carboxyl group and a chemical group reactive thereto; 

(i) a sulfhydryl group! and a chemical group reactive thereto; 



(j) a combination jtffipeof. 

38. The compositionuaf cl&im 36, wherein the cysteine residues 
corresponding to amino acids 48 and fl 07 in SEQ TD NO: 134 have been either 
deleted or substituted with another amino acid residue. 



39. The composition of claim 37_^h£rein said Hepatitis B virus capsid 



protein and said antigen or antigemj>d€terminant are attached by an attachment 
comprising interacting leucipe'zipper polypeptides. 



40. 



le composition of claim 39, wherein said interacting leucine 



zipper polypeptides are FOS and/or JUN polypeptides. 



1. The composition of any one of claims >28 3 34, 35, 36 and 38, 
wherein said antigen is selected from the group consisting of: 

(a) an antigen suited to induce /n immune response against 

bacteria, 

(b) an antigen suited to indiy^an immune response against 

viruses, 

(c) an antigen suited /o ii$uce an immunp^fesponse against 

parasites, 

(d) an antigen sujted tj$ inducp^h immune response against 

cancer cells, 

(e) an antigen suited/to induce an immune response against 

allergens, 



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(f) an antigen suited to induce an immune response in a farm 

animals, and 

(g) a protein suited to induce an imrfiune response in a pet. 

42. The composition of claim 41, whereiy the antigen is a protein, 
polypeptide, or a fragment thereof 

43. The composition of claim 41, wheilein said antigen induces an 
immune response against one or more allergens. 

44. The composition of c laim 41, wherein said antigen is: 

(a) a recombinant protein of HIV, 

(b) a recombinant protein of Influenza virus, 

(c) a recombinant protein ofl Hepatitis C virus, 

(d) a recombinant protein of Toxoplasma, 

(e) a recombinant protein of Plasmodium falciparum, 

(f) a recombinant proteir^f Plasmodium vivax, 

(g) a recombinant projeia of Plasmodium ovale, 

(h) a recombinant protein of Plasmodium malariae, 

(i) a recombina^protern of breast cancer cells, 
(j) a recombinant p^tein of kidney cancer-cells, 
(k) a recomWnan^rptein ofjjj^sfate cancer cells, 
(1) a recomgipant protein of skin cancer cells, 
(m) a recombinant orotein of brain cancer cells, 
(n) a recombinant jprotein of leukemia cells, 
(o) a recombinant? profiling, 
(p) a recombinant protein of bee sting allergy, 
(q) a recombin^it protein of nut allergy, 
(r) a recombinant protein of food allergies, 
(s) a recombinant protein of asthma, or 



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(t) a recombinant protein of Chlamydia. 

45. The composition of any one of claims /, 1 1 and 21, wherein said 
antigen is selected from the group consisting of: 

(a) an antigen suited to induce ^n immune response against 

bacteria, 

(b) an antigen suited to inducjfe an immune response against 

viruses, 

(c) an antigen suited to indi/ce an immune response against 

parasites, 

(d) an antigen suited to induce an immune response against 

cancer cells, 

(e) an antigen suited to induce an immune response in a farm 

animals, and 

(f) an antigen suited t^ induce an immune response in a pet, 

and 

(g) any other antiger^nvolved in a pathophysiological context. 

46. The composition of clai m 45 , wherein the antigen is a protein, a 
polypeptide, or a fragment thereof. 

47. The composition of any one of claims 1, 11 or 21, wherein said 
antigen is: / 

(a) a recombinant protein of HIV, 

(b) a recombinant protein of Influenza virus, 

(c) a recombinant protein of Hepatitis C virus, 

(d) a recombinant protein of Toxoplasma, 

(e) a recombinant protein of Plasmodium falciparum, 

(f) a recombinant protein of Plasmodium vivax, 

(g) a recombinant protein of Plasmodium ovale, 



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(h) a recombinant 

(i) a recombinant 
(j) a recombinant 
(k) a recombinant 
(1) a recombinant 
(m) a recombinant 
(n) a recombinant 
(o) a recombinant 
(p) a recorpfbinant 



protein ofyPlasmodium malariae, 
protein pf breast cancer cells, 
protein of kidney cancer cells, 
protein of prostate cancer cells, 
protein of skin cancer cells, 
►rotein of brain cancer cells, 
protein of leukemia cells, 
profiling, 

protein of Chlamydia. 



48. A pharmaceutical composition comprising the composition of any 
one of claims 1, 11,/21, 28, 34, 35, 36, f8, 41 or 44, and a pharmaceutical^ 
acceptable"carrier. 



49. A vaccine composition comprising the composition of any one of 
claims 1, 11, 21, 28, 34, 35, 36, 38, 41 ir 44. 



51. A method of irafmuni^ 
vaccine composition of claim 49 oi 

52. The methods claim 
immune response. 



53. The method of claim 
humoral immune response. 




50. The vaccine compositippofsJaim 49, further comprising at least 
one adjuvant. 



comprising administering to a subject the 



1, wherein said administering produces an 



51, wherein said administering produces a 



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54. The method of claymj&fi, wherein said administering produces a 
cellular immune response. 

55. The method of claim 51, wherein sai coadministering produces a 
humoral immune response and annular immujje^fesponse. 

56. The method/offcliirp^l, wherein said administering produces a 

it ' 

protective immune response. 



57. A method of making the composition of clainiX, comprising 




combining said pilus and said antigen or antigenic determinan^wherein sa ^d pilus 
and said antigen or antigenic determinant interact to forai an antigen array. 

58, The method of claim 57, wherein said antigen array is ordered 
and/or repetitive. "~ 



59. A method of makmg the composition of claim 11, comprising 
combining said pilin polypeotfae and said antigen or antigenic determinant, 
wherein said pilin polypeptide and said antigen or antigenic determinant interact 
to form an antigen array. 



60. /The method of claim 59, wherein said antigen array is ordered 
and/or readitive. 



61. A method of making the composition of claim_ 21, 28, 34, 35, 36 
of 38, comprising combining said-tfoi'f-n^tural molecular scaffold and said antigen 
or antigenic determinant, v^rehysaid non-na^atlrTolecular scaffold and said 
antigen or antigenic deteminajp^ntej^eTto form an antigen array. 



62. The metho 
and/or repetitive. 




wherein said antigen array is ordered 



63. A composition comprising: 

(a) a non-natural molecular scaffold comprising^ 

(i) a core particle selected from the group consisting 



of: 



pilin protein; and 



.site, 



(1) a bacterial pilus; and 

(2) a recombinant form/of a bacterial pilus or 

(ii) an organizer comprising at least one first attachment 



> I wherein said organizer is connected to s^dd core particle by at least one 

covalent bond; and 



(b) an antigen or antigenic determinant with at least one second 
attachment site, said second attachmerjt site being selected from the group 
consisting of 

(i) an attachment site not naturally occurring with said 
antigen or antigenic determinant; at 

(ii) an Attachment site naturally . occurring with said 
antigen or antigenic determinant, 

wherein said second attachment site is capable of association through at 
least one non-peptide bond to said first attachment site; 

wherein said antigen or antigenic determinant and said scaffold interact 
through said association io form an ordered and repetitive antigen array, and 

wherein said antigen or antigenic determinant is selected from the group 
consisting of an infmenza M2 peptide, the GRA2 polypeptide, the DP 178c 
peptide, the tumor necrosis factor polypeptide, a tumor necrosis factor peptide, 
the B2 peptide, the D2 peptide, and the Ap peptide. 



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64. The composition of cl aim 6 3, wherein said antigen or/antigenic 
determinant is the influenza M2 peptide or variants thereof. 

65. The composition of claim 63, wherein said antigen or antigenic 
determinant is the GRA2 polypeptide. 

66. The composition of claim 63, wherein said' antigen or antigenic 
determinant is the DP 178c peptide. 

67. The composition of claim 63, wherein said antigen or antigenic 
determinant is the tumor necrosis factor polypeptide. 



A / 68. The composition of claim 63, wherein said antigen or antigenic 

determinant is a tumor necrosis factor peptid^ 

69. The composition of clairr/63, wherein said antigen or antigenic 
determinant is the B2 peptide. 

70. The composition of claim 63, wherein said antigen or antigenic 
determinant is the D2 peptide. 

71. The composition of claim 63, wherein said antigen or antigenic 
determinant is the Ap peptide. 

72. The composition of claim 63, wherein said organizer is a 
polypeptide or residue thereof, and wherein said second attachment site is a 
polypeptide or residue thereof 

73 . /The composition of claim 6 3 , wherein said first and/or said second 
attachment sites comprise: 



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(a) an antigen and an antibody or antibody fragment the/eto; 

(b) biotin and avidin; 

(c) strepavidin and biotin; 

(d) a receptor and its ligand; 

(e) a ligand-binding protein and its ligand, 

(f) interacting leucine zipper polypeptides; 

(g) an amino group and a chemical group reactive thereto; 

(h) a carboxyl group and a chemical group /eactive thereto; 

(i) a sulfhydryl group and a chemical gro^p reactive thereto; 

(j) a combination thereof 



74. The composition of claim 63, whereip said first and/or said second 
attachment sites comprise interacting leucine zipper polypeptides. 

75 . The composition of claim 63 ^herein said bacterial pilus is a Type- 
1 pilus of Eschericia coli. 



76. The composition of claim 63, wherein pilus subunits of said type-1 
pilus comprise the amino acid sequence of SEQ ID No. 146 or a sequence having 
at least 65, 70, 75, 80, 85, 90 of 95% sequence identity to SEQ ID NO: 146. 



77. 



The composition of claim 63, wherein said interacting leucine 
zipper polypeptides are/the JUN and/oFFOS leucine zipper polypeptides. 



78. 
claim 43 . 

79. 



A vaccine composition comprising the composition of claim 63 or 



vaccine composition 




A methodof i 



rising administering to a subject the 




80. The method of claim/79/^herein sai^adrrTinistering produces an 
immune response. 

81. A method of making the composipj^fTof claim 63, comprising 
combining said non-natural molecular sc^-ffSld and said antigen or antigenic 
determinant, wherein said non-natpr<u molecular scaffold and said antigen or 
antigenic determinant interacHo form an antigen array. 



82. 

and/or rem 



method of claim 81, wherein said antigen array is ordered 



ftive. 



83. A method of immunizing, comprising administering the 
composition of any one of claims y, 1 1, 21, 49 or 50 to a subject, wherein for 
inducing a Th2 response, wherein said administering produces a Th2 response that 
is specific for said antigen or antigenic determinant. 



84. 

antigen or antigenic^ 
are induced in th 



f claim 83, wherein antibodies specific for said 
t of a subtype corresponding to the Th2 subtype 




85. / The rriopod of chyj^rlT?, wherein the subject does not generate a 
Thl response th^isipeciTic for said pilus, said pilin polypeptide, or said antigen 
or antigenic determinant.