Methods of using compositions comprising variants and fusions of FGF19 polypeptides for treatment of diabetes

1. A method of treating diabetes in a subject, comprising administering to the subject an effective amount of a peptide, wherein the peptide comprises:

a) an N-terminal region comprising at least seven amino acid residues, the N-terminal region having a first amino acid position and a last amino acid position, wherein the N-terminal region comprises DSSPL (SEQ ID NO:121) or DASPH (SEQ ID NO:122); and

b) a C-terminal region comprising a portion of SEQ ID NO:99 [FGF19], the C-terminal region having a first amino acid position and a last amino acid position, wherein the C-terminal region comprises

(i) a first C-terminal region sequence comprising WGDPIRLRHLYTSG (amino acids 16 to 29 of SEQ ID NO:99 [FGF19]), wherein the W residue corresponds to the first amino acid position of the C-terminal region; and

(ii) a second C-terminal region sequence comprising PHGLSSCFLRIRADGVVDCARGQSAHSLLEIKAVALRTVAIKGVHS VRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYRSEKHRL PVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESD MFSSPLETDSMDPFGLVTGLEAVRSPSFEK (amino acid residues 30 to 194 of SEQ ID NO:99 [FGF19]);

wherein the peptide

(i) binds to fibroblast growth factor receptor 4 (FGFR4) with an affinity equal to or greater than FGF19 binding affinity for FGFR4;

(ii) activates FGFR4 to an extent or amount equal to or greater than FGF19 activates FGFR4;

(iii) has at least one of reduced hepatocellular carcinoma (HCC) formation; greater glucose lowering activity, less lipid increasing activity, less triglyceride activity, less cholesterol activity, less non-HDL activity or less HDL increasing activity, as compared to FGF19, or as compared to an FGF19 variant sequence having any of GQV, GDI, WGPI (SEQ ID NO:171), WGDPV (SEQ ID NO:172), WGDI (SEQ ID NO:173), GDPI (SEQ ID NO:174), GPI, WGQPI (SEQ ID NO:175), WGAPI (SEQ ID NO:176), AGDPI (SEQ ID NO:177), WADPI (SEQ ID NO:178), WGDAI (SEQ ID NO:179), WGDPA (SEQ ID NO:180), WDPI (SEQ ID NO:181), WGDI (SEQ ID NO:182), WGDP (SEQ ID NO:183) or FGDPI (SEQ ID NO:184) substituted for the FGF19 WGDPI (SEQ ID NO:170) sequence at amino acids 16-20 of FGF19 (SEQ ID NO:99); and/or

(iv) has less lean mass reducing activity as compared to FGF21;

thereby treating diabetes in said subject.

2. The method of claim 1 , wherein the second C-terminal region sequence of the peptide comprises from 1 to 5 amino acid substitutions, deletions or insertions.

3. The method of claim 1 , wherein the peptide is less than about 250 amino acids in length.

4. The method of claim 1 , wherein the N-terminal region of the peptide comprises amino acid residues VHYG (SEQ ID NO:101), DASPHVHYG (SEQ ID NO:102), or DSSPLVHYG (SEQ ID NO:103).

5. The method of claim 4 , wherein the G corresponds to the last position of the N-terminal region of the peptide.

6. The method of claim 5 , wherein the N-terminal region of the peptide further comprises:

RHPIP (SEQ ID NO:106), wherein R is the first amino acid position of the N-terminal region;

HPIP (SEQ ID NO:107), wherein H is the first amino acid position of the N-terminal region;

RPLAF (SEQ ID NO:108), wherein R is the first amino acid position of the N-terminal region;

PLAF (SEQ ID NO:109), wherein P is the first amino acid position of the N-terminal region; or

R, wherein R is the first amino acid position of the N-terminal region.

7. The method of claim 1 , wherein the N-terminal region of the peptide comprises amino acid residues DSSPLLQ (SEQ ID NO:104), and wherein the Q residue is the last amino acid position of the N-terminal region.

8. The method of claim 7 , wherein the N-terminal region of the peptide further comprises:

RHPIP (SEQ ID NO:106), wherein R is the first amino acid position of the N-terminal region;

HPIP (SEQ ID NO:107), wherein H is the first amino acid position of the N-terminal region;

RPLAF (SEQ ID NO:108), wherein R is the first amino acid position of the N-terminal region;

PLAF (SEQ ID NO:109), wherein P is the first amino acid position of the N-terminal region; or

R, wherein R is the first amino acid position of the N-terminal region.

9. The method of claim 1 , wherein the N-terminal region of the peptide comprises amino acid residues DSSPLLQFGGQV (SEQ ID NO:105), and wherein the V residue corresponds to the last position of the N-terminal region.

10. The method of claim 1 , wherein amino acid residues HPIP (SEQ ID NO:107) are the first 4 amino acid residues of the N-terminal region of the peptide.

11. The method of claim 1 , wherein

the first position of the N-terminal region of the peptide is a R or M residue;

the first and second positions of the N-terminal region of the peptide is a MR, RM, RD, DS, MD or MS sequence;

the first through third positions of the N-terminal region of the peptide is a MDS, RDS, MSD, MSS, or DSS sequence;

the first through fourth positions of the N-terminal region of the peptide is a RDSS (SEQ ID NO:115) or MDSS (SEQ ID NO:116) sequence;

the first through fifth positions of the N-terminal region of the peptide is an MRDSS (SEQ ID NO:117) sequence;

the first through sixth positions of the N-terminal region of the peptide is an MDSSPL (SEQ ID NO:119) sequence; or

the first through seventh positions of the N-terminal region of the peptide is an MSDSSPL (SEQ ID NO:120) sequence.

12. The method of claim 1 , wherein the peptide comprises an N-terminal region and a first C-terminal region having an amino acid sequence comprising or consisting of any of:

RPLAFSDASPHVHYGWGDPIRLRHLYTSG (M1) (amino acids 1-29 of SEQ ID NO:1);

PLAFSDASPHVHYGWGDPIRLRHLYTSG (M1-R) (amino acids 2-29 of SEQ ID NO:1);

RPLAFSDSSPLVHYGWGDPIRLRHLYTSG (M2) (amino acids 1-29 of SEQ ID NO:2);

PLAFSDSSPLVHYGWGDPIRLRHLYTSG (M2-R) (amino acids 2-29 of SEQ ID NO:2);

RHPIPDSSPLLQWGDPIRLRHLYTSG (M8) (amino acids 1-26 of SEQ ID NO:8);

RHPIPDSSPLLQFGWGDPIRLRHLYTSG (M9) (amino acids 1-28 of SEQ ID NO:9);

RPLAFSDSSPLVHWGDPIRLRHLYTSG (M26) (amino acids 1-27 of SEQ ID NO:26);

PLAFSDSSPLVHWGDPIRLRHLYTSG (M26-R) (amino acids 2-27 of SEQ ID NO:26);

HPIPDSSPLLQWGDPIRLRHLYTSG (M47) (amino acids 1-25 of SEQ ID NO:47);

RDSSPLLQWGDPIRLRHLYTSG (M52) (amino acids 1-22 of SEQ ID NO:52);

DSSPLLQWGDPIRLRHLYTSG (M52-R) (amino acids 2-22 of SEQ ID NO:52);

MDSSPLVHYGWGDPIRLRHLYTSG (M53) (amino acids 1-24 of SEQ ID NO:53);

RDSSPLVHYGWGDPIRLRHLYTSG (M69) (amino acids 1-24 of SEQ ID NO:69);

DSSPLVHYGWGDPIRLRHLYTSG (M69-R) (amino acids 2-24 of SEQ ID NO:69);

MRDSSPLVHYGWGDPIRLRHLYTSG (M70) (amino acids 1-25 of SEQ ID NO:70);

DSSPLVHYGWGDPIRLRHLYTSG (M141) (amino acids 1-23 of SEQ ID NO:141);

or

HPIPDSSPLLQFGWGDPIRLRHLYTSG (M163) (amino acids 1-27 of SEQ ID NO:163).

13. The method of claim 1 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:1 (M1), SEQ ID NO:2 (M2), SEQ ID NO:8 (M8), SEQ ID NO:9 (M9), SEQ ID NO:26 (M26), SEQ ID NO:47 (M47), SEQ ID NO:52 (M52), SEQ ID NO:53 (M53), SEQ ID NO:69, (M69), SEQ ID NO:70 (M70); SEQ ID NO:141 or SEQ ID NO:163.

14. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:1.

15. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:2.

16. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:8.

17. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:9.

18. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:26.

19. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:47.

20. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:52.

21. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:53.

22. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:141.

23. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NO:163.

24. The method of claim 13 , wherein the peptide has an amino acid sequence comprising or consisting of SEQ ID NOs:1, 2, 8, 9, 26, 52 or 69, wherein the arginine (R) residue at the first amino acid position of the N-terminal region of the sequence is deleted.

25. The method of claim 1 , wherein the N-terminal region first amino acid position of the peptide is a methionine (M), arginine (R), serine (S), histidine (H), proline (P), leucine (L) or aspartic acid (D) residue.

26. The method of claim 1 , wherein the N-terminal region of the peptide does not have a methionine (M) or arginine (R) residue at the first amino acid position of the N-terminal region.

27. The method of claim 1 , wherein the N-terminal region of the peptide comprises any one of the following amino acid sequences: MDSSPL (SEQ ID NO:119), MSDSSPL (SEQ ID NO:120), or SDSSPL (SEQ ID NO:112).

28. The method of claim 1 , wherein the peptide is fused with an immunoglobulin Fc region.

29. The method of claim 1 , wherein the peptide has at least one of reduced HCC formation; greater glucose lowering activity, or less lipid increasing activity as compared to FGF19, or as compared to an FGF19 variant having any of GQV, GDI, WGPI, WGDPV, WGDI, GDPI, GPI, WGQPI, WGAPI, AGDPI, WADPI, WGDAI, WGDPA, WDPI, WGDI, WGDP or FGDPI substituted for the WGDPI sequence at amino acids 16-20 of FGF19 (SEQ ID NO:99).

30. The method of claim 29 , wherein the HCC formation, glucose lowering activity, or lipid increasing activity is ascertained in a db/db mouse.

31. The method of claim 1 , wherein the peptide has less lean mass reducing activity as compared to the lean mass reducing activity of FGF21.

32. The method of claim 31 , wherein the lean mass reducing activity is ascertained in a db/db mouse.

33. The method of claim 1 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

34. The method of claim 1 , wherein the method further comprises administration of a supplementary therapy.

35. The method of claim 34 , wherein said supplemental therapy is a weight loss surgery, gastric bypass, gastrectomy, gastric banding, gastric balloon, or gastric sleeve.

36. The method of claim 34 , wherein said supplemental therapy is a glucose lowering agent, insulin, GLP1 analogue, biguanide, sulphonylurea, thiazolidinedione, a dipeptidyl peptidase-4 (DPP-4) inhibitor, a bromocriptine formulation, a bile acid sequestrant, metformin, a thiazolidinedione, a SGLT-2 inhibitor, or any combination thereof.

37. The method of claim 36 , wherein said biguanide or sulphonylurea is selected from the group consisting of tolbutamide, chlorpropamide, acetohexamide, tolazamide, glibenclamide, glipizide or any combination thereof.

38. The method of claim 36 , wherein said thiazolidinedione is rosiglitazone or pioglitazone, or combination thereof.

39. The method of claim 36 , wherein said bile acid sequestrant is colesevelam.

40. The method of claim 36 , wherein said insulin is bolus insulin, basal insulin, or an analogue thereof.

41. The method of claim 36 , wherein said metformin is metformin hydrochloride.

42. The method of claim 34 , wherein said supplemental therapy is administered prior to, contemporaneously with or following administration of said peptide.

43. The method of claim 1 , wherein the diabetes is type 2 diabetes.

44. The method of claim 1 , wherein the diabetes is insulin-dependent (type I) diabetes.

45. The method of claim 1 , wherein the diabetes is gestational diabetes.

46. The method of claim 1 , wherein the diabetes is prediabetes.

47. The method of claim 1 , wherein said subject has a fasting plasma glucose (FPG) level of greater than 100 mg/dl.

48. The method of claim 1 , wherein said subject has an FPG of 125 mg/dl or above.

49. The method of claim 1 , wherein said subject has an FPG of between about 100 and 125 mg/dl.

50. The method of claim 1 , wherein said subject has a hemoglobin A1c (HbA1c) level above 6%.

51. A method of treating diabetes in a subject, comprising administering to the subject an effective amount of a peptide, wherein the peptide has an amino acid sequence comprising or consisting of MRDSSPLVHYGWGDPIRLRHLYTSGPHGLSSCFLRIRADGVVDCARGQSAHSLLE IKAVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYR SEKHRLPVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESDMFSSP LETDSMDPFGLVTGLEAVRSPSFEK (SEQ ID NO:70), thereby treating diabetes in said subject.

52. The method of claim 51 , wherein the peptide has an amino acid sequence comprising SEQ ID NO: 70.

53. The method of claim 52 , wherein the peptide is fused with an immunoglobulin Fc region.

54. The method of claim 51 , wherein the peptide has an amino acid sequence consisting of SEQ ID NO: 70.

55. The method of claim 54 , wherein the peptide is fused with an immunoglobulin Fc region.

56. The method of claim 51 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

57. The method of claim 51 , wherein the method further comprises administration of a supplementary therapy.

58. The method of claim 57 , wherein said supplemental therapy is a weight loss surgery, gastric bypass, gastrectomy, gastric banding, gastric balloon, or gastric sleeve.

59. The method of claim 57 , wherein said supplemental therapy is a glucose lowering agent, insulin, GLP1 analogue, biguanide, sulphonylurea, thiazolidinedione, a DPP-4 inhibitor, a bromocriptine formulation, a bile acid sequestrant, metformin, a thiazolidinedione, a SGLT-2 inhibitor, or any combination thereof.

60. The method of claim 59 , wherein said biguanide or sulphonylurea is selected from the group consisting of tolbutamide, chlorpropamide, acetohexamide, tolazamide, glibenclamide, glipizide or any combination thereof.

61. The method of claim 59 , wherein said thiazolidinedione is rosiglitazone or pioglitazone, or combination thereof.

62. The method of claim 59 , wherein said bile acid sequestrant is colesevelam.

63. The method of claim 59 , wherein said insulin is bolus insulin, basal insulin, or an analogue thereof.

64. The method of claim 59 , wherein said metformin is metformin hydrochloride.

65. The method of claim 57 , wherein said supplemental therapy is administered prior to, contemporaneously with or following administration of said peptide.

66. The method of claim 51 , wherein the diabetes is type 2 diabetes.

67. The method of claim 51 , wherein the diabetes is insulin-dependent (type I) diabetes.

68. The method of claim 51 , wherein the diabetes is gestational diabetes.

69. The method of claim 51 , wherein the diabetes is prediabetes.

70. The method of claim 51 , wherein said subject has a FPG level of greater than 100 mg/dl.

71. The method of claim 51 , wherein said subject has an FPG of 125 mg/dl or above.

72. The method of claim 51 , wherein said subject has an FPG of between about 100 and 125 mg/dl.

73. The method of claim 51 , wherein said subject has a HbA1c level above 6%.

74. A method of treating diabetes in a subject, comprising administering to the subject an effective amount of a peptide, wherein the peptide has an amino acid sequence comprising or consisting of RDSSPLVHYGWGDPIRLRHLYTSGPHGLSSCFLRIRADGVVDCARGQSAHSLLEIK AVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYRSE KHRLPVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESDMFSSPLE TDSMDPFGLVTGLEAVRSPSFEK (SEQ ID NO:69), thereby treating diabetes in said subject.

75. The method of claim 74 , wherein the peptide has an amino acid sequence comprising SEQ ID NO: 69.

76. The method of claim 75 , wherein the peptide is fused with an immunoglobulin Fc region.

77. The method of claim 74 , wherein the peptide has an amino acid sequence consisting of SEQ ID NO: 69.

78. The method of claim 77 , wherein the peptide is fused with an immunoglobulin Fc region.

79. The method of claim 74 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

80. The method of claim 74 , wherein the method further comprises administration of a supplementary therapy.

81. The method of claim 80 , wherein said supplemental therapy is a weight loss surgery, gastric bypass, gastrectomy, gastric banding, gastric balloon, or gastric sleeve.

82. The method of claim 80 , wherein said supplemental therapy is a glucose lowering agent, insulin, GLP1 analogue, biguanide, sulphonylurea, thiazolidinedione, a DPP-4 inhibitor, a bromocriptine formulation, a bile acid sequestrant, metformin, a thiazolidinedione, a SGLT-2 inhibitor, or any combination thereof.

83. The method of claim 82 , wherein said insulin is bolus insulin, basal insulin, or an analogue thereof.

84. The method of claim 82 , wherein said metformin is metformin hydrochloride.

85. The method of claim 82 , wherein said biguanide or sulphonylurea is selected from the group consisting of tolbutamide, chlorpropamide, acetohexamide, tolazamide, glibenclamide, glipizide or any combination thereof.

86. The method of claim 82 , wherein said thiazolidinedione is rosiglitazone or pioglitazone, or combination thereof.

87. The method of claim 82 , wherein said bile acid sequestrant is colesevelam.

88. The method of claim 80 , wherein said supplemental therapy is administered prior to, contemporaneously with or following administration of said peptide.

89. The method of claim 74 , wherein the diabetes is type 2 diabetes.

90. The method of claim 74 , wherein the diabetes is insulin-dependent (type I) diabetes.

91. The method of claim 74 , wherein the diabetes is gestational diabetes.

92. The method of claim 74 , wherein the diabetes is prediabetes.

93. The method of claim 74 , wherein said subject has a FPG level of greater than 100 mg/dl.

94. The method of claim 74 , wherein said subject has an FPG of 125 mg/dl or above.

95. The method of claim 74 , wherein said subject has an FPG of between about 100 and 125 mg/dl.

96. The method of claim 74 , wherein said subject has a HbA1c level above 6%.

97. A method of treating Type 2 diabetes in a subject, comprising administering to the subject an effective amount of a peptide, wherein the peptide has an amino acid sequence comprising MRDSSPLVHYGWGDPIRLRHLYTSGPHGLSSCFLRIRADGVVDCARGQSAHSLLE IKAVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYR SEKHRLPVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESDMFSSP LETDSMDPFGLVTGLEAVRSPSFEK (SEQ ID NO:70), thereby treating Type 2 diabetes in said subject.

98. The method of claim 97 , wherein the peptide is fused with an immunoglobulin Fc region.

99. The method of claim 98 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

100. The method of claim 98 , wherein the method further comprises administration of a supplementary therapy.

101. The method of claim 97 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

102. The method of claim 97 , wherein the method further comprises administration of a supplementary therapy.

103. A method of treating Type 2 diabetes in a subject, consisting administering to the subject an effective amount of a peptide, wherein the peptide has an amino acid sequence consisting of MRDSSPLVHYGWGDPIRLRHLYTSGPHGLSSCFLRIRADGVVDCARGQSAHSLLE IKAVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYR SEKHRLPVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESDMFSSP LETDSMDPFGLVTGLEAVRSPSFEK (SEQ ID NO:70), thereby treating Type 2 diabetes in said subject.

104. The method of claim 103 , wherein the peptide is fused with an immunoglobulin Fc region.

105. The method of claim 104 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

106. The method of claim 104 , wherein the method further comprises administration of a supplementary therapy.

107. The method of claim 103 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

108. The method of claim 103 , wherein the method further comprises administration of a supplementary therapy.

109. A method of treating Type 2 diabetes in a subject, comprising administering to the subject an effective amount of a peptide, wherein the peptide has an amino acid sequence comprising RDSSPLVHYGWGDPIRLRHLYTSGPHGLSSCFLRIRADGVVDCARGQSAHSLLEIK AVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYRSE KHRLPVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESDMFSSPLE TDSMDPFGLVTGLEAVRSPSFEK (SEQ ID NO:69), thereby treating Type 2 diabetes in said subject.

110. The method of claim 109 , wherein the peptide is fused with an immunoglobulin Fc region.

111. The method of claim 110 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

112. The method of claim 110 , wherein the method further comprises administration of a supplementary therapy.

113. The method of claim 109 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

114. The method of claim 109 , wherein the method further comprises administration of a supplementary therapy.

115. A method of treating Type 2 diabetes in a subject, consisting administering to the subject an effective amount of a peptide, wherein the peptide has an amino acid sequence consisting of RDSSPLVHYGWGDPIRLRHLYTSGPHGLSSCFLRIRADGVVDCARGQSAHSLLEIK AVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYRSE KHRLPVSLSSAKQRQLYKNRGFLPLSHFLPMLPMVPEEPEDLRGHLESDMFSSPLE TDSMDPFGLVTGLEAVRSPSFEK (SEQ ID NO:69), thereby treating Type 2 diabetes in said subject.

116. The method of claim 115 , wherein the peptide is fused with an immunoglobulin Fc region.

117. The method of claim 116 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

118. The method of claim 116 , wherein the method further comprises administration of a supplementary therapy.

119. The method of claim 115 , wherein the peptide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

120. The method of claim 115 , wherein the method further comprises administration of a supplementary therapy.