Extended recombinant polypeptides and compositions comprising same
Abstract
The present invention relates to compositions comprising biologically active proteins linked to extended recombinant polypeptide (XTEN), isolated nucleic acids encoding the compositions and vectors and host cells containing the same, and methods of using such compositions in treatment of glucose- related diseases, metabolic diseases, coagulation disorders, and growth hormone-related disorders and conditions.

Term
3.4 yearsleft in the term
Expires 3 February 2030.
- Priority and filed
- Granted
- Today
- Expires
161 claims: 69 independent, 92 dependent
- 1I» WHAT IS CLAIMED IS:1. An isolated extended recombinant polypeptide (XTEN) comprising at least 36 to 3000 amino acid residues, wherein the XTEN is characterized in that;(a) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than about 90% of the total amino acid sequence of the XTEN;(b) at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95% of the XTEN sequence consists of non-overlapping sequence motifs, wherein the sequence motifs are selected from the group consisting of SEQ IND NOS: 182-203 and 1715-1722;(c) the XTEN sequence is substantially non-repetitive such that (i) the XTEN sequence contains no three contiguous amino acids that are identical unless the amino acids are serine residues, or (ii) within each of the sequence motifs, any two contiguous amino acid residues does not occur more than twice in each of the sequence motifs;(d) the XTEN sequence lacks a predicted T-cell epitope when analyzed by TEPITOPE algorithm, wherein the TEP1TOPE algorithm prediction for epitopes within the XTEN sequence is based on a score of-6 or greater;(e) the XTEN sequence has greater than 90% random coil formation as determined by Garnier-Osguthorpe-Robson (GOR) algorithm;and (f) the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by Chou-Fasman algorithm.
- 13An isolated fusion protein, comprising a growth hormone (GH) sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO:1750, wherein said growth hormone is linked to an extended recombinant polypeptide (XTEN) wherein the XTEN is characterized in that: (a) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than about 90% of the total amino acid sequence of the XTEN;(b) at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95% of the XTEN sequence consists of non-overlapping sequence motifs, wherein the sequence motifs are selected from the group consisting of SEQ IND NOS: 182-203 and 1715-1722;(c) the XTEN sequence is substantially non-repetitive such that (i) the XTEN sequence contains no three contiguous amino acids that are identical unless the amino acids are serine residues, or (ii) within each of the sequence motifs, any two contiguous amino acid residues does not occur more than twice in each of the sequence motifs;(d) the XTEN sequence lacks a predicted T-cell epitope when analyzed by TEPITOPE algorithm, wherein the TEPITOPE algorithm prediction for epitopes within the XTEN sequence is based on a score of -6 or greater;(e) the XTEN sequence has greater than 90% random coil formation as determined by Garnier-Osguthorpe-Robson (GOR) algorithm;and (f) the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by Chou-Fasman algorithm.
- 30An isolated fusion protein comprising an amino acid sequence having at least 90% sequence identity to the sequence of SEQ ID NO:1750 linked to an extended recombinant polypeptide (XTEN) sequence having at least 90% sequence identity to the sequence of SEQ ID NO: 217 and wherein the fusion protein retains at least a portion of the biologic activity of the corresponding sequence of SEQ ID NO: 1750 not linked to XTEN.
- 39A method of producing a fusion protein comprising a growth hormone (GH) fused to one or more extended recombinant polypeptides (XTEN), comprising:(a) providing a cell culture host cell comprising a recombinant polynucleotide molecule encoding the fusion protein of any one of claims 13-37;(b) culturing the cell culture host 447 CA 2748314 2018-01-24 Il cell in nutrient media under conditions permitting the expression of the fusion protein;and (c) recovering the fusion protein.
- 45Use of a therapeutically effective amount of a fusion protein of any one of claims 13-37 for treating a growth-hormone related condition in a subject, wherein the growth-hormone related condition is growth-hormone deficiency. Turner's Syndrome, Prader-Willi Syndrome, idiopathic short stature, AIDS wasting, multiple sclerosis, Crohn's disease, ulcerative colitis, or muscular dystrophy.
- 46An isolated fusion protein, comprising a glucose regulating peptide (GRP) sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS:1-42, wherein said glucose regulating peptide is linked to an extended recombinant polypeptide (XTEN) comprising at least 36 to 3000 amino acid residues wherein the XTEN is characterized in that: (a) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than about 90% of the total amino acid sequence of the XTEN;(b) at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95% of the XTEN sequence consists of non-overlapping sequence motifs, wherein the sequence motifs are selected from the group consisting of SEQ IND NOS: 182-203 and 1715-1722;(c) the XTEN sequence is substantially non-repetitive such that (i) the XTEN sequence contains no three contiguous amino acids that are identical unless the 448 CA 2748314 2018-01-24 amino acids are serine residues, or (ii) within each of the sequence motifs, any two contiguous amino acid residues does not occur more than twice in each of the sequence motifs;(d) the XTEN sequence lacks a predicted T-celi epitope when analyzed by TEPITOPE algorithm, wherein the TEPITOPE algorithm prediction for epitopes within the XTEN sequence is based on a score of-6 or greater;(e) the XTEN sequence has greater than 90% random coil formation as determined by Garnier-Osguthorpe-Robson (GOR) algorithm;and (f) the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by Chou-Fasman algorithm.
- 61An isolated fusion protein comprising an amino acid sequence having at least 90% sequence identity to the sequence of SEQ ID NO:12 linked to an extended recombinant polypeptide (XTEN) sequence having at least 90% sequence identity to the sequence of SEQ ID NO: 213 and wherein the fusion protein retains at least a portion of the biologic activity of the corresponding sequence of SEQ ID NO: 12 not linked to XTEN.
- 65The isolated fusion protein ofclaim 61, comprising an amino acid sequence that has at least 90% sequence identity to SEQ ID NO:1059.
- 70A method of producing a fusion protein comprising a glucose regulating peptide fused to one or more extended recombinant polypeptides (XTEN), comprising:(a) providing a cell culture host cell comprising a recombinant polynucleotide molecule encoding the fusion protein of any one of claims 46-68;(b) culturing the cell culture host cell in nutrient media under conditions permitting the expression of the fusion protein;and (c) recovering the fusion protein.
- 74Use of a therapeutically effective amount of a fusion protein of any one of claims 46-68 for treating a glucose homeostasis related condition in a subject, wherein the glucose homeostasis related condition is type I diabetes, type II diabetes, syndrome X, insulin resistance, gestational diabetes, juvenile diabetes, obesity, excessive appetite, insufficient satiety, metabolic disorder, glucagonomas, retinal neurodegenerative processes, or the honeymoon period of Type 1 diabetes.
- 86An isolated fusion protein comprising an amino acid sequence having at least 90% sequence identity to the sequence of SEQ ID NO:20 linked to an extended recombinant polypeptide (XTEN) sequence having at least 90% sequence identity to the sequence of SEQ ID NO: 213 and wherein the fusion protein retains at least a portion of the biologic activity of the corresponding sequence of SEQ ID NO: 20 not linked to XTEN. 452 CA 2748314 2018-01-24
- 95A method of producing a fusion protein comprising a glucose regulating peptide fused to one or more extended recombinant polypeptides (XTEN), comprising:(a) providing a cell culture host cell comprising a recombinant polynucleotide molecule encoding the fusion protein of any one of claims 75-93;(b) culturing the cell culture host cell in nutrient media under conditions permitting the expression of the fusion protein;and (c) recovering the fusion protein.
- 99An isolated fusion protein comprising an amino acid sequence having at least 90% sequence identity to a sequence selected from the group consisting of SEQ ID NOS:30, 453 CA 2748314 2018-01-24 37-42 linked to an extended recombinant polypeptide (XTEN) sequence having at least 90% sequence identity to the sequence of SEQ ID NO;213 and wherein the fusion protein retains at least a portion of the biologic activity of the corresponding sequences of SEQ ID NOS: 30 and 37-42 not linked to XTEN.
- 100Use of a therapeutically effective amount of a fusion protein of any one of claims 75-93 and 99 for treating a glucose homeostasis related condition in a subject wherein the glucose homeostasis related condition is type I diabetes, type II diabetes, syndrome X, insulin resistance, gestational diabetes, juvenile diabetes, obesity, excessive appetite, insufficient satiety, metabolic disorder, glucagonomas, retinal neurodegenerative processes, or the honeymoon period of Type 1 diabetes.
- 108An isolated fusion protein comprising an amino acid sequence having at least 90% sequence identity to the sequence of SEQ ID NO:24 linked to an extended 454 CA 2748314 2018-01-24 recombinant polypeptide (XTEN) sequence having at least 90% sequence identity to the sequence of SEQ ID NO: 213 and wherein the fusion protein retains at least a portion of the biologic activity of the corresponding sequence of SEQ ID NO: 24 not linked to XTEN.
- 113A method of producing a fusion protein comprising a glucose regulating peptide fused to one or more extended recombinant polypeptides (XTEN), comprising:(a) providing a cell culture host cell comprising a recombinant polynucleotide molecule encoding the fusion protein of any one of claims 101-111;(b) culturing the cell culture host cell in nutrient media under conditions permitting the expression of the fusion protein;and (c) recovering the fusion protein.
- 117Use of a therapeutically effective amount of a fusion protein of any one of claims 101-111 for treating a condition in a subject, wherein the condition is Crohn’s disease, ulcerative colitis, gestational diabetes, excessive appetite, insufficient satiety, metabolic disorders, or irritable bowel syndrome.
- 118An isolated fusion protein, comprising a metabolic protein sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS:1723-1734, wherein said metabolic protein (MP) is linked to an extended 455 CA 2748314 2018-01-24 recombinant polypeptide (XTEN) comprising at least 36 to 3000 amino acid residues wherein the XTEN is characterized in that: (a) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than about 90% of the total amino acid sequence of the XTEN;(b) at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95% of the XTEN sequence consists of non-overlapping sequence motifs, wherein the sequence motifs are selected from the group consisting of SEQ IND NOS: 182-203 and 1715-1722;(c) the XTEN sequence is substantially non-repetitive such that (i) the XTEN sequence contains no three contiguous amino acids that are identical unless the amino acids are serine residues, or (ii) within each of the sequence motifs, any two contiguous amino acid residues does not occur more than twice in each of the sequence motifs;(d) the XTEN sequence lacks a predicted T-cell epitope when analyzed by TEPITOPE algorithm, wherein the TEPITOPE algorithm prediction for epitopes within the XTEN sequence is based on a score of -6 or greater;(e) the XTEN sequence has greater than 90% random coil formation as determined by Garnier-Osguthorpe-Robson (GOR) algorithm;and (f) the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by Chou-Fasman algorithm.
- 130A method of producing a fusion protein comprising a metabolic protein fused to one or more extended recombinant polypeptides (XTEN), comprising:(a) providing a cell culture host cell comprising a recombinant polynucleotide molecule encoding the fusion protein of any one of claims 118-128;(b) culturing the cell culture host cell in nutrient media under conditions permitting the expression of the fusion protein;and (c) recovering the fusion protein.
- 133The method ofclaim 130, wherein the fusion protein is recovered from the host cell cytoplasm.
- 134Use of a therapeutically effective amount of a fusion protein of any one of claims 118-128 for treating a metabolic condition in a subject, wherein the metabolic condition is aneurysm, angina, atherosclerosis, stroke, cerebrovascular disease, congestive heart failure, coronary artery disease, myocardial infarction, reduced cardiac output, peripheral vascular disease, hypertension, hypotension,, diuresis inducement, natriuresis inducement, renal diseases, or asthma.
- 135An isolated fusion protein, comprising a coagulation factor sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS:1735-1747, wherein said metabolic protein is linked to an extended recombinant polypeptide (XTEN) comprising at least 36 to 3000 amino acid residues wherein the XTEN is characterized in that: (a) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than about 90% of the total amino acid sequence of the XTEN;(b) at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95% of the XTEN sequence consists of non-overlapping sequence motifs, wherein the sequence motifs are selected from the group consisting of SEQ IND NOS: 182-203 and 1715-1722;(c) the XTEN sequence is substantially non-repetitive such that (i) the XTEN sequence contains no three contiguous amino acids that are identical unless the amino acids are serine residues, or (ii) within each of the sequence motifs, any two contiguous amino acid residues does not occur more than twice in each of the sequence motifs;(d) the XTEN sequence lacks a predicted T-cell epitope when analyzed by TEPITOPE algorithm, wherein the TEPITOPE algorithm prediction for epitopes within the XTEN sequence is based on a score of-6 or greater;(e) the XTEN sequence has greater than 90% random coil formation as determined by Garnier-Osguthorpe-Robson (GOR) algorithm;and 458 CA 2748314 2018-01-24 Il (f) the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by Chou-Fasman algorithm.
- 143The isolated fusion protein of any one of claims 135-141, wherein the coagulation factor is linked to an XTEN comprising a sequence which is at least 95% identical to a sequence selected from the group consisting of SEQ ID NOS:204,206,210, 213,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388.389, 390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407, 408, and 409. 459 CA 2748314 2018-01-24 Il
- 144The isolated fusion protein of any one of claims 135-141, wherein the coagulation factor is linked to an XTEN comprising a sequence which is at least 99% identical to a sequence selected from the group consisting of SEQ ID NOS:204,206,210, 213,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389, 390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407, 408, and 409.
- 145An isolated fusion protein comprising an amino acid sequence that has at least 90% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS:1785-1811 and wherein the fusion protein retains at least a portion of the biologic activity of the corresponding sequences of SEQ ID NOS: 1785-1811 not linked to XTEN.
- 150A method of producing a fusion protein comprising a coagulation factor fused to one or more extended recombinant polypeptides (XTEN), comprising:(a) providing a cell culture host cell comprising a recombinant polynucleotide molecule encoding the fusion protein of any one of claims 135-148;(b) culturing the cell culture host cell in nutrient media under conditions permitting the expression of the fusion protein;and (c) recovering the fusion protein.
- 154Use of a therapeutically effective amount of a fusion protein of any one of claims 135-148 for treating a bleeding disorder in a subject, wherein the bleeding disorder is factor Vll deficiency, factor X deficiency, factor XII deficiency, hemophilia A, hemophilia B (Christmas Disease), hemophilia C, idiopathic thrombocytopenic purpura (1TP), Von Willebrand's disease (type I and type II), trauma-associated bleeding, or surgical bleeding.
- 155A kit comprising a fusion protein for use in treating a condition, wherein the kit comprises (a) a first container; (b) a fusion protein composition comprising an XTEN which is at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS:210,213,216, 217,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389, 390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407, 408, and 409 fused to a biologically active protein having at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% or 100% sequence identity to a sequence selected from the group of sequences set forth in SEQ ID NOS: 1-42,48-179,1723-1747, and 17501777 and wherein the biologically active protein retains at least a portion of the biologic activity of the corresponding biologically active protein of SEQ ID NOS: 1-42,48-179,17231747, and 1750-1777 not linked to XTEN;(c) an amount of a pharmaceutically acceptable carrier;(d) a label identifying drug and storage and handling conditions;and (e) a sheet of the approved indications for the drug.
- 156Use of a therapeutically effective amount of a fusion protein of any one of claims 13-37 in the manufacture of a medicament for treating a growth-hormone related condition in a subject, wherein the growth-hormone related condition is growth-hormone deficiency, Turner's Syndrome, Prader-Willi Syndrome, idiopathic short stature, AIDS wasting, multiple sclerosis, Crohn’s disease, ulcerative colitis, or muscular dystrophy. 461 CA 2748314 2018-01-24
- 157Use of a therapeutically effective amount of a fusion protein of any one of claims 46-68 in the manufacture of a medicament for treating a glucose homeostasis related condition in a subject, wherein the glucose homeostasis related condition is type I diabetes, type II diabetes, syndrome X, insulin resistance, gestational diabetes, juvenile diabetes, obesity, excessive appetite, insufficient satiety, metabolic disorder, glucagonomas, retinal neurodegenerative processes, or the honeymoon period of Type I diabetes.
- 158Use of a therapeutically effective amount of a fusion protein of any one of claims 75-93 and 99 in the manufacture of a medicament for treating a glucose homeostasis related condition in a subject, wherein the glucose homeostasis related condition is type I diabetes, type II diabetes, syndrome X, insulin resistance, gestational diabetes, juvenile diabetes, obesity, excessive appetite, insufficient satiety, metabolic disorder, glucagonomas, retinal neurodegenerative processes, or the honeymoon period of Type I diabetes.
- 159Use of a therapeutically effective amount of a fusion protein of any one of claims 101-111 in the manufacture of a medicament for treating a condition in a subject, wherein the condition is Crohn’s disease, ulcerative colitis, gestational diabetes, excessive appetite, insufficient satiety, metabolic disorders, or irritable bowel syndrome.
- 160Use of a therapeutically effective amount of a fusion protein of any one of claims 118-128 for treating a metabolic condition in a subject, wherein the metabolic condition is aneurysm, angina, atherosclerosis, stroke, cerebrovascular disease, congestive heart failure, coronary artery disease, myocardial infarction, reduced cardiac output, peripheral vascular disease, hypertension, hypotension,, diuresis inducement, natriuresis inducement, renal diseases, or asthma.
- 161Use of a therapeutically effective amount of a fusion protein of any one of claims 135-148 in the manufacture of a medicament for treating a bleeding disorder in a subject, wherein the bleeding disorder is factor VII deficiency, factor X deficiency, factor XII deficiency, hemophilia A, hemophilia B (Christmas Disease), hemophilia C, idiopathic thrombocytopenic purpura (ITP), Von Willebrand's disease (type I and type II), traumaassociated bleeding, or surgical bleeding. 462 CA 2748314 2018-01-24
Independent claims69
8 paragraphs in 8 sections, as filed
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Numbers
- Publication
- 2748314
- Application
- 2748314
Titles2
- English
- EXTENDED RECOMBINANT POLYPEPTIDES AND COMPOSITIONS COMPRISING SAME
- French
- POLYPEPTIDES RECOMBINANTS ETENDUS ET COMPOSITIONS LES COMPRENANT
Classification
- CPC, 45
- C07K14/001
- C07K1/00
- C07K14/47
- C07K2319/31
- C07K14/61
- C07K14/745
- C07K2319/35
- C12N9/6437
- C12N9/644
- C07K14/605
- A61P1/00
- A61P1/04
- A61P1/14
- A61P19/02
- A61P21/00
- A61P21/04
- A61P25/00
- A61P25/02
- A61P27/02
- A61P29/00
- A61P3/04
- A61P31/18
- A61P3/06
- A61P3/08
- A61P43/00
- A61P5/00
- A61P5/06
- A61P5/10
- A61P5/22
- A61P5/48
- A61P5/50
- A61P7/00
- A61P7/02
- A61P7/04
- A61P7/06
- A61P9/00
- A61P9/10
- A61P9/12
- A61P9/14
- A61P3/10
- A61K38/16
- C07K14/00
- C07K14/435
- C07K19/00
- C07K14/545
- IPC, 6
- C07K14 00
- C07K1 00
- C07K7 08
- C07K19 00
- C08G69 10
- C12N15 00