Fibronectin type III domain based scaffold compositions, methods and uses

• US 10,654,913 B2
• Filed: 07/11/2018
• Issued: 05/19/2020
• Est. Priority Date: 10/31/2008
• Status: Active Grant

• Current Assignee: Janssen Biotech, Inc. (Johnson & Johnson)
• Original Assignee: Janssen Biotech, Inc. (Johnson & Johnson)
• Inventors: Jacobs, Steven, O'Neil, Karyn
• Primary Examiner(s): Boesen, Christian C
• Application Number:
  US16/032,691
• Publication Number:
  US 20180334492A1
• Time in Patent Office: 678 Days
• Field of Search: None
• CPC Class Codes: A61P 1/00 Drugs for disorders of the alimentary tract or the digestive system
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 13/00 Drugs for disorders of the urinary system
• CPC Class Codes: A61P 15/00 Drugs for genital or sexual disorders for disorders of sex hormones A61P5/24; Contraceptives
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 33/00 Antiparasitic agents
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 39/02 Antidotes
• CPC Class Codes: A61P 7/00 Drugs for disorders of the blood or the extracellular fluid
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: C07K 14/78 Connective tissue peptides, e.g. collagen, elastin, laminin, fibronectin, vitronectin or cold insoluble globulin [CIG]
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 50/06 : Biochemical methods, e.g. using enzymes or whole viable microorganisms

Abstract

A protein scaffold based on a consensus sequence of fibronectin type III (FN3) proteins, such as the tenth FN3 repeat from human fibronectin (human Tenascin), including isolated nucleic acids that encode a protein scaffold, vectors, host cells, and methods of making and using thereof have applications in diagnostic and/or therapeutic compositions, methods and devices. In particular, protein scaffold molecules binding to IgG have been identified as useful for diagnostic and/or therapeutic applications.

Claims

1. A library produced by a method of constructing a library of a protein scaffold based on a fibronectin type III (FN3) domain derived from a consensus sequence of an FN3 domain, comprising the steps of:

providing a polypeptide derived from a consensus sequence of an FN3 domain having at least 90% identity to the amino acid sequence of SEQ ID NO;

16; and

introducing diversity into copies of the polypeptide to form the protein scaffold library.

2. A method of generating a protein scaffold binding to a specific target protein or nucleotide with a predefined binding affinity, comprising contacting the library of claim 1 with the specific target protein or nucleotide and isolating a protein scaffold binding to the specific target protein or nucleotide with the predefined affinity.

3. The method of claim 2, wherein the isolating step comprises isolating scaffold molecules binding to the specific target protein or nucleotide and testing the isolated scaffold molecules for binding affinity to the specific target protein or nucleotide.

4. The method of claim 3, wherein the isolating step comprises panning the library with the specific target protein or nucleotide, identifying scaffold molecules binding to the specific target protein or nucleotide, and isolating the binding scaffold molecules.

5. The method of claim 3, wherein the affinity is less than or equal to about 10⁻

7M.

6. A library produced by a method of constructing a library of a protein scaffold based on a fibronectin type III (FN3) domain, comprising the steps of:

providing a polypeptide having the amino acid sequence of SEQ ID NO;

16; and

introducing diversity into copies of the polypeptide having the amino acid sequence of SEQ ID NO;

16 to form the protein scaffold library, wherein the introducing diversity step comprises mutating at least one loop region selected from the group consisting of residues at or about positions 13-16, 22-28, 38-43, 51-54, 60-64, and 75-81 of SEQ ID NO;

16.

7. A method of generating a protein scaffold binding to a specific target with a predefined binding affinity, comprising contacting the library of claim 6 with the specific target protein or nucleotide and isolating a protein scaffold binding to the specific target protein or nucleotide with the predefined affinity.

8. The method of claim 7, wherein the isolating step comprises isolating scaffold molecules binding to the specific target protein or nucleotide and testing the isolated scaffold molecules for binding affinity to the specific target protein or nucleotide.

9. The method of claim 8, wherein the isolating step comprises panning the library with the specific target protein or nucleotide, identifying scaffold molecules binding to the specific target protein or nucleotide, and isolating the binding scaffold molecules.

10. The method of claim 8, wherein the affinity is less than or equal to about 10⁻

7M.

11. A medical device, comprising an isolated protein scaffold comprising a fibronectin type III (FN3) domain having at least 90% identity to the amino acid sequence of SEQ ID NO:

16, wherein said device is suitable for contacting or administering said protein scaffold by at least one mode selected from parenteral, subcutaneous, intramuscular, intravenous, intrarticular, intrabronchial, intraabdominal, intracapsular, intracartilaginous, intracavitary, intracelial, intracerebellar, intracerebroventricular, intracolic, intracervical, intragastric, intrahepatic, intramyocardial, intraosteal, intrapelvic, intrapericardiac, intraperitoneal, intrapleural, intraprostatic, intrapulmonary, intrarectal, intrarenal, intraretinal, intraspinal, intrasynovial, intrathoracic, intrauterine, intravesical, intralesional, bolus, vaginal, rectal, buccal, sublingual, intranasal, and transdermal.