Supercharged proteins for cell penetration

• US 9,221,886 B2
• Filed: 04/28/2010
• Issued: 12/29/2015
• Est. Priority Date: 04/28/2009
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Liu, David R., McNaughton, Brian R., Cronican, James Joseph, Thompson, David B.
• Primary Examiner(s): RAGHU, GANAPATHIRAM
• Application Number:
  US13/318,032
• Publication Number:
  US 20120100569A1
• Time in Patent Office: 2,071 Days
• Field of Search: 435/69.7, 435/188, 435/375, 435/377, 424/94.1, 536/23.4, 530/350
• US Class Current: 1/1
• CPC Class Codes: A61P 31/18 for HIV
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/001 by chemical synthesis
• CPC Class Codes: C07K 14/43595 from coelenteratae, e.g. medusae
• CPC Class Codes: C07K 2319/01 containing a localisation/targetting motif
• CPC Class Codes: C07K 7/06 having 5 to 11 amino acids
• CPC Class Codes: C07K 7/08 having 12 to 20 amino acids gastrins C07K14/595; somatostatins C07K14/655; melanotropins C07K14/68
• CPC Class Codes: C12N 2501/40 Regulators of development
• CPC Class Codes: C12N 2501/60 Transcription factors
• CPC Class Codes: C12N 2740/13043 viral genome or elements thereof as genetic vector
• CPC Class Codes: C12N 5/0602 Vertebrate cells

Abstract

Compositions, preparations, systems, and related methods for delivering a supercharged protein, or a complex of a supercharged protein and an agent (e.g., nucleic acids, peptides, proteins, small molecules) to cells are provided. Such systems and methods include the use of supercharged proteins. For example, superpositively charged proteins may be associated with nucleic acids (which typically have a net negative charge) via electrostatic interactions. In some embodiments, such systems and methods involve altering the primary sequence of a protein in order to “supercharge” the protein (e.g., to generate a superpositively-charged protein). In some embodiments, complexes comprising supercharged proteins and one or more agents to be delivered are useful as therapeutic agents. In some embodiments, complexes and/or pharmaceutical compositions thereof are administered to a subject in need thereof. The inventive complexes or pharmaceutical compositions thereof may be used to treat proliferative diseases, infectious diseases, cardiovascular diseases, inborn errors in metabolism, genetic diseases, etc.

Claims

1. A supercharged protein associated with a functional peptide or protein, comprising

a supercharged protein having

a molecular weight of 4-100 kDa, a theoretical net charge of at least +10 at physiological pH, and a charge to molecular weight ratio of at least 0.8, wherein the supercharged protein is a supercharged protein variant of a wild-type protein and comprises a modified primary amino acid sequence as compared to the wild-type sequence,

wherein the modified primary amino acid sequence comprises replacement of a plurality of charged or polar, solvent-exposed residues with a natural amino acid residue that is positively charged at physiological pH;

and

a functional peptide or protein selected from the group consisting of enzymes, DNA-binding proteins, histones, cytoskeletal proteins, receptor proteins, chaperone proteins, transcription factors, tumor suppressors, developmental regulators, growth factors, metastasis suppressors, pro-apoptotic proteins, and reprogramming factors,

wherein the supercharged protein is covalently bound to the functional peptide or protein, and wherein the supercharged protein associated with the functional peptide or protein is able to penetrate a cell and deliver the functional peptide or protein to the cell.

2. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein is bound to the functional protein or peptide via a peptide bond, thus forming a fusion protein.

3. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein and the functional protein or peptide are bound to a linker connecting the supercharged protein and the functional peptide or protein.

4. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein or the linker can be cleaved by a cellular enzyme.

5. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein is a globular protein.

6. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein is a protein comprising a β

-barrel.

7. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein is a supercharged green fluorescent protein (GFP).

8. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the functional protein is a protein chosen from the group consisting of histone acetyltransferases, histone deacetylases, DNA methyltransferases, kinases, phosphatases, proteases, oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, nucleases, zinc finger nucleases, and recombinases.

9. The supercharged protein associated with a functional peptide or protein of claim 8, wherein the functional protein is a protein selected from the group consisting of BCL-2 family proteins, caspases, TIMP-family proteins, BMP-family growth factors, GDF-family growth factors, and zinc finger nucleases targeting a site within the human CCR5 gene.

10. A method of delivering a functional peptide or protein to a cell, comprising:

contacting the cell with a supercharged protein covalently bound to the functional peptide or protein of claim 1, under conditions sufficient for the functional peptide or protein to enter the cell.

11. The method of claim 10, wherein the functional peptide or protein is a nuclear peptide or protein, and the step of contacting results in delivery of the functional protein or peptide to the nucleus of the cell.

12. The method of claim 10, wherein the functional protein or peptide delivered to the cell is a transcription factor or a reprogramming factor.

13. The method of claim 12, wherein the cell is a somatic cell from a subject diagnosed with a disease and is contacted with a supercharged protein covalently bound to a reprogramming factor in an amount, for a time, and under conditions sufficient to induce reprogramming of the somatic cell to a pluripotent state.

14. The method of claim 13, further comprising:

isolating a pluripotent cell generated from the somatic cell;

differentiating the isolated pluripotent cell, or progeny thereof, into a differentiated cell type; and

/or

using the pluripotent cell, or differentiated progeny thereof, in a cell replacement therapeutic approach.

15. The method of claim 10, wherein the cell is a cell carrying a genomic allele associated with a disease and the supercharged protein is associated with a nuclease specifically targeting the allele.

16. The method of claim 15, wherein the nuclease targets the human CCR5 gene in a T-lymphocyte of a subject diagnosed with HIV/AIDS.

17. The method of claim 10, wherein the functional protein is a recombinase, and the cell comprises a recombination site recognized by the recombinase in its genome.

18. The method of claim 17, wherein the cell comprises a plurality of recombination sites recognized by the recombinase, and recombinase-mediated recombination of the plurality of recombination sites results in deletion of a genomic region.

19. The method of claim 10, wherein the cell is a tumor cell, and the functional protein is a tumor suppressor protein, a metastasis suppressor protein, a cytostatic protein, or a cytotoxic protein.

20. The supercharged protein covalently bound to a functional peptide or protein of claim 1, wherein the supercharged protein has a molecular weight of 10-100 kDa, a theoretical net charge of at least +10 at physiological pH, and a charge to molecular weight ratio of at least 0.8.

21. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the supercharged protein is covalently bound to the functional peptide or protein using a linker comprising an amide, ester, or disulfide bond.

22. The supercharged protein associated with a functional peptide or protein of claim 7, wherein the supercharged protein is +25 GFP, +36 GFP, +42 GFP, +48 GFP, or +49 GFP.

23. The supercharged protein associated with a functional peptide or protein of claim 3, wherein the linker comprises an amino acid sequence chosen from the group consisting of:

X-AGVF-X (SEQ ID NO;

     136), X-GFLG-X (SEQ ID NO;

     137), X-FK-X (SEQ ID NO;

     138), X-AL-X (SEQ ID NO;

     139), X-ALAL-X (SEQ ID NO;

     140), and X-ALALA-X (SEQ ID NO;

     141), wherein X denotes the supercharged protein or the functional peptide or protein.

24. The supercharged protein associated with a functional peptide or protein of claim 8, wherein the functional protein is a protein selected from the group consisting of:

p53, Rb (retinoblastoma protein), BRCA1, BRCA2, PTEN, APC, CD95, ST7, ST14, BRMS1, CRSP3, DRG1, KAI1, KISS1, NM23, EGF, EPO, FGF, G-CSF, GM-CSF, HGF, HDGF, IGF, PDGF, TPO, TGF-α

, TGF-β

, VEGF, Cre recombinase, Dre recombinase, and FLP recombinase.

25. The supercharged protein associated with a functional peptide or protein of claim 1, wherein the modified primary amino acid sequence comprises replacement of a plurality of charged or highly polar, solvent-exposed residues with a natural amino acid residue that is positively charged at physiological pH.