Hydrolysis of mannose-1-phospho-6-mannose linkage to phospho-6-mannose

• US 10,392,609 B2
• Filed: 11/14/2016
• Issued: 08/27/2019
• Est. Priority Date: 09/29/2009
• Status: Active Grant

• Current Assignee: Universiteit Gent Vzw, V1B Vzw, Co., VIB VZW, Vrije Universiteit Brussel
• Original Assignee: Oxyrane UK Limited
• Inventors: Callewaert, Nico Luc Marc, Vervecken, Wouter, Tiels, Petra Sophie, Remaut, Han Karel, Piens, Kathleen Camilla Telesphore Alida Maria
• Primary Examiner(s): Prouty, Rebecca E
• Application Number:
  US15/350,648
• Publication Number:
  US 20170226493A1
• Time in Patent Office: 1,016 Days
• CPC Class Codes: A61P 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: C07K 14/00 Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
• CPC Class Codes: C12N 9/2428 Glucan 1,4-alpha-glucosidase (3.2.1.3), i.e. glucoamylase
• CPC Class Codes: C12N 9/2465 acting on alpha-galactose-glycoside bonds, e.g. alpha-galactosidase (3.2.1.22)
• CPC Class Codes: C12N 9/2488 Mannanases
• CPC Class Codes: C12P 19/04 Polysaccharides, i.e. compounds containing more than five saccharide radicals attached to each other by glycosidic bonds
• CPC Class Codes: C12P 19/14 produced by the action of a carbohydrase (EC 3.2.x), e.g. by alpha-amylase , e.g. by cellulase, hemicellulase
• CPC Class Codes: C12P 21/00 Preparation of peptides or proteins single cell protein C12N1/00
• CPC Class Codes: C12P 21/005 Glycopeptides, glycoproteins
• CPC Class Codes: C12Y 302/01 Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
• CPC Class Codes: C12Y 302/01003 Glucan 1,4-alpha-glucosidase (3.2.1.3), i.e. glucoamylase
• CPC Class Codes: C12Y 302/01022 Alpha-galactosidase (3.2.1.22)
• CPC Class Codes: Y02P 20/52 using catalysts, e.g. selective catalysts

Abstract

Described herein are methods and genetically engineered cells useful for uncapping a mannose-6-phosphate residue on an oligosaccharide.

Claims

1. A method for uncapping a mannose-6-phosphate residue on an oligosaccharide, said method comprising

a) providing said oligosaccharide having a mannose-1-phospho-6-mannose linkage;

and

b) contacting said oligosaccharide with a mannosidase capable of hydrolyzing said mannose-1-phospho-6-mannose residue to phospho-6-mannose, wherein said mannosidase is a member of glycosyl hydrolase family 92 and wherein said mannosidase does not contain a catalytic acid residue capable of protonating the anomeric oxygen, and

wherein said mannosidase comprises an amino acid sequence having (i) a GVGXXGXGG motif where X is Gly, Ala, Ser, Thr, or Cys;

(ii) a VRXE motif, where X is any amino acid other than Pro;

(iii) an X₁YQGX₂ motif, where X₁ is Leu, Ile, Val, Ala, Phe, Tyr or Met, and X₂ is Thr, Ser, or Asn; and

(iv) GDXGN, where X can be any amino acid other than Pro, and

wherein said mannosidase comprises an amino acid sequence having at least 90% identity to residues 1 to 774 of SEQ ID NO;

50 or an amino acid sequence having at least 95% identity to SEQ ID NO;

50.

2. The method of claim 1, wherein for said mannosidase, the three dimensional protein coordinates of the atoms in the amino acid side chains located in the minimal catalytic center fall within 1.5 Å

deviation of the coordinates of the equivalent atoms in FIG. 33.

3. The method of claim 1, wherein said contacting step is performed using a purified mannosidase, a recombinant mannosidase, a cell lysate containing said recombinant mannosidase, or a fungal cell containing said recombinant mannosidase.

4. The method of claim 1, wherein said oligosaccharide is attached to a protein.

5. The method of claim 4, wherein said protein is a human protein expressed in a fungal organism.

6. The method of claim 5, wherein said fungal organism is Yarrowia lipolytica or Arxula adeninivorans.

7. The method of claim 5, wherein said fungal organism is a methylotrophic yeast.

8. The method of claim 7, wherein said methylotrophic yeast is Pichia pastoris, Pichia methanolica, Oogataea minuta, or Hansenula polymorpha.

9. The method of claim 5, wherein said fungal organism is a filamentous fungus.

10. The method of claim 9, wherein said filamentous fungus is selected from the group consisting of Aspergillus caesiellus, Aspergillus candidus, Aspergillus carneus, Aspergillus clavatus, Aspergillus deflectus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus oryzae, Aspergillus parasiticus, Aspergillus penicilloides, Aspergillus restrictus, Aspergillus sojae, Aspergillus sydowii, Aspergillus tamari, Aspergillus terreus, Aspergillus ustus, and Aspergillus versicolor.

11. The method of claim 5, said fungal organism further comprising a nucleic acid encoding a polypeptide capable of promoting mannosyl phosphorylation.

12. The method of claim 5, wherein said fungal organism is genetically engineered to be deficient in OCH1 (Outer CHain elongation) activity.

13. The method of claim 5, said fungal organism further comprising a nucleic acid encoding a polypeptide capable of promoting mannosyl phosphorylation, and wherein said fungal organism is genetically engineered to be deficient in OCH1 activity.

14. The method of claim 11, wherein said polypeptide capable of promoting mannosyl phosphorylation is a MNN4 polypeptide.

15. The method of claim 11, wherein said polypeptide capable of promoting mannosyl phosphorylation is a P. pastoris PNO1 polypeptide.

16. The method of claim 4, wherein said protein is a pathogen protein, a lysosomal protein, a growth factor, a cytokine, a chemokine, an antibody or antigen-binding fragment thereof, or a fusion protein.

17. The method of claim 16, wherein said lysosomal protein is a lysosomal enzyme.

18. The method of claim 17, wherein said lysosomal enzyme is associated with a lysosomal storage disorder (LSD).

19. The method of claim 18, wherein said LSD is selected from the group consisting of Fabry'"'"'s disease, mucopolysaccharidosis I, Farber disease, Gaucher disease, GM1-gangliosidosis, Tay-Sachs disease, Sandhoff disease, GM2 activator disease, Krabbe disease, metachromatic leukodystrophy, Niemann-Pick disease, Scheie disease, Hunter disease, Sanfilippo disease, Morquio disease, Maroteaux-Lamy disease, hyaluronidase deficiency, aspartylglucosaminuria, fucosidosis, mannosidosis, Schindler disease, sialidosis type 1, Pompe disease, Pycnodysostosis, ceroid lipofuscinosis, cholesterol ester storage disease, Wolman disease, Multiple sulfatase deficiency, galactosialidosis, mucolipidosis, cystinosis, sialic acid storage disorder, chylomicron retention disease with Marinesco-Sjö

gren syndrome, Hermansky-Pudlak syndrome, Chediak-Higashi syndrome, Danon disease, and Geleophysic dysplasia.

20. The method of claim 18, wherein said LSD is Pompe disease or Fabry'"'"'s disease.

21. The method of claim 17, wherein said lysosomal enzyme is acid alpha glucosidase or alpha galactosidase.

22. The method of claim 1, wherein said mannosidase comprises a targeting sequence to target the mannosidase to an intracellular compartment.

23. The method of claim 1, wherein the residue of said mannosidase corresponding to glutamic acid residue Glu 585 of the Bacteroides thetaiotaomicron alpha-1,2-mannosidase Bt3990 is a non-acidic residue.

24. The method of claim 23, wherein the residue of the mannosidase corresponding to the glutamic acid residue Glu 585 of the Bacteroides thetaiotaomicron alpha-1,2-mannosidase Bt3990 is a threonine or serine residue.

25. The method of claim 1, wherein said mannosidase is a C. cellulans mannosidase.

26. A method for uncapping a mannose-6-phosphate residue on an oligosaccharide, said method comprising

a) providing said oligosaccharide having a mannose-1-phospho-6-mannose linkage;

and

b) contacting said oligosaccharide with a mannosidase capable of hydrolyzing said mannose-1-phospho-6-mannose residue to phospho-6-mannose, wherein said mannosidase is a member of glycosyl hydrolase family 92 and wherein said mannosidase does not contain a catalytic acid residue capable of protonating the anomeric oxygen, and

wherein for said mannosidase, the three dimensional protein coordinates of the atoms in the amino acid side chains located in the minimal catalytic center fall within 1.5 Å

deviation of the coordinates of the equivalent atoms in FIG. 33, and

wherein said mannosidase comprises an amino acid sequence having at least 90% identity to residues 1 to 774 of SEQ ID NO;

50 or an amino acid sequence having at least 95% identity to SEQ ID NO;

50.

27. The method of claim 26, wherein said contacting step is performed using a purified mannosidase, a recombinant mannosidase, a cell lysate containing said recombinant mannosidase, or a fungal cell containing said recombinant mannosidase.

28. The method of claim 26, wherein said oligosaccharide is attached to a protein.

29. The method of claim 28, wherein:

said protein is a human protein expressed in a fungal organism;

or

said protein is a pathogen protein, a lysosomal protein, a growth factor, a cytokine, a chemokine, an antibody or antigen-binding fragment thereof, or a fusion protein.

30. The method of claim 26, wherein said mannosidase comprises a targeting sequence to target the mannosidase to an intracellular compartment.

31. The method of claim 26, wherein:

the residue of said mannosidase corresponding to glutamic acid residue Glu 533 of the Bacteroides thetaiotaomicron alpha-1,2-mannosidase Bt3990 is a non-acidic residue; and

/or

the residue of said mannosidase corresponding to glutamic acid residue Glu 585 of the Bacteroides thetaiotaomicron alpha-1,2-mannosidase Bt3990 is a non-acidic residue.

32. The method of claim 26, wherein said mannosidase is a C. cellulans mannosidase.

33. A method for uncapping a mannose-6-phosphate residue on an oligosaccharide, said method comprising

a) providing said oligosaccharide having a mannose-1-phospho-6-mannose linkage;

and

b) contacting said oligosaccharide with a mannosidase capable of hydrolyzing said mannose-1-phospho-6-mannose residue to phospho-6-mannose, wherein said mannosidase is a member of glycosyl hydrolase family 92 and wherein said mannosidase does not contain a catalytic acid residue capable of protonating the anomeric oxygen, and

wherein said mannosidase comprises an amino acid sequence having at least the following residues forming the catalytic center;

G71, G72, D355, R405, Q536, N588, Q589, T626, D660 and D662, and

wherein said mannosidase comprises an amino acid sequence having at least 90% identity to residues 1 to 774 of SEQ ID NO;

50 or an amino acid sequence having at least 95% identity to SEQ ID NO;

50.

34. The method of claim 33, wherein for said mannosidase, the three dimensional protein coordinates of the atoms in the amino acid side chains located in the minimal catalytic center fall within 1.5 Å

deviation of the coordinates of the equivalent atoms in FIG. 33.

35. The method of claim 33, wherein said contacting step is performed using a purified mannosidase, a recombinant mannosidase, a cell lysate containing said recombinant mannosidase, or a fungal cell containing said recombinant mannosidase.

36. The method of claim 33, wherein said oligosaccharide is attached to a protein.

37. The method of claim 36, wherein:

said protein is a human protein expressed in a fungal organism;

or

said protein is a pathogen protein, a lysosomal protein, a growth factor, a cytokine, a chemokine, an antibody or antigen-binding fragment thereof, or a fusion protein.

38. The method of claim 33, wherein said mannosidase comprises a targeting sequence to target the mannosidase to an intracellular compartment.

39. The method of claim 33, wherein said mannosidase is a C. cellulans mannosidase.