CA2493509A1 - Rationally designed polysaccharide lyases derived from chondroitinase b - Google Patents

Rationally designed polysaccharide lyases derived from chondroitinase b Download PDF

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Publication number
CA2493509A1
CA2493509A1 CA002493509A CA2493509A CA2493509A1 CA 2493509 A1 CA2493509 A1 CA 2493509A1 CA 002493509 A CA002493509 A CA 002493509A CA 2493509 A CA2493509 A CA 2493509A CA 2493509 A1 CA2493509 A1 CA 2493509A1
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CA
Canada
Prior art keywords
chondroitinase
modified
recombinant
amino acid
native
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Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
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CA002493509A
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French (fr)
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CA2493509C (en
Inventor
Kevin Pojasek
Rahul Raman
Ram Sasisekharan
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Massachusetts Institute of Technology
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Publication of CA2493509C publication Critical patent/CA2493509C/en
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Expired - Fee Related legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C08—ORGANIC MACROMOLECULAR COMPOUNDS; THEIR PREPARATION OR CHEMICAL WORKING-UP; COMPOSITIONS BASED THEREON
    • C08B—POLYSACCHARIDES; DERIVATIVES THEREOF
    • C08B37/00—Preparation of polysaccharides not provided for in groups C08B1/00 - C08B35/00; Derivatives thereof
    • C08B37/006—Heteroglycans, i.e. polysaccharides having more than one sugar residue in the main chain in either alternating or less regular sequence; Gellans; Succinoglycans; Arabinogalactans; Tragacanth or gum tragacanth or traganth from Astragalus; Gum Karaya from Sterculia urens; Gum Ghatti from Anogeissus latifolia; Derivatives thereof
    • C08B37/0063—Glycosaminoglycans or mucopolysaccharides, e.g. keratan sulfate; Derivatives thereof, e.g. fucoidan
    • C08B37/0069—Chondroitin-4-sulfate, i.e. chondroitin sulfate A; Dermatan sulfate, i.e. chondroitin sulfate B or beta-heparin; Chondroitin-6-sulfate, i.e. chondroitin sulfate C; Derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/88—Lyases (4.)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/527—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving lyase
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides

Abstract

The invention relates to rationally designed polysaccharide lyases and uses thereof. In particular, the invention relates to modified chondroitinase B. The modified chondroitinase B enzymes of the invention are useful for a variety of purposes, including cleaving and sequencing polysaccharides such as glycosaminoglycans (GAGs) as well as removing polysaccharides from a solutio n. The invention also includes methods of inhibiting anticoagulant activity, inhibiting angiogenesis, treating cancer, and inhibiting maternal malarial infection.

Claims (35)

1. A modified chondroitinase B having an amino acid sequence of the mature peptide of SEQ ID NO: 2 or conservative substitutions thereof, wherein at least one residue at a position selected from the group consisting of 116, 184, 213, 219, 245, 250, 271, 272, 296, 298, 318, 333, 363 and 364 of SEQ ID NO: 2 has been substituted or deleted.
2. The chondroitinase B of claim 1, wherein the substituted amino acid is a conservative amino acid substitution.
3. The chondroitinase B of claim 1, wherein the chondroitinase B is a substantially purified recombinant form.
4. A modified chondroitinase B having a modified product profile, wherein the modified product profile of the modified chondroitinase B is at least 10%
different than a native product profile of a native chondroitinase B.
5. The chondroitinase B of claim 4, wherein the modified chondroitinase B has a modified product profile that is at least 50% different than a native product profile of a native chondroitinase B.
6. The chondroitinase B of claim 4, wherein the modified chondroitinase B has a modified product profile that is at least 20% different than a native product profile of a native chondroitinase B.
7. The chondroitinase B of claim 4, wherein the modified chondroitinase B has the amino acid sequence of the mature peptide of SEQ ID NO: 2 wherein at least one amino acid residue has been substituted and wherein the substituted amino acid is at a position selected from the group consisting of 272, 333, and 364 of SEQ ID NO:
2.
8. A modified chondroitinase B having a k cat, or K M value for a substrate that is at least 10% different than a native chondroitinase B k cat or K M value.
9. The chondroitinase B of claim 8, wherein the modified chondroitinase B kcat or KM value is at least 20% different than a native chondroitinase B kcat or KM value.
10. The chondroitinase B of claim 8, wherein the modified chondroitinase B
kcat or KM value is at least 50% different than a native chondroitinase B kcat or KM value.
11. The chondroitinase B of claim 8, wherein the modified chondroitinase B has the amino acid sequence of the mature peptide of SEQ ID NO: 2 wherein at least one amino acid residue has been substituted and wherein the substituted amino acid is at a position selected from the group consisting of 272, 333, 363 and 364 of SEQ ID
NO: 2.
12. The chondroitinase B of claim 9, wherein the substrate is a glycosaminoglycan.
13. A pharmaceutical preparation comprising a sterile formulation of chondroitinase B of any one of claims 1-12 and a pharmaceutically acceptable carrier.
14. A method of specifically cleaving chondroitin sulfate, comprising:
contacting chondroitin sulfate with the chondroitinase B of any one of claims 12.
15. A method of specifically cleaving dermatan sulfate, comprising:
contacting dermatan sulfate with the chondroitinase B of any one of claims 1-12.
16. The method of claim 14, wherein the method is a method of removing chondroitin sulfate from a chondroitin sulfate containing fluid.
17. The method of claims 15, wherein the method is a method of removing dermatan sulfate from a dermatan sulfate containing fluid.
18. The method of claim 14, wherein the method is a method for sequencing chondroitin sulfate oligosaccharides.
19. The method of claim 15, wherein the method is a method for sequencing dermatan sulfate oligosaccharides.
20. A method of analyzing a sample of polysaccharides, comprising:
contacting the sample with the chondroitinase B of any one of claims 1-12.
21. A method of identifying the presence of a particular polysaccharide in a sample, comprising:
contacting the sample with the chondroitinase B of any one of claims 1-12.
22. A method of determining the purity of sample of polysaccharides, comprising:
contacting the sample with the chondroitinase B of any one of claims 1-12.
23. A method for determining the composition of a sample of polysaccharides, comprising:
contacting the sample with the chondroitinase B of any one of claims 1-12.
24. A method for inhibiting angiogenesis, comprising administering to a subject an effective amount for inhibiting angiogenesis of the chondroitinase B of any one of claims 1-12, or a GAG fragment produced by the chondroitinase B of any one of claims 1-12.
25. The method of claim 24 wherein the chondroitinase B or GAG fragment is administered to a tumor.
26. The method of claim 24, wherein the chondroitinase B or GAG fragment is administered in a biodegradable, biocompatible polymeric delivery device.
27. The method of claim 24, wherein the chondroitinase B or GAG fragment is administered in a pharmaceutically acceptable vehicle for injection.
28. An immobilized modified chondroitinase B comprising:
a modified chondroitinase B as in any one of claims 1-12, and a solid support membrane, wherein the modified chondroitinase B is immobilized on the solid support membrane.
29. A method for purifying a recombinant chondroitinase, comprising:
inducing a culture of cells containing a recombinant chondroitinase with an inducing agent for greater than four hours, and isolating the recombinant chondroitinase from the cells to produce a purified chondroitinase.
30. The method of claim 29, wherein the cells are incubated with the inducing agent at a temperature of between 20° and 26° C.
31. The method of claim 30, wherein the cells are incubated with the inducing agent for at least 8 hours.
32. The method of claims 29, wherein the chondroitinase is selected from the group consisting of chondroitinase AC and B.
33. The method of claim 29, wherein the recombinant chondroitinase includes an terminal Histidine tag.
34. The method of claim 33, further comprising passing the recombinant chondroitinase over a charged Ni 2+ column to isolate the recombinant chondroitinase.
35. A method for isolating a recombinant chondroitinase, comprising:
lysing a cell culture containing a recombinant chondroitinase having a terminal Histidine tag, and passing the recombinant chondroitinase over a charged Ni 2+ column to isolate the recombinant chondroitinase.
CA002493509A 2002-06-03 2003-06-03 Rationally designed polysaccharide lyases derived from chondroitinase b Expired - Fee Related CA2493509C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US38550902P 2002-06-03 2002-06-03
US60/385,509 2002-06-03
PCT/US2003/017680 WO2003102160A2 (en) 2002-06-03 2003-06-03 Rationally designed polysaccharide lyases derived from chondroitinase b

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CA2493509A1 true CA2493509A1 (en) 2003-12-11
CA2493509C CA2493509C (en) 2010-03-09

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US (4) US6962699B2 (en)
EP (1) EP1532241B1 (en)
AT (1) ATE481478T1 (en)
AU (1) AU2003243396A1 (en)
CA (1) CA2493509C (en)
DE (1) DE60334220D1 (en)
WO (1) WO2003102160A2 (en)

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EP1532241B1 (en) 2010-09-15
US20050227320A1 (en) 2005-10-13
DE60334220D1 (en) 2010-10-28
EP1532241A2 (en) 2005-05-25
US20050233419A1 (en) 2005-10-20
CA2493509C (en) 2010-03-09
AU2003243396A8 (en) 2003-12-19
WO2003102160A3 (en) 2004-09-16
US20070065424A1 (en) 2007-03-22
EP1532241A4 (en) 2005-12-14
US20040091472A1 (en) 2004-05-13
AU2003243396A1 (en) 2003-12-19
US7129335B2 (en) 2006-10-31
ATE481478T1 (en) 2010-10-15
US6962699B2 (en) 2005-11-08
WO2003102160A2 (en) 2003-12-11
US7105334B2 (en) 2006-09-12

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