WO1999033994A1 - Desacetoxycephalosporine c synthase (daocs) modifies et structure aux rayons x - Google Patents
Desacetoxycephalosporine c synthase (daocs) modifies et structure aux rayons x Download PDFInfo
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- WO1999033994A1 WO1999033994A1 PCT/GB1998/003860 GB9803860W WO9933994A1 WO 1999033994 A1 WO1999033994 A1 WO 1999033994A1 GB 9803860 W GB9803860 W GB 9803860W WO 9933994 A1 WO9933994 A1 WO 9933994A1
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Classifications
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- 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
- C12N9/0004—Oxidoreductases (1.)
- C12N9/0071—Oxidoreductases (1.) acting on paired donors with incorporation of molecular oxygen (1.14)
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
- A61P1/12—Antidiarrhoeals
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P19/00—Drugs for skeletal disorders
- A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
Definitions
- Penicillin and cephalosporin antibiotics are produced either directly by fermentation or by modification of fermentation derived materials containing a beta-lactam ring.
- the biosynthetic pathway to the penicillins and cephalosporins has been extensively studied and reviewed (J. E. Baldwin and C. J. Schofield, in 'The Chemistry of ⁇ -lactams (Ed. M. I. Page), Chapter 1 , Blackie, London 1992; ingolia and Queener, Med. Res. Rev., 1989, 9, 245-264; Aharonowitz, Cohen and Martin, Ann. Rev.
- D-valine (ACV) to isopenicillin N in a step catalysed by isopenicillin N synthase (IPNS). This step is common to both penicillin and cephalosporin biosynthesis.
- isopenicillin N is converted by exchange of its L- ⁇ - ⁇ - aminoadipoyl side chain to penicillins with other side chains, which are normally more hydrophobic than the side chain of isopenicillin N. This conversion is catalysed by an amidohydrolase/ acyltransferase enzyme.
- penicillins produced by this biosynthetic process include penicillin G (which has a phenylacetyl side chain) and penicillin V (which has a phenoxyacetyl side chain). These hydrophobic penicillins may be commercially produced via fermentation under the appropriate conditions.
- DOCS deacetoxycephalosporin C synthase
- DAOC/DACS deacetoxy/deacetylcephalosporin C synthase
- DAOC deacetylcephalosporin C
- Penicillins with hydrophobic side chains may be used for the preparation of cephalosporins or intermediates used in the preparation of cephalosporins, e.g. penicillins (including penicillin G and penicillin V) may be used to prepare C-3 exomethylene cephams which may be used as intermediates in the preparation of the commercial antibiotics, e.g. Cefachlor.
- IPNS The enzymes IPNS, DAOCS, DACS and DAOC/DACS are members of an extended family of Fe(ll) utilising oxidase and oxygenase enzymes. Most of this family (including DAOCS, DACS and DAOC/DACS) utilise a 2-oxo acid (normally 2-oxoglutarate) as a cosubstrate in addition to dioxygen and the 'prime' substrate (e.g. penicillin N in the case of DAOCS). Since IPNS, does not use 2-oxoglutarate, it has a substantially different mechanism to the 2-oxoglutarate dependent oxygenases, and this gives rise to a significantly different active site.
- 2-oxo acid normally 2-oxoglutarate
- the 'prime' substrate e.g. penicillin N in the case of DAOCS
- This invention is based on the determination of the three dimensional crystal structure of DAOCS and the information and developments which come from it.
- the X-ray co-ordinates provide very detailed 3-dimensional information on the relationships between amino acid residues in the structure of DAOCS and on the binding modes of the Fe-cofactor and the substrates to DAOCS.
- the structure allows the modification of DAOCS and related enzymes of penicillin and cephalosporin biosynthesis (including DACS and DAOC/DACS) in order to alter their substrate and product selectivities. Since the DAOCS structures are the first from the family of 2-oxoglutarate dependent dioxygenases they also allow for the design of new inhibitors of this family of enzymes.
- IPNS gene sequence (and therefore the amino acid sequence) is related but significantly different to those of DAOCS, DACS, DAOC/DACS. It is likely that gross elements of the fold (i.e. significant elements within the 3-dimensional structure) of these enzymes will be conserved but that the active site architecture will be very significantly different. Structural elements conserved are likely to include the beta- barrel 'jelly roll' core and certain alpha-helices (including alpha helix-10, as defined in Roach et al., Nature, 1995, 375, 700-704). The degree of similarity is insufficient to define the precise structure of DAOCS, DACS, or DAOC/DACS from the IPNS structures.
- the three-dimensional structure of DAOCS is defined by the X-ray co-ordinates set out below (Structure A).
- the present invention relates to the use of the structures of DAOCS in order to make modifications to it or DACS or DAOC/DACS in order that the modified enzymes catalyse the conversion of unnatural penicillins (e.g. penicillin G and penicillin V) to cephalosporins more efficiently than the wild-type enzyme.
- Further aspects of the invention relate to the use of the DAOCS structure in order to produce unnatural products in micro-organisms. Such products include exomethylene cephalosporins, with or without alpha-aminoadipoyl or hydrophobic side chain (e.g. phenylacetyl or phenoxyacetyl).
- one aspect of this invention refers to the use of the structure of DAOCS for modifying DAOCS (or the closely related enzymes DACS or DAOC/DACS) in order to: (i) permit the enzyme to accept (or accept more efficiently) unnatural penicillin substrates for the preparation of new or commercially valuable antibacterial materials. (ii) enable the modified enzyme to produce unnatural (e.g. exomethylene cephams) or optimise the production of minor products (e.g. 3- ⁇ -hydroxycephams) for use as antibacterials or as intermediates in the preparation of antibacterials or commercially valuable compounds.
- unnatural e.g. exomethylene cephams
- optimise the production of minor products e.g. 3- ⁇ -hydroxycephams
- this invention provides modified enzymes that result from application of the aforementioned techniques.
- These are enzymes having significant (as defined below) sequence and thus structural similarity with DAOCS.
- structures of these enzymes may be predicted on the basis of the DAOCS structures.
- sequence similarity/identity between most of the modified enzyme and a major part of DAOCS.
- two enzymes may have structures in which secondary structural elements are largely or wholly conserved, differences in the structures of the two enzymes may result from the side chains of the amino acids forming the secondary structural elements. The effect of these differences, which alter the substrate/product selectivities of the compared enzymes, is predictable once the three-dimensional structure of one of the enzymes is known.
- the invention provides an enzyme having significant (as herein defined) sequence similarity to DAOCS wherein the side chain binding site of penicillin N or DAOC is modified and at at least one of the following sites at least one amino acid residue is changed to another amino acid residue or is deleted: Thr72, Arg74, Arg75, Glu156, Leu158, Arg160, Arg162, Leu186, Ser187, Phe225, Phe264, Arg266, Asp301 , Tyr302, Val303, Asn304; and/or at least one additional amino acid residue is inserted within the region 300-311 ; provided that other residues interacting with the above may be changed in order to accommodate the change in one of the above.
- the side chain binding pocket of DAOCS is made of residues from different parts of the peptide chain, so it is likely that more than one residue will have to be altered to make a better penicillin G/V expander. Nevertheless some residues are more important than others.
- the penam C-3 carboxylate group probably occupies an analogous position to that of Ala- 311 from a symmetry related molecule in the active site, forming electrostatic interactions with Arg-162 and Arg-160.
- the side chain of Arg-160 may also form a hydrogen bonding interaction with the ⁇ -lactam carbonyl.
- Arg-266 This residue binds with the -aminoadipate side chain of the natural substrate and should be changed to a residue of more hydrophobic character, e.g. Phe, Ala, Val, Leu, He. b) Thr-72. This should be changed to a hydrophobic residue e.g.
- Arg-74 may be usefully changed to a neutral or hydrophobic residue (Phe, Tyr, Val, Leu, He, Ala). Modification of Arg-75 may be necessary in addition because it forms a hydrogen-bonding network with Arg-74.
- Glu-156 This residue binds with the ⁇ -aminoadipate side chain. It should be changed to one of Ala, Val, Leu, He, Phe, Tyr, Trp, Asn, Gin, Ser.
- the insertion or deletion of residues into the DAOCS sequence may also be of use in constructing a hydrophobic binding pocket for the penicillin side chain. Insertion of hydrophobic residues into the
- C-terminal region may assist in the construction of a hydrophobic binding pocket for penicillin side chains.
- the invention provides an enzyme having significant (as herein defined) sequence similarity to DAOCS wherein the penicillin/cephalosporin binding site of penicillin N or DAOC is modified and at at least one of the following amino acid residues is changed or deleted: Ile88, Arg160, Arg162, Phe164, Met180, Thr190, Ile192, Phe225, Pro241 , Val245, Val262, Phe264, Asn304, Ile305, Arg306, Arg307; and/or at least one additional amino acid residue is inserted within the region 300-31 1 ; provided that other residues interacting with the above may be changed in order to accommodate the change in one of the above.
- Another aspect of the invention refers to the use of the structure of DAOCS in order to modify its active site (or that of a structurally related 2-oxoglutarate dependent dioxygenase) in order that the modified enzyme accepts non beta lactam substrates in order to produce oxidised compounds of value.
- Oxidised amino acids e.g. 4-hydroxyprolines, hydroxylysines, hydroxyaspartic acids and others
- specific residues can be targeted for modification in order that the modified enzyme can be used to produce oxidised amino acids or peptides.
- the process may include modification of the following residues: Arg74, Glu156, Leu158, Arg160, Arg162, Leu186, Ser187, Phe225, Phe264, Arg266, Asp301 , Tyr302, Val303, Asn304, Ile88, Arg162, Phe164, Met180, Thr190, Ile192, Pro241 , Val245, Val262, Ile305, Arg306, Arg307.
- Another aspect of the invention refers to the use of the use of the
- DAOCS structure for the design of selective inhibitors of 2-oxoglutarate dependent dioxygenases.
- the 2-oxoglutarate dependent dioxygenase prolyl 4-hydroxylase has been the target of inhibition in order to provide a therapeutic treatment for fibrotic diseases (e.g. liver cirrhosis, arthritis).
- fibrotic diseases e.g. liver cirrhosis, arthritis.
- no inhibitors are in clinical use, probably because it is difficult to achieve selective inhibition of the target enzyme for inhibition over other enzymes (including 2-oxoglutarate dependent enzymes).
- the structure of DAOCS provides a template for the design of inhibitors of 2-oxoglutarate dependent dioxygenases. Set out below are two high resolution crystal structures for
- DAOCS from S. clavuligerus the structure of the iron-free apoenzyme (Structure A) and the structure of the complex with Fe(ll) and 2-oxoglutarate (Structure B).
- Structure A the structure of the iron-free apoenzyme
- Structure B the structure of the complex with Fe(ll) and 2-oxoglutarate
- the results imply a mechanism by which the enzyme-Fe(ll) complex reacts with 2-oxoglutarate and dioxygen to give the reactive ferryl species, a process common to many non-haem oxygenases.
- 2-oxoacid-dependent ferrous enzymes are prolyl hydroxylase, involved in collagen biosynthesis, gibberellin 3 ⁇ -hydroxylase, a mutation of which influences stem length in plants, and clavaminic acid synthase, involved in the biosynthesis of the ⁇ -lactamase inhibitor, clavulanic acid.
- DAOCS belongs to a sub-family, the members of which show sequence similarity with IPNS and 1-aminocyclopropane-1-carboxylate oxidase (the ethylene forming enzyme), enzymes that do not use a 2-oxoacid in catalysis.
- the iron-free form of DAOCS crystallises in space group R3 as a crystallographic trimer.
- the main chain of the protein folds into a conserved jelly roll core with flanking helices.
- Figure 1 the biosynthetic pathway to the penicillins and cephalosporins.
- Figure 2 is a view of the active site of DAOCS showing
- Structure A is a three-dimensional structure of DAOCS.
- Structure B is a high resolution crystal structure for prokaryotic DAOCS from S. clavuligerus as a complex with Fe(ll) and 2- oxoglutarate.
- DAOCS The peptide sequence of DAOCS (with the numbering used herein) is set out below:
- ATOM 92 CD2 LEU 10 16.852 29.603 44.869 1.000 21.93
- ATOM 271 CE2 PHE 32 19.267 22.348 49.138 1.000 15.49
- ATOM 364 CD2 LEU 44 6.793 29.259 57.653 1.000 51.56
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Abstract
Priority Applications (6)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
PL98341396A PL341396A1 (en) | 1997-12-24 | 1998-12-24 | Modified syntheses of diacetoxycephalosporin c (daocs) and its roentgenographic structure |
JP2000526650A JP2002500015A (ja) | 1997-12-24 | 1998-12-24 | 改変型デアセトキシセファロスポリンcシンターゼ(daocs)およびx線構造 |
SK976-2000A SK9762000A3 (en) | 1997-12-24 | 1998-12-24 | Modified deacetoxycephalosporin c synthase (daocs) and x-ray structure |
CA002316401A CA2316401A1 (fr) | 1997-12-24 | 1998-12-24 | Desacetoxycephalosporine c synthase (daocs) modifies et structure aux rayons x |
EP98962587A EP1047785A1 (fr) | 1997-12-24 | 1998-12-24 | Desacetoxycephalosporine c synthase (daocs) modifies et structure aux rayons x |
AU17720/99A AU1772099A (en) | 1997-12-24 | 1998-12-24 | Modified deacetoxycephalosporin c synthase (daocs) and x-ray structure |
Applications Claiming Priority (4)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
GB9727370.0 | 1997-12-24 | ||
GBGB9727370.0A GB9727370D0 (en) | 1997-12-24 | 1997-12-24 | Processed based on the structure of deacetoxycephalosporin c synthase |
GB9813644.3 | 1998-06-24 | ||
GBGB9813644.3A GB9813644D0 (en) | 1998-06-24 | 1998-06-24 | Structure of a cephalosporin synthase |
Publications (1)
Publication Number | Publication Date |
---|---|
WO1999033994A1 true WO1999033994A1 (fr) | 1999-07-08 |
Family
ID=26312856
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/GB1998/003860 WO1999033994A1 (fr) | 1997-12-24 | 1998-12-24 | Desacetoxycephalosporine c synthase (daocs) modifies et structure aux rayons x |
Country Status (8)
Country | Link |
---|---|
EP (1) | EP1047785A1 (fr) |
JP (1) | JP2002500015A (fr) |
CN (1) | CN1284997A (fr) |
AU (1) | AU1772099A (fr) |
CA (1) | CA2316401A1 (fr) |
PL (1) | PL341396A1 (fr) |
SK (1) | SK9762000A3 (fr) |
WO (1) | WO1999033994A1 (fr) |
Cited By (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2001085951A1 (fr) * | 2000-05-09 | 2001-11-15 | Acs Dobfar Uk Limited | Expandase modifiee et utilisations |
EP1348759A1 (fr) * | 2002-03-26 | 2003-10-01 | Synmax Biochemical Co., Ltd | Expandase de penicillin mutée et un procédé de production de 7-ADCA en utilisant ladite expandase |
Families Citing this family (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US9404139B2 (en) * | 2012-01-10 | 2016-08-02 | Orchid Chemicals & Pharmaceuticals Limited | Mutated cephalosporin hydroxylase and its application in deacetylcephalosporanic acid synthesis |
CN114958877B (zh) * | 2022-06-14 | 2024-02-20 | 河南省健康元生物医药研究院有限公司 | 去乙酰氧基头孢菌素c合成酶突变体及其编码基因与应用 |
Citations (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0366354A2 (fr) * | 1988-10-24 | 1990-05-02 | Eli Lilly And Company | Déacétoxycéphalosporine C synthase purifiée |
EP0532341A1 (fr) * | 1991-09-11 | 1993-03-17 | Gist-Brocades B.V. | Nouveau procédé biologique de préparation de 7-AADC |
WO1997020053A2 (fr) * | 1995-11-27 | 1997-06-05 | Gist-Brocades B.V. | Procede ameliore de production de cephalosporines semi-synthetiques par l'activite de l'expandase sur la penicilline g |
WO1998016648A2 (fr) * | 1996-10-15 | 1998-04-23 | Isis Innovation Limited | Enzymes isopenicilline n synthetase et desacetoxycephalosporine c synthetase et procedes |
-
1998
- 1998-12-24 WO PCT/GB1998/003860 patent/WO1999033994A1/fr not_active Application Discontinuation
- 1998-12-24 JP JP2000526650A patent/JP2002500015A/ja not_active Withdrawn
- 1998-12-24 CA CA002316401A patent/CA2316401A1/fr not_active Abandoned
- 1998-12-24 SK SK976-2000A patent/SK9762000A3/sk unknown
- 1998-12-24 AU AU17720/99A patent/AU1772099A/en not_active Abandoned
- 1998-12-24 CN CN98813793A patent/CN1284997A/zh active Pending
- 1998-12-24 EP EP98962587A patent/EP1047785A1/fr not_active Withdrawn
- 1998-12-24 PL PL98341396A patent/PL341396A1/xx unknown
Patent Citations (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0366354A2 (fr) * | 1988-10-24 | 1990-05-02 | Eli Lilly And Company | Déacétoxycéphalosporine C synthase purifiée |
EP0532341A1 (fr) * | 1991-09-11 | 1993-03-17 | Gist-Brocades B.V. | Nouveau procédé biologique de préparation de 7-AADC |
WO1997020053A2 (fr) * | 1995-11-27 | 1997-06-05 | Gist-Brocades B.V. | Procede ameliore de production de cephalosporines semi-synthetiques par l'activite de l'expandase sur la penicilline g |
WO1998016648A2 (fr) * | 1996-10-15 | 1998-04-23 | Isis Innovation Limited | Enzymes isopenicilline n synthetase et desacetoxycephalosporine c synthetase et procedes |
Non-Patent Citations (11)
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2001085951A1 (fr) * | 2000-05-09 | 2001-11-15 | Acs Dobfar Uk Limited | Expandase modifiee et utilisations |
EP1348759A1 (fr) * | 2002-03-26 | 2003-10-01 | Synmax Biochemical Co., Ltd | Expandase de penicillin mutée et un procédé de production de 7-ADCA en utilisant ladite expandase |
US6905854B2 (en) | 2002-03-26 | 2005-06-14 | Synmax Biochemical Co., Ltd. | Mutated penicillin expandase and process for preparing 7-ADCA using the same |
Also Published As
Publication number | Publication date |
---|---|
EP1047785A1 (fr) | 2000-11-02 |
PL341396A1 (en) | 2001-04-09 |
SK9762000A3 (en) | 2001-02-12 |
JP2002500015A (ja) | 2002-01-08 |
CN1284997A (zh) | 2001-02-21 |
CA2316401A1 (fr) | 1999-07-08 |
AU1772099A (en) | 1999-07-19 |
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