US20190152981A1

US20190152981A1 - Compositions and Methods For Making Alkaloid Morphinans

Info

Publication number: US20190152981A1
Application number: US16/247,972
Authority: US
Inventors: Peter James FACCHINI
Original assignee: EPIMERON Inc
Current assignee: Willow Biosciences Inc
Priority date: 2014-08-22
Filing date: 2019-01-15
Publication date: 2019-05-23
Also published as: WO2016026048A1; US20170267686A1; EP3183348A1; EP3183348A4; AU2015306046A1; US10227353B2; CA2958719A1

Abstract

Methods that may be used for the manufacture of a class of chemical compounds known as morphinans, including neopine, are provided. Compositions useful for the synthesis of morphinans, including neopine, are also provided.

Description

RELATED APPLICATIONS

This application is a continuation application of U.S. patent application Ser. No. 15/505,625 (now allowed), which is a national phase entry application of Patent Cooperation Treaty Application No. PCT/CA2015/050796 filed Aug. 21, 2015 (designed the U.S.), which claims the benefit under 35 USC § 119(e) from U.S. Provisional Patent Application No. 62/040,754, filed on Aug. 22, 2014 (now abandoned), all of which are incorporated by reference herein in their entirety.

INCORPORATION OF SEQUENCE LISTING

A computer readable form of the Sequence Listing “21806-P46963US02_SequenceListing.txt” (53,248 bytes), submitted via EFS-WEB and created on Jan. 15, 2019, is herein incorporated by reference.

FIELD OF THE DISCLOSURE

The compositions and methods disclosed herein relate to a class of chemical compounds known as alkaloids and methods for making alkaloids. More particularly, the present disclosure relates to alkaloid morphinans and processes for making the same.

BACKGROUND OF THE DISCLOSURE

The following paragraphs are provided by way of background to the present disclosure. They are not however an admission that anything discussed therein is prior art or part of the knowledge of persons skilled in the art.
Alkaloids belonging to the class of chemical compounds known as morphinans (i.e. alkaloid morphinans) have long been recognized to be useful as therapeutic agents, and as precursor compounds for use in the manufacture of therapeutic agents. Neopine, for example, is produced by plants belonging to the Papaveraceae and has been isolated from opium poppy (Papaver somniferum) (Dobbie J. J. and Lauder, A. (1911), J. Chemical Society, 34-5). It is known that neopine in planta is produced from a precursor compound named thebaine. However it is not clear which plant genes and polypeptides are involved in catalyzing the conversion reaction(s) resulting in the production of neopine. Currently neopine may be harvested from natural sources, such as opium poppy. Alternatively, neopine may be prepared synthetically. The latter may be achieved by oxymercuration of thebaine or by reduction of or 14-bromocodeinone or 14-bromo-codeine (NaBH₄) which yields neopine and its isomers (Poppy, the genus Papaver, 1998, pp 116, Harwood Academic Publishers, Editor: Bernàth, J.)
The existing manufacturing methods for neopine and related morphinans however suffer from low yields of neopine and morphinans and/or are expensive. No methods exist to biosynthetically make neopine. There exists therefore in the art a need for improved methods for the synthesis of neopine and related morphinans.

SUMMARY OF THE DISCLOSURE

The following paragraphs are intended to introduce the reader to the more detailed description that follows and not to define or limit the claimed subject matter of the present disclosure.
The present disclosure relates to certain alkaloids belonging to the class of morphinans, as well as to methods of making such morphinans. Accordingly, the present disclosure provides in at least one aspect a method of making a second morphinan having a C₇-C₈saturated carbon bond and a C₈-C₁₄mono-unsaturated carbon bond comprising:

- (a) providing a first morphinan having a C₇-C₈mono-unsaturated carbon bond and a C₈-C₁₄saturated carbon bond; and
- (b) contacting the first morphinan with a codeine isomerase or codeinone reductase capable of converting the first morphanin into the second morphinan.

In preferred embodiments, the method further comprises a step

- (c) recovering the second morphinan.

In preferred embodiments, the first morphinan and the second morphinan possess a bridging oxygen atom between carbon atoms C₄and C₅forming a tetrahydrofuranyl ring within the morphinan structure (furanyl-morphinan).
The present disclosure further provides, in at least one aspect, a method of making a second morphinan comprising:

- (a) providing a first morphinan;
- (b) contacting the first morphinan with a codeine isomerase or codeinone reductase capable of converting the first morphinan under conditions that permit the conversion of the first morphinan into the second morphinan;
  - wherein the first morphinan has the chemical formula (I):

and
wherein the second morphinan has the chemical formula (II):
wherein, in the first and the second morphinan, R₁represents a hydroxyl group or a methoxy group; wherein in the first and the second morphinan R₂represents a hydroxyl group and R_2′ represents a hydrogen atom, or taken together, R₂and R_2′ form an oxo group; and wherein in the first and the second morphinan R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group, the nitrogen atom bonded to R₃is optionally in the form of an N-oxide.
In further preferred embodiments, the nitrogen atom in the morphinan is methylated (i.e. R₃is a methyl group).
In further preferred embodiments, the nitrogen atom in the morphinan is hydrogenated (i.e. R₃is a hydrogen).
In further preferred embodiments, the nitrogen is a methylated and N-oxidized.
In further particularly preferred embodiments, in the first and the second morphinan, R₁is a methoxy group; R₂is a hydroxyl group and R_2′ is a hydrogen atom; and R₃is a methyl group, providing for the first morphinan having the chemical formula (III):
also known as codeine; and, providing for the second morphinan having the chemical formula (IV):
also known as neopine.
In further preferred embodiments, the codeine isomerase or the codeinone reuctase are a codeine isomerase or codeinone reductase obtainable from or obtained from Papaver somniferum.
In accordance with the present disclosure, the methods may be conducted in vitro or in vivo including, but not limited to, in plants, plant cell cultures, microorganisms, and cell-free systems.
In further embodiments, provided herein is a method for preparing a morphinan having chemical formula (II) comprising:

- (a) providing a chimeric nucleic acid sequence comprising as operably linked components:
  - (i) a nucleic acid sequence encoding a codeine isomerase or codeinone reductase polypeptide;
  - (ii) one or more nucleic acid sequences capable of controlling expression in a host cell;
- (b) introducing the chimeric nucleic acid sequence into a host cell that endogenously produces or is exogenously supplied with a morphinan substrate;
- (c) growing the host cell to produce codeine isomerase or codeinone reductase and to produce the morphinan having chemical formula (II); and
- (d) recovering morphinan having chemical formula (II) from the cell;
  wherein R₁represents a hydroxyl group or a methoxy group; wherein R₂represents a hydroxyl group or an oxo group; and wherein R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group the N is optionally an N-oxide.

Provided herein is further a method for preparing a codeine isomerase, the method comprising:

- (a) providing a chimeric nucleic acid sequence comprising as operably linked components:
  - (i) a nucleic acid sequence encoding a codeine isomerase or codeinone reductase; and
  - (ii) one or more a nucleic acid sequences capable of controlling expression in a host cell;
- (b) introducing the chimeric nucleic acid sequence into a host cell and growing the host cell to produce the codeine isomerase or codeinone reductase; and
- (c) recovering the codeine isomerase polypeptide or codeinone reductase from the host cell.

The present disclosure, still further, provides compositions for making a morphinan, comprising a polypeptide capable of, in a first morphinan having a mono-unsaturated C₇-C₈bond and a saturated C₈-C₁₄bond:

- (i) saturating the C₇-C₈bond; and
- (ii) unsaturating the C₈-C₁₄bond, to form a second morphinan having a saturated C₇-C₈and a mono-unsaturated C₈-C₁₄bond.

In preferred embodiments, the polypeptide is a codeine isomerase or codeinone reductase obtainable or obtained from Papaver somniferum.
The present disclosure, still further, provides compositions comprising nucleic acid sequences encoding a polypeptide capable of, in a first morphinan having a mono-unsaturated C₇-C₈bond and a saturated C₈-C₁₄bond:

Other features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description, while indicating preferred implementations of the disclosure, are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those of skill in the art from the detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The disclosure is in the hereinafter provided paragraphs described in relation to its Figures. The Figures provided herein are provided for illustration purposes and are not intended to limit the present disclosure.

FIG. 1A-B depicts a prototype chemical structure of morphinan (FIG. 1A) and furanyl morphinan (FIG. 1B). Various atoms within the structures have been numbered for ease of reference.

FIG. 2A-H depicts the chemical structures of certain morphinans, notably morphinans having a methylated N₁₇: codeine (FIG. 2A), neopine (FIG. 2B), morphine (FIG. 2C), neomorphine (FIG. 2D), codeinone (FIG. 2E), neopinone (FIG. 2F), morphinone (FIG. 2G), neomorphinone (FIG. 2H).

FIG. 3A-H depicts the chemical structures of certain morphinans, notably, morphinans having a hydrogenated N₁₇: norcodeine (FIG. 3A), norneopine (FIG. 3B) normorphine (FIG. 3C), norneomorphine (FIG. 3D), norcodeinone (FIG. 3E), norneopinone (FIG. 3F), normorphinone (FIG. 3G), norneomorphinone (FIG. 3H).

FIG. 4A-H depicts the chemical structures of certain morphinans, notably morphinans having a methylated N-oxidized N₁₇: codeine N-oxide (FIG. 4A), neopine N-oxide (FIG. 4B), morphine N-oxide (FIG. 4C), neomorphine N-oxide (FIG. 4D), codeinone N-oxide (FIG. 4E), neopinone N-oxide (FIG. 4F), morphinone N-oxide (FIG. 4G) and neomorphinone N-oxide (FIG. 4H).

FIG. 5A and FIG. 5B depicts HPLC traces showing the in-vitro production of neopine from codeine using codeine isomerase. The reaction was performed for varying amounts of time (right hand panels; t=1 min (Panel A); t=30 mins (Panel C); t=80 min (Panel E) and t=640 mins (Panel G)). The control using codeinone reductase is shown in the left hand panels; t=1 min (Panel B); t=30 mins (Panel D); t=80 min (Panel F) and t=640 mins (Panel H).

FIG. 6 depicts a comparison between the polynucleotide sequences of codeine isomerase (also set forth in SEQ.ID NO: 2) (sequence labeled “CDI”) and codeinone reductase, used as a control as further described in Example 1 (sequence labeled “COR 1.3”). Amino acids are numbered from the N-terminus.

FIG. 7A-B depicts HPLC traces showing the in-vivo production of neopine in E. coli from codeine using codeinone reductase (FIG. 7A) and codeine isomerase (FIG. 7B). The reaction was performed for varying amounts of time (t=12 hours (blue); t=24 hours (green); t=48 hours (orange); and t=72 hours (red)).

FIG. 8A-B depicts HPLC traces showing the in-vivo production of neopine in S. cerevisiae from codeine using codeinone reductase (FIG. 8A) and codeine isomerase (FIG. 8B). The reaction was performed for varying amounts of time (t=12 hours (blue); t=24 hours (green); t=48 hours (orange); and t=72 hours (red)).

FIG. 9 depicts HPLC traces showing the in-vitro production of neomorphine from morphine using codeine isomerase in the presence of NADP+, NADPH and in the absence of co-factor.

FIG. 10 depicts HPLC traces showing the in-vitro production of neopine from codeine using codeine isomerase in the presence of NADP+, NADPH and in the absence of co-factor.

FIG. 11 depicts HPLC traces showing the in-vitro production of neomorphine N-oxide from morphine N-oxide using codeine isomerase in the presence of NADP+, NADPH and in the absence of co-factor.

FIG. 12 depicts HPLC traces showing the in-vitro production of neopine N-oxide from codeine N-oxide using codeine isomerase in the presence of NADP+, NADPH and in the absence of co-factor.

FIG. 13 depicts a chemical reaction involving the conversion of codeine to neopine via intermediate morphinan compounds, neopinone and codeinone.

FIG. 14 depicts a chemical reaction involving the conversion of neopine from codeine using thebaine as a codeine precursor compound, and codeinone and neopinone as intermediate precursor compounds.

DETAILED DESCRIPTION OF THE DISCLOSURE

Various compositions and processes will be described below to provide an example of an embodiment of each claimed subject matter. No embodiment described below limits any claimed subject matter and any claimed subject matter may cover processes, compositions or systems that differ from those described below. The claimed subject matter is not limited to compositions or processes having all of the features of any one composition, system or process described below or to features common to multiple or all of the compositions, systems or processes described below. It is possible that a composition, system or process described below is not an embodiment of any claimed subject matter. Any subject matter disclosed in a composition, system or process described below that is not claimed in this document may be the subject matter of another protective instrument, for example, a continuing patent application, and the applicants, inventors or owners do not intend to abandon, disclaim or dedicate to the public any such subject matter by its disclosure in this document.
All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

Definitions

The term “morphinan”, as used herein, refers to a class of chemical compounds comprising the prototype chemical structure shown in FIG. 1A. Certain specific carbon and nitrogen atoms are referred to herein by reference to their position within the morphinan structure e.g. C₁, C₂, N₁₇etc. The pertinent atom numbering is shown in FIG. 1A
The term “furanyl-morphinan” as used herein refers to a class of chemical compounds comprising the prototype chemical structure shown in FIG. 1B. Furanyl-morphinans may be derived from morphinans by the formation of a tetrahydrofuranyl ring structure established by a bridging oxygen between C₄and C₅. It is noted that the tetrahydrofuranyl group may also be referred to as a 2,3 dihydrofuranyl ring structure due to benzene resonance.
The term “codeine” as used herein refers to a chemical compound having the structure set forth in FIG. 2A, and further represented by the chemical formula (III).
The term “neopine” as used herein refers to a chemical compound having the structure set forth in FIG. 2B, and further represented by the chemical formula (IV).
The term “morphine” as used herein refers to a chemical compound having the structure set forth in FIG. 2C.
The term “neomorphine” as used herein refers to a chemical compound having the structure set forth in FIG. 2D.
The term “codeinone” as used herein refers to a chemical compound having the structure set forth in FIG. 2E.
The term “neopinone” as used herein refers to a chemical compound having the structure set forth in FIG. 2F.
The term “morphinone” as used herein refers to a chemical compound having the structure set forth in FIG. 2G.
The term “neomorphinone” as used herein refers to a chemical compound having the structure set forth in FIG. 2H.
The term “norcodeine” as used herein refers to a chemical compound having the structure set forth in FIG. 3A.
The term “norneopine” as used herein refers to a chemical compound having the structure set forth in FIG. 3B.
The term “normorphine” as used herein refers to a chemical compound having the structure set forth in FIG. 3C.
The term “norneomorphine” as used herein refers to a chemical compound having the structure set forth in FIG. 3D.
The term “norcodeinone” as used herein refers to a chemical compound having the structure set forth in FIG. 3E.
The term “norneopinone” as used herein refers to a chemical compound having the structure set forth in FIG. 3F.
The term “normorphinone” as used herein refers to a chemical compound having the structure set forth in FIG. 3G.
The term “norneomorphinone” as used herein refers to a chemical compound having the structure set forth in FIG. 3H.
The term “codeine N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4A.
The term “neopine N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4B.
The term “morphine N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4C.
The term “neomorphine N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4D.
The term “codeinone N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4E.
The term “neopinone N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4F.
The term “morphinone N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4G.
The term “neomorphinone N-oxide” as used herein refers to a chemical compound having the structure set forth in FIG. 4H.
The term “oxo group” means a group represented by “C═O”.
The term “morphinan substrate” is any codeine isomerase or codeinone reductase substrate molecule, or precursor molecule thereof, that may be exogenously or endogenously provided to perform, in vivo or in vitro, a reaction which results in the conversion of the first morphinan into the second morphinan. In respect of the performance of in vitro reactions the morphinan substrate may be a first morphinan selected from the morphinans set forth in FIGS. 2A, 2C, 2E, 2G, 3A, 3C, 3E, 3G, 4A, 4C, 4E and 4G. In respect of the performance of in vivo reactions the morphinan substrate may be first morphinan selected from the morphinans set forth in FIGS. 2A, 2C, 2E, 2G, 3A, 3C, 3E, 3G, 4A, 4C, 4E and 4G, and furthermore the first morphinan may be a precursor of a first morphinan which can be metabolized by the cell to form one of the morphinans set forth in FIGS. 2A, 2C, 2E, 2G, 3A, 3C, 3E, 3G, 4A, 4C, 4E and 4G.
The terms “codeine isomerase” and “neopinone reductase”, which may be used interchangeably herein, refer to any and all enzymes comprising a sequence of amino acid residues which is (i) substantially identical to the amino acid sequences constituting any codeine isomerase polypeptide set forth herein, including, for example, SEQ. ID NO: 2, or (ii) encoded by a nucleic acid sequence capable of hybridizing under at least moderately stringent conditions to any nucleic acid sequence encoding any codeine isomerase polypeptide set forth herein, but for the use of synonymous codons.
The term “codeinone reductase” refers to any and all enzymes comprising a sequence of amino acid residues which is (i) substantially identical to the amino acid sequences constituting any codeinone reductase polypeptide set forth herein, including, for example, SEQ. ID NO: 10, or (ii) encoded by a nucleic acid sequence capable of hybridizing under at least moderately stringent conditions to any nucleic acid sequence encoding any codeinone reductase polypeptide set forth herein, but for the use of synonymous codons.
The term “6-O-demethylase” refers to any and all enzymes comprising a sequence of amino acid residues which is (i) substantially identical to the amino acid sequences constituting any 6-O-demethylase polypeptide set forth herein, including, for example, SEQ. ID NO: 22, or (ii) encoded by a nucleic acid sequence capable of hybridizing under at least moderately stringent conditions to any nucleic acid sequence encoding any 6-O-demethylase polypeptide set forth herein, but for the use of synonymous codons.
The term “nucleic acid sequence” as used herein refers to a sequence of nucleoside or nucleotide monomers consisting of naturally occurring bases, sugars and intersugar (backbone) linkages. The term also includes modified or substituted sequences comprising non-naturally occurring monomers or portions thereof. The nucleic acid sequences of the present disclosure may be deoxyribonucleic acid sequences (DNA) or ribonucleic acid sequences (RNA) and may include naturally occurring bases including adenine, guanine, cytosine, thymidine and uracil. The sequences may also contain modified bases. Examples of such modified bases include aza and deaza adenine, guanine, cytosine, thymidine and uracil, and xanthine and hypoxanthine.
The term “nucleic acid sequence encoding codeine isomerase”, “nucleic acid sequence encoding a codeine isomerase polypeptide”, nucleic acid sequence encoding a neopinone reductase” and “nucleic acid sequence encoding a neopinone reductase polypeptide” refer to any and all nucleic acid sequences encoding a codeine isomerase polypeptide, including, for example, SEQ. ID NO: 1. Nucleic acid sequences encoding a codeine isomerase polypeptide further include any and all nucleic acid sequences which (i) encode polypeptides that are substantially identical to the codeine isomerase polypeptide sequences set forth herein; or (ii) hybridize to any codeine isomerase nucleic acid sequences set forth herein under at least moderately stringent hybridization conditions or which would hybridize thereto under at least moderately stringent conditions but for the use of synonymous codons.
The term “nucleic acid sequence encoding codeinone reductase”, “nucleic acid sequence encoding a codeinone reductase polypeptide”, refer to any and all nucleic acid sequences encoding a codeinone reductase polypeptide, including, for example, SEQ. ID NO: 5. Nucleic acid sequences encoding a codeinone reductase polypeptide further include any and all nucleic acid sequences which (i) encode polypeptides that are substantially identical to the codeinone reductase polypeptide sequences set forth herein; or (ii) hybridize to any codeinone reductase nucleic acid sequences set forth herein under at least moderately stringent hybridization conditions or which would hybridize thereto under at least moderately stringent conditions but for the use of synonymous codons.
The term “nucleic acid sequence encoding 6-O-demethylase”, “nucleic acid sequence encoding a 6-O-demethylase polypeptide”, refer to any and all nucleic acid sequences encoding a codeinone reductase polypeptide, including, for example, SEQ. ID NO: 21. Nucleic acid sequences encoding a 6-O-demethylase polypeptide further include any and all nucleic acid sequences which (i) encode polypeptides that are substantially identical to the 6-O-demethylase polypeptide sequences set forth herein; or (ii) hybridize to any 6-O-demethylase nucleic acid sequences set forth herein under at least moderately stringent hybridization conditions or which would hybridize thereto under at least moderately stringent conditions but for the use of synonymous codons.
By the term “substantially identical” it is meant that two polypeptide sequences preferably are at least 70% identical, and more preferably are at least 85% identical and most preferably at least 95% identical, for example 96%, 97%, 98% or 99% identical. In order to determine the percentage of identity between two polypeptide sequences the amino acid sequences of such two sequences are aligned, using for example the alignment method of Needleman and Wunsch (J. Mol. Biol., 1970, 48: 443), as revised by Smith and Waterman (Adv. Appl. Math., 1981, 2: 482) so that the highest order match is obtained between the two sequences and the number of identical amino acids is determined between the two sequences. Methods to calculate the percentage identity between two amino acid sequences are generally art recognized and include, for example, those described by Carillo and Lipton (SIAM J. Applied Math., 1988, 48:1073) and those described in Computational Molecular Biology, Lesk, e.d. Oxford University Press, New York, 1988, Biocomputing: Informatics and Genomics Projects. Generally, computer programs will be employed for such calculations. Computer programs that may be used in this regard include, but are not limited to, GCG (Devereux et al., Nucleic Acids Res., 1984, 12: 387) BLASTP, BLASTN and FASTA (Altschul et al., J. Molec. Biol., 1990:215:403). A particularly preferred method for determining the percentage identity between two polypeptides involves the Clustal W algorithm (Thompson, J D, Higgines, D G and Gibson T J, 1994, Nucleic Acid Res 22(22): 4673-4680 together with the BLOSUM 62 scoring matrix (Henikoff S & Henikoff, J G, 1992, Proc. Natl. Acad. Sci. USA 89: 10915-10919 using a gap opening penalty of 10 and a gap extension penalty of 0.1, so that the highest order match obtained between two sequences wherein at least 50% of the total length of one of the two sequences is involved in the alignment.
By “at least moderately stringent hybridization conditions” it is meant that conditions are selected which promote selective hybridization between two complementary nucleic acid molecules in solution. Hybridization may occur to all or a portion of a nucleic acid sequence molecule. The hybridizing portion is typically at least 15 (e.g. 20, 25, 30, 40 or 50) nucleotides in length. Those skilled in the art will recognize that the stability of a nucleic acid duplex, or hybrids, is determined by the Tm, which in sodium containing buffers is a function of the sodium ion concentration and temperature (Tm=81.5° C.−16.6 (Log 10 [Na+])+0.41(% (G+C)−600/l), or similar equation). Accordingly, the parameters in the wash conditions that determine hybrid stability are sodium ion concentration and temperature. In order to identify molecules that are similar, but not identical, to a known nucleic acid molecule a 1% mismatch may be assumed to result in about a 1° C. decrease in Tm, for example if nucleic acid molecules are sought that have a >95% identity, the final wash temperature will be reduced by about 5° C. Based on these considerations those skilled in the art will be able to readily select appropriate hybridization conditions. In preferred embodiments, stringent hybridization conditions are selected. By way of example the following conditions may be employed to achieve stringent hybridization: hybridization at 5× sodium chloride/sodium citrate (SSC)/5×Denhardt's solution/1.0% SDS at Tm (based on the above equation) −5° C., followed by a wash of 0.2×SSC/0.1% SDS at 60° C. Moderately stringent hybridization conditions include a washing step in 3×SSC at 42° C. It is understood however that equivalent stringencies may be achieved using alternative buffers, salts and temperatures. Additional guidance regarding hybridization conditions may be found in: Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 1989, 6.3.1.-6.3.6 and in: Sambrook et al., Molecular Cloning, a Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989, Vol. 3.
The term “chimeric” as used herein in the context of nucleic acid sequences refers to at least two linked nucleic acid sequences which are not naturally linked. Chimeric nucleic acid sequences include linked nucleic acid sequences of different natural origins. For example a nucleic acid sequences constituting a yeast promoter linked to a nucleic acid sequence encoding a codeine isomerase or codeinone reductase protein is considered chimeric. Chimeric nucleic acid sequences also may comprise nucleic acid sequences of the same natural origin, provided they are not naturally linked. For example a nucleic acid sequence constituting a promoter obtained from a particular cell-type may be linked to a nucleic acid sequence encoding a polypeptide obtained from that same cell-type, but not normally linked to the nucleic acid sequence constituting the promoter. Chimeric nucleic acid sequences also include nucleic acid sequences comprising any naturally occurring nucleic acid sequences linked to any non-naturally occurring nucleic acid sequence.
The terms “substantially pure” and “isolated”, as may be used interchangeably herein describe a compound, e.g., a morphinan or a polypeptide, which has been separated from components that naturally accompany it. Typically, a compound is substantially pure when at least 60%, more preferably at least 75%, more preferably at least 90%, 95%, 96%, 97%, or 98%, and most preferably at least 99% of the total material (by volume, by wet or dry weight, or by mole percent or mole fraction) in a sample is the compound of interest. Purity can be measured by any appropriate method, e.g., in the case of polypeptides, by chromatography, gel electrophoresis or HPLC analysis.
The term “functional variant” as used herein in reference to nucleic acid sequences or polypeptide sequences refers to nucleic acid sequences or polypeptide sequences capable of performing the same function as one a noted nucleic acid sequence or polypeptide sequence. Thus, for example, a functional variant of the codeine isomerase polypeptide set forth in SEQ. ID NO: 2, refers to a polypeptide capable of performing the same function as the polypeptide set forth in SEQ. ID NO: 2.
The term “recovered” as used herein in association with an enzyme or protein or morphinan refers to a more or less pure form of the enzyme or protein or morphinan.
The term “in vivo” as used herein to describe methods of making morphinans refers to contacting a first morphinan with an enzyme capable of catalyzing conversion of a first morphinan within a living cell, including, for example, a microbial cell or a plant cell, to form a second morphinan.
The term “in vitro” as used herein to describe methods of making morphinans refers to contacting a first morphinan with an enzyme capable of catalyzing conversion of the first morphinan in an environment outside a living cell, including, without limitation, for example, in a microwell plate, a tube, a flask, a beaker, a tank, a reactor and the like, to form a second morphinan.
It should be noted that terms of degree such as “substantially”, “about” and “approximately” as used herein mean a reasonable amount of deviation of the modified term such that the end result is not significantly changed. These terms of degree should be construed as including a deviation of the modified term if this deviation would not negate the meaning of the term it modifies.
As used herein, the wording “and/or” is intended to represent an inclusive-or. That is, “X and/or Y” is intended to mean X or Y or both, for example. As a further example, “X, Y, and/or Z” is intended to mean X or Y or Z or any combination thereof.

General Implementation

As hereinbefore mentioned, the present disclosure relates to certain alkaloids belonging to the class of chemical compounds known as morphinans. The current disclosure further relates to certain enzymes capable of catalyzing reactions resulting in the conversion of a first morphinan into a second morphinan. The herein provided methods represent a novel and efficient means of making certain morphinans, including, in a preferred embodiment, neopine. The methods provided herein do not rely on chemical synthesis of the subject morphinans and may be conducted at commercial scale. To the best of the inventor's knowledge, the current disclosure provides for the first time a methodology to manufacture certain morphinans, including neopine, using living cells not normally capable of synthesizing such morphinans. Such cells may be used as a source whence these morphinans may economically be extracted. The morphinans produced in accordance with the present disclosure are useful inter alia in the manufacture of pharmaceutical compositions.
Accordingly, the present disclosure provides, in at least one aspect, a method of making a second morphinan having a C₇-C₈saturated carbon bond and a C₈-C₁₄mono-unsaturated carbon bond comprising:

- (a) providing a first morphinan having a C₇-C₈mono-unsaturated carbon bond and a C₈-C₁₄saturated carbon bond; and
- (b) contacting the first morphinan with a codeine isomerase capable of converting the first morphinan into the second morphinan.

In preferred embodiments the method further comprises a step
(c) recovering the second morphinan.
In preferred embodiments, the first morphinan and the second morphinan each possess a bridging oxygen atom between carbon atoms C₄and C₅forming a tetrahydrofuranyl ring within the morphinan structure, thus having the prototype chemical structure shown in FIG. 1B.
The present disclosure provides, in at least one aspect, a method of making a morphinan comprising:

- (b) providing a first morphinan;
- (b) contacting the first morphinan with a codeine isomerase or codeinone reductase capable of converting the first morphinan under conditions that permit the conversion of the first morphinan into the second morphinan;
  wherein the first morphinan has the chemical formula (I):

and
wherein the second morphinan has the chemical formula (II):
wherein, in the first and the second morphinan, R₁represents a hydroxyl group or a methoxy group; wherein in the first and the second morphinan R₂represents a hydroxyl group and R_2′ represents a hydrogen atom, or taken together, R₂and R_2′ form an oxo group; and wherein in the first and the second morphinan R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group, the nitrogen atom bonded to R₃is optionally in the form of an N-oxide.

Synthesis of Morphinans Comprising a Methylated N₁₇

In preferred embodiments hereof, the N₁₇of the first and second morphinan are methylated, as shown in compounds (V) and (VI), respectively:
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated, and R₁is a methoxy group, R₂is a hydroxyl group and R_2′ is a hydrogen atom, providing codeine (compound (III)) for the first morphinan and neopine (compound (IV)) for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated, and R₁is a hydroxyl group, R₂is a hydroxyl group and R_2′ is a hydrogen atom, providing morphine for the first morphinan and neomorphine for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated, and R₁is a methoxy group, and taken together, R₂and R_2′ form an oxo group, providing codeinone for the first morphinan and neopinone for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated, and R₁is a hydroxyl group, and taken together, R₂and R_2′ form an oxo group, providing morphinone for the first morphinan and neomorphinone for the second morphinan.
It is noted that in each of the foregoing embodiments, R₁in the first morphinan is identical to R₁in the second morphinan. Similarly, R₂and R_2′ in the first morphinan are identical to R₂and R_2′ in the second morphinan.

Synthesis of Morphinans Comprising a Hydrogenated N₁₇

In preferred embodiments hereof, the N₁₇of the first and second morphinan are hydrogenated as shown in compounds (VII) and (VIII), respectively:
In a further preferred embodiment, in the first and second morphinan the N₁₇is hydrogenated, and R₁is a methoxy group, R₂is a hydroxyl group and R_2′ is a hydrogen atom, providing norcodeine for the first morphinan and norneopine for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is hydrogenated, and R₁is a hydroxyl group, R₂is a hydroxyl group and R_2′ is a hydrogen atom, providing normorphine for the first morphinan and norneomorphine for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is hydrogenated, and R₁is a methoxy group, and taken together, R₂and R_2′ form an oxo group, providing norcodeinone for the first morphinan and norneopinone for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is hydrogenated, and R₁is a hydroxyl group, and taken together R₂and R_2′ form an oxo group, providing normorphinone for the first morphinan and norneomorphinone for the second morphinan.
It is noted that in each of the foregoing embodiments, R₁in the first morphinan is identical to R₁in the second morphinan. Similarly, R₂and R_2′ in the first morphinan are identical to R₂and R_2′ in the second morphinan.

Synthesis of Morphinans Comprising a Methylated and N-Oxidized N₁₇.

In preferred embodiments hereof, the N₁₇of the first and second morphinan are methylated and N-oxidized as shown in compounds (IX) and (X), respectively:
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated and N-oxidized, and R₁is a methoxy group, R₂is a hydroxyl group and R_2′ is a hydrogen atom, providing codeine N-oxide for the first morphinan and neopine N-oxide for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated and N-oxidized, and R₁is a hydroxyl group, R₂is a hydroxyl group and R_2′ is a hydrogen atom, providing morphine N-oxide for the first morphinan and neomorphine N-oxide for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated and N-oxidized, and R₁is a methoxy group, and taken together R₂and R_2′ form an oxo group, providing codeinone N-oxide for the first morphinan and neopinone N-oxide for the second morphinan.
In a further preferred embodiment, in the first and second morphinan the N₁₇is methylated and N-oxidized, and R₁is a hydroxyl group, and taken together R₂and R_2′ form an oxo group, providing morphinone N-oxide for the first morphinan and neomorphinone N-oxide for the second morphinan.
It is noted that in each of the foregoing embodiments, R₁in the first morphinan is identical to R₁in the second morphinan. Similarly, R₂and R_2′ in the first morphinan are identical to R₂and R_2′ in the second morphinan.
In order to convert the first morphinan to the second morphinan, the first morphinan is contacted with a codeine isomerase or a codeinone reductase under reaction conditions that permit the conversion of the first morphinan to the second morphinan. The codeine isomerase may be any codeine isomerase capable of converting the first morphinan to the second morphinan, including in preferred embodiments the codeine isomerase set forth in SEQ. ID NO: 2, and functional variants thereof. The codeinone reductase may be any codeinone reductase capable of converting the first morphinan to the second morphinan, including in preferred embodiments the codeinone reductase set forth in SEQ. ID NO: 10, and functional variants thereof. The reaction conditions may be any reaction conditions that permit the catalysis. The reaction conditions include in vivo or in vitro conditions, as hereinafter further detailed. The reaction conditions further typically include the presence of water and buffering agents, and the reaction is preferably conducted at neutral pH or mild basic pH (from approximately pH 7.5 to approximately pH 9.5). Further typically included are a reducing agent or an oxidizing agent. In particularly preferred embodiments, the oxidizing agent may be nicotine amide adenine dinucleotide phosphate (NAPP+). In further particularly preferred embodiments, the reducing agent is the reduced form of nicotine amide adenine dinucleotide phosphate (NADPH). In embodiments hereof, where codeine isomerase is used, when the reaction is conducted using NADP⁺, the pH is preferably selected to be approximately 7.5. When the reaction is conducted using NADPH, the pH is preferably selected to be approximately 9.0.
In certain embodiments, the first morphinan may be converted to the second morphinan via one or more intermediate morphinan compounds, wherein such intermediate morphinan compounds are morphinan compounds other than the first or second morphinan compound. In certain embodiments, the intermediate morphinan compound is a furanyl-morphinan, and the furanyl-morphinan is a compound other than the first or second morphinan. In certain embodiments, the intermediate morphinan has the chemical formula (XI):
wherein in each formula (XI) and (XII): R₁represents a hydroxyl group or a methoxy group; R₂represents a hydroxyl group and R_2′ represents a hydrogen atom, or taken together, R₂and R_2′ form an oxo group; and R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group, the nitrogen atom bonded to R₃is optionally in the form of an N-oxide, and wherein the intermediate morphinan compound is a compound other than the first or second morphinan compound.
The time period during which an intermediate morphinan compound exists may vary and may depend on the reaction conditions selected. Furthermore an equilibrium between the first morphinan, second morphinan and an intermediate morphinan compound may form wherein the reaction may comprise various amounts of the first morphinan, the second morphinan and, optionally, one or more intermediate morphinan compounds. The relative amounts of each of these compounds may vary depending on the reaction conditions selected. In general, in accordance herewith the molar fraction of the second morphinan, upon substantial completion of the reaction, is at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least, 95%, at least 99% or at least 99.9%.
In certain embodiments, the first morphinan is codeine and the second morphinan is neopine, and codeinone and neopinone are formed, as a first and second intermediate morphinan compound, respectively. The foregoing embodiment is further illustrated in FIG. 13. In embodiments hereof where one or more intermediate morphinan compounds are formed, no enzymes other than codeine isomerase or codeinone reductase are required to perform the reaction. Thus in accordance herewith, the conversion of the first morphinan into the second morphinan occurs in a manner wherein a codeinone reductase or a codeine isomerase are contacted with the first morphinan, and wherein the first morphinan is converted into the second morphinan without enzymatic compounds other than codeinone reductase or codeine isomerase.
In some embodiments, the reaction may be conducted by including in the reaction a precursor molecule of a first morphinan. In some embodiments, the precursor molecule is a morphinan other than the first or second morphinan. In some embodiments, the precursor molecule is a furanyl-morphinan other than the first or second morphinan.
In some embodiments, the precursor molecule has the chemical formula (XIII):
wherein, R₁represents a hydroxyl group or a methoxy group; wherein R₂represents a hydroxyl group or a methoxy group; and wherein R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group the nitrogen atom bonded to R₃is optionally in the form of an N-oxide, and wherein precursor molecule is a molecule other than the first or second morphinan.
In further embodiments, the reaction may be conducted by including in the reaction a precursor molecule of a first morphinan and one or more enzymes capable of converting the precursor molecule of the first morphinan into the first morphinan.
In embodiments encompassing the inclusion of a precursor molecule of a first morphinan, the conversion of a precursor molecule into the first morphinan may proceed via one or more intermediate precursor molecules.
In some embodiments, the intermediate precursor molecule is a morphinan other than the first or the second morphinan. In some embodiments, the intermediate precursor molecule is a furanyl-morphinan, other than the first or second morphinan.
In some embodiments, the intermediate precursor molecule has the chemical formula (XI) or (XII), wherein in each formula (XI) and (XII): R₁represents a hydroxyl group or a methoxy group; R₂represents a hydroxyl group and R_2′ represents a hydrogen atom, or taken together, R₂and R_2′ form an oxo group; and R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group, the nitrogen atom bonded to R₃is optionally in the form of an N-oxide, and wherein the intermediate precursor molecule is a morphinan other than the first or second morphinan.
In certain embodiments, the reaction may include a morphinan other than the first or the second morphinan, wherein the morphinan other than the first morphinan or the second morphinan is thebaine. In this embodiment, the reaction may further include a demethylase, for example an O-demethylase, capable of demethylating thebaine, including the 6-O-demethylase set forth in SEQ. ID NO: 22. In this embodiment, the precursor molecule, thebaine, may be converted into the intermediate precursor molecules neopinone and codeinone. This embodiment of the present disclosure is further illustrated in FIG. 14.
In certain embodiments, the reaction may include a morphinan other than the first or the second morphinan, wherein the morphinan other than the first morphinan or the second morphinan is oripavine. In this embodiment, the reaction may further include a demethylase, for example an O-demethylase, capable of demethylating oripavine. In this embodiment the precursor molecule, oripavine may be converted into the intermediate precursor molecules, neomorphinone and morphinone.
In certain embodiments, mixtures of enzymes may be used mixtures of two or more codeinone reductases, or two or more codeine isomerases, or a codeinone reductase and a codeine isomerase.
Thus it will be clear from the foregoing that the present disclosure includes embodiments wherein the first morphinan is provided by providing a precursor molecule to the first morphinan, and one or more enzymes capable of converting the precursor molecule into the first morphinan. This embodiment is further illustrated in Examples 2 and 3.
In other embodiments, the first morphinan is provided substantially free of other morphinans, including substantially free from precursor molecules to the first morphinan, and/or substantially free of enzymes capable of converting a precursor molecule to the first morphinan into the first morphinan.

In Vitro Synthesis of Morphinans

In accordance with certain aspects of the present disclosure, a first morphinan is brought in contact with catalytic quantities of the enzyme codeine isomerase or codeinone reductase under reaction conditions permitting an enzyme catalyzed chemical conversion of the first morphinan under in vitro reaction conditions. Under such in vitro reaction conditions the initial reaction constituents are provided in more or less pure form and are mixed under conditions that permit the chemical reaction to substantially proceed.
Substantially pure forms of the first morphinan may be purchased as a substantially pure chemical compound, chemically synthesized from precursor compounds, or isolated from natural sources including Papaver somniferum. Other plant species that may be used in accordance herewith to obtain the first morphinan include, without limitation, plant species belonging to the plant families of Eupteleaceae, Lardizabalaceae, Circaeasteraceae, Menispermaceae, Berberidaceae, Ranunculaceae, and Papaveraceae (including those belonging to the subfamilies of Pteridophylloideae, Papaveroideae and Fumarioideae) and further includes plants belonging to the genus Argemone, including Argemone mexicana (Mexican Prickly Poppy), plants belonging to the genus Berberis, including Berberis thunbergii (Japanese Barberry), plants belonging to the genus Chelidonium, including Chelidonium majus (Greater Celandine), plants belonging to the genus Cissampelos, including Cissampelos mucronata (Abuta), plants belonging to the genus Cocculus, including Cocculus trilobus (Korean Moonseed), plants belonging to the genus Corydalis, including Corydalis chelanthifolia (Ferny Fumewort), Corydalis cava; Corydalis ochotenis; Corydalis ophiocarpa; Corydalis platycarpa; Corydalis tuberosa; and Cordyalis bulbosa, plants belonging to the genus Eschscholzia, including Eschscholzia californica (California Poppy), plants belonging to the genus Glaucium, including Glaucium flavum (Yellowhorn Poppy), plants belonging to the genus Hydrastis, including Hydrastis canadensis (Goldenseal), plants belonging to the genus Jeffersonia, including Jeffersonia diphylla (Rheumatism Root), plants belonging to the genus Mahonia, including Mahonia aquifolium (Oregon Grape), plants belonging to the genus Menispermum, including Menispermum canadense (Canadian Moonseed), plants belonging to the genus Nandina, including Nandina domestica (Sacred Bamboo), plants belonging to the genus Nigella, including Nigella sativa (Black Cumin), plants belonging to the genus Papaver, including Papaver bracteatum (Persian Poppy), Papaver somniferum, Papaver cylindricum, Papaver decaisnei, Papaver fugax, Papaver nudicale, Papaver oreophyllum, Papaver orientale, Papaver paeonifolium, Papaver persicum, Papaver pseudo-orientale, Papaver rhoeas, Papaver rhopalothece, Papaver armeniacum, Papaver setigerum, Papaver tauricolum, and Papaver triniaefolium, plants belonging to the genus Sanguinaria, including Sanguinaria canadensis (Bloodroot), plants belonging to the genus Stylophorum, including Stylophorum diphyllum (Celandine Poppy), plants belonging to the genus Thalictrum, including Thalictrum flavum (Meadow Rue), plants belonging to the genus Tinospora, including Tinospora cordifolia (Heartleaf Moonseed), plants belonging to the genus Xanthoriza, including Xanthoriza simplicissima (Yellowroot) and plants belonging to the genus Romeria including Romeria carica.
More or less pure forms of the codeine isomerase enzyme or codeinone reductase may be obtained by isolation of these enzymes from natural sources, including, but not limited to, Papaver somniferum, Papaver bracteatum, Papaver nudicale, Papaver orientale and Papaver rhoeas, or the enzymes may be prepared recombinantly, or synthetically. Thus provided herein is further a method for preparing a codeine isomerase or a codeinone reductase comprising:

- (a) providing a chimeric nucleic acid molecule comprising as operably linked components:
  - (i) a nucleic acid sequence encoding a codeine isomerase or codeinone reductase; and
  - (ii) one or more a nucleic acid sequences capable of controlling expression in a host cell;
- (b) introducing the chimeric nucleic acid molecule into a host cell and growing the host cell to produce the codeine isomerase or codeinone reductase; and
- (c) recovering the codeine isomerase or codeinone reductase polypeptide from the host cell.

The nucleic acid sequence encoding codeine isomerase or codeinone reductase may be obtained from Papaver somniferum. Other plant species from which a nucleic acid encoding a codeine isomerase or codeinone reductase may be obtained in accordance herewith include, without limitation, plant species belonging to the plant families of Eupteleaceae, Lardizabalaceae, Circaeasteraceae, Menispermaceae, Berberidaceae, Ranunculaceae, and Papaveraceae (including those belonging to the subfamilies of Pteridophylloideae, Papaveroideae and Fumarioideae) and further includes plants belonging to the genus Argemone, including Argemone mexicana (Mexican Prickly Poppy), plants belonging to the genus Berberis, including Berberis thunbergii (Japanese Barberry), plants belonging to the genus Chelidonium, including Chelidonium majus (Greater Celandine), plants belonging to the genus Cissampelos, including Cissampelos mucronata (Abuta), plants belonging to the genus Cocculus, including Cocculus trilobus (Korean Moonseed), plants belonging to the genus Corydalis, including Corydalis chelanthifolia (Ferny Fumewort), Corydalis cava; Corydalis ochotenis; Corydalis ophiocarpa; Corydalis platycarpa; Corydalis tuberosa; and Cordyalis bulbosa, plants belonging to the genus Eschscholzia, including Eschscholzia californica (California Poppy), plants belonging to the genus Glaucium, including Glaucium flavum (Yellowhorn Poppy), plants belonging to the genus Hydrastis, including Hydrastis canadensis (Goldenseal), plants belonging to the genus Jeffersonia, including Jeffersonia diphylla (Rheumatism Root), plants belonging to the genus Mahonia, including Mahonia aquifolium (Oregon Grape), plants belonging to the genus Menispermum, including Menispermum canadense (Canadian Moonseed), plants belonging to the genus Nandina, including Nandina domestica (Sacred Bamboo), plants belonging to the genus Nigella, including Nigella sativa (Black Cumin), plants belonging to the genus Papaver, including Papaver bracteatum (Persian Poppy), Papaver somniferum, Papaver cylindricum, Papaver decaisnei, Papaver fugax, Papaver nudicale, Papaver oreophyllum, Papaver orientale, Papaver paeonifolium, Papaver persicum, Papaver pseudo-orientale, Papaver rhoeas, Papaver rhopalothece, Papaver armeniacum, Papaver setigerum, Papaver tauricolum, and Papaver triniaefolium, plants belonging to the genus Sanguinaria, including Sanguinaria canadensis (Bloodroot), plants belonging to the genus Stylophorum, including Stylophorum diphyllum (Celandine Poppy), plants belonging to the genus Thalictrum, including Thalictrum flavum (Meadow Rue), plants belonging to the genus Tinospora, including Tinospora cordifolia (Heartleaf Moonseed), plants belonging to the genus Xanthoriza, including Xanthoriza simplicissima (Yellowroot) and plants belonging to the genus Romeria including Romeria carica.
In preferred embodiments, the nucleic acid sequence encoding the codeine isomerase comprises the nucleic acid sequence set forth in SEQ. ID NO: 1.
In preferred embodiments, the nucleic acid sequence encoding the codeinone reductase comprises the nucleic acid sequence set forth in SEQ. ID NO: 5.
In further embodiments, the nucleic acid sequence encoding the codeinone reductase comprises SEQ. ID NO: 3; SEQ. ID NO: 4; SEQ. ID NO: 6; SEQ. ID NO: 7; SEQ. ID NO: 13; SEQ. ID NO: 15; SEQ. ID NO: 17; or SEQ. ID NO: 19.
Growth of the host cells leads to production of the codeine isomerase or codeinone reductase polypeptides. The polypeptides subsequently may be recovered, isolated and separated from other host cell components by a variety of different protein purification techniques including, e.g. ion-exchange chromatography, size exclusion chromatography, affinity chromatography, hydrophobic interaction chromatography, reverse phase chromatography, gel filtration, etc. Further general guidance with respect to protein purification may for example be found in: Cutler, P. Protein Purification Protocols, Humana Press, 2004, Second Ed. Thus substantially pure preparations of the codeine isomerase or codeinone reductase polypeptides may be obtained. The protein preparation thus obtained is capable of catalyzing a chemical reaction resulting into the formation of a second morphinan from a first morphinan. Accordingly, the present disclosure further provides compositions for making a morphinan comprising a polypeptide capable of, in a first morphinan having a mono-unsaturated C₇-C₈bond and a saturated C₈-C₁₄bond:

In accordance herewith in order to perform a reaction under in vitro conditions, a first morphinan is brought in contact with catalytic quantities of codeine isomerase or codeinone reductase, under reaction conditions permitting an enzyme catalyzed chemical conversion of the first morphinan. In preferred embodiments, the agents are brought in contact with each other and mixed to form a mixture. In preferred embodiments the mixture is an aqueous mixture comprising water and further optionally additional agents to facilitate enzyme catalysis, including buffering agents, salts, pH modifying agents. As hereinbefore mentioned it is particularly preferred that the reaction mixture comprises NADPH or NADP⁺. The reaction may be performed at a range of different temperatures. In preferred embodiments the reaction is performed at a temperature between about 18° C. and 37° C. Upon completion of the in vitro reaction the second morphinan may be obtained in more or less pure form.
In further embodiments, the reaction conditions may be arranged to include one or more enzymes capable of converting a precursor of first morphinan into the first morphinan, as well as the precursor to the first morphinan. Thus in certain embodiments, the reaction conditions may be arranged to include thebaine and a demethylase, capable of forming codeine from thebaine.

In Vivo Synthesis of Morphinans

In accordance with certain aspects of the present disclosure, a first morphinan is brought in contact with catalytic quantities of codeine isomerase or codeinone reductase under reaction conditions permitting an enzyme catalyzed chemical conversion of a first morphinan under in vivo reaction conditions. Under such in vivo reaction conditions living cells are modified in such a manner that they produce a second morphinan. In certain embodiments the living cells are microorganisms, including bacterial cells and fungal cells. In other embodiments the living cells are multicellular organisms, including plants and plant cell cultures.
In one embodiment, the living cells are selected to be host cells not naturally capable of producing the second morphinan. In another embodiment, the cells are able to produce the second morphinan but the levels at which the second morphinan are produced are lower than desirable, and by implementation of the methods of the present disclosure, the cells are modified such that the levels of the second morphinan in the cells are modulated relative to the levels in the unmodified cells. In a specific embodiment, the levels of the second morphinan in the modified cells are higher than the levels in the unmodified cells. Such cells include, without limitation, bacteria, yeast, other fungal cells, plant cells, or animal cells. The produced morphinan may be recovered from the modified cells.
Accordingly, provided herein still further, is a method for preparing a morphinan having chemical formula (II) comprising:

- (a) providing a chimeric nucleic acid molecule comprising as operably linked components:
  - (i) a nucleic acid sequence encoding a codeine isomerase or codeinone reductase polypeptide;
  - (ii) one or more nucleic acid sequences capable of controlling expression in a host cell;
- (b) introducing the chimeric nucleic acid molecule into a host cell that endogenously produces or is exogenously supplied with a morphinan substrate;
- (c) growing the host cell to produce codeine isomerase or codeinone reductase and to produce the morphinan having chemical formula (II); and
- (d) recovering morphinan having chemical formula (II) from the cell; and

wherein in formula (II), R₁represents a hydroxyl group or a methoxy group;
wherein R₂represents a hydroxyl group and R_2′ represents a hydrogen atom, or taken together, R₂and R_2′ form an oxo group; and wherein R₃represents a hydrogen atom, or a methyl group, wherein when R₃represents a methyl group, the nitrogen atom bonded to the R₃is optionally in the form of an N-oxide.
In preferred embodiments, the nucleic acid sequence encoding codeine isomerase is the sequence set forth herein as SEQ. ID NO: 1 or a functional variant thereof. In further preferred embodiments, the codeine isomerase is the polypeptide having the sequence set forth in SEQ. ID NO: 2, or a functional variant thereof.
In preferred embodiments, the nucleic acid sequence encoding codeinone reductase is the sequence set forth herein as SEQ. ID NO: 5 or a functional variant thereof. In further preferred embodiments, the codeinone reductase is the polypeptide having the sequence set forth in SEQ. ID NO: 10, or a functional variant thereof.
In further preferred embodiments, the nucleic acid sequence encoding codeinone reductase is the sequence set forth herein as SEQ. ID NO: 3; SEQ. ID NO: 4; SEQ. ID NO: 6; SEQ. ID NO: 7; SEQ. ID NO: 13; SEQ. ID NO: 15; SEQ. ID NO: 17; or SEQ. ID NO: 19, or a functional variant thereof. In further preferred embodiments, the codeinone reductase is the polypeptide having the sequence set forth in SEQ. ID NO: 8; SEQ. ID NO: 9; SEQ. ID NO: 11; SEQ. ID NO: 12; SEQ. ID NO: 14; SEQ. ID NO: 16; SEQ. ID NO: 18; or SEQ. ID NO: 20.
Referring to FIG. 6, in further preferred embodiments, the codeine isomerase that is used in accordance herewith is a codeine isomerase having a sequence substantially identical to SEQ.ID NO: 2 provided however, that such codeine isomerase has the following amino acid residues (AAs) in the denoted positions (wherein each of the positions is numbered consecutively from the N-terminus of the polypeptide chain): (1) AA25=valine; (2) AA29=glutamic acid; (3) AA58=threonine (4) AA178=threonine; (5) AA180=asparagine; (6) AA181=serine; (7) AA219=valine; (8) AA 220=glycine; (9) AA222=alanine; (10) AA225=threonine; (11) AA230=histidine; (12) AA268=alanine; (13) AA285=aspartic acid; (14) AA 301=alanine; (15) AA318=glycine; (16) AA319=glutamic acid; and (17) AA320=valine.
In further preferred embodiments, the codeine isomerase is codeine isomerase having a sequence substantially identical to SEQ.ID NO: 2, provided however, that the codeine isomerase comprises at least 16, at least 15, at least 14, at least 13, at least 12, at least 11, at least 10, at least 9, at least 8, at least 7, at least 6, at least 5, at least 4, at least 3, at least 2, or at least 1 of the following amino acids in the denoted positions (1) AA25=valine; (2) AA29=glutamic acid; (3) AA58=threonine (4) AA178=threonine; (5) AA180=asparagine; (6) AA181=serine; (7) AA219=valine; (8) AA 220=glycine; (9) AA222=alanine; (10) AA225=threonine; (11) AA230=histidine; (12) AA268=alanine; (13) AA285=aspartic acid; (14) AA 301=alanine; (15) AA318=glycine; (16) AA319=glutamic acid; and (17) AA320=valine.
The cells may be capable of endogenously producing a morphinan having chemical formula (I) wherein R₁represents a hydroxyl group or a methoxy group; wherein R₂represents a hydroxyl group and R_2′ represents a hydrogen atom, or taken together, R₂and R_2′ form an oxo group; and wherein R₃represents a hydrogen atom, or a methyl group, and wherein when R₃represents a methyl group, the nitrogen atom bonded to R₃is optionally in the form of an N-oxide. Alternatively such morphinan may be exogenously supplied to the cells.
In accordance herewith, the nucleic acid sequence encoding the codeine isomerase or codeinone reductase are linked to a nucleic acid sequence capable of controlling expression isomerase or codeinone reductase in a host cell. Accordingly, the present disclosure also provides a nucleic acid sequence encoding codeine isomerase and codeinone reductase linked to a promoter capable of controlling expression in a host cell. Nucleic acid sequences capable of controlling expression in host cells that may be used herein include any transcriptional promoter capable of controlling expression of polypeptides in host cells. Generally, promoters obtained from bacterial cells are used when a bacterial host is selected in accordance herewith, while a fungal promoter will be used when a fungal host is selected, a plant promoter will be used when a plant cell is selected, and so on. Further nucleic acid elements capable elements of controlling expression in a host cell include transcriptional terminators, enhancers and the like, all of which may be included in the chimeric nucleic acid molecules of the present disclosure. It will be understood by those ordinary skill in the art that operable linkage of nucleic acid sequences includes linkage of promoters and sequences capable of controlling expression to coding sequences in the 5′ to 3′ direction of transcription.
In accordance with the present disclosure, the chimeric nucleic acid molecules comprising a promoter capable of controlling expression in host cell linked to a nucleic acid sequence encoding codeine isomerase or a codeinone reductase, can be integrated into a recombinant expression vector which ensures good expression in the host cell. Accordingly, the present disclosure includes a recombinant expression vector comprising as operably linked components:

- (i) a nucleic acid sequence capable of controlling expression in a host cell; and
- (ii) a nucleic acid sequence encoding a codeine isomerase or a codeinone reductase

wherein the expression vector is suitable for expression in a host cell.
The term “suitable for expression in a host cell” means that the recombinant expression vector comprises the chimeric nucleic acid molecule of the present disclosure linked to genetic elements required to achieve expression in a host cell. Genetic elements that may be included in the expression vector in this regard include a transcriptional termination region, one or more nucleic acid sequences encoding marker genes, one or more origins of replication and the like. In preferred embodiments, the expression vector further comprises genetic elements required for the integration of the vector or a portion thereof in the host cell's genome, for example if a plant host cell is used the T-DNA left and right border sequences which facilitate the integration into the plant's nuclear genome.
Pursuant to the present disclosure the expression vector may further contain a marker gene. Marker genes that may be used in accordance with the present disclosure include all genes that allow the distinction of transformed cells from non-transformed cells, including all selectable and screenable marker genes. A marker gene may be a resistance marker such as an antibiotic resistance marker against, for example, kanamycin or ampicillin. Screenable markers that may be employed to identify transformants through visual inspection include β-glucuronidase (GUS) (U.S. Pat. Nos. 5,268,463 and 5,599,670) and green fluorescent protein (GFP) (Niedz et al., 1995, Plant Cell Rep., 14: 403).
One host cell that particularly conveniently may be used is Escherichia coli. The preparation of the E. coli vectors may be accomplished using commonly known techniques such as restriction digestion, ligation, gelectrophoresis, DNA sequencing, the Polymerase Chain Reaction (PCR) and other methodologies. A wide variety of cloning vectors are available to perform the necessary steps required to prepare a recombinant expression vector. Among the vectors with a replication system functional in E. coli, are vectors such as pBR322, the pUC series of vectors, the M13 mp series of vectors, pBluescript etc. Typically, these cloning vectors contain a marker allowing selection of transformed cells. Nucleic acid sequences may be introduced in these vectors, and the vectors may be introduced in E. coli by preparing competent cells, electroporation or using other well known methodologies to a person of skill in the art. E. coli may be grown in an appropriate medium including but not limited to, Luria-Broth medium and harvested. Recombinant expression vectors may readily be recovered from cells upon harvesting and lysing of the cells. Further, general guidance with respect to the preparation of recombinant vectors and growth of recombinant organisms may be found in, for example: Sambrook et al., Molecular Cloning, a Laboratory Manual, Cold Spring Harbor Laboratory Press, 2001, Third Ed.
Further included in the present disclosure are a host cell wherein the host cell comprises a chimeric nucleic acid molecule comprising as operably linked components one or more nucleic acid sequences encoding a codeine isomerase or codeinone reductase. As hereinbefore mentioned, the host cell is preferably a host cell capable of producing the first morphinan, but not capable of naturally producing the second morphinan. In another embodiment, the host cell is able to produce the second morphinan, however the levels of second morphinan produced are lower than desirable and the levels of second morphinan are modulated relative to the levels of morphinan in the unmodified cells. In yet other embodiments, the cells are unable to naturally produce the first morphinan, and the first morphinan is provided to the cells as part of the cell's growth medium. Cells that may be used in accordance herewith include, without limitation, bacterial, yeast, or other fungal cells, plant cells, animal cells, or synthetic cells.
The present disclosure still further provides compositions comprising nucleic acid sequences encoding a polypeptide capable of, in a first morphinan having a mono-unsaturated C₇-C₈bond and a saturated C₈-C₁₄bond:

- (i) saturating the C₇-C₈bond; and
- (ii) unsaturating the C₈-C₁₄bond, to form a second morphinan having a saturated C₇-C₈and a mono-unsaturated C₈-C₁₄bond. In a preferred embodiment, the nucleic acid sequence is SEQ. ID NO: 1. In a further preferred embodiment, the nucleic acid sequence is SEQ. ID NO: 5.

In further aspects, the nucleic acid sequences encoding codeine isomerase, including the nucleic acid sequence set forth in SEQ. ID NO: 1, and the nucleic acid sequences encoding codeinone reductase, including the nucleic acid sequence set forth in SEQ. ID NO: 1, and SEQ. ID NO: 5, respectively, may be used to produce a cell that has modulated levels of expression of codeine isomerase or codeinone reductase. Such a cell is preferably a plant cell natively expressing codeine isomerase or codeinone reductase and, more preferably, a plant cell obtained from a plant belonging to the plant families Papaveraceae, Lauraceae, Annonaceae, Euphorbiaceae or Moraceae, and, most preferably, the plant belongs to the species Papaver somniferum, Papaver bracteatum, Papaver nudicale, Papaver orientale or Papaver rhoeas. Thus the present disclosure further provides a method for modulating expression of nucleic acid sequences in a cell naturally expressing codeine isomerase or codeinone reductase comprising:

- (a) providing a cell naturally expressing codeine isomerase or codeinone reductase;
- (b) mutagenizing the cell;
- (c) growing the cell to obtain a plurality of cells; and
- (d) determining if the plurality of cells comprises a cell comprising modulated levels of codeine isomerase or codeinone reductase.

In preferred embodiments, the method further comprises a step (e) as follows:

- (e) selecting a cell comprising modulated levels of codeine isomerase or codeinone reductase and growing such cell to obtain a plurality of cells.

In further preferred embodiments, plant seed cells are used to perform the mutagenesis. Mutagenic agents that may be used are chemical agents, including without limitation, base analogues, deaminating agents, alkylating agents, intercalating agents, transposons, bromine, sodium azide, ethyl methanesulfonate (EMS) as well as physical agents, including, without limitation, radiation, such as ionizing radiation and UV radiation. Thus the present disclosure further provides a method for producing a seed setting plant comprising modulated expression of nucleic acid sequences in a cell naturally expressing codeine isomerase or codeinone reductase, the method comprising:

- (a) providing a seed setting plant naturally expressing codeine isomerase or codeinone reductase;
- (b) mutagenizing seed of the plant to obtain mutagenized seed;
- (c) growing the mutagenized seed into the next generation mutagenized plants capable of setting the next generation seed; and
- (d) obtaining the next generation seed, or another portion of the mutagenized plants, and analyzing if the next generation plants or next generation seed exhibits modulated codeine isomerase expression or modulated codeinone reductase expression.

In preferred embodiments, a plurality of generations of plants and/or seed may be obtained, and portions of plants and/or seed in any or all of such generations may be analyzed. Analysis is typically performed by comparing expression levels (e.g. RNA levels or protein levels) in non-mutagenized (wild type) plants or seed with expression in mutagenized plants or seed. In further preferred embodiments, the analysis in step (d) may be performed by analyzing heteroduplex formation between wildtype DNA and mutated DNA. Thus in preferred embodiments, the analysing in step (d) comprises

- i. extracting DNA from mutated plants;
- ii. amplifying a portion of the DNA comprising a nucleic acid sequence encoding codeine isomerase or codeinone reductase to obtain amplified mutated DNA;
- iii. extracting DNA from wild type plants;
- iv. mixing the DNA from wild type plants with the amplified mutated DNA and form a heteroduplexed polyucleotide;
- v. incubating the heteroduplexed polynucleotide with a single stranded restriction nuclease capable of restricting at a region of the heteroduplexed polynucleotide that is mismatched; and
- vi. determining the site of mismatch in the heteroduplex polynucleotide.

In preferred embodiments, the nucleic acid sequence encoding codeine isomerase that is used is set forth in SEQ. ID NO: 1.
In preferred embodiments, the nucleic acid sequence encoding codeinone reductase that is used is set forth in SEQ. ID NO: 5.
In further aspects, the nucleic acid sequences encoding codeine isomerase or codeinone reductase may be used to produce a cell that has modulated levels of expression of codeine isomerase or codeinone reductase by gene silencing. Thus the present disclosure further includes a method of reducing the expression of codeine isomerase or codeinone reductase in a cell, comprising:

- (a) providing a cell expressing codeine isomerase or codeinone reductase; and
- (b) silencing expression of codeine isomerase or codeinone reductase in the cell.

In preferred embodiments, the cell is a plant cell. Preferably, the plant is a member belonging to the plant families Papaveraceae, Lauraceae, Annonaceae, Euphorbiaceae or Moraceae, and more preferably, the plant belongs to the species Papaver somniferum, Papaver bracteatum, Papaver nudicale, Papaver orientale or Papaver rhoeas. A preferred methodology to silence codeine isomerase or codeinone reductase that is used is virus induced gene silencing (known to the art as VIGS). In general, in plants infected with unmodified viruses, the viral genome is targeted. However, when viral vectors have been modified to carry inserts derived from host genes (e.g. portions of sequences encoding codeine isomerase or codeinone reductase), the process is additionally targeted against the corresponding mRNAs. Thus the present disclosure further includes a method of producing a plant expressing reduced levels of codeine isomerase or codeinone reductase, the method comprising

- (a) providing a plant expressing codeine isomerase or codeinone reductase; and
- (b) reducing expression of codeine isomerase or codeinone reductase in the plant using virus induced gene silencing.

The hereinbefore mentioned methods to modulate expression levels of codeine isomerase or codeinone reductase may result in modulations in the levels of plant alkaloid morphinans, in plants including, without limitation, morphine, codeine, neopine. Thus the present disclosure includes the use of the methodologies to modify the levels of plant alkaloids in a plant naturally capable of producing plant alkaloids. Preferably, such plants belong to the plant families Papaveraceae, Lauraceae, Annonaceae, Euphorbiaceae or Moraceae, and more preferably, the plant belongs to the species Papaver somniferum, Papaver bracteatum, Papaver nudicale, Papaver orientale or Papaver rhoeas.
In yet further aspects of the present disclosure, the nucleic acid sequences encoding codeine isomerase or codeinone reductase may be used to genotype plants. Preferably, the plant is a member belonging to the plant families Papaveraceae, Lauraceae, Annonaceae, Euphorbiaceae or Moraceae, and more preferably, the plant belongs to the species Papaver somniferum, Papaver bracteatum, Papaver nudicale, Papaver orientale or Papaver rhoeas. In general, genotyping provides a means of distinguishing homologs of a chromosome pair and can be used to identify segregants in subsequent generations of a plant population. Molecular marker methodologies can be used for phylogenetic studies, characterizing genetic relationships among plant varieties, identifying crosses or somatic hybrids, localizing chromosomal segments affecting monogenic traits, map based cloning, and the study of quantitative inheritance. See, e.g., Plant Molecular Biology: A Laboratory Manual, Chapter 7, Clark, Ed., Springer-Verlag, Berlin (1997). For molecular marker methodologies, see generally, The DNA Revolution by Andrew H. Paterson 1996 (Chapter 2) in: Genome Mapping in Plants (ed. Andrew H. Paterson) by Academic Press/R. G. Landis Company, Austin, Tex., pp. 7-21. The particular method of genotyping in accordance with the present disclosure may involve the employment of any molecular marker analytic technique including, but not limited to, restriction fragment length polymorphisms (RFLPs). RFLPs reflect allelic differences between DNA restriction fragments caused by nucleotide sequence variability. As is known to those of skill in the art, RFLPs are typically detected by extraction of plant genomic DNA and digestion of the genomic DNA with one or more restriction enzymes. Typically, the resulting fragments are separated according to size and hybridized with a nucleic acid probe. Restriction fragments from homologous chromosomes are revealed. Differences in fragment size among alleles represent an RFLP. Thus, the present disclosure further provides a means to follow segregation of a portion or genomic DNA encoding codeine isomerase or codeinone reductase, as well as chromosomal nucleic acid sequences genetically linked to these codeine isomerase or codeinone reductase encoding nucleic acid sequences using such techniques as RFLP analysis. Linked chromosomal nucleic sequences are within 50 centiMorgans (cM), often within 40 or 30 cM, preferably within 20 or 10 cM, more preferably within 5, 3, 2, or 1 cM of a genomic nucleic acid sequence encoding codeine isomerase or codeinone reductase. Thus, in accordance with the present disclosure the codeine isomerase or codeinone reductase encoding sequences of the present disclosure may be used as markers to evaluate in a plant population the segregation of nucleic acid sequences genetically linked thereto. Preferably, the plant population comprises or consists of plants belonging to the plant families Papaveraceae, Lauraceae, Annonaceae, Euphorbiaceae or Moraceae, and more preferably, the plant population comprises or consists of plants belonging to the species Papaver somniferum, Papaver bracteatum Papaver nudicale, Papaver orientale or Papaver rhoeas.
In accordance with the present disclosure, the nucleic acid probes employed for molecular marker mapping of plant nuclear genomes selectively hybridize, under selective hybridization conditions, to a genomic sequence encoding codeine isomerase or codeinone reductase. In preferred embodiments, the probes are selected from the nucleic acid sequences encoding codeine isomerase or codeinone reductase provided by the present disclosure. Typically, these probes are cDNA probes. Typically these probes are at least 15 bases in length, more preferably at least 20, 25, 30, 35, 40, or 50 bases in length. Generally, however, the probes are less than about 1 kilobase in length. Preferably, the probes are single copy probes that hybridize to a unique locus in a haploid plant chromosome complement. Some exemplary restriction enzymes employed in RFLP mapping are EcoRI, EcoRv, and SstI. As used herein the term “restriction enzyme” includes reference to a composition that recognizes and, alone or in conjunction with another composition, cleaves a polynucleotide at a specific nucleotide sequence.
Other methods of differentiating polymorphic (allelic) variants of the nucleic acid sequences of the present disclosure can be used by utilizing molecular marker techniques well known to those of skill in the art, including, without limitation: 1) single stranded conformation analysis (SSCP); 2) denaturing gradient gel electrophoresis (DGGE); 3) RNase protection assays; 4) allele-specific oligonucleotides (ASOs); 5) the use of proteins which recognize nucleotide mismatches, such as the E. coli mutS protein; and 6) allele-specific PCR. Other approaches based on the detection of mismatches between the two complementary DNA strands include, without limitation, clamped denaturing gel electrophoresis (CDGE); heteroduplex analysis (HA), and chemical mismatch cleavage (CMC). Thus, the present disclosure further provides a method of genotyping comprising the steps of contacting, under stringent hybridization conditions, a sample suspected of comprising a nucleic acid encoding codeine isomerase or codeinone reductase, with a nucleic acid probe capable of hybridizing thereto. Generally, the sample is a plant sample; preferably, a sample suspected of comprising a Papaver somniferum nucleic acid sequence encoding codeine isomerase or codeinone reductase (e.g., gene, mRNA). The nucleic acid probe selectively hybridizes, under stringent conditions, to a subsequence of the nucleic acid sequence encoding codeine isomerase or codeinone reductase comprising a polymorphic marker. Selective hybridization of the nucleic acid probe to the polymorphic marker nucleic acid sequence yields a hybridization complex. Detection of the hybridization complex indicates the presence of that polymorphic marker in the sample. In preferred embodiments, the nucleic acid probe comprises a portion of a nucleic acid sequence encoding codeine isomerase or codeinone reductase.

Use of Morphinans

The morphinans obtained in accordance with the present disclosure may be formulated for use as a pharmaceutical drug, therapeutic agent or medicinal agent. Thus the present disclosure further includes a pharmaceutical composition comprising a morphinan prepared in accordance with the methods of the present disclosure. Pharmaceutical compositions comprising a morphinan in accordance with the present disclosure preferably further comprise vehicles, excipients and auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like. These vehicles, excipients and auxiliary substances are generally pharmaceutical agents that may be administered without undue toxicity. Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol and ethanol. Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, benzoates, and the like. It is also preferred, although not required, that the preparation will contain a pharmaceutically acceptable excipient that serves as a stabilizer. Examples of suitable carriers that also act as stabilizers for peptides include, without limitation, pharmaceutical grades of dextrose, sucrose, lactose, sorbitol, inositol, dextran, and the like. Other suitable carriers include, again without limitation, starch, cellulose, sodium or calcium phosphates, citric acid, glycine, polyethylene glycols (PEGs), and combinations thereof. The pharmaceutical composition may be formulated for oral and intravenous administration and other routes of administration as desired. Dosing may vary and may be optimized using routine experimentation.
In further embodiments, the present disclosure provides methods for treating a patient with a pharmaceutical composition comprising a morphinan prepared in accordance with the present disclosure. Accordingly, the present disclosure further provides a method for treating a patient with a morphinan prepared according to the methods of the present disclosure, said method comprising administering to the patient a composition comprising a morphinan, wherein the morphinan is administered in an amount sufficient to ameliorate a medical condition in the patient.

EXAMPLES

Hereinafter are provided examples of specific embodiments for performing the methods of the present disclosure, as well as embodiments representing the compositions of the present disclosure. The examples are provided for illustrative purposes only, and are not intended to limit the scope of the present disclosure in any way.

Example 1—In Vitro Production of Neopine from Codeine

This example illustrates the in vitro production of neopine from codeine using codeine isomerase and codeinone reductase from Papaver somniferum.
E. coli cells were transformed with a nucleic acid sequence construct comprising SEQ. ID NO: 1 encoding a codeine isomerase having SEQ. ID NO:2, and or codeinone reductase comprising SEQ. ID NO: 5 encoding a codeinone reductase having SEQ. ID NO: 10. The polypeptide further was designed to comprise a histidine tag. Cells were grown and the codeine isomerase and codeinone reductase were isolated by affinity purification using the histidine tag. In order to assay for activity of the enzyme, codeine (15 μmol), NADP (1.8 μmol), and glycine buffer (1.8 mmol; pH 9.00) were incubated with the enzyme in a total volume of 10 mls under mild agitation at 30° C., before extraction at various time points (t=1 min; t=30 min; t=80 min and t=640 min) with two volumes (20 ml) of CHCl₃. The volume of the combined organic phase was reduced in vacuo and resolved using HPLC.
The results are shown in FIG. 5. It is noted that at retention time 1.5 mins, the codeine isomerase preparations yields substantial quantities of neopine, particularly following incubation for 640 mins. Smaller quantities of neopine were observed in the codeinone reductase preparations.

Example 2—In Vivo Production of Neopine in E. coli

This example illustrates the in vivo production in E. coli of neopine from codeine using codeine isomerase from Papaver somniferum.
Cloning of Papaver somniferum Thebaine 6-O-Demethylase (T6ODM) with Either COR1.3 or CDI—Full-length coding region of T6ODM (SEQ. ID NO: 21) was amplified using Q5 Taq (NEB) with a FLAG sequence at the 5′ end and subcloned into the E. coli expression vector pACE (MultiColi, Geneva-Biotech). CDI or COR1.3 were subcloned into the pACE vector using similar approach with a 5′ His-tag sequence. The cassette of T7_pro-CDI-T7_teror T7_pro-CDI-T7_terwas obtained via restriction digestion of the corresponding pACE construct using I-CeuI and BstXI enzymes. The construct of pACE-T6ODM was digested with only I-CeuI serving as the accepting vector. The insert, i.e. T7_pro-CDI-T7_teror T7_pro-CDI-T7_terwas ligated into pACE-T6ODM using T4 DNA ligase (NEB). The final constructs were designated as pACE-T6ODM-CDI and pACE-T6ODM-COR1.3, which were then individually transformed into E. coli strain Rosetta (DE3) for expression. Expression of T6ODM, COR1.3 and CDI were confirmed by immunoblot analysis.
In Vivo Feeding Experiments—Single colony of E. coli strain harboring pACE-T6ODM-CDI or pACE-T6ODM-COR1.3 was cultured in LB medium at 30° C. for overnight. Overnight cultures were inoculate in fresh LB medium to an OD₆₀₀of 0.2 and grown until an OD₆₀₀of 0.8 at 37° C. A 100 μl-aliquote of the individual cultures was then supplemented with 0.2 mM IPTG, 0.15 mM thebaine, 10 mM sodium ascorbate, 10 mM 2-oxoglutarate and 1.8 mM iron (II) sulfate and grown for 12, 24, 48 and 72 h. The supernatant was collected and diluted in methanol. An empty vector strain was used as a negative control.
LC-MS/MS Analysis—Products in the culture medium derived from thebaine were analyzed using a 6410 Triple Quadruple LC-MS/MS (Agilent) for identification and quantification. Liquid chromatography was carried out using a Poroshell 120 SB C18 column (2.1×50 mm, 2.7 μm particle size; Agilent) at a flow rate of 0.6 mL min⁻¹. Liquid chromatography was initiated at 100% solvent A (10 mM ammonium acetate, pH5.5, 5% acetonitrile), ramped to 60% solvent B (acetonitrile) using a linear gradient over 8 min, further ramped to 99% solvent B using a linear gradient over 2 min, held constant at 99% solvent B for 1 min and returned to original conditions over 0.1 min for a 3 min equilibration period. Eluate was applied to the mass analyzer using an electrospray ionization probe operating in positive mode with the following conditions: capillary voltage, 4000 V; fragmentor voltage, 100 V; source temperature, 350° C.; nebulizer pressure, 50 PSI; gas flow, 10 L/min. For full-scan analysis, quadrupole 1 and 2 were set to RF only, whereas the third quadrupole scanned from 200-700 m/z. Positive-mode electrospray ionization (ESI [+]), collision-induced dissociation (CID) spectra were analyzed, the precursor m/z was selected in quadrupole 1 and collision energy of 30 eV was applied in quadrupole 2 and an argon collision gas pressure of 1.8×10⁻³torr. The resulting MS²fragments were resolved by quadrupole 3 scanning from 40 m/z to 2 m/z greater than the precursor ion m/z. Produce Compounds were identified based on retention times and ESI [+]-CID spectra compared with authentic standards or compared with previously published spectra.
Results—Feeding thebaine to pACE-T6ODM-COR1.3 resulted in the formation of primarily codeine over 24-hour time course. After 24 h incubation until 72 h, neopine was the major product while the amount of codeine continued to decline (FIG. 7A). In contrast, feeding thebaine to pACE-T6ODM-CDI resulted in the formation of primarily neopine over the 72-hour time course (FIG. 7B).

Example 3—In Vivo Production of Neopine in Yeast

This example illustrates the in vivo production in yeast (Saccharomyces cerevisiae) of neopine from codeine using codeine isomerase from Papaver somniferum.
Cloning of Papaver somniferum Thebaine 6 O-Demethylase (T6ODM) with COR1.3 and CDI—Full-length coding regions of T6ODM (see: SEQ. ID NO: 21), Gal10-Gal1 promoter region and PsCOR1.3 were amplified using PfuTurbo Hotstart DNA polymerase (Agilent). The PCR products were cloned to pCfB259 using the USER cloning system. The construct was designated pCfB259-T6ODM-COR1.3. Similarly, full-length coding regions of T6ODM, Gal10-Gal1 promoter region and CDI were amplified and cloned into pCfB259, and the construct was designated pCfB259-T6ODM-CDI. The two constructs were independently transformed into yeast strain CENPK102-5B and integrated to yeast chromosome. Expression of T6ODM, COR1.3 and CDI were confirmed by immunoblot analysis. The yeast strains were designated CENPK102-5B (T6ODM-COR1.3) and CENPK102-5B (T6ODM-CDI).
In Vivo Feeding Experiments—Yeast strains CENPK102-5B (T6ODM-COR1.3) and CENPK102-5B (T6ODM-CDI) were cultured in SC growth medium (leucine dropout, 2% dextrose) and incubated at 30° C. for overnight. Cultures were then back-diluted 20× into SC medium (leucine dropout, 2% galactose) containing 200 μM thebaine and 50 mM 2-oxoglutarate (Sigma). Strains were grown for 12, 24, 48 and 72 h, and supernatant was collected and diluted in methanol. An empty vector strain was used as a negative control.
LC-MS/MS Analysis—Products in the culture medium derived from thebaine were analyzed using a 6410 Triple Quadruple LC-MS/MS (Agilent) for identification and quantification. Liquid chromatography was carried out using a Poroshell 120 SB C18 column (2.1×50 mm, 2.7 μm particle size; Agilent) at a flow rate of 0.7 mL min⁻¹. Liquid chromatography was initiated at 100% solvent A (1% formic acid), ramped to 60% solvent B (acetonitrile) using a linear gradient over 6 min, further ramped to 99% solvent B using a linear gradient over 1 min, held constant at 99% solvent B for 1 min and returned to original conditions over 0.1 min for a 3.9 min equilibration period. Eluate was applied to the mass analyzer using an electrospray ionization probe operating in positive mode with the following conditions: capillary voltage, 4000 V; fragmentor voltage, 100 V; source temperature, 350° C.; nebulizer pressure, 50 PSI; gas flow, 10 L/min. For full-scan analysis, quadrupole 1 and 2 were set to RF only, whereas the third quadrupole scanned from 200-700 m/z. Positive-mode electrospray ionization (ESI [+]), collision-induced dissociation (CID) spectra were analyzed, the precursor m/z was selected in quadrupole 1 and collision energy of 30 eV was applied in quadrupole 2 and an argon collision gas pressure of 1.8×10⁻³torr. The resulting MS²fragments were resolved by quadrupole 3 scanning from 40 m/z to 2 m/z greater than the precursor ion m/z. Produce Compounds were identified based on retention times and ESI [+]-CID spectra compared with authentic standards or compared with previously published spectra.
Results—Feeding thebaine to CENPK102-5B (T6ODM-COR1.3) resulted in the formation of codeine and neopine in similar quantities, slightly favoring the accumulation of codeine, over the 72-hour time course (FIG. 8A). In contrast, feeding thebaine to CENPK102-5B (T6ODM-CDI) resulted in the formation of primarily neopine over the 72-hour time course (FIG. 8B).

Example 4—Production of Neomorphine Using Morphine as a Substrate

This example illustrates the in vitro production of neomorphine from morphine using codeine isomerase from Papaver somniferum.
Codeine isomerase preparations were obtained from E. coli recombinantly expressing codeine isomerase, as described in Example 1. Morphine substrate was incubated with the enzyme, in the presence of NADPH and NADP+ and the resulting reaction products were evaluated. In order to assay for activity of the enzyme, substrate (15 μmol), NADP (1.8 μmol), and glycine buffer (1.8 mmol; pH 9.00) were incubated with the enzyme in a total volume of 10 mls under mild agitation at 30° C., before extraction at time point t=640 min with two volumes (20 ml) of CHCl₃. The volume of the combined organic phase was reduced in vacuo and resolved using HPLC.
The results are shown in FIG. 9.

Example 5—Production of Neopine Using Codeine as a Substrate

This example illustrates the in vitro production of neopine from codeine using codeine isomerase from Papaver somniferum.
Codeine isomerase preparations were obtained from E. coli recombinantly expressing codeine isomerase, as described in Example 1. Codeine-substrate was incubated with the enzyme, in the presence of NADPH and NADP⁺ and the resulting reaction products were evaluated. In order to assay for activity of the enzyme, substrate (15 μmol), NADP (1.8 μmol), and glycine buffer (1.8 mmol; pH 9.00) were incubated with the enzyme in a total volume of 10 mls under mild agitation at 30° C., before extraction at time point t=640 min with two volumes (20 ml) of CHCl₃. The volume of the combined organic phase was reduced in vacuo and resolved using HPLC.
The results are shown in FIG. 10.

Example 6—Production of Neomorphine N-Oxide Using Morphine N-Oxide as a Substrate

This example illustrates the in vitro production of neomorphine N-oxide from morphine N-oxide using codeine isomerase from Papaver somniferum.
Codeine isomerase preparations were obtained from E. coli recombinantly expressing codeine isomerase, as described in Example 1. Morphine N-oxide substrate was incubated with the enzyme, in the presence of NADPH and NADP⁺ and the resulting reaction products were evaluated. In order to assay for activity of the enzyme, substrate (15 μmol), NADP (1.8 μmol), and glycine buffer (1.8 mmol; pH 9.00) were incubated with the enzyme in a total volume of 10 mls under mild agitation at 30° C., before extraction at time point t=640 min with two volumes (20 ml) of CHCl₃. The volume of the combined organic phase was reduced in vacuo and resolved using HPLC.
The results are shown in FIG. 11.

Example 7—Production of Neopine N-Oxide Using Codeine N-Oxide as a Substrate

This example illustrates the in vitro production of neopine N-oxide from codeine N-oxide using codeine isomerase from Papaver somniferum.
Codeine isomerase preparations were obtained from E. coli recombinantly expressing codeine isomerase, as described in Example 1. Codeine N-oxide substrate was incubated with the enzyme, in the presence of NADPH and NADP+ and the resulting reaction products were evaluated. In order to assay for activity of the enzyme, substrate (15 μmol), NADP (1.8 μmol), and glycine buffer (1.8 mmol; pH 9.00) were incubated with the enzyme in a total volume of 10 mls under mild agitation at 30° C., before extraction at time point t=640 min with two volumes (20 ml) of CHCl₃. The volume of the combined organic phase was reduced in vacuo and resolved using HPLC.
The results are shown in FIG. 12.
While the present invention has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the invention is not limited to the disclosed examples. To the contrary, the invention is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.
All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

SUMMARY OF SEQUENCES

SEQ. ID NO: 1 and 2 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of a codeine isomerase polypeptide of Papaver somniferum.
SEQ. ID NO: 3, 4, 5, 6 and 7 and SEQ. ID NO: 8, 9, 10, 11 and 12 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of codeinone reductase polypeptides of Papaver somniferum.
SEQ. ID NO: 13; and SEQ. ID NO: 14 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of a codeinone reductase polypeptide of Papaver rhoeas.
SEQ. ID NO: 15; and SEQ. ID NO: 16 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of a codeinone reductase polypeptide of Papaver orientale.
SEQ. ID NO: 17; and SEQ. ID NO: 18 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of a codeinone reductase polypeptide of Papaver nudicale.
SEQ. ID NO: 19; and SEQ. ID NO: 20 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of a codeinone reductase polypeptide of Papaver bracteatum.
SEQ. ID NO: 21; and SEQ. ID NO: 22 set forth the nucleotide sequence and deduced amino acid sequence, respectively, of a 6-O-demethylase polypeptide of Papaver somniferum.

Claims

1. An isolated nucleic acid sequence encoding a polypeptide comprising SEQ. ID. NO: 2 or a polypeptide substantially identical thereto, wherein SEQ. ID NO: 2 is capable of, in a first morphinan having a mono-unsaturated C₇-C₈bond and a saturated C₈-C₁₄bond:

(i) saturating the C₇-C₈bond; and

(ii) unsaturating the C₈-C₁₄bond, to form a second morphinan having a saturated C₇-C₈and a mono-unsaturated C₈-C₁₄bond.

2. The isolated nucleic acid sequence according to claim 1 encoding the polypeptide substantially identical to SEQ ID NO:2, wherein the polypeptide comprises at least 16, at least 15, at least 14, at least 13, at least 12, at least 11, at least 10, at least 9, at least 8, at least 7, at least 6, at least 5, at least 4, at least 3, at least 2, or at least 1 of the following amino acids in the following positions in SEQ ID NO:2 (1) AA25=valine; (2) AA29=glutamic acid; (3) AA58=threonine (4) AA178=threonine; (5) AA180=asparagine; (6) AA181=serine; (7) AA219=valine; (8) AA 220=glycine; (9) AA222=alanine; (10) AA225=threonine; (11) AA230=histidine; (12) AA268=alanine; (13) AA285=aspartic acid; (14) AA 301=alanine; (15) AA318=glycine; (16) AA319=glutamic acid; and (17) AA320=valine.

3. The isolated nucleic acid sequence according to claim 1 encoding the polypeptide substantially identical to SEQ ID NO:2, wherein the polypeptide comprises the following amino acid residues in the following positions in SEQ ID NO: 2 (1) AA25=valine; (2) AA29=glutamic acid; (3) AA58=threonine (4) AA178=threonine; (5) AA180=asparagine; (6) AA181=serine; (7) AA219=valine; (8) AA 220=glycine; (9) AA222=alanine; (10) AA225=threonine; (11) AA230=histidine; (12) AA268=alanine; (13) AA285=aspartic acid; (14) AA 301=alanine; (15) AA318=glycine; (16) AA319=glutamic acid; and (17) AA320=valine.

4. The isolated nucleic acid sequence according to claim 1, wherein the nucleic acid sequence comprises SEQ. ID NO: 1.

5. The isolated nucleic acid sequence according to claim 1 wherein the polypeptide substantially identical to SEQ ID NO:2 has at least 98% identity with SEQ ID NO:2.

6. The isolated nucleic acid sequence according to claim 1 wherein the polypeptide substantially identical to SEQ ID NO:2 has at least 99% identity with SEQ ID NO:2.

7. The isolated nucleic acid sequence according to claim 1, wherein the first morphinan has the chemical formula (V)

and wherein the second morphinan has the chemical formula (VI)

and wherein in the first and second morphinan R₁is a methoxy group, R₂is a hydroxyl group and R_2′ a hydrogen atom.

8. The isolated nucleic acid sequence according to claim 1, wherein the first morphinan has the chemical formula (V)

and wherein the second morphinan has the chemical formula (VI)

and wherein in the first and second morphinan R₁is a hydroxyl group, R₂is a hydroxyl group and R_2′ is a hydrogen atom.

9. The isolated nucleic acid sequence according to claim 1, wherein the first morphinan has the chemical formula (VII)

and wherein the second morphinan has the chemical formula (VIII)

and wherein in the first and second morphinan R₁is a methoxy group, R₂is a hydroxyl group and R_2′ is a hydrogen atom.

10. The isolated nucleic acid sequence according to claim 1, wherein the first morphinan has the chemical formula (VII)

and wherein the second morphinan has the chemical formula (VIII)

11. The isolated nucleic acid sequence according to claim 1, wherein the first morphinan has the chemical formula (IX)

and wherein the second morphinan has the chemical formula (X)

12. The isolated nucleic acid sequence according to claim 1, wherein the first morphinan has the chemical formula (IX)

and wherein the second morphinan has the chemical formula (X)

13. A chimeric nucleic acid sequence comprising as operably linked components:

(i) a nucleic acid sequence according to claim 1; and

(ii) one or more nucleic acid sequences capable of controlling expression in a host cell.

14. A recombinant expression vector comprising the chimeric nucleic acid sequence according to claim 13.

15. A host cell comprising the chimeric nucleic acid sequence according to claim 13.

16. A host cell according to claim 15, wherein the host cell is a microbial cell.

17. A host cell according to claim 16, wherein the host cell is a plant cell.

18. A host cell according to claim 17 wherein the microbial cell is a yeast cell.

19. A host cell according to claim 16 wherein the microbial cell is an Escherichia coli cell.

20. A host cell according to claim 17 wherein the plant cell is a Papaver cell.