austlii:cth/APO/2025/38
General information, not legal advice.
APO
2025-11-04
Original judgment source is linked above.
Title: Methods of producing nor-opioid and nal-opioid benzylisoquinoline alkaloids
Medicinal opioids are used for treating moderate to severe pain, but may exhibit addictive properties. Due to the mechanism by which medicinal opioids relieve pain, these medications are among the most effective painkillers in modern medicine. Additionally, however, medicinal opioids are also widely abused. In addressing the use of medicinal opioids, policy makers are tasked with balancing the under-treatment of pain, while mitigating the risk for opioid abuse. Pharmacotherapies have proven effective in treating and preventing opioid addiction but the high cost of these therapeutics is a limiting factor in the scope and reach of treatment programs.
The present disclosure provides methods for demethylating a first opioid to a second opioid. The present disclosure further provides methods for demethylating an opioid to a nor-opioid. Additionally, the present disclosure provides methods for altering an opioid to a nal-opioid. Further, the present disclosure provides engineered cells for producing a nor-opioid from an opioid present within the engineered cell. The present disclosure also provides engineered cells for producing a nal-opioid from a nor-opioid present within the engineered cell.
An aspect of the disclosure provides a method for demethylating a first opioid to a second opioid. The method comprises contacting the first opioid with at least one enzyme, wherein contacting the first opioid with the at least one enzyme converts the first opioid to a second opioid through loss of an O-linked methyl group, wherein the first opioid is not selected from the group consisting of codeine and thebaine.
Another aspect of the disclosure provides a method of demethylating an opioid to a nor-opioid. The method comprises contacting the first opioid with at least one enzyme, wherein contacting the first opioid with the at least one enzyme converts the first opioid to a second opioid through loss of an O-linked methyl group. The method also comprises contacting the second opioid with at least one enzyme, wherein contacting the opioid with the at least one enzyme converts the second opioid to a nor-opioid through loss of an N-linked methyl group.[2]
[00345] To identify engineered enzymes with improved O-demethylation activity, sequences encoding enzymes listed in Table 3 were subjected to random mutagenesis and then screened via a high-throughput colorimetric assay. Initial libraries were generated by error-prone PCR using Mutazyme II (Agilent Technologies), and variants were cloned into the pA24 (or similar) vector by gap repair in the Cen.PK2 screening host. Strains expressing mutated enzymes, with either individual mutations or combinations of mutations introduced by gene shuffling or other methods, were grown in selective medium in 96-well plate format under varying fermentation conditions (different media components, pH, and temperature, for example), pelleted, and lysed by glass bead disruption. Lysates were incubated with substrates (listed in FIG. 23) and assayed for formaldehyde production in the purpald assay. Enzymes with improved O-demethylation activity were verified by directly measuring O-demethylated product (oxymorphone, for example) formation in the culture medium by LC-MS.
[00348] To identify engineered enzymes with improved N-demethylation activity, sequences encoding enzymes listed in Table 4 were subjected to random mutagenesis and then screened via a high-throughput colorimetric assay. Initial libraries were generated by error-prone PCR using Mutazyme II (Agilent Technologies), and variants were cloned into the pA24 (or similar) vector by gap repair in the Cen.PK2 screening host. Strains expressing mutated enzymes, with either individual mutations or combinations of mutations introduced by gene shuffling or other methods, were grown in selective medium in 96-well plate format under varying fermentation conditions (different media components, pH, and temperature, for example), pelleted, and lysed by glass bead disruption. Lysates were incubated with substrates (listed in FIG. 24) and assayed for formaldehyde production in the purpald assay. Enzymes with improved N-demethylation activity were verified by direct measurement of N-demethylated product (noroxymorphone, for example) formation in the culture medium by LC-MS.
[00351] To identify engineered enzymes with improved BIA modifying activity, sequences encoding enzymes listed in Table 5 were subjected to random mutagenesis and then screened via a high-throughput colorimetric assay. Initial libraries were generated by error-prone PCR using Mutazyme II (Agilent Technologies), and variants were cloned into the pA24 (or similar) vector by gap repair in the Cen.PK2 screening host. Strains expressing mutated enzymes, with either individual mutations or combinations of mutations introduced by gene shuffling or other methods, were grown in selective medium in 96-well plate format under varying fermentation conditions (different media components, pH, and temperature, for example), pelleted, and lysed by glass bead disruption. To detect N-methylation activity in a high-throughput screen, lysates were incubated with substrates (such as noroxymorphone) in the presence of a BM3 variant with demethylating activity, and assayed for formaldehyde production in the purpald assay (for indirect measurement of methylation). In this case, formaldehyde formation can only result from the activity of BM3 on a substrate that has been N-methylated by an enzyme of interest. Enzymes with improved modifying activity were additionally tested for activity in cell lysates using various SAM analogues as cosubstrates (see FIG. 25), and verified by direct measurement of product formation by LC-MS. The best variant enzymes were selected for the efficient bioconversion of substrate molecules to nal-opioid compounds.
contacting the opioid with an N-demethylase enzyme, wherein contacting the opioid with the enzyme converts the opioid to the nor-opioid through removal of a N-linked methyl group from the opioid,
wherein the nor-opioid is produced by culturing an engineered yeast cell comprising a coding sequence for encoding the N-demethylase enzyme,
wherein the opioid is selected from the group consisting of codeine, oxycodone, thebaine, hydrocodone, dihydrocodeine, 14-hydroxycodeine, codeinone, and 14- hydroxycodeinone, morphine, oxymorphone, oripavine, hydromorphone, dihydromorphine, 14-hydroxy-morphine, morphinone, or 14-hydroxy-morphinone.
contacting a first opioid with an O-demethylase enzyme, wherein contacting the first opioid with the O-demethylase enzyme converts the first opioid to a second opioid through loss of an O-linked methyl group; and
contacting the second opioid with the N-demethylase enzyme, wherein contacting the opioid with the N-demethylase enzyme converts the second opioid to the nor-opioid through loss of an N-linked methyl group,
wherein the nor-opioid is produced by culturing the engineered cell, wherein the cell further comprises a coding sequence for encoding the O-demethylase enzyme.
contacting the nor-opioid with a N-methyltransferase enzyme, wherein contacting the nor-opioid with the N-methyltransferase enzyme in the presence of a cofactor converts the nor-opioid to the nal-opioid through transfer of a sidechain from the cofactor,
wherein the nal-opioid is produced by culturing the engineered cell, wherein the cell further comprises a coding sequence for encoding the N-methyltransferase enzyme.
A document constituting, reporting, recording or evidencing each sequence of the O-demethylation enzymes that was verified by the Applicant and identified in paragraph [00345] of the Specification as displaying improved activity.
A document constituting, reporting, recording or evidencing each sequence of the N-demethylation enzymes that was verified by the Applicant and identified in paragraph [00348] of the Specification as displaying improved activity.
A document constituting, reporting, recording or evidencing each sequence of the best variant enzymes that were verified and selected by the Applicant for the efficient bioconversion of substrate molecules to nal-opioid compounds identified in paragraph [00351] of the Specification
(1) The Commissioner may, for the purposes of this Act:
(b) receive written or oral evidence on oath or affirmation; and
(c) require the production of documents or articles; and
(d) award costs against a party to proceedings before the Commissioner.
(2) The Commissioner must not summon a witness under paragraph (1)(a) unless:
(a) the Commissioner is satisfied, on the balance of probabilities, of the following matters:
(i) the witness has a substantial interest in the proceedings before the Commissioner;
(ii) the witness is likely to provide oral evidence of substantial relevance to a matter before the Commissioner;
(iii) receiving oral evidence from the witness is necessary or desirable in all the circumstances; and
(b) the Commissioner notifies the witness of the actions the Commissioner may take under section 210A if the witness fails or refuses to comply with the summons.
(3) The Commissioner may summon a witness under paragraph (1)(a) whether the witness is in or out of the patent area.
Exercise of power to require production of document or article
(4) The Commissioner must not require a person to produce a document or article under paragraph (1)(c) unless:
(a) the Commissioner is satisfied, on the balance of probabilities, of the following matters:
(i) the person has a substantial interest in the proceedings before the Commissioner;
(ii) the document or article is likely to be of substantial relevance to a matter before the Commissioner; and
(b) the Commissioner notifies the person of the actions the Commissioner may take under section 210A if the person fails or refuses to comply with the requirement.
(5) The Commissioner may require a person to produce a document or article under paragraph (1)(c) whether the person is in or out of the patent area.
Exercise of powers in relation to bodies corporate
(6) The Commissioner's powers in subsection (1) to make a requirement of a person extend, if the person is a body corporate, to making that requirement of any person who is an officer, agent or employee of the body corporate.
"...in my view 'substantial relevance' means more than just 'substantive relevance' or 'not of limited relevance' as suggested by Mr Cordiner. It must be something that is likely to be, if not determinative, highly significant in the determination of a relevant issue in dispute in the proceedings."
"It follows that section 210 as amended is unlike the scheme for discovery and production in other jurisdictions. It is not to be invoked by one party as a general means of exploring the other party's case and particularly is not to be used in a fishing expedition or a hunt for a 'smoking gun'. Usually it will be necessary to identify a real and specific factual issue in dispute, not merely speculation that production or summons might reveal such a matter and a plausible basis for concluding that the order will in some way be likely to provide substantial assistance in resolving the matter. Otherwise the Commissioner cannot be satisfied on the balance of probabilities that what is sought is 'likely to be of substantial relevance'."
and pointed out that the power is discretionary (at [33]):
"The power exercised by the Commissioner is discretionary and must only be exercised after considering the respective interests involved and the purpose of the legislation. Some relevant factors will include fairness to the respective parties, whether any order made would be onerous, delay in the resolution of the proceedings and in the granting of the patent, the correctness of the determination of the proceedings and the efficiency of IP Australia in administering the process."
"Rather [section 210] is intended to allow existing documents to be produced in limited circumstances where they would provide significant assistance in a determination by the Commissioner." (emphasis added)
"The subpoena must specify, with reasonable particularity, the documents to be produced and must avoid becoming a mechanism for "fishing" for evidence or documents. Broad subpoenas that contain imprecise or ambiguous terms may fail to obtain leave."
"Likely to be of substantial relevance" means that the documents or articles required are likely to be of substantial probative value in the determination of a matter before the Commissioner. This goes beyond evidence that may be merely relevant to the Commissioner's determination. It requires a realistic expectation that the documents or articles are of such significance that they may be determinative of a matter before the Commissioner.
Unless a document or article is identified with sufficient particularity for its relevance to be determined it cannot be the subject of a requirement to produce. Section 210 is not an opportunity to discover what relevant documents are in possession of another party or to obtain documents of potential relevance. Requests of this nature will be refused."
"In Example 19, the Patent Applicant describes the biological production of N-demethylated opioid molecules... For the purposes of the Notice, River Stone refers the delegate to the first 4 lines of [00358] which state:
Enzymes described in Example 15 and listed in Table 4, that displayed N demethylase activity on BIA molecules (such as those listed in Table 2), were incorporated into a microbial strain (either Saccharomyces cerevisiae or Escherichia coli) which biosynthesizes morphinan alkaloids de nova. (Emphasis added)
This passage presents clear circumstantial evidence that the Patent Applicant was in possession of the sequences at the time of filing the Patent Application, for the following reasons:
(a) First, the above passage refers to the use of enzymes that displayed "N-demethylase activity on BIA molecules". The only enzymes that were tested for N demethylase activity on BIA molecules were the improved enzymes identified in paragraph [00348]. The enzymes produced in paragraph [00346] were not tested for the identified enzyme activity; they were merely isolated, verified by PCR and sequenced.
(b) Second the Enzymes were then "incorporated" into the select microbial strain. Without knowing the sequence of the enzyme, it would not have been possible to incorporate the sequence into the strain.
Therefore, the circumstantial evidence would strongly suggest that the Patent Applicant must have been in possession of the sequences with N demethylase activity on BIA molecules revealed in Example 15."
[3] (Domino's) [2016] APO 13 at [31]
[4] Allsop CJ (25 October 2016) Subpoenas and Notices to Produce Practice Note (GPN -SUBP) Federal Court of Australia, https://www.fedcourt.gov.au/law-and-practice/practice-documents/practice-notes/gpn-subp
[5] (Sanofi) [2018] APO 3
[8] The NOCO Company v Brown and Watson International Pty Ltd [2025] FCA 887 at [389].
River Stone Biotech ApS
Antheia, Inc [2025] APO 38