Methods of producing morphinan alkaloids and derivatives

1. An engineered microbial cell, comprising:

i) an engineered epimerase, wherein the engineered epimerase converts an (S)-1-benzylisoquinoline precursor to an (R)-1-benzylisoquinoline product within the engineered microbial cell;

ii) a thebaine synthase, wherein the thebaine synthase has measurable activity within the engineered microbial cell; and

iii) at least one modification selected from the group consisting of: a) a substrate inhibition alleviating mutation, b) a product inhibition alleviating mutation, c) a cofactor recovery promoting mechanism, d) a feedback inhibition alleviating mutation, e) transcriptional modulation modification, and f) an inactivating mutation; and

iv) wherein the cell further comprises the enzymes of:

(a) tyrosinase or tyrosine hydroxylase (TYR or TyrH), L-DOPA decarboxylase (DODC), 6-O-methyltransferase (6OMT), coclaurine-N-methyltransferase (CNMT), cytochrome P450 80B1 (CYP80B1), (4′-O-methyltransferase) (4′OMT), dehydroreticuline synthase and dehydroreticuline reductase (DRS-DRR), salutaridine synthase (SalSyn), salutaridine reductase SalR), and salutaridinol 7-O-acetyltransferase (SalAT); or

(b) TYR or TyrH, DODC, monoamine oxidase (maoA), 6OMT, CNMT, 4′OMT, DRS-DRR, SalSyn, SalR, and SalAT, and

wherein, within the engineered microbial cell, the engineered microbial cell converts a plurality of tetracyclic promorphinan precursor molecules to a category of alkaloid products selected from the group consisting of: i) a morphinan alkaloid, ii) a nal-opioid alkaloid, and iii) a nor-opioid alkaloid, and

wherein the engineered microbial cell produces at least 10% more thebaine relative to a same microbial cell that lacks the thebaine synthase.

2. The engineered microbial cell of claim 1 , wherein the engineered epimerase is a split epimerase.

3. The engineered microbial cell of claim 1 , wherein the engineered epimerase converts (S)-reticuline to (R)-reticuline.

4. The engineered microbial cell of claim 3 , wherein at least 50% of the (S)-1-benzylisoquinoline alkaloid molecules within the engineered microbial cell are converted to the (R)-1-benzylisoquinoline product.

5. The engineered microbial cell of claim 1 , wherein the thebaine synthase is an engineered thebaine synthase.

6. The engineered microbial cell of claim 1 , wherein the plurality of tetracyclic promorphinan precursor molecules are fed to the engineered microbial cell.

7. The engineered microbial cell of claim 1 , wherein the plurality of tetracyclic promorphinan precursor molecules are produced within the engineered microbial cell.

8. The engineered microbial cell of claim 1 , wherein the plurality of tetracyclic promorphinan precursor molecules are selected from the group consisting of reticuline, 3′hydroxy-N-methylcoclaurine, coclaurine, norcoclaurine, norlaudanosoline, methylnorlaudanosoline, laudanosoline, methylnorlaudanosoline, norreticuline, 3′hydroxy-N-methylcoclaurine, 4′-O′-methylaudanosoline, L-Dopa, tyrosine, dopamine, 3,4-dihydroxyphenylacetaldehyde (3,4-DHPA), hydroxyphenylpyruvate, prephenate, chorismate, 5-enolpyruvylshikimate-3-phosphate (EPSP), 3-deoxy-D-arabinoheptulosonate-7-phosphate (DAHP), erythrose-4-phosphate (E4P), phosphoenolpyruvate (PEP), and glucose.

9. The engineered microbial cell of claim 1 , wherein at least 50% of the tetracyclic promorphinan precursor molecules within the engineered microbial cell are converted to thebaine.

10. The engineered microbial cell of claim 9 , wherein the tetracyclic promorphinan molecules are selected from the group consisting of salutaridine, salutaridinol, or salutaridinol-7-O-acetate.

11. The engineered microbial cell of claim 1 , wherein the plurality of tetracyclic promorphinan precursor molecules are an (S)-substrate of Formula I:

or a salt thereof, wherein:

R 1 , R 2 , R 3 , and R 4 are independently selected from hydrogen and methyl; and

R 5 is selected from hydrogen, hydroxy, and methoxy.

12. The engineered microbial cell of claim 11 , wherein at least one of R 1 , R 2 , R 3 , R 4 , and R 5 is hydrogen.

13. The engineered microbial cell of claim 1 , wherein a precursor of a promorphinan molecule is (S)-substrate is a compound of Formula II:

or a salt thereof, wherein:

R 3 is selected from hydrogen and C 1 -C 4 alkyl;

R 6 and R 7 are independently selected at each occurrence from hydroxy, fluoro, chloro, bromo, carboxaldehyde, C 1 -C 4 acyl, C 1 -C 4 alkyl, and C 1 -C 4 alkoxy;

n is 0, 1, 2, 3, or 4; and

n′ is 0, 1, 2, 3, 4 or 5.

14. The engineered microbial cell of claim 1 , wherein the plurality of tetracyclic promorphinan precursor molecules are tyrosine.

15. The engineered microbial cell of claim 1 , wherein the plurality of tetracyclic promorphinan precursor molecules are sugar.

16. The engineered microbial cell of claim 1 , further comprising at least one modification selected from the group consisting of: i) a BIA-generating modification, ii) an O-demethylation modification, iii) an N-demethylation modification, and iv) an N-linked modification.

17. The engineered microbial cell of claim 1 , wherein the morphinan alkaloid product is a thebaine, codeinone, codeine, morphine, morphinone, oripavine, neopinone, neopine, neomorphine, hydrocodone, dihydrocodeine, 14-hydroxycodeinone, oxycodone, 14-hydroxycodeine, morphinone, hydromorphone, dihydromorphine, dihydroetorphine, ethylmorphine, etorphine, metopon, buprenorphine, pholcodine, heterocodeine, or oxymorphone.

18. The engineered microbial cell of claim 1 , wherein the nal-opioid alkaloid product is a naltrexone, naloxone, nalmefene, nalorphine, nalorphine, nalodeine, naldemedine, naloxegol, 6β-naltrexol, naltrindole, methylnaltrexone, methylsamidorphan, alvimopan, axelopran, bevenpran, dinicotinate, levallorphan, samidorphan, buprenorphine, dezocine, eptazocine, butorphanol, levorphanol, nalbuphine, pentazocine, phenazocine, norbinaltorphimine, or diprenorphine.

19. The engineered microbial cell of claim 1 , wherein (a) and (b) further comprise norcoclaurine synthase (NCS).