Patent Grant
11965195
This application is a national stage application of International Application No. PCT/EP2020/084508, filed 3 Dec. 2020, which claims priority from Great Britain Patent Application No. 1917694.0, filed 4 Dec. 2019, both of which applications are incorporated herein by reference.
Attached to this Amendment is a Sequence Listing as filed in the International application. The Sequence Listing includes sequences for SEQ ID NOS: 1-23. Please add the Sequence Listing to the present application.
The present invention generally relates to 3a-ethyl-6,6,9a-trmethyldodecahydro-naphtho[2,1-b]furan and to a method of making 3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan using squalene-hopene cyclase (SHC) enzyme or enzyme variant. The invention further relates to compositions comprising 3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan and the various uses of 3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan and compositions comprising 3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan. The present invention also relates to consumer products comprising 3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan and compositions comprising 3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan.
There is an ongoing need in the fragrance industry to provide new compounds for use in fragrance compositions. (−)-Ambrox provides an ambery, dry, woody odour that is useful in fragrance compositions alone or in combination with other woody or ambery ingredients. It is therefore desirable to provide new compounds that may provide an ambery odour. US 2009/0131300, the contents of which are incorporated herein by reference, discloses a mixture of stereoisomers of structure I below, as well as the individual isomeric components:
However, US 2009/0131300 teaches that the substituents on the tetrahydrofuranyl ring are cis-configured. In addition, the stereoisomers of structure I of US 2009/0131300 are synthesized in racemic form by a lengthy process involving 9 steps from ethyl-dihydro-ionone. It is therefore desirable to provide new compounds and compositions that provide an ambery odour and to provide new methods for making said compounds. It would not be obvious to make a compound of formula (I) as specified in the present claims in view of the teaching of US 2009/0131300 because US 2009/0131300 teaches that another isomer is preferred and there is no teaching at all with regard to specific enantiomers. The novel method disclosed herein provides access to specific enantiomers.
In accordance with a first aspect of the present invention there is provided a method for making a compound of formula (I),
wherein the method comprises contacting a compound of formula (II) with a squalene-hopene cyclase (SHC) enzyme or enzyme variant.
In certain embodiments, the method comprises contacting a compound of formula (IIa) with a squalene-hopene cyclase (SHC) enzyme or enzyme variant,
In certain embodiments, the method comprises contacting composition comprising a compound of formula (IIa) and a compound of formula (IIb) with a squalene-hopene cyclase SHC) enzyme or enzyme variant,
In certain embodiments, the weight ratio of the compound of formula (IIa) to the compound of formula (IIb) ranges from about 5:1 to about 15:1, for example from about 8:1 to about 10:1.
In accordance with a second aspect of the present invention there is provided a compound of formula (I),
In accordance with a third aspect of the present invention there is provided a composition comprising, consisting essentially of, or consisting of a compound of formula (and a compound of formula (III),
In accordance with a fourth aspect of the present invention there is provided a compound or composition obtainable by or obtained by the method of the first aspect of the present invention. The compound or composition may, for example, be as defined in the second or third aspect of the present invention respectively, including any embodiment thereof.
In accordance with a fifth aspect of the present invention there is provided a use of a compound or composition of the second, third, or fourth aspect of the present invention in or as a fragrance composition.
In accordance with a sixth aspect of the present invention there is provided a consumer product comprising a compound or composition of the second, third, or fourth aspect of the present invention.
In accordance with a seventh aspect of the present invention there is provided a compound of formula (II),
In accordance with an eighth aspect of the present invention there is provided a composition comprising, consisting essentially of, or consisting of a compound of formula (II). The composition of the eighth aspect of the present invention may, for example, comprise, consist essentially of, or consist of a compound of formula (IIa) alone, or of a compound of formula (IIa) and a compound of formula (IIb)
In certain embodiments, the weight ratio of the compound of formula (IIa) to the compound of formula (IIb) ranges from about 5:1 to about 15:1, for example from about 8:1 to about 10:1.
Certain embodiments of the present invention may provide one or more of the following advantages:
The details, examples and preferences provided in relation to any particular one or more of the stated aspects of the present invention will be further described herein and apply equally to all aspects of the present invention. Any combination of the embodiments, examples and preferences described herein in all possible variations thereof is encompassed by the present invention unless otherwise indicated herein, or otherwise clearly contradicted by context.
SEQ ID NO: 1 is the wild-type Alicyclobacillus acidocaldarius (Aac) SHC amino acid sequence.
SEQ ID NO: 2 corresponds to SEQ ID NO: 1 with the substitutions M132R, A224V, I432T, A557T and H431L and may be referred to as SHC enzyme variant #49 herein.
SEQ ID NO: 3 corresponds to SEQ ID NO: 1 with the substitutions M132R. A224V, I432T, A557T and R613S and may be referred to as SHC enzyme variant #65 herein.
SEQ ID NO: 4 corresponds to SEQ ID NO: 1 with the substitutions M132R, A224V, I432T, Y81H, A557T and R613S and may be referred to as SHC enzyme variant #66 herein.
SEQ ID NO: 5 corresponds to SEQ ID NO: 1 with the substitutions M132R, A224V, I432T, Y81H, H431L and A557T and may be referred to as SHC enzyme variant #110B8 herein.
SEQ ID NO: 6 is the nucleic acid sequence encoding the polypeptide of SEQ ID NO: 2 (SHC enzyme variant #49).
SEQ ID NO: 7 is the nucleic acid sequence encoding the polypeptide of SEQ ID NO: 3 (SHC enzyme variant #65).
SEQ ID NO: 8 is the nucleic acid sequence encoding the polypeptide of SEQ ID NO: 4 (SHC enzyme variant #66).
SEQ ID NO: 9 is the nucleic acid sequence encoding the polypeptide of SEQ ID NO: 5 (SHC enzyme variant #110B8).
SEQ ID NO: 10 may be referred to as 215G2SHC and corresponds to the wild-type AacSHC amino acid sequence with the mutations M132R, A224V and I432T.
SEQ ID NO: 11 is the wild-type amino acid sequence of ZmoSHC1.
SEQ ID NO: 12 is the wild-type amino acid sequence of ZmoSHC2.
SEQ ID NO: 13 is the wild-type amino acid sequence of BjpSHC/BjaSHC.
SEQ ID NO: 14 is the wild-type amino acid sequence of GmoSHC.
SEQ ID NO: 15 is the nucleotide sequence encoding the wild-type AacSHC.
SEQ ID NO: 16 is the nucleotide sequence encoding 215G2SHC.
SEQ ID NO: 17 corresponds to SEQ ID NO: 1 with the substitutions M132R, A224V, I432T, T90A and R613S and may be referred to as SHC enzyme variant #90C7 herein.
SEQ ID NO: 18 corresponds to SEQ ID NO: 1 with the substitutions M132R, A224V, I432T, A172T and M277K and may be referred to as SHC enzyme variant #115A7 herein.
SEQ ID NO: 19 is the wild-type amino acid sequence of TelSHC.
SEQ ID NO: 20 is the wild-type amino acid sequence of ApaSHC1.
SEQ ID NO: 21 is a GmoSHC variant.
SEQ ID NO: 22 is the nucleotide sequence encoding the polypeptide of SEQ ID NO: 17 (SHC enzyme variant #90C7).
SEQ ID NO: 23 is the nucleotide sequence encoding the polypeptide of SEQ ID NO: 18 (SHC enzyme variant #115A7).
The present invention is based, at least in part, on the surprising finding that (3aR,5aS,9aS,9bR)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan, i.e. one enantiomer of formula (I), provides a strong odour. This is surprising in view of the teaching in US 2009/0131300 that another isomer is preferred. The present invention is further based on the surprising finding that squalene-hopene cyclase (SHC) enzyme or enzyme variant can be used to make the compound of formula (I) from a compound of formula (II) having a non-regular terpene chain.
Thus, there is provided herein a method of making a compound of formula (I),
wherein the method comprises contacting a compound of formula (II) with a squalene-hopene cyclase (SHC) enzyme or enzyme variant.
The compound of formula (I) is a new compound that has surprisingly been found to have a strong odour. Therefore, there is also provided herein a compound of formula (I). There is further provided herein the use of compound of formula (I) as fragrance, a composition comprising a compound of formula (I) and optionally a compound of formula (III).
The methods provided herein enzymatically convert a compound of formula (II) to a compound of formula (I) using an SHC enzyme or enzyme variant.
Compound of Formula (II)
The compound of formula (II) may, for example, be referred to as ethyl-homofarnesol. The compound of formula (II) may, for example, be a compound of formula (IIa) (having E,E-configuration) or a compound of formula (IIb) (having E,Z-configuration). The compounds of formula (IIa) and (IIb) are stereoisomers of the compound of formula (II). Other stereoisomers of the compound of formula (II) are compounds of formula (IIc) and (IId) shown below.
The compound of formula (II) may, for example, be a mixture of stereoisomers comprise, consist essentially of or consist of a compound of formula (IIa) and a compound of formula (IIb). The mixture may or may not, for example, comprise any other stereoisomers of formula (II).
In certain embodiments, the method comprises contacting a compound of formula (IIa) with a squalene-hopene cyclase (SHC) enzyme or enzyme variant,
In certain embodiments, the method comprises contacting a compound of formula (IIa) with a squalene-hopene cyclase (SHC) enzyme or enzyme variant in the absence of any other stereoisomers of formula (II) (e.g. in the absence of a compound of formula (IIb)),
In other embodiments, the compound of formula (II) may, for example, be a mixture of stereoisomers of formula (II). In certain embodiments, the mixture comprises a compound of formula (IIa) and one or more other stereoisomers of formula (II). In certain embodiments, the mixture comprises a compound of formula (Jib) and one or more other stereoisomers of formula (ii).
In certain embodiments, the method comprises contacting a composition comprising, consisting essentially of, or consisting of a compound of formula (IIa) and a compound of formula (IIb) with an SHC enzyme or enzyme variant. In certain embodiments, the composition does not comprise any other stereoisomers of formula (II).
The weight ratio of the compound of formula (IIa) to total other stereoisomers of formula (II) may, for example, be equal to or greater than about 10:90. For example, the weight ratio of the compound of formula (IIa) to total other stereoisomers of formula (II) may be equal to or greater than about 20:80 or equal to or greater than about 30:70 or equal to or greater than about 40:60 or equal to or greater than about 50:50 or equal to or greater than about 60:40 or equal to or greater than about 70:30 or equal to or greater than about 80:20 or equal to or greater than about 90:10 or equal to or greater than about 95:5.
The weight ratio of the compound of formula (IIa) to total other stereoisomers of formula (II) may, for example, be equal to or less than about 99:1. For example, the weight ratio of the compound of formula (IIa) to total other stereoisomers of formula (II) may be equal to or less than about 95:5 or equal to or less than about 90:10 or equal to or less than about 85:15 or equal to or less than about 80:20.
For example, the weight ratio of the compound of formula (IIa) to total other stereoisomers of formula (II) may range from about 10:90 to about 99:1 or from about 10:90 to about 90:10 or from about 20:80 to about 80:20 or from about 50:50 to about 80:20 or from about 60:40 to about 80:20.
The weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may, for example, be equal to or greater than about 10:90. For example, the weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may be equal to or greater than about 20:80 or equal to or greater than about 30:70 or equal to or greater than about 40:60 or equal to or greater than about 50:50 or equal to or greater than about 60:40 or equal to or greater than about 70:30 or equal to or greater than about 80:20 or equal to or greater than about 90:10 or equal to or greater than about 95:5.
The weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may, for example, be equal to or less than about 99:1. For example, the weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may be equal to or less than about 96:5 or equal to or less than about 90:10 or equal to or less than about 85:15 or equal to or less than about 80:20.
The weight ratio of compound of formula (IIa) to compound of formula (IIb) may, for example, range from about 5:1 to about 15:1. For example, the weight ratio of compound of formula (IIa) to compound of formula (IIb) may range from about 6:1 to about 14:1 or from about 7:1 to about 13:1 or from about 8:1 to about 12:1 or from about 8:1 to about 11:1 or from about 8:1 to about 10:1. For example, the weight ratio of compound of formula (IIa) to compound of formula (IIb) may be about 9:1. Other stereoisomers of formula (II) include the compound of formula (IIc) and the compound of formula (IId),
The amount of each stereoisomer in a mixture of stereoisomers may, for example, be identified by gas chromatography or NMR spectroscopy.
In certain embodiments, not all compounds of formula (II) are converted to a compound of formula (I) or a by-product of the reaction. Thus, in certain embodiments, the compositions described herein, for example the compositions obtained by or obtainable by the methods described herein, may comprise a compound of formula (I) and a compound of formula (II), for example one or more of a compound of formula (IIIa), (IIb), (IIc) and/or (IId). In particular, the compositions described herein may comprise a compound of formula (IIIa) and/or a compound of formula (IIb). In certain embodiments, any remaining compound of formula (II) in the compositions made by the methods described herein may be separated from the other reaction products such that the composition does not comprise a compound of formula (II).
In alternative embodiments, all compounds of formula (II) are converted to a compound of formula (I) or a compound of formula (III).
The number of stereoisomers of the compound of formula (II) present may influence the speed of the reaction. An SHC enzyme or enzyme variant may be capable of cyclizing a compound of formula (IIa) to a compound of formula (I) from a complex mixture of stereoisomers of the compound of formula (II). However, a lower conversion rate may be observed, which is consistent with the view that stereoisomers of formula (IIb), (IIc) and/or (IId) may compete with the compound of formula (IIa) for access to the SHC enzyme or enzyme variant and thus may act as competitive inhibitors for the conversion of the compound of formula (IIIa) to the compound of formula (I) and/or also act as alternative substrates. Accordingly, the compound of formula (II) substrate may comprise an isomeric mixture of 2-4 isomers, preferably two isomers. In one particular embodiment, the compound of formula (II) substrate comprises, consists essentially of or consists of an (IIa):(IIb) isomeric mixture.
A composition comprising a compound of formula (IIa) and a compound of formula (IIb) may, for example, be made by the method described in Example 1 below.
In a further particular embodiment, the compound of formula (II) substrate comprises, consists essentially of or consists of (IIa).
Compound of Formula (I) and Stereoisomers Thereof
The compound of formula (I) has the relative configuration shown in the structures provided herein which encompasses two enantiomers ((3aR,5aS,9aS,9bR)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan and (3aS,5aR,9aR,9bS)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan).
The compound of formula (I) contains a number of chiral carbon atoms and thus other stereoisomers may also exist, including enantiomers and diastereomers, for example a compound of formula (III) which encompasses two enantiomers (3aR,5aS,9aS,9bS)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan and (3aS,5aR,9aR,9bR)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan). In addition to the compound of formula (I), the products made by the methods described herein may include a compound of formula (III)
In certain embodiments, no other stereoisomers of the compound of formula (I) are made by the method or are present in the product of the method, e.g. in certain embodiments a compound of formula (III) is not made by the method or are present in the product of the method.
The methods described herein may, for example, make a compound of formula (I) and optionally a compound of formula (III)). Thus, the compositions described herein, for example the compositions obtained by or obtainable by the methods described herein may comprise a compound of formula (I) and optionally a compound of formula (III).
The weight ratio of the compound of formula (I) to the compound of formula (III) may, for example be equal to or greater than about 50:50. For example, the weight ratio of the compound of formula (I) to the compound of formula (III) may be equal to or greater than about 55:45 or equal to or greater than about 60:40 or equal to or greater than about 65.35 or equal to or greater than about 70:30 or equal to or greater than about 75:25 or equal to or greater than about 80:20 or equal to or greater than about 85:15 or equal to or greater than about 90:10 or equal to or greater than about 95:5 or equal to or greater than about 97:3 or equal to or greater than about 98:2 or equal to or greater than about 99:1.
In one embodiment, the mixture comprising a compound of formula (I) and other stereoisomers may comprise from about 50 wt % to about 100 wt % or from about 60 wt % to about 99 wt % or from about 70 wt % to about 98 wt % or from about 80 wt % to about 97 wt % or from about 90 wt % to about 97 wt % of the compound of formula (I) based on the total weight of the compound of formula (I) and other stereoisomers.
For example, the weight ratio of the compound of formula (I) to total other stereoisomers may be from about 50:50 to about 100:0 or from about 60.40 to about 99:1 or from about 70:30 to about 98:2 or from about 80:20 to about 97:3 or from about 90:10 to about 97:3.
In certain embodiments the compound of formula (I) is enantioenriched.
By “enantioenriched” we mean a mixture comprising (3aR,5aS,9aS,9bR)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan and (3aS,5aR,9aR,9bS)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan in a weight ratio from 55:45 to 100:0. For example, the weight ratio may be equal to or greater than about 60:40 or equal to or greater than about 65:35 or equal to or greater than about 70:30 or equal to or greater than about 75:25 or equal to or greater than about 80:20 or equal to or greater than about 85.15 or equal to or greater than about 90:10 or equal to or greater than about 95:5 or equal to or greater than about 97:3 or equal to or greater than about 98:2 or equal to or greater than about 99:1.
The amount of each stereoisomer in a mixture of stereoisomers may, for example, be identified by gas chromatography or NMR spectroscopy.
The term “isolated” as used herein refers to a cyclization product such as the compound of formula (I) which has been separated or purified from components which accompany it. The purity can be measured by any appropriate method, e.g. gas chromatography (GC), HPLC or NMR analysis.
Desirably, the amount of compound of formula (I) produced can be from about 1 mg/l to about 20,000 mg/l (20 g/l) or higher such as from about 20 g/l to about 200 g/l or from 100-200 g/l, preferably about 125 g/l or 150 g/l or about 188 g/l.
For example about 1 to about 100 mg/1, about 30 to about 100 mg/l, about 50 to about 200 mg/l, about 100 to about 500 mg/l, about 100 to about 1,000 mg/l, about 250 to about 5,000 mg/l, about 1,000 (1 g/l) to about 15.000 mg/l (15 g/l), or about 2,000 (2 g/l) to about 10,000 mg/l (10 g/l) or about 2,000 (2 g/l) to about 25,000 mg/l (25 g/l) or about 2,000 (2 g/l) to about 25,000 mg/l (25 g/l), 26.000 mg/l (26 g/l), 27,000 mg/l (27 g/l), 28,000 mg/l (28 g/l), 29,000 mg/l (29 g/l), 30,000 mg/l (30 g/l), 40 g/l, 50 g/l, 60 g/l, 70 g/l, 80 g/l, 90 g/l, 100 g/l, 110 g/l, 120 g/l, 125 g/l, 130 g/l, 140 g/l, 150 g/l, 160 g/l, 170 g/l, 1809/1, 190 g/l or 200 g/l or 300 g/l or 400 g/i or 500 g/l of compound of formula (I) may be produced.
Preferably a compound of formula (I) at a concentration of at least 100 g/l is produced within a period of time from 48 to 72 hours.
Preferably compound of formula (I) at a concentration of about 150 g/l is produced within a time period of from about 48 to 72 hours. Preferably compound of formula (I) at a concentration of about 200 g/l is produced within a time period of from about 48 to 72 hours.
Preferably compound of formula (I) at a concentration of about 250 g/1 is produced within a time period of from about 48 to 72 hours.
Products Obtained by the Methods Described Herein
There is also provided herein the products of the methods described herein. Thus, there is also provided herein a compound or a composition obtained by or obtainable by the method described herein, including all embodiments thereof.
Thus, there is provided herein a compound of formula (I) or a composition comprising a compound of formula (I).
There is also provided herein a composition comprising, consisting essentially of, or consisting of a compound of formula (I) and a compound of formula (III). Additionally or alternatively, the composition may further comprise any unreacted compound of formula (II).
The weight ratio of the compound of formula (I) to the compound of formula (III) in the compositions described herein may, for example, range from about 60:40 to about 99:1. For example, the weight ratio of the compound of formula (I) to the compound of formula (III) may range from about 65:35 to about 99:1 or from about 70:30 to about 99:1 or from about 75:25 to about 99:1 or from about 80:20 to about 99:1 or from about 85:15 to about 99:1 or from about 90:10 to about 99:1 or from about 95:5 to about 99:1. For example, the weight ratio of the compound of formula (I) to the compound of formula (III) may range from about 65:35 to about 98:2 or from about 70:30 to about 97:3 or from about 75:25 to about 96:4 or from about 80:20 to about 95:5 or from about 85:15 to about 90:10.
The weight ratio of the compound of formula (I) to the compound of formula (II) in the compositions described herein may, for example, range from about 90:10 to about 100:0. For example, the weight ratio of the compound of formula (I) to the compound of formula (II) in the compositions described herein may range from about 92:8 to about 100:0 or from about 94:6 to about 100:0 or from about 95:5 to about 100:0 or from about 96:4 to about 99.5:0.5 or from about 97:3 to about 99.0:1.0 or from about 98:2 to about 99.0:1.0.
Fragrance Compositions
There is further provided herein the use of the compounds and compositions described herein as or in a fragrance composition.
Thus, there is also provided herein a fragrance composition comprising a compound of formula (I). By “fragrance composition” is meant any composition comprising a compound of formula (I) and a base material.
As used herein, the “base material” includes all known fragrance ingredients selected from the extensive range of natural products, and synthetic molecules currently available, such as essential oils, alcohols, aldehydes and ketones, ethers and acetals, esters and lactones, macrocycles and heterocycles, and/or in admixture with one or more ingredients or excipients conventionally used in conjunction with odorants in fragrance compositions, for example, carrier materials, diluents, and other auxiliary agents commonly used in the art.
Fragrance ingredients known to the art are readily available commercially from the major fragrance manufacturers. Non-limiting examples of such ingredients include:
As used herein, “carrier material” means a material which is practically neutral from an odorant point of view, i.e. a material that does not significantly alter the organoleptic properties of odorants.
By “diluents” is meant any diluent conventionally used in conjunction with odorants, such as diethyl phthalate (DEP), dipropylene glycol (DPG), isopropyl myristate (IPM), triethyl citrate (TEC) and alcohol (e.g. ethanol).
The term “auxiliary agent” refers to ingredients that might be employed in a fragrance composition for reasons not specifically related to the olfactive performance of said composition. For example, an auxiliary agent may be an ingredient that acts as an aid to processing a fragrance ingredient or ingredients, or a composition containing said ingredient(s), or it may improve handling or storage of a fragrance ingredient or composition containing same, such as anti-oxidant adjuvant. Said anti-oxidant may be selected, for example, from Tinogard® TT (BASF), Tinogard® Q (BASF), Tocopherol (including its isomers, CAS 59-02-9; 364-49-8; 18920-62-2; 121854-78-2), 2,6-bis(1,1-dimethylethyl)-4-methylphenol (BHT, CAS 128-37-0) and related phenols, hydroquinones (CAS 121-31-9).
It might also be an ingredient that provides additional benefits such as imparting colour or texture. It might also be an ingredient that imparts light resistance or chemical stability to one or more ingredients contained in a fragrance composition. A detailed description of the nature and type of auxiliary agent commonly used in fragrance compositions containing same cannot be exhaustive, but it has to be mentioned that said ingredients are well known to a person skilled in the art.
Various applications for the compound of formula (I) include but are not limited to a fine fragrance or a consumer product such as fabric care, toiletries, beauty care and leaning products, detergent products, and soap products.
There is also provided herein a consumer product comprising a compound or a composition or fragrance composition as described herein, including any embodiment thereof. The consumer product may, for example, be a cosmetic product (e.g. an eau de parfum or eau de toilette), a cleaning product, a detergent product, or a soap product
Intermediates and Starting Materials
There is also provided herein the intermediates and starting materials used in the methods described herein.
Thus, there is also provided herein a compound of formula (II),
There is also provided herein a composition comprising, consisting essentially of, or consisting of a compound of formula (II). For example, the composition may comprise, consist essentially of, or consist of a compound of formula (IIa) and a compound of formula (IIb).
The weight ratio of the compound of formula (IIa) to the compound of formula (Ib) may, for example, be equal to or greater than about 10:90. For example, the weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may be equal to or greater than about 20:80 or equal to or greater than about 30:70 or equal to or greater than about 40:60 or equal to or greater than about 50:50 or equal to or greater than about 60:40 or equal to or greater than about 70:30 or equal to or greater than about 80.20 or equal to or greater than about 90:10 or equal to or greater than about 95:5.
The weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may, for example, be equal to or less than about 99:1. For example, the weight ratio of the compound of formula (IIa) to the compound of formula (IIb) may be equal to or less than about 95:5 or equal to or less than about 90:10 or equal to or less than about 85:15 or equal to or less than about 80:20.
The weight ratio of compound of formula (IIa) to compound of formula (IIb) may, for example, range from about 5:1 to about 15:1. For example, the weight ratio of compound of formula (IIa) to compound of formula (IIb) may range from about 6:1 to about 14:1 or from about 7:1 to about 13:1 or from about 8:1 to about 12:1 or from about 8:1 to about 11:1 or from about 8:1 to about 10:1. For example, the weight ratio of compound of formula (IIa) to compound of formula (IIb) may be about 9:1.
The compound of formula (II) or composition comprising one or more compound(s) of formula (II) may, for example, be used to make a compound of formula (I), for example in accordance with the methods described herein using a SHC enzyme or enzyme variant.
The composition comprising a compound of formula (II) may, for example, further comprise one or more other materials. The one or more other materials may, for example, be a diluent, excipient, or carrier material.
SHC Enzyme or Enzyme Variant
The methods described herein use an SHC enzyme or enzyme variant to enzymatically convert a compound of formula (II) to a compound of formula (I).
As used herein, the term “SHC enzyme” means a wild-type (WT) Squalene Hopene Cyclase enzyme that is naturally occurring, for example, in a thermophilic bacterium such as Alicyclobacillus acidocaldarius.
As used herein, the term “variant” is to be understood as a polypeptide which differs in comparison to the polypeptide from which it is derived by one or more changes in the amino acid sequence. The polypeptide from which a variant is derived is also known as the parent or reference polypeptide. Typically a variant is constructed artificially, preferably by gene-technological means. Typically, the polypeptide from which the variant is derived is a wild-type protein or wild-type protein domain. However, the variants usable in the present disclosure may also be derived from homologs, orthologs, or paralogs of the parent polypeptide or from artificially constructed variants, provided that the variant exhibits at least one biological activity of the parent polypeptide. The changes in the amino acid sequence may be amino acid exchanges (substitutions), insertions, deletions, N-terminal truncations, or C-terminal truncations, or any combination of these changes, which may occur at one or several sites.
As used herein, the term “SHC enzyme variant” means an enzyme that is derived from a wild-type SHC enzyme but has one or more amino acid alterations compared to the wild-type SHC enzyme and is therefore not naturally occurring. The one or more amino acid alterations may, for example, modify (e.g. increase) the enzymatic activity for a substrate (e.g. compound of formula (II)).
A number of wild-type and variant SHC enzymes from a variety of bacteria are disclosed, for example, in the following documents: WO 2016/170099; WO 2018/157021; Neumann & Simon 1986, Biol Chem Hoppe-Seyler 367, 723-729; JP2009060799; Seckler & Poralla 1986, Biochem Biophys Act 356-363; Ochs et at 1990, J Bacteriol 174, 298-302; WO 2010/139719; U.S. Pat. No. 8,759,043; WO 2012/066059; Seitz et al 2012, J Molecular Catalysis 8; Enzymatic 84, 72-77; Eichhorn et al 2018, Adv Synth Catal 360, 2339-2351, and Seitz 2012 PhD thesis (http://elib.uni-stuttgart.de/handle/11682/1400), the contents of which are incorporated herein by reference). These SHC enzymes and variants may be used in the methods described herein.
Assays for determining and quantifying SHC enzyme and/or SHC enzyme variant activity are described herein and are known in the art. By way of example, SHC enzyme and/or SHC enzyme variant activity can be determined by incubating purified SHC enzyme or enzyme variant or extracts from host cells or a complete recombinant host organism that has produced the SHC enzyme or enzyme variant with an appropriate substrate under appropriate conditions and carrying out an analysis of the reaction products (e.g. by gas chromatography (GC) or HPLC analysis). Further details on SHC enzyme and/or SHC enzyme variant activity assays and analysis of the reaction products are provided in the Examples. These assays may include producing the SHC enzyme variant in recombinant host cells (e.g. E. coli).
As used herein, the term “activity” means the ability of an enzyme to react with a substrate to provide a desired product. The activity can be determined in what is known as an activity test for monitoring the formation of the desired product. The SHC enzyme derivatives of the present disclosure may be characterized by their ability to cyclize the compound of formula (II) to the compound of formula (I).
A “biological activity” as used herein, refers to any activity a polypeptide may exhibit, including without limitation: enzymatic activity; binding activity to another compound (e.g. binding to another polypeptide, in particular binding to a receptor, or binding to a nucleic acid); inhibitory activity (e.g. enzyme inhibitory activity); activating activity (e.g. enzyme-activating activity); or toxic effects. It is not required that the variant exhibits such an activity to the same extent as the parent or wild-type polypeptide. A variant is regarded as a variant within the context of the present application, if it exhibits the relevant activity to a degree of at least 10% of the activity of the parent polypeptide. Likewise, a variant is regarded as a variant within the context of the present application, if it exhibits the relevant biological activity to a degree of at least 10% of the activity of the parent polypeptide (as the terms derivative and variant are used interchangeably throughout the present disclosure). In other embodiments, the SHC enzyme variants used herein allows a better yield than the reference SHC enzyme (e.g. a wild-type SHC enzyme or a known SHC enzyme variant). The term “yield” refers to the gram of recoverable product per gram of feedstock (which can be calculated as a percent molar conversion rate). In additional embodiments, the SHC enzyme variants used herein may show a modified (e.g. increased) productivity relative to the reference SHC enzyme (e.g. wild-type AacSHC or 215G2SHC). The term “productivity” refers to the amount of recoverable product in grams per liter of reaction per hour of reaction time (i.e. time after the substrate was added).
In further embodiments, the SHC enzyme variants of the present disclosure show a modified yield compared with the reference SHC enzyme (e.g. wild-type AacSHC (SEQ ID NO: 1) or 215G2SHC (SEQ ID NO: 10) or wild-type ZmoSHC1 (SEQ ID NO: 11) or wild-type ZmoSHC2 (SEQ ID NO: 12) or wild-type BjpSHC (SEQ ID NO: 13) or wild-type GmoSHC (SEQ ID NO: 14) or wild-type TelSHC (SEQ ID NO: 19) or wild-type ApaSHC1 (SEQ ID NO: 20)). The term “target yield factor” refers to the ratio between the product concentration obtained and the concentration of the SHC variant enzyme (for example, purified SHC enzyme variant or whole cells, or an extract from the recombinant host cells producing the SHC enzyme variant) in the reaction medium. In various embodiments, the SHC enzyme variants of the present disclosure show a modified (e.g. increased) fold increase in enzymatic activity (e.g. a modified/increased cyclization of a compound of formula (II)) relative to the reference SHC protein (e.g. SEQ ID No. 1 or SEQ ID NO: 10 or SEQ ID NO: 11 or SEQ ID NO: 12 or SEQ ID NO: 13 or SEQ ID NO: 14 or SEQ ID NO: 19 or EQ ID NO: 20). This increase in activity may be at least by a factor of: 2, 3, 4, 8, 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 45, 50, 55, 80, 65, 70, 75, 80, 85, 90, 95, and/or 100.
As used herein, the term “amino acid alteration” means an insertion of one or more amino acids between two amino acids, a deletion of one or more amino acids or a substitution (which may be conservative or non-conservative) of one or more amino acids with one or more different amino acids relative to the amino acid sequence of a reference amino acid sequence. Substitutions replace the amino acids of the reference sequence with the same number of amino acids in the variant sequence. Reference amino acid sequences may, for example, be a wild-type (WT) amino acid sequence (for example SEQ ID NO: 1 or SEQ ID NO: 11 or SEQ ID NO: 12 or SEQ ID NO: 13 or SEQ ID NO: 14 or SEQ ID NO: 19 or SEQ ID NO: 20) or may, for example, itself be a SHC enzyme variant sequence (for example the Aac 215G2SHC variant—SEQ ID NO: 10).
The amino acid alterations can be easily identified by a comparison of the amino acid sequences of the SHC enzyme variant with the amino acid sequence of the reference amino acid sequence.
Conservative amino acid substitutions may be made, for instance, on the basis of similarity in polarity, charge, size, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the amino acid residues involved. The 20 naturally occurring amino acids as outlined above can be grouped into the following six standard amino acid groups:
Accordingly, as used herein, the term “conservative substitutions” means an exchange of an amino acid by another amino acid listed within the same group of the six standard amino acid groups shown above. For example, the exchange of Asp by Glu retains one negative charge in the so modified polypeptide. In addition, glycine and praline may be substituted for one another based on their ability to disrupt alpha-helices. Some preferred conservative substitutions within the above six groups are exchanges within the following sub-groups: (i) Ala, Val, Leu and Ile; (ii) Ser and Thr, (ii) Asn and Gln; (iv) Lys and Arg; and (v) Tyr and Phe. Given the known genetic code, and recombinant and synthetic DNA techniques, the skilled scientist readily can construct DNAs encoding the conservative amino acid variants.
As used herein, “non-conservative substitutions” or “non-conservative amino acid exchanges” are defined as exchanges of an amino acid by another amino acid listed in a different group of the six standard amino acid groups (1) to (6) as shown above. Typically the SHC enzyme variants described herein are prepared using non-conservative substitutions which alter the biological function of the disclosed SHC enzyme variants. For ease of reference, the one-letter amino acid symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission are indicated as follows. The three letter codes are also provided for reference purposes.
Amino acid alterations such as amino acid substitutions may be introduced using known protocols of recombinant gene technology including PCR, gene cloning, site-directed mutagenesis of cDNA, transfection of host cells, and in vitro transcription which may be used to introduce such changes to the reference sequence resulting in an SHC enzyme variant. The enzyme variants can then be screened for SHC functional activity.
Suitable sources of SHC enzymes include, for example, Alicyclobacillus acidocaldarius (Mc), Zymomonas mobilis (Zmo), Bradyrhizobium japonicum (Bjp), Gluconobacter morbifer (Gmo), Burkholderia ambifaria, Bacillus anthracis, Methylococcus capsulatus, Frankia alni, Acetobacter pasteurianus (Apa), Thermosynechococcus elongatus (Tel). Streptomyces coelicolor (Sco), Rhodopseudomonas palustris (Rpa), Teredinibacter turnerae (Ttu), Pelobacter carbinolicus (Pca), and Tetrahymena pyriformis (see, for example WO 2010/139719, US 2012/01345477, WO 2012/086059, the contents of which are incorporated herein by reference).
In particular, the SHC enzyme (e.g. from which the SHC enzyme variant may be derived) may be the Alicyclobacillus acidocaldarius (Aac) SHC enzyme, the Zymomonas mobilis (Zmo) SHC enzyme, the Bradyrhizobium japonicum (Bjp or Bja) SHC enzyme or the Gluconobacter morbifer (Gmo) SHC enzyme. In particular, the SHC enzyme (e.g. from which the SHC enzyme variant may be derived) may be the Alicyclobacillus acidocaldarius (Aac) SHC enzyme.
For ease of reference, the designation “AacSHC” may be used to refer to the Alicyclobacillus acidocaldarius (Aac) SHC enzyme, “ZmoSHC” may be used to refer to the Zymomonas mobilis (Zmo) SHC enzyme, “BjpSHC” or “BjaSHC” may be used to refer to the Bradyrhizobium japonicum (Bjp or Bja) SHC enzyme and “GmoSHC” may be used to refer to the Gluconobacter morbifer (Gmo) SHC enzyme.
AacSHC, ZmoSHC and BjpSHC enzyme sequences are disclosed in BASF WO 2010/139719, US 2012/01345477A1, Seitz et al (as cited above) and Seitz (2012 PhD thesis as cited above). Two different sequences are disclosed for ZmoSHC, referred to as ZmoSHC1 and ZmoSHC2. The Gmo SHC enzyme sequence is disclosed in WO 2018/157021.
Alicyclobacillus
acidocaldarius
Zymomonas mobilis
Bradryhizobium
japonicum
Burkholderia
ambifaria
Burkholderia
ambifaria
Bacillus anthracis
Frankia alni
Rhodopseudomonas
palustris
The sequences of the wild-type AacSHC, wild-type ZmoSHC1, wild-type ZmoSHC2, wild-type BjpSHC, wild-type GmoSHC, wild-type TelSHC and wild-type ApaSHC1 are also disclosed herein (SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13. SEQ ID NO: 14, SEQ ID NO: 19 and SEQ ID NO: 20 respectively).
An alignment of WT SHC sequences prepared by Hoshino and Sato (2002 as cited above) indicates that multiple motifs were detected in all four sequences and consists of the core sequence Gln-X-X-X-Gly-X-Trp which is found six times in the SHC sequences of both Z. mobilis and A. acidocaldarius (See FIG. 3 of Reipen et al 1995, Microbiology 141, 155-161). Hoshino and Sato (2002 as cited above) report that aromatic amino acids are unusually abundant in SHCs and that two characteristic motifs were noted in the SHCs: one is a QW motif represented by specific amino acid motifs [(K/R)(G/A)X2-3(F/Y/W)(1/IV)3X3QX2-5GXW] and the alternative is a DXDDTA motif. Wendt et al (1997, Science 277, 1811-1815 and 1999, J Mol Biol 286, 175-187) reported on the X-ray structure analysis of A. acidocaldarius SHC. The DXDDTA motif appears to correlate with the SHC active site.
Functional homologues of the wild-type SHC enzymes or the SHC enzyme variants described herein are also suitable for use in cyclization reactions, for example for producing a compound of formula (II), for example in a recombinant host. Thus, the recombinant host may include one or more heterologous nucleic acid(s) encoding functional homologs of the polypeptides described above and/or a heterologous nucleic acid encoding a SHC variant enzyme as described herein.
A functional homolog is a polypeptide that has sequence similarity to a reference polypeptide, and that carries out one or more of the biochemical or physiological function(s) of the reference polypeptide. A functional homolog and the reference polypeptide may be natural occurring polypeptides, and the sequence similarity may be due to convergent or divergent evolutionary events. As such, functional homologs are sometimes designated in the literature as homologs, or orthologs, or paralogs. Variants of a naturally occurring functional homolog, such as polypeptides encoded by mutants of a wild-type coding sequence, may themselves be functional homologs. Functional homologs can also be created via site-directed mutagenesis of the coding sequence for a polypeptide, or by combining domains from the coding sequences for different naturally-occurring polypeptides (“domain swapping”). Techniques for modifying genes encoding functional homologs described herein are known and include, inter alia, directed evolution techniques, site-directed mutagenesis techniques and random mutagenesis techniques, and can be useful to increase specific activity of a polypeptide, alter substrate specificity, alter expression levels, alter subcellular location, or modify polypeptide:polypeptide interactions in a desired manner. Such modified polypeptides are considered functional homologs. The term “functional homolog” is sometimes applied to the nucleic acid that encodes a functionally homologous polypeptide.
Functional homologs can be identified by analysis of nucleotide and polypeptide sequence alignments. For example, performing a query on a database of nucleotide or polypeptide sequences can identify homologs of the nucleic acid sequences encoding the SHC derivative polypeptides and the like.
Hybridization can also be used to identify functional homologs and/or as a measure of homology between two nucleic acid sequences. A nucleic acid sequence encoding any of the proteins disclosed herein, or a portion thereof, can be used as a hybridization probe according to standard hybridization techniques. The hybridization of a probe to DNA or RNA from a test source (e.g. a mammalian cell) is an indication of the presence of the relevant DNA or RNA in the test source. Hybridization conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, New York, 6.3.1-6.3.6, 1991. Moderate hybridization conditions are defined as equivalent to hybridization in 2×sodium chloride/sodium citrate (SSC) at 30° C. followed by a wash in 1×SSC, 0.1% SDS at 50° C. Highly stringent conditions are defined as equivalent to hybridization in 6× sodium chloride/sodium citrate (SSC) at 45° C. followed by a wash in 0.2×SSC, 0.1% SDS at 65° C. Sequence analysis to identify functional homologs can also involve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of non-redundant databases using a relevant amino acid sequence as the reference sequence. Amino acid sequence is, in some instances, deduced from the nucleotide sequence. Those polypeptides in the database that have greater than 40% sequence identity are candidates for further evaluation for suitability for use in the SHC cyclization reaction. Amino acid sequence similarity allows for conservative amino acid substitutions, such as substitution of one hydrophobic residue for another or substitution of one polar residue for another. If desired, manual inspection of such candidates can be carried out in order to narrow the number of candidates to be further evaluated. Manual inspection can be performed by selecting those candidates that appear to have for e.g. conserved functional domains.
Typically, polypeptides that exhibit at least about 30% amino acid sequence identity are useful to identify conserved regions. Conserved regions of related polypeptides exhibit at least 30%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 81%, 62%, 63%, 64%, 65%, 86%, 67%, 68%, 69%, amino acid sequence identity. In some embodiments, a conserved region exhibits at least, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 88%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity. Sequence identity can be determined as set forth above and below.
The SHC enzymes or enzyme variants described herein and used in the methods described herein may, for example, be based on an amino add sequence of SEQ ID NO: 1, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14. SEQ ID NO: 19, SEQ ID NO: 20 or a variant, homologue, mutant, derivative or fragment thereof. The SHC enzyme or enzyme variant may, for example, have an amino acid sequence with at least 30%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, β0%, 131%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO: 1, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12. SEQ ID NO: 13, SEQ ID NO: 14 or SEQ ID NO: 19 or SEQ ID NO: 20.
The SHC enzymes or enzyme variants described herein and used in the methods described herein may, for example, have a selectivity equal to or greater than about 75%. For example, the SHC enzyme or enzyme variant may have a selectivity equal to or greater than about 80% or equal to or greater than about 85% or equal to or greater than about 90% or equal to or greater than about 95%. For example, the SHC enzyme or enzyme variant may have a selectivity up to 100%, for example less than 100%, for example equal to or less than about 99.5% or equal to or less than about 99.0% or equal to or less than about 98.0% or equal to or less than about 97.0%.
“Percent (%) identity” with respect to the nucleotide sequence of a gene is defined as the percentage of nucleotides in a candidate DNA sequence that is identical with the nucleotides in the DNA sequence, after aligning the sequence and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent nucleotide sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. The terms “polypeptide” and “protein” are used interchangeably herein and mean any peptide-linked chain of amino acids, regardless of length or post-translational modification.
As used herein the term “derivative” includes but is not limited to a variant. The terms “derivative” and “variant” are used interchangeably herein.
In certain embodiments, the SHC enzyme variants described herein only include substitutions and do not include any deletions or insertions.
Specific SHC enzymes and enzymes variants that may be used in the methods described herein are further described below.
Wild-Type (WT) SHC Enzymes
The methods described herein may, for example, use an SHC enzyme having 100% sequence identity to a wild-type SHC enzyme. The wild-type SHC enzyme does not have to have been obtained directly from its natural organism and may have been produced heterologously in a host organism.
The wild-type SHC enzyme may, for example, be an SHC found in Alicyclobacillus acidocaldarius (Aac), Zymomonas mobilis (Zmo), Bradyrhizobium japonicum (Bjp or Bja), Gluconobacter morbifer (Gmo), Burkholderia ambifaria, Bacillus anthracis, Methylococcus capsulatus, Frankia alni, Acetobacter pasteurianus (Ape), Thermosynechococcus elongates (Tel). Streptomyces coelicolor (Sco), Rhodopseudomonas palustris (Rpa), Teredinibacter tumerae (Ttu), Pelobacter carbinolicus (Pca), or Tetrahymena pyriformis (see, for example WO 2010/139719, US 2012/01345477, WO 2012/066059, the contents of which are incorporated herein by reference).
In particular, the wild-type SHC enzyme may be the Alicyclobacillus acidocaldarius (Aac) SHC enzyme, the Zymomonas mobilis (Zmo) SHC enzyme, the Bradyrhizobium japonicum (Bjp/Bja) SHC enzyme or the Gluconobacter morbifer (Gmo) SHC enzyme. In particular, the wild-type SHC may be the Alicyclobacillus acidocaldarius (Aac) SHC enzyme.
For ease of reference, the designation “AacSHC” may be used to refer to the Alicyclobacillus acidocaldarius (Aac) SHC enzyme. “ZmoSHC” may be used to refer to the Zymomonas mobilis (Zmo) SHC enzyme, “BjpSHC” or “BjaSHC” may be used to refer to the Bradyrhizobium japonicum (Bjp) SHC enzyme, “GmoSHC” may be used to refer to the Gluconobacter morbifer (Gmo) SHC enzyme. “TelSHC” may be used to refer to the Thermosynechococcus elongates SHC enzyme and “ApaSHC” may be used to refer to the Acetobacter pasteurianus SHC enzyme.
The wild-type SHC enzyme amino add sequence may, for example, be AacSHC (SEQ ID NO: 1). ZmoSHC1 (SEQ ID NO: 11), ZmoSHC2 (SEQ ID NO: 12), BjpSHC (SEQ ID NO: 13), GmoSHC (SE) ID NO: 14), TelSHC (SEQ ID NO: 19) or ApaSHC1 (SEQ ID NO. 20). For example, the wild-type SHC enzyme may be AacSHC (SEQ ID NO: 1).
SHC Variant Enzyme
The methods described herein may, for example, use an SHC enzyme variant (i.e. an SHC enzyme having less than 100% sequence identity to a wild-type SHC enzyme).
The methods described herein may, for example, use a SHC enzyme variant as described in WO 2016/170099 or WO 2018/157021, the contents of which are incorporated herein by reference. For example, the SHC enzyme variant used in the methods described herein may be the SHC enzyme variant 215G2, which is described in WO 2016/170099.
The SHC enzyme variant may, for example, have an amino acid sequence having at least about 70.0% identity to a wild-type SHC enzyme amino acid sequence. For example, the SHC enzyme variant may have an amino acid sequence having at least about 75.0% or at least about 80.0% or at least about 85.0% or at least about 90.0% or at least about 95.0% or at least about 95.5% or at least about 96.5% or at least about 97.0% or at least about 97.5% or at least about 98.0% or at least about 98.5% or at least about 99.0% identity to a wild-type SHC enzyme amino acid sequence.
The SHC enzyme variant has an amino acid sequence having less than 100% identity, for example equal to or less than about 99.5% or equal to or less than about 99.0% identity to a wild-type SHC enzyme amino acid sequence.
For example, the SHC enzyme variant may have from about 70.0% to about 99.5% or from about 80.0% to about 99.0% or from about 85.0% to about 98.5% or from about 90.0% to about 98.0% identity to a wild-type SHC enzyme amino acid sequence.
The wild-type SHC enzyme may, for example, be from Alicyclobacillus acidocaldarius (Aac), Zymomonas mobilis (Zmo), Bradyrhizobium japonicum (Bjp), Gluconobacter morbifer (Gmo), Burkholderia ambifaria, Bacillus anthraces, Methylococcus capsulatus, Frankia alni, Acetobacter pasteurianus (Apa), Thermosynechococcus elongatus (Tel), Streptomyces coelicolor (Sco), Rhodopseudomonas palustris (Rpa), Teredinibacter tumerae (Ttu), Pelobacter carbinolicus (Pca), or Tetrahymena pyriformis (see, for example WO 2010/139719, US 2012/01345477, WO 2012/066059, the contents of which are incorporated herein by reference).
The wild-type SHC enzyme amino add sequence may, for example, be AacSHC (SEQ ID NO: 1), ZmoSHC1 (SEQ ID NO: 11), ZmoSHC2 (SEQ ID NO: 12), BjpSHC (SEQ ID NO: 13), GmoSHC (SEQ ID NO: 14), TelSHC (SEQ ID NO: 19) or ApaSHC1 (SEQ ID NO: 20). For example, the wild-type SHC enzyme may be AacSHC (SEQ ID NO: 1).
Therefore, in certain embodiments, the SHC enzyme or SHC enzyme variant may have an amino acid sequence having at least about 70.0% identity to SEQ ID NO: 1. SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the SHC enzyme or SHC enzyme variant has an amino acid sequence having at least about 75.0% or at least about 80.0% or at least about 85.0% or at least about 90.0% or at least about 95.0% or at least about 95.5% or at least about 96.5% or at least about 97.0% or at least about 97.5% or at least about 98.0% or at least about 98.5% or at least about 99.0% identity to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20.
For example, the SHC enzyme variant may, for example, have an amino acid sequence having less than 100% identity, for example equal to or less than about 99.5% or equal to or less than about 99.0% identity to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20.
For example, the SHC enzyme variant may have from about 70.0% to about 99.5% or from about 80.0% to about 99.0% or from about 85.0% to about 98.5% or from about 90.0% to about 98.0% identity to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO. 12, SEQ ID NO: 13 SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20 “Percent (%) identity” with respect to a polypeptide or nucleotide sequence is defined respectively as the percentage of amino acids or nucleotides in a candidate sequence that are identical with the amino acids or nucleotides in the reference sequence, after aligning the sequence and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. The terms “polypeptide” and “protein” are used interchangeably herein and mean any peptide-linked chain of amino acids, regardless of length or post-translational modification.
The similarity of nucleotide and amino acid sequences, i.e. the percentage of sequence identity, can be determined via sequence alignments. Such alignments can be carried out with several art-known algorithms, preferably with the mathematical algorithm of Karlin and Altschul (Karlin & Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5877), with hmmalign (HMMER package, http.//hmmer.wustl.edu/) or with the CLUSTAL algorithm (Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-80) available eg, on https://www.ebi.ac.uk/Tools/msa/clustalo/ or the GAP program (mathematical algorithm of the University of Iowa) or the mathematical algorithm of Myers and Miller (1989—Cabios 4: 11-17). Preferred parameters used are the default parameters as they are set on https://www.ebi.ac.uk/Tools/msa/clustalo/.
Percentage sequence identity may be calculated using, for example, BLAST. BLAT or BlastZ (or BlastX). A similar algorithm is incorporated into the BLASTN and BLASTP programs of Altschul et al (1990) J. Mol. Biol. 215, 403-410 BLAST polynucleotide searches may be performed with the BLASTN program, score=100, word length=12, to obtain polynucleotide sequences that are homologous to those nucleic acids which encode the relevant protein. BLAST protein searches may be performed with the BLASTP program, score=50, word length=3, to obtain amino acid sequences homologous to the polypeptide.
To obtain gapped alignments for comparative purposes, Gapped BLAST may be utilized as described in Altschul et al (1997) Nucleic Acids Res. 25, 3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs are used. Sequence matching analysis may be supplemented by established homology mapping techniques like Shuffle-LAGAN (Brudno M., Bioinformatics 2003b, 19 Suppl 1: 154-162) or Markov random fields. When percentages of sequence identity are referred to in the present application, these percentages are calculated in relation to the full length of the longer sequence, if not specifically indicated otherwise.
In particular embodiments, % identity between two sequences is determined using CLUSTAL O (version 1.2.4).
In certain embodiments, the SHC enzyme variant may have equal to or less than about 200 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the SHC enzyme variant may have equal to or less than about 150 or equal to or less than about 120 or equal to or less than about 100 or equal to or less than about 95 or equal to or less than about 90 or equal to or less than about 85 or equal to or less than about 80 or equal to or less than about 75 or equal to or less than about 70 or equal to or less than about 65 or equal to or less than about 60 or equal to or less than about 55 or equal to or less than about 50 or equal to or less than about 45 or equal to or less than about 40 or equal to or less than about 35 or equal to or less than about 30 or equal to or less than about 25 or equal to or less than about 20 or equal to or less than about 15 or equal to or less than about 10 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20.
The SHC enzyme variant may, for example, have at least about 1 or at least about 2 or at least about 3 or at least about 4 or at least about 5 or at least about 6 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13. SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO. 20
For example, the SHC enzyme variant may have from about 1 to about 30 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO. 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the SHC enzyme variant may have from about 2 to about 25 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 1, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the SHC enzyme variant may have from about 3 to about 20 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 1. SEQ ID NO: 14. SEQ ID NO: 19 or SEQ ID NO: 20. For example, the SHC enzyme variant may have from about 4 to about 15 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the SHC enzyme variant may have from about 5 to about 10 amino acid alterations compared to the wild-type SHC enzyme, for example compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20.
The amino acid alterations may, for example, be insertions, deletions and/or substitutions as described above. For example, the amino acid alterations may be substitutions, for example, non-conservative substitutions.
In certain embodiments, the only amino acid alterations compared to the wild-type SHC enzyme (e.g. compared to SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13. SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20) are substitutions (i.e. there are no insertions or deletions).
Amino acid alterations are defined relative to a reference sequence. An amino acid alteration relative to a reference sequence means that the amino acid sequence of the variant sequence is different to the reference sequence.
Amino acids in the reference sequence and the variant sequence may be assigned a number, where the numbering starts with the amino acid at the N-terminus of the polypeptide (i.e. the amino acid at the N-terminus of the polypeptide is numbered 1, the next amino acid is numbered 2 etc.). The “position” of a reference sequence refers to a specific amino acid residue present in the reference sequence as identified by the specific numbering of the amino acids in the reference sequence. The “position” of a variant sequence refers to a specific amino acid residue present in the variant sequence as identified by the specific numbering of the amino acids in the variant sequence.
Since the variant sequence may include deletions or insertions compared to the reference sequence, the amino acids in the variant sequence may be numbered differently to the same amino acids in the reference sequence. By way of example, if an amino acid is inserted between amino acids 131 and 132 of SEQ ID NO: 1, the amino acid following the insertion will have the numbering 133 in the variant sequence while it retains the numbering 132 in the reference sequence. In this example, the position of the variant sequence that corresponds to position 132 of the reference sequence is position 133. Therefore, amino acids in the variant sequence that have been retained from the reference sequence may be defined by referring to the “corresponding position” of the reference sequence. In other words, a “position” in the variant sequence may be defined by reference to a “corresponding position” in the reference sequence. In particular, substitutions in the variant sequence compared to the reference sequence may be defined by referring to the “corresponding position” of the reference sequence in spite of any insertions and/or deletions in the reference sequence. Where the amino acids of a reference sequence have been deleted, there is no “corresponding position” in the variant sequence. Where there are no insertions or deletions compared to the reference sequence (i.e. there are only substitutions), the “corresponding position” of the reference sequence will be the same as the position in the variant sequence.
Wild-type SHC enzymes from different species have different polypeptide lengths. The wild-type sequences may be aligned using algorithms as described above in order to identify “corresponding positions” in two different wild-type SHC enzymes. Therefore, the amino acid at a position of the variant sequence corresponding to a position in a reference sequence may, for example, be a different amino acid residue and/or may have a different number to that of the reference sequence. By way of example, the amino acid M at position 132 of AacSHC (SEQ ID NO: 1) may correspond to the amino acid Y at position 185 of ZmoSHC1 (SEQ ID NO: 11).
The amino acid alteration may therefore be defined relative to two different reference sequences. For example, the amino acid alteration may be a change compared to a first reference sequence (e.g. a wild-type SHC enzyme sequence from which the variant is derived) and the position of the amino acid alteration in the variant sequence may be defined by reference to a second reference sequence (e.g. the AacSHC (SEQ ID NO: 1)). Thus, the amino acid alteration in the SHC enzyme variant may be relative to a first wild-type SHC enzyme at a position defined by reference to a second wild-type SHC enzyme.
The SHC enzyme variant may have one or more of the specific substitutions, or combinations of substitutions, at one or more positions corresponding to positions 81, 90, 132, 172, 224, 277, 431, 432, 557 and 613 of SEQ ID NO: 1.
In particular, the SHC enzyme variant may have one or more of the following combinations of substitutions:
The SHC enzyme variant amino acid sequence may have one or more amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at a position selected from positions corresponding to positions 81, 90, 172, 277, 431, 557 and 613 of SEQ ID NO: 1. For example, the amino acid alterations may be at one or more positions selected from positions corresponding to positions 81, 431, 557 and 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
In certain embodiments, the SHC enzyme variant amino acid sequence has an amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 557 of SEQ ID NO: 1 and at least one position corresponding to position 81, 431 or 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20 For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence may have an amino acid alteration relative to a wild-type SHC enzyme amino acid sequence at a position corresponding to position 557 of SEQ ID NO: 1 and one position corresponding to position 81, 431 or 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to a wild-type SHC enzyme amino acid sequence at a position corresponding to position 557 of SEQ ID NO: 1 and two positions selected from positions corresponding to positions 81, 431 and 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to a wild-type SHC enzyme amino acid sequence at a position corresponding to position 557 of SEQ ID NO: 1 and all positions corresponding to positions 81, 431 and 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13. SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence has amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 90 and 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1. SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1
For example, the SHC enzyme variant amino acid sequence has amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 172 and 277 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12. SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence has amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 557 and 431 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence has amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 557 and 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence has amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 81, 557 and 613 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence has amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 81, 431 and 557 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 557 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 557.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 557 of SEQ ID NO: 1 may, for example, be Met. Val, Leu, Ile, Cys, Ser, Thr, Asn, Gln, Asp, Glu, His, Lys, Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a neutral hydrophilic amino acid (i.e. Cys, Ser, Thr, Asn or Gln). For example, the new amino acid in the SHC enzyme variant may be threonine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 81 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) may not be 81.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 81 of SEQ ID NO: 1 may, for example, be Met, Ala, Val, Leu, Ile, Cys, Ser, Thr, Asn, Gln, Asp, Glu, His, Lys, Arg, Gly, Pro, Trp, or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a basic amino acid (i.e. His, Lys or Arg). For example, the new amino acid in the SHC enzyme variant may be histidine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 90 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 90.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 90 of SEQ ID NO: 1 may, for example, be Met, Ala, Val, Leu, Ile, Cys, Ser, Asn, Gin, Asp, Glu, His, Lys, Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a hydrophobic amino acid (i.e. Met, Ala, Val, Leu, Ile). Far example, the new amino acid in the SHC enzyme variant may be alanine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 172 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 172.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 172 of SEQ ID NO: 1 may, for example, be Met, Val, Leu, Ile, Cys, Ser, Thr, Asn, Gin, Asp, Glu, His, Lys, Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a neutral hydrophilic amino acid (i.e. Cys, Ser, Thr, Asn, Gin). For example, the new amino acid in the SHC enzyme variant may be threonine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 277 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 277.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 277 of SEQ ID NO: 1 may, for example, be Ala, Val, Leu, Ile, Cys, Ser, Thr, Asn. Gin, Asp. Glu, His, Lys. Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a basic amino acid (i.e. His, Lys, Arg). For example, the new amino acid in the SHC enzyme variant may be lysine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 431 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) may not be 431.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 431 of SEQ ID NO: 1 may, for example, be Met, Ala, Val, Leu, Ile, Cys, Ser, Thr, Asn, Gin, Asp, Glu, Lys, Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a hydrophobic amino acid (i.e. Met, Ala. Val, Leu or Ile). For example, the new amino acid in the SHC enzyme variant may be leucine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 613 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X) As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) may not be 613.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 613 of SEQ ID NO: 1 may, for example, be Met, Ala, Val. Leu, Ile, Cys, Ser. Thr, Asn, Gin, Asp, Glu, His, Lys, Gly. Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a neutral hydrophilic amino acid (i.e. Cys, Ser, Thr, Asn or Gln). For example, the new amino acid in the SHC enzyme variant may be threonine.
The amino acids and positions in the wild-type ZmoSHC1, ZmoSHC2, BjpSHC, GmoSHC, TelSHC and ApaSHC1 sequences (SEQ ID NOs: 11, 12, 13, 14, 19 and 20 respectively) that correspond to the amino acids of AacSHC (SEQ ID NO: 1) (e.g. the amino acids at positions 81, 431, 557 and 613 of AacSHC) are shown in
Amino acid positions 81, 90, 132, 224, 172, 277, 431, 432, 557 and 613 in wild-type AacSHC are highlighted with a white letter on a black background. The amino acids directly above or below the highlighted amino acid are therefore the amino acids and positions in ZmoSHC2, BjaSHC, GmoSHC, ApaSHC1, ZmoSHC1 and TelSHC that correspond to positions 81, 90, 132, 224, 172, 277, 431, 432, 557 and 613 of AacSHC (SEQ ID NO: 1). For example, the amino acid in BjaSHC, GmoSHC, ApaSHC1 and ZmoSHC1 that corresponds to the amino acid Y a position 81 of AacSHC (SEQ ID NO. 1) is Y. The amino acid in ZmoSHC2 and TelSHC that corresponds to the amino acid Y at position 81 of AacSHC (SEQ ID NO: 1) is F. Position 84 of TelSHC is the position of TelSHC that corresponds to position 81 of AacSHC (SEQ ID NO: 1).
The SHC enzyme variant amino acid sequence may have one or more amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132, 224 and 432 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions.
For example, the SHC enzyme variant amino acid sequence may have one, two, or three amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions selected from positions corresponding to positions 132, 224 and 432 of SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132 and 432 of SEQ ID NO: 1.
For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132, 224 and 432 of SEQ ID NO. 1.
For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 90, 132, 224, 432 and 613 of SEQ ID NO. 1 For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132, 172, 224, 277 and 432 of SEQ ID NO: 1. For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132, 224, 432 and 557 of SEQ ID NO: 1 and one or more positions selected from positions corresponding to positions 81, 431 and 613 of SEQ ID NO: 1. For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132, 224, 431, 432 and 557 of SEQ ID NO: 1. For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 132, 224, 432, 557 and 613 of SEQ ID NO: 1. For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 81, 132, 224, 432, 557 and 613 of SEQ ID NO. 1. For example, the SHC enzyme variant amino acid sequence may have amino acid alterations relative to the wild-type SHC enzyme amino acid sequence at positions corresponding to positions 81, 132, 224, 431, 432 and 557 of SEQ ID NO: 1. The amino acid alterations may, for example, be substitutions, for example non-conservative substitutions. The wild-type SHC enzyme amino acid sequence may, for example, be SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13. SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 20. For example, the wild-type sequence may be SEQ ID NO: 1.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 132 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 132.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 132 of SEQ ID NO: 1 may, for example, be Ala, Val, Leu, Ile, Cys, Ser, Thr, Asti. Gin, Asp. Glu, His, Lys. Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a basic amino acid (i.e. His, Lys or Arg). For example, the new amino acid in the SHC enzyme variant may be arginine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 224 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 224.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 224 of SEQ ID NO: 1 may, for example, be Met, Val, Leu, Ile, Cys, Ser, Thr, Asn, Gin, Asp, Glu, His, Lys, Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a hydrophobic amino acid (i.e. Met, Val, Leu or Ile). For example, the new amino acid in the SHC enzyme variant may be valine.
The amino acid alteration relative to the wild-type SHC enzyme amino acid sequence at a position corresponding to position 432 of SEQ ID NO: 1 may, for example, be a substitution of the amino acid of the wild-type SHC enzyme for a different amino acid (X). As noted above, since the wild-type sequence may have a different length to SEQ ID NO: 1 and since the variant may additionally comprise insertions and/or deletions, the numbering of the new amino acid (X) in the variant sequence may not be 432.
The new amino acid (X) in the SHC enzyme variant amino acid sequence at a position corresponding to position 432 of SEQ ID NO: 1 may, for example, be Met, Ala, Val, Leu, Cys, Ser. Thr, Asn, Gin. Asp, Glu, His, Lys, Arg, Gly, Pro, Trp, Tyr or Phe. For example, the new amino acid (X) in the SHC enzyme variant may be a neutral hydrophilic amino acid (i.e. Cys, Ser, Thr, Asn or Gln). For example, the new amino acid in the SHC enzyme variant may be threonine.
The amino acids and positions in the wild-type ZmoSHC1. ZmoSHC2, BjpSHC, GmoSHC, TelSHC and ApaSHC1 sequences (SEQ ID NOs: 11, 12, 13, 14, 19 and 20 respectively) that correspond to the amino acids of AacSHC (SEQ ID NO: 1) (e.g. at positions 132, 224 and 432 of AacSHC) are shown in
The SHC enzyme variants described herein may, for example, have one or more other amino acid alterations (e.g. substitutions) at the other positions of AacSHC identified in WO 2016/170099.
Any combination of the amino acid alterations described herein is envisaged. In particular, combinations of amino acid alterations at positions corresponding to the combinations of amino acid alterations identified in AaCSHC herein and in WO 2016/17009 are envisaged.
In certain embodiments, the SHC enzyme variant is identical to SEQ ID NO: 1 except for the following amino acid substitutions:
The SHC enzyme variant may, for example, have the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3. SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6. SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 22, or SEQ ID NO: 23
The SHC enzyme variants may, for example, have increased enzymatic activity for the conversion of the compound of formula (II) to the compound of formula (I) compared to the wild-type SHC enzyme. Increased enzymatic activity may refer to any aspect of the enzymatic conversion of the compound of formula (II) to the compound of formula (I) including, for example, increased total conversion of the compound of formula (II) to the compound of formula (I), increased rate of conversion of the compound of formula (II) (e.g. in the first 6 hours or in the first 12 hours of reaction), increased production of the compound of formula (I), and decreased production of by-products. Increased enzymatic activity may be defined by increased productivity in general, which may be defined in terms of compound of formula (I) produced per hour, per gram of biocatalyst and per liter of reaction.
The SHC enzyme variants may, for example, provide increased conversion of compound of formula (II) compared to the wild-type SHC enzyme. Therefore, the process described herein may have an increased level of compound of formula (11) conversion compared to the process using the wild-type SHC enzyme. The SHC enzyme variants may, for example, provide increased rate of compound of formula (II) conversion compared to the wild-type SHC enzyme. Therefore, the process described herein may have an increased rate of compound of formula (II) conversion compared to the wild-type SHC enzyme. The SHC enzyme variant may, for example, provide increased rate of compound of formula (II) conversion over the first 4 hours or over the first 6 hours or over the first 8 hours or over the first 12 hours or over the first 24 hours of the reaction compared to the wild-type SHC enzyme. Therefore, the process described herein may have an increased rate of compound of formula (II) conversion over the first 4 hours or over the first 6 hours or over the first 8 hours or over the first 12 hours or over the first 24 hours of the reaction compared to the wild-type SHC enzyme. This may be when compared to using both enzymes (i.e. the SHC enzyme variant and the wild-type SHC enzyme) under the same reaction conditions (e.g. same pH and temperature) or when compared to using each enzymes under their optimized reaction conditions (e.g. optimized pH and temperature) which may be different to each other.
For example, the new SHC enzyme variant may provide or the process may have at least about 5% compound of formula (II) conversion in the first 24 hours of the reaction. For example, the new SHC enzyme variant may provide or the process may have at least about 6% or at least about 8% or at least about 10% or at least about 12% or at least about 14% or at least about 15% compound of formula (II) conversion in the first 24 hours of the reaction. For example, the new SHC enzyme variant may provide or the process may have at least about 1.5% compound of formula (II) conversion in the first 4 hours of the reaction. For example, the new SHC enzyme variant may provide or the process may have at least about 2.0% or at least about 2.5% or at least about 3.0% or at least about 3.5% or at least about 4.0% or at least about 4.5% or at least about 5.0 compound of formula (II) conversion in the first 4 hours of the reaction. This may be when compared to using both enzymes (i.e. the new SHC enzyme variant and the enzyme of SEQ ID NO: 1 or SEQ ID NO: 10) under the same reaction conditions (e.g. same pH and temperature) or when compared to using each enzymes under their respective optimized reaction conditions (e.g. optimized pH and temperature) which may be different to each other.
The conversion of compound of formula (II) to compound of formula (I) may, for example, be determined using an activity assay as described above and may be calculated as gram of recoverable product per gram of feedstock (which can be calculated as a percent molar conversion rate).
The optimum temperature for the SHC enzyme variant may, for example, be equal to or greater than about 30° C. For example, the optimum temperature for the SHC enzyme variant may range from about 30° C. to about 50° C., for example from about 35° C. to about 50° C. or from about 40° C. to about 50° C. or from about 35° C. to about 45° C. For example, the optimum temperature of the SHC enzyme variant may be about 35° C. or about 45° C. The processes for making the compound of formula (I) disclosed herein may be carried out at the optimum temperature of the SHC enzyme variant.
The optimum pH for the SHC enzyme variant may, for example, be equal to or greater than about 5.0. For example, the optimum pH for the SHC enzyme variant may range from about 5.0 to about 6.0, for example from about 5.2 to about 5.8, for example from about 5.4 to about 5.8, for example from about 5.6 to about 5.8. For example, the optimum pH of the SHC enzyme variant may be about 5.4 or about 5.6 or about 5.8. The processes for making the compound of formula (I) disclosed herein may be carried out at the optimum pH of the SHC enzyme variant.
The optimum concentration of sodium dodecyl sulfate (SDS) in the reaction medium of the processes for making the compound of formula (I) disclosed herein may, for example, be from about 0.010 w/w % to about 0.10 w/w %. For example, the optimum concentration of SDS may be from about 0.040 w/w % to about 0.080 w/w %, for example about 0.050 w/w % when Ethyl-homofarnesol is used at 4 WI with cells to an OD650 nm of 10.
The processes for making the compound of formula (I) disclosed herein may be carried out at the optimum temperature range or optimum temperature and/or the optimum pH range or optimum pH and/or the SOS optimum concentration range or optimum SDS concentration for the specific enzyme used, as set out in the Examples below.
Nucleic Acids and Methods of Making Nucleic Acids
The SHC enzyme and enzyme variants described herein may be encoded by a nucleic acid. The nucleic acid may, for example, be an isolated nucleic acid.
Thus, there is provided herein a construct comprising a nucleic acid sequence encoding a SHC enzyme or enzyme variant as described herein. As used herein, a “construct” is an artificially created segment of nucleic acid that is to be transfected into a target cell. The construct may comprise the nucleic acid encoding the SHC enzyme or enzyme variant and an expression controller (e.g. promoter).
There is further provided herein a vector comprising a construct as described herein. As used herein, a “vector” is a DNA molecule that is used as a vehicle to artificially carry foreign genetic material into a cell where it can be replicated and/or expressed. The vector may, for example, be a plasmid, a viral vector, a cosmid, or an artificial chromosome.
The terms “construct” and “vector” may overlap, for example where the construct is a plasmid.
In particular, there is provided herein a nucleic acid encoding an amino acid sequence of any one of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 17, SEQ ID NO: 18.
In particular, there is provided herein a nucleic acid having the sequence of SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 22 and SEQ ID NO: 23 which may, for example, be comprised in a construct or a vector as described herein.
The term “nucleic acid” or “nucleic acid molecule” as used herein shall specifically refer to polynucleotides of the disclosure which can be DNA, cDNA, genomic DNA, synthetic DNA, or RNA, and can be double-stranded or single-stranded, the sense and/or an antisense strand. The term “nucleic acid” or “nucleic acid molecule” shall particularly apply to the polynucleotide(s) as used herein, e.g. as full-length nucleotide sequence or fragments or parts thereof, which encodes a polypeptide with enzymatic activity, e.g. an enzyme of a metabolic pathway, or fragments or parts thereof, respectively.
The term also includes a separate molecule such as a cDNA where the corresponding genomic DNA has introns and therefore a different sequence; a genomic fragment that lacks at least one of the flanking genes; a fragment of cDNA or genomic DNA produced by polymerase chain reaction (PCR) and that lacks at least one of the flanking genes; a restriction fragment that lacks at least one of the flanking genes; a DNA encoding a non-naturally occurring protein such as a fusion protein (e.g. a His tag), mutein, or fragment of a given protein; and a nucleic acid which is a degenerate variant of a cDNA or a naturally occurring nucleic acid. In addition, it includes a recombinant nucleotide sequence that is part of a hybrid gene, i.e. a gene encoding a non-naturally occurring fusion protein. Fusion proteins can add one or more amino acids (such as but not limited to Histidine (His)) to a protein, usually at the N-terminus of the protein but also at the C-terminus or fused within regions of the protein. Such fusion proteins or fusion vectors encoding such proteins typically serve three purposes: (i) to increase production of recombinant proteins; (ii) to increase the solubility of the recombinant protein; and (iii) to aid in the purification of the recombinant protein by providing a ligand for affinity purification.
The term “nucleic acid” or “nucleic acid molecule” also includes codon optimised sequences suitable for expression in a particular microbial host cell (e.g. E. coli host cell). As used herein, the term “codon optimized” means a nucleic acid protein coding sequence which has been adapted for expression in a prokaryotic or a eukaryotic host cell, particularly bacterial host cells such as E. coli host cells by substitution of one or more or preferably a significant number of colons with colons that are more frequently used in bacterial (e.g. E. coli host cell genes.
In this regard, the nucleotide sequence encoding the reference amino acid sequence (e.g. SEQ ID NO: 1 or SEQ ID NO: 10) and variants/derivatives thereof may be the original one as found in the source (e.g. SEQ ID NO: 1 found in AacSHC) or the gene can be colon-optimized for the selected host organisms, such as e.g. E. coli.
A ribonucleic acid (RNA) molecule can be produced by in vitro transcription. Segments of DNA molecules are also considered within the scope of the disclosure, and can be produced by, for example, the polymerase chain reaction (PCR) or generated by treatment with one or more restriction endonucleases. Segments of a nucleic acid molecule may be referred to as DNA fragments of a gene, in particular those that are partial genes. A fragment can also contain several open reading frames (ORF), either repeats of the same ORF or different ORF's. The term shall specifically refer to coding nucleotide sequences, but shall also include nucleotide sequences which are non-coding, e.g. untranscribed or untranslated sequences, or encoding polypeptides, in whole or in part. The genes as used herein, e.g. for assembly, diversification or recombination can be non-coding sequences or sequences encoding polypeptides or protein encoding sequences or parts or fragments thereof having sufficient sequence length for successful recombination events. More specifically, said genes have a minimum length of 3 bp, preferably at least 100 bp, more preferred at least 300 bp. It will be apparent from the foregoing that a reference to an isolated DNA does not mean a DNA present among hundreds to millions of other DNA molecules within, for example, cDNA or genomic DNA libraries or genomic DNA restriction digests in, for example, a restriction digest reaction mixture or an electrophoretic gel slice. An isolated nucleic acid molecule of the present disclosure encompasses segments that are not found as such in the natural state.
As used herein, the term “isolated DNA” can refer to (1) a DNA that contains sequence not identical to that of any naturally occurring sequence, a polynucleotide or nucleic acid which is not naturally occurring, (e.g. is made by the artificial combination (e.g. artificial manipulation of isolated segments of nucleic acids, e.g. by genetic engineering techniques) of two otherwise separated segments of sequences through human intervention) or (2), in the context of a DNA with a naturally-occurring sequence (e.g. a cDNA or genomic DNA), a DNA free of at least one of the genes that flank the gene containing the DNA of interest in the genome of the organism in which the gene containing the DNA of interest naturally occurs.
The term “isolated DNA” as used herein, specifically with respect to nucleic acid sequences may also refer to nucleic acids or polynucleotides produced by recombinant DNA techniques, e.g. a DNA construct comprising a polynucleotide heterologous to a host cell, which is optionally incorporated into the host cell. A chimeric nucleotide sequence may specifically be produced as a recombinant molecule. The term “recombination” shall specifically apply to assembly of polynucleotides, joining together such polynucleotides or parts thereof, with or without recombination to achieve a cross-over or a gene mosaic. For example, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. A recombinant gene encoding a polypeptide described herein may include the coding sequence for that polypeptide, operably linked, in sense orientation, to one or more regulatory regions suitable for expressing the polypeptide. Because many microorganisms are capable of expressing multiple gene products from a polycistronic mRNA, multiple polypeptides can be expressed under the control of a single regulatory region for those microorganisms, if desired. A coding sequence and a regulatory region are considered to be operably linked when the regulatory region and coding sequence are positioned so that the regulatory region is effective for regulating transcription or translation of the sequence.
The term “recombinant” as used herein, specifically with respect to enzymes shall refer to enzymes produced by recombinant DNA techniques, i.e. produced from cells transformed by an exogenous DNA construct encoding the desired enzyme. “Synthetic” enzymes are those prepared by chemical synthesis. A chimeric enzyme may specifically be produced as recombinant molecule. The term “recombinant DNA” therefore includes a recombinant DNA incorporated into a vector into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote (or the genome of a homologous cell, at a position other than the natural chromosomal location).
In a further aspect the nucleic acid molecule(s) of the present disclosure is/are operatively linked to expression control sequences allowing expression in prokaryotic and/or eukaryotic host cells. As used herein, “operatively linked” means incorporated into a genetic construct so that expression control sequences effectively control expression of a coding sequence of interest. The transcriptional/translational regulatory elements referred to above include but are not limited to inducible and non-inducible, constitutive, cell cycle regulated, metabolically regulated promoters, enhancers, operators, silencers, repressors and other elements that are known to those skilled in the art and that dove or otherwise regulate gene expression. Such regulatory elements include but are not limited to regulatory elements directing constitutive expression or which allow inducible expression like, for example, CUP-1 promoter, the tet repressor as employed, for example, in the tet-on or tet-off systems, the lac system, the trp system regulatory elements. By way of example, Isopropyl β-D-1-thiogalactopyranoside (IPTG) is an effective inducer of gene expression in the concentration range of 100 μM to 1.0 mM. This compound is a molecular mimic of allolactose, a lactose metabolite that triggers transcription of the lac operon, and it is therefore used to induce gene expression when the gene is under the control of the lac operator. Another example of a regulatory element which induces gene expression is lactose. Similarly, the nucleic acid molecule(s) of the present disclosure can form part of a hybrid gene encoding additional polypeptide sequences, for example, a sequence that functions as a marker or reporter. Examples of marker and reporter genes including beta-lactamase, chloramphenicol acetyltransferase (CAT), adenosine deaminase (ADA), aminoglycoside phosphotransferase dihydrofolate reductase (DHFR), hygromycin-B-phosphotransferase (MPH), thymidine kinase (TK), lacZ (encoding beta-galactosidase), and xanthine guanine phosphoribosyltransferase (XGPRT). As with many of the standard procedures associated with the practice of the disclosure, skilled artisans will be aware of additional useful reagents, for example, additional sequences that can serve the function of a marker or reporter.
There is also provided herein a recombinant polynucleotide encoding the SHC enzyme or variant thereof, which may be inserted into a vector for expression and optional purification. One type of vector is a plasmid representing a circular double stranded DNA loop into which additional DNA segments are ligated. Certain vectors can control the expression of genes to which they are functionally linked. These vectors are called “expression vectors”. Usually expression vectors suitable for DNA recombination techniques are of the plasmid type. Typically, an expression vector comprises a gene such as the SHC enzyme or variant thereof as described herein. In the present description, the terms “plasmid” and “vector” may be used interchangeably since the plasmid is the vector type most often use.
Such vectors can include DNA sequences which include but are not limited to DNA sequences that are not naturally present in the host cell, DNA sequences that are not normally transcribed into RNA or translated into a protein (“expressed”) and other genes or DNA sequences which one desires to introduce into the non-recombinant host. It will be appreciated that typically the genome of a recombinant host described herein is augmented through the stable introduction of one or more recombinant genes. However, autonomous or replicative plasmids or vectors can also be used within the scope of this disclosure. Moreover, the present disclosure can be practiced using a low copy number, e.g. a single copy, or high copy number (as exemplified herein) plasmid or vector.
The vector of the present disclosure includes plasmids, phagemids, phages, cosmids, artificial bacterial and artificial yeast chromosomes, knock-out or knock-in constructs, synthetic nucleic acid sequences or cassettes and subsets may be produced in the form of linear polynucleotides, plasmids, megaplasmids, synthetic or artificial chromosomes, such as plant, bacterial, mammalian or yeast artificial chromosomes.
It is preferred that the proteins encoded by the introduced polynucleotide are expressed within the cell upon introduction of the vector. The diverse gene substrates may be incorporated into plasmids. The plasmids are often standard cloning vectors, e.g. bacterial multicopy plasmids. The substrates can be incorporated into the same or different plasmids. Often at least two different types of plasmid having different types of selectable markers are used to allow selection for cells containing at least two types of vectors.
Typically bacterial or yeast cells may be transformed with any one or more nucleotide sequences as is well known in the art. For in vivo recombination, the gene to be recombined with the genome or other genes is used to transform the host using standard transforming techniques. In a suitable embodiment DNA providing an origin of replication is included in the construct. The origin of replication may be suitably selected by the skilled person. Depending on the nature of the genes, a supplemental origin of replication may not be required if sequences are already present with the genes or genome that are operable as origins of replication themselves.
Host Cells, Methods of Making Host Cells and Methods of Making the Compound of Formula (I) Using Host Cells
Recombinant host cells may be used in the methods described herein.
There is further provided herein a recombinant host cell comprising a nucleic acid sequence or a construct or a vector as described herein. There is further provided herein a recombinant host cell that produces a SHC enzyme or enzyme variant as described herein.
The processes described herein for producing the compound of formula (I) may, for example, comprise culturing a recombinant host cell as described herein. As used herein, the term “culturing” refers to a process of maintaining living cells such that they produce a SHC enzyme or enzyme variant as described herein that can be used in a process for producing the compound of formula (I) as described herein. It is not necessary for the cells to divide and replicate themselves, although this is not excluded.
A bacterial or yeast cell may be transformed by exogenous or heterologous DNA when such DNA has been introduced inside the cell. The transforming DNA may or may not be integrated, i.e. covalently linked into the genome of the cell. In prokaryotes, and yeast, for example, the transforming DNA may be maintained on an episomal element such as a plasmid. With respect to eukaryotic cells, a stably transfected cell is one in which the transfected DNA has become integrated into a chromosome so that it is inherited by daughter cells through chromosome replication. This stability is demonstrated by the ability of the eukaryotic cell to establish cell lines or clones comprised of a population of daughter cells containing the transforming DNA.
Generally, the introduced DNA is not originally resident in the host that is the recipient of the DNA, but it is within the scope of the disclosure to isolate a DNA segment from a given host, and to subsequently introduce one or more additional copies of that DNA into the same host, e.g. to enhance production of the product of a gene or alter the expression pattern of a gene. In some instances, the introduced DNA will modify or even replace an endogenous gene or DNA sequence, e.g. by homologous recombination or site-directed mutagenesis. Suitable recombinant hosts include microorganisms, plant cells, and plants.
The present disclosure also features recombinant hosts. The term “recombinant host”, also referred to as a “genetically modified host cell” or a “transgenic cell” denotes a host cell that comprises a heterologous nucleic acid or the genome of which has been augmented by at least one incorporated DNA sequence. A host cell of the present disclosure may be genetically engineered with the polynucleotide or the vector as outlined above.
The host cells that may be used for purposes of the disclosure include but are not limited to prokaryotic cells such as bacteria (for example, E. coli and B. subtilis), which may, for example, be transformed with, for example, recombinant bacteriophage DNA, plasmid DNA, bacterial artificial chromosome, or cosmid DNA expression vectors containing the polynucleotide molecules of the disclosure; simple eukaryotic cells like yeast (for example, Saccharomyces and Pichia), which may, for example, be transformed with, for example, recombinant yeast expression vectors containing the polynucleotide molecule of the disclosure. Depending on the host cell and the respective vector used to introduce the polynucleotide of the disclosure the polynucleotide can integrate, for example, into the chromosome or the mitochondria) DNA or can be maintained extrachromosomally like, for example, episomally or can be only transiently comprised in the cells.
The term “cell” as used herein in particular with reference to genetic engineering and introducing one or more genes or an assembled cluster of genes into a cell, or a production cell is understood to refer to any prokaryotic or eukaryotic cell. Prokaryotic and eukaryotic host cells are both contemplated for use according to the disclosure, including bacterial host cells like E. coli or Bacillus sp. yeast host cells, such as S. cerevisiae, insect host cells, such as Spodoptera frugiperda or human host cells, such as HeLa and Jurkat.
Specifically, the cell is a eukaryotic cell, preferably a fungal, mammalian or plant cell, or a prokaryotic cell. Suitable eukaryotic cells include, for example, without limitation, mammalian cells, yeast cells, or insect cells (including Sf9), amphibian cells (including melanophore cells), or worm cells including cells of Caenorhabditis (including Caenorhabditis elegans). Suitable mammalian cells include, for example, without limitation, COS cells (including Cos-1 and Cos-7), CHO cells, HEK293 cells, HEK293T cells, HEK293 T-Rex™ cells, or other transfectable eucaryotic cell lines. Suitable bacterial cells include without limitation E. coli.
Preferably prokaryotes, such as E. coli, Bacillus, Streptomyces, or mammalian cells, like HeLa cells or Jurkat cells, or plant cells, like Arabidopsis, may be used.
The cell may, for example, be selected from prokaryotic, yeast, plant, and/or insect host cells.
Preferably the cell is an Aspergillus sp. or a fungal cell, preferably, it can be selected from the group consisting of the genera Saccharomyces, Candida, Kluyveromyces, Hansenula, Schizosaccharomyces, Yarrowia, Pichia and Aspergillus.
Preferably, the cell us a bacteria cells, for example, having a genus selected from Escherichia, Streptomyces. Bacillus. Pseudomonas. Lactobacillus and Lactococcus. For example, the bacteria may be E. coli.
Preferably the E. coli host cell is an E. coli host cell which is recognized by the industry and regulatory authorities (including but not limited to an E. coli K12 host cell or an E. coli BL21 host cell).
One preferred host cell to use with the present disclosure is E. coli, which may be recombinantly prepared as described herein. Thus, the recombinant host may be a recombinant E. coli host cell. There are libraries of mutants, plasmids, detailed computer models of metabolism and other information available for E. coli, allowing for rational design of various modules to enhance product yield. Methods similar to those described above for Saccharomyces can be used to make recombinant E. coli micro-organisms.
In one embodiment, the recombinant E. coli microorganism comprises nucleotide sequences encoding SHC enzyme or enzyme variant genes.
Preferably, the recombinant E. coli microorganism comprises a vector construct as described herein. In another preferred embodiment, the recombinant E. coli microorganism comprises nucleotide sequences encoding the SHC enzymes and enzyme variants disclosed herein.
Another preferred host cell to use with the present disclosure is S. cerevisiae which is a widely used chassis organism in synthetic biology. Thus, the recombinant host may be S. cerevisiae. There are libraries of mutants, plasmids, detailed computer models of metabolism and other information available for S. cerevisiae, allowing for rational design of various modules to enhance product yield. Methods are known for making recombinant S. cerevisiae microorganisms.
Culturing of cells may be performed in a conventional manner. The culture medium may contain a carbon source, at least one nitrogen source and inorganic salts, and vitamins are added to it. The constituents of this medium can be the ones which are conventionally used for culturing the species of microorganism in question. Carbon sources of use in the instant method include any molecule that can be metabolized by the recombinant host cell to facilitate growth and/or production of the compound of formula (I). Examples of suitable carbon sources include, but are not limited to, sucrose (e.g. as found in molasses), fructose, xylose, glycerol, glucose, cellulose, starch, cellobiose or other glucose containing polymer.
In embodiments employing yeast as a host, for example, carbon sources such as sucrose, fructose, xylose, ethanol, glycerol, and glucose are suitable. The carbon source can be provided to the host organism throughout the cultivation period or alternatively, the organism can be grown for a period of time in the presence of another energy source, e.g. protein, and then provided with a source of carbon only during the fed-batch phase.
The suitability of a recombinant host cell microorganism for use in the methods of the present disclosure may be determined by simple test procedures using well known methods. For example, the microorganism to be tested may be propagated in a rich medium (e.g. LB-medium, Bacto-tryptone yeast extract medium, nutrient medium and the like) at a pH, temperature and under reaction conditions commonly used for propagation of the microorganism. Once recombinant microorganisms (i.e. recombinant host cells) are selected that produce the desired products of cyclization, the products are typically produced by a production host cell line on the large scale by suitable expression systems and fermentations, e.g. by microbial production in cell culture. In one embodiment of the present disclosure, a defined minimal medium such as M9A is used for cell cultivation.
The components of M9A medium comprise: 14 g/l KH2PO4, 16 g/l K2HPO4, 1 g/l Na3Citrate.2H2O, 7.5 g/l (NH4)2SO4, 0.25 g/l MgSO4.7H2O, 0.015 g/l CaCl2.2H2O, 5 g/l glucose and 1.25 g/l yeast extract).
In another embodiment of the present disclosure, nutrient rich medium such as LB was used. The components of LB medium comprise: 10 g/l tryptone, 5 g/l yeast extract, 5 g/l NaCl. Other examples of Mineral Medium and M9 Mineral Medium are disclosed, for example, in U.S. Pat. No. 6,524,831B2 and US 2003/0092143A1.
Another example of a minimal medium may be prepared as follows: for 350 ml culture: to 35 ml citric acid/phosphate stock (133 g/l KH2PO4, 40 g/l (NH4)2HPO4, 17 g/l citric acid.H2O with pH adjusted to 6.3) was added 307 ml H2O, the pH adjusted to 6.8 with 32% NaOH as required. After autoclaving 0.850 ml 50% MgSO4, 0.035 ml trace elements solution (see below) solution, 0.035 ml Thiamin solution and 7 ml 20% glucose were added.
Trace elements solution: 50 g/i Na2EDTA.2H2O, 20 g/l FeSO4.7H2O, 3 g/l H3BO3, 0.9 g/l MnSO4.2H2O, 1.1 g/l CoCl2, 80 g/L CuCl2, 240 g/l NiSO4.7H2O, 100 g/l KI, 1.4 g/l (NH4)6Mo7O24.4H2O, 1 g/l ZnSO4.7H2O, in deionized water
Thiamin solution: 2.25 g/l Thiamin.HCl in deionized water
MgSO4 solution: 50% (w/v) MgSO4.7H2O in deionized water
The recombinant microorganism may be grown in a batch, fed batch or continuous process or combinations thereof. Typically, the recombinant microorganism is grown in a fermenter at a defined temperature(s) in the presence of a suitable nutrient source. e.g. a carbon source, for a desired period of time to produce sufficient enzyme to cyclize the compound of formula (II) (e.g. a compound of formula (IIa) and or (fib)) to the compound of formula (I) and to produce a desired amount of the compound of formula (I). The recombinant host cells may be cultivated in any suitable manner, for example by batch cultivation or fed-batch cultivation.
As used herein, the term “batch cultivation” is a cultivation method in which culture medium and/or nutrients is neither added nor withdrawn during the cultivation.
As used herein, the term “fed-batch” means a cultivation method in which culture medium and/or nutrients is added during the cultivation but no culture medium is withdrawn.
One embodiment of the present disclosure provides a method of producing the compound of formula (I) in a cellular system comprising expressing SHC enzymes or enzyme variants under suitable conditions in a cellular system, feeding the compound of formula (H) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) to the cellular system, converting the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (fib)) to the compound of formula (I) using the SHC enzymes or enzyme variants produced using the cellular system, collecting the compound of formula (I) (e.g., a compound of formula (IIa) and/or a compound of formula (fib)) from cellular system and optionally isolating the compound of formula (I) from the system. Expression of other nucleotide sequences may serve to enhance the method. The cyclization method can include the additional expression of other nucleotide sequences in the cellular system. The expression of other nucleotide sequences may enhance the cyclization pathway for making the compound of formula (I).
A further embodiment of the present disclosure is a cyclization method of making the compound of formula (I) comprising growing host cells comprising SHC enzyme or enzyme variant genes, producing SHC enzymes or enzyme variants in the host cells, feeding the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) to the host cells, incubating the host cells under conditions of pH, temperature and solubilizing agent suitable to promote the conversion of the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) to the compound of formula (I) and collecting the compound of formula (I). The production of the SHC enzymes or enzyme variants in the host cells provides a method of making the compound of formula (I) when the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) is added to the host cells under suitable reaction conditions. Achieved conversion may be enhanced by adding more biocatalyst and SOS to the reaction mixture.
The recombinant host cell microorganism may be cultured in a number of ways in order to provide cells in suitable amounts expressing the SHC enzymes or enzyme variants for the subsequent cyclization step. Since the microorganisms applicable for the cyclization step vary broadly (e.g. yeasts, bacteria and fungi), culturing conditions are, of course, adjusted to the specific requirements of each species and these conditions are well known and documented. Any of the art known methods for growing cells of recombinant host cell microorganisms may be used to produce the cells utilizable in the subsequent cyclization step of the present disclosure. Typically the cells are grown to a particular density (measurable as optical density (OD)) to produce a sufficient biomass for the cyclization reaction.
The cultivation conditions chosen influence not only the amount of cells obtained (the biomass) but the quality of the cultivation conditions also influences how the biomass becomes a biocatalyst. The recombinant host cell microorganism expressing the SHC enzyme or enzyme variant gene and producing the SHC enzyme or enzyme variant is termed a biocatalyst which is suitable for use in a cyclization reaction. In some embodiments the biocatalyst is a recombinant whole cell producing SHC enzymes or enzyme variants or it may be in suspension or an immobilized format. In other embodiments, the biocatalyst is a membrane fraction or a liquid fraction prepared from the recombinant whole cell producing the SHC enzyme or enzyme variant (as disclosed for example in Seitz et a/2012—as cited above). The recombinant whole cell producing SHC enzymes or enzyme variants include whole cells collected from the fermenter (for the cyclization reaction) or the cells in the fermenter (which are then used in a one-pot reaction). The recombinant whole cell producing SHC enzymes or enzyme variants can include intact recombinant whole cell and/or cell debris. Either way, the SHC enzyme or enzyme variant is associated with a membrane (such as a cell membrane) in some way in order to receive and/or interact with a substrate (e.g. compound of formula (II)), which membrane (such as a cell membrane) can be part of or comprise a whole cell (e.g. a recombinant whole cell). The SHC enzymes or enzyme variants may also be in an immobilized form (e.g. associated with an enzyme carrier) which allows the SHC enzymes or enzyme variants to interact with a substrate (e.g. compound of formula (II)). The SHC enzymes or enzyme variants may also be used in a soluble form.
In one embodiment, the biocatalyst is produced in sufficient amounts (to create a sufficient biomass), harvested and washed (and optionally stored, e.g. refrigerated, frozen or lyophilized)) before starting the bioconversion step.
In a further embodiment, the cells are produced in sufficient amounts (to create a sufficient biocatalyst) and the reaction conditions are then adjusted without the need to harvest and wash the biocatalyst for the cyclization reaction. This one step (or “one pot”) method is advantageous as it simplifies the process while possibly reducing costs. The culture medium used to grow the cells is also suitable for use in the cyclization reaction provided that the reaction conditions are adjusted to facilitate the cyclization reaction.
The optimum pH for growing the cells is in the range of 6.0-7.0. The optimum pH for the cyclization reaction is dependent on the type of SHC enzyme or enzyme variant used in the cyclization reaction. The pH is regulated using techniques which are well known to the Skilled Person.
Whilst the terms “mixture” or “reaction mixture” may be used interchangeably with the term “medium” in the present disclosure (especially as it relates to a “one pot” reaction), it should be noted that growing the cells to create a sufficient biomass requires a cell culture/fermentation medium but a medium is not required for the cyclization step as a reaction buffer will suffice at a suitable pH.
The cyclization methods of the present disclosure are carried out under conditions of time, temperature, pH and solubilizing agent to provide for conversion of the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) to the compound of formula (I).
The pH of the reaction mixture may be in the range of 4-8, preferably, 5 to 6.5, more preferably 4.8-6.0 for the SHC enzyme variants and in the range of from about pH 5.0 to about pH 7.0 for the wild-type SHC enzymes and can be maintained by the addition of buffers to the reaction mixture. An exemplary buffer for this purpose is a citric acid buffer, a phosphate buffer, an acetic acid buffer and/or a succinic acid buffer.
The preferred temperature is between from about 15° C. and about 60° C., for example from about 15° C. to about 50° C. or from about 15° C. to about 45 C or from about 30° C. to about 60 C or from about 40° C. to about 50° C. The temperature can be kept constant or can be altered during the cyclization process.
It may be useful to include a solubilizing agent (e.g. a surfactant, detergent, solubility enhancer, water miscible organic solvent and the like) in the cyclization reaction.
As used herein, the term “surfactant” means a component that lowers the surface tension (or interfacial tension) between two liquids or between a liquid and a solid.
Surfactants may act as detergents, wetting agents, emulsifiers, foaming agents, and dispersants. Examples of surfactants include but are not limited to Triton X-100, Tween 80, taurodeoxycholate, Sodium taurodeoxycholate, Sodium dodecyl sulfate (SDS), and/or sodium lauryl sulfate (SLS).
Whilst Triton X-100 may be used to partially purify the SHC enzyme or enzyme variant (in soluble or membrane fraction/suspension form), it may also be used in the cyclization reaction (see for example the disclosure in Seitz (2012 PhD thesis as cited above) as well as the disclosure in Neumann and Simon (1986—as cited above) and JP2009060799. SDS may be used as a solubilizing agent.
Without wishing to be bound by theory, the use of SDS with recombinant microbial host cells may be advantageous as the SDS may interact advantageously with the host cell membrane in order to make the SHC enzyme or enzyme variant (which is a membrane bound enzyme) more accessible to the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (fib)) substrate. In addition, the inclusion of SOS at a suitable level in the reaction mixture may improve the properties of the emulsion (e.g. compound of formula (II) in water) and/or improve the access of the compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) substrate to the SHC enzyme within the host cell while at the same time preventing the disruption (e.g. denaturation of the SHC (WT or SHC variant) enzyme). The concentration of the solubilising agent (e.g. SDS) used in the cyclization reaction is influenced by the biomass amount and the substrate concentration. That is, there is a degree of interdependency between the solubilising agent (e.g. SDS) concentration, the biomass amount and the substrate concentration. By way of example, as the concentration of compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) substrate increases, sufficient amounts of biocatalyst and solubilising agent (e.g. SDS) are required for an efficient cyclization reaction to take place. If, for example, the solubilising agent (e.g. SDS) concentration is too low, a suboptimal compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) conversion may be observed. On the other hand, if, for example, the solubilising agent (e.g. SDS) concentration is too high, then there may be a risk that the biocatalyst is affected through either the disruption of the intact microbial cell and/or denaturation/inactivation of the SHC enzyme or enzyme variant. The selection of a suitable concentration of SOS in the context of the biomass amount and, substrate (concentration is within the knowledge of the Skilled Person).
The temperature of the cyclization reaction for a WT SHC enzyme (eg. AacSHC) may be from about 30° C. to about 60° C., for example from about 45° C. to about 60° C., for example from about 50° C. to about 60° C., for example about 55° C.
The pH range of the cyclization reaction for a WT SHC enzyme (eg. AacSHC) may be from about 5.0 to 7.0, more preferably from about 5, 6 to about 6.2, even more preferably about 6.0.
The temperature of the cyclization reaction for a SHC enzyme variant may be about 30 C to about 55° C., for example from about 40° C. to about 50° C., for example about 45° C.
The pH of the cyclization reaction for a SHC enzyme variant may be about 4.8-6.4, preferably about 5.2-6.0.
The [SDS]/[cells] ratio may be in the range of about, 10:1-20:1, preferably about 15:1-18:1, preferably about 16:1 when the ratio of biocatalyst to compound of formula (II) is about 2:1.
The optimum temperature for the SHC enzyme variants may, for example, be equal to or greater than about 35° C. For example, the optimum temperature for the SHC enzyme variants may range from about 40° C. to about 50° C., for example from about 42° C. to about 48° C. or from about 44° C. to about 46° C. For example, the optimum temperature of the SHC enzyme variants may be about 45° C. The processes for making the compound of formula (I) disclosed herein may be carried out at the optimum temperature of the SHC enzyme variant.
The optimum pH for the SHC enzyme variants may, for example, be equal to or greater than about 5.4. For example, the optimum pH for the SHC enzyme variants may range from about 5.2 to about 6.0, for example from about 5.4 to about 5.8, for example from about 5.6 to about 5.8. For example, the optimum pH of the SHC enzyme variants may be about 5.6 or about 5.8. The process for making the compound of formula (I) disclosed herein may be carried out at the optimum pH of the SHC enzyme variant.
The optimum concentration of sodium dodecyl sulfate (SDS) in the reaction medium of the process for making the compound of formula (I) disclosed herein may, for example, be from about 0.010 w/w % to about 0.10 w/w %. For example, the optimum concentration of SDS may be from about 0.040 w/w % to about 0.080 w/w %, for example about 0.050 w/w % when the substrate is used at 4 g/l with cells to an OD650 nm, of 10. The process for making the compound of formula (I) disclosed herein may be carved out using the optimum concentration of SDS described herein.
The processes for making the compound of formula (I) disclosed herein may be carried out within the optimum temperature range or at the optimum temperature and/or within the optimum pH range or at the optimum pH and/or within the SOS optimum concentration range or at the optimum SDS concentration for the specific enzyme used, as set out in Table 3 in the Examples below.
In some embodiments, the compound of formula (I) is produced using a biocatalyst to which the compound of formula (II) substrate is added.
It is possible to add the substrate by feeding using known means (e.g. peristaltic pump, infusion syringe and the like). The compound of formula (II) may be oil soluble and provided in an oil format. Given that the biocatalyst (microbial cells such as intact recombinant whole cell and/or cell debris and/or immobilised enzyme) is present in an aqueous phase, the cyclization reaction may be regarded as a three phase system (comprising an aqueous phase, a solid phase and an oil phase) when compound of formula (II) is added to the reaction mixture. This is the case even when SDS is present. By way of clarification, when a soluble WT SHC or a SHC enzyme variant is used as a biocatalyst, this is considered a two phase system.
A fermenter may be used to grow recombinant host cells expressing the SHC enzyme or enzyme variant gene and producing active SHC enzymes or enzyme variants to a sufficient biomass concentration suitable for use as a biocatalyst in the same fermenter vessel which is used to convert the compound of formula (II) source to the compound of formula (I), for example in admixture with one or more of the by product of formula (III).
The Skilled Person will understand that higher cumulative production titers can be achieved by implementing a continuous process, such as product removal, substrate feed, and biomass addition or (partial) replacement. Preferably the cyclization of compound of formula (II) into compound of formula (I) in the presence of a recombinant host cell comprising a SHC enzyme or enzyme variant generates an compound of formula (I) yield of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, given in mol percent and based on the mols of compound of formula (II) employed; especially preferably, the yield is between 5 and 100, 10 and 100, and 100, 25 and 100, 30 and 100, 35 and 100, in particular between 40 and 100, 45 and 100, 50 and 100, 60 and 100, 70 and 100 mol percent.
The activity of the SHC enzyme or enzyme variant is defined via the reaction rate (amount of product/(amount of product+amount of remaining starting material))×100) in mot percent. Preferably, the cyciization of compound of formula (II) into compound of formula (I) in the presence of a SHC enzyme or enzyme variant produces compound of formula (I) yield of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, given in mol percent and based on the mols of compound of formula (II) employed; especially preferably, the yield is between 5 and 100, 10 and 100, 20 and 100, 25 and 100, 30 and 100, 35 and 100, in particular between 40 and 100, 45 and 100.50 and 100, 60 and 100, 70 and 100.
In a preferred embodiment of the invention, the yield and/or the reaction rate are determined over a defined time period of, for example, 4, 6, 8, 10, 12, 16, 20, 24, 36 or 48 hours, during which compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) is converted into compound of formula (I) by a recombinant host cell comprising a nucleotide sequence encoding a SHC enzyme or enzyme variant. In a further variant, the reaction is carried out under precisely defined conditions of, for example, 25° C., 30° C., 40° C. 50° C. or 60° C. In particular, the yield and/or the reaction rate are determined by carrying out the reaction of converting compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) into compound of formula (I) by the SHC enzymes or enzyme variants according to the invention at 35 C over a period of 24-72 hours.
In a further embodiment of the present invention, a recombinant host cell comprising a nucleotide sequence encoding a SHC enzyme variant is characterized in that it shows a 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 11-, 12-, 13-, 14-, 15-, 16-, 17-, 18-, 19-, 20-, 21-, 22-, 23-, 24-, 25-, 26-, 27-, 28-, 29-, 30-, 31-, 32-, 33-, 34-, 35-, 36-, 37-, 38-, 39-, 40-, 41-, 42-, 43-, 44-, 45-, 46-, 47-, 48-, 49-, 50-, 51-, 52-, 53-, 54-, 55-, 56-, 57-, 58-, 59-, 60-, 61-, 62-, 63-, 64-, 65-, 68-, 67-, 68-, 69-, 70-, 71-, 72-, 73-, 74-, 75-, 76-, 77-, 78-, 79-, 80-, 81-, 82-, 83-, 84-, 85-, 86-, 87-, 88-, 89-, 90-, 91-, 92-, 93-, 94-, 95-, 96-, 97-, 98-, 99-, 100-, 200-, 500-, 1000-fold or higher yield and/or reaction rates in the reaction of compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (Ib)) to give compound of formula (I) in comparison with the WT SHC or SHC derivative enzyme under the same conditions. Here, the term condition relates to reaction conditions such as substrate concentration, enzyme concentration, reaction time and/or temperature.
The successful development of a cyclization process for making compound of formula (I) from compound of formula (II) (e.g., a compound of formula (IIa) and/or a compound of formula (IIb)) in a recombinant strain of E. coli comprising a nucleotide sequence encoding a Wt/reference SHC or a SHC derivative can offer a low cost and industrially economical process for compound of formula (I) production.
Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. The term “comprising” also means “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y. It must be noted also that, as used in this specification and the appended claims, the singular forms “a”, “an” and “the” include plural referents unless the content dearly dictates otherwise. By way of example, a reference to “a gene” or “an enzyme” is a reference to “one or more genes” or “one or more enzymes”.
It is to be understood that this disclosure is not limited to the particular methodology, protocols and reagents described herein as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present disclosure which will be limited only by the appended claims. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by the person skilled in the art. In accordance with the present disclosure there may be conventional molecular biology, microbiology, and recombinant DNA techniques employed which are within the skill of the art.
This disclosure is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The disclosure is capable of other embodiments and of being practiced or of being carried out in various ways. Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. Preferably, the terms used herein are defined as described in “A multilingual glossary of biotechnological terms: (IUPAC Recommendations)”, Leuenberger, H. G. W, Nagel, B. and Kolbl, H. eds. (1995), Helvetica Chimica Acta, CH-4010 Basel, Switzerland).
Several documents are cited throughout the text of this specification. Each of the documents cited herein (including all patents, patent applications, scientific publications, manufacturer's specifications, instructions, GenBank Accession Number sequence submissions etc.), whether supra or infra, is hereby incorporated by reference in its entirety.
The examples described herein are illustrative of the present disclosure and are not intended to be limitations thereon. Different embodiments of the present disclosure have been described according to the present disclosure. Many modifications and variations may be made to the techniques described and illustrated herein without departing from the spirit and scope of the disclosure. Accordingly, it should be understood that the examples are illustrative only and are not limiting upon the scope of the disclosure.
A composition comprising a mixture of E,E- and E,2-stereoisomers of ethyl-homofarnesol was made by the scheme illustrated in
To a suspension of potassium carbonate (79.4 g, 575 mmol, 1.0 equiv) in DMF (1250 ml) was added ethyl 3-oxopentanoate (91.2 g, 632 mmol) and the mixture was stirred for 20 minutes at room temperature. Geranylbromide (125 g, 575 mmol, 1 equiv) was added and the mixture was stirred at room temperature for 16 h. After the addition of ice and stirring for 10 minutes, the product was extracted with ethyl acetate (3 times 650 ml). The combined organic layer were washed with water (twice 650 ml) and brine (650 ml), dried over Na2SO4, filtered and concentrated under vacuum. The crude product was purified by column chromatography over silica gel using 0-4% of EtOAc in petrolether to yield methyl (E)-5,9-dimethyl-2-propionyldeca-4,8-dienoate (2) (120 g, 74%) as a liquid.
To a solution of 2 (57 g, 203.2 mmol, 1.0 Equiv) in methanol (210 ml) was added aqueous 5N KOH solution (114 ml) at room temperature. The solution was then heated to reflux under stirring for 2.5 h, then cooled to room temperature and 2N HCl until pH 3-4. The product was extracted with ethyl acetate (twice 250 ml) and the combined organic layer was washed with water (twice 100 ml) and brine (100 ml), dried over anhydrous Na2SO4 and the solvent was removed under reduced pressure. The crude (E)-7,11-dimethyldodeca-6,10-dien-3-one (3) thus obtained (35 g, 83%) was further converted without purification.
To a stirred suspension of sodium hydride (23.3 g, 576 mmol, 3.0 equiv) in THE (200 ml) was added triethyl phosphonoacetate (129.1 g, 576 mmol, 3.0 equiv) in THF (100 ml) dropwise over a period of 2 h at −10° C. and stirred at room temperature for additional 30 min. A solution of 3 prepared above (40 g, 192 mmol, 1.0 equiv) in THF (100 ml) was added drowise over a period of one hour. The reaction mixture was stirred at room temperature for 3-4 h. The reaction mixture was poured on to ice and then the product was extracted with ethyl acetate (0.8 L) and organic layer was washed with water (400 ml) and brine (400 ml). The organic layer was dried over Na2SO4 and the solvent was evaporated under reduced pressure to yield ethyl 3-ethyl-7,11-dimethyldodeca-2,6,10-trienoate (4) (40 g, 75%) as a liquid. The crude compound was used in the next step without purification.
To an ice cooled solution of DIBAL-H (593 ml, 593 mmol, 3.0 equiv) in THE (500 ml) was added dropwise a solution of 4 (55 g, 197.5 mmol, 1.0 equiv) in THF (100 ml). The reaction mixture was stirred at room temperature for 4 h. The reaction was quenched with saturated ammonium chloride solution (300 ml) at 0° C. and stirred for 30 minutes. The mixture was filtered through Celite and the Celite bed was washed with ethyl acetate (1 L). The filtrate was washed with water and brine. The organic layer was dried over Na2SO4 and solvent was evaporated on rotary evaporator. The crude product was purified by column chromatography over silica gel using 0-15% of EtOAc in petrolether to afford 3-ethyl-7,11-dimethyldodeca-2,6,10-trien-1-ol (5) (43 g, 92%) as a liquid.
To a solution of 5 (50 g, 212 mmol, 1.0 equiv) in DMF (500 ml) was dropwise added s-collidine (103 g, 846 mmol, 4.0 equiv) at room temperature. The reaction mixture was cooled to 0° C., then mesyl chloride (48.3 g, 423 mmol, 2.0 equiv) was added dropwise over a period of one hour. The reaction mixture was stirred at room temperature for 2 h. Lithium chloride (35.7 g, 846 mmol) was added and the mixture was stirred at room temperature for 16 h. The reaction was quenched with ice-water (1 L) and the product was extracted with petrol ether (1 L). The organic layer was washed with water (three times 500 ml) and brine (500 ml). The organic layer was dried over sodium sulphate and concentrated under reduced pressure to yield 1-chloro-3-ethyl-7,11-dimethyldodeca-2,6,10-triene (6) (50 g). The crude product was used without any purification.
To a stirred solution of KCN (34.7 g, 533 mmol, 2.3 equiv) in DMSO (500 ml) was drop wise added a solution of 6 (59 g, 232 mmol) in DMSO (100 ml) at room temperature. The reaction mixture was stirred at room temperature overnight. The reaction was quenched with ice cold water (2.0 L) and the product was extracted with ethyl acetate (twice 1 L). The combined organic layer was washed with water (three times 750 ml) and brine (750 ml). The organic layer was dried over sodium sulfate and concentrated under reduced pressure to afford 4-ethyl-8,12-dimethyltrideca-3,7,11-trienenitrile (7) (56 g, 98%) as a liquid.
To a stirred solution of 7 prepared above (29 g, 118 mmol, 1.0 equiv) in ethanol (232 ml) was added a solution of KOH (53.0 g, 945 mmol, 8.0 equiv) in water (232 ml). The reaction mixture was stirred at reflux for overnight. Ethanol was removed under reduced pressure and the residue was cooled to 5-10° C. The mixture was acidified with 1.5 N HCl to pH 3-4 and diluted with water. The product was extracted with DCM (twice 500 ml) and the combined organic layer was washed with water (500 ml). The organic layer was dried and concentrated under vacuum. The crude product was purified by column chromatography over silica gel using 0-60% of EtOAc in petrolether to yield 4-ethyl-8,12-dimethyltrideca-3,7,11-trienoic acid (8) (14 g, 45%) as a liquid.
To a suspension of LAH (2.75 g, 72.6 mmol, 1.2 equiv) in THF (140 ml) was added a solution of 8 as prepared above (16 g, 60.5 mmol, 1.0 equiv) in THF (40 ml) at −10° C. The reaction mixture was stirred at room temperature for 3 h. The reaction mixture was cooled to 0° C. and slowly quenched with water (2.75 ml), 10% sodium hydroxide solution (2.75 ml) and again water (8.25 ml). The suspension was stirred at room temperature for 30 minutes and then filtered through a Celite bed. The filtrate was concentrated and the residue was purified by column chromatography followed by fractional distillation to yield 4-ethyl-8,12-dimethyltrideca-3,7,11-trien-1-ol as a liquid (10.5 g, 69%) as a slightly yellow mixture. GC-MS analysis indicates the presence of 6 double bond and E,Z-isomers (relative peak areas 39; 23; 23; 3; 2; 2%).
1H-NMR (400 MHz, CDCl3): 5.06-5.17 (m, 3H), 3.59-3.68 (m, 2H), 2.27-2.37 (m, 2H), 1.95-2.15 (m, 11H), 1.69 (br. s, 3H), 1.61 (br. s, 6H), 0.96-1.06 (m, 3H). 13C-NMR (100 MHz, COCl3, major 3 isomers): 144.6 (s), 144.4 (s), 135.3 (s), 135.1 (s), 135.0 (s), 131.3 (s), 131.3 (s), 131.2 (s), 124.4 (d), 124.3 (d), 124.3 (d), 124.2 (d), 124.1 (d), 124.1 (d), 124.0 (d), 119.3 (d), 118.8 (d), 62.8 (t), 62.6 (t), 62.5 (t), 39.7 (t), 39.7 (t), 36.8 (t), 36.5 (t), 33.2 (t), 31.3 (t), 31.1 (t), 31.1 (t), 30.5 (t), 29.8 (t), 29.6 (t), 27.0 (t), 26.7 (t), 26.7 (t), 26.6 (t), 25.7 (q), 23.4 (t), 23.2 (t), 17.7 (q), 16.0 (q), 15.9 (q), 13.3 (q), 13.2 (q), 13.2 (q), 12.8 (q). MS (EI, 70 eV): (isomer 1, rt 9.29 min, 3%) 136(11), 123(12), 107(12), 93(10), 81(40), 69(100), 55(13), 41(56); (isomer 2, rt 9.31 min, 2%) 250 (<1, M+), 136(5), 123(16), 107(11), 81(32), 69(100), 55(13), 41(40); (isomer 3, rt 9.56 min, 2%) 181(4), 166(4), 137(15), 109(15), 95(36), 81(83), 69(100), 55(33), 41(60); (isomer 4, rt 9.67 min, 23%), 250 (<1, M), 235(<1), 181(2), 136(1), 121(11), 107(7), 95(19), 81(49), 69(100), 55(21), 41(49); (isomer 5, rt 9.72 min, 39%) 250 (<1, M+), 235(<1), 181(4), 136(13), 121(10), 107(9), 95(21), 81(36), 69(100), 55(20), 41(48); (isomer 6, rt 9.82 min, 23%), 250 (<1, M+), 235(<1), 181(3), 136(7), 121(12), 107(9), 95(25), 81(36), 69(100), 55(16), 41(51);
A solution of (E)-6,10-dimethylundeca-5,9-dien-1-yne (8.0 g, 45.4 mmol) and bis-dicyclopentadienyl zirconium dichloride (13.3 g, 45.4 mmol) in dichloromethane (150 mL) was cooled under stirring to −50° C. A solution of Methyl aluminium in hexane (1.0 M, 136 mL, 136 mmol, 3 equiv.) was added dropwise, upon which the temperature rose to −45° C. After complete addition, the cooling bath was removed and stirring continued at room temperature for 8 hours. After cooling to −10° C., the solution of ethylene oxide in THE (2.5 M, 20 mL, 50 mmol, 1.1 equiv.) was added dropwise, upon which the temperature rose to 0° C. After complete addition the cooling bath was removed and stirring was continued for 19 hours at room temperature. The mixture was filtered and the filtrate was poured carefully on 300 mL ice-cold 2 M aqueous HCl-solution. After extraction with MTBE (150 mL), the organic layer was washed with water (200 mL) and with dilute aqueous NaCl solution (pH neutral). The organic layer was dried over MgSO4, suction filtered and the filtrate was concentrated on a rotary evaporator to yield 15.3 g of a clear, yellow liquid, which was purified by flash chromatography on silica gel, eluting with heptane/MTBE 4:1 to isolate (3E,7E)-4-ethyl-8,12-dimethyltrideca-3,7,11-trien-1-ol (3.26 g, 29%) as a clear, colourless liquid (gas chromatographical purity 81%).
1H-NMR (400 MHz, CDCl3): 4.93-5.02 (m, 3H), 3.49 (t, J=6.5 Hz, 2H), 2.17 (q, J=6.7 Hz, 2H), 1.82-2.01 (m, 11H), 1.56 (d, J=1.0 Hz, 3H), 1.48 (s, 6H), 0.86 (t, J=7.5 Hz, 3H). 13C-NMR (100 MHz, CDCl3): 144.8 (s), 135.2 (s), 131.3 (s), 124.3 (d), 124.1 (d), 119.3 (d), 62.6 (t), 39.7 (t), 36.5 (t), 31.2 (t), 28.7 (t), 26.7 (t), 25.7 (q), 23.2 (t), 17.7 (q), 16.0 (q), 13.3 (q). MS (EI, 70 eV): 250 (<1), 235 (<1), 221 (<1), 207 (2), 181 (5), 166 (4), 137 (17), 121 (14), 107 (11), 95 (25), 81 (42), 69 (100), 55 (22), 41 (49).
SHC Plasmid Preparation
The gene encoding a wild-type or variant squalene hopene cyclase (SHC) enzyme was inserted into plasmid pET-28a(+), where it is under the control of an IPTG inducible T7-promotor for protein production in Escherichia coli. The plasmid was transformed into E. coli strain BL21(DE3) using a standard heat-shock transformation protocol.
Media Preparation
The minimal medium chosen as default was prepared as follows for 350 ml culture: to 35 ml citric acid/phosphate stock (133 g/l KH2PO4, 40 g/l (NH4)2HPO4, 17 g/l citric acid.H2O with pH adjusted to 6.3) was added 307 ml H2O, the pH adjusted to 6.8 with 32% NaOH as required. After autoclaving 0.850 ml 50% MgSO4, 0.035 ml trace elements solution (see below), 0.035 ml Thiamin solution and 7 ml 20% glucose were added.
Trace elements solution: 50 g/l Na2EDTA.2H2O, 20 g/l FeSO4.7H2O, 3 g/l H3BO3, 0.9 g/l MnSO4.2H2O, 1.1 g/l CoCl2, 80 g/L CuCl2, 240 g/l NiSO4.7H2P, 100 g/l KI, 1.4 g/l (NH4)5Mo7O24.4H2O, 1 g/l ZnSO4.7H2O, in deionized water
Thiamin solution: 2.25 g/l Thiamin.HCl in deionized water
MgSO4 solution: 50% (w/v) MgSO4.7H2O in deionized water
SHC Enzyme of Enzyme Variant Production (Biocatalyst Production)
Small Scale Biocatalyst Production (Wild-Type SHC or SHC Variants)
350 ml culture (medium supplemented with 50 μg/ml kanamycin) were inoculated from a preculture of the E. coli strain BL21(DE3) containing the SHC production plasmid. Cells were grown to an optical density of approximately 0.5 (OD650 nm) at 37° C. with constant agitation (250 rpm). Enzyme production was then induced by the addition of IPTG to a concentration of 300 μM followed by incubation for a further 5-6 hours with constant shaking. The resulting biomass was finally collected by centrifugation and washed with e.g. 50 mM Tris-HCl buffer pH 7.5. The cells were stored as pellets at 4° C. or −20° C. until further use. In general 2.5 to 4 grams of cells (wet weight) were obtained from 1 litre of culture, independently of the medium used.
Biocatalyst Production in Fermenters
Fermentations were prepared and run in 750 ml InforsHT reactors. To the fermentation vessel was added 168 ml deionized water. The reaction vessel was equipped with all required probes (pO2, pH, sampling, antifoam), C+N feed and sodium hydroxide bottles and autoclaved. After autoclaving is added to the reactor
The fermenter was inoculated from a seed culture to an OD650 nm of 0.4-0.5. This seed culture was grown in LB medium (+Kanamycin) at 37° C., 220 rpm for 8 h. The fermentation was run first in batch mode for 11.5 h, where after was started the C+N feed with a feed solution (sterilized glucose solution (143 ml H2O+35 g glucose) to which had been added after sterilization: 17.5 ml (NH4)2SO4 solution, 1.8 ml MgSO4 solution, 0.018 ml trace elements solution, 0.360 ml Thiamine solution, 0.180 ml kanamycin stock. The feed was run at a constant flow rate of approx. 4.2 mi/h. Glucose and NH4+ measurements were done externally to evaluate availability of the C- and N-sources in the culture. Usually glucose levels stay very low.
Cultures were grown for a total of approximately 25 hours, where they reached typically an OD650 nm of 40-45. SHC production was then started by adding IPTG to a concentration of approx. 1 mM in the fermenter (as IPTG pulse or over a period of 3-4 hours using an infusion syringe), setting the temperature to 40 C and pO2 to 20%. Induction of SHC production lasted for 16 h at 40° C. At the end of induction the cells were collected by centrifugation, washed with 0.1 M citric acid/sodium citrate buffer pH 5.4 and stored as pellets at 4° C. or −20° C. until further use.
Results
Six SHC enzyme variants were derived from the AacSHC enzyme variant 21562 disclosed in WO 2016/170099. The six new SHC enzyme variants have the mutations (compared to wild-type AacSHC) listed in Table 2 below. These mutations are in addition to the mutations M132R, A224V and 14321, which were present in the 21562 SHC enzyme variant (parent enzyme).
The new mutations identified in the SHC variants created are not in the vicinity of the active site of the enzyme as was observed previously when evolving wild-type Alicyclobacillus acidocaldarius SHC to 215G2SHC. The majority of the new mutations identified are located again in domain 2 of the crystal structure of the enzyme (T90A, A1721, M277K and H431L). Two are located in domain 1 (A557T and R613S) and 1 at the interface between the 2 domains (Y81H).
Reaction parameters investigated: temperature, SOS concentration and pH
The reaction conditions for the SHC variants listed in Table 2 above in relation to Example 3 were individually optimized with regards to temperature, pH and SDS concentration.
Biocatalyst was prepared from the different variants by fermentation as described above using the E. coli cells transformed with the corresponding plasmid. Cells were collected by centrifugation, and stored at −20° C. until further used. The biocatalysts produced showed very similar SHC content. It could therefore be concluded that the differences in activity observed were due to the inserted mutations.
Results
Reactions of 2-5 ml volume with 4 g/l EEH and biocatalyst loaded at an OD650 nm of 10.0 were run in 0.1 M citric acid/sodium phosphate buffer pH 5.0-6.8, in the presence of 0.0125-0.125% SOS at temperatures ranging from 28 to 50° C. and under constant agitation (Heidolph synthesis 1 Liquid device, 900 rpm).
The conditions listed in Table 3 below appeared to be the individual optimal conditions. They were confirmed in reactions run in 0.1 M succinic acid/NaOH buffer at pH around pH defined earlier as optimal.
Some deviation from the 215G2SHC parent enzyme was noted. With only one exception the introduction of the new mutations shifted optimal temperature by 10° C. from 35° C. to about 45° C.
Method—SHC Cyclization of Ethyl-Homofarnesol
The activity of wild-type and variant SHC enzymes was tested under reaction conditions individually defined as optimal and as set out in Example 4 (temperature, pH, SDS concentration), or at pH 6.0, 55T and in the presence of 0.060% SOS with wild type Alicyclobacillus acidocaldarius (Aac) SHC. The reactions (5 ml volume) contained 4 g/l Ethyl-homofarnesol prepared according to Example 1. Cells that had produced the SHC variants or WT Aac SHC were added to an OD650 nm of 10.0 to start the reaction. The reactions were incubated on a Heidolph Synthesis 1 Liquid 16 device under constant agitation (900 rpm).
Results—SHC Cyclization of Ethyl-Homofarnesol
Ethyl-homofarnesol cyclization was successful with 21502 SHC and variants of this enzyme. The amino acid mutations introduced in 215G2 SHC slightly increased conversion with all variants, and significantly with one of them (SHC #65) (see Table 4 below).
Ethyl-homofarnesol conversion in reactions run at 4 g/i substrate and with biocatalyst loaded at an OD650 nm of 10.0 applying individually optimized reaction conditions (1, pH, [SDS]).
The reaction vessel (0.75 l Infors fermenter) was loaded with a total amount of 2.9 g Ethyl-homofarnesol prepared according to Example 1 (2.0 g were added at reaction start and a further 0.9 g approximately 48 hours later), 1.95 g SDS was added from a 15.5% (w/w) solution prepared in deionized water. A cell suspension was prepared from E. coli cells that had produced the 215G2 SHC variant (as outlined in Example 3) by suspending the cells in 0.1 M succinic acid/NaOH buffer pH 5.1. After determination of the cell wet weight concentration of this cell suspension by centrifugation for 10 min at 10° C. and 17210 g, the appropriate volume of cells was added to the reaction vessel in order to introduce 37.5 g of cells into the reaction.
The volume of the reaction was completed to 150 g with the required amount of reaction buffer pH 5.1. The reaction was run at 35° C. and pH 5.4 under constant stirring (700 rpm). The pH was set to 5.4 using 85% H3PO4. pH regulation was done manually using 85% phosphoric acid as required. The reaction was sampled over time (1 ml), extracted with 5 volumes of MTBE/tBME (5 ml). The substrate and product content of the reaction was determined by GC analysis after clarification of the solvent phase by centrifugation (table top centrifuge, 13000 rpm, 2 min). About 75% Ethyl-homofarnesol conversion was obtained in the reaction that was run for approx. 4 days.
The crude MTBE extract was concentrated on a rotary evaporator and the residue was filtered over silica gel with MTBE as eluent. After removal of the solvent, a brown liquid (4.3 g) was obtained, which was purified by flash chromatography over silica gel with heptane/MTBE 50:1. From this a white, crystalline solid was obtained (300 mg, 10% isolated yield), which consisted of 85% of compound of Formula (I) and 14% of compound of Formula (III). The identity of compound of Formula (I) was confirmed by comparison of its NMR and MS data with the pure compound of Formula (I) obtained in Example 7. Its enantiomeric excess was determined as >99.% (for the preparation of a racemic reference sample see Example 7). The unequivocal assignment of the relative configuration of compound of Formula (III) required the use of 3D-HSQC-NOESY NMR-spectroscopy due to signal crowding in diagnostically important areas of the 1H-NMR spectra. The NMR-data of the compound of Formula (III) are given in the following.
1H-NMR (600 MHz, C6D6) 3.82 (td, J=8.8, 2.1 Hz, 1H), 3.63-3.69 (m, 1H), 1.73-1.84 (m, 2H), 1.65-1.73 (m, 2H), 1.48-1.63 (m, 4H), 1.36 (br dd, J=12.8, 3.0 Hz, 3H), 1.06-1.14 (m, 8H), 0.97 (s, 3H), 0.87 (s, 3H), 0.78 (s, 3H). 13C-NMR (C6D6, extracted from HMBC): 82.3 (s), 64.7 (1), 54.7 (d), 47.5 (d), 42.5 (t), 39.5 (t), 36.2 (s), 33.7 (q), 33.5 (t), 33.0 (s), 32.1 (t), 29.0 (t), 22.3 (q), 22.0 (q), 20.6 (t), 18.9 (t), 8.7 (q). MS (EI, 70 eV): 250 (<1, M+), 235 (1), 221 (100, [M-C2H5]+), 137 (32), 121 (9), 109 (13), 97 (50), 81 (19), 69 (17), 55 (17), 41 (15), 29 (5).
A racemic reference of the compound of Formula (III) was prepared by preparative GC-chromatography from a commercial sample of Grisalva®. This sample was subjected to analytical separation on a GC-apparatus equipped with an FID detector, a sniffing port (split ratio 1:1) and a chiral column (Hydrodex-beta-3P, Machery-Nagel, P/N 723358.25). Further conditions: 11.11 injection volume (1000 ng/μl in MtBE), split 20:1, hot needle injection technique, injector 230° C., carrier gas H2, constant flow 1.5 ml/min, temperature program 2 min at 50° C.-2° C./min-2 min at 230° C. Under these conditions, the two enantiomers of the compound of the racemic sample of Formula (III) eluted at 63.78 and 64.10 min. The compound of Formula (III) obtained with SHC as described above (14% in mixture with compound of Formula (I)) eluted at 63.78 min. Thus, the first peak corresponds to (3aR,5aS,9aS,9bS)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan. The enantiomeric excess was >99%. The odour of both peaks of the racemic product was assessed by experienced panelists. The first peak was perceived as strong woody, warm, ambra, tobacco and slightly animalic, whereas the second peak was perceived as weak, woody, ambra at the injected sample amount. Thus, the herein prepared enantiomer of Formula (III), (3aR,5aS,9aS,9bS)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan, is preferred and stronger than (3aS,5aR,9aR,9bR)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan.
The reaction vessel (0.75 l Infors fermenter) was loaded with a total amount of 2.1 g E,E-Ethyl-homofarnesol prepared according to Example 2 (1.0 g were added at reaction start, a further 0.6 g and 0.5 g at approximately 7 and 23 hours later); 1.9 g SOS was added from a 31.0% (w/w) solution prepared in deionized water. A cell suspension was prepared from E. coli cells that had produced the 215G2 SHC variant (as outlined in Example 3) by suspending the cells in 0.1 M succinic acid/NaOH buffer pH 5.1. After determination of the cell wet weight concentration of this cell suspension by centrifugation for 10 min at 10° C. and 17210 g, the appropriate volume of cells was added to the reaction vessel in order to introduce 41.8 g of cells into the reaction. The volume of the reaction was completed to 135 g with the required amount of reaction buffer pH 5.1. The reaction was run at 35° C. and pH 5.4 under constant stirring (700 rpm). The pH was set to 5.4 using 85% H3PO4. pH regulation was done manually using 85% phosphoric acid as required. The reaction was sampled overtime (1 ml), extracted with 5 volumes of MTBE/tBME (5 ml). The substrate and product content of the reaction was determined by GC analysis after clarification of the solvent phase by centrifugation (table top centrifuge, 13000 rpm, 2 min).
About 90% Ethyl-homofarnesol conversion was obtained in the reaction that was run for approx. 2 days. The reaction was extracted 5 times with 100 ml MTBE by vigorous shaking followed by phase separation (centrifugation at 3500 g for 10 min, room temperature). This allowed full extraction of the reaction product and remaining unconverted substrate as judged from GC-analysis of the recovered solvent phases.
The crude MTBE (methyl tert butyl ether) extract of the biotransformation was concentrated to 100 mL and diluted with heptane (100 mL). The solution was filtered over a plug of silica gel. After removal of the solvents, a dark yellow liquid was obtained (2.15 g), which was purified by flash column chromatography on silica gel, eluting with heptane/MTBE 15:1 to isolate (3aR,5aS,9aS,9bR)-3a-ethyl-6,6,9a-trimethyldodecahydronaphtho[2,1-b]furan (600 mg, 38%) as a white crystalline solid (m.p. 60.4-61.3° C., purity according to GC-MS 99%).
[α]D=−34° (c=006, CHCl3)
1H-NMR (400 MHz, CDCl3): 3.75-3.87 (m, 2H), 2.11-2.17 (m, 1H), 1.60-1.79 (m, 4H), 1.36-1.54 (m, 6H), 1.13-1.32 (m, 3H), 0.96-1.09 (m, 2H), 0.88 (s, 3H), 0.84 (s, 3H), 0.85 (t, J=7.5 Hz, 3H), 0.83 (s, 3H). 13C-NMR (100 MHz, COCl3); 81.5 (s), 64.7 (t), 61.3 (d), 57.6 (d), 42.5 (t), 40.0 (t), 36.3 (s), 35.3 (t), 33.6 (q), 33.1 (s), 23.3 (t), 22.6 (t), 21.1 (q), 20.4 (t), 18.4 (t), 15.5 (q), 7.9 (q). MS (EI, 70 eV): 250 (<1, M+), 235 (2), 221 (100, (M-C2H4), 137 (40), 121 (9), 109 (8), 97 (51), 81 (22), 69 (20), 55 (25), 41 (27), 29 (13).
A racemic sample of the compound of Formula (I) was prepared as follows. To the stirred solution of E,E-Ethylhomofarnesol prepared according to Example 2 (580 mg, 2.34 mmol) in CH2Cl2 (40 mL) at −78° C. was added dropwise fluorosulfonic acid (0.27 mL, 2 equiv.) stirring was continued for 45 min. The solution was poored on 100 mL of water and extracted with MTBE. The organic layer was washed with water and brine and dried over MgSO4. The crude yellow liquid was purified by flash chromatography on silica gel eluting with heptane/MTBE 10:1 to yield a colourless liquid (370 mg, 64%), which contained, according to GC-MS, besides other isomers 49% of the compound of Formula (I) in racemic form. This compound was isolated in pure form by preparative GC-chromatography and served as the racemic reference for the SHC-derived pure product. The racemic sample and the compound obtained by SHC-cyclization were subjected to chiral GC-analysis and chiral GC-sniff as described in Example 6. The two enantiomers present in the racemic sample eluted at 66.00 min and 66.69 min. The (−)-enantiomer of Formula (I) prepared by SHC-cyclization as described hereabove eluted at 66.00 min and its e.e. was 99.94% (see
The foregoing broadly describes certain embodiments of the present invention without limitation. Variations and modifications as will be readily apparent to those skilled in the art are intended to be within the scope of the present invention as defined in and by the appended claims
| Number | Date | Country | Kind |
|---|---|---|---|
| 1917694 | Dec 2019 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2020/084508 | 12/3/2020 | WO |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2021/110858 | 6/10/2021 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20090131300 | Boden et al. | May 2009 | A1 |
| Number | Date | Country |
|---|---|---|
| 2060567 | May 2009 | EP |
| 2013156398 | Oct 2013 | WO |
| 2016170099 | Oct 2016 | WO |
| 2017182542 | Oct 2017 | WO |
| WO-2018157021 | Aug 2018 | WO |
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| Number | Date | Country | |
|---|---|---|---|
| 20230009254 A1 | Jan 2023 | US |
