Patent Application
20250059537
The project leading to this application has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 656872.
The present invention relates to oligonucleotides.
Oligonucleotides (ONs) are fundamental to many areas of molecular biology and are essential tools in technologies such as DNA sequencing, forensic and genetic analysis. They can also be used therapeutically.
Although the concept of binding RNA to correct disease was first demonstrated in 1978, antisense oligonucleotides (ASOs) are only just starting to deliver on their initial promise. To date, nine ASOs have now been approved for clinical use indicating their increasing therapeutic potential. All of these, however, are for rare, severe life limiting diseases.
The field recently received a boost by the approval by the European regulators of the oligonucleotide drug Inclisiran for lowering LDL cholesterol levels in patients with hypercholesterolemia. Unlike previous oligonucleotide therapeutics, Inclisiran is used to treat a common disease. However, although a major advance, and an insight into what the field can offer, Inclisiran is a special case of delivery to the liver. For other organs, inefficient biodistribution, poor cellular delivery, and toxicity prevent the wider adoption of this technology.
To address these issues new oligonucleotide analogues are greatly sought after. There are RNA targets for many more diseases than there are conventional protein targets, including incurable cancers, genetic disorders, and debilitating infectious diseases, hence improvements in ASO chemistry is likely to have huge societal benefit.
Therapeutic oligonucleotides are short single-stranded analogues of DNA that bind to RNA to regulate gene expression and alter protein synthesis1, 2. They act as steric blockers of translation3, recruit RNase-H leading to degradation of mRNA4, or modulate pre-mRNA splicing5-7. They can also be formulated as double-stranded siRNA constructs for gene silencing8. Oligonucleotides have attracted much attention as therapeutic agents due to their logical design criteria based on Watson Crick base pairing, high target specificity, and extensive range of potential disease targets. Indeed, there are far more potential RNA targets than conventional protein targets for human diseases such as cancers, genetic disorders, and debilitating infectious diseases, many of which are undruggable using existing approaches9. Hence improvements in ASO chemistry are likely to have huge societal benefit.
Therapeutic oligonucleotides hold great promise against currently untreatable diseases, but are hampered by poor cellular uptake and limited bioavailability.
To achieve a therapeutic response an oligonucleotide must be stable in vivo, bind to its target RNA with high selectivity and affinity, and display good pharmacokinetic properties2. Unmodified oligonucleotides are rapidly digested by nucleases in cells and are therefore unsuitable for use as drugs. This limitation has led to a plethora of modifications aiming to provide nuclease resistance whilst retaining high target affinity10. The most successful constructs combine 2′-sugar substitutions, including 2′-OMe (2′OMe), 2′-O-(2-methoxyethyl) and 2′-fluoro,11-13 with phosphorothioate (PS) backbones12, 14 The PS group is essential; it provides resistance to in vivo degradation and improves cell uptake. However, it also reduces RNA target affinity, which is overcome by the additional 2′-sugar modifications2. Whilst these developments have led to the FDA and EMA approval of several oligonucleotide therapies15, limited efficacy, off-target effects and toxicity issues inhibit the wider adoption of oligonucleotides in the clinic16. Improvements in these areas would be transformative.
Poor uptake into cells remains a major obstacle; generally less than 1% of an administered oligonucleotide typically reaches its target17. Reducing the net anionic charge of the oligonucleotide by full or partial replacement of the phosphodiester backbone with neutral linkages is a potential means of increasing cell permeability and nuclease resistance10, 18 However, most of the current modifications suffer from reduced duplex stability when hybridised to RNA10. In contrast, peptide nucleic acid (PNA),19 which is uncharged, has high target affinity, but poor aqueous solubility and inefficient cell penetration. This makes it therapeutically unsuitable,21 although studies to address this issue are ongoing22.
Oligonucleotides containing the artificial amide backbone AM1 have shown initial promise23-25 (
Locked nucleic acid oligonucleotides (LNA-ONs) are well established32; binding to complementary RNA targets with very high affinity33, 34, 35. However, LNA-ONs have not yet been clinically approved, largely due to challenges with toxicity.32 The extreme duplex stabilising effects of LNA can result in binding to imperfectly matched RNA strands, causing undesirable off-target effects. Nevertheless, LNA is a powerful modification for enhancing target affinity, and combining it with artificial DNA backbones is an exciting prospect. In this context LNA has been mixed with charge-neutral backbones including various triazoles36-38, carbamates39, and amides40, 41. In all cases where duplex stability was determined, stabilisation with RNA targets only occurred when the LNA was positioned on the 3′-side of the modified backbone where it directly influences the attached phosphodiester backbone. The LNA sugar has consistently failed to stabilise artificial linkages when located on their 5′-side.
The present invention was devised with the foregoing in mind.
According to one aspect of the present invention, there is provided an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
According to a second aspect of the present invention, there is provided a process for making an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
According to a third aspect of the present invention, there is provided an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof, for use in therapy.
According to a fourth aspect of the present invention, there is provided a use of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof, as antisense RNA or interference RNA (RNAi, e.g. siRNA or miRNA) or an RNA component of a CRISPR-Cas system (e.g. crRNA, tracrRNA or gRNA).
According to another aspect of the present invention, there is provided a method for amplifying an oligonucleotide sequence as defined herein.
According to another aspect of the present invention, there is provided a method for replicating an oligonucleotide sequence as defined herein.
According to another aspect of the present invention, there is provided a method for producing a ribonucleic acid (RNA) sequence or deoxyribonucleic acid (DNA) sequence as defined herein.
Unless otherwise stated, the following terms used in the specification and claims have the following meanings set out below.
Throughout the description and claims of this specification, the words “comprise” and “contain” and variations of them mean “including but not limited to”, and they are not intended to (and do not) exclude other moieties, additives, components, integers or steps. Throughout the description and claims of this specification, the singular encompasses the plural unless the context otherwise requires. In particular, where the indefinite article is used, the specification is to be understood as contemplating plurality as well as singularity, unless the context requires otherwise.
Features, integers, characteristics, compounds, chemical moieties or groups described in conjunction with a particular aspect, embodiment or examples of the invention are to be understood to be applicable to any other aspect, embodiment or example described herein unless incompatible therewith. All of the features disclosed in this specification (including any accompanying claims, abstract and drawings), and/or all of the steps of any method or process so disclosed, may be combined in any combination, except combinations where at least some of such features and/or steps are mutually exclusive. The invention is not restricted to the details of any foregoing embodiments. The invention extends to any novel one, or any novel combination, of the features disclosed in this specification (including any accompanying claims, abstract and drawings), or to any novel one, or any novel combination, of the steps of any method or process so disclosed.
The term “alkyl” includes both straight and branched chain alkyl groups. References to individual alkyl groups such as “propyl” are specific for the straight chain version only and references to individual branched chain alkyl groups such as “isopropyl” are specific for the branched chain version only. For example, “(1-6C)alkyl” includes (1-4C)alkyl, (1-3C)alkyl, propyl, isopropyl and t-butyl. A similar convention applies to other radicals, for example “phenyl(1-6C)alkyl” includes phenyl(1-4C)alkyl, benzyl, 1-phenylethyl and 2-phenylethyl.
The term “(m-nC)” or “(m-nC) group” used alone or as a prefix, refers to any group having m to n carbon atoms.
The term “halo” refers to fluoro, chloro, bromo and iodo.
Where optional substituents are chosen from “one or more” groups it is to be understood that this definition includes all substituents being chosen from one of the specified groups or the substituents being chosen from two or more of the specified groups.
The phrase “oligonucleotide of the invention” means those oligonucleotides which are disclosed herein, both generically and specifically, or pharmaceutically acceptable salts or solvates thereof.
The term “oligonucleotide” refers to a polynucleotide strand. It will be appreciated by those skilled in the art that an oligonucleotide has a 5′ and a 3′ end and comprises a sequence of nucleosides linked together by inter-nucleoside linkages.
The terms “oligonucleotide analogue” and “nucleotide analogue” refer to any modified synthetic analogues of oligonucleotides or nucleotides respectively that are known in the art. Examples of oligonucleotide analogues include peptide nucleic acids (PNAs), morpholino oligonucleotides, phosphorothioate oligonucleotides, phosphorodithioate oligonucleotides, alkylphosphonate oligonucleotides, acylphosphonate oligonucleotides and phosphoramidate oligonucleotides.
“Nucleobase” refers to a substituted or unsubstituted nitrogen-containing parent heteroaromatic ring of a type that is commonly found in nucleic acids. typically, but not necessarily, the nucleobase is capable of forming Watson-Crick and/or Hoogsteen hydrogen bonds with an appropriately complementary nucleobase. The nucleobases may be naturally occurring, such as the naturally-occurring encoding nucleobases A, G, C, T and U, or they may be modified or synthetic. The term “nucleobase” as defined herein therefore refers to both naturally occurring nucleobases which function as the fundamental units of genetic code (i.e. adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)) and also any modified or synthetic nucleobases which are known in the art. The skilled person will appreciate there to be numerous natural and synthetic nucleobase analogues available in the art which could be employed in the present invention. As such, the skilled person will readily be able to identify suitable nucleobase analogues for use in the present invention. Commonly available nucleobase analogues are commercially available from a number of sources (for example, see the Glen Research catalogue).
It will also be appreciated that the term “modified nucleobases” covers but is not limited to universal/degenerate bases (e.g. 3-nitropyrrole, 5-nitroindole and hypoxanthine); fluorescent bases (e.g. tricyclic cytosine analogues (tCO, tCS) and 2-aminopurine); base analogues bearing reactive groups selected from alkynes, thiols or amines; and base analogues that can crosslink oligonucleotides to DNA, RNA or proteins (e.g. 5-bromouracil or 3-cyanovinyl carbazole).
Common modified or synthetic nucleobases include 2-aminoadenine, 5-propynylcytosine, 5-propynyluracil, 5-methylcytosine, 3-methyluracil, 5,6-dihydrouracil, 4-thiouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, 6-dimethyl aminopurine, 6-methyl amino purine, 2-amino purine, 2,6-diamino purine, 6-amino-8-bromo purine, inosine, 5-methyl cytosine, 7-deazaadenine, 7-deazaguanosine, 3-cyanovinyl carbazole, 3-nitropyrrole, 5-nitroindole, hypoxanthine and G-clamp (a tricyclic aminoethyl-phenoxazine 2′-deoxyCytidine analogue which has the structure
Additional non-limiting examples of modified or synthetic nucleobases of which the target nucleic acid may be composed can be found in Fasman, CRC PRACTICAL HANDBOOK OF BIOCHEMISTRY AND McOLECULAR BIOLOGY, 1985, pp. 385-392; Beilstein's Handbuch der Organischen Chemie, Springer Verlag, Berlin and Chemical Abstracts, the entirety of which is incorporated herein by reference, and which provide references to publications describing the structures, properties and preparation of such nucleobases.
As will be recognized by those of skill in the art, many of the above-described modified or synthetic nucleobases are capable of forming Watson-Crick base pairing interactions with the naturally occurring encoding nucleobases A, T, C, G and U. However, in certain embodiments of the invention, it may be desirable to include in a nucleobase polymer synthetic nucleobases which are not capable of forming Watson-Crick base pairs with either the naturally occurring encoding nucleobases A, T, C, G, and U and/or common analogs thereof, but that are capable of forming non-standard (i.e., non-Watson-Crick) base pairs with one another. Nucleobases having these properties are referred to herein as “non-standard synthetic” nucleobases. Examples of such non-standard synthetic nucleobases include, but are not limited to, iso-guanine (iso-G), iso-cytosine (iso-C), xanthine (X), kappa (K), nucleobase H, nucleobase J, nucleobase M and nucleobase N (see U.S. Pat. No. 6,001,983). These non-standard synthetic nucleobases base-pair with one another to form the following non-standard base pairs: iso-C·iso-G, K·X, H·J and M·N. Each of these non-standard base pairs has three hydrogen bonds. Additional non-standard synthetic nucleobases, as well as methods for their synthesis and methods for incorporating them into nucleobase polymers are found in U.S. Pat. Nos. 5,432,272, 5,965,364 and 6,001,983, the disclosures of which are incorporated herein by reference.
The nucleobase is attached to a sugar moiety (typically ribose or deoxyribose) or a ribose or deoxyribose mimic, for example a chemically modified sugar derivative (e.g. a chemically modified ribose or deoxyribose) or a cyclic group that functions as a synthetic mimic of a ribose or deoxyribose sugar moiety (e.g. the morpholino ring present in morpholino oligonucleotides).
A chemically modified sugar derivative includes sugars modified at the 2′ position, for example to include 2′-O-methyl, 2′-O-methoxy-ethyl, 2′-NH2 and 2′-F modifications. Such sugars may be located in any of the nucleotides present in the oligonucleotides of the present invention.
The term “nucleoside” is used herein to refer to a moiety composed of a sugar/a ribose or deoxyribose mimic bound to a nucleobase/nucleobase analogue. The term nucleoside as used herein excludes the inter-nucleoside linkage that connects adjacent nucleosides together. An “inter-nucleoside linkage” is a linking group that connects the rings of the sugar/ribose or deoxyribose mimic of adjacent nucleosides. Thus, a “nucleotide” is a nucleoside with one or more inter-nucleoside linkage attached.
The terms “locked nucleic acid”, “LNA” or “locked nucleoside” are used herein to refer to nucleic acids or nucleosides comprising a ribose or deoxyribose moiety in which the conformation of the ribose or deoxyribose ring is fixed or locked in a specific conformation, typically by a bridging group. Typically the bridging group connects the 2′ and 4′ carbon atoms of the ribose or deoxyribose rings and locks the ribose or deoxyribose in the 3′-endo conformation (which is often found in A-form duplexes). Examples of locked nucleic acid/nucleoside structures are well known in the art and are commercially available.
A suitable pharmaceutically acceptable salt of an oligonucleotide of the invention is, for example, an acid-addition salt of an oligonucleotide of the invention which is sufficiently basic, for example, an acid-addition salt with, for example, an inorganic or organic acid, for example hydrochloric, hydrobromic, sulfuric, phosphoric, trifluoroacetic, formic, citric methane sulfonate or maleic acid. In addition, a suitable pharmaceutically acceptable salt of an oligonucleotide of the invention which is sufficiently acidic is an alkali metal salt, for example a sodium or potassium salt, an alkaline earth metal salt, for example a calcium or magnesium salt, an ammonium salt or a salt with an organic base which affords a pharmaceutically acceptable cation, for example a salt with methylamine, dimethylamine, trimethylamine, piperidine, morpholine or tris-(2-hydroxyethyl)amine.
It is also to be understood that certain oligonucleotides of the invention may exist in solvated as well as unsolvated forms such as, for example, hydrated forms.
According to one aspect of the present invention, there is provided an oligonucleotide having a 5′ and a 3′ end and comprising a sequence of nucleosides linked together by inter-nucleoside linkages, wherein:
It will be appreciated by those skilled in the art that an inter-nucleoside linkage will have a 5′ end (or 5′ side) that links to the nucleoside on the 5′ side, and 3′ end (or 3′ side) that links to the nucleoside on the 3′ side of linkage. The 3′ and 5′ nomenclature is well established in the nucleic acid field.
The inventors have surprisingly found that the provision of an amide linker moiety, a phosphorothioate linker moiety and a locked nucleoside is associated with increased cell uptake of the modified oligonucleotide and also associated with reduced toxicity.
In addition, the oligonucleotides of the present invention are much more stable to nuclease degradation when compared to corresponding oligonucleotides comprising just locked nucleosides alone. This indicates that the oligonucleotides of the present invention will be suitable for use in vivo.
The combination of the two aforementioned advantages (namely the increased nuclease stability together with the increase in the thermal melting temperatures observed upon binding of the oligonucleotides of the present invention to complimentary DNA or RNA stands) makes the oligonucleotides of the present invention particularly advantageous.
In an embodiment, the at least one locked nucleoside is either directly attached to the 3′ end of the amide linker moiety. Suitably, the amide linker is attached to the 4′ carbon of the locked ribose or deoxyribose ring of the locked nucleoside.
The oligonucleotide may comprise multiple locked nucleosides in its sequence, for example there may be two, three, four, five or more locked nucleosides present. The additional locked nucleosides may be present at any position in the oligonucleotide.
In an embodiment, a the at least one locked nucleoside is directly attached to the 5′ end of the amide linker moiety. Suitably, the amide linker is attached to the 3′ carbon atom of the ribose or deoxyribose ring of the locked nucleoside.
In a particular embodiment, the oligonucleotide comprises at least two locked nucleosides, one of which is directly attached to the 3′ end of the amide linker moiety and the other of which is directly attached to the 5′ end of the amide linker moiety. This particular embodiment of the invention is expected to result in the oligonucleotide binding to complementary RNA tighter than in embodiments in which there is only one locked nucleoside or in comparison to an oligonucleotide comprising no locked nucleosides.
Amide linkages known in the art are present in the oligonucleotides of the present invention. The amide linker moeity is an inter-nucleoside linkage that acts as a charge neutral mimic of the phosphodiester linkages found in naturally occurring polynucleotides.
Amide linkages suitably have the structure shown below:
Suitably, R1 and R2 are each independently selected from hydrogen or methyl.
Suitably, R3 and R4 are each independently selected from hydrogen or methyl.
Suitably, RN is selected from hydrogen or methyl.
Suitably, each of R1, R2, R3, R4 and RN is hydrogen.
Phosphorothioate linkages known in the art are present in the oligonucleotides of the present invention. The phosphorothioate linker moeity is an inter-nucleoside linkage that acts as a mimic of the phosphodiester linkages found in naturally occurring polynucleotides.
The at least one phosphorothioate linkage may be located at any suitable position throughout the oligonucleotide. For example, the at least one phosphorothioate linker may be located at one or more of the following positions:
Suitably, the at least one phosphorothioate linker is:
A phosphorothioate linkage can be represented by either of the following structures:
In some embodiments, it may be that all phosphodiester Inkages in the oligonucleotide are replaced with a phosphorothioate linkage. In some embodiments however, some phosphodiester Inkages may be present in the oligonucleotide.
Suitably, more than 75% of the phosphodiester Inkages in the oligonucleotide are replaced with a phosphorothioate linkage. More suitably, more than 90% of the phosphodiester Inkages in the oligonucleotide are replaced with a phosphorothioate linkage. In some embodiments 100% of the phosphodiester Inkages in the oligonucleotide are replaced with a phosphorothioate linkage.
Locked nucleic acids are well known in the art. Any suitable locked nucleoside may be used in the present invention.
The locked nucleic acid may be at a terminal position or may be located centrally.
Typically, the locked nucleoside has the general structure shown below:
In another embodiment, the oligonucleotide of the present invention comprises at least one inter-nucleoside linkage which is a phosphorothioate linker moiety, and a moiety of the formula:
wherein:
Particular oligonucleotides of the invention include, for example, oligonucleotides comprising a moeity formula I, or pharmaceutically acceptable salts and/or solvates thereof, wherein, unless otherwise stated, each of Q1, Q2, bond a, bond b, X1, X2, X3, X4, R1, R2, R3, R4 and RN, and any associated substituent groups has any of the meanings defined hereinbefore or in any of paragraphs (1) to (76) hereinafter:—
Suitably, Q1 is as defined in any one of paragraphs (1) to (3). Most Suitably, Q1 is as defined in paragraph (3).
Suitably, X1 and X2 are as defined in any one of paragraphs (4) to (8). More suitably, X1 and X2 are as defined in any one of paragraphs (6) to (8). Most Suitably, X1 and X2 are as defined in paragraph (8).
Suitably, Q2 is as defined in any one of paragraphs (9) to (11). Most Suitably, Q2 is as defined in paragraph (11).
Suitably, X3 and X4 are as defined in any one of paragraphs (12) to (16). More suitably, X3 and X4 are as defined in any one of paragraphs (14) to (16). Most Suitably, X3 and X4 are as defined in paragraph (16).
Suitably, R1 and R2 are as defined in paragraph (17) or (18). Most Suitably, R1 and R2 are as defined in paragraph (18).
Suitably, R1 and R2 are as defined in paragraph (17) or (18). Most Suitably, R1 and R2 are as defined in paragraph (18).
Suitably, RN is as defined in paragraph (21) or (22). Most Suitably, RN is defined in paragraph (22).
Bonds a and b are as defined in any one of paragraphs (23) to (26). Most suitably, bonds a and b are as defined in paragraph (26).
In the oligonucleotides according to Formula (I), it may be that:
wherein C3, C4, Q1, Q2, B, B′, X1, X2, X3, X4, R1, R2, R3, R4 and RN are as defined herein.
In a particular group of oligonucleotides of the present invention, both of bonds a and b are present, thus the oligonucleotide comprises a moiety of Formula (Ia) below:
wherein C3, C4, Q1, Q2, B, B′, X1, X2, X3, X4, R1, R2, R3, R4 and RN are as defined herein.
In a particular group of oligonucleotides of the present invention, at least one phosphorothioate linkage is adjacent to the moeity of Formula (I), thus the oligonucleotide comprises a moiety of Formula (IIa) or (IIb) below:
wherein C3, C4, Q1, Q2, B, B′, X1, X2, X3, X4, R1, R2, R3, R4 and RN are as defined herein.
In a particular group of oligonucleotides of the present invention, at least one phosphorothioate linkage is adjacent to the moeity of Formula (I), and both of bonds a and b are present, thus the oligonucleotide comprises a moiety of Formula (IIc) or (IId) below:
wherein C3, C4, Q1, Q2, B, B′, X1, X2, X3, X4, R1, R2, R3, R4 and RN are as defined herein.
In a particular group of oligonucleotides of the present invention, at least one phosphorothioate linkage is adjacent to the moeity of Formula (I), both of bonds a and b are present, X1 is CH2, X2 is O, X3 is CH2, X2 is O, Q1 is O, Q2 is O, and R1, R2, R3 and R4 are hydrogen, thus the oligonucleotide comprises a moiety of Formula (IIe) or (IIf) below:
wherein B and B′ are as defined herein.
The oligonucleotides of the present invention will also comprise further nucleotides as part of the oligonucleotide chain. Such nucleotides may include an unmodified or modified sugar moiety as part of the nucleoside. Sugar modified nucleosides are known to the skilled person. The oligonucleotides of the present invention may therefore comprise one or more modified sugar moieties in the sequence (e.g. a 2′OMe sugar).
Suitable nucleosides in the oligonucleotide may have the structural formula shown below:
More suitably, R50 is selected from H, OH or OMe.
In an “unmodified” sugar moiety, R50 is H (DNA) or OH (RNA). In a “modified” sugar moiety, R50 may be OMe, O(CH2)2OMe or F, suitably OMe.
In a particular group of oligonucleotides of the present invention, the oligonucleotide comprises a moiety of Formula (III) below:
wherein C3, C4, Q1, Q2, B, B′, X1, X2, X3, X4, R1, R2, R3, R4, RN and R50 are as defined herein.
In a particular group of oligonucleotides of the present invention, in the moiety of formula (III), both of bonds a and b are present, thus the oligonucleotide comprises a moiety of Formula (III):
wherein C3, C4, Q1, Q2, B, B′, X1, X2, X3, X4, R1, R2, R3, R4 and RN are as defined herein.
In a particular group of oligonucleotides of the present invention, in the moiety of formula (III), both of bonds a and b are present, X1 is CH2, X2 is O, X3 is CH2, X2 is O, Q1 is O, Q2 is O, and R1, R2, R3 and R4 are hydrogen, thus the oligonucleotide comprises a moiety of Formula (lie) or (IIf) below:
wherein B, B′, B″ and R50 are as defined herein.
The oligonucleotides of the present invention can be prepared using techniques known in the art.
The preparation of oligonucleotides comprising one or more locked nucleosides in their sequence is known in the art.
Further examples of how to synthesise the oligonucleotides of the present invention are set out in the accompanying examples.
The oligonucleotides of the present invention may be used for a wide variety of applications in fields such as, for example, medicine, genetic testing, gene editing, diagnostics, agriculture, industrial biotechnology, biological research and forensics.
It will be appreciated that certain oligonucleotides of the present invention will have potential therapeutic applications. Examples include antisense RNA oligonucleotides of the present invention as well as certain siRNA and miRNA oligonucleotides.
Another example, is oligonucleotides associated with Clustered Regularly Interspaced Short Palindromic Repeats in combination with CRISPR Associated sequences (CRISPR-Cas) systems, such as for example CRISPR RNA (crRNA), pre-crRNA, tracrRNA and guideRNA (gRNA). Such oligonucleotides find therapeutic utility in the treatment of diseases via e.g. gene therapy as well as in the treatment of infections via selective killing of pathogenic organisms.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in therapy. Examples of potential therapeutic uses of such oligonucleotides include the treatment of cancer, genetic disorders, metabolic disorders, viral infections and bacterial infections. Thus, the present invention provides an oligonucleotide as defined herein a viral infection, cancer, a genetic disorder, a metabolic disease or a bacterial infection.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the treatment of a viral infection.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the inhibition of viral messenger RNA.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the treatment of cancer.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the inhibition of messenger RNA of a cancer-causing gene.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the treatment of a genetic disorder, for example diseases caused by loss of function of important endogenous genes, typically in exon-skipping applications (see for example Crooke et al, Antisense technology: A review; JBC Reviews, Vol 296, January 2021), e.g. Duchenne muscular dystrophy, spinal muscular atrophy (SMA).
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the treatment of a metabolically-related disease that is caused by over-production of a specific protein.
In another aspect, the present invention provides an oligonucleotide as defined herein for use in the treatment of a bacterial infection.
In another aspect, the present invention provides a method of treating a viral infection in a subject in need of such treatment, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
In another aspect, the present invention provides a method of treating cancer in a subject in need of such treatment, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
In another aspect, the present invention provides a method of treating a genetic disorder in a subject in need of such treatment, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
In another aspect, the present invention provides a method of inhibiting viral messenger RNA in a subject, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
In another aspect, the present invention provides a method of treating a bacterial infection in a subject in need of such treatment, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
In another aspect, the present invention provides a method of treating metabolically-related disease that is caused by over-production of a specific protein in a subject in need of such treatment, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof.
In another aspect, the present invention provides a method of inhibiting messenger RNA in a subject, the method comprising administering to said subject a therapeutically effective amount of an oligonucleotide as defined herein, or a pharmaceutically acceptable salt or solvate thereof. Suitably, the messenger RNA is messenger RNA of a cancer causing gene.
The present invention further relates to the use of the oligonucleotides of the present invention as
In general terms, there are two main classes of CRISPR-Cas systems (Makarova et al. Nat Rev Microbiol. 13:722-736 (2015)), which encompass five major types and 16 different subtypes based on cas gene content, cas operon architecture, Cas protein sequences, and process steps (Makarova et al. Biol Direct. 6:38 (2011); Makarova and Koonin Methods Mol Biol. 1311:47-75 (2015); Barrangou, R. Genome Biology 16:247 (2015)). This classification in either Class 1 or Class 2 is based upon the Cas genes involved in the interference stage.
Class 1 systems have a multi-subunit crRNA-effector complex such as Cascade-Cas3, whereas Class 2 systems have a crRNA-effector complex having a single Cas protein, such as Cas9, Cas12 (previously referred to as Cpf1) and Cas 13a (previously referred to as C2c2). For Type II systems there is a second RNA component tracrRNA which hybridises to crRNA to form a crRNA:tracr RNA duplex, these two RNA components may be linked to form single guide RNA.
RNA components in such CRISPR-Cas systems may be adapted to be an oligonucleotide in accordance with the invention. It would be a matter of routine for a person of ordinary skill in the art to synthesise a crRNA, pre-crRNA, tracrRNA or guideRNA having at least one inter-nucleoside linkage which is a triazole linker moiety between two nucleosides with a locked nucleoside positioned at the 3′ end of the triazole linker moiety, and which retains the desired function of the RNA component (e.g., to guide the crRNA:effector complex to a target site). Standard methods are known in the art for testing whether oligonucleotides of the invention when used as such CRISPR RNA components retain the desired function (e.g. by comparing the desired function to that of a control CRISPR RNA component which has the same nucleosides without any-triazole linker moieties between nucleosides or locked nucleosides).
The term “CRISPR RNA components” or “RNA component of a CRISPR-Cas system” is used herein, as in most CRISPR-Cas systems, the nucleic acid sequences which guide the effector protein(s) to a desired target sequence are RNA components. However, CRISPR hybrid DNA/RNA polynucleotides which can also function to guide effector protein(s) to a desired target site in a DNA or RNA sequence are also known in the art—see for example Rueda et al. (Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease, Nature Communications 8, Article Number: 1610 (2017)). Accordingly, reference to CRISPR RNA components herein may also encompass hybrid RNA/DNA components such as crDNA/RNA, tracrDNA/RNA or gDNA/RNA.
Advantageously the oligonucleotides of the invention may have particular utility in in vivo gene therapy applications. For example, one way of carrying out in vivo therapy using a Type II CRISPR-Cas system involves delivering the Cas9 and tracrRNA via a virus, which can assemble inactive complexes inside of cells. The crRNA can then be administered later to assemble and selectively activate CRISPR/Cas9 complexes, which would then go on to target and edit specific sites in the human genome, such as disease relevant genes (Gagnon and Corey, Proc. Natl. Acad. Sci. USA 112:15536-15537, 2015; Rahdar, et al, Proc. Natl. Acad. Sci. USA 112:E7110-71 17, 2015). For this gene therapy approach to work the crRNA should be extremely resistant to nucleases and cellular degradation, as well as confer high activity and specificity to the assembled CRISPR/Cas9 complex. Hence, the increased stability of the oligonucleotides of the invention to degradation is highly desirable. Alternatively, crRNA:effector complexes (i.e. CRISPR-Cas complexes, such as CRISPR/Cas9) can be assembled in vitro and directly transfected into cells for genome editing (Liang, et al, J. Biotechnol. 208:44-53, 2015; Zuris, et al, Nat. Biotechnol. 33:73-80, 2015). Special transfection reagents, such as CRISPRMAX (Yu, et al, Biotechnol. Lett. 38:919-929, 2016), have been developed for this purpose. Oligonucleotides of the invention when used as crRNAs may improve this approach by offering stability against degradation.
Accordingly, the oligonucleotides of the invention when used as CRISPR RNA components can advantageously be used for the various applications of CRISPR-Cas systems known in the art including: gene-editing, gene activation (CRISPRa) or gene interference (CRISPRi), base-editing, multiplex engineering (CRISPRm), DNA amplification, diagnostics (e.g. SKERLOCK or DETECTR), cell recording (e.g. CAMERA), typing bacteria, antimicrobial applications, synthesising new chemicals etc.
Suitably, in diagnostic applications such as SHERLOCK and DETECTR the oligonucleotides of the invention can be used as RNA components such as the “sacrificial RNA molecules” used to create a signal.
Embodiments of the invention will be described, by way of example only, with reference to the accompanying drawings, which are described below:
Therapeutic oligonucleotides hold great promise against currently untreatable diseases, but are hampered by poor cellular uptake and limited bioavailability.
We investigated if combining the amide linkage (AM1) with locked-nucleic acid (LNA)30, 31 and phosphorothioate would overcome the specific limitations of each modification individually (
We show that antisense oligonucleotides containing artificial amide linkages flanked with locked nucleic acid (LNA) within a phosphorothioate backbone have improved cellular uptake, RNA target affinity, nuclease resistance and potency.
To construct such oligonucleotides, analogues of LNA (A, T, C, 5-methyl-C and G), where the 3′—OH group is replaced with an ethanoic acid group, were synthesised in 8 steps, comparable with LNA phosphoramidite synthesis. These were coupled to 5′-amino groups in growing oligonucleotides during standard solid-phase assembly to form inter-nucleoside amide bonds in high yield. X-ray crystal structures of the modified oligonucleotides hybridised to complementary RNA show that the artificial backbone causes minimal structural deviation. 2′OMe phosphorothioate splice-switching oligonucleotides containing just four LNA-amide linkages display greatly improved gymnotic activity relative to oligonucleotides lacking amides, highlighting the therapeutic potential of this technology.
Herein is described the synthesis of LNA-amide-phosphorothioate and LNA-amide-phosphodiester chimeric oligonucleotides, we demonstrate duplex stabilisation and mismatch discrimination, and show that oligonucleotides containing this modification are very stable to nucleases. X-ray crystallography studies with complementary RNA show that the LNA-amide combination does not significantly perturb the A-form duplex. In a biological context, we show that LNA-amide ONs containing 2′OMe sugars and PS backbones are highly effective in a cellular exon-skipping (RNA splice modulation) assay and show greatly improved cellular uptake.
Oligonucleotide segment synthesis. Oligonucleotide synthesis was performed on an Applied Biosystems 394 automated DNA/RNA synthesiser on a 1.0 μmole scale using a standard phosphoramidite cycle of detritylation, coupling, and oxidation. No capping step was used. All β-cyanoethyl phosphoramidite monomers were dissolved in anhydrous MeCN (10% CH2Cl2 was added when 2′OMe U phosphoramidite was used) to a concentration of 0.1 M immediately prior to use. 5-(Benzylthio)-1H-tetrazole (BTT) activator (0.3 M) was used with a coupling time of 50 s for normal dA, dG, dC and T phosphoramidites, this was extended to 6 min for 2′OMe and LNA phosphoramidites. Standard iodine oxidiser was used for phosphodiester oligonucleotides. For the phosphorothioate oligonucleotides, 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH) was used as the sulfurisation agent, and the solid support was washed with MeCN after each phosphoramidite coupling before the sulfurisation step. Sulfurisation time was initially 3 min, and after this period fresh EDITH was sent to the synthesis column and left for another 3 min. Further details are given below.
Amino monomer addition. The MMT-protected 5′-amino phosphoramidite monomer (either LNA 1050 or commercially available deoxythymidyl 11) was dissolved in anhydrous MeCN to a concentration of 0.1 M immediately prior to use. The same coupling conditions as above were used, but the coupling time was extended to 10 min. The MMT protecting group was cleaved on the Applied Biosystems 394 automated synthesiser using 3% TCA in CH2Cl2 with an extended cleavage time of 2 min. The solid support was then washed with acetonitrile on the synthesiser for 3 min. To improve the coupling efficiency in the next step, the solid support was washed with 0.5% (v/v) N-methylmorpholine in DMF (1×1 mL) followed by DMF (3×1 mL).
Amide bond formation on resin (peptide coupling). All amide couplings were performed manually on the synthesis column. A solution with 10 equivalents of acid monomer, 10 equivalents of PyBOP and 30 equivalents of N-methylmorpholine was first prepared in 400 μL of DMF. This was then taken up into a 1 mL syringe and loaded onto the column before a second 1 mL syringe was attached to the other end of the synthesis column. The mixture was agitated every 10 min for 1 h. The columns were then washed with DMF (3×1 mL) followed by MeCN (5×1 mL) and dried by passing argon through the column. The column was then returned to the synthesiser to continue oligonucleotide synthesis.
Cleavage of oligonucleotides from resin, deprotection and purification. LNA-amide containing oligonucleotides were isolated with the final 5′-DMT protecting group still in place (DMT-ON). Following solid phase synthesis, the cyanoethyl groups were removed by a 15 min treatment with 20% diethylamine in MeCN. The resin was then washed with MeCN (5×1 mL) and dried by passing a stream of argon through the synthesis column. The oligonucleotides were cleaved from the solid support and deprotected by heating in concentrated aqueous ammonia in a sealed glass vial at 55° C. for 5 hours. The ammonia was removed under reduced pressure prior to oligonucleotide purification. The DMT-ON oligonucleotides were purified by reverse-phase high performance liquid chromatography (RP-HPLC) and lyophilised. They were then dissolved in 0.5 mL of 80% acetic acid and left for 1 hour at room temperature to remove the DMT group. The solution was neutralised with 0.5 mL of triethylammonium acetate buffer (2 M, pH 7) and the detritylated oligonucleotides were desalted using a NAP-10 column (Cytiva) then freeze dried.
Efficient synthesis of chemically modified oligonucleotides is essential for fundamental studies and therapeutic applications. We have devised a combined solid-phase phosphoramidite coupling/amide bond formation approach which enables the straightforward assembly of oligonucleotides containing LNA-flanked amides, and which could be easily automated and/or adapted by others in the field. In our strategy a maximum of eight monomers are required to make all possible nucleobase sequences containing amide linkages (four carboxylic acids and four amines).
Synthesis of the required 5′-dimethoxytrityl (DMT)-protected 3-ethanoic acid LNA-monomers was achieved in just 8 steps from 1, the same as for standard LNA phosphoramidites following the most commonly cited route43 (
The pathways to each monomer then diverged, with Vorbruggen conditions43, 49 utilised for addition of the nucleobases to access 7a-e. Subsequent simultaneous unmasking of the 3′-carboxyl and 2′-hydroxyl groups by treatment with hydroxide, followed by cyclisation to form the 2′-4′-oxymethylene bridge, then 5′-mesyl deprotection, gave the hydroxy-LNA acid compounds 8a-e. The progress of the reaction was rapid; mesyl deprotection using hydroxide ion conventionally requires several days under reflux conditions43. We postulate that the acceleration in rate is due to neighbouring group participation whereby the carboxylate anion displaces the 5′-mesyl group, forming a lactone that is subsequently opened by hydrolysis (
Using this strategy we were able to access all four canonical nucleoside analogues along with the 5-methylcytidine version which is often used in antisense experiments to increase target affinity16. Additionally, we required phosphoramidites 1050 and commercially available 11 with monomethoxytrityl (MMT)-protected 5′-amino groups, and the 5′-DMT-protected thymidine 3′-ethanoic acid monomer 1251, 52 (
An overview of our oligonucleotide synthesis strategy is shown in
The process can be repeated to install multiple non-contiguous amides in the same oligonucleotide. To demonstrate this, DMT-protected LNA acids 9a-e, phosphoramidites 10 and 11, and DNA acid 1251, 52 (
To evaluate the compatibility of AM1 with LNA, we synthesised ONs with a single amide linkage flanked by either no LNA (ON1DNA-Am-DNA), an LNA 5′ to the amide (ON2LNA-Am-DNA) an LNA 3′ to the amide (ON3DNA-Am-LNA), or LNA on both sides of the amide (ON4LNA-Am-LNA) along with LNA without amide (ON5LNA-LNA) and DNA without amide (ON6DNAcontrol). We compared the duplex denaturation temperatures (Tms) after hybridisation with DNA and RNA complementary strands. In the DNA:RNA hybrids, ON2LNA-Am-DNA showed a significant increase in duplex stability (+3.0° C.) compared to the unmodified ON6DNAcontrol, and an increase of +3.4° C. compared to ‘amide only’ ON1DNA-Am-DNA. This supports our hypothesis that LNA can stabilise artificial backbones that are close analogues of canonical phosphodiester linkages. As expected, ON4LNA-Am-LNA in which the amide is surrounded by LNA sugars, gave the greatest increase in stability of the amide modified ONs (+5.1° C.). It is noteworthy that ON2LNA-Am-DNA and ON4LNA-Am-LNA provide the first examples of an LNA sugar with an immediate 3′-non-phosphorus DNA backbone stabilising a duplex.
RNA sequence selectivity of the amide-containing ONs was excellent; ONs 1-4 all showed significant duplex destabilisation when hybridised to an RNA strand with a single mismatched base pair. ON2-4 with the various combinations of LNA and the amide linkage all had lower duplex stability than the LNA alone (ON5LNA-LNA), allowing several amide linkages to be incorporated into an oligonucleotide without producing excessively high duplex stability (Table 2, discussed further below). In summary, an amide linkage flanked by LNA on both sides gives excellent DNA:RNA duplex stabilisation and mismatch discrimination.
In duplexes with DNA targets, ONs with all combinations of LNA and DNA sugars around the amide linkage were very slightly destabilising (between −0.1° C. to −2.6° C.), indicating their selectivity for RNA over DNA.
Am-DNA
Am-DNA
Am-LNA
Am-LNA
LNA
Tm values were measured using 3.0 μM concentrations of each oligonucleotide strand in 10 mM phosphate buffer (pH 7.0) containing 200 mM NaCl. T indicates a locked sugar and * is an amide bond in place of a phosphodiester. Tm values were calculated as the maximum of the first derivative of the melting curve (A260 vs temperature) and reported as the average of at least two independent experiments. ΔTm for matched sequences=modified−ON6DNAcontrol; ΔTm for mismatched=RNA mismatch−match. Target ON sequences, where an underlined base denotes the mismatch: ON7=GCTGCAAGCGTCG; ON8=GCUGCAAGCGUCG; ON9=GCUGCACGCGUCG; ON10=GCUGCCAGCGUCG; RNA ON11=GCUGCAGGCGUCG. ON12=GCUGCGAGCGUCG. Representative melting curves are given (
The stabilisation induced by the LNA amide combination is cumulative and general (Table 2a). In a different biologically relevant sequence context from above, addition of one amide flanked with LNA to unmodified DNA (ON13DNA/1LAL/16PO) increases duplex stability by 1.8° C., whereas addition of four amides flanked by LNA (ON14DNA/4LAL/13PO) gives an increase of 5.1° C. A much stronger trend is observed for duplexes with RNA, where a single amide flanked by LNA increases the DNA:RNA hybrid Tm by 2.2° C., and four LNA-flanked amides increase it by an impressive 13.0° C. This selectivity for RNA over DNA is an important advantage when developing therapeutic oligonucleotides to selectively target RNA.
It was not possible to directly determine the duplex melting temperatures of the 2′OMe oligonucleotides containing multiple LNA amide additions as the duplexes were too stable. Instead, duplex melting temperatures were measured against shorter 10-mer DNA (ON23) and RNA (ON24) targets complementary to the 5′-portion (Table 2b-d). In all cases the combination of LNA and amide greatly increased duplex stability and, as expected, PS linkages reduced the stability of duplexes relative to phosphodiesters.
Experimental conditions as in Table 1. a. comparison of DNA ONs against full length targets, b. comparison of DNA ONs against 10-mer targets, c. comparison of 2′OMe/PO ONs, d. comparison of 2′OMe/PS ONs. Backbone: PO=phosphodiester, PS=phosphorothioate, DNA=deoxyribose sugars, 2′OMe=2′OMe RNA sugars. Underlined bases indicate a locked sugar and * indicates an amide bond in place of a phosphodiester. The ON code indicates the number of each backbone linkage where LAL stands for LNA-flanked amide bonds. DNA target (ON21)=TGTAACTGAGGTAAGAGG; RNA target (ON22)=UGUAACUGAGGUAAGAGG. Truncated DNA target (ON23)=AGGTAAGAGG. Truncated RNA target (ON24)=AGGUAAGAGG. ΔTm=modified−control. Bases in lowercase italic remain single stranded on duplex formation and do not contribute to Tm. Representative melting curves are given (
To evaluate whether the combination of LNA and amide confers greater nuclease resistance than LNA alone, we incubated unmodified DNA (ON15DNAN17PO) and DNA with four amide linkages flanked with LNA (ON14DNA4LAL/13PO) in a 1:1 mixture of phosphate buffered saline (PBS) and foetal bovine serum (FBS) to mimic the in vivo environment, and compared it with DNA with the same eight LNA sugars without amide linkages (ON25DNA8LNA/17PO). We sampled aliquots at different time intervals, and analysed them by gel electrophoresis (
X-Ray Crystallography Reveals that LNA Amide Modifications Cause Minimal Structural Deviation.
X-ray structures were carried out to determine the effects of LNA and amide modifications on duplex conformation. These are the first crystal structures of DNA:RNA hybrids that contain amide linkages. The X-ray structure of an amide-modified RNA:RNA duplex was determined previously, but this was a self-complementary sequence with amide linkages in both strands. Moreover, the amide linkages were surrounded by multiple mismatched base pairs, an unusual construct that cannot exist outside the solid-state27. The sequence of the LNA-amide modified DNA:RNA hybrid duplexes was based on the corresponding unmodified hybrid PDB 1PJO4 (Table 3). Crystals of DNA with a single amide linkage flanked entirely by DNA (ON28xDNA-Am-DNA) an LNA 5′ to the amide (ON29xLNA-Am-DNA), and LNA on both sides of the amide (ON30xLNA-Am-LNA) all hybridised to complementary RNA (ON27xRNA), diffracted to between 2.5-2.8 A resolution (
T indicates a locked sugar and * indicates an amide bond in place of a phosphodiester.
The hybrids all adopt an A-form duplex structure. Importantly, structures of the modified duplexes containing the amide and LNA-amide backbones (
In agreement with the amide-DNA:RNA hybrid NMR structure by Rosners28 in which the DNA strand contained multiple amides, our X-ray studies indicate that the amide linkage is a close mimic of the phosphodiester backbone (
In
Poor cellular uptake and cellular toxicity remain major obstacles when developing therapeutic oligonucleotide agents. We sought to evaluate the biological activity of the LNA-amide combination using the HeLa pLuc/705 cell line55. This cell line carries a luciferase-encoding gene that is interrupted by a mutated ß-globin intron55. The mutation creates a 5˜-splice site which in turn activates a cryptic 3′-splice site, resulting in incorrect mRNA splicing and the production of non-functional luciferase. An oligonucleotide that hybridises to the mutant 5′-splice site prevents incorporation of the aberrant intron. This restores the luciferase pre-mRNA splicing pattern to produce functional luciferase, which is quantified by LIuminometry. The oligonucleotides in Table 2 were designed to be complementary to this aberrant splice site. Oligonucleotides ON14DNA/4LAL/13PO ON162′OMe/4LAL/13PO, and ON182′OMe/4LAL/13PS have the LNA-amide modification in the same position and were designed to evaluate LNA-amide in combination with the DNA, 2′OMe/phosphodiester, and 2′OMe/phosphorothioate backbones respectively. We decided to evaluate ONs 14 and 16 with phosphodiester backbones in these exon-skipping studies as neither LNA or the amide linkages are compatible with RNase-H2,56, and the LNA-amide modification strongly protects ONs against nuclease degradation. In addition, it allowed us to determine the consequences of the absence of the PS linkages on delivery/activity of LNA-amide ONs. Three controls were included: ON202′OMe/17PS to determine whether the LNA-amide linkage can improve the biological activity of a therapeutic oligonucleotide55, ON172′OMe/17PO to evaluate the importance of the PS linkage independent of LNA or amide linkages, and ON192′OMe/8LNA/17PS with LNA sugars but no amide linkages to determine if the enhanced duplex stability of LNA was responsible for any observed increase in activity. A scrambled control (ON312′OMe/17PS scrambled,
To compare the biological activity independent of cell uptake, Lipofectamine 2000 (LF2000), a cationic liposome transfection/delivery reagent, was used. All three target-complementary PS-ONs were active in the assay (ON202′OMe/17PS, ON182′OMe/4LAL/13PS, and ON192′OMe/8LNA/17PS), whereas the PO-ONs (ON14DNA/4LAL/13PO, ON162′OMe/4LAL/13PO and ON172′OMe/17PO) were all inactive at 100 nM (
Next, we compared the naked (gymnotic) uptake of the ONs. These conditions more closely represent in vivo applications where transfection agents such as LF2000 cannot be used. We seeded cells at low confluency, added the oligonucleotides in fresh media after 16 h, and measured luciferase activity after a further 96 h. The presence of just four amide bonds flanked both sides by LNA (ON182′OMe/4LAL/13PS) significantly increased the activity in a dose-dependent manner when compared with ON202′OMe/17PS (
We compared the viability of the HeLa cells following lipofection using a WST-1 cell proliferation assay (
Given that cell uptake remains a major challenge when developing new therapeutic oligonucleotides, the results shown in
We have developed methodology to synthesise LNA monomers with 3′-ethanoic acid and 5-amino groups and incorporate them into oligonucleotides that combine the favourable properties of LNA sugars, amide backbones, and phosphorothioate groups synergistically. The methodology is high yielding and has the potential to be automated, an important consideration for therapeutic oligonucleotide development. The resulting constructs have remarkable resistance to enzymatic degradation, and bind to complementary RNA with affinity and selectivity superior to unmodified ONs, but crucially not as tightly as LNA. X-ray crystallography revealed that the artificial backbone causes minimal structural deviation in DNA:RNA hybrids, consistent with the excellent affinity of the modified ONs for complementary RNA. Oligonucleotides with alternating LNA-amide and phosphodiester (or phosphorothioate) backbones cannot give rise to LNA mononucleotides (modified dNTPs) in the presence of cellular nucleases, and their favourable toxicity profile relative to LNA may reflect this. Cell studies with gymnotic delivery revealed that the substitution of just four LNA-flanked amides in a 2′OMe phosphorothioate background significantly improves naked (gymnotic) uptake. Poor cellular uptake is currently a major barrier in oligonucleotide technologies in general, and we propose that combining the PS and LNA modifications with charge-neutral amide backbones such as AM1 could lead to more potent oligonucleotides for clinical applications.
Unless otherwise stated, reactions were performed in oven-dried glassware under an inert argon using anhydrous solvents. Anhydrous solvents were collected from an mBraun SPS-800 bench top solvent purification system, having passed through anhydrous alumina columns. Solvents for phosphitylation reaction were degassed by bubbling with argon before used and pyridine and CH2Cl2 were further purified by distillation over KOH or CaH respectively. Anhydrous dichloroethane (Aldrich) was used as supplied without further purification. 3-O-Benzyl 4-C-(methanesulfonyloxymethyl)-5-O-methanesulfonyl-1,2-O-isopropylidene-a-D-ribofuranose was purchased from Carbosynth. All other chemicals were used as obtained from commercial sources without further purification.
Thin layer chromatography (TLC) was performed using Merck pre-coated 0.23 mm thick plates of Kieselgel 60 F254 and visualised using UV (λ=254 nm) or by staining with KMnO4, p-anisaldehyde, dinitrophenylhydrazine, iodine, or ninhydrin (depending on functionality). All retention factors (Rf) are given to 0.01 with the solvent system reported in parentheses. Column chromatography was carried out using Geduran Silica Gel 60 from Merck.
Melting points (mp) were measured using Gallenkamp melting point apparatus and are uncorrected.
1H, 13C and 31P NMR spectra were recorded on a BrukerAVIIIHD 400, BrukerAVII 500 (with a 13C cryoprobe), or Bruker NEO 600 (with broadband helium cryoprobe) spectrometer operating at 400, 500 or 600 MHz respectively using an internal deuterium lock at ambient probe temperatures. 1H NMR chemical shifts (6) are quoted to the nearest 0.01 ppm and are referenced relative to residual solvent peak. Coupling constants (J) are given to the nearest 0.1 Hz. The following abbreviations are used to indicate the multiplicity of signals: s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet, and br=broad. Data is reported as follows: chemical shift (multiplicity, coupling constant(s), integration). 13C NMR chemical shifts (6) are quoted to the nearest 0.1 ppm and are reference relative to the deuterated solvent peak. NMR assignments are supported by DEPT, COSY, HMQC, and HMBC where necessary.
High resolution mass spectra (HRMS) were recorded on a Thermo Scientific Exactive Mass Spectrometer equipped with a Waters Equity autosampler and pump by the University of Oxford Chemistry Departmental Mass Spectrometry Service, and reported mass values are within ±5 ppm mass units unless otherwise stated.
Unless otherwise stated, yields refer to analytically pure compounds.
Commercially available 3-O-benzyl 4-C-(methanesulfonyloxymethyl)-5-O-methanesulfonyl-1,2-O-isopropylidene-a-D-ribofuranose 1 (9.8 g, 21.1 mmol) and ammonium formate (10 g, 159 mmol, 7.5 eq) were dissolved in MeOH (250 mL) and 20 wt % palladium hydroxide on carbon (1.48 g, 2.11 mmol, 10 mol %) was added. The flask was flushed with argon and the reaction was stirred at 60° C. overnight. A large volume of gas is generated within the first hour of the reaction presenting a risk of over-pressurisation. The reaction was filtered through celite to remove the catalyst and the solvent was removed under vacuum. The resulting solid was dissolved in EtOAc (100 mL), washed with a half-saturated aqueous solution of NaCl (2×100 mL), dried over MgSO4, and evaporated to dryness to give 2 (7.9 g, 21.0 mmol) as a white solid in quantitative yield.
TLC (EtOAc:40-60 petroleum ether (PE), 7:3 v/v) Rf: 0.36;
1H NMR (400 MHz, CDCl3): δ 5.87 (d, J=4.0 Hz, 1H), 4.75 (dd, J=6.1, 4.0 Hz, 1H), 4.65 (d, J=11.6 Hz, 1H), 4.50 (d, J=11.6 Hz, 1H), 4.39 (dd, J=7.7, 6.1 Hz, 1H), 4.33 (d, J=10.9 Hz, 1H), 4.29 (d, J=10.9 Hz, 1H), 3.12 (s, 3H), 3.08 (s, 3H), 2.88 (d, J=7.7 Hz, 1H), 1.67-1.66 (s, 3H), 1.38 (s, 3H);
13C NMR (101 MHz, CDCl3): δ 114.1, 104.7, 84.3, 79.2, 72.7, 69.3, 68.6, 38.0, 37.7, 26.2, 26.0; HRMS (m/z): [M+Na]+ calcd. for C11H20O10NaS2+, 399.0390; found, 399.0389.
Alcohol 2 (17.4 g, 46.3 mmol) and Dess-Martin periodinane (29.7 g, 70.0 mmol, 1.5 eq) were dissolved in CH2Cl2 (300 mL) and the reaction was stirred at room temperature overnight. A solution of Na2S2O3 in saturated aqueous NaHCO3 (10% w/v, 200 mL) was added slowly to the reaction and stirring was continued until bubbling ceased. The biphasic mixture was filtered through celite to remove the white precipitate and the organic layer collected. The organic layer was washed twice more with saturated NaHCO3 (200 mL), dried over Na2SO4, and evaporated to dryness to give 3 (16.7 g, 44.7 mmol) as colourless oil in 97% yield which crystallised on standing. This was used without further purification
TLC (EtOAc:40-60 PE, 6:4 v/v) Rf: 0.24;
1H NMR (400 MHz, CDCl3): δ 6.16 (d, J=4.1 Hz, 1H), 4.52 (d, J=4.1 Hz, 1H), 4.46 (d, J=11.0 Hz, 1H), 4.45 (d, J=11.7 Hz, 1H), 4.33 (d, J=11.7 Hz, 1H), 4.32 (d, J=11.0 Hz, 1H), 3.11 (s, 3H), 3.03 (s, 3H), 1.56 (s, 3H), 1.39 (s, 3H);
13C NMR (101 MHz, CDCl3): δ 205.0, 115.6, 103.0, 84.3, 76.7, 69.5, 68.9, 38.2, 37.9, 27.2, 26.8; HRMS (m/z): [M+Na]+ calcd. for C11H18O10NaS2+, 397.0234; found, 397.0231.
A solution of compound 3 (15.1 g, 40.4 mmol) and (carbethoxymethylene)triphenylphosphorane (16.9 g, 48.5 mmol, 1.2 eq) in CH2Cl2 (80 mL) was stirred at room temperature overnight. After removal of the solvent the resulting orange gum was triturated with EtOH, forming a white precipitate. The precipitate was collected by filtration, washed with cold EtOH, and dried under vacuum. The crude product was then purified by recrystallisation from hot EtOH to yield alkene 4 (15.4 g, 33.1 mmol) in 86% yield.
TLC (EtOAc:40-60 PE, 6:4 v/v) Rf: 0.64;
mp: 88-93° C. (crystallised from EtOH);
1H NMR (400 MHz, CDCl3): δ 6.07 (d, J=1.3 Hz, 1H), 5.93 (d, J=3.7 Hz, 1H), 5.79 (dd, J=3.7, 1.3 Hz, 1H), 4.53-4.19 (m, 6H), 3.11 (s, 3H), 3.07 (s, 3H), 1.59 (s, 3H+H2O), 1.41 (s, 3H), 1.32 (t, J=7.1 Hz, 3H);
13C NMR (101 MHz, CDCl3): δ 164.0, 151.2, 121.4, 114.5, 105.6, 85.0, 78.7, 70.1, 69.5, 61.5, 38.2, 37.9, 27.2, 26.4, 14.2;
HRMS (m/z): [M+Na]+ calcd. for C15H24O11NaS2+, 467.0652; found, 467.0652. Ethyl 2-((3aR,6S,6aR)-2,2-dimethyl-5,5-bis(((methylsulfonyl)oxy)methyl)tetrahydrofuro[2,3-d][1,3]dioxol-6-yl)acetate 5
A solution of 4 (13.0 g, 29.3 mmol) in EtOAc (300 mL) was placed under an atmosphere of argon before 5% palladium on activated carbon (1.3 g, 1.5 mmol, 5 mol %) was added. The flask was evacuated under vacuum and refilled with H2 gas three times to ensure a hydrogen atmosphere and vigorously stirred overnight. The reaction was monitored by NMR. Once complete, the mixture was filtered through a pad of celite and the solvent removed under reduced pressure to yield 5 (12.7 g, 28.4 mmol) as a colourless solid in 97% yield which was used without further purification. The use of Pd/C and hydrogen gas along with flammable solvents poses a significant fire risk.
TLC (EtOAc:40-60 PE, 6:4 v/v) Rf: 0.64;
mp: 88-95° C. (crystallised from a mixture of MeOH and EtOH);
1H NMR (400 MHz, CDCl3): δ 5.85 (d, J=3.9 Hz, 1H), 4.87 (dd, J=5.2, 3.9 Hz, 1H), 4.59 (d, J=10.8 Hz, 1H), 4.31 (d, J=10.7 Hz, 1H), 4.30 (d, J=10.8 Hz, 1H), 4.23 (d, J=10.7 Hz, 1H), 4.18 (apparent dq, J=7.1, 2.2 Hz, 2H), 3.12 (s, 3H), 3.07 (s, 3H), 2.91-2.65 (m, 2H), 2.57 (dd, J=16.9, 5.5 Hz, 1H), 1.60 (s, 3H), 1.30 (s, 3H), 1.28 (t, J=7.2 Hz, 3H);
13C NMR (101 MHz, CDCl3): δ 171.3, 112.9, 105.3, 84.1, 81.7, 70.1, 68.2, 61.3, 42.7, 38.1, 37.7, 28.6, 26.3, 25.5, 14.2;
HRMS (m/z): [M+Na]+ calcd. for C15H26O11NaS2+, 469.0809; found, 469.0811.
To a solution of compound 5 (4.9 g, 11.0 mmol) in acetic acid (50 mL) and acetic anhydride (38 mL) was added camphorsulfonic acid (CSA) (120 mg, 0.52 mmol) and the solution was stirred at 80° C. for 90 min. A second portion of CSA (120 mg, 0.52 mmol) was added and stirring continued at 80° C. for 90 min. This was repeated twice more, and the reaction left to stir overnight at 80° C. The volatiles were removed under reduced pressure and the resulting brown gum was co-evaporated with toluene (3×50 mL), dissolved in EtOAc (150 mL), washed with a saturated aqueous solution of NaHCO3 (5×100 mL), washed with brine (1×100 mL), dried over Na2SO4, and evaporated to dryness to yield crude compound 6 (5.3 g, assume quantitative) which was used without purification in the next step. We found the compound was not stable to column chromatography.
TLC (EtOAc:40-60 PE, 6:4 v/v) Rf: 0.38;
1H NMR (400 MHz, CDCl3): δ 6.10 (s, 1H), 5.32 (d, J=5.0 Hz, 1H), 4.40 (d, J=3.3 Hz, 2H), 4.28 (s, 2H), 4.20-4.11 (m, 2H), 3.08 (s, 3H), 3.07 (s, 3H), 3.03 (dd, J=7.7, 4.9 Hz, 1H), 2.62 (t, J=7.5 Hz, 2H), 2.14 (s, 3H), 2.11 (s, 3H), 1.26 (t, J=7.2 Hz, 3H);
13C NMR (101 MHz, CDCl3): δ 170.9, 169.5, 169.3, 97.8, 84.6, 77.8, 71.4, 66.9, 61.6, 40.4, 38.0, 37.6, 28.6, 21.1, 20.8, 14.2;
HRMS (m/z): [M+Na]+ calcd. for C16H26O13NaS2+, 513.0707; found, 513.0706.
Crude compound 6 (2.5 g, 5.1 mmol) and thymine (0.8 g, 6.4 mmol, 1.25 eq) were co-evaporated with anhydrous MeCN (3×15 mL). The mixture was then dissolved in anhydrous MeCN (12.5 mL) and bis(trimethylsilyl)acetamide (BSA) (3.5 mL, 14.2 mmol, 2.8 eq) was added. The solution was heated to reflux for 1 h. The reaction was cooled to room temperature and TMSOTf (1.25 mL, 6.8 mmol, 1.4 eq) was added. The reaction was then heated to reflux overnight resulting in a dark red solution. The reaction was cooled to room temperature, diluted with CH2Cl2 (12.5 mL), and a half saturated aqueous solution of NaHCO3 (25 mL) was added with stirring (bubbles are generated). The organic layer became a pale-yellow colour and was subsequently washed with saturated aqueous NaHCO3 (25 mL) and brine (25 mL). The organic phase was dried over Na2SO4 and evaporated to dryness. The crude brown foam was purified by column chromatography (0-7% MeOH in CH2Cl2) to give compound 7a (2.42 g, 4.4 mmol) as a beige foam in 85% yield.
TLC (CH2Cl2:MeOH, 17:1 v/v) Rf: 0.55;
1H NMR (400 MHz, CDCl3): δ 9.29 (s, 1H), 7.03 (d, J=1.2, 1H), 5.58 (dd, J=7.6, 1.7, 1H), 5.49 (d, J=1.7, 1H), 4.47 (s, 2H), 4.38 (d, J=11.0, 1H), 4.32 (d, J=11.0, 1H), 4.15 (q, J=7.1, 2H), 3.55 (ddd, J=9.6, 7.6, 6.2, 1H), 3.10 (s, 3H), 3.09 (s, 3H), 2.65 (dd, J=16.8, 9.6, 1H), 2.57 (dd, J=16.8, 6.2, 1H), 2.14 (s, 3H), 1.91 (d, J=1.2, 3H), 1.25 (t, J=7.1, 3H);
13C NMR (101 MHz, CDCl3): δ 170.8, 170.3, 163.9, 150.3, 138.5, 111.6, 95.8, 85.5, 78.5, 70.1, 67.4, 61.5, 41.4, 37.9, 37.6, 29.1, 20.8, 14.3, 12.4;
HRMS (m/z): [M+Na]+ calcd. for C19H28N2O13NaS2+, 579.0925; found 579.0924.
Compound 6 (1.04 g, 2.1 mmol) and N4-benzoylcytosine (0.912 g, 4.0 mmol, 2.0 eq) were co-evaporated with anhydrous MeCN (3×15 mL). The mixture was then dissolved in anhydrous MeCN (12.5 mL) and BSA (1.0 mL, 4.1 mmol, 1.9 eq) was added. The suspension was heated to reflux for 1 h. The reaction was cooled to room temperature and TMSOTf (0.45 mL, 2.5 mmol, 1.2 eq) was added. The reaction was then heated to reflux overnight resulting in a dark red solution. The reaction was cooled to room temperature, diluted with CH2Cl2 (12.5 mL), and a half saturated aqueous solution of NaHCO3 was added with stirring. The organic layer was subsequently washed with saturated aqueous NaHCO3 (25 mL) and brine (25 mL). The organic phase was dried over Na2SO4 and evaporated to dryness. The crude brown foam was purified by column chromatography (50-100% EtOAc in 40-60 PE) to give 7b (1.25 g, 1.9 mmol) as a pale-yellow foam in 92% yield.
TLC (CH2Cl2:MeOH, 17:1 v/v) Rf: 0.53;
1H NMR (400 MHz, CDCl3): δ 8.97 (s, 1H), 7.93 (d, J=7.7, 2H), 7.73 (d, J=7.5, 1H), 7.65-7.50 (m, 4H), 5.67 (dd, J=7.4, 1.5, 1H), 5.58 (d, J=1.5, 1H), 4.62-4.49 (m, 2H), 4.45-4.36 (m, 2H), 4.16 (q, J=7.1, 2H), 3.66 (apparent dt, J=9.1, 7.0, 1H), 3.11 (s, 3H), 3.09 (s, 3H), 2.69 (dd, J=16.8, 9.1, 1H), 2.59 (dd, J=16.7, 6.8, 1H), 2.17 (s, 3H), 1.26 (t, J=7.1, 3H);
13C NMR (151 MHz, CDCl3): δ 170.7, 170.4, 166.3 (broad due to rotamers), 162.6, 153.3 (broad due to rotamers), 148.5, 133.8, 132.4, 129.3, 128.2, 97.8, 96.9 (broad due to rotamers), 86.7, 78.7, 70.1, 67.6, 61.5, 41.4, 38.0, 37.7, 29.3, 20.8, 14.3;
HRMS (m/z): [M+H]1 calcd. for C25H32O13N3S2+, 646.1371; found, 646.1367.
A suspension of N4-benzoyl methylcytosine (808 mg, 3.5 mmol, 1.5 eq), compound 6 (1.13 g, 2.3 mmol) and BSA (1.5 mL, 6.1 mmol, 2.7 eq) in anhydrous MeCN (13.5 mL) was heated to reflux for 1 h. The solution was cooled to room temperature, TMSOTf (0.5 mL, 2.8 mmol, 1.2 eq) was added dropwise with stirring and the reaction was then heated to reflux overnight. After cooling to room temperature, the reaction was diluted with EtOAc (30 mL) and a saturated aqueous solution of NaHCO3 (30 mL) was added slowly (generates bubbles). Stirring the biphasic mixture generated a precipitate, which was filtered removing the precipitate prior to workup. The organic layer was collected, washed with saturated aqueous NaHCO3 (2×30 mL) followed by brine (30 mL), dried over MgSO4, and evaporated to dryness to give an orange foam. This was purified by column chromatography (0-10% MeOH in CH2Cl2) to give 7c (885 mg, 1.3 mmol) as a beige foam in 58% yield.
TLC (CH2Cl2:MeOH, 17:1 v/v) Rf: 0.5;
1H NMR (400 MHz, CDCl3): δ 13.24 (s, 1H), 8.34-8.29 (m, 2H), 7.54 (tt, J=7.4, 1.4, 1H), 7.45 (t, J=7.4, 2H), 7.21 (d, J=1.2, 1H), 5.62 (dd, J=7.5, 1.7, 1H), 5.54 (d, J=1.7, 1H), 4.49 (d, J=10.8, 2H), 4.46 (d, J=10.8, 1H), 4.41 (d, J=11.0, 1H), 4.33 (d, J=11.0, 1H), 4.17 (q, J=7.1, 2H), 3.58 (apparent dt, J=9.2, 6.9, 1H), 3.11 (s, 3H), 3.09 (s, 3H), 2.67 (dd, J=16.8, 9.2, 1H), 2.58 (dd, J=16.8, 6.6, 1H), 2.17 (s, 3H), 2.12 (d, J=1.2, 3H), 1.27 (t, J=7.1, 3H);
13C NMR (151 MHz, CDCl3): δ 180.0, 170.7, 170.2, 159.7, 147.8, 139.1, 137.1, 132.8, 130.2, 128.3, 112.7, 96.1, 85.7, 78.5, 69.8, 67.3, 61.5, 41.3, 38.0, 37.7, 29.1, 20.8, 14.3, 13.5;
HRMS (m/z): [M+H]+ calcd. for C26H34O13N3S2+, 660.1528; found, 660.1522.
N6-Benzoyladenine (1.15 g, 4.8 mmol) and compound 6 (2.63 g, 5.3 mmol, 1.1 eq) were suspended in anhydrous 1,2-dichlorethane (22 mL) and BSA (3.13 mL, 12.8 mmol, 2.7 eq) was added. The solution was heated to reflux for 1 h. The reaction was cooled to room temperature and TMSOTf (2.0 mL, 11 mmol, 2.3 eq) was added. The reaction was then heated to reflux overnight resulting in a dark red solution. The reaction was cooled to room temperature, diluted with CH2Cl2 (12.5 mL), and added to a saturated aqueous solution of NaHCO3 (22 mL) slowly with stirring (bubbles are generated). The organic layer was subsequently washed with saturated aqueous NaHCO3 (25 mL) and brine (25 mL), dried over Na2SO4, and evaporated to dryness. The crude brown foam was purified by silica column chromatography (0-100% EtOAc in 40-60 PE) to give compound 7d (2.29 g, 3.4 mmol) as a beige foam in 71% yield.
TLC (EtOAc) Rf: 0.35;
1H NMR (400 MHz, CDCl3): δ 9.17 (s, 1H), 8.80 (s, 1H), 8.12 (s, 1H), 8.04-7.93 (m, 2H), 7.64-7.55 (m, 1H), 7.51 (t, J=7.51, 2H), 6.13 (d, J=1.1, 1H), 5.88 (dd, J=6.7, 1.1, 1H), 4.55 (d, J=1.9, 2H), 4.48 (d, J=10.9, 1H), 4.40 (d, J=10.9, 1H), 4.16 (q, J=7.1, 2H), 4.12-4.02 (m, 1H), 3.11 (s, 3H), 2.95 (s, 3H), 2.72 (apparent dd, J=7.8, 4.9, 2H), 2.19 (s, 3H), 1.25 (t, J=7.1, 3H);
13C NMR (101 MHz, CDCl3): δ 170.7, 170.1, 164.8, 152.8, 151.1, 150.0, 142.6, 133.7, 133.0, 129.0, 128.0, 123.7, 90.8, 86.0, 79.0, 69.6, 67.0, 61.5, 41.6, 37.9, 37.6, 28.9, 20.8, 14.2;
HRMS (m/z): [M+H]1 calcd. for C26H32O12N5S2, 670.1483; found, 670.1482.
Compound 6 (2.6 g, 5.3 mmol) and N2-isobutyrylguanine (1.34 g, 6.1 mmol, 1.1 eq) were suspended in anhydrous 1,2 dichloroethane (22 mL) and BSA (3.1 mL, 12.5 mmol, 2.4 eq) was added. The suspension was heated to reflux for 1.5 h. The reaction was cooled to room temperature and TMSOTf (2.0 mL, 11 mmol, 2.1 eq) was added. The reaction was then heated to reflux for 2 h. The reaction was cooled to room temperature and added to a stirring solution of saturated aqueous NaHCO3 (22 mL). The organic layer was subsequently washed with saturated aqueous NaHCO3 (25 mL) and brine (25 mL). The organic phase was dried over Na2SO4 and evaporated to dryness. Purification by column chromatography (0-10% MeOH in EtOAc) gave 7e (2.64, 4.1 mmol) as a pale-yellow foam in 78% yield.
TLC (EtOAc:MeOH, 9:1 v/v) Rf: 0.45;
1H NMR (400 MHz, CDCl3): δ 12.16 (s, 1H), 9.44 (s, 1H), 7.75 (s, 1H), 5.96 (d, J=1.1, 1H), 5.72 (dd, J=6.5, 1.1, 1H), 4.72 (d, J=10.5, 1H), 4.49 (d, J=11.1, 1H), 4.42 (d, J=10.5, 1H), 4.32 (d, J=11.1, 1H), 4.25 (dt, J=8.9, 6.6, 1H), 4.13 (apparent qd, J=7.2, 1.1, 2H), 3.12 (s, 3H), 3.06 (s, 3H), 2.77-2.57 (m, 3H), 2.16 (s, 3H), 1.30-1.16 (m, 9H);
13C (101 MHz, CDCl3): δ 179.4, 171.1, 170.0, 155.5, 148.1, 147.4, 139.2, 122.0, 91.0, 85.4, 78.5, 69.6, 67.6, 61.5, 41.4, 38.0, 37.7, 36.4, 28.6, 20.7, 19.0, 18.9, 14.2; HRMS (m/z): [M+H]1 calcd. for C23H34O13N5S2+, 652.1589; found, 652.1586.
Compound 7a (1.0 g, 1.8 mmol) was dissolved in 1,4-dioxane (4.5 mL) and water (4.5 mL) and 2 M NaOH in water (9 mL, 18 mmol, 10 eq) was added. The reaction was stirred at room temperature for 2 h until the locking step and ester hydrolysis was complete (reaction progress monitored using LCMS). The reaction was then heated to 55° C. for 1 h. The reaction was evaporated to dryness and partitioned between CH2Cl2 (40 mL) and water (30 mL). The aqueous layer was washed with CH2Cl2 (3×10 mL). The aqueous phase was acidified using 1 M HCl and washed with CH2Cl2 (3×20 mL). The product was then extracted from the aqueous layer using 25% iPrOH in CH2Cl2 (4×10 mL, until no product remained in the aqueous layer as determined by TLC), dried over Na2SO4, and evaporated to dryness to give 8a (516 mg, 1.7 mmol) as a white solid in 92% yield which was used without further purification.
TLC (CH2Cl2:MeOH, 3:2 v/v+2% Et3N) Rf: 0.26;
1H NMR (400 MHz, d6-DMSO): δ 11.39 (s, 1H), 7.62 (d, J=1.3, 1H), 5.44 (s, 1H), 4.35 (s, 1H), 3.81 (d, J=13.0, 1H), 3.77 (d, J=13.0, 1H), 3.73 (d, J=8.5, 1H), 3.60 (d, J=8.4, 1H), 3.31 (s, 1H), 2.41 (dd, J=15.5, 2.7, 1H), 2.33-2.07 (m, 2H), 1.79 (d, J=1.2, 3H);
13C NMR (101 MHz, d6-DMSO): δ 173.4, 164.3, 150.5, 135.4, 108.8, 91.1, 86.8, 80.2, 71.5, 57.1, 39.7, 29.0, 12.9;
HRMS (m/z): [M−H]− calcd. for C13H15O7N2−, 311.0885; found, 311.0882.
Compound 7b (400 mg, 0.62 mmol) was dissolved in 1,4-dioxane (4 mL) and 1 M NaOH in water (2 mL, 2 mmol, 3.2 eq) was added. The reaction was stirred at room temperature for 2 h until the locking step and ester hydrolysis was complete (reaction progress monitored using LCMS). The reaction was then heated to 55° C. for 2 h. The reaction was evaporated to dryness and partitioned between CH2Cl2 (40 mL) and water (30 mL). The aqueous phase was washed with CH2Cl2 (3×10 mL), acidified using 1 M HCl and further washed with CH2Cl2 (3×20 mL). The product was then extracted from the aqueous layer using 25% iPrOH in CH2Cl2 (4×10 mL, until no product remains in the aqueous layer as determined by TLC), dried over Na2SO4, and evaporated to dryness to give 8b (198 mg, 0.49 mmol) as a white solid in 80% yield which was used without further purification.
TLC (CH2Cl2:MeOH, 3:2 v/v, +2% Et3N) Rf: 0.4;
1H NMR (500 MHz, d6-DMSO): δ 8.26 (d, J=7.5, 1H), 8.00 (dd, J=8.5, 1.3, 2H), 7.63 (tt, J=7.5, 1.3, 1H), 7.55-7.48 (m, 2H), 7.41 (d, J=7.5, 1H), 5.55 (s, 1H), 4.45 (s, 1H), 3.82 (d, J=13.1, 1H), 3.77 (d, J=13.1, 1H), 3.77 (d, J=8.4, 1H), 3.65 (d, J=8.4, 1H), 2.30 (s, 1H), 2.31-2.05 (m, 3H);
13C NMR (126 MHz, d6-DMSO): δ 167.9, 167.4, 163.3, 154.0, 144.3, 133.2, 132.7, 128.5, 128.4, 95.9, 91.2, 87.4, 79.8, 71.1, 56.8, 40.1, 29.9;
HRMS (m/z): [M−H]− calcd. for C19H18O7N3−, 400.1150; found, 400.1141.
Compound 7c (400 mg, 0.61 mmol) was dissolved in 1,4-dioxane (4 mL) and 1 M LiOH in water (2 mL, 2 mmol, 3.3 eq) was added. The reaction was stirred at room temperature for 2 h and then heated to 55° C. After 1 h the reaction was complete as determined by LCMS. The reaction was evaporated to dryness and partitioned between CH2Cl2 (40 mL) and water (30 mL). The aqueous layer was washed with CH2Cl2 (3×40 mL), acidified with 1 M HCl, and washed once more with CH2Cl2 (40 mL). The product was then extracted from the aqueous layer using 15% iPrOH in CH2Cl2 (5×20 mL), until no product remained in the aqueous layer as determined by TLC, dried over Na2SO4, and evaporated to dryness to give 8c (198 mg, 0.48 mmol) as a white solid in 78% yield which was used without further purification.
TLC (CH2Cl2:MeOH, 3:2 v/v, +2% Et3N) Rf: 0.36;
1H NMR (500 MHz, d6-DMSO): δ 8.23-8.16 (m, 2H), 7.95 (s, 1H), 7.60 (t, J=7.3, 1H), 7.51 (t, J=7.6, 2H), 5.53 (s, 1H), 5.25 (br s, 1H), 4.46 (s, 1H), 3.85 (d, J=13.1, 1H), 3.82 (d, J=13.1, 1H), 3.77 (d, J=8.5, 1H), 3.65 (d, J=8.5, 1H), 2.42 (dd, J=15.8, 3.2, 1H), 2.30-2.19 (m, 2H), 2.04 (s, 3H);
13C NMR (126 MHz, d6-DMSO): δ 177.9, 172.9, 159.1, 147.2, 137.8, 136.5, 132.5, 129.3, 128.4, 109.1, 91.1, 87.0, 79.5, 71.1, 56.6, 39.0, 28.5, 13.4;
HRMS (m/z): [M+H]+ calcd. for C20H22O7N3+, 416.1452; found, 416.1452.
Compound 7d (500 mg, 0.75 mmol) was dissolved in 1,4-dioxane (4.8 mL) and 1 M LiOH in water (2.4 mL, 2.4 mmol, 3.2 eq). The reaction was stirred at room temperature for 2 h and then heated to 55° C. After 2 h the product formation was analysed by LCMS. The reaction was not complete and a further 0.33 eq of 1 M LiOH (266 L) was added and the reaction stirred at 55° C. for 1 h. Once complete, the reaction was evaporated to dryness and partitioned between CH2Cl2 (20 mL) and water (20 mL). The aqueous layer was washed with CH2Cl2 (3×20 mL), acidified with 1 M HCl, and washed once more with CH2Cl2 (20 mL). The product was then extracted from the aqueous layer using 15% iPrOH in CH2Cl2 (5×20 mL), dried over Na2SO4, and evaporated to dryness to give 8d (230 mg, 0.54 mmol) as a white solid in 72% yield which was used without further purification.
TLC (CH2Cl2:MeOH, 3:2 v/v, +2% Et3N) Rf: 0.24;
1H NMR (400 MHz, d6-DMSO): δ 12.36 (s, 1H), 11.21 (s, 1H), 8.76 (s, 1H), 8.53 (s, 1H), 8.09-8.02 (m, 2H), 7.69-7.60 (m, 1H), 7.60-7.51 (m, 2H), 6.09 (s, 1H), 4.74 (s, 1H), 3.86 (m, 3H), 3.77 (d, J=8.5, 1H), 3.32 (s, 1H), 2.57 (dd, J=9.8, 4.1, 1H), 2.54-2.47 (m, 1H+solvent peak), 2.33 (dd, J=17.1, 9.8, 1H);
13C NMR (101 MHz, d6-DMSO): δ 173.4, 165.8, 152.3, 151.8, 150.8, 141.5, 133.8, 132.9, 129.0, 128.9, 126.2, 90.8, 86.0, 80.5, 72.0, 57.6, 41.3, 29.1; HRMS (m/z): [M+H]+ calcd. for C20H20O6N5+, 426.1406; found, 426.1407.
To a solution of compound 7e (105 mg, 0.17 mmol) in 1,4-dioxane (2 mL) was added 1 M NaOH in water (0.5 mL, 0.5 mmol, 3.0 eq). The reaction was stirred at room temperature for 3 h and then heated to 55° C. After 1 h the reaction was complete as determined by LCMS. The reaction was evaporated to dryness and was partitioned between CH2Cl2 (20 mL) and water (20 mL). The aqueous layer was washed with CH2Cl2 (3×20 mL), acidified with 1 M HCl, and washed once more with CH2Cl2 (20 mL). NaCl was added to saturate the aqueous layer and the product was extracted from the aqueous layer using 25% iPrOH in CH2Cl2 (5×20 mL), dried over Na2SO4, and evaporated to dryness to give 8e (52 mg, 0.13 mmol) as a white solid in 75% yield which was used without further purification.
TLC (CH2Cl2:MeOH, 3:2 v/v, +2% Et3N) Rf: 0.18;
1H NMR (400 MHz, d6-DMSO): δ 12.14 (s, 1H), 11.80 (s, 1H), 8.14 (s, 1H), 5.82 (s, 1H), 4.61 (s, 1H), 3.82 (apparent d, J=9.8, 3H), 3.69 (d, J=8.6, 1H), 2.78 (app h, J=6.8, 1H), 2.55-2.46 (m, 2H and d6-DMSO), 2.29 (dd, J=17.8, 10.5, 1H), 1.11 (d, J=6.8, 6H);
13C NMR (101 MHz, d6-DMSO): δ 180.2, 172.9, 154.6, 148.4, 147.6, 136.1, 120.0, 90.3, 85.3, 80.1, 71.5, 57.1, 40.6, 34.7, 28.6, 18.9, 18.8;
HRMS (m/z): [M−H]− calcd. for C17H20O7N5−, 406.1368; found, 406.1359.
Compound 8a (400 mg, 1.28 mmol) was dissolved in pyridine (18 mL) and Et3N (0.25 mL, 1.8 mmol, 1.1 eq) and activated 3 A molecular sieves were added. The solution was stirred at room temperature for 15 min before 4-dimethylaminopyridine (DMAP) (78 mg, 0.64 mmol, 0.5 eq) and 4,4′-dimethoxytrityl chloride (DMT-Cl) (1 g, 2.95 mmol, 2.3 eq) were added. The reaction was stirred at room temperature for 4 h before a second portion of DMT-Cl (0.8 g, 2.36 mmol, 1.8 eq) was added and the reaction was stirred at room temperature for 16 h. The molecular sieves were removed by filtration and the organic solvents were removed under vacuum. The resulting residue was purified by column chromatography (0-30% MeOH in EtOAc with a constant additive of 2% Et3N). Following column chromatography, NMR showed significant amounts of Et3N salts and the material was dissolved in EtOAc (25 mL) and was washed with H2O (3×25 mL), dried over Na2SO4, and evaporated to dryness to yield 9a (687 mg). Rather than risk degradation, the final product was not evaporated to complete dryness and was stored and used with 0.5 eq of Et3N present (as determined by NMR), making the final yield 81%.
TLC (CH2Cl2:MeOH, 4:1 v/v, +2% Et3N) Rt: 0.18;
1H NMR (400 MHz, DMSO-d6): δ 11.43 (s, 1H), 7.61 (d, J=1.1, 1H), 7.49-7.37 (m, 2H), 7.37-7.21 (m, 7H), 6.91 (dd, J=9.0, 3.0, 4H), 5.48 (s, 1H), 4.42 (s, 1H), 3.74 (s, 6H), 3.64 (d, J=8.6, 1H), 3.60 (d, J=8.6, 1H), 3.50 (d, J=11.4, 1H), 3.30 (d, J=11.4, 1H underwater peak), 2.50-2.45 (m, 8H, Et3N counterion under solvent peak), 2.42 (dd, J=9.4, 4.3, 1H), 2.17 (dd, J=16.9, 9.4, 1H), 2.00 (dd, J=16.9, 4.3, 1H), 1.59 (d, J=1.1, 3H), 0.95 (t, J=7.2, 4.5H, Et3N);
13C NMR (151 MHz, d6-DMSO): δ 172.6, 163.8, 158.2, 149.9, 144.6, 135.2, 135.0, 134.3, 129.7, 129.7, 128.0, 127.6, 126.9, 113.3, 113.3, 108.5, 89.2, 86.6, 85.8, 79.7, 71.3, 58.6, 55.0, 45.5 (Et3N), 40.7, 28.6, 12.4, 10.7 (Et3N);
HRMS (m/z): [M−H]− calcd. for C34H33O9N2−, 613.2192; found, 613.2184.
Compound 8b (100 mg, 0.25 mmol) was dissolved in pyridine (4 mL) and Et3N (0.05 mL, 0.36 mmol, 1.4 eq) and activated 3 A molecular sieves were added. The solution was stirred at room temperature for 15 min before DMAP (16 mg, 0.13 mmol, 0.5 eq) and DMT-Cl (204 mg, 0.6 mmol, 2.5 eq) were added. The reaction was stirred at room temperature for 16 h before the molecular sieves were removed by filtration and the organic solvents removed under vacuum. The resulting residue was purified by column chromatography (0-30% MeOH in EtOAc with a constant additive of 2% pyridine) to give 9b (122 mg) in 69% yield.
TLC (CH2Cl2:MeOH, 3:2 v/v, +2% Et3N) Rf: 0.37;
1H NMR (400 MHz, DMSO-d6): δ 11.17 (s, 1H), 8.33 (d, J=7.5, 1H), 8.01 (d, J=7.4, 2H), 7.64 (t, J=7.4, 1H), 7.52 (t, J=7.6, 2H), 7.46-7.22 (m, 10H), 6.94 (d, J=8.7, 4H), 5.62 (s, 1H), 4.53 (s, 1H), 3.77 (s, 6H), 3.67-3.63 (m, 2H), 3.51 (d, J=11.1, 1H), 3.41 (d, J=11.1, 1H), 2.39 (dd, J=9.3, 4.0, 1H), 2.21-2.09 (m, 1H), 1.97 (dd, J=16.6, 4.0, 1H);
13C NMR (151 MHz, d6-DMSO): δ 173.2, 168.0. 163.4, 158.2, 154.0, 149.6 (pyridine), 144.4, 143.9, 135.1, 135.1, 133.2, 132.7, 129.7, 129.7, 128.5, 128.4, 128.0, 127.7, 126.9, 123.9, 113.3, 113.3, 95.8, 89.3, 87.6, 86.0, 79.3, 71.3, 58.4, 55.0, 40.1, 28.7.
HRMS (m/z): [M+H]+ calcd. for C40H38O9N3+, 704.2603; found, 704.2602.
Compound 8c (100 mg, 0.24 mmol) was dissolved in pyridine (4 mL) and Et3N (0.05 mL, 0.7 mmol, 1.5 eq) and activated 3 A molecular sieves were added. The solution was stirred at room temperature for 15 min before DMAP (16 mg, 0.36 mmol, 1.5 eq) and DMT-Cl (204 mg, 0.6 mmol, 2.5 eq) were added. The reaction was left to stir at room temperature for 16 h before the molecular sieves were removed by filtration and the organic solvents removed under vacuum. The resulting residue was purified by column chromatography (0-30% MeOH in EtOAc with a constant additive of 2% pyridine) to yield 9c (114 mg). Rather than risk degradation, the final product was not evaporated to complete dryness and was stored and used with 1 eq of pyridine present (as determined by NMR), making the final yield 60%.
TLC (CH2Cl2:MeOH, 3:2 v/v, +2% Et3N) Rf: 0.37;
1H NMR (500 MHz, DMSO-d6): δ 8.65-8.45 (m, 2H, pyridine), 8.22-8.12 (m, 2H), 7.89 (s, 1H), 7.78 (tt, J=7.6, 1.9, 1H, pyridine), 7.60 (t, J=7.4, 1H), 7.50 (t, J=7.7, 2H), 7.48-7.42 (m, 2H), 7.44-7.30 (m, 8H, pyridine), 7.29-7.24 (m, 1H), 6.93 (dd, J=8.9, 4.0, 4H), 5.58 (s, 1H), 4.54 (s, 1H), 3.75 (s, 6H), 3.69 (d, J=8.7, 1H), 3.66 (d, J=8.7, 1H), 3.55 (d, J=11.4, 1H), 3.36 (d, J=11.4, 1H), 3.34 (br s, 1H), 2.47 (m, 1H under solvent peak), 2.25 (dd, J=17.0, 8.9, 1H), 2.05 (dd, J=17.0, 4.4, 1H), 1.87-1.75 (m, 3H);
13C NMR (126 MHz, d6-DMSO): δ 177.6, 172.5, 159.2, 149.6 (pyridine), 147.1, 144.6, 137.1, 136.1 (pyridine), 135.2, 135.1, 132.6, 129.8, 129.3, 129.2, 128.4, 128.0, 127.6, 126.9, 123.9 (pyridine), 113.4, 113.3, 109.2, 89.6, 87.3, 85.9, 79.5, 71.3, 58.5, 55.1, 39.4, 28.4, 13.6; HRMS (m/z): [M+H]+ calcd. for C41H40N3O9+, 718.2759, found, 718.2756.
Compound 8d (62.5 mg, 0.15 mmol) was dissolved in pyridine (1.5 mL) and Et3N (0.031 mL, 0.22 mmol, 1.5 eq) and activated 3 A molecular sieves were added. The solution was stirred at room temperature for 15 min before DMAP (18 mg, 2 mmol, 1.3 eq) and DMT-Cl (100 mg, 0.29 mmol, 2 eq) were added. The reaction was stirred at room temperature for 2 h, and a second portion of DMT-Cl (100 mg, 0.29 mmol, 2.0 eq) was added. After 16 h the molecular sieves were removed by filtration and the organic solvents removed under vacuum. The resulting residue was purified by column chromatography (5-15% MeOH in EtOAc with a constant additive of 2% pyridine) to yield 9d (76 mg). Rather than risk degradation, the final product was not evaporated to complete dryness and was stored and used with 0.72 eq of pyridine present (as determined by NMR), making the final yield 65%.
TLC (EtOAc:MeOH, 3:7 v/v, +2% Et3N) Rf: 0.50;
1H NMR (500 MHz, DMSO-d6): δ 12.63 (s, 1H), 11.27 (s, 1H), 8.78 (s, 1H), 8.60-8.55 (m, 1H, pyridine), 8.48 (s, 1H), 8.08-8.02 (m, 2H), 7.78 (tt, J=7.6, 1.9, 0.5H, pyridine), 7.68-7.61 (m, 1H), 7.55 (t, J=7.7, 2H), 7.43-7.22 (m, 10H, includes pyridine), 6.90-6.85 (m, 4H), 6.14 (s, 1H), 4.81 (s, 1H), 3.84 (d, J=8.5, 1H), 3.77 (d, J=8.5, 1H), 3.73 (s, 6H), 3.47 (d, J=11.2, 1H), 3.44 (d, J=11.2, 1H), 2.73 (dd, J=9.7, 4.2, 1H), 2.24-2.16 (m, 1H), 2.08 (dd, J=16.8, 4.2, 1H);
13C NMR (126 MHz, d6-DMSO): δ 173.2, 165.7, 158.2, 151.8, 151.4, 150.4, 149.6 (pyridine), 144.6, 140.8, 133.3, 136.1 (pyridine), 135.2, 135.2, 133.4, 132.5, 129.8, 129.7, 128.5, 128.5, 127.9, 127.6, 126.9, 126.8, 125.6, 123.9 (pyridine), 113.3, 88.8, 85.7, 85.6, 80.0, 71.8, 59.5, 55.0, 41.6, 29.2;
HRMS (m/z): [M+H]+ calcd. for C41H38O8N5+, 728.2711; found, 728.2715.
Compound 8e (41 mg, 0.10 mmol) was dissolved in pyridine (1.7 mL) and Et3N (0.023 mL, 0.17 mmol, 1.7 eq) and activated 3 A molecular sieves were added. The solution was stirred at room temperature for 15 min before DMAP (6.7 mg, 0.05 mmol, 0.5 eq) and DMT-Cl (85 mg, 0.25 mmol, 2.5 eq) were added. The reaction was left to stir at room temperature for 16 h. The molecular sieves were removed by filtration and the organic solvents removed under vacuum. The resulting residue was purified by column chromatography (5-15% MeOH in EtOAc with a constant additive of 2% pyridine) to yield 9e (52 mg). Rather than risk degradation, the final product was not evaporated to complete dryness and was stored and used with 0.65 eq of pyridine present (as determined by NMR), making the final yield 68%.
TLC (EtOAc:MeOH, 3:7 v/v, +2% Et3N) Rf: 0.53;
1H NMR (500 MHz, DMSO-d6): δ 8.97-8.40 (m, 1.2H, pyridine), 8.11 (s, 1H), 7.91-7.56 (m, 0.6H, pyridine) 7.39-7.34 (m, 3.4H, with 1.4H from pyridine), 7.30 (dd, J=8.6, 6.9, 2H), 7.29-7.17 (m, 5H), 6.93-6.84 (m, 4H), 5.85 (s, 1H), 4.71 (s, 1H), 3.76 (d, J=8.4, 1H), 3.73 (s, 6H), 3.71 (d, J=8.4, 1H), 3.41 (d, J=11.1, 1H), 3.31 (d, J=11.1, 1H), 3.16 (s, 1H, MeOH), 2.79 (p, J=6.9, 1H), 2.67 (dd, J=10.2, 3.9, 1H), 2.10-1.94 (m, 2H), 1.11 (dd, J=6.9, 1.9, 6H);
13C NMR (126 MHz, d6-DMSO): δ 180.2, 175.1 (broad), 158.2, 154.9, 148.4, 148.0, 144.7, 136.0, 135.2, 135.1, 129.7, 127.9, 127.6, 126.8, 120.4, 113.3, 113.3, 88.7, 85.6, 85.1, 80.1, 71.9, 59.5, 55.1, 42.5, 34.7, 30.4, 18.9, 18.9;
HRMS (m/z): [M+H]+ calcd. for C40H4O9N5+, 710.2821; found 710.2817.
Compound S14 was prepared based on a similar procedure outlined by Thorpe et al.1 Compound S82 (3.5 g, 8.0 mmol) and NaN3 (1.04 g, 16 mmol, 2 eq) were dissolved in DMF (40 mL) and the reaction was stirred at 50° C. for 5 h. Sodium azide is potentially explosive if handled in correctly. The solvent was removed under vacuum and the resulting residue was partitioned between EtOAc (40 mL) and water (40 mL). The organic layer was washed with water (2×40 mL), dried over Na2SO4, and evaporated to dryness to yield S14 (2.96 g, 7.7 mmol) as a white solid in 96% yield which was used without purification. If required the compound can be purified by column chromatography (50-100% EtOAc in 40-60 PE).
Data consistent with literature1.
Compound S11 (2.0 g, 5.2 mmol) and ammonium formate (4.0 g, 63 mmol, 12 eq) were dissolved in MeOH (100 mL) and 20 wt % palladium hydroxide on carbon (0.36 g, 0.52 mmol, 10 mol %) was added. The flask was flushed with argon and the reaction was stirred at 60° C. for 4 h. A large volume of gas is generated within the first hour of the reaction presenting a risk of over-pressurisation. The reaction was filtered through celite to remove the catalyst and the solvent was removed under vacuum. The resulting solid was purified by column chromatography (0-30% MeOH in EtOAc) to give S11 (1.17 g, 4.3 mmol) as a white solid in 83% yield.
Data consistent with literature1.
Amine S11 (1.17 g, 4.3 mmol) was dissolved in anhydrous pyridine (50 mL) and 4-methoxytriphenylmethyl chloride (1.6 g, 5.2 mmol, 1.2 eq) was added in small portions. The reaction was stirred at room temperature for 2 h before the solvents were removed under vacuum. The resulting residue was purified by column chromatography (0-30% EtOAc in 40-60 PE with a constant additive of 0.1% pyridine) to give S12 (1.93 g, 3.6 mmol) as a pale-yellow foam in 83% yield.
TLC (EtOAc:hexane, 3:2 v/v, +0.5% pyridine) Rf: 0.5;
1H NMR (400 MHz, CDCl3): δ 9.32 (s, 1H), 7.65 (s, 1H), 7.48-7.45 (m, 4H), 7.38-7.37 (m, 2H), 7.29-7.24 (m, 4H), 7.17 (t, J=7.3, 2H), 6.81 (d, J=9.0, 2H), 5.61 (s, 1H), 4.46 (s, 1H), 4.26 (s, 1H), 4.00 (br s, 1H), 3.92 (d, J=8.3, 1H), 3.78 (d, J=8.2, 1H), 3.74 (s, 3H), 2.65-2.49 (m, 2H), 2.09 (t, J=8.5, 1H), 1.92 (d, J=1.2, 3H).
13C NMR (101 MHz, CDCl3): δ 164.1, 158.3, 150.0, 145.9, 145.8, 137.4, 134.7, 129.9, 128.5, 128.2, 126.8, 113.5, 110.5, 88.8, 87.2, 79.8, 72.7, 70.7, 70.4, 55.4, 40.2, 12.8;
HRMS (m/z): [M+Na]+ calcd. for C31H31O6N3Na+, 564.2105, found, 564.2103;
No spectroscopic data reported previously3.
Nucleoside 10 (1.1 g, 2.0 mmol) was dissolved in anhydrous degassed CH2Cl2 (10 mL). Degassed N,N-diisopropylethylamine (DIPEA) (883 μL, 5.1 mmol, 2.5 eq) and 2-cyanoethyl N,N-diisopropylchlorophosphoramidite (677 μL, 3.0 mmol, 1.5 eq) were added and the reaction was stirred under an argon atmosphere at room temperature for 2 h. The reaction mixture was diluted with CH2Cl2 (40 mL) and washed with a saturated aqueous solution of KCl (30 mL). The organic phase was dried over Na2SO4 and the solvents were removed under vacuum. The resulting pale-yellow oil was purified by column chromatography (40% EtOAc in hexane with a constant additive of 0.5% pyridine) to give the phosphoramidite 10 (1.3 g, 1.8 mmol) as a white foam in 90% yield.
TLC (EtOAc:hexane, 2:3 v/v, +0.5% pyridine) Rf: 0.4;
31P NMR (162 MHz, CDCl3): δ 148.7, 148.3
HRMS (m/z): [M−H]− calcd. for C40H47O7N5P−, 740.3219; found 740.3219.
DNA synthesis was performed on an Applied Biosystems 394 automated DNA/RNA synthesiser using a standard phosphoramidite cycle of detritylation, coupling, capping (unless stated elsewhere), and oxidation on a 1.0 μmole scale. Trichloroacetic acid (TCA) (3% in CH2Cl2) was used for detritylation, 5-benzylthio-1H-tetrazole (BTT) (0.25 M in MeCN) was used as an activator, and oxidation was achieved using iodine (0.02 M in THF, pyridine and water). Pre-packed nucleoside SynBase™ CPG 1000/110 (Link Technologies) were used and β-cyanoethyl phosphoramidite monomers (dA(Bz), dG(iBu), dC(Bz) and dT, Sigma-Aldrich) were dissolved in anhydrous MeCN (0.1 M) immediately prior to use with coupling time of 50 s. LNA β-cyanoethyl phosphoramidite monomers (QIAGEN) were dissolved to a concentration of 0.1 M in either MeCN (LNA-T) or 25% THF/MeCN (LNA-mC(Bz)) immediately prior to use with a coupling time of 6 min. Stepwise coupling efficiencies were determined by automated trityl cation conductivity monitoring and were >98% in all cases. Cleavage and deprotection were achieved by exposure to concentrated aqueous ammonia solution for 60 min at room temperature followed by heating in a sealed tube for 5 h at 55° C.
RNA synthesis was performed on an Applied Biosystems 394 automated DNA/RNA synthesiser using a standard phosphoramidite cycle of detritylation, coupling, capping, and oxidation on a 1.0 μmole scale. Coupling, capping and oxidation reagents were identical to those used for DNA synthesis except a solution of ethylthiotetrazole (ETT) (0.25 M in MeCN, Link Technologies) was used instead of BTT as the activator. Standard CPG resin (Link Technologies) was used and 2′-thiomorpholine-4-carbothioate (TC) protected monomers (A(Bz), C(Ac), G(iBu) and U, Sigma-Aldrich) were dissolved in anhydrous toluene/MeCN (1:1 v/v, 0.1 M) immediately prior to use. The coupling time for all monomers was 3 min. Stepwise coupling efficiencies were determined by automated trityl cation conductivity monitoring and in all cases were >97%. To deprotect and cleave the RNA, the solid support was exposed to dry ethylenediamine:toluene (1:1 v/v) for 6 h at room temperature, washed with toluene (3×1 mL), then MeCN (3×1 mL) and dried using argon. The cleaved RNA was eluted from the solid support with water.
2′OMe oligonucleotides were synthesised on an Applied Biosystems 394 automated DNA/RNA synthesiser using a standard phosphoramidite cycle of detritylation, coupling (unless otherwise stated), capping, and oxidation on a 1.0 μmole scale. Detritylation, coupling, capping, oxidation and activation reagents are identical to those used for DNA synthesis. Pre-packed nucleoside SynBase™ CPG 1000/110 (Link Technologies) were used, and β-cyanoethyl phosphoramidite monomers (DMT-2′O-Methyl-rA(Bz), DMT-2′O-Methyl-rG(iBu), DMT-2′O-Methyl-rC(Ac) and DMT-2′O-Methyl-rU, Sigma-Aldrich) were dissolved in anhydrous MeCN (10% CH2Cl2 was added when 2′OMe U phosphoramidite was used) to a concentration of 0.1 M immediately prior to use with a coupling time of 6 min. LNA β-cyanoethyl phosphoramidite monomers (QIAGEN) were dissolved to a concentration of 0.1 M in either MeCN (LNA-T) or 25% THF/MeCN (LNA-mC(Bz)) immediately prior to use with a coupling time of 6 min. Stepwise coupling efficiencies were determined by automated trityl cation conductivity monitoring and were >98% in all cases. Cleavage and deprotection were achieved by exposure to concentrated aqueous ammonia solution for 60 min at room temperature followed by heating in a sealed tube for 5 h at 55° C.
Oligonucleotides were purified using a Gilson reverse-phase high performance liquid chromatography (RP-HPLC) system with ACE® C8 column (particle size: 10 μm, pore size: 100 Å, column dimensions: 10 mm×250 mm) with a gradient of buffer A (0.1 M TEAB, pH 7.5) to buffer B (0.1 M TEAB, pH 7.5 containing 50% v/v MeCN) and flow rate of 4 mL/min. The gradient of MeCN in triethylammonium bicarbonate (TEAB) was increased from 0% to 50% buffer B over 30 min. Elution was monitored by UV absorbance at 298 nm. After HPLC purification, oligonucleotides were freeze dried then dissolved in water without the need for desalting.
Oligonucleotides with a phosphorothioate rather than a phosphodiester backbone were synthesised as described above, except for a solution of 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH, Link Technologies) in MeCN (0.05 M) was used as a sulfurising reagent in place of the oxidising solution. The sulfurisation time was extended to 3 min followed by sending fresh EDITH to the synthesis column and leaving it for another 3 min. Phosphorothioate modified oligonucleotides were isolated with the final 5′-DMT protecting group still in place (DMT-On). Following solid phase synthesis, the cyanoethyl groups were removed by a 15 min treatment with 20% diethylamine in MeCN. The resin was then washed with MeCN (5×1 mL) and dried by passing a stream of argon through the synthesis column. The oligonucleotides were cleaved from the solid support and deprotected by heating in a sealed glass vial at 55° C. for 5 h. The ammonia was removed under reduced pressure prior to oligonucleotide purification. The DMT-On oligonucleotides were purified by RP-HPLC and lyophilised. They were then dissolved in 0.5 mL of 80% acetic acid and incubated for 1 h at room temperature to remove the DMT group. The solution was neutralised with 0.5 mL of triethylammonium acetate buffer (2 M, pH 7) and the detritylated oligonucleotides were desalted using a NAP-10 column (Cytiva) then freeze dried.
All oligonucleotides were characterised by negative-mode ultra-performance liquid chromatography (UPLC) mass spectrometry using a Waters Xevo G2-XS QT of mass spectrometer with an Acquity UPLC system, equipped with an Acquity UPLC oligonucleotide BEH C18 column (particle size: 1.7 μm; pore size: 130 A; column dimensions: 2.1 mm×50 mm). Data were analysed using Waters MassLynx software or Waters UNIFI Scientific Information System software.
Oligonucleotide segments were synthesised as described, except that the capping step was omitted.
The MMT-protected 5′-amino phosphoramidite monomer (either LNA 103 or commercially available deoxythymidyl 11) was dissolved in anhydrous MeCN (0.1 M) immediately prior to use. The same conditions as above were used, but the coupling time was extended to 10 min. No capping step was used. The 5′-MMT protecting group was cleaved on the Applied Biosystems 394 automated synthesiser using TCA (3% in CH2Cl2) with an extended cleavage time of 2 min. The solid support was then washed with MeCN on the synthesiser for 3 min. To improve the coupling efficiency in the next step the solid support was washed with N-methylmorpholine in DMF (0.5% v/v, 1 mL) followed by DMF (3×1 mL).
All amide couplings were performed manually in the synthesis column. A solution with 10 equivalents of acid monomer, 10 equivalents of PyBOP and 30 equivalents of N-methylmorpholine was first prepared in 400 μL of DMF. This was then taken up into a 1 mL syringe and loaded into the column before a second 1 mL syringe was attached to the other end of the synthesis column. The mixture was agitated every 10 min for 1 h. The columns were then washed with DMF (3×1 mL) followed by MeCN (5×1 mL) and dried by passing argon through the column. The column was then returned to the synthesiser to continue oligonucleotide synthesis.
Cleavage of Oligonucleotides from Resin, Deprotection and Purification
LNA-amide containing oligonucleotides were isolated with the final 5′-DMT protecting group still in place (DMT-On). Following solid phase synthesis, the cyanoethyl groups were removed by a 15 min treatment with 20% diethylamine in MeCN. The resin was then washed with MeCN (5×1 mL) and dried by passing a stream of argon through the synthesis column. The oligonucleotides were cleaved from the solid support and deprotected by heating in concentrated aqueous ammonia solution in a sealed glass vial at 55° C. for 5 h. The ammonia was removed under reduced pressure prior to oligonucleotide purification. The DMT-On oligonucleotides were purified by RP-HPLC. The elution of oligonucleotides was monitored by UV absorbance at 298 nm. The oligonucleotides were lyophilised and then dissolved in 0.5 mL of 80% acetic acid, and incubated for 1 h at room temperature to remove the DMT group. The solution was neutralised with 0.5 mL of triethylammonium acetate buffer (2 M, pH 7) and the detritylated oligonucleotides were desalted using a NAP-10 column (Cytiva), then freeze dried.
UV melting experiments were performed using a Cary 4000 scan UV-vis spectrophotometer. 3 nmol of each oligonucleotide was dissolved in 1 mL of 10 mM phosphate buffer containing 200 mM NaCl at pH 7.0. The samples were first denatured by heating to 85° C. (10° C./min) and then annealed by slowly cooling to 20° C. (1° C./min). Six successive cycles of heating and cooling were performed at a gradient of 1° C./min whilst recording the change in UV absorbance at 260 nm. The built-in software was then used to calculate the melting temperature from the first derivative of the melting curve.
DNA and RNA oligonucleotides were purified by HPLC, desalted by gel filtration (NAP-10) and then freeze dried. Oligonucleotide stock solutions (2 mM) were prepared in aqueous KCl (10 mM). DNA samples were combined with an equimolar ratio of complementary RNA to form their respective modified DNA:RNA hybrids to form 1 mM duplex (60 μL). Single crystals of the DNA:RNA duplexes were obtained by the sitting drop vapour diffusion method. The Natrix HT sparse matrix screen (Hampton Research, HR2-131) was used to identify crystallisation hits for each modified duplex sample using high throughput (HT) methods. All HT screens were performed in CrystalMation Intelli-Plate 96-3 low-profile plates (Hampton Research, HR3-119). Reservoirs and drops were dispensed using an Art Robbins Phoenix automatic liquid handler. Reservoirs contained 80 μL of Natrix HT solution and crystallisation drops (200-300 nL total volume) were placed in each of the three subwells; subwell 1, 200 nL oligo:100 nL well solution; subwell 2, 100 nL oligo: 100 nL well solution; subwell 3, 100 nL oligo: 200 nL well solution (stock duplex concentration was 1 mM). Plates were sealed using optically clear Xtra-Clear Advanced Polyolefin StarSeal (StarLab) and incubated at 19° C., crystals usually formed within one week (range 2-90 days, crystal size <10-200 m). The unmodified DNA:RNA duplex was crystallised using adapted conditions from Kopka et al.4 Optimisation of these conditions were done in 24 well Cryschem sitting drop plates (Hampton Research, USA) using 4 μL sitting drops consisting of 0.5 mM duplex, 12 mM Mg(OAc)2, 0.6 mM spermidine·HCl, 0.075% (w/v) β-octylglucoside, 12 mM sodium cacodylate and 12% 2-methyl-2,4-pentanediol (MPD). This was equilibrated against a reservoir of H2O:MPD (1:1 v/v, 400 μL). To screen conditions, components of the drop were varied (6-16 mM Mg(OAc)2, 0.2-1.2 mM spermidine·HCl, 0.075% (w/v) β-octylglucoside, 12 mM sodium cacodylate and 6-16% MPD. All other structures were obtained using hits from the NatrixHT screen (Hampton Research, USA). All samples were crystallised at 19° C. using the conditions outlined in Table S6.
Sample wells were opened and cryo protectant 20% glycerol in reservoir solution (2 μL) was added. Crystals were harvested using cryoloops (0.01-0.05 mm) and immediately cryo-cooled by plunging into liquid N2 (77 K), transferred into a cryo-vial and stored under liquid nitrogen at 77 K until data collection. Data collection was performed at Diamond Light Source (beamlines i03 or i04) or DESY in Hamburg (beamline P13). The high radiation damage resistance of the oligo duplex crystals permitted 100% beam transmission. Oscillation images (3600 images, 0.1° osc) were collected. The detector distance was set to obtain a maximum resolution of 0.5 A greater than the expected diffraction limit to maximise spot separation (see Table S5) and reduce overlapping reflections and obtain maximal completeness. Data were auto processed using either fast dp5, xia2_dials6 or xia2_3dii7. CC1/2>0.3 and completeness >90%, crystal data quality was reviewed using Phenix.Xtriage. ON26xDNA, ON29xDNA-Am-DNA, and ON29xLNA-Am-DNA duplexes all crystallised in the high symmetry space group P61 and contained a single DNA:RNA hybrid in the asymmetric unit. In contrast, the ON30xLNA-Am-LNA duplex was in the lower symmetry Space Group P 3221 with two DNA:RNA hybrids in each asymmetric unit.
The structures were solved using the Molecular Replacement method and 1PJO PDB ID as the search model6, 9 using PHASER 2.8.210. Structure solutions resulted in TFZ score>8.0 and LLG>50 and correct solution was confirmed by visual inspection of electron density maps. The DNA:RNA models (some with modified backbone) were built and fit to the electron density using winCOOT11. Model refinement was performed using REFMAC512 and PHENIX.REFINE13. Geometric restraints for the non-standard phosphoribosyl backbones were generated using JLIGAND8 or ACEDRG14. Model building continued until the observed electron density was satisfied and the Rfree no longer decreased. Software packages and project management was handled using CCP415 and Phenix13. Images were made using PYMOL graphic software (The PyMOL Molecular Graphics System, Version 2.3.2 Schrödinger, LLC).
Where necessary, data were reprocessed to achieve acceptable final statistics (i.e. CC ½>0.3). Reprocessing was performed using iMosflm, XDS or in-house using automated xia2 pipelines7. The data were then scaled and merged using Aimless16.
Five nmol of each oligonucleotide was dissolved in Dulbecco's PBS (50 μL) and FBS (50 μL, Gibco, standard sterile-filtered) was added. The sample was mixed by pipetting and 20 μL of this solution was immediately removed, mixed with formamide (20 μL), snap frozen in liquid N2, and stored at −80° C. as a control (0 h). The remaining reaction mixtures were incubated at 37° C. and aliquots (20 μL) were taken at different time intervals, mixed with formamide (20 μL), snap frozen in liquid N2 and stored at −80° C. The samples were then analysed by denaturing 20% polyacrylamide gel.
HeLa pLuc/705 cells17 were cultured in Dulbecco's Modified Eagle Medium with GlutaMAX-I (Gibco) supplemented with 10% (v/v) FBS (Gibco) and 1×Antibiotic-Antimycotic (Gibco) at 37° C. in a humidified incubator with 5% CO2.
Transfection with Lipofectamine 2000
Cells were seeded at a density of 7000 cells/well in 100 μL of culture media in 96 well plates 16 h before transfection to reach 70-80% cell confluency. Immediately prior to transfection, 5 μL of Lipofectamine 2000 (Invitrogen) was diluted in 500 μL OptiMEM (Gibco) and incubated at room temperature for 5 min before mixing with 4 pmol of lyophilised oligonucleotide dissolved in 500 μL of OptiMEM. The resulting mixture was incubated at room temperature allowing complexation to occur. The complexes were then further diluted in OptiMEM to the concentrations required for the experiments. Culture media was removed from the cells and 100 μL of the complexes added per well. The cells were then incubated at 37° C. in a humidified incubator with 5% CO2. After 4 h the media was replaced with 100 μL of culture media and the cells were returned to the incubator for a further 20 h.
Cells were seeded at a density of 800 cells/well in 100 μL in culture media in 96 well plates 16 h before the oligonucleotides were added. Lyophilised oligonucleotides were dissolved in OptiMEM immediately before addition to the cells. The media in each well was removed and replaced with 100 μL of the oligonucleotide containing OptiMEM. The cells were then incubated for 96 h at 37° C. in a humidified incubator with 5% CO2.
The culture media was removed from the well and the cells were washed with 200 μL of PBS. 100 μL of GloLysis™ buffer (Promega) was added to each well. The plate was incubated at room temperature on the orbital shaker for 10 min to lyse the cells. 50 μL of the cell lysate was added to 50 μL of Bright-Glo™ luciferase reagent (Promega) in a white 96 well plate and the luminescence was measured using a Clariostar plate reader. 25 μL of the cell lysate was then used for protein quantification using a Pierce BCA protein assay kit in accordance with the manufacturer's guidelines, using GloLysis buffer as a blank standard. The luminescence values were divided by the total protein quantities and normalised to the values for untreated cells.
The cell viability was evaluated using the WST-1 cell proliferation reagent (Roche) in accordance with the manufacturer's guidelines. Briefly, cells were seeded, transfected using Lipofectamine 2000, and the media was changed to culture media after 4 h, as described above. The cells were then incubated for 20 h at 37° C. in a humidified incubator with 5% CO2 before WST-1 reagent (10 μL) was added to each well. The cells were returned to the incubator for 4 h. The cells were shaken at 500 rpm for 1 min before 10 μL of media was removed from each well and added to a clear 96 well plate containing 90 μL of water in each well and the absorbance at 440 nm was measured using a ClarioStar plate reader. This dilution step was necessary as the absorbance went above the accurate range of the instrument. Cells that were treated with OptiMEM instead of the oligonucleotide complexes were used as a 100% viability reference.
GCGUCG
AGCGUCG
GCGUCG
AGCGUCG
Underlined bases indicates a locked sugar; * is an amide bond in place of a phosphodiester, underlined italic and highlighted bases indicates the position of the mismatch. Backbone denotes to the chemistry of inter-sugar linkages and the sugars not flanking an amide bond.
DNA-
Am-
DNA
LNA-
Am-
DNA
DNA-
Am-
LNA
LNA-
Am-
LNA
LNA-
LNA
DNAcontrol
Tm values were measured using 3.0 μM concentrations of each oligonucleotide strand in 10 mM phosphate buffer (pH 7.0) containing 200 mM NaCl. Underlined, e.g. T indicates a locked sugar and * is an amide bond in place of a phosphodiester. Tm values were calculated as the maximum of the first-derivative of the melting curve (A260 vs T) and reported as the average of at least two independent experiments. ΔTm for matched sequences=modified−ON6DNAcontrol; ΔTm for mismatched=Match−RNA mismatch. Target ON sequences, where X denotes the mismatch. ON7=GCTGCAAGCGTCG; ON8=GCUGCAAGCGUCG; ON9=GCUGCACGCGUCG; ON10=GCUGCCAGCGUCG; RNA ON11=GCUGCAGGCGUCG. ON12=GCUGCGAGCGUCG. Representative melting curves are given (
Experimental conditions as in Table S2. a=comparison of DNA ONs against full length targets, b=comparison of DNA ONs against 10-mer targets, c=comparison of 2′OMe/PO ONs, d=comparison of 2′OMe/PS ONs. Backbone: PO=phosphodiester, PS=phosphorothioate, DNA=deoxyribose sugars, 2′OMe=2′OMe RNA sugars. X indicate a locked sugar and * indicates an amide bond in place of a phosphodiester, LAL indicates the number of LNA-flanked amide bonds. DNA target (ON21)=TGTAACTGAGGTAAGAGG; RNA target (ON22)=UGUAACUGAGGUAAGAGG. Truncated DNA target (ON23)=AGGTAAGAGG. Truncated RNA target (ON24)=AGGUAAGAGG. ΔTm=modified−control. Bases in lower case italic remain single stranded on duplex formation and do not contribute to Tm. Representative melting curves are given (
DNA
DNA
LNA
T indicates a locked sugar and * indicates an amide bond in place of phosphodiester.
T indicates a locked sugar and * indicates an amide bond in place of a phosphodiester.
While specific embodiments of the invention have been described for the purpose of reference and illustration, various modifications will be apparent to a person skilled in the art without departing from the scope of the invention as defined by the appended claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2118332.2 | Dec 2021 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/GB2022/053283 | 12/16/2022 | WO |
