2′-O-Lysylaminohexyladenosine modified oligonucleotides

Abstract  

Development of therapeutically active oligonucleotides for sequence-specific gene knockdown relies on chemical modifications that confer high stability and target affinity and ideally enable cellular uptake. 2′-O-Lysylaminohexyluridine-containing antisense and siRNA oligonucleotides have been shown to be well suited for gene knockdown. They are highly resistant to enzymatic degradation while having good affinity for the targeted RNA strand and efficiently down-regulate their target in cell culture tumor models. The 2′-O-lysylaminohexyl modification was expanded to adenosine nucleosides. The corresponding phosphoramidite building block was prepared in a straightforward procedure comprising six steps starting from adenosine. After 2′-O-alkylation with N-(6-bromohexyl)phthalimide and removal of the N-protecting group, the protected lysine was specifically attached to the alkylamino group. Incorporation of 2′-O-lysylaminohexyladenosine nucleotides in a test sequence confirmed that the cationic chains lead only to minor duplex destabilization and do not disturb the duplex structure. Results further emphasize the advantageous properties of 2′-O-lysylaminohexyl modified oligonucleotides for therapeutic applications.     

Reversible diselenide cross-links are formed between oligonucleotides containing 2′-deoxy-6-selenoinosine

We have synthesized and characterized a phosphoramidite derivative of 2′-deoxy-6-selenoinosine (d^6SeI) and incorporated this modification into an oligonucleotide by solid-phase synthesis. During cleavage from the solid-support and deprotection, spontaneous dimerization of this oligonucleotide occurs via formation of a diselenide cross-link between the modified nucleobases. This cross-link can be readily reduced to restore the single-stranded oligonucleotide. UV thermal denaturation and circular dichroism spectroscopy of duplexes with d^6SeI paired against all four native nucleobases revealed minor differences in stability and structure relative to 2′-deoxyinosine. This selenium containing nucleobase modification may be useful for applications in DNA nanomaterials and X-ray crystallography.     

1,1-Bis-(4-methoxyphenyl)-1′-pyrenyl methyl (bmpm): a new fluorescent 5′ protecting group for the purification of unmodified and modified oligonucleotides

By replacing the phenyl by a pyrenyl in the dimethoxytrityl (DMTr) group commonly used for 5′-protection in oligonucleotide synthesis, we have obtained a fluorescent acid-labile protecting group which exhibits similar chemical properties to those of DMTr. Here we demonstrate the usefulness of the new protecting group in the purification of both charged and neutral DNA fragments.     

Structural characterization of melphalan modified 2′-oligodeoxynucleotides by miniaturized LC-ES MS/MS

In this study a miniaturized LC coupled to electrospray tandem mass spectrometry was used to analyze modifications originating from the interaction between the chemotherapeutic agent melphalan and 2'-oligodeoxynucleotides. Low energy CAD product ion spectra gave information about the specificity of melphalan alkylation with regard to certain DNA sequences. These data can be very useful to estimate the risk in the development of secondary leukaemia as a result of a melphalan cure. In the study of the interaction between melphalan and d(GG), differentiation could be made between alkylation on the 5'-side and alkylation on the 3'-side, because of the presence or absence of the alkylated w1 fragment in the low energy CAD spectra. In the other di-mers alkylation specificity for the different bases could be observed. Melphalan alkylation occurs in the sequence G > A > C > T. The study of the alkylated d(GGGG) revealed the presence of mainly 5'-end alkylation. Furthermore studies were performed which investigated other melphalan treated di-, tetra-, hepta-, and octa-mers.     

Synthesis of 3′-fluoro-4′-amino-hexitol nucleosides with a pyrimidine nucleobase as building blocks for oligonucleotides

The synthesis of 3′-fluoro-4′-amino-hexitol nucleosides with a uracil and cytosine nucleobase was performed. The synthesis started from 1,5:2,3-dianhydro-4,6-benzylidene-allitol and afforded the target compounds in 15 steps. These protected hexitol nucleosides are valuable building blocks for the preparation of a new class of oligonucleotides.     

Synthesis of 5,5′-Dialkyl-6,6′-dichloro-2, 2′-bipyridines

5,5′-Dialkyl-6,6′-dichloro-2,2′-bipyridines were synthesized starting from 3-substituted 2-chloro-6-iodopyridines using Pd-catalyzed coupling conditions. 6-Alkyl-3,5-dichloro-2H-1,4-oxazin-2-ones were excellent precursors for the synthesis of these functionalized 2-iodo-6-chloropyridines.     

Darstellung von 2′,3′-Dideoxy-2′-hydroxymethyl-nucleosiden

Zusammenfassung Die Synthese von geschützten 2,3-Dideoxy-2-hydroxymethyl-nucleosiden wird beschrieben. Die durch ein Mehrstufenverfahren aus Isopropylidenglycerol erhaltenen Nucleoside können als Bausteine zur Darstellung von Oligonucleotiden verwendet werden, deren 2- und 5-Positionen über eine Etherbrücke verbunden sind.

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Synthesis of 2,3-dideoxy-2-hydroxymethyl nucleosides

Summary The synthesis of protected 2,3-dideoxy-2-hydroxymethyl nucleosides is presented. The nucleosides, obtained in a multi-step procedure starting from isopropylideneglycerol, may be used as building blocks for the synthesis of 2,5-ether linked oligonucleotides.

     

Synthesis of 2′-deoxy-2′-fluororibo- and 2′-deoxy-2′,2′-difluororibonucleosides derived from 6-(het)aryl-7-deazapurines

A series of novel sugar-modified derivatives of cytostatic 6-hetaryl-7-deazapurine ribonucleosides (2′-deoxy-2′-fluororibo- and 2′-deoxy-2′,2-difluororibonucleosides) bearing an aryl or hetaryl group in position 6, was prepared and screened for biological activity. The fluororibo derivatives were prepared by aqueous palladium catalyzed cross-coupling reactions of the corresponding 6-chloro-7-deazapurine 2′-deoxy-2′-fluororibonucleoside 11 with (het)arylboronic acids. The key intermediate 11 was prepared by a six-step sequence from the corresponding arabinonucleoside by selective protection of 3′- and 5′-hydroxyls by acid-labile groups followed by stereoselective S_N2 fluorination and deprotection. The difluororibo-series was prepared by non-stereoselective glycosidation of 6-chloro-7-deazapurine with benzoyl-protected 2-deoxy-2,2-difluoro-d-erythro-pentofuranosyl-1-mesylate followed by cross-couplings, separation of anomers and deprotection. The title nucleosides did not show considerable cytostatic or antiviral activity.     

In vitro metabolism of 2′-ribose unmodified and modified phosphorothioate oligonucleotide therapeutics using liquid chromatography mass spectrometry

Antisense oligonucleotides (ASOs) have been touted as an emerging therapeutic class to treat genetic disorders and infections. The evaluation of metabolic stability of ASOs during biotransformation is critical due to concerns regarding drug safety. Because the effects of the modifications in ASOs on their metabolic stabilities are different from unmodified ASOs, studies that afford an understanding of these effects as well as propose proper methods to determine modified and unmodified ASO metabolites are imperative. An LC–tandem mass spectrometry method offering good selectivity with a high-quality separation using 30 mm N,N-dimethylcyclohexylamine and 100 mm 1,1,1,3,3,3-hexafluoro-2-propanol was utilized to identify each oligonucleotide metabolite. Subsequently, the method was successfully applied to a variety of in vitro systems including endo/exonuclease digestion, mouse liver homogenates, and then liver microsomes, after which the metabolic stability of unmodified versus modified ASOs was compared. Typical patterns of chain-shortened metabolites generated by mainly 3′-exonucleases were observed in phosphodiester and phosphorothioate ASOs, and endonuclease activity was identically observed in gapmers that showed relatively more resistance to nuclease degradation. Overall, the degradation of each ASO occurred more slowly corresponding to the degree of chemical modifications, while 5′-exonuclease activities were only observed in gapmers incubated in mouse liver homogenates. Our findings provide further understanding of the impact of modifications on the metabolic stability of ASOs, which facilitates the development of future ASO therapeutics.     

Oxidation of the 2′-NHR Analogues of 2′-OR-Chalcones; Conversion of 2′-NHR-Chalcone Epoxides

Synthesis of 2′-NHR-chalcone expoxides and their reaction with acidic reagents are discussed.     

Synthesis of 2′,3′-Dideoxy-2′-Fluorokanamycin A

2′,3′-Dideoxy-2′-fluorokanamycin A (23) was prepared by condensation of 6-azido-4-0-benzoyl-2,3,6-trideoxy-2-fluoro-α-D-ribo-hexopyranosyl bromide (13) and a protected disaccharide (19). Methyl 4,6-0-benzylidene-3-deoxy-β-D-arabino-hexopyranoside (5) prepared from methyl 4,6-0-benzylidene-3-chloro-3-deoxy-β-D-allo-hexopyranoside (1) by oxidation with pyridinium chlorochromate followed by reduction with Na₂ S₂O₄ was fluorinated with the DAST reagent to give methyl 4,6-O-benzylidene-2,3-dideoxy-2-fluoro-β-D-ribo-hexopyranoside (7). Successive treatment of 7 with NBS, NaN₃ and SOBr₂ gave 13. The structure of the final product (23) was determined by the ¹H and ¹⁹F and shift-correlated 2D NMR spectra.     

Chiral enrichment of 2-amino-2′-hydroxy-1,1′-binaphthyl

A new synthetic procedure for the formation of 2-amino-2′-hydroxy-1,1′-binaphthyl, and a new purification procedure through the formation of Schiff bases, purification of the Schiff bases, and breakdown of the Schiff bases through amine exchange, are described. Through the new purification procedure, greater than 99% purity of the compound can be obtained easily and reliably. A set of procedures were examined to compare the efficiency and reliability to resolve 2-amino-2′-hydroxy-1,1′-binaphthyl into enantiomers. A new procedure was discovered to enrich enantiomeric excess from less than 10% to 95–99% in one step. Even a racemic mixture from an achiral procedure can be enriched to 67% e.e. in about 4% yield. The X-ray crystal structure of the racemic mixture [rhombohedral, space group Iba2, a=15.718(2) Å, b=21.703(2) Å, c=8.5398(9) Å, V=2913.2(5) ų, R1=0.0705, Z=8, d_calcd=1.301 g/cm³, F(000)=1200 e] was solved to elucidate the intriguing behavior of this compound.     

Stereodefined dinucleoside (3′,5′)-propionamidophosphonates and β-cyanoethylphosphonates and their incorporation into modified oligonucleotides

Base-catalyzed stereospecific anti-Markovnikov addition of dinucleoside (3′,5′)-H-phosphonates to the activated alkenes acrylamide and acrylonitrile resulting in the synthesis of P-chiral diastereomerically pure dinucleoside (3′,5′)-alkylphosphonates is reported.     

2′-5′连接寡聚核苷酸——2′-5′A核的固相合成

本文用磷酸三酯法,在交联聚丙烯酰吗福啉载体上,以1,3,5-三甲苯磺酰氯(MS)加N-甲基咪唑(N-Mein)为缩合剂,合成了2′-5′相连的寡聚腺苷酸——2′-5′A核。每个保护的单体接到载体上的收率是令人满意的,分别是100％,64％和89％。在合成过程中,我们对合成一系列中间体和制备载体的方法进行了改进,使产物收率大大提高,分离操作得以简化。     

Synthesis of β-L-2′,3′-Dideoxy-2′-fluoro-3′-hydroxymethylarabinofuranosyl Pyrimidine Nucleosides

β-2′,3′-Dideoxy-2′-fluoro-3′-hydroxymethylarabinofuranosylthymine 10 and cytosine 12 were synthesized from L-xylose and were found to be inactive against HIV-1 in acutely infected lymphocytes.     

A Click-Chemistry Linked 2′3′-cGAMP Analogue

2′3′-cGAMP is an uncanonical cyclic dinucleotide where one A and one G base are connected via a 3′-5′ and a unique 2′-5′ linkage. The molecule is produced by the cyclase cGAS in response to cytosolic DNA binding. cGAMP activates STING and hence one of the most powerful pathways of innate immunity. cGAMP analogues with uncharged linkages that feature better cellular penetrability are currently highly desired. Here, the synthesis of a cGAMP analogue with one amide and one triazole linkage is reported. The molecule is best prepared via a first Cu^I-catalyzed click reaction, which establishes the triazole, while the cyclization is achieved by macrolactamization.     

New boron-containing 2′-deoxyadenosines

Conjugates of polyhedral boron hydrides with deoxyadenosine were synthesized by the opening of cyclic oxonium derivatives of closo-dodecaborate and cobalt bis(1,2-dicarbollide) with 2′-deoxyadenosine derivatives containing a nucleophilic group in the substituent at C(8). Biological studies of the derivatives obtained for cytotoxicity revealed that the derivatives based on closo-dodecaborate did not exhibit cytotoxicity. The conjugates obtained can be used in further biological trials as potential agents for boron neutron capture therapy of cancer.     

2′-Fluoro-3-deazaaristeromycin

The carbocyclic nucleoside 3-deazaaristeromycin has shown biological promise but a library of its derivatives upon which to expand this property is lacking. To address this situation, the synthesis of the two diastereomers of 2′-fluoro-3-deazaaristeromycin is described in a multistep convergent process that calls upon d-ribose for construction of the cyclopentyl fluoro units.