Deprotection Conditions Research Articles

Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid Phase Synthesis.

Nucleosides containing ester groups that are sensitive to nucleophiles were incorporated into oligodeoxynucleotides (ODNs) through solid phase chemical synthesis. The sensitive esters are located on a purine nucleobase. They are the esters of ethyl, 2-methoxyethyl, 4-methoxyphenyl and phenyl groups, and a thioester. These esters cannot survive the deprotection and cleavage conditions used in known ODN synthesis technologies, which involve strong nucleophiles such as ammonium hydroxide and potassium methoxide (potassium carbonate in anhydrous methanol). To incorporate these sensitive groups into ODNs, the Dmoc phosphoramidites and linker were used for solid phase synthesis, which allowed ODN deprotection and cleavage to be carried out under non-nucleophilic oxidative conditions. Sixteen ODN sequences containing these groups were synthesized and characterized with MALDI MS. In addition, the synthesis and characterization of three ODNs containing a nucleophile sensitive 6-chloropurine using the same strategy are described.

An amine protecting group deprotectable under nearly neutral oxidative conditions.

The 1,3-dithiane-based dM-Dmoc group was studied for the protection of amino groups. Protection was achieved under mild conditions for aliphatic amines, and under highly reactive conditions for the less reactive arylamines. Moderate to excellent yields were obtained. Deprotection was performed by oxidation followed by treating with a weak base. The yields were good to excellent. The new amino protecting group offers a different dimension of orthogonality in reference to the commonly used amino protecting groups in terms of deprotection conditions. It is expected to allow a collection of transformations to be carried out on the protected substrates that are unattainable using any known protecting groups.

Automatic procedures for the synthesis of difficult peptides using oxyma as activating reagent: A comparative study on the use of bases and on different deprotection and agitation conditions

Solid-Phase Peptide Synthesis (SPPS) is a rapid and efficient methodology for the chemical synthesis of peptides and small proteins. However, the assembly of peptide sequences classified as “difficult” poses severe synthetic problems in SPPS for the occurrence of extensive aggregation of growing peptide chains which often leads to synthesis failure. In this framework, we have investigated the impact of different synthetic procedures on the yield and final purity of three well-known “difficult peptides” prepared using oxyma as additive for the coupling steps. In particular, we have comparatively investigated the use of piperidine and morpholine/DBU as deprotection reagents, the addition of DIPEA, collidine and N-methylmorpholine as bases to the coupling reagent. Moreover, the effect of different agitation modalities during the acylation reactions has been investigated. Data obtained represent a step forward in optimizing strategies for the synthesis of “difficult peptides”.

Facile Synthesis, Geometry, and 2'-Substituent-Dependent in Vivo Activity of 5'-(E)- and 5'-(Z)-Vinylphosphonate-Modified siRNA Conjugates.

(E)-Vinylphosphonate ((E)-VP), a metabolically stable phosphate mimic at the 5'-end of the antisense strand, enhances the in vivo potency of siRNA. Here we describe a straightforward synthetic approach to incorporate a nucleotide carrying a vinylphosphonate (VP) moiety at the 5'-end of oligonucleotides under standard solid-phase synthesis and deprotection conditions by utilizing pivaloyloxymethyl (POM) protected VP-nucleoside phosphoramidites. The POM protection enhances scope and scalability of 5'-VP-modified oligonucleotides and, in a broader sense, the synthesis of oligonucleotides modified with phosphonate moieties. Trivalent N-acetylgalactosamine-conjugated small interfering RNA (GalNAc-siRNA) comprising (E)-geometrical isomer of VP showed improved RISC loading with robust RNAi-mediated gene silencing in mice compared to the corresponding (Z)-isomer despite similar tissue accumulation. We also obtained structural insights into why bulkier 2'-ribosugar substitutions such as 2'-O-[2-(methylamino)-2-oxoethyl] are well tolerated only when combined with 5'-(E)-VP.

Deprotection of durable benzenesulfonyl protection for phenols — efficient synthesis of polyphenols

ABSTRACTA robust protection method for phenol was demonstrated by the use of durable benzenesulfonyl group, which survives various harsh reaction conditions using Grignard reagent, organolithium reagent, metal alkoxide, phosgene, mineral, and Lewis acids. A facile deprotection condition utilizing pulverized KOH (5 equiv) and t-BuOH (10 equiv) in hot toluene makes this protocol as a practical method, which can be applied to the multistep synthesis of biologically and medicinally important polyphenol compounds.

Synthesis and Multiple Incorporations of 2'-O-Methyl-5-hydroxymethylcytidine, 5-Hydroxymethylcytidine and 5-Formylcytidine Monomers into RNA Oligonucleotides.

The synthesis of 2′‐O‐methyl‐5‐hydroxymethylcytidine (hm5Cm), 5‐hydroxymethylcytidine (hm5C) and 5‐formylcytidine (f5C) phosphoramidite monomers has been developed. Optimisation of mild post‐synthetic deprotection conditions enabled the synthesis of RNA containing all four naturally occurring cytosine modifications (hm5Cm, hm5C, f5C plus 5‐methylcytosine). Given the considerable interest in RNA modifications and epitranscriptomics, the availability of synthetic monomers and RNAs containing these modifications will be valuable for elucidating their biological function(s).

A Flexible Strategy for the Regiocontrolled Synthesis of Pyrazolo[1,5-a]pyrazines.

A four-step protocol for the synthesis of pyrazolo[1,5-a]pyrazines has been developed. Commercially available pyrazoles were alkylated and formylated in a regiocontrolled manner to give pyrazole-5-aldehydes bearing 2,2-dialkoxyethyl substitution on N-1. Efficient conditions for the subsequent deprotection and cyclization of these intermediates allowed access to pyrazolo[1,5-a]pyrazines with multiple substitution patterns. The versatility of the pyrazole-5-aldehyde intermediates was further demonstrated through a deprotection and double-reductive amination sequence to give 4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazines.

Efficient synthesis of hydrocarbon-bridged diaminodiacids through nickel-catalyzed reductive cross-coupling

Solid-phase incorporation of pre-prepared diaminodiacids has been established as an efficient strategy for the chemical synthesis of peptide disulfide bond mimics. Hydrocarbon-bridged diaminodiacids represent one important category of diaminodiacids but they remain difficult to synthesize. In the present work, we reported the use of newly-developed nickel catalyzed reductive cross-coupling reaction to efficiently synthesize diaminodiacids with hydrocarbon bridges. Through optimization of the reaction conditions, the yield of the hydrocarbon bridge formation reached about 50%, even when the reaction was scaled up to the gram level. Subsequently, using our recently developed Dmab/ivDde protecting group system, we obtained a new hydrocarbon-bridged diaminodiacid that are suitable for metal-free deprotection conditions. We demonstrated the utility of this Dmab/ivDde protected hydrocarbon-bridged diaminodiacid in the synthesis of a disulfide surrogate of oxytocin.

Photo‐Triggered Fluorometric Hydrophobic Benzyl Alcohol for Soluble Tag‐Assisted Liquid‐Phase Peptide Synthesis

AbstractSolid phase methods have been central to the chemical synthesis of peptides, yet a liquid phase method would arguably be more appropriate with modern synthetic chemistry approaches to fine‐tune the molecular structures of peptides. Herein, we describe a simple and rational design for the synthesis of 2,5‐substituted hydrophobic benzyl alcohol (HBA) as a new soluble tag for liquid phase peptide synthesis. This tag allows the use of both 9‐fluorenylmethoxycarbonyl (Fmoc) and HF‐free tert‐butoxycarbonyl (Boc) methods. The HBA‐tagged peptides can be detected both colorimetrically and fluorometrically, enabling their quantitative assay. The Boc method is compatible with the HBA tag because it is mildly acid resistant, whereas commonly used acidic global deprotection conditions lead to the simultaneous cleavage of the side chain protecting groups and the HBA tag. The HBA tag was successfully applied to the synthesis of the angiotensin III selective antagonist peptide.

Efficient synthesis of N-nosyl-protected 3-azabicyclo[4.3.0]nonen-8-one by an aniline- and nitrobenzene-mediated Pauson–Khand cyclization

ABSTRACTThe intramolecular Pauson–Khand cyclization in the presence of both aniline and nitrobenzene was used to improve the construction of N-nitrobenzenesulfonyl-protected 3-azabicyclo[4.3.0]nonane skeletons. We found that aniline enhanced the cyclization and that nitrobenzene prevents the concurrent reduction in this process. This combination of mediators allows for the efficient synthesis of bioactive azabicyclic nonane-type alkaloids and the use of milder deprotection conditions in the synthetic route.

DDQ mediated regiospecific protection of primary alcohol and deprotection under neutral conditions: Application of new p -methoxy benzyl-pixyl ether as reagent of choice for nucleoside protection

A simple and efficient protocol is described for regiosepecific protection of primary hydroxyl group both in nucleosides and other molecules with p-methoxy-benzyl 2,7-dimethyl pixylether (MBDPE) in presence of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). Furthermore, swift deprotection of 2, 7-dimethylpixyl (DMPx) is accomplished with DDQ in MeOH. Both procedures are successfully implemented on gram-scale synthesis of modified nucleosides. This protocol offers mild and neutral conditions for selective protection and deprotection of DMPx group while compatible in presence of other conventional protecting groups such as benzoyl, benzyl, THP, TBDPS and acetonide.

Stability of Oligonucleotide-Small Molecule Conjugates to DNA-Deprotection Conditions.

Oligonucleotide conjugates of small molecules are widely used in chemical biology and have found increasing interest in the context of DNA-encoded chemical libraries for drug discovery. Attachment of molecules to DNA bound to the solid support is an attractive small-molecule conjugation method that permits the use of organic solvents, rigorous reaction conditions, and simple workup. However, the conjugated structures must be resistant to the harsh DNA deprotection/cleavage conditions and the stabilities of building blocks under various deprotection conditions are mostly unexplored. In the present study, we analyzed the stability of 131 structurally diverse fragments that contain amides and amide-like elements during DNA deprotection protocols. Structural features susceptible to decomposition in DNA deprotection conditions were identified and a protocol that enabled the synthesis of DNA conjugates with labile fragments on solid support was identified.

Reaction of S-geranyl-2-thiouracil modified oligonucleotides with alkyl amines leads to the N2-alkyl isocytosine derivatives.

S-Geranylated 2-thiouridines (geS2Us) are unique hydrophobic modified nucleosides identified very recently in bacterial tRNAs. Our study on the synthesis of geS2Ura-containing oligonucleotides (geS2U-RNA and geS2dU-DNA) revealed a fast substitution of the S-geranyl moiety by methylamine (frequently used in oligonucleotide deprotection procedures) or n-butylamine, providing the corresponding N2-alkyl isocytosine (R2isoCyt) derivatives. To retain the S-geranyl moiety in the DNA or RNA chains, the optimized deprotection protocol with 8 M ethanolic ammonia should be applied. The oligomers bearing the R2isoCyt heterocycle (R2isoC-RNA and R2isodC-DNA) are less hydrophobic than the corresponding S2U- and geS2U-modified oligomers, whereas, contrary to the previously reported data, geS2dU-DNA and geS2U-RNA exhibit significantly higher lipophilicity than the parent S2Ura-containing oligonucleotides. Thermodynamic studies revealed that: (a) both geS2Ura- and R2isoCyt-modified oligomers exhibit similar hybridization properties towards DNA and RNA templates, and (b) the R2isoCyt nucleobase preferentially hybridizes to guanine moiety in the DNA/DNA and RNA/RNA duplexes.

Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis.

We report a new method to assess protective groups (PGs) reactivity as a function of reaction conditions (catalyst, solvent) using raw reaction data. It is based on an intuitive similarity principle for chemical reactions: similar reactions proceed under similar conditions. Technically, reaction similarity can be assessed using the Condensed Graph of Reaction (CGR) approach representing an ensemble of reactants and products as a single molecular graph, i.e., as a pseudomolecule for which molecular descriptors or fingerprints can be calculated. CGR-based in-house tools were used to process data for 142,111 catalytic hydrogenation reactions extracted from the Reaxys database. Our results reveal some contradictions with famous Greene's Reactivity Charts based on manual expert analysis. Models developed in this study show high accuracy (ca. 90%) for predicting optimal experimental conditions of protective group deprotection.

Glycosylation Reaction of Thioglycosides by Using Hypervalent Iodine(III) Reagent as an Excellent Promoter.

Thioglycosides are available donors in glycosylation due to the stability of the anomeric C-S bond under general reaction conditions of protection and deprotection, and offer orthogonality in their activation. We report now that the hypervalent iodine effectively induced glycosylation reaction of thioglycosides with various alcohols. This method features a high efficiency, completion in a short time, and proceeding under very mild conditions.

Toward the Control of the Creation of Mixed Monolayers on Glassy Carbon Surfaces by Amine Oxidation.

A versatile and simple methodology for the creation of mixed monolayers on glassy carbon (GC) surfaces was developed, using an osmium-bipyridyl complex and anthraquinone as model redox probes. The work consisted in the electrochemical grafting on GC of a mixture of mono-protected diamine linkers in varying ratios which, after attachment to the surface, allowed orthogonal deprotection. After optimisation of the deprotection conditions, it was possible to remove one of the protecting groups selectively, couple a suitable osmium complex and cap the residual free amines. The removal of the second protecting group allowed the coupling of anthraquinone. The characterisation of the resulting surfaces by cyclic voltammetry showed the variation of the surface coverage of the two redox centres in relation to the initial ratio of the linking amine in solution.

Enantioselective Michael Reaction of Acetals with Nitroalkenes: An Improvement of the Oseltamivir Synthesis

Synthesis of key chiral intermediates for oseltamivir and its derivatives from corresponding alkyloxyacetaldehyde acetals is described. Acetals are deprotected in the presence of acidic ionic liquid and water. These deprotection conditions are compatible with subsequent stereoselective Michael addition. The key chiral intermediate in the organocatalytic synthesis of oseltamivir can be obtained in yields of up to 90%, syn:anti ratios of up to 83:17, and enantiomeric purities of the required syn isomer of up to 98:2 e.r. Even further cyclization can be realized in a one-pot fashion. Therefore, a three-step sequence comprising acetal deprotection, Michael addition, and cyclization can be performed in a convenient one-pot operation.

A new method testing the orthogonality of different protecting groups

A new test was elaborated to identify a new set of orthogonal protecting groups. With the developed method eight different protecting groups were tested under various deprotection conditions and the complex reaction mixtures were analysed by HPLC. The developed method allows for quick identification of orthogonality using simple model structures.

ChemInform Abstract: Multifunctionality of the N‐Trichloroacetyl Group Developed in the Synthesis of Tetrodotoxin, a Puffer Fish Toxin

AbstractReview: [32 refs.

Solid- and solution-phase synthesis and application of R6G dual-labeled oligonucleotide probes

A novel N-TFA-protected carboxyrhodamine 6G (R6G) phosphoramidite was synthesized for use in an automated DNA synthesis to prepare 5′-labeled oligonucleotides. Deprotection and purification conditions were optimized for 5′-labeled and dual-labeled oligonucleotide probes. As an alternative we synthesized an azide derivative of R6G for CuAAC post-synthetic oligonucleotide labeling. Dual-labeled probes obtained by both methods showed the same efficacy in a quantitative PCR assay. R6G-labeled probes demonstrated superior properties in a qPCR assay in comparison with alternative HEX, JOE and SIMA dyes due to more efficient fluorescence quenching by BHQ-1. We successfully used R6G dual-labeled probes for rotavirus genotyping.