Metal/Non-Metal Catalyzed Activation of Organic Nitriles.

Nitrile activation is a prominent topic in recent developments in chemistry, especially in organic, inorganic, biological chemistry, as well as in the natural synthesis of products and in the pharmaceutical industry. The activation of nitriles using both metal and non-metal precursors has attracted several researchers, who are exploring newer ways to synthesize novel compounds. Nitrile activation can be achieved by combining various catalytic double hydroelementation reactions, such as hydrosilylation, hydroboration, and hydrogenation of organonitriles using silanes, pinacolborane, and other sources of hydrogen. These methodologies have garnered considerable attention since they are effective in the reduction of organonitriles, whose end products are extensively applied in synthetic organic chemistry. In this review, we summarize the development of selective hydroborylation, hydrosilylation, dihydroborysilylation, and hydrogenation of organonitriles, as well as their reaction mechanisms and the role of metal complexes in the catalytic cycles. This review article explains various synthetic methodologies applied toward the reduction of organonitriles into corresponding amines.

Transition metal-catalyzed double Cvinyl-H bond activation: synthesis of conjugated dienes.

Conjugated dienes have occupied a pivotal position in the field of synthetic organic chemistry and medicinal chemistry. They act as important synthons for the synthesis of various biologically important molecules and therefore, gain tremendous attention worldwide. A wide range of synthetic routes to access these versatile molecules have been developed in the past decades. Transition metal-catalyzed cross-dehydrogenative coupling (CDC) has emerged as one of the utmost front-line research areas in current synthetic organic chemistry due to its high atom economy, efficiency, and viability. In this review, an up-to-date summary including scope, limitations, mechanistic studies, stereoselectivities, and synthetic applications of transition metal-catalyzed double Cvinyl-H bond activation for the synthesis of conjugated dienes has been reported since 2013. The literature reports mentioned in this review have been classified into three different categories, i.e. (a) Cvinyl-Cvinyl bond formation via oxidative homo-coupling of terminal alkenes; (b) Cvinyl-Cvinyl bond formation via non-directed oxidative cross-coupling of linear/cyclic alkenes and terminal/internal alkenes, and (c) Cvinyl-Cvinyl bond formation via oxidative cross-coupling of directing group bearing alkenes and terminal/internal alkenes. Overall, this review aims to provide a concise overview of the current status of the considerable development in this field and is expected to stimulate further innovation and research in the future.

Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues.

Conformationally restricted diastereomeric homoarabinofuranosylpyrimidines (AZT analogue), i.e., (5'R)-3'-azido-3'-deoxy-2'-O,5'-C-bridged-ß-ᴅ-homoarabinofuranosylthymine and -uracil had been synthesized starting from diacetone ᴅ-glucofuranose following chemoenzymatic and chemical routes in 34-35% and 24-25% overall yields, respectively. The quantitative and diastereoselective acetylation of primary hydroxy over two secondary hydroxy groups present in the key nucleoside precursor was mediated with Lipozyme® TL IM in 2-methyltetrahydrofuran following a chemoenzymatic pathway. Whereas, the protection of the primary hydroxy over the lone secondary hydroxy group in the key azido sugar precursor was achieved using bulky tert-butyldiphenylsilyl chloride (TBDPS-Cl) in pyridine in 92% yield following a chemical synthetic pathway. The chemoenzymatic method was found to be superior over the chemical method in respect of the number of synthetic steps and overall yield of the final product.

Double-headed nucleosides: Synthesis and applications.

Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.

Enzymatic separation of epimeric 4-C-hydroxymethylated furanosugars: Synthesis of bicyclic nucleosides.

Conversion of D-glucose to 4-C-hydroxymethyl-1,2-O-isopropylidene-α-D-ribofuranose, which is a key precursor for the synthesis of different types of bicyclic/spiro nucleosides, led to the formation of an inseparable 1:1 mixture of the desired product and 4-C-hydroxymethyl-1,2-O-isopropylidene-α-D-xylofuranose. A convenient environment friendly Novozyme®-435 catalyzed selective acetylation methodology has been developed for the separation of an epimeric mixture of ribo- and xylotrihydroxyfuranosides in quantitative yields. The structure of both the monoacetylated epimers, i.e., 5-O-acetyl-4-C-hydroxymethyl-1,2-O-isopropylidene-α-D-ribo- and xylofuranose obtained by enzymatic acetylation, has been confirmed by an X-ray study on their corresponding 4-C-p-toluenesulfonyloxymethyl derivatives. Furthermore, the two separated epimers were used for the convergent synthesis of two different types of bicyclic nucleosides, which confirms their synthetic utility.

Proline-glutamate chimera's side chain conformation directs the type of ß-hairpin structure.

Our aim was to study the impact of two proline chimeras, containing a glutamic acid side chain in cis- or trans-configuration, on secondary structure formation. We further investigated to what extent the configuration of the side chain contributes to the overall peptide conformation. We used a 10 residue peptide (IYSNPDGTWT) that forms a ß-hairpin in water. The turn-forming proline was substituted with either a cis- or trans-proline-glutamic acid chimera, resulting in the peptides IYSNPcis -E DGTWT (P1_Pcis-E) and IYSNP(trans-E)DGTWT (P1_Ptrans-E). We studied the conformation of the modified peptides by circular dichroism (CD) and NMR-spectroscopy, and SEC/static light scattering (SLS) analysis. NMR analysis reveals that the modified peptides maintain the ß-hairpin conformation in aqueous solution. At 5 °C and pH 4.3, the peptide (P1_Pcis-E) was found to adopt two coexisting ß-hairpin conformations (2:2 ß-hairpin, and 3:5 ß-hairpin). In contrast to that, the peptide (P1_Ptrans-E) adopts a 2:2 ß-hairpin that exists in equilibrium with a 4:4 ß-hairpin conformation. The adoption of ordered ß-hairpin structures for both modified peptides could be confirmed by CD spectroscopy, while SEC/SLS analysis showed a monomeric oligomerization state for all three investigated peptides. With the combination of several NMR methods, we were able to elucidate that even small alterations in the side chain conformation of the proline-glutamate chimera (cis or trans) can significantly influence the conformation of the adopted ß-hairpin.

Synthesis and evaluation of antineurotoxicity properties of an amyloid-ß peptide targeting ligand containing a triamino acid.

Peptide-like compounds containing an arginine have been shown to bind and stabilize the central helix of the Alzheimer's disease related amyloid-ß peptide (Aß) in an α-helical conformation, thereby delaying its aggregation into cytotoxic species. Here we study a novel Aß targeting ligand AEDabDab containing the triamino acid, N(γ)-(2-aminoethyl)-2,4-diaminobutanoic (AEDab) acid. The new AEDab triamino acid carries an extra positive charge in the side chain and is designed to be incorporated into a ligand AEDabDab where the AEDab replaces an arginine moiety in a previously developed ligand Pep1b. This is done in order to increase the Aß-ligand interaction, and molecular dynamics (MD) simulation of the stability of the Aß central helix in the presence of the AEDabDab ligand shows further stabilization of the helical conformation of Aß compared to the previously reported Pep1b as well as compared to the AEOrnDab ligand containing an N(δ)-(2-aminoethyl)-2,5-diaminopentanoic acid unit which has an additional methylene group. To evaluate the effect of the AEDabDab ligand on the Aß neurotoxicity the AEDab triamino acid building block is synthesized by reductive alkylation of N-protected-glycinal with α-amino-protected diaminobutanoic acid, and the Aß targeting ligand AEDabDab is prepared by solid-phase synthesis starting with attachment of glutarate to the Wang support. Replacement of the arginine residue by the AEDab triamino acid resulted in an improved capability of the ligand to prevent the Aß1-42 induced reduction of gamma (γ) oscillations in hippocampal slice preparation.

An efficient and facile methodology for bromination of pyrimidine and purine nucleosides with sodium monobromoisocyanurate (SMBI).

An efficient and facile strategy has been developed for bromination of nucleosides using sodium monobromoisocyanurate (SMBI). Our methodology demonstrates bromination at the C-5 position of pyrimidine nucleosides and the C-8 position of purine nucleosides. Unprotected and also several protected nucleosides were brominated in moderate to high yields following this procedure.

Chemoenzymatic synthesis of bridged homolyxofuranosyl pyrimidine nucleosides: Bicyclic AZT analogues.

A greener chemo-enzymatic methodology has been developed for the synthesis of conformationally restricted diastereomeric homolyxofuranosyl pyrimidines (AZT analogue), i.e., (5'R)-3'-azido-3'-deoxy-2'-O,5'-C-bridged-ß-d-homolyxofuranosyl-uracil and thymine starting from inexpensive diacetone-d-glucofuranose in 18% and 21% overall yields, respectively. In one of the key steps in multistep synthesis of bicyclic AZT analogues, the primary hydroxyl group of 3'-azido-3'-deoxy-ß-d-glucofuranosyl pyrimidines has been acetylated using Novozyme® 435 in THF in 92% and 97% yields, respectively. The monoacetylated nucleoside was converted to desired bicyclic AZT analogue in two steps in an overall yield of 82% and 83%, respectively.

Efficient and stereoselective synthesis of sugar fused pyrano[3,2-c]pyranones as anticancer agents.

A highly stereoselective, efficient and facile route was achieved for the synthesis of novel and biochemically potent sugar fused pyrano[3,2-c]pyranone derivatives starting from inexpensive, naturally occurring d-galactose and d-glucose. First, ß-C-glycopyranosyl aldehydes were synthesized from these d-hexose sugars in six steps, with overall yields 41-55%. Next, two different 1-C-formyl glycals were synthesized from these ß-C-glycopyranosyl aldehydes by treatment in basic conditions. The optimization of reaction conditions was carried out following reactions between 1-C-formyl galactal and 4-hydroxycoumarin. Next, 1-C-formyl galactal and 1-C-formyl glucal were treated with nine substituted 4-hydroxy coumarins at room temperature (25 °C) in ethyl acetate for ∼1-2 h in the presence of l-proline to obtain exclusively single diastereomers of pyrano[3,2-c]pyranone derivatives in excellent yields. Four compounds were found to be active for the MCF-7 cancer cell line. The MTT assay, apoptosis assay and migration analysis showed significant death of the cancer cells induced by the synthesized compounds.

Synthesis and applications of bicyclic sugar modified locked nucleic acids: A review.

A large number of Locked Nucleic Acids (LNAs) with variety of modifications and restricted conformations have been developed in the last few decades. These modifications have significantly improved the biological properties of oligonucleotides, when LNAs moieties were incorporated into them. Herein, the synthesis and applications of these modified locked nucleic acids as antisense oligonucleotides are discussed.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2022.2052316 .

2'-O-(N-(Aminoethyl)carbamoyl)methyl Modification Allows for Lower Phosphorothioate Content in Splice-Switching Oligonucleotides with Retained Activity.

2'-O-(N-(Aminoethyl)carbamoyl)methyl (2'-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2'-O-methyl oligonucleotides (2'-OMe ONs) with phosphodiester linkers as well as with partial and full phosphorothioate (PS) inclusion were synthesized and functionally evaluated as splice-switching oligonucleotides in several different reporter cell lines originating from different tissues. This was enabled by first preparing the AECM-modified A, C, G and U, which required a different strategy for each building block. The AECM modification has previously been shown to provide high resistance to enzymatic degradation, even without PS linkages. It is therefore particularly interesting and unprecedented that the 2'-O-AECM ONs are shown to have efficient splice-switching activity even without inclusion of PS linkages and found to be as effective as 2'-OMe PS ONs. Importantly, the PS linkages can be partially included, without any significant reduction in splice-switching efficacy. This suggests that AECM modification has the potential to be used in balancing the PS content of ONs. Furthermore, conjugation of 2'-O-AECM ONs to an endosomal escape peptide significantly increased splice-switching suggesting that this effect could possibly be due to an increase in uptake of ON to the site of action.

Synthesis of d-glycopyranosyl depsipeptides using Passerini reaction.

A protocol based on Passerini multi-component reaction has been developed for facile, efficient and atom economical synthesis of a small library of twenty potential bioactive (2R)-2-(d-glycopyranosyl)-2-acyloxyacetamides using perbenzylated d-glycopyranosyl aldehydes, substituted isocyanides and different aliphatic/aromatic carboxylic acids. All twenty synthesized d-glycopyranosyl α-acyloxy amides, commonly known as depsipeptides were unambiguously identified on the basis of their spectral (IR, 1H, 13C NMR, COSY, HSQC, NOESY and HRMS) data analysis.

Novel insights into the use of Glowing LNA as nucleic acid detection probes--influence of labeling density and nucleobases.

Appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA (locked nucleic acid) display large increases in fluorescence intensity and remarkably high quantum yields upon hybridization with nucleic acid targets. Thermal denaturation and fluorescence spectroscopy studies on ONs modified with known thymine monomer X and novel 5-methylcytosine monomer Y provide new insights into the design principles and mechanism of these Glowing LNA nucleic acid detection probes.

Chemo-enzymatic route to bridged homolyxofuranosyl-pyrimidines.

Synthesis of 2'-O,5'-C-bridged-ß-d-homolyxofuranosyl nucleosides U and T have been achieved starting from diacetone-d-glucose in overall yields 55.7 and 57.1%, respectively. Quantitative regioselective monoacetylation of the lone primary hydroxyl group in trihydroxy nucleoside intermediate, i.e. 3'-O-benzyl-ß-d-glucofuranosyl nucleosides mediated by Novozyme®-435 has been utilized as the key step in the synthesis of homolyxofuranosyl nucleosides. The structure of the synthesized 2'-O,5'-C-bridged-ß-d-homolyxofuranosyl uracil and -thymine has been established on the basis of their spectral (IR, 1H, 13C NMR and HRMS) data analysis and the structure of earlier nucleoside was confirmed by its X-rays diffraction analysis which revealed that these 2'-O,5'-C-bridged homo-nucleosides are locked into S-type sugar puckering.

Synthesis and hybridization studies of alpha-configured arabino nucleic acids.

Synthesis of alpha-L-arabino- and alpha-D-arabino-configured pentofuranosyl nucleosides of four of the natural bases [thymine (ara-T), adenine (ara-A), cytosine (ara-C) and guanine (ara-G)] is reported together with hybridization properties of oligonucleotides containing alpha-L-ara-T and -A, alpha-D-ara-T and -A, and 2'-amino-alpha-L-ara-T monomers. 2'-O-Acetylated alpha-L-ara-T, -A, -C and -G, alpha-D-ara-T, -A, -C and -G, and N2'-acylated-alpha-L-ara-T phosphoramidite building blocks were synthesized and used together with standard DNA phosphoramidites for solid-phase synthesis of 18-mer oligonucleotides. Thermal denaturation experiments showed that incorporation of three or six of the arabino-configured monomers into DNA-oligonucleotides reduced the binding affinity towards antiparallel DNA/RNA complements. Fully modified alpha-L-ara-oligonucleotides did not hybridize with DNA/RNA complements, whereas hybridization of fully modified alpha-D-ara-oligonucleotides with complementary DNA/RNA in parallel strand orientation was confirmed.

Amyloid-ß Peptide Targeting Peptidomimetics for Prevention of Neurotoxicity.

A new generation of ligands designed to interact with the α-helix/ß-strand discordant region of the amyloid-ß peptide (Aß) and to counteract its oligomerization is presented. These ligands are designed to interact with and stabilize the Aß central helix (residues 13-26) in an α-helical conformation with increased interaction by combining properties of several first-generation ligands. The new peptide-like ligands aim at extended hydrophobic and polar contacts across the central part of the Aß, that is, "clamping" the target. Molecular dynamics (MD) simulations of the stability of the Aß central helix in the presence of a set of second-generation ligands were performed and revealed further stabilization of the Aß α-helical conformation, with larger number of polar and nonpolar contacts between ligand and Aß, compared to first-generation ligands. The synthesis of selected novel Aß-targeting ligands was performed in solution via an active ester coupling approach or on solid-phase using an Fmoc chemistry protocol. This included incorporation of aliphatic hydrocarbon moieties, a branched triamino acid with an aliphatic hydrocarbon tail, and an amino acid with a 4'- N, N-dimethylamino-1,8-naphthalimido group in the side chain. The ability of the ligands to reduce Aß1-42 neurotoxicity was evaluated by gamma oscillation experiments in hippocampal slice preparations. The "clamping" second-generation ligands were found to be effective antineurotoxicity agents and strongly prevented the degradation of gamma oscillations by physiological concentration of monomeric Aß1-42 at a stoichiometric ratio.

Efficient and selective enzymatic acylation reaction: separation of furanosyl and pyranosyl nucleosides.

Candida antarctica lipase-B (CAL-B) immobilized on lewatite selectively acylated the primary hydroxyl group of the furanosyl nucleoside in a mixture of 1-(alpha-D-arabinofuranosyl)thymine and 1-(alpha-D-arabinopyranosyl)thymine. This selective biocatalytic acylation of furanosyl nucleoside has enabled us an easy separation of arabinofuranosyl thymine from an inseparable mixture with arabinopyranosyl thymine. The primary hydroxyl selective acylation methodology of arabinonucleoside has also been successfully used for the separation of 1-(beta-D-xylofuranosyl)thymine and 1-(beta-D-xylopyranosyl)thymine from a mixture of the two, which demonstrate the generality of the enzymatic methodology for separation of furanosyl and pyranosyl nucleosides.

Synthesis of novel 3'-azido-3'-deoxy-α-L-ribo configured nucleosides: A comparative study between chemical and chemo-enzymatic methodologies.

Syntheses of novel 3'-azido-3'-deoxy-2'-O,4'-C-methylene-α-L-ribofuranosyl nucleosides have been carried out from 3'-azido-3'-deoxy-4'-C-hydroxymethyl-ß-D-xylofuranosyl nucleosides following both chemical and chemo-enzymatic methodologies. The precursor nucleoside in turn was synthesized from a common glycosyl donor 4-C-acetoxymethyl-1,2,5-tri-O-acetyl-3-azido-3-deoxy-α,ß-D-xylofuranose, which was obtained by the acetolysis of 4-C-acetoxymethyl-5-O-acetyl-3-azido-3-deoxy-1,2-O-isopropylidene-α-D-xylofuranose in 96% yield. It has been observed that a chemo-enzymatic pathway for the synthesis of targeted nucleosides is much more efficient than a chemical pathway, leading to the improvement in yield for the synthesis of 3'-azido-3'-deoxy-α-L-ribofuranosyl thymine and uracil from 49 to 89% and 55 to 93%, respectively.

Synthesis and Photophysical Studies on N1-(2'-O,4'-C-Methyleneribofurano-nucleoside-3'-yl)-C4-(coumarin-7-oxymethyl)-1,2,3-triazoles.

A series of eight N1-(2'-O,4'-C-methylene-ß-D-ribofuranonucleoside-3'-yl)-C4-(coumarin-7-oxymethyl)-1,2,3-triazoles have been synthesized by Cu(I)-catalyzed azide-alkyne cycloaddition reaction of 3'-azido-3'-deoxy-2'-O,4'-C-methyleneuridine and 3'-azido-3'-deoxy-2'-O,4'-C-methylene-5-methyluridine with 7-propargyloxy coumarins in 82-88% yields. The synthesized coumarintriazolyl-bicyclonucleoside conjugates possess an extra bridge between 2'-O and 4'-C in the nucleoside moiety, which facilitates its pre-organization into N-type sugar puckering. This was confirmed by X-ray crystal structure studies on one of the conjugates, i.e. on N1-(3'-deoxy-2'-O,4'-C-methylene-5-methyluridin-3'-yl)-C4-(4-phenylcoumarin-7-oxymethyl)-1,2,3-triazole. Photophysical studies carried out on the synthesized compounds demonstrate that they possess useful level of fluorescence with Stokes shift of approximately 70 nm.