Regio- and Enantioselective Synthesis of Chiral Pyrimidine Acyclic Nucleosides via Rhodium-Catalyzed Asymmetric Allylation of Pyrimidines

Recent Advances in the Synthesis of Acyclic Nucleosides and Their Therapeutic Applications

DNA is commonly known as the "molecule of life" because it holds the genetic instructions for all living organisms on Earth. The utilization of modified nucleosides holds the potential to transform the management of a wide range of human illnesses. Modified nucleosides and their role directly led to the 2023 Nobel prize. Acyclic nucleosides, due to their distinctive physiochemical and biological characteristics, rank among the most adaptable modified nucleosides in the field of medicinal chemistry. Acyclic nucleosides are more resistant to chemical and biological deterioration, and their adaptable acyclic structure makes it possible for them to interact with various enzymes. A phosphonate group, which is linked via an aliphatic functionality to a purine or a pyrimidine base, distinguishes acyclic nucleoside phosphonates (ANPs) from other nucleotide analogs. Acyclic nucleosides and their derivatives have demonstrated various biological activities such as anti-viral, anti-bacterial, anti-cancer, anti-microbial, etc. Ganciclovir, Famciclovir, and Penciclovir are the acyclic nucleoside-based drugs approved by FDA for the treatment of various diseases. Thus, acyclic nucleosides are extremely useful for generating a variety of unique bioactive chemicals. Their biological activities as well as selectivity is significantly influenced by the stereochemistry of the acyclic nucleosides because chiral acyclic nucleosides have drawn a lot of interest due to their intriguing biological functions and potential as medicines. For example, tenofovir's (R) enantiomer is roughly 50 times more potent against HIV than its (S) counterpart. We can confidently state, "The most promising developments are yet to come in the realm of acyclic nucleosides!" Herein, we have covered the most current developments in the field of chemical synthesis and therapeutic applications of acyclic nucleosides based upon our continued interest and activity in this field since mid-1990's.

Rhodium-Catalyzed Asymmetric N2-C5 Allylation of Indazoles with Dienyl Allylic Alcohols

The development of site-selective and regio- and enantioselective reactions of substrates with multiple active sites is an important topic and remains a substantial challenge in synthetic chemistry. Here, we describe a rhodium-catalyzed asymmetric N2-C5 allylation of indazoles with dienyl allylic alcohols under mild conditions. In the presence of a Rh/(P/olefin) catalyst and formic acid, chiral N2-C5 allylic indazoles were formed in good yields with excellent enantioselectivities (up to 97% ee). The mechanism proceeds through an elusive intermediate Int B, which represents a challenging task on asymmetric allylic substitution (AAS) of dienyl substrates.

Synthesis of Chiral Acyclic Pyrimidine Nucleoside Analogues from DHAP-Dependent Aldolases

Dihydroxyacetone phosphate (DHAP)-dependent aldolases catalyze the aldol addition of DHAP to a variety of aldehydes and generate compounds with two stereocenters. This reaction is useful to synthesize chiral acyclic nucleosides, which constitute a well-known class of antiviral drugs currently used. In such compounds, the chirality of the aliphatic chain, which mimics the open pentose residue, is crucial for activity. In this work, three DHAP-dependent aldolases: fructose-1,6-biphosphate aldolase from rabbit muscle, rhanmulose-1-phosphate aldolase from Thermotoga maritima, and fuculose-1-phosphate aldolase from Escherichia coli, were used as biocatalysts. Aldehyde derivatives of thymine and cytosine were used as acceptor substrates, generating new acyclic nucleoside analogues containing two new stereocenters with conversion yields between 70% and 90%. Moreover, structural analyses by molecular docking were carried out to gain insights into the diasteromeric excess observed.

Synthesis of Chirally Enriched Pyrazolylpyrimidinone-Based Glycohybrids via Annulation of Glycals with 2-Hydrazineylpyrimidin-4(3H)-ones

A new strategy for synthesizing chirally enriched pyrazolylpyrimidinone-based glycohybrids has been achieved, employing an annulation approach in ethanol without any additives or catalysts under microwave conditions. The designed compounds were obtained within a short reaction time (5 min). This method offers several advantages, including mild reaction conditions, a green solvent, and a metal-free approach. Furthermore, the protocol demonstrated a broad substrate scope, successfully incorporating various functional groups with stereochemical diversity and furnishing chirally enriched molecules.

Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides

Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.

Rhodium-Catalyzed Asymmetric Synthesis of 1,2-Disubstituted Allylic Fluorides

Although there are many methods for the asymmetric synthesis of monosubstituted allylic fluorides, construction of enantioenriched 1,2-disubstituted allylic fluorides has not been reported. To address this gap, we report an enantioselective synthesis of 1,2-disubstituted allylic fluorides using chiral diene-ligated rhodium catalyst, Et3 N ⋅ 3HF as a source of fluoride, and Morita Baylis Hillman (MBH) trichloroacetimidates. Kinetic studies show that one enantiomer of racemic MBH substrate reacts faster than the other. Computational studies reveal that both syn and anti π-allyl complexes are formed upon ionization of allylic substrate, and the syn complexes are slightly energetically favorable. This is in contrast to our previous observation for formation of monosubstituted π-allyl intermediates, in which the syn π-allyl conformation is strongly preferred. In addition, the presence of an electron-withdrawing group at C2 position of racemic MBH substrate renders 1,2-disubstituted π-allyl intermediate formation endergonic and reversible. To compare, formation of monosubstituted π-allyl intermediates was exergonic and irreversible. DFT calculations and kinetic studies support a dynamic kinetic asymmetric transformation process wherein the rate of isomerization of the 1,2-disubstituted π-allylrhodium complexes is faster than that of fluoride addition onto the more reactive intermediate. The 1,2-disubstituted allylic fluorides were obtained in good yields, enantioselectivity, and branched selectivity.

Highly Diastereoselective Synthesis of Oxindoles Containing Vicinal Quaternary and Tertiary Stereocenters by a Domino Heck/Decarboxylative Alkynylation Sequence

A palladium-catalyzed domino Heck/decarboxylative alkynylation reaction of trisubstituted alkenes or enamines is reported. For two different types of substrates, the current domino reaction employing different solvents and bases led to 3,3-disubstituted oxindoles and hydropyrimidinyl spirooxindoles containing vicinal quaternary and tertiary stereocenters in moderate to good yields, respectively. The general applicability of this method was shown by gram-scale syntheses and diverse transformations of the reaction products. The enantioselective version for this domino process was also studied.

Acyclic Twisted Amides

In this contribution, we provide a comprehensive overview of acyclic twisted amides, covering the literature since 1993 (the year of the first recognized report on acyclic twisted amides) through June 2020. The review focuses on classes of acyclic twisted amides and their key structural properties, such as amide bond twist and nitrogen pyramidalization, which are primarily responsible for disrupting nN to π*C═O conjugation. Through discussing acyclic twisted amides in comparison with the classic bridged lactams and conformationally restricted cyclic fused amides, the reader is provided with an overview of amidic distortion that results in novel conformational features of acyclic amides that can be exploited in various fields of chemistry ranging from organic synthesis and polymers to biochemistry and structural chemistry and the current position of acyclic twisted amides in modern chemistry.

Palladium-catalyzed asymmetric allylic amination of a vinylethylene carbonate with N-heteroaromatics

Highly enantioselective allylic amination of a vinylethylene carbonate with N-heteroaromatics is enabled by asymmetric palladium catalysis for the synthesis of chiral acyclic nucleosides and isonucleosides.

Synthesis of Aza-acyclic Nucleoside Libraries of Purine, Pyrimidine, and 1,2,4-Triazole

Under the aegis of the Pilot Scale Library Program of the NIH Roadmap Initiative, a new library of propan-1-amine containing aza acyclic nucleosides was designed and prepared, and we now report a diverse set of 157 purine, pyrimidine, and 1,2,4-triazole- N-acetamide analogues. These new nucleoside analogues were prepared in a parallel high throughput solution-phase format. A set of diverse amines was reacted with several nucleobase N-propaldehydes utilizing reductive amination with sodium triacetoxyborohydride coupling to produce a small and diverse aza acyclic nucleoside library. All reactions were performed using 24-well reaction blocks and an automatic reagent-dispensing platform under an inert atmosphere. Final targets were purified on an automated system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS and were analyzed for purity by HPLC prior to submission to the Molecular Libraries Small Molecule Repository (MLSMR). Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) demonstrated diverse and interesting biological activities.

Dynamic Kinetic Resolution of α-Purine Substituted Alkanoic Acids: Access to Chiral Acyclic Purine Nucleosides

An efficient route to construct chiral acyclic purine nucleoside analogues via dynamic kinetic resolution of α-purine substituted alkanoic acids is reported. Using ( S)-BTM as the catalyst, diverse chiral acyclic purine nucleoside analogues were obtained in moderate to good yields (up to 93%) and high enantioselectivities (up to 98% ee). Chiral acyclic purine nucleosides could be obtained from the esterified products via reduction reaction, which could then be transferred into Tenofovir analogues.

Organocatalytic enantioselective synthesis of acyclic pyrimidine nucleosides by aza-Michael reaction

An efficient diarylprolinol triphenylsilyl ether-catalyzed enantioselective aza-Michael reaction of pyrimidines as N-centered nucleophiles to α,β-unsaturated aldehydes, followed by reduction, provided chiral acyclic pyrimidine nucleosides in good yields (51-78% yields for two steps) and excellent enantioselectivities (91-98% ee). In addition, the chiral acyclic pyrimidine nucleoside having the tert-butyldiphenylsilyl-protected hydroxyl substituent was successfully applied to the synthesis of the corresponding chiral cyclic pyrimidine nucleoside analogue bearing the tetrahydrofuranyl ring.

Cyclization Reaction of Donor-Acceptor Oxiranes with N,N'-Disubstituted Thioureas: A Domino Process to trans-Dihydropyrimidines

An unprecedented cyclization reaction of donor-acceptor oxiranes with N,N'-disubstituted thioureas to construct trans-dihydropyrimidines is presented. Preliminary reaction mechanism studies demonstrated that the reaction underwent sequential cycloaddition/amine ester exchange/oxygen-sulfur exchange/desulfuration/Michael addition process. A wide range of trans-dihydropyrimidines were produced with high yields up to 94% by using this method.

Regio- and Enantioselective Rhodium-Catalyzed Allylic Alkylation of Racemic Allylic Alcohols with 1,3-Diketones

Highly regio- and enantioselective rhodium-catalyzed allylic alkylation of 1,3-diketones with racemic secondary allylic alcohols is reported. In the presence of a Rh-catalyst derived from the Carreira (P, olefin)-ligand and TFA as an additive, chiral branched α-allylated 1,3-diketones could be obtained in good to excellent yields, with excellent regio- and enantioselectivity ( b/ l > 19/1, 86-98% ee). The direct utilization of allyl alcohols as electrophiles represents an improvement from the viewpoint of an atom economy. Both aryl- and aliphatic-substituted allyl alcohols are suitable substrates with excellent reaction outcomes. This reaction features mild conditions, broad substrate scope, and readily available substrates.

Enantioselective Synthesis of Carbocyclic Nucleosides via Asymmetric [3 + 2] Annulation of α-Purine-Substituted Acrylates with MBH Carbonates

An efficient route to chiral carbocyclic nucleoside analogues containing a quaternary stereocenter and a C═C double bond has been established via a highly enantioselective [3 + 2] annulation of Morita-Baylis-Hillman (MBH) carbonates with α-purine-substituted acrylates. With 20 mol % (S)-SITCP as the catalyst, various chiral carbocyclic nucleoside analogues with a quaternary stereocenter and a C═C double bond were obtained in high yields (up to 92%) with good diastereoselectivities (up to 10:1 dr) and excellent enantioselectivities (up to 96% ee). Furthermore, the corresponding products were subjected to diverse transformations to afford interesting and potentially useful chiral carbocyclic nucleosides.

Enantioselective and regiodivergent allylation of pyrimidines with terminal allenes: an approach to pyrimidine acyclic nucleosides

An atom-economic addition of pyrimidines to allenes has been developed for the diverse synthesis of branched or linear N-allylpyrimidine analogues.