Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• and diagnostics that depend on Watson–Crick hydrogen bonding to natural nucleic acids. An unexpected discovery of early studies was that the triplex-forming PNAs built of pyrimidine monomers formed a 2:1 PNA–DNA–PNA strand-invasion triplex instead of the expected 1:1 PNA–dsDNA triplex (c.f., Figure 2A

• and 2B) [1][23]. This unprecedented binding mode was enabled by PNA’s unique ability to displace the pyrimidine-rich strand of dsDNA as the so-called P-loop, which was clearly facilitated by the neutral backbone [1]. Later studies showed that there was a delicate balance between the two binding modes

• recognition of pyrimidines in hypothetical X•T–A or X•C–G triplets is complicated by two problems: 1) pyrimidines present only one hydrogen bond acceptor (C=O in T or U) or donor (-NH2 in C) in the major groove, and 2) the six-membered pyrimidine ring extends further out in the major groove than the five

Synthesis of 1-indolyl-3,5,8-substituted γ-carbolines: one-pot solvent-free protocol and biological evaluation

• Premansh Dudhe,
• Mena Asha Krishnan,
• Kratika Yadav,
• Diptendu Roy,
• Krishnan Venkatasubbaiah,
• Biswarup Pathak and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2021, 17, 1453–1463, doi:10.3762/bjoc.17.101

• shown promising biological activities in preclinical and clinical studies (Figure 1) [2][3][4][5][6]. The pyrimidine-γ-carboline alkaloid ingenine B (isolated from an Indonesian sponge) exhibits a pronounced cytotoxicity against a murine lymphoma cell line [7] and several isocanthine analogs are

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• of deoxyribonucleic acids (DNA) or ribonucleic acids (RNA), which contain either a purine or pyrimidine nucleobase and a furanosyl moiety of pentose sugars, 2′-deoxyribose or ribose [1][2]. Nucleotides are constituted by addition of a phosphate group at the 5′-position of the nucleosides and these

• ribonuclease A [36]. Lazrek et al. [51] synthesized C-3'-modified double-headed nucleosides 54a–g where a 1,2,3-triazol ring acts as linker of the nucleobase and the sugar moiety. First, seven N9/N1-propargylpurine/pyrimidine nucleobases 13b, 45, and 53a–g were synthesized by treating the nucleobases with

• nucleoside 92 (Scheme 20) [13]. Lazrek et al. [51] synthesized C-5′-modified double-headed nucleosides 96a–g, where a 1,2,3-triazolo ring acted as the linker between the nucleobase and the sugar moiety. First, seven N9/N1-propargylpurine/pyrimidine nucleobases 13b, 45 and 53a–e were synthesized by treating

Icilio Guareschi and his amazing “1897 reaction”

• Gian Cesare Tron,
• Alberto Minassi,
• Giovanni Sorba,
• Mara Fausone and
• Giovanni Appendino

Beilstein J. Org. Chem. 2021, 17, 1335–1351, doi:10.3762/bjoc.17.93

• Guareschi pyridine synthesis is a modified two-component version, mechanistically similar to the Biginelli pyrimidine synthesis [33] and based on the condensation of cyanoacetamide and a β-dicarbonyl derivative [45][46]. This is the most famous Guareschi pyridine synthesis, both in textbooks and in other

A comprehensive review of flow chemistry techniques tailored to the flavours and fragrances industries

• Guido Gambacorta,
• James S. Sharley and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2021, 17, 1181–1312, doi:10.3762/bjoc.17.90

Synthetic accesses to biguanide compounds

• Oleksandr Grytsai,
• Cyril Ronco and
• Rachid Benhida

Beilstein J. Org. Chem. 2021, 17, 1001–1040, doi:10.3762/bjoc.17.82

Microwave-assisted multicomponent reactions in heterocyclic chemistry and mechanistic aspects

• Shivani Gulati,
• Stephy Elza John and
• Nagula Shankaraiah

Beilstein J. Org. Chem. 2021, 17, 819–865, doi:10.3762/bjoc.17.71

• solvent to successfully furnish 5,6-disubstituted pyrrolo[2,3-d]pyrimidine-2,4-diones 89. Similarly, excellent yields were obtained when the thiol was replaced by malononitrile (51) even in the absence of catalyst or any promoter. The malononitrile undergoes hydrolysis forming an amide, thus giving rise

• to a series of pyrrolo[2,3-d]pyrimidine-2,4-diones acetamides 90 under microwave irradiation (Scheme 32). An interesting observation by the authors surfaced that the conventional approach to the malononitrile protocol delivered comparable yields in longer reaction time (5–8 h). A gram-scale attempt

• condensation of aromatic aldehydes and heterocyclic ketones followed by a [3 + 3] cycloaddition between A and amidine giving off the intermediate B, which undergoes 1,5-hydrogen transfer followed by 1,3-hydrogen transfer to give the final products (101, Scheme 39). 6.2.4 Imidazo(1,2-a)pyrimidine: The

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• cell-based applications. Illustration of H-bonding in a DNA duplex and a parallel triplex. A) Depiction of Watson–Crick base-paring (left: T-A and right: C-G); B) parallel triple helices: pyrimidine-rich third strand interactions are stabilised by Hoogsteen hydrogen bonds (the duplex is in black, TFO

Facile preparation and conversion of 4,4,4-trifluorobut-2-yn-1-ones to aromatic and heteroaromatic compounds

• Takashi Yamazaki,
• Yoh Nakajima,
• Minato Iida and
• Tomoko Kawasaki-Takasuka

Beilstein J. Org. Chem. 2021, 17, 132–138, doi:10.3762/bjoc.17.14

• a variety of pyrimidine derivatives, 6, using amidines including guanidine [34]. First of all, various bases were employed for the reaction of the model substrate 2a. During initial testing, guanidine hydrochloride at 25 °C for 4 h in acetonitrile (Table 5, entries 1–7) as well as sodium carbonate

• as shown in Table 5, entry 14, which included heating the reaction mixture at 80 °C for 8 h in MeCN, furnishing the desired pyrimidine 6aa in 60% isolated yield. Then, four types of ynones, 2a–d, were reacted with formamidine and acetamidine as well as guanidine under the optimized conditions

• point. The unfavorable yield may be reasoned by the fact that there have been very limited reports for the syntheses of, for example, pyrimidine 6ca [35][36][37][38], with such drawbacks as the formation of a regioisomeric mixture [35] and the requirement of harsh conditions [38]. At the same time, for

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• building blocks of the purine nucleosides with functionalities suitable for post-synthetic conjugation at the nucleobase are basically missing, and also in the pyrimidine series, the few existing derivatives of uridine do not offer much variety. Motivated by this lack of functional building blocks, we have

• synthesized a number of pyrimidine and purine derivatives carrying amino linkers of different length and flexibility [13][20]. Linker-modified uridine derivatives, upon conversion into phosphoramidite building blocks, were incorporated in RNA and used for a systematic study of distance determination of

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• with 1-chloropropan-2-one to give 3-acetylimidazo[1,2-a]pyrimidine, which, following degradation of the pyridimine ring with hydrazine, yielded 9. The coupled HSQC experiments measured 1JC,H = 215 Hz for the H-2/C-2 pair in 8 (Figure S26, Supporting Information File 1) and 201 Hz for H-5/C-5 in 9

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• found that phosphorolysis of uridine, thymidine, and Ara-U in the presence of Dowex® 1X8 (phosphate; Dowex-nPi) proceeded smoothly in the presence of magnesium cations in water at 20–50 °C for 54–96 h giving rise to quantitative formation of the corresponding pyrimidine bases and PF-1Pis. The resulting

• pyrimidine nucleoside phosphorylase (PyNP-Y04 and PyNP-Y02) [29] was studied and the corresponding Rib-1Pi, dRib-1Pi, and Ara-1Pi were obtained in the form of barium salts in yields within 13–37%. At the same time, the strategy by Hennen and Wong [30][31] was used to synthesize Rib-1Pi and dRib-1Pi

• important purine and pyrimidine nucleosides. A scrutiny of the results of these studies vs the transglycosylation reaction showed that both methods have certain advantages along with obvious disadvantages, namely, problems with obtaining individual PF-1Pis (in particular removal of excess inorganic

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• corresponding pyrimidines. An efficient C–N bond-forming process is also observed by using boronic acid pinacol esters as coupling partners in the presence of Cu(II) acetate and boric acid. The 4-fluoroalkyl group on the pyrimidine ring significantly assists in the formation of the target N1-substituted

• chemistry, given the great importance of fluorinated groups in drug discovery [26][27][28][29]. On the strength of these results, herein we aim at extending the range of available compounds I by the introduction of (het)aryl and alkenyl substituents at the N1 position of the pyrimidine ring. Such

• derivatives have been hitherto unknown due to their synthetic inaccessibility by the conventional approach based on the formation of the pyrimidine moiety. For example, the attempted heterocyclization of ethoxyenones II (e.g., 4-ethoxy-1,1,1-trifluorobut-3-en-2-one) with N-arylureas, unlike the reaction with

Synthesis of 3(2)-phosphonylated thiazolo[3,2-a]oxopyrimidines

• Ksenia I. Kaskevich,
• Anastasia A. Babushkina,
• Vladislav V. Gurzhiy,
• Dmitrij M. Egorov,
• Nataly I. Svintsitskaya and
• Albina V. Dogadina

Beilstein J. Org. Chem. 2020, 16, 1947–1954, doi:10.3762/bjoc.16.161

• Thiazolopyrimidines, whose molecules includes both thiazole and pyrimidine rings, have a structural analogy with the antipsychotic drugs ritanserin and setoperone (Figure 1) [1][2][3]. To date, a wide spectrum of biological activity of thiazolopyrimidines has been determined: anticancer [4][5], antimicrobial [6][7

• most accessible approach to the synthesis of 5H-thiazolo[3,2-a]pyrimidine-5(7)-ones is the reaction of 2-thiouracil derivatives with α-halo ketones and α-halo acids, involving successive alkylation and condensation steps (Scheme 3) [17][18][19][20][21]. A convenient one-step synthesis of

• between 2-thiouracil and propargyl bromide yielded 5H-thiazolo[3,2-a]pyrimidine-5-one (Scheme 5) [20][21][22][23][24]. Despite the wide variety of thiazolopyrimidines reported to date, phosphonylated analogues of compounds of this series are unknown. Of special interest is the design of molecules

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• trifluoride diethyl etherate as an activator (Table 1, entry 5). Nevertheless, the isolated yield of the product decreased to 71%. Next, the reaction performed with HBr/AcOH was extended to alkylidene oxetanes substituted by an alkyl chain, and a pyrimidine base. The presence of the alkyl chain in place of

Regiodivergent synthesis of functionalized pyrimidines and imidazoles through phenacyl azides in deep eutectic solvents

• Paola Vitale,
• Luciana Cicco,
• Ilaria Cellamare,
• Filippo M. Perna,
• Antonio Salomone and
• Vito Capriati

Beilstein J. Org. Chem. 2020, 16, 1915–1923, doi:10.3762/bjoc.16.158

• imidazole (32–98% yield) and pyrimidine derivatives (45–88% yield), with a broad substrate scope, when using deep eutectic solvents [choline chloride (ChCl)/glycerol (1:2 mol/mol) and ChCl/urea (1:2 mol/mol)] as environmentally benign and non-innocent reaction media, by modulating the temperature (25 or 80

• the preparation of aroylpyrimidines. In 1995, Yamamoto et al. reported the direct introduction of acyl groups into pyrimidine rings by reacting trimethylstannyl derivatives with acylformyl chlorides in dry benzene under a N2 stream [33]. Results and Discussion During our studies on the synthesis of

• undergo a base-promoted loss of nitrogen to form α-imino ketones upon protonation [38]. A plausible mechanism for the formation of pyrimidine derivative 7a from 2a, in competition with imidazoles 3a/3a', is depicted in Scheme 5. The key intermediate 5a, formed by elimination of nitrogen from the enol

When metal-catalyzed C–H functionalization meets visible-light photocatalysis

• Lucas Guillemard and
• Joanna Wencel-Delord

Beilstein J. Org. Chem. 2020, 16, 1754–1804, doi:10.3762/bjoc.16.147

• Figure 31. As previously, distinct catalytic cycles involving photoredox catalysis and C–H activation act in a cooperative way to promote the formation of a new bond. The strategy is based on the presence of a pyrimidine DG at the N1-position of the indole in order to facilitate the C–H activation step

Recent synthesis of thietanes

• Jiaxi Xu

Beilstein J. Org. Chem. 2020, 16, 1357–1410, doi:10.3762/bjoc.16.116

•  89). Pyrimidine-2,4(1H,3H)-diones 413 were derivatized with chloromethylthiirane (398a), giving rise to 1-(thietane-3-yl)pyrimidin-2,4(1H,3H)-dione derivatives 414 in low yields [114] (Scheme 90). 4.1.2 Synthesis via nucleophilic ring expansion of thiiranes: The nucleophilic ring expansion of

Photocatalytic trifluoromethoxylation of arenes and heteroarenes in continuous-flow

• Alexander V. Nyuchev,
• Ting Wan,
• Borja Cendón,
• Carlo Sambiagio,
• Job J. C. Struijs,
• Michelle Ho,
• Moisés Gulías,
• Ying Wang and
• Timothy Noël

Beilstein J. Org. Chem. 2020, 16, 1305–1312, doi:10.3762/bjoc.16.111

• poor yields. Other synthetically useful substituents, including cyano, nitro, phenylsulphonyl, (pinacolato)boron, and alkyl groups could be tolerated in the reaction (24–30), leading to a yield range between 26 and 65%. The trifluoromethoxylation of pyridine, pyrimidine, and thiophene derivatives also

Synthesis and properties of quinazoline-based versatile exciplex-forming compounds

• Rasa Keruckiene,
• Simona Vekteryte,
• Ervinas Urbonas,
• Matas Guzauskas,
• Eigirdas Skuodis,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 1142–1153, doi:10.3762/bjoc.16.101

• is to employ both donor and acceptor moieties in a single molecular structure [1][2][3][4]. Quinazoline is a planar aromatic heterocyclic compound with the fused bicyclic structure consisting of benzene and pyrimidine rings. Quinazoline derivatives were investigated and used in medicinal applications

Copper-based fluorinated reagents for the synthesis of CF₂R-containing molecules (R ≠ F)

• Louise Ruyet and
• Tatiana Besset

Beilstein J. Org. Chem. 2020, 16, 1051–1065, doi:10.3762/bjoc.16.92

• , pyrimidine and quinolone derivatives, for instance, when the PhenCuCF2CF3 complex was used as the pentafluoroethyl source (24 examples, up to 99% 19F NMR yield and up to 93% isolated yield, Scheme 15). Note that a complete mechanistic study was recently reported to explain the reactivity of this well

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• ]. It should be noted that TOI3-rev in this article is different from TOI3 in the previous reporting [12]. Here, the 1,2-diazole ring has been replaced with that of a pyrimidine core. Given the abundance of literature regarding analogues having modifications of the indole amine unit and vinylogous

• mode of binding for each compound was similar to panobinostat in HDAC8 (Figure 2). Two differences were however observed in the mode of binding of TOI4. It was shown that the pyridazine ring did not lay as planar in the gorge as the pyrazine and pyrimidine rings of TOI1 and TOI2, respectively. The

• interaction with the Zn2+ ion. TOI3-rev, like that of TOI1, TOI2, and TOI4 produces two parallel-displaced π–π interactions with Phe-152 and Phe-208 (Figure 2). The pyrimidine ring of TOI3-rev also lays planar in the gorge similar to the pyrazine and pyrimidine rings of TOI1 and TOI2. The indole ring of TOI3

Synthesis of 4-amino-5-fluoropyrimidines and 5-amino-4-fluoropyrazoles from a β-fluoroenolate salt

• Tobias Lucas,
• Jule-Philipp Dietz and
• Till Opatz

Beilstein J. Org. Chem. 2020, 16, 445–450, doi:10.3762/bjoc.16.41

• stage [15][16][17][18][19]. Fluorinated pyrimidines, pyrimidine analogues and pyrazoles [20][21] play a prominent role in several clinically important pharmaceuticals [22][23][24][25]. These compounds act against HIV or HIV-related diseases [26], such as opportunistic fungal infections, and represent

• producing alkyl-substituted pyrimidine derivatives was investigated (Scheme 2). Starting from formamidine hydrochloride, compound 10a was synthesized in 85% yield. A variety of amidines with different steric hindrance such as methyl, cyclopropyl and tert-butyl substitution was used, and all substituents

• product was detected by LC–MS). This side reaction could also be observed in the attempted synthesis of the triazolo derivative 10r, where the desired pyrimidine could only be detected in traces by LC–MS. Another limitation of the substrate scope was observed in the cyclization with an Nα-protected

Ultrasonic-assisted unusual four-component synthesis of 7-azolylamino-4,5,6,7-tetrahydroazolo[1,5-a]pyrimidines

• Yana I. Sakhno,
• Maryna V. Murlykina,
• Oleksandr I. Zbruyev,
• Anton V. Kozyryev,
• Svetlana V. Shishkina,
• Dmytro Sysoiev,
• Vladimir I. Musatov,
• Sergey M. Desenko and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2020, 16, 281–289, doi:10.3762/bjoc.16.27

• and pyruvic acid (3a) in acetic acid at room temperature under ultrasonication for 90 min gave 3-cyano-7-((4-cyano-1H-pyrazol-5-yl)amino)-5-aryl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-7-carboxylic acids 4a–c. There is also the possibility of applying ethyl pyruvate (3b) instead of pyruvic acid as

• -aryl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-7-carboxylates (substituents = H, CH3) 4d–o were isolated in 45–80% yields (Scheme 4, Table 1). The same products were isolated while carrying out this reaction in acetic acid at room temperature with intensive stirring instead of ultrasonic irradiation

• -1,2,4-triazole (1c) with aromatic aldehydes 2a–f and pyruvic acid (3a) carried out in acetic acid at a room temperature under ultrasonication for 120 min gave 7-((1H-1,2,4-triazol-5-yl)amino)-5-aryl-4,5,6,7-tetrahydro[1,2,4]triazolo[1,5-a]pyrimidine-7-carboxylic acids 4p–u in 34–76% yields (Scheme 4

Extension of the 5-alkynyluridine side chain via C–C-bond formation in modified organometallic nucleosides using the Nicholas reaction

• Renata Kaczmarek,
• Dariusz Korczyński,
• James R. Green and
• Roman Dembinski

Beilstein J. Org. Chem. 2020, 16, 1–8, doi:10.3762/bjoc.16.1

• , triethylamine, in DMF, and at room temperature – to avoid cycloisomerization to furopyrimidines (Scheme 1). The modified pyrimidine nucleoside scaffolds, propargyl acetate-substituted 2'-deoxyuridine (R = Ac, 2) and propargyl methyl ether-substituted uridine (R = Me, 3), were obtained in 87% and 61% yield