Silver Ions in Non‐canonical DNA Base Pairs: Metal‐Mediated Mismatch Stabilization of 2′‐Deoxyadenosine and 7‐Deazapurine Derivatives with 2′‐Deoxycytidine and 2′‐Deoxyguanosine

Novel silver‐mediated dA?dC, dA*?dC, and dA*?dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA). 7‐Deazapurine nucleosides enforce silver ion binding and direct metal‐mediated base pair formation to their Watson–Crick face. New phosphoramidites were prepared from 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA, which contain labile isobutyryl protecting groups. Solid‐phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher T_m values) were observed for oligonucleotide duplexes with non‐canonical dA*?dC and dA?dC pairs in the presence of silver ions. The stability of the silver‐mediated base pairs was pH dependent. Silver ion binding was not observed for the dA?dG mismatch but took place when mismatches were formed between 7‐deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair.     

Enzymatic Synthesis of 7′,5′‐Bicyclo‐DNA Oligonucleotides

The selection of artificial genetic polymers with tailor‐made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo‐DNA triphosphate (i.e., 7′,5′‐bc‐TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7′,5′‐bc‐TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA‐dependent DNA synthesis and potentially also XNA‐dependent XNA synthesis. However, DNA‐dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7′,5′‐bc‐TTP.     

7‐Substituted 7‐Deaza‐2′‐deoxyadenosines and 8‐Aza‐7‐deaza‐2′‐deoxyadenosines: Fluorescence of DNA‐Base Analogues Induced by the 7‐Alkynyl Side Chain

7‐Alkynylated 7‐deazaadenine (pyrrolo[2,3‐d]pyrimidin‐4‐amine) 2′‐deoxyribonucleosides show strong fluorescence which is induced by the 7‐alkynyl side chain (Table 3). A large Stokes shift with an emission around 400 nm is observed when the compound is irradiated at 280 nm. The solvent dependence indicates the formation of a charged transition state. The fluorescence appears when the triple bond is in conjugation with the heterocyclic base. Electron‐donating substituents at the triple bond increase the fluorescence, while electron‐withdrawing residues reduce it. In comparison, the 7‐alkynylated 8‐aza‐7‐deazaadenine (pyrazolo[3,4‐d]pyrimidin‐4‐amine) 2′‐deoxyribonucleosides are rather weakly fluorescent (Table 4). Quantum yields and fluorescence decay times are measured. The synthesis of the 7‐alkynylated 7‐deaza‐2′‐deoxyadenosines and 8‐aza‐7‐deaza‐2′‐deoxyadenosines was performed with 7‐deaza‐2′‐deoxy‐7‐iodoadenosine ( 6 ) or 8‐aza‐7‐deaza‐2′‐deoxy‐7‐iodoadenosine ( 22 ) as starting materials and employing the Pd⁰‐catalyzed cross‐coupling reaction with the corresponding alkynes (Schemes 1, 4, and 5). Catalytic hydrogenation of the side chain of the unsaturated nucleosides 5 and 17 afforded the 7‐alkyl derivatives 18 and 19 , respectively, which do not show significant fluorescence (Scheme 2).     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

2‐Substituted dATP Derivatives as Building Blocks for Polymerase‐Catalyzed Synthesis of DNA Modified in the Minor Groove

2′‐Deoxyadenosine triphosphate (dATP) derivatives bearing diverse substituents (Cl, NH₂, CH₃, vinyl, ethynyl, and phenyl) at position 2 were prepared and tested as substrates for DNA polymerases. The 2‐phenyl‐dATP was not a substrate for DNA polymerases, but the dATPs bearing smaller substituents were good substrates in primer‐extension experiments, producing DNA substituted in the minor groove. The vinyl‐modified DNA was applied in thiol–ene addition and the ethynyl‐modified DNA was applied in a CuAAC click reaction to form DNA labelled with fluorescent dyes in the minor groove     

A locked derivative of 8‐aza‐7‐deazaadenosine

The title compound [systematic name: (1S,3S,4R,7S)‐3‐(4‐amino‐1H‐pyrazolo[3,4‐d]pyrimidin‐1‐yl)‐1‐hydroxymethyl‐2,5‐dioxabicyclo[2.2.1]heptan‐7‐ol], C₁₁H₁₃N₅O₄, belongs to a family of nucleosides with modifications in both the sugar and nucleobase moieties: these modifications are known to increase the thermodynamic stability of DNA and RNA duplexes. There are two symmetry‐independent molecules in the asymmetric unit that differ significantly in conformation, and both exhibit a high‐anti conformation about the N‐glycosidic bond, with χ torsion angles of −85.4 (3) and −87.4 (3)°. The sugar C atom attached to the nucleobase N atom is −0.201 (4) and 0.209 (4) Å from the 8‐aza‐7‐deazaadenine skeleton plane in the two molecules. The molecules are assembled into layers via hydrogen bonds and π–π stacking interactions between the modified nucleobases.     

Base‐Pairing Properties of 8‐Aza‐7‐deazaadenine Linked via the 8‐Position to the DNA Backbone

The base‐pairing properties of oligonucleotides containing the unusual N⁸‐linked 8‐aza‐7‐deazaadenine 2′‐deoxyribonucleoside ( 2a ) as well as its 7‐bromo derivative 2b are described. The oligonucleotides were prepared by solid‐phase synthesis employing phosphoramidite chemistry. Compound 2a forms a strong base pair with T_d for which a reverse Watson‐Crick pair is suggested (Fig. 9). Compound 2a displays a lower N‐glycosylic‐bond stability than its N⁹‐nucleoside and shows strong stacking interactions when incorporated into oligonucleotides. The replacement of 2′‐deoxyadenosine by 2a does not significantly influence the duplex stability. However, this behavior depends on the position of the incorporation.     

An easy route to 2‐substituted‐2,3‐dihydro‐5(7)H‐oxazolo[3,2‐a]pyrimidin‐5‐ones and 7‐ones starting from the corresponding 2‐amino‐2‐oxazolines

The isomeric 2‐substituted‐7(5)‐methyl‐2,3‐dihydro‐5(7)H‐oxazolo[3,2‐a]pyrimidin‐5‐ones 3a‐b and 7‐ones 2a‐b,7a were synthesized by cyclocondensation from the 5‐substituted‐2‐amino‐2‐oxazolines 1a‐b with biselectrophiles. In boiling ethanol, the reaction of 1a‐b with acetylenic esters led to a mixture of 2a‐b,7a with a small amount of (E)‐2‐N‐(2‐ethoxycarbonylethylene)‐5‐substituted‐2‐iminooxazolines 5a‐b . The ring annulation between 1a‐b and diketene gave the 2‐substituted‐7‐hydroxy‐7‐methyl‐2,3,6,7‐tetrahydro‐5H‐oxazolo[3,2‐ a ]pyrimidin‐5‐ones 4a‐b which can be easily dehydrated to provide the 2‐substituted‐7‐methyl‐2,3‐dihydro‐5H‐oxazolo[3,2‐a]pyrimidin‐5‐ones 3a‐b .     

Synthesis of 2,4‐disubstituted 6‐phenyl‐7H‐pyrrolo[3,2‐d]‐pyrimidin‐7‐one 5‐oxides

A relatively short and efficient method for the utilization of 4,6‐dichloro‐2‐methylthio‐5‐nitropyrimidine ( 1 ) in the synthesis of the poly substituted pyrrolo[3,2‐d]pyrimidin‐7‐one 5‐oxides ( 6a ‐g) is reported. Some new 4‐substituted 6‐chloro‐2‐methylthio‐5‐nitropyrimidines ( 2a‐e ) were prepared by reaction of 4,6‐dichloro‐2‐methylthio‐5‐nitropyrimidine ( 1 ) with amines. 4‐Substituted 2‐methylthio‐5‐nitro‐6‐phenylethynylpyrimidines ( 3a‐e ), obtained from 4‐substituted 6‐chloro‐2‐methylthio‐5‐nitropyrimidines ( 2a‐e ) via palladium‐catalyzed Sonagashira coupling reaction with 1‐phenylacetylene, underwent smooth cyclization reaction in boiling 2‐propanol in the presence of catalytic amount of pyridine to give 4‐substituted 2‐methylthio‐6‐phenyl‐7H‐pyrrolo[3,2‐d]pyrimidin‐7‐one 5‐oxides ( 4a‐e ). The methylthio group of the latter compounds can be easily and selectively oxidized by m‐chloroperbenzoic acid and replaced with different amines.     

Synthesis and Antimicrobial Activities of Novel Series of 3‐(4‐(2‐substituted thiazol‐4‐yl)phenyl)‐2‐(4‐methyl‐2‐substituted thiazol‐5‐yl)thiazolidin‐4‐one Derivatives

In the present investigation, a novel series of 3‐(4‐(2‐substituted thiazol‐4‐yl)phenyl)‐2‐(4‐methyl‐2‐substituted thiazol‐5‐yl)thiazolidin‐4‐one derivatives were synthesized by condensation of 2‐substituted‐4‐methylthiazole‐5‐carbaldehyde with 4‐(2‐substituted thiazol‐4‐yl)benzenamine followed by cyclo‐condensation with thioglycolic acid in toluene. All the newly synthesized compounds were characterized by spectral (IR, ¹H NMR, ¹³C NMR, and Mass) methods. The title compounds were screened for quantitative antibacterial activity (minimal inhibitory concentration). All compounds 7a , 7b , 7c , 7d , 7e , 7f , 7g , 7h and 8a , 8b , 8c , 8d , 8e , 8f , 8g , 8h show moderate to good antimicrobial activity, whereas compounds ( 7a , 7b , 7c , 7d , 7e , 7f , 7g , 7h ) also show moderate antifungal activity.     

Preparation of 2‐amino‐5‐methyl‐7H‐1,3,4‐thiadiazolo[3,2‐α]pyrimidin‐7‐ones

2‐Amino substituted 7H‐1,3,4‐thiadiazolo[3,2‐α]pyrimidin‐7‐ones 11a‐e were prepared by the reaction of 2‐bromo‐5‐amino‐1,3,4‐thiadiazole ( 1b ) and diketene ( 8 ), subsequent cyclocondensation ( 9b → 3b ) and displacement of the bromo substituents by the reaction with primary or secondary amines ( 3b → 11a‐e ). The hydrogen atom 6‐H in the heterobicycle 3b is replaced by a Cl or Br atom in the transformation of 3b → 14a,b. The 2‐bromo‐6‐chloro compound 14a reacts chemoselectively in the 2‐position with dimethylamine ( 14a → 15 ). The structure elucidations are based on one‐ and two‐dimensional NMR techniques including a heteronuclear NOE measurement.     

Ultrasonic and Grinding Aptitudes of One‐Pot Synthesis of 5‐(4‐Chlorophenyl)‐7‐(3,4‐Dimethyl Phenyl)‐2‐oxo‐2H‐Pyrano[2,3‐b]Pyridine Derivatives as Antibacterial Agents

A simple facile “one‐pot” synthesis of 5‐(4‐chlorophenyl)‐7‐(3,4‐dimethyl phenyl)‐2‐oxo‐2H‐pyrano[2,3‐b]pyridine derivatives via three‐component reaction of chalcone, ethyl‐2‐substituted acetate, and ammonium acetate under ultrasonic irradiation and grinding tools. The newly synthesized compounds were evaluated for their antibacterial activity against ATCC 25923, ATCC 10987, ATCC 274, and SM514. All the synthesized compounds have been characterized on the basis of their elemental analyses and spectral data.     

Ferrocenylethynyl derivatives of nucleoside triphosphates: synthesis, incorporation, electrochemistry, and bioanalytical applications

Modified dATP (2'-deoxyadenosine-5'-triphosphate) and dUTP (2'-deoxyuridine-5'-triphosphate) bearing ferrocene (Fc) labels linked via a conjugate acetylene spacer were prepared by single-step aqueous-phase cross-coupling reactions of 7-iodo-7-deaza-dATP or 5-iodo-dUTP with ethynylferrocene. The Fc-labeled dNTPs were good substrates for DNA polymerases and were efficiently incorporated to DNA by primer extension (PEX). Electrochemical analysis of the 2'-deoxyribonucleoside triphosphates (dNTPs) and PEX products revealed significant differences in redox potentials of the Fc label bound either to U or to 7-deazaA and between isolated dNTPs and conjugates incorporated to DNA. Prospective bioanalytical applications are outlined.     

Synthesis and fluorescence properties of substituted 7‐aminocoumarin‐3‐carboxylate derivatives

4‐Trifluoromethyl‐ or 6‐bromo‐substituted 7‐diethylaminocoumarin‐3‐carboxamide derivatives 2 and 3, each containing a maleimide have been synthesized as potential fluorescent labeling reagents for thiol groups in proteins and their fluorescence properties have been determined. The 4‐trifluoromethyl substituted compound 2 has a significantly greater Stokes shift than the comparable compound lacking this group, but both the new coumarins have low fluorescence quantum yields (?_f). When a 4‐trifluoromethyl substituent is present, the 3‐carboxamide is unusually labile to hydrolysis. Bromination of ethyl 7‐diethylaminocoumarin‐3‐carboxylate 17 gave the 6‐ and 8‐bromo derivatives 18 and 19 respectively, and also the 8‐bromo‐7‐monoethylamino compound 20. ?_f for the latter compound is 100‐fold greater than for its diethylamino analogue 19. Fluorescence lifetime measurements support an interpretation based on the twisted intramolecular charge transfer (TICT) model to explain these large differences in ?_f.     

Stereochemistry and opioid receptor affinity of 2,4‐dipyridine‐3,7‐diazabicyclo[3.3.1]nonanones ‐ influence of the substituent in position N7

The stereochemistry the 2,4‐di‐arene substituted 3,7‐diazabicyclo[3.3.1]nonan‐9‐one 1,5‐dicarboxylate skeleton was found to be regulated by the kind of substituents attached to the arene rings as well as to the nitrogens N3 and N7. Conformational isomers, i.e., chair/chair, boat/chair and chair/boat, in addition to cis/trans conflgurational isomerism with respect to the arene rings were reported. Since the analgesic potency of the diazabicyclononanones, which is related to their affinity toward the κ‐opioid receptor, is governed by the stereochemistry of the molecules, the influence of the substituents at nitrogen N7 was studied herein. The various differently N7 substituted diazabicyclononanones were found to crystallise in a highly symmetrical chair/chair conformation. However, beside HZ2 none of the compounds exhibits high affinity to the κ receptor. In contrast, some compounds with affinity to the μ receptor could be identified. In addition, the N7‐(4‐carboxybenzyl) substituted compound was found to have affinity to the δ receptor in the submi‐cromolar range of concentration.     

Synthesis,Modification, and Anticonvulsant Activity of 3′‐R1‐Spiro[indoline‐3,6′‐[1,2,4]triazino[2,3‐c]quinazolin]‐2,2′(7′H)‐diones Derivatives

Previously unknown 3′‐R¹‐5‐R²‐spiro[indoline‐3,6′‐[1,2,4]triazino[2,3‐c]quinazoline]‐2,2′‐(7′H)‐diones and their N‐substituted analogues were obtained via reaction of 6‐R¹‐3‐(2‐aminophenyl)‐1,2,4‐triazin‐5‐ones with isatin and its substituted derivatives. It was shown that alkylation of 3′‐R¹‐5‐R²‐spiro[indoline‐3,6′‐[1,2,4]triazino[2,3‐c]quinazolin]‐2,2′‐(7′H)‐diones by N‐R³‐chloroacetamides or chloroacetonitrile in the presence of а base proceeds by N‐1 atom of isatin fragment. The spectral properties (¹H and ¹³C NMR spectra) of synthesized compounds were studied, and features of spectral patterns were discussed. The high‐effective anticonvulsant and radical scavenging agents among 3′‐R¹‐5‐R²‐spiro[indoline‐3,6′‐[1,2,4]triazino[2,3‐c]quinazolin]‐2,2′(7′H)‐diones and their N‐substituted derivatives were detected. It was shown that compounds 2.2 , 2.8 , and 3.1 exceed or compete the activity of the most widely used in modern neurology drug—lamotrigine on the pentylenetetrazole‐induced seizures model. The aforementioned fact may be considered as a reason for further profound study of synthesized compounds using other pathology models.     

Synthesis of Some 7H‐s‐Triazolo[3,4‐b]‐1,3,4‐thiadiazine Derivatives

The cyclization of 1‐amino‐2‐mercapto‐5‐[5‐methyl‐1‐(4‐methylphenyl)‐1,2,3‐triazol‐4‐yl]‐1,3,4‐triazole with various α‐haloketone in absolute ethanol yields 7H‐3‐[5‐methyl‐1‐(4‐methylphenyl)‐1,2,3‐triazol‐4‐yl]‐6‐substituted‐s‐triazolo[3,4‐b]‐1,3,4‐thiadiazines and their structures are established by elemental analysis, MS, IR and ¹H NMR spectral data.     

Synthesis and spectral properties of 2‐[(o‐ and p‐substituted)aminophenyl] ‐3H‐5‐[(o‐ and p‐substituted)phenyl]‐7‐chloro‐1,4‐benzodiazepines

A series of twelve new 2‐[(o‐ and p‐substituted)aminophenyl]‐3H‐5‐[(o‐ and p‐substituted)phenyl]‐7‐chloro‐1,4‐benzodiazepines, which have possible pharmacological properties has been obtained. The synthesis was carried out following six steps. The structure of all products was corroborated by ir, ¹H nmr, ¹³C nmr and ms. In addition for the compound 2‐(o‐chloroaminophenyl)‐3H‐5‐(o‐fluorophenyl)‐7‐chloro‐1,4‐benzodiazepine 7, its structure was confirmed by X‐ray diffraction.     

Synthesis and Characterization of New 7‐Substituted 6,14‐Ethenomorphinane Derivatives: N‐{5‐[(5α,7α)‐4,5‐Epoxy‐3,6‐dimethoxy‐17‐methyl‐6,14‐ethenomorphinan‐7‐yl]‐1,3,4‐oxadiazol‐2‐yl}arenamines

In this study, (5α,7α)‐4,5‐epoxy‐3,6‐dimethoxy‐17‐methyl‐6,14‐ethenomorphinan‐7‐carboxylic acid hydrazide ( 5 ) was synthesized by the condensation of methyl (5α,7α)‐4,5‐epoxy‐3,6‐dimethoxy‐17‐methyl‐6,14‐ethenomorphinan‐7‐carboxylate ( 4 ) with NH₂NH₂⋅H₂O. The (5α,7α)‐4,5‐epoxy‐3,6‐dimethoxy‐17‐methyl‐6,14‐ethenomorphinan‐7‐carboxylic acid 2‐[(arylamino)carbonyl]hydrazides 6a – 6q were prepared by the reaction of 5 with corresponding substituted aryl isocyanates, and the N‐{5‐[(5α,7α)‐4,5‐epoxy‐3,6‐dimethoxy‐17‐methyl‐6,14‐ethenomorphinan‐7‐yl]‐1,3,4‐oxadiazol‐2‐yl}arenamines 7a – 7q were obtained via the cyclization reaction of 6a – 6q in the presence of POCl₃. The synthesized compounds have a rigid morphine structure, including the 6,14‐endo‐etheno bridge and the 5‐(arylamino)‐1,3,4‐oxadiazol‐2‐yl residue at C(7) adopting the (S)‐configuration (7α). The structures of the compounds were confirmed by high‐resolution mass spectrometry (HR‐MS) and various spectroscopic methods such as FT‐IR, ¹H‐NMR, ¹³C‐NMR, APT, and 2D‐NMR (HETCOR, COSY, INADEQUATE).     

Synthesis of Novel 3‐(3‐(5‐Methylisoxazol‐3‐yl)‐7H‐[1,2,4]Triazolo [3,4‐b][1,3,4]Thiadiazin‐6‐yl)‐2H‐Chromen‐2‐Ones

A novel series of coumarin substituted triazolo‐thiadiazine derivatives were designed and synthesized by using 5‐methyl isoxazole‐3‐carboxylic acid ( 1 ), thiocarbohydrazide ( 2 ), and various substituted 3‐(2‐bromo acetyl) coumarins ( 4a , 4b , 4c , 4e , 4d , 4f , 4g , 4h , 4i , 4j ). Fusion of 5‐methyl isoxazole‐3‐carboxylic acid with thiocarbohydrazide resulted in the formation of the intermediate 4‐amino‐5‐(5‐methylisoxazol‐3‐yl)‐4H‐1,2,4‐triazole‐3‐thiol ( 3 ). This intermediate on further reaction with substituted 3‐(2‐bromo acetyl) coumarins under simple reaction conditions formed the title products 3‐(3‐(5‐methylisoxazol‐3‐yl)‐7H‐[1,2,4]triazolo[3,4‐b][1,3,4]thiadiazin‐6‐yl‐2H‐chromen‐2‐ones ( 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j ) in good to excellent yields. All the synthesized compounds were well characterized by physical, analytical, and spectroscopic techniques.