Novel C-6 Fluorinated Acyclic Side Chain Pyrimidine Derivatives: Synthesis, 1H and 13C NMR Conformational Studies, and Antiviral and Cytostatic Evaluations

N-Heterocycles as Promising Antiviral Agents: A Comprehensive Overview

Viruses are a real threat to every organism at any stage of life leading to extensive infections and casualties. N-heterocycles can affect the viral life cycle at many points, including viral entrance into host cells, viral genome replication, and the production of novel viral species. Certain N-heterocycles can also stimulate the host's immune system, producing antiviral cytokines and chemokines that can stop the reproduction of viruses. This review focused on recent five- or six-membered synthetic N-heterocyclic molecules showing antiviral activity through SAR analyses. The review will assist in identifying robust scaffolds that might be utilized to create effective antiviral drugs with either no or few side effects.

[Msim]CuCl3: as an efficient catalyst for the preparation of 5-amino-1H-pyrazole-4-carbonitriles by anomeric based oxidation

3-Methyl-1-sulfonic acid imidazolium trichlorido copper (II) {[Msim]CuCl3} was prepared and used as a new catalyst for the preparation of 5-amino-1H-pyrazole-4-carbonitriles. In this reaction, the pyrazole ring was formed by an anomeric and vinylogous anomeric effect in the structure of the product.

Cascade annulation reaction (CAR): highly diastereoselective synthesis of pyranopyrazole scaffolds

An unprecedented domino protocol for the novel synthesis of highly diverse and functionalized tetrahydro pyranopyrazole scaffolds using chalcone epoxide has been reported for the first time. This synthetic protocol generates three consecutive stereogenic centres in a highly diastereoselective manner with the formation of vicinal diol and a quaternary carbon centre. A wide range of substrates were utilized for the scope of this methodology and provided very good yields of pyranopyrazoles. The pyranopyrazoles were also transformed into densely functionalized tetrasubstituted olefins.

An unprecedented domino protocol for the novel synthesis of highly diverse and functionalized tetrahydro pyranopyrazole scaffolds using chalcone epoxide has been reported.

Hybridized Quinoline Derivatives as Anticancer Agents: Design, Synthesis, Biological Evaluation and Molecular Docking

Objective:

Conjugating quinolones with different bioactive pharmacophores to obtain potent anticancer active agents.

Methods:

Fused pyrazolopyrimidoquinolines 3a-d, Schiff bases 5, 6a-e, two hybridized systems: pyrazolochromenquinoline 7 and pyrazolothiazolidinquinoline 8, different substituted thiazoloquinolines 13-15 and thiazolo[3,2-a]pyridine derivatives 16a-c were synthesized. Their chemical structures were characterized through spectral and elemental analysis, cytotoxic activity on five cancer cell lines, caspase-3 activation, tubulin polymerization inhibition and cell cycle analysis were evaluated.

Results:

Four compounds 3b, 3d, 8 and 13 showed potent activity than doxorubicin on HCT116 and three compounds 3b, 3d and 8 on HEPG2. These promising derivatives showed increase in the level of caspase-3. The trifloromethylphenyl derivatives of pyrazolopyrimidoquinolines 3b and 3d showed considerable tubulin polymerization inhibitory activity. Both compounds arrested cell cycle at G2/M phase and induced apoptosis.

Conclusion:

Compounds 3b and 3d can be considered as promising anticancer active agents with 70% of colchicine activity on tubulin polymerization inhibition and represent hopeful leads that deserve further investigation and optimization.

Polyfluorinated groups in medicinal chemistry

Introduction of novel and diverse functional groups in drug discovery is always seen with hesitancy until good activity and low toxicity characteristics are proven. The introduction of fluorine in drug-like compounds is now a well-accepted strategy in medicinal chemistry. However, polyfluoroalkyl groups, with the exception of trifluoromethyl substituents, are not well explored yet. Our aim is to show to the readers how polyfluorinated groups can be beneficial to the properties of pharmaceutically active compounds by highlighting the structure–activity relationship (SAR) studies that led to the selection of polyfluorinated moieties as key structural features. Despite the fact that the use of higher polyfluoroalkyl/aryl moieties is still in its infancy, we believe that they will soon acquire the same importance of their lower parents.

Catalytic applications of {[HMIM]C(NO2)3}: as a nano ionic liquid for the synthesis of pyrazole derivatives under green conditions and a mechanistic investigation with a new approach

1-Methylimidazolium trinitromethanide {[HMIM]C(NO₂)₃} as a nano structure ionic liquid was applied for the synthesis of pyrazole derivatives with high yields under mild and green conditions.

Quantum chemical calculations on the geometrical, conformational, spectroscopic and nonlinear optical parameters of 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine

The optimized geometry, (1)H and (13)C NMR chemical shifts, conformational and natural bond orbital (NBO) analyses, thermodynamic parameters, molecular surfaces, Mulliken, NBO and APT charges for 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine [C7H7Cl3N2] were investigated by the ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The calculated structural parameters (bond lengths, bond angles and dihedral angles) and (1)H and (13)C NMR chemical shifts values are compared with experimental values of the investigated compound. The observed and the calculated values are found to be in good agreement. The energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were calculated, and the obtained energies displayed that charge transfer occurs in 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine compound. In addition, the linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated compound have been computed by using HF and DFT methods.

Significance and biological importance of pyrimidine in the microbial world

Microbes are unique creatures that adapt to varying lifestyles and environment resistance in extreme or adverse conditions. The genetic architecture of microbe may bear a significant signature not only in the sequences position, but also in the lifestyle to which it is adapted. It becomes a challenge for the society to find new chemical entities which can treat microbial infections. The present review aims to focus on account of important chemical moiety, that is, pyrimidine and its various derivatives as antimicrobial agents. In the current studies we represent more than 200 pyrimidines as antimicrobial agents with different mono-, di-, tri-, and tetrasubstituted classes along with in vitro antimicrobial activities of pyrimidines derivatives which can facilitate the development of more potent and effective antimicrobial agents.

Theoretical investigation of 5-(2-acetoxyethyl)-6-methylpyrimidin-2,4-dione: conformational study, NBO and NLO analysis, molecular structure and NMR spectra

Structural and conformational, natural bond orbital (NBO) and nonlinear optical (NLO) analysis was performed, and (1)H and (13)C NMR chemical shifts values of 5-(2-Acetoxyethyl)-6-methylpyrimidin-2,4-dione [C9H12N2O4] in the ground state were calculated by using Density Functional Theory (DFT-B3LYP/6-311++G(d,p)) and Hartree-Fock (HF/6-311++G(d,p)) methods. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. In addition, the molecular frontier orbital energies, thermodynamic parameters (in the range of 200-700 K), molecular surfaces, Mulliken charges and atomic polar tensor-based charges were investigated. Besides, the analysis of all possible conformational of the title compound, a detailed potential energy curve for τ1(C8O3C10O4), τ2 (C8O3C10C11) and τ3 (C5C7C8O3) dihedral angles were performed in steps of 10° from 0° to 360°, and depicted to find the most stable form. Finally, the calculated HOMO and LUMO energies show that charge transfer occurs within the title compound.

Synthesis, characterization and RHF/ab initio simulations of 2-amino-1,3,4-thiadiazole and its annulated ring junction pyrimidine derivatives

Michael addition reaction of the 2-amino-1,3,4-thiadiazole to chalcone as biselectrophile afforded 5,7-diphenyl-6-[1,3-diphenylpropan-1-on-3-yl][1,3,4]thiadiazolo[3,2-a]pyrimidine (3) instead of 5,7-diphenyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidine (5) via further Michael addition at C₅ in pyrimidine moiety. The structure 3 was established through the aspect of ab initio calculations, elemental analysis and spectral data.

Methoxymethyl (MOM) group nitrogen protection of pyrimidines bearing C-6 acyclic side-chains

Novel N-methoxymethylated (MOM) pyrimidine (4−13) and pyrimidine-2,4-diones (15−17) nucleoside mimetics in which an isobutyl side-chain is attached at the C-6 position of the pyrimidine moiety were synthesized. Synthetic methods viaO-persilylated or N-anionic uracil derivatives have been evaluated for the synthesis of N-1- and/or N-3-MOM pyrimidine derivatives with C-6 acyclic side-chains. A synthetic approach using an activated N-anionic pyrimidine derivative afforded the desired N,N-1,3-diMOM and N-1-MOM pyrimidines 4 and 5 in good yield. Introduction of fluorine into the side-chain was performed with DAST as the fluorinating reagent to give a N,N-1,3-diMOM pyrimidine 13 with a 1-fluoro-3-hydroxyisobutyl moiety at C-6. Conformational study of the monotritylated N-1-MOM pyrimidine 12 by the use of the NOE experiments revealed the predominant conformation of the compound to be one where the hydroxymethyl group in the C-6 side-chain is close to the N-1-MOM moiety, while the OMTr is in proximity to the CH₃-5 group. Contrary to this no NOE enhancements between the N-1-MOM group and hydroxymethyl or fluoromethyl protons in 13 were observed, which suggested a nonrestricted rotation along the C-6 side-chain. Fluorinated N,N-1,3-diMOM pyrimidine 13 emerged as a model compound for development of tracer molecules for non-invasive imaging of gene expression using positron emission tomography (PET).

Synthesis, structural studies and antitumoral evaluation of C-6 alkyl and alkenyl side chain pyrimidine derivatives

The synthetic route for introduction of fluorophenylalkyl (compounds 5, 7, 14 and 15) and fluorophenylalkenyl (compounds 4E and 13) side chains at C-6 of the pyrimidine nucleus involved the lithiation of the pyrimidine derivatives 1, 2 and 11 and subsequent nucleophilic addition or substitution reactions of the organolithium intermediate thus obtained with 2-fluorophenylacetone, 4-fluoroacetophenone or ethyl 4-fluorobenzoate as electrophiles. The structures of novel compounds were confirmed by ¹H-, ¹⁹F- and ¹³C-NMR and MS. Compounds 8 and 10 containing unsaturated fluorophenylalkyl side chains showed better inhibitory effect than their saturated fluorophenylalkylated pyrimidine counterparts 7 and 9. A conformational study based on NOE enhancements showed the importance of the double bond and substitution in the side chain for the conformational preferences in relation to inhibitory activity. Among all tested compounds, C-5 furyl (12) and phenyl (13 and 15) substituted pyrimidine derivatives showed significant cytostatic activities against all tested tumor cell lines.

Synthesis, characterization, crystal structure and ab initio studies on 5-ethoxycarbonly-6-methyl-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine

The title compound, 5-ethoxycarbonly-6-methyl-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine, has been synthesized and characterized by elemental analysis, IR, UV-vis and X-ray single crystal diffraction. Ab initio calculations have been carried out for the title compound by using B3LYP and HF methods at 6-31G* basis set. The calculated results show that the predicted geometries can reproduce the structural parameters, although the intermolecular interactions have some influences on the molecular geometry in the solid state. Predicted vibrational frequencies by two methods are consistent with each other. They have been assigned and compared with experimental IR spectra. The theoretical electronic absorption spectra have been calculated by both TD-DFT and HF-CIS methods, and the results indicate that only the former can approximately predict the electronic spectra for the title compound. Molecular orbital coefficients analyses suggest that the electronic transitions are mainly assigned to n-->pi* and pi-->pi* electronic transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C(p,m)(0), S(m)(0), H(m)(0) and temperatures.

Synthesis and structural characterization of the 5-(2-haloethyl)pyrimidines--hydrogen-bonded chains in alpha-(1-carbamyliminomethylene)-gamma-butyrolactone

Three novel 5-(2-haloethyl)pyrimidine derivatives were synthesized and characterized by 1H-NMR, 13C-NMR, MS, IR spectra and elemental analysis. Iodine and chlorine atoms in the C-5 side chain were introduced by reaction of 5-(2-hydroxyethyl)pyrimidine with hydroiodic acid and phosphoryl chloride, respectively. The structure of the intermediate alpha-(1-carbamyliminomethylene)-gamma-butyrolactone was determined by X-ray crystal structure analysis. The molecule deviates very slightly from planarity. Three N-H...O hydrogen bonds link the molecules into one-dimensional chains of edge-fused rings.