Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers

The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.     

3-Methoxalylchromone--a novel versatile reagent for the regioselective purine isostere synthesis

The first synthesis of 3-methoxalylchromone was described. The reaction of the latter with electron-rich aminoheterocycles afforded a set of heteroannelated pyridines bearing a CO(2)Me substituent located at the α-position of the pyridine core.     

Design,Synthesis, Antibacterial Evaluations and In Silico Studies of Novel Thiosemicarbazides and 1,3,4-Thiadiazoles

The emergence of drug-resistant bacterial strains continues to be one of the major challenges of medicine. For this reason, the importance of searching for novel structures of antibacterial drugs chemically different from the currently known antibiotics is still of great importance. In this study, we synthesized the thiosemicarbazide and 1,3,4-thiadiazole derivatives and tested them for antibacterial activity. In in vitro tests, we examined the activity of the synthesized substances against Gram-positive and Gram-negative bacteria strains. While all 1,3,4-thiadiazoles tested lacked significant activity, the antimicrobial response of the thiosemicarbazides was moderate and it was also dependent on the type and position of the substituent on the phenyl ring. The highest activity towards all Gram-positive bacteria strains was shown by all three linear compounds containing the trifluoromethylphenyl group in the structure. The MIC (minimum inhibitory concentration) values were in the range of 3.9–250 µg/mL. Additionally, we try to explain the mechanism of the antibacterial activity of the tested compounds using the molecular docking to DNA gyrase and topoisomerase IV, following previous reports on the molecular basis of the activity of thiosemicarbazides. Docking simulations allow the purposing dual mechanism of the antibacterial activity of the synthesized compounds through inhibition of topoisomerase IV DNA gyrase with the moderate prevalence of the topoisomerase pathway.     

Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+

The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O.Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the P=O-->Mg and Mg<--N7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O.Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.     

Synthesis,spectroscopic, structural characterization of Cd(II) and Zn(II) complexes based on the N-methyl-C-(2-pyridyl)nitrone

Zinc and cadmium complexes, ML₂(NO₃)₂ (L = N-methyl-C-(2-pyridyl)nitrone) were synthesized and characterized by means of X-ray diffraction crystallography and IR and NMR spectroscopy. The organic ligands in the complexes are coordinated via the oxygen atom of the nitrone group and the nitrogen atom of the pyridine moiety. The coordination environment of the central atoms is a distorted octahedron. The bond lengths and angles of the complexes were calculated using the DFT method with B3LYP functional. Theoretical studies revealed that the geometric parameters are in agreement with the experimental data. The fluorescent properties for the zinc and cadmium complexes were investigated at room temperature.     

Efficient synthesis of purines by inverse electron-demand Diels-Alder reactions of 1-substituted-1H-imidazol-5-amines with 1,3,5-triazines

The reaction of 1,3,5-triazine and 2,4,6-tri(trifluoromethyl)-1,3,5-triazine with in situ generated 1-substituted 5-amino-1H-imidazoles led to a set of functionalized purines. The developed practical route could serve as a fundament for the preparation of related ADA inhibitors.     

Synthesis of fluorinated purine and 1-deazapurine glycosides as potential inhibitors of adenosine deaminase

The synthesis of 2- and 6-trifluoromethylated purines and 1-deazapurines was performed by formal [3 + 3]-cyclization reactions of 5-aminoimidazoles with a set of trifluoromethyl-substituted 1,3-CCC- and 1,3-CNC-dielectrophiles. The corresponding fluorinated nucleosides were synthesized by glycosylation of 9-unsubstituted purines and 1-deazapurines with peracetylated β-ribose, β-glucose, and rhamnose and subsequent deprotection. These scaffolds can be considered as potential inhibitors of adenosine deaminase (ADA) and inosine monophosphate dehydrogenase (IMPDH) enzymes.     

Spiro[3.3]heptane as a Saturated Benzene Bioisostere**

The spiro[3.3]heptane core, with the non-coplanar exit vectors, was shown to be a saturated benzene bioisostere. This scaffold was incorporated into the anticancer drug sonidegib (instead of the meta-benzene), the anticancer drug vorinostat (instead of the phenyl ring), and the anesthetic drug benzocaine (instead of the para-benzene). The patent-free saturated analogs obtained showed a high potency in the corresponding biological assays.     

Features of two- and multicomponent heterocyclization reactions involving 3,4-disubstituted 5-aminopyrazoles and alkyl pyruvates

Three-component heterocyclizations of pyruvic acids and their esters with 5-aminopyrazoles and aromatic aldehydes, in addition to the sequential versions of these reactions, under different activating conditions were studied. Under conventional heating, pyrazolopyrimidine derivatives containing a hydroxyl group in the 6-position were formed in both two- and three-component treatments. Whereas the application of an inert atmosphere did not influence the outcome of these reactions, the use of ultrasonic irradiation led to the formation of 7-hydroxy-tetrahydropyrazolopyrimidines in multi-component reactions and 6-hydroxy-dihydropyrazolopyrimidines in the case of a step-by-step approach. The products of the latter treatment were further transformed into heteroaromatized 6-hydroxy-pyrazolopyrimidines by conventional heating.