Moscow University Chemistry Bulletin最新文献

This paper reviews the protein engineering of Bst polymerase using various methods. To modify the enzyme, approaches such as the production of chimeric proteins, directed evolution, and directed and random mutagenesis are used. Examples of successful changes in enzyme properties such as catalytic activity, processivity, thermal stability, and resistance to inhibitors are described.

World-wide introduction of high throughput screening (HTS) methods in drug discovery research did not result in the increased number of novel medications on the market. We discuss novel trends in drug discovery that came from the understanding that majority of diseases are multifactorial and that one enzyme has many protein substrates. Hence, new approaches are focused on development of drugs, which (1) trigger survival pathways to return the organism to homeostatic balance, and (2) inhibit enzymes modifying histones or transcription factors not at the active site, but by displacement of protein substrates from the enzyme complexes. A good example for both approaches comes from the development of activators of antioxidant defense. We analyze and illustrate problems of commonly used in vitro HTS assays, and briefly discuss advantages and limitations of small animal models. The novel approaches are complementary to the standard HTS and do not substitute for testing in mammals. Development of transgenic reporter mice to monitor drug effects by means of in vivo imaging is extremely promising to select proper dosage and administration regimes for full-range PK studies.

The combined quantum mechanics/molecular mechanics method is most often used to describe the molecular mechanisms of enzymatic reactions. The review discusses the main methodological issues, gives practical recommendations, and also illustrates the progress of the method over the past 20 years using an important example of the reaction of guanosine triphosphate hydrolysis by a protein complex.

The transition of active Mycolicibacterium smegmatis cells to a dormant state under acidification conditions is accompanied by the intracellular accumulation of tetramethyl ester of coproporphyrin (TMC). At the same time, the dormant forms of mycobacteria develop resistance to a number of damaging factors. The addition of 5-aminolevulinic acid (ALA), a precursor of porphyrin synthesis, into the bacterial culture medium leads to the accumulation of TMC in actively growing cells, which simulates the situation with dormant mycobacteria. Upon threefold increasing the concentration of TMC, the bacteria become sevenfold more resistant to the action of 40 mM hydrogen peroxide and 90-fold more resistant to heating up to 80°C. At the same time, in M. smegmatis cells with an increased concentration of TMC, the activity of dichlorophenolindophenol reductase that is a marker of respiratory chain activity decreases by 18%. The detected inhibition of activity can lead to a decrease in side oxidative reactions in the cell. Therefore, the accumulation of methylated coproporphyrin is possibly one of the mechanisms for the development of mycobacterium resistance at dormancy.

Aptamers are promising for a wide application range in biomedicine and various diagnostic systems due to their unique properties as selective ligands specifically obtained or a selected target using methods of artificial evolution and combinatorial chemistry. Strategies for obtaining aptamers in vitro and using their chemical modifications, as well as approaches to design the initial libraries of compounds based on in silico prestructuring are discussed. Limitations are formulated, and a direction for the development of the field of obtaining new aptamers is proposed.

The main types of oxidative post-translational modifications of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDН) targeting the sulfhydryl group of the catalytic cysteine residue Cys152 are reviewed. The highly reactive sulfhydryl group of Cys152 in the active center of GAPDH undergoes oxidation and S-nitrosylation, leading to inactivation and destabilization of the enzyme. Upon reversible oxidation of the sulfhydryl group to form cysteine-sulfenic acid, the enzyme loses dehydrogenase activity, but gains the ability to catalyze the acyl-phosphatase reaction. Hydrolysis of the product of the dehydrogenase reaction, 1,3-diphosphoglycerate, under the action of oxidized GAPDH leads to uncoupling of oxidation and phosphorylation at this stage of glycolysis. The action of nitric oxide results in S-nitrosylation of Cys152 in GAPDH with the subsequent formation of cysteine-sulfenic acid due to hydrolysis of the S-NO-group. Data are presented on the relationship between S-nitrosylation, oxidation and S-glutathionylation of Cys152 in GAPDH. The role of post-translational modifications of the sulfhydryl group of the catalytic cysteine residue in the regulation of enzyme activity, as well as the mechanisms ensuring the reversibility of such modifications are discussed.

In this review the methods used to study internal rotation (IR) in the ground (S₀) and excited (S₁) electronic states for compounds of the benzoic series C₆H₅–COR, where R = H, F, and CI, are compared. In the (S₀) electronic state, differences in the values of (0–v) transitions of the torsional vibration for the studied compounds are revealed in the methods of analysis of the vibrational structure of the n–π* transition of high-resolution UV absorption spectra and Fourier-transform IR spectra. The reasons for such differences are established. In the excited (S₁) state for benzaldehyde, the method of analyzing the vibrational structure of the n–π* transition of high-resolution UV absorption spectra and the method of analyzing the excitation spectra of the sensitized phosphorescence of this compound in a cooled jet are compared. It is concluded that the method of analyzing the vibrational structure of the n–π* transition of the high-resolution UV absorption spectra of vapors of the investigated compounds is more reliable and accurate when studying the IR in both electronic states.

Solubility behavior of amlodipine besylate (ADB) was investigated in the binary mixtures of ethylene glycol + 2-propanol at five different temperatures (293.2–313.2 K). The solubility results obtained from the shake-flask method are correlated with some reported cosolvency models (i.e. the van’t Hoff, combined nearly ideal binary solvent/Redlich–Kister, the Jouyban–Acree, the Jouyban–Acree–van’t Hoff, the mixture response surface, the modified Wilson, and Buchowski–Ksiazczak models). The accuracy of these models is investigated with the mean relative deviations of the back-calculated solubility data.

This article studies the development of a simple chromatographic method for the simultaneous determination of well-known antiseptics—chlorhexidine and triclosan—in new-generation antiseptic liquids. The dependencies of the retention times of chlorhexidine and triclosan on the concentration of acetonitrile in the mobile phase (30 to 60%) and pH (in a range of 3–8 units) for Luna C18, Nucleosil CN, and Diasfer C4 sorbents are studied. Ideal separation of chlorhexidine, p-chloroaniline (the most toxic decomposition product of chlorhexidine), dibutyl phthalate (as a component of cosmetic alcohol), triclosan, and ionol (butylhydroxytoluene (BHT) and E321—an antioxidant agent) during 20 min in the gradient elution mode on a column with a domestic Diasfer C4 sorbent is demonstrated.

The structures of small silver clusters (Ag_n, n = 1–3, 13) and their complexes with molecules of the antibacterial drug 2,3-bis-(hydroxymethyl)quinoxaline-N,N′-dioxide–dioxidine (Dx) are calculated using the electron density functional method in the DFT/B3LYP5 version. The features of the geometric structure and energy of the metal cluster–dioxidine ligand interaction are considered depending on the size (nuclearity) of the metal cluster. For small clusters (n = 1–3), a tendency for the metal to be coordinated to only one of the oxygen atoms of the ligand molecule is revealed. The most stable complexes are the silver trimers Dx–Ag₃ and the icosahedral silver cluster Dx–Ag₁₃, which are coordinated simultaneously with two oxygen atoms of the hydroxyl groups of the dioxidine molecule. The difference between the obtained optimized structures of the silver–dioxidine complexes and the previously studied silver complexes with hydroxide ligands, for which the hydrogen atom of the ligand hydroxyl group is displaced during the interaction, is shown.