Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry (v.12, #4)

Searching for Essential Genes in the Cancer Genome by M. A. Pyatnitskiy; D. S. Karpov; S. A. Moshkovskii (283-296).
The concept of essential genes, whose loss of functionality results in cell death, is one of the fundamental concepts of genetics and is important for basic and applied research. This field is particularly promising in oncology, because using the search for genetic vulnerabilities of cancer cells it is possible to identify new potential targets for antitumor therapy. The modern biotechnology capacities are used in large-scale projects for sequencing of somatic mutations in tumors, as well as for direct action on the genetic apparatus of cancer cells. They provided accumulation of a considerable body of knowledge about genetic variants and their phenotypic manifestations in tumors. In the near future this knowledge will find application in clinical practice. This review describes the main experimental and computational approaches to the search for essential genes with special emphasis on application of these methods in molecular oncology.
Keywords: cancer genome; essential genes; CRISPR; RNA interference; synthetic lethals

Apolipoprotein A-I Stimulates Secretion of Insulin and Matrix Metalloproteinases by Islets of Langerhans by I. F. Usynin; O. N. Poteryaeva; G. S. Russkikh; A. V. Zubova; K. Yu. Boiko; L. M. Polyakov (297-302).
The development of type 2 diabetes mellitus (DM2) is accompanied by impairments in lipid metabolism. These include the increase in serum levels of atherogenic fractions of very low-density (VLDL) and low-density lipoproteins (LDL), total cholesterol, triglycerides, and apoB. The level of antiatherogenic high density lipoproteins (HDL) and the content of apolipoprotein A-I (apoA-I) decreased. To study the effect of the observed metabolic changes on insulin secretion in vitro, we have used the islets of Langerhans isolated from the rat pancreas. It has been found that incubation of the islets in the presence of serum of obese patients and patients with decompensated DM2 leads to a 2.4-fold and 5.0-fold decrease in insulin secretion, respectively. On the contrary, addition of HDL to the incubation medium caused a 3.4-fold increase in the insulin secretion. A similar effect was observed in the presence of apoA-I, the main protein component of HDL. In the presence of apoA-I, the extracellular activity of matrix metalloproteinases (MMPs) demonstrated a 10-fold increase. The addition of LDL and VLDL to the islets did not change the insulin secretion and MMP activity. Our results emphasize an important role of HDL and apoA-I in the regulation of the insulin secretion by β-cells and the MMP activity in the islets of Langerhans.
Keywords: type 2 diabetes mellitus; apolipoprotein A-I; insulin; matrix metalloproteinases; islets of Langerhans

The Effect of Acute Hypoxia with Hypercapnia on the Monoamine Content in Symmetrical Brain Areas of Albino Mice by I. V. Karpova; V. V. Mikheev; V. V. Marysheva; N. A. Kuritcyna; N. A. Popkovskii; E. R. Bychkov; P. D. Shabanov (303-307).
Changes in the activity of monoaminergic systems of the left and right hemispheres of the brain were investigated in male albino mice after acute hypoxia with hypercapnia. The concentrations of dopamine (DA), serotonin (5-HT) and their metabolites dihydroxyphenylacetic (DOPAC), homovanillic (HVA), and 5-hydroxyindoleacetic (5-HIAA) acids were measured by HPLC in the brain cortex, hippocampus, and striatum of the right and the left hemispheres. In the control mice (which were not exposed to hypoxia with hypercapnia), a higher concentration of DA in the left cortex was detected. No asymmetry in the content of other substances was identified in the investigated structures. Acute hypoxia with hypercapnia led to the right-sided increase of DA and 5-HT levels and to the left-sided reduction DOPAC in the cerebral cortex. Under the condition of hypoxia with hypercapnia, the left-sided increase of the DA content was detected in the hippocampus. In the striatum the contents of monoamines and their metabolites were insignificantly changed. It has been concluded that acute hypoxia with hypercapnia causes asymmetric changes in monoaminergic systems of the archicortex and the neocortex.
Keywords: hypoxia with hypercapnia; dopamine; serotonin; striatum; hippocampus; brain cortex

Lipoylcarnosine: Synthesis, Study of Physico-Chemical and Antioxidant Properties, Biological Activity by S. L. Stvolinsky; N. A. Antonova; O. I. Kulikova; A. V. Lopachev; D. A. Abaimov; I. Al-Baidani; O. M. Lopacheva; T. N. Fedorova; A. P. Kaplun; G. M. Sorokoumova (308-315).
Synthesis of lipoylcarnosine (LipС), a conjugated molecule based on two natural antioxidants, carnosine and α-lipoic acid, is described and its physico-chemical, antioxidant properties and biological activity are characterized. According to reversed-phase HPLC with a UV detector, purity of the final product was 89.3%. The individuality of the obtained sodium salt of LipС was confirmed by tandem HPLC-mass spectrometry. LipC demonstrated high resistance to hydrolysis with serum carnosinase. The antioxidant activity of LipC evaluated by the reaction with the formation of thiobarbituric acid reacting substances and kinetic parameters of iron-induced chemiluminescence was higher than that of carnosine and lipoic acid. LipC did not affect viability of SH-SY5Y human neuroblastoma cells, differentiated to the dopaminergic phenotype, at concentrations not exceeding 5 mM. In the concentration range of 0.1–0.25 mM LipC protected neuronal cells against 1-methyl-4-phenylpyridinium (MPP+)-induced toxicity.
Keywords: carnosine; α-lipoic acid; lipoylcarnosine; antioxidant; carnosinase; parkinsonism

A Rational Approach for Obtaining High-Specific Polyclonal Antibodies against Recombinant Alpha-Synuclein by K. V. Barinova; A. K. Melnikova; E. V. Schmalhausen; V. I. Muronetz (316-321).
An approach for quick and efficient production of polyclonal antibodies to the target antigen, alpha-synuclein, has been proposed. Two methods have been employed to purify specific rabbit polyclonal antibodies against recombinant human alpha-synuclein, produced by subcutaneous immunization with complete Freund’s adjuvant. It was shown that purification on CNBr-activated Sepharose with immobilized alpha-synuclein resulted in antibody preparation with rabbit serum histidine-rich glycoprotein as a contaminant. Two-stage antibody purification procedure first on Sepharose with immobilized protein G, and then on alpha-synuclein immobilized column helps to avoid contamination and to obtain homogenous antibody preparation. Antibodies recognize different conformations of alpha-synuclein and can be used in a variety of immunochemical approaches, including immunocytochemistry.
Keywords: polyclonal antibodies; alpha-synuclein; adjuvant; immunization

Preliminary results of construction of an overall model for prediction of IC50 values of inhibitors of neuraminidase from any influenza virus strains are presented. We used MM-PBSA (MM-GBSA) energy terms calculated for the complexes obtained after modeling of 30 variants of neuraminidase structures, subsequent docking and molecular dynamics simulation as independent variables in prediction equations. The structures of known neuraminidase-inhibiting drugs (oseltamivir, zanamivir and peramivir) and a neuraminidase substrate (MUNANA) were used as ligands. Use of calculation parameters of neuraminidase-inhibitor complexes did not result in the correlation equation with acceptable parameters (R2 ≤ 0.3). However, if information about binding energy of the substrate used for neuraminidase assay (and IC50 detection) is included the resultant IC50 prediction equations became significant (R2 ≥ 0.55). It is concluded that models joining not only various ligands but also numerous variants of the target protein involved in their binding should take into consideration not only the IC50 value as the target parameter but also binding of the neuraminidase substrate used for experimental determination of the IC50 value. In this case the use of modelled proteins is reasonable. The predictive power of such models depends critically on the quality of the modeling of the ligand-protein complexes.
Keywords: influenza virus neuraminidase; inhibitors; computational methods; QSAR

Early Changes in Hyppocampal Neurogenesis Induced by Soluble Aβ1-42 Oligomers by Yu. K. Komleva; O. L. Lopatina; Ya. V. Gorina; A. I. Chernykh; A. N. Shuvaev; A. B. Salmina (330-338).
Alzheimer’s disease (AD) is characterized by the loss of neurons, the accumulation of intracellular neurofibrillary tangles and extracellular amyloid plaques in the brain. However, contradicting data exist on differences in neurogenesis at the onset of the disease or before the formation of amyloid plaques. Taking into consideration growing awareness of the importance of the pre-symptomatic phase in neurodegenerative diseases in the context of early diagnosis and pathogenesis, we have analyzed critical periods of adult hippocampal neurogenesis at the early stage under the action of soluble forms of amyloid-beta (Aβ1-42). Using the mouse AD model induced by injection of soluble Aβ oligomers we investigated proliferation, migration, and neuronal cells survival. The injection of Aβ1-42 oligomers caused a decrease in cell proliferation in the mouse hippocampus. Despite preservation of the neuroblast pool in animals treated with Aβ injection, the process of radial migration impaired, and apoptosis increased. Thus, our results demonstrate that Aβ administration impaired critical stages of neurogenesis including progenitor cells, neuroblast migration, integration of immature neurons, and survival of neurons under application of soluble beta-amyloid oligomers. The data obtained indicate the decline in proliferation rate in the subgranular zone, which is accompanied by ectopic differentiation and disturbed migration, producing, apparently, abnormal neurons that have lower survival rates. That could lead to a decrease in the number of mature neurons and in the number of cells in the granular layer of the dentate gyrus.
Keywords: Alzheimer’s disease; neurogenesis; subgranular zone; cell migration; apoptosis; stem cells

The Effect of the Primula Veris Solid Herbal Extract on the Development of Oxidative Stress and the Functional State of Cardiomyocyte Mitochondria of Rats with Experimental Chronic Heart Failure by T. A. Popova; E. A. Muzyko; M. V. Kustova; M. A. Bychenkova; V. N. Perfilova; I. I. Prokofiev; M. A. Samoylova; I. N. Tyurenkov; G. M. Latypova; V. A. Kataev (339-349).
Experimental chronic heart failure (CHF), caused by intraperitoneal administration of L-isoproterenol (2.5 mg/kg twice a day for 21 days), promotes uncoupling of respiration and oxidative phosphorylation in rat cardiac mitochondria. The rate of mitochondrial oxygen consumption in the metabolic state V3 by Chance in animals with CHF decreased by 53.3% (p < 0.05) with malate (as an oxidation substrate feeding complex I of the electron transport chain (ETC)), by 70.6% (p < 0.05) with succinate (complex II substrate) and by 63.6% (p < 0.05) when malate and succinate were added simultaneously. The respiratory control ratio (RCR) of mitochondria from CHF rats demonstrated a significant decrease for complex I substrate (2.3-fold), complex II substrate (2.5-fold) and 2.6-fold in the case of simultaneous addition of complex I and II substrates and 2.6 times as compared to cardiac mitochondria of intact animals. Mitochondrial dysfunction in experimental CHF is evidently associated with the development of oxidative stress: the malondialdehyde (MDA) content in the group of CHF rats was higher by 54.7% (p < 0.05), as compared with intact animals. The activity of superoxide dismutase (SOD) and catalase was lower by 17.5% (p < 0.05), and by 18.4%, respectively, than in the intact group. Administration of the Primula veris solid herbal extract (PVSHE) attenuated the development of mitochondrial dysfunction in rats with experimental CHF as evidenced by an increase in the V3 respiration using complex I (77.2%; p < 0.05), complex II (114.6%; p < 0.05) substrates and a 1.7- and 2-fold increase in the RCR value (p < 0.05) determined versus negative control with complex I and complex II substrates, respectively. Under these conditions the MDA concentration was lower by 15.7% (p < 0.05), while SOD activity was higher by 56.3% (p < 0.05).
Keywords: chronic heart failure; mitochondrial dysfunction; oxidative stress; Primula veris solid herbal extract

Isatin (indol-2,3-dione) is an endogenous indole found in the brain, peripheral tissues and biological body fluids of humans and animals. Its wide spectrum of biological activity is realized via interaction with numerous isatin-binding proteins; these include proteins playing an important role in the development of neurodegenerative pathology. In the context of the neuroprotective effect, the effect of isatin is comparable to the effects of deprenyl, a pharmacological agent used for treatment of Parkinson’s disease. In this study, the effects of the course of deprenyl (1 mg/kg) and isatin (20 mg/kg) administration for 21 days on the profile of the isatin-binding proteins of the liver of mice have been investigated. Proteomic profiling of liver isatin-binding proteins of control mice by means of 5-aminocaproylisatin as an affinity ligand resulted in identification of 105 proteins. Treatment of animals with a low dose of isatin slightly decreased (up to 91), while injections of deprenyl slightly increased (up to 120) the total number of isatin-binding proteins. 75 proteins were common for all three groups; they represented from 62.5% (in deprenyl treated mice) and 71% (in control mice), to 82% (isatin treated mice) of the total number of identified liver isatin-binding proteins. The proteomic analysis of the isatin-binding proteins of mice treated with isatin (20 mg/kg) or deprenyl (1 mg/kg) for 21 days revealed a representative group of proteins (n = 30) that were sensitive to the administration of these compounds. Taking into consideration the previously obtained results, it is reasonable to suggest that the change in the profile of isatin-binding proteins may be attributed to accumulation of isatin and deprenyl in the liver and interaction with target proteins prevents their subsequent binding to the affinity sorbent. In this context, the identified isatin-binding liver proteins of control animals that do not bind to the affinity sorbent (immobilized isatin analogue) after treatment of animals with either deprenyl or isatin appear to be specific targets directly interacting with isatin in vivo.
Keywords: isatin; deprenyl; isatin-binding proteins; mouse liver; proteomic profiling