The prediction of main protease SARS-CoV-2 inhibition based on models of enzyme-inhibitor complexes.

A set of linear regression equations predicting the IC50 values for SARS-CoV-2 main protease inhibitors was analyzed. For 180 competitive inhibitors, we have simulated the molecular dynamics of enzyme-inhibitor complexes with known structures or modeled using molecular docking. In the docking procedure, the selection of final poses was restricted by similarity to known structural analogs. The values of the energy contributions obtained by means of calculation of the free energy change of the enzyme-inhibitor complex performed by two variants of the MMPBSA (MMGBSA) method and a number of physicochemical characteristics of the inhibitors were used as independent variables. During the learning process, indicator variables were used for inhibitor subsets obtained from various literature sources to compensate the existing systematic deviations from the target value. A leave one out and leave 20% out cross validation procedures were used to evaluate the prediction quality. For the total logarithmic range width of 3.71, the mean error in predicting the lg(IC50) value was 0.45 log units. The stability of the prediction depending on the variability of the complex in molecular dynamics was investigated.

Quality of life in patients with primary hyperparathyroidism before and after parathyroidectomy: long term single center experience.

BACKGROUND: Primary hyperparathyroidism (PHPT) is a common endocrine disorder caused by a parathyroid tumor or hyperplasia, which is often accompanied with quality of life (QoL) impairment. A parathyroidectomy (PTX) is the preferred standard treatment for PHPT patients. In this single center study we aimed to evaluate the impact of PHPT on patient's QoL and identify QoL changes at early and long-term follow-up after surgery. METHODS: All the patients underwent routine PTX with the removal of the suspected hyperparathyroid gland(s). Patients filled out generic QoL questionnaire RAND SF-36, specific questionnaire PHPQoL and specific symptom assessment questionnaire PAS upon admission to the hospital before surgery, at 3 months, 12 months and 24 months after surgery. RESULTS: A total of 92 patients with PHPT (median age was 56 years, 95.7% females) were included in the study. Before PTX patient's QoL by SF-36 scores was significantly lower as compared to healthy controls (p < 0.01). Almost 40% of patients had poor or very poor QoL. The most frequent symptoms by PAS before surgery were as follows: tiredness (97.8% of patients), weakness (94.6%), forgetfulness (94.6%), mood changes (90%), feeling "blue"/depression (88%), joint pains (83.3%), headaches (80.2%), constant irritability (77.2%), bone pains (75%), thirst (70.7%) and trouble getting out of a chair (67.4%). The half of the patients had moderate-to-severe (≥ 40 scores) tiredness, weakness, joint pains, forgetfulness, as well as mood changes. Post-operative QoL changes were analysed in the group of 72 patients. After surgery there was significant improvement in QoL by all scales of SF-36 questionnaire, excluding bodily pain, and the PHPQoL total score (GEE, p < 0.01) as compared with their values before surgery. Also severity of tiredness, mood changes, weakness and forgetfulness significantly decreased after surgery as compared to their baseline values (GEE, p < 0.05). Decreased mental component of QoL by PHPQoL (OR = 0.927, 95%CI = 0.874-0.984, p = 0.013) predicted improved QoL after surgery. CONCLUSIONS: Patients with PHPT demonstrated significantly impaired QoL in physical, psychological and social functioning as well experienced a wide profile of common PHPT symptoms. Successful PTX was accompanied with remarkable QoL improvement and decrease in subjective symptoms for at least 24 months after surgery.

[The prediction of SARS-CoV-2 main protease inhibition with filtering by position of ligand]. / Predskazanie ingibirovaniia glavnoi proteazy SARS-CoV-2 c uchetom fil'tratsii dannykh o polozhenii ligandov.

The paper analyzes a set of equations that adequately predict the IC50 value for SARS-CoV-2 main protease inhibitors. The training set was obtained using filtering by criteria independent of prediction of target value. It included 76 compounds, and the test set included nine compounds. We used the values of energy contributions obtained in the calculation of the change of the free energy of complex by MMGBSA method and a number of characteristics of the physical and chemical properties of the inhibitors as independent variables. It is sufficient to use only seven independent variables without loss of prediction quality (Q² = 0.79; R²prediction = 0.89). The maximum error in this case does not exceed 0.92 lg(IC50) units with a full range of observed values from 1.26 to 4.95.

[Acetylation, methylation, and ubiquitination of proteins in experimental ischemic stroke in mice: a bioinformatics analysis]. / Atsetilirovanie, metilirovanie i ubikvitinirovanie belkov pri éksperimental'nom ishemicheskom insul'te u myshei: bioinformaticheskii analiz.

The experimental results available in the ProteomeXchange database (accession code PXD016538) (Simats et al. (2020) Molecular and Cellular Proteomics, 19(12), 1921-1936) obtained using a comprehensive multi-omics approach were analyzed in mouse blood to identify potential biomarkers of ischemic stroke. Acetylation, methylation, and ubiquitination were considered as post-translational modifications. The analysis of the significance of changes in the level of protein modification was evaluated for ischemic tissue in comparison with tissue undamaged by stroke and control taken from mice after sham operation. At the level of statistically significant differences according to the Mann-Whitney test (p < 0.05), 2 proteins were found (Q02248 and Q8BL66); for additional 7 proteins, the differences were at the level of a statistical trend (p < 0.1). For 7 of 9 selected proteins there are reports in the literature, for their association with cerebral ischemia.

[The bioinformatic identification of proteins with varying levels of post-translational modifications in experimental ischemic stroke in mice]. / Bioinformaticheskaia identifikatsiia belkov s meniaiushchimsia urovnem posttransliatsionnykh modifikatsii pri éksperimental'nom ishemicheskom insul'te u myshei.

The experimental data obtained by Simats A. et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936) was analysed using a bioinformatic approach. Original experimental results available in the ProteomeXchange database were obtained using a comprehensive multidomain approach to identify potential blood biomarkers in ischemic stroke in mice. The identification of peptides with post-translational modification (PTM) was performed by us using the raw data (accession code PXD016538). Only phosphorylation and deamination were considered as PTMs. Different combinations of data sets (ischemic tissue with intact tissue, ischemic tissue with control taken from mice after sham surgery, etc.) were compared both in terms of the ratio of abundance for the modified peptide to the unmodified variant and in terms of absolute values of abundance. The most likely change in precisely PTM levels was shown for 27 proteins, which include dynamin, glycogen phosphorylase and 70 kDa heat shock protein.

Prediction of the Inhibition of Influenza Virus Neuraminidase Various Strains by Means of a Generalized Model Constructed Using the Data on the Position of Known Ligands.

Several variants of models for predicting the IC50 values of inhibitors of influenza virus neuraminidase are presented for both individual strains and also for combinations of data for neuraminidases of several strains. They are based on the use of calculated energy contributions to the amount of change in the free energy of enzyme-inhibitor complexes. In contrast to previous works, aimed at the complex modeling, we added a procedure of comparison of the docking variants with one of the neuraminidase inhibitors, for which the structure of the complexes was determined experimentally. Selection of reference molecules for the comparison of structure similarity was made using the Tanimoto metrics and the limit of the RMSD value for a similar part of the structure was no more than 2 Å. Using this limitation and filtering datasets for a particular strain by the Q2 value obtained in the leave-one-out control procedure it was possible to construct equations for predicting the IC50 value with a Q2 value close to the minimum confidence threshold (0.57 in this work). Taking into consideration that in this version of the prediction models, a minimum set of energy contributions is used, which does not employ expensive calculations of entropy contributions, the result obtained supports the correctness of using a generalized model based on the data on the position of known ligands to predict the inhibition of neuraminidase of the influenza virus of various strains.

[Prediction of inhibition of influenza virus neuraminidase of various strains by using a generalized model constructed using the data on the position of known ligands]. / Predskazanie ingibirovaniia neiraminidazy virusa grippa razlichnykh shtammov s ispol'zovaniem obobshchennoi modeli, postroennoi c uchetom dannykh o polozhenii izvestnykh ligandov.

Several variants of models for predicting the IC50 values of inhibitors of influenza virus neuraminidase are presented for both individual strains and for combinations of data for neuraminidases of several strains. They are based on the use of calculated energy contributions to the amount of change in the free energy of enzyme-inhibitor complexes. In contrast to previous works, aimed at the complex modeling, we added a procedure of comparison of the docking variants with one of the neuraminidase inhibitors, for which the structure of the complexes was determined experimentally. The choice of the comparison structure was made according to the similarity of structures evaluated using the Tanimoto metrics and the limit of the RMSD value for a similar part of the structure was no more than 2 Å. Using this limitation and filtering datasets for a particular strain by the Q2 value obtained in the leave-one-out control procedure it is possible to construct equations for predicting the IC50 value with a Q2 value close to the minimum confidence threshold (0.57 in this work). Taking into consideration that in this version of the prediction, a minimum set of energy contributions is used, which does not provide for expensive calculations of entropy contributions, the result obtained supports the correctness of using a generalized model based on the data on the position of known ligands to predict the inhibition of neuraminidase of the influenza virus of various strains.

[The model of prediction of the inhibition of neuraminidases of influenza A and B based on a reduced set of energy terms]. / Model' predskazaniia ingibirovaniia neiraminidaz virusa grippa A i B na baze ogranichennogo nabora énergeticheskikh vkladov.

The overall model for prediction of IC50 values for inhibitors of neuraminidase influenza virus A and B has been created. It combines data about IC50 values of complexes of 40 variants of neuraminidases of influenza A (7 serotypes) and B and three known inhibitors (oseltamivir, zanamivir, peramivir). The model also uses only data of enthalpy contributions to the potential energy of inhibitor/protein and substrate (MUNANA)/protein complexes. The calculation procedures are ported to use software with support of GPU accelerators, that significant decrease the computation time. The corresponding correlation coefficient (R²) for pIC50 prediction was within 0.45-0.58, the SEM values of around 0.7 (the range of used pIC50 data set is from 4.55 to 10.22).

[Difficulties and mistakes in the diagnosis of abdominal tuberculosis in the practice of the general practitioner].

The relevance of the research is determined by the growth of cases of abdominal tuberculosis (AT), which is difficult to diagnose. AIM: Identify clinical features and possibilities of timely AT diagnosis. MATERIALS AND METHODS: Medical reports of 116 AT patients. The results of clinical, microbiological, immunological, radiological, endoscopic and morphological studies were analyzed. THE RESULTS: AT proceeded under the mask of ulcerative colitis and Crohn's disease (26.3%), alcoholic and biliary hepatitis (11.8%), lymphoproliferative and oncological diseases (61.8%), often generalized against the background of HIV-infection. The duration of the diagnostic search for disease verification exceeded 3 months due to incorrect (erroneous) interpretation of intoxication (26.3%) and radiological pattern in the lungs (23.7%), non - application and late application of laparoscopy (39.5%). CONCLUSION: When diagnosing AT, it is necessary to consider the peculiarities of its clinic and to conduct timely laparoscopy.

[Creation of a generalized model prediction of inhibition of neuraminidase of influenza virus of various strains]. / Sozdanie obobshchennoi modeli predskazaniia ingibirovaniia neiraminidazy virusa grippa razlichnykh shtammov.

Preliminary results of construction of overall model for prediction of IC50 value of ligands of influenza virus neuraminidase of any strain 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 simulation of molecular dynamics 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. The correlation equation based on calculated energetic parameters of inhibitor complexes with neuraminidase did not result in the prediction of IC50 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 resulting IC50 prediction equations become significant (R2³0.55). It is concluded that models based on IC50 values as a predictable variable and combining information about binding of different ligands to different variants of the target proteins must take into account the binding properties of the substrate (used for IC50 determination). The predictive power of such models depends critically on the quality of the modeling of the ligand-protein complexes.

[The sequence coverage in different methods of mass spectrometry data analysis obtained on model proteins]. / Stepen' pokrytiia aminokislotnoi posledovatel'nosti pri ispol'zovanii razlichnykh metodov analiza mass-spektrometricheskikh dannykh, poluchennykh na model'nykh belkakh.

The aim of this study was to evaluate sequence coverage of five model proteins (CYB5A, SMAD4, RAB27B, FECH, and CXXC1) by means of shotgun proteomic data analysis employing different methods of data treatment including database-dependent search engines (MASCOT and X!Tandem) and de novo sequencing software ((PEAKS, Novor, and PepNovo+). In order to achieve maximal results, multiprotease hydrolysis including enzymes trypsin, LYS-C, ASPN and GluC was performed in solution and using the FASP method. High resolution mass spectrometry was carried out with a Q EXACTIVE HF hybrid mass spectrometer in the positive ionization mode; parent ions with the highest intensity and a charge range from +2 to +6 were fragmented in the HCD mode. 27 experiments were carried out (hydrolysis with each of 5 enzymes in solution, 4 for the FASP protocol, three technical repeats). Using parameters limiting false identification of peptides, the search engines and de novo sequencing software gave similar results. The degree of sequence coverage was not at least 40%, and in the best cases it reached 80-90%. The use of de novo sequencing software resulted in identification of the Y12H amino acid substitution in one model protein (CYB5A).

[Use of de novo sequencing for proteins identification]. / Primenenie metodov de novo sekvenirovaniia dlia identifikatsii belkov.

Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) ("Sigma-Aldrich", USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS was performed using pure UPS2 and UPS2 mixtures with E. coli extract and human plasma samples. Protein detection was based on identification of at least two peptides of 9 residues in length or one peptide containing at least 13 residues. Using these criteria 13 (Novor), 20 (PEAKS) and 11 (PepNovo+) proteins were detected in pure UPS2 sample. Protein identifications in mixed samples were comparable or worse. Better results (by ~20%) were obtained using prediction included high quality identified fragment (TAG) containing at least 7 residues and unidentified additional masses at N- and C-termini (PepNovo+). The latter approach confidently recognized mass-spectrometric artefacts (and probably PTM). Atypical mass changes missed in UNIMOD DB were found (PepNovo+) to be statistically significant at the C-terminus (+23.02, +26.04 and +27.03). Using peptides containing these modifications and milder detection threshold 41 of 48 UPS2 proteins were identified.

[Correction of the electrophoretic shift in virtual 2D SDS-PAGE electrophoresis]. / Korrektsiia élektroforeticheskogo sdviga v virtual'nom 2D SDS-PAGE élektroforeze.

Virtual electrophoresis in proteomics can be used to search localization of proteins and their proteoforms (especially those existing in low concentrations), to identify proteoforms found in experiments etc. Although the problem of predicting the isoelectric point is well studied, the need of electrophoretic shift correction is usually ignored. Researchers simply use the brutto molecular weight of the protein. In this study four data sets taken from the literature sources and the SWISS-2DPAGE database have been used to build correction equations for prediction of the electrophoretic shift (123, 72, 118 and 470 points, respectively). Two groups of models were built. The first model was based on the amino acid composition of proteins, the second one, on analysis of parameters calculated by amino acid sequences (theoretical molecular weight, hydrophobicity, charge distribution, ability to form helix structures). The coefficient of determination ranged from 0.35 to 0.75 in each single set, but cross-prediction between samples did not gave satisfactory results. At the same time, the direction of correction was predicted correctly in 74% of cases. After combining of the samples and dividing pooled data into 2 representative sets, the coefficient of determination during in the process of learning ranged from 0.44 to 0.51, and R2 of predictions were not less than 0.39. The direction of correction was predicted correctly in 80% of cases. This prediction models have been integrated into the program pIPredict v.2, freely available at http://www.ibmc.msk.ru/LPCIT/pIPredict.

[The modern characteristics of species identification of coagulase-positive bacteria of Staphylococcus genus.]

The development of molecular techniques of research in the end of XX century permitted to broaden nomenclature of species forming genus Staphylococcus that nowadays numbers 51 species and 27 sub-species. The pathogenic species of genus have a capacity to coagulate blood plasma of mammals forming group of coagulase-positive staphylococci including 7 species: S. aureus, S. delphini, S. intermedius, S. pseudintermedius, S. lutrae, S. schleiferi ssp. сoagulans, S hyicus. In clinical practice, S.aureus is considered as the most virulent among staphylococci. The cumulated data testifies increasing etiologic significance of other representatives of group of coagulase-positive staphylococci in human and animal infection pathology. The keen attention is needed to be paid to Staphylococcus intermedius of group (SIG), uniting three close kindred species: S. pseudintermedius, S. intermedius, S. delphini. Among them the most broadly prevailed are methicillin-resistant clones of S. pseudintermedius, capable to bring on in patient various pyoinflammatory diseases. The laboratory methods based on phenotype tests, provide no opportunity to differentiate coagulase-positive staphylococci because of significant similarity of phenotype characteristics in certain representatives of this group. Te comparative analysis was implemented concerning efficiency of various methods of species identification of coagulase-positive staphylococci: biochemical, molecular genetic (multi-primer polymerase chain reaction for identifying differences in gene structure of thermonuclease, analysis of polymorphism of lengths of restricting fragments of catalase gene and their sequencing), matrix-activated laser desorptional/ionizing time-of-flight mass-spectrometry (MALDI-ToF MS) with various modes of probe preparation. The analysis was applied to 117 isolates of representatives of SIG, separated from ill and healthy individuals of small domestic animals, clinical isolates form patients of hospitals. The multi-primer polymerase chain reaction permitted to identify 97% of isolates, analysis of polymorphism of lengths of restricting fragments of catalase gene - 100% of isolates that confirms efficiency of molecular genetic methods of analysis. The MALDI-ToF MS requires replenishment data base of mass-spectrometer and application of the mode of preliminary protein extraction of samples fo increasing efficiency of species identification of coagulase-positive staphylococci.

[Prediction of selective inhibition of neuraminidase from various influenza virus strains by potential inhibitors]. / Predskazanie selektivnogo tormozheniia neiraminidazy virusa grippa razlichnykh shtammov potentsial'nymi ingibitorami.

A universal model of inhibition of neuraminidases from various influenza virus strains by a particular has been developed. It is based on known 3D data for neuraminidases from three influenza virus strains (A/Tokyo/3/67, A/tern/Australia/G70C/75, B/Lee/40) and modeling of 3D structure of neuraminidases from other strains (A/PR/8/34 è A/Aichi/2/68). Using docking and molecular dynamics, we have modeled 235 enzyme-ligand complexes for 89 compounds with known IC50 values. Selection of final variants among three results obtained for each enzyme-ligand pair and calculation of independent variables for generation of linear regression equations was performed using MM-PBSA/MM-GBSA. This resulted in the set of equations individual strains and the equations pooling all the data. Thus using this approach it is possible to predict inhibition for neuraminidase from each the considered strains by a particular inhibitor and to predict the range of its action on neuraminidases from various influenza virus strains.

[Cytotoxic activity and molecular modeling of progestins - pregna-D'-pentarans]. / Tsitotoksicheskaia aktivnost' i molekuliarnoe modelirovanie progestinov - pregna-D'-pentaranov.

The cytotoxic activity of synthetic progestins (pregna-D'-pentaranes) II-V full agonists of the progesterone receptor (PR) for PR-positive and PR-negative cells of human breast carcinoma was studied. These compounds were more active in the PR-positive MCF-7 cells than in the PR-negative MDA-MB-453 cells. Cytotoxic effects of tested compounds against normal epithelial MDCK cells were not found. Molecular modeling of studied steroids with PR showed that all progestins with close energy values can bind to the ligand binding domain (LBD) of PR and the magnitude of the energy exceeds the value estimated for the progesterone molecule. Thus, the studied progestins are active against different molecular subtypes of breast cancer and represent a promising class of chemical compounds for oncology.

[MODERN PROBLEMS OF DIAGNOSTICS AND TREATMENT OF FUNCTIONAL (UNULCEROUS) DYSPEPSIA].

This review elucidates the data on etiology and pathogenesis of functional (unulcerous) dyspepsia, clinical features, diagnostic, therapeutic and prophylactic approaches to this pathology.

The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin.

Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains. Two adjacent genes coding maltose O-acetyltransferase and uridine phosphorylase which were presented in the genomes of all optochin-susceptible strains and missed in the optochin-resistant strain were revealed. Non-synonymous substitutions in 14 protein-coding genes were discovered, including the Ala49Ser mutation in the C-subunit of the F0 part of the ATP synthase rotor usually associated with pneumococcal optochin resistance. Modeling of a process of optochin interaction with the F0 part of the ATP synthase rotor indicates that the complex of optochin with "domain C" composed by wild-type C-subunits is more stable than the same complex composed of Ala49Ser mutant C-subunits.

[SPECIFIC FEATURES OF ECOLOGY, PATHOGENIC PROPERTIES, AND ROLE OF THE STAPHYLOCOCCUS INTERMEDIUS GROUP MEMBERS IN ANIMAL AND HUMAN INFECTIOUS PATHOLOGY.]

The changes in the nomenclature of species in the genus Staphylococcus, including the most pathogenic cluster of the coagulase-positive staphylococci, are represented. Presently, besides S. aureus, this cluster consists of 6 species: S. intermedius, S. schleiferi ssp. coagulans, S. lutrae, S. hyicus, S. pseudintermedius, and S. delphini. A particular attention was paid to the Staphylococcus intermedius group (SIG), which includes three closely related coagulase-positive bacterial species: S. intermedius, S. pseudintermedius, and S. delphini. The hosts of SIG species are various mammals and birds, which live in a close contact with humans. The current knowledge about the virulence factors and pathogenicity for animals and humans are analyzed. The diffic6lties of the species identification, the features of ecology and epidemiology, antimicrobial resistance were reviewed. The biological features of S. pseudintermedius, which has the greatest similarity with S. aureus, are considered in the context of the properties of newly emerging pathogens.

[ProteoСat: a tool for planning of proteomic experiments].

ProteoCat is a computer program has been designed to help researchers in the planning of large-scale proteomic experiments. The central part of this program is the subprogram of hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases AspN and GluC). For the peptides obtained after virtual hydrolysis or loaded from data file a number of properties important in mass-spectrometric experiments can be calculated or predicted. The data can be analyzed or filtered to reduce a set of peptides. The program is using new and improved modification of our methods developed to predict pI and probability of peptide detection; pI can also be predicted for a number of popular pKa's scales, proposed by other investigators. The algorithm for prediction of peptide retention time was realized similar to the algorithm used in the program SSRCalc. ProteoCat can estimate the coverage of amino acid sequences of proteins under defined limitation on peptides detection, as well as the possibility of assembly of peptide fragments with user-defined size of "sticky" ends. The program has a graphical user interface, written on JAVA and available at http://www.ibmc.msk.ru/LPCIT/ProteoCat.