The quantitative structure−activity relationship (QSAR) analysis with comparative molecular field (CoMFA) of indole derivatives−monoamine oxidase (MAO) inhibitors were done. pharmacophore model included four features: two hydrophobic rings, one donor atom, and acceptor site. predictive values (cross-validated r2) QSAR for the inhibition MAO-A MAO-B 0.743 0.603, respectively. contributions steric electrostatic fields in interaction between enzymes equal. three-dimensional arrangement these...

The data on approximate values of isoelectric point (pI) peptides obtained during their fractionation by focusing can be successfully used for the calculation pKa's scale amino acid residues. This pI prediction. peptide also provides information about various posttranslational modifications (PTM), so that prediction may performed a wide range protein forms. In this study, pKa were calculated using set 13448 (including 300 with PTMs significant calculation). constants N-terminal, internal and...

Quantitative descriptions of hydrogen bonding for use in QSAR and molecular modeling by means H-bond descriptors have been analyzed detail this paper. Ten new surface enthalpy integral were proposed. The usefulness these descriptors, as well previously developed was verified using a set 154 drugs which data intestinal absorption humans available. results showed that such the number acceptor donor atoms polar area (PSA) did not sufficiently describe actual H-bonding ability molecules. Thus,...

Data from a mass spectrometry experiment of mouse line developed to study the mechanisms fibromuscular dysplasia and deposited by d'Escamard et al. in ProteomeXchange (PXD051750) have been analyzed. Identification peptides with post-translational modifications (PTMs) was repeated using more stringent conditions than original work. The following were considered during analysis changes PTM levels experimental control groups mice: acetylation lysine residue N-terminal protein peptide,...

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

The antibodies of schizophrenic patients that hydrolyze myelin basic protein (MBP) have been actively studied recently, but the mechanism catalytic properties immunoglobulin molecules remains unknown. Determination specific sequences associated with high activity MBP proteolysis will help to understand mechanisms abzyme catalysis. In course comparative mass spectrometric analysis IgG peptides from blood serum acute schizophrenia and healthy people, 12 were identified, which found only in...

Pneumonia caused by the COVID-19 virus has led to quick search of drugs that would able block spread this virus. A standard way drug development is a long process. One approach can significantly accelerate reposition. In study virtual screening database approved been used for inhibitors against 3СLpro COVID-19, main protease COVID-19. Molecular docking, simulation molecular dynamics and binding energy estimation MM-GBSA method allowed select several compounds further experimental testing....

A universal model of inhibition neuraminidases from various influenza virus strains by a particular has been developed. It is based on known 3D data for three (A/Tokyo/3/67, A/tern/Australia/G70C/75, B/Lee/40) and modeling structure other (A/PR/8/34 è A/Aichi/2/68). Using docking molecular dynamics, we have modeled 235 enzyme-ligand complexes 89 compounds with IC50 values. Selection final variants among results obtained each pair calculation independent variables generation linear regression...

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 results available in the ProteomeXchange database were comprehensive multidomain approach to identify potential blood biomarkers ischemic stroke mice. identification of peptides with post-translational modification (PTM) performed us raw (accession code PXD016538). Only phosphorylation deamination considered as PTMs. Different...

QSPR analyses of the solubility in water 558 vapors, 786 liquids and 2045 solid organic neutral chemicals drugs are presented. Simultaneous consideration H-bond acceptor donor factors leads to a good description vapors liquids. A volume-related term was found have an essential negative contribution Consideration polarizability, indicators for few functional groups, as well experimental values structurally nearest neighbors yielded correlations The application Yalkowsky's "General Solubility...

Preliminary results of construction overall model for prediction IC50 value ligands influenza virus neuraminidase any strain are presented. We used MM-PBSA (MM-GBSA) energy terms calculated the complexes obtained after modeling 30 variants structures, subsequent docking and simulation molecular dynamics as independent variables in equations. The structures known neuraminidase-inhibiting drugs (oseltamivir, zanamivir peramivir) a substrate (MUNANA) were ligands. correlation equation based on...

A set of models for preliminary estimation the inhibition constant values potential ligands 4 acetylcholine muscarinic receptors M1-M4 was developed. The study uses an information about three-dimensional structure human M1, M2 and M4 receptors, as well M3 receptor model, constructed by homology based on rat receptor. Ki 42 compounds were obtained from sources. Modeling “protein-ligand” complexes performed using molecular docking dynamics procedures. component energy characteristics...

A series of 42 steroid ligands was used to predict a binding affinity progesterone receptor. The molecules were the derivatives 16alpha,17alpha-cycloalkanoprogesterones. Different methods prediction and analyzed such as CoMFA artificial neural networks. best result (Q2 = 0.91) obtained for combination molecular docking, dynamics simulation predictive power model validated by group 8 pentarans synthesized separately tested in vitro (R2test 0.77). This can be determine level ligand receptor...

ProteoCat is a computer program has been designed to help researchers in the planning of large-scale proteomic experiments. The central part this subprogram hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases AspN and GluC). For peptides obtained after virtual or loaded from data file number properties important mass-spectrometric experiments can be calculated predicted. analyzed filtered reduce set peptides. using new improved modification our methods...

A new program ONIX v.2.00 was specially designed with adaptation for the purposes of biochemist's education. works proteins and nucleic acids, contained in PDB, has interface based on molecular structure hierarchy. also multimolecules multiwindows environment, error control PDB files, 3D presentation space handling models, calculation solvent-accessible surface, macro-language, saving work results (working history). The is oriented widely accessible PC computers running Windows 3.1xx.

Three-dimensional Quantitative Structure-Аctivity Relationship models were designed for irreversible and reversible acetylcholinesterase inhibitors by molecular modeling methods. In case of CoMFA (the comparative analysis fields) or CoMSIA indexes similarity) descriptors together with HYBOT 3D fields provide more statistically valid 3D-QSAR models. This indicates importance donor-acceptor interactions inhibition. organophosphorous good quality model structure-activity relationships was...

The scale of virtual pKa values for calculating the isoelectric point peptides and proteins with chemical post-translational modifications (PTM) is presented. learning set based on data from 25 experiments focusing subsequent mass spectrometric identification (ProteomeXchange accession codes: PXD000065, PXD005410, PXD006291, PXD010006 PXD017201). In order to enrich resulting sets containing was repeated using raw spectrometry all datasets. final have included satisfying following conditions:...