Computer simulation of the spatial structure of MUC 1 peptides capable of inhibiting apoptosis

Identification of new effective inhibitors of apoptosis is an important task for drug development for treatment of a number diseases including neurogenerative diseases. Initiation of apoptosis occurs via the formationof macromolecular protein complexes. In these complexes, activation of key enzymes in apoptosis, caspases, takes place. One of those macromolecular complexes is DISC (death- inducing signaling complex) playing a central role in the induction of the extrinsic apoptosis pathway. The adaptor protein FA DD has a major role in the formation of the DISC. Therefore, inhibitors of FA DD, preventing its function in the DISC, can act as potential drugs inhibiting apoptosis. Furthermore, the study of the mechanisms of action of these inhibitors is of great interest for understanding the mechanisms of the signal transduction pathways of apoptosis. It has been reported that a natural protein inhibitor of FA DD is mucin-type 1 glycoprotein (MUC1). In particular, two fragments of the primary structure of the cytoplasmic domain of MUC1 (MUC1- CD) are capable of inhibiting the binding of caspase-8 to FA DD. However, the three-dimensional structure of MUC1 has not been obtained yet. It complicates significantly the rational design of potential drugs on the basis of these peptides. In this context, the aim of the present study was in silico prediction ofthree-dimensional structures of MUC1-CD peptides corresponding to protein fragments (1-20 and 46-72), as well as analysis of their conformational properties. The main focus of the work was given to the peptide MUC1-CD (46-72), which is capable of binding to FA DD. Using the methods of molecular dynamics in the implicit water it was shown that the peptide MUC1-CD (46-72) can take conformations similar to the conformations of a number of fragments of the caspase-8 DED domain. It was found that  the structure of the peptide MUC1-CD (46-72) is similar to the spatial structure of at least four fragments of caspase-8. These results indicate that the molecular mechanism of the inhibitory activity of the peptide can be explained by competitive binding with FA DD due to the structural and conformational similarity with the fragments of the caspase-8 DED domain

Structural modeling of NAD+ binding modes to PARP-1

The nuclear protein poly (ADP-ribose) polymerase-1 (PARP-1) plays an important role in the signaling and repair of DNA. PARP-1 catalyses covalent binding of poly (ADP-ribose) polymers with itself as well as with other acceptor proteins using NAD+ as a donor of ADP-ribose. Inhibitors of poly (ADP-ribose) polymerase have been shown to be effective in improvement of radiation therapy and chemotherapy of cancer in clinical testing. Development of new poly (ADP-ribose) polymerase-1 inhibitors based on derivatives of natural compounds such as NAD+ represents a novel and promising strategy. The structure of complex of human poly (ADP-ribose) polymerase-1 with NAD+ can be a starting point for rational design of small molecule inhibitors based on NAD+ derivatives. Indeed there is no crystal structure of complex poly (ADP-ribose) polymerase-1 with nicotinamide adenine dinucleotide (NAD+) available yet. In this work using molecular modeling approaches we have predicted NAD+ binding modes with PARP-1 at the donor binding site of the catalytic domain. Using structures of PARP-1 homologs in complex with NAD+ we predicted pharmacophore restraints of NAD+ binding to PARP-1. Based on clustering of PARP-1 conformations in complex with co-crystallized inhibitors and predicted pharmacophore restraints, we proposed several possible models of NAD+ binding to PARP-1 at the donor binding site of the catalytic domain. According to the predicted models, two conformations of pyrophosphate group of NAD+ in complex with PARP-1 at the donor binding site are possible. Validation of the proposed models of NAD+ binding with PARP-1 can be achieved by quantitative structure-activity analysis of NAD+ derivatives. We designed two NAD+ derivatives, which can be used for validation of predicted NAD+ binding models

Design and experimental validation of the action of small molecule-based inhibitors of the FADD protein

CD95 is one of the best studied members of the death receptor family. Activation of CD95 leads to the induction of the cell death programme, apoptosis, via formation of the death-inducing signaling complex (DISC). FA DD is a key adaptor protein for the formation of the C D95 DISC and activation of caspase-8 in the receptor complex. FA DD comprises the death domain and the death effector domain (DED). The death domain is essential for the interactions of FA DD with CD95, while DED is necessary for the recruitment of procaspase-8, -10 and the protein c-FLIP into the DISC. The search for the inhibitors that would block the interactions of FA DD with the other core proteins of the DISC is essential for the studies of the structure and function of this complex, investigation of the apoptosis mechanisms and development of new treatments for neurodegenerative diseases. In the course of this work, the screening for small inhibitors in silico that selectively interact with DED has been performed. For this purpose, the molecular modeling of the protein complexes and virtual screening of the potential inhibitors of FA DD has been performed. In addition, a new technology to test the activity of these inhibitors has been developed. The computational and experimental analysis performed allowed us to characterize the optimal conformation of the FA DD protein for the design of the small molecules that can bind in the region of amino acid residue Y25. We presume that further optimization of the structures of chemical compounds that can bind with the hydrophobic pocket next to the residue Y25 of FA DD will allow for the creation of the new perspective inhibitors of the programmed cell death

The effect of alloying on the microstructure and mechanical properties of Mo-Fe-B boride hard alloys

Mo2FeB2 based cermets with different Cr and Ni contents were prepared by liquid phase sintering. The effects of Ni and Cr content on the microstructure, hardness and fracture toughness were investigated. The results reveal that alloying of cermet with nickel leads to formation of structure сharacterized by high austenite volume fraction and low ferrite conten

Molecular-genetic mechanisms of the interaction between processes of cell response to mechanical stress and neuronal apoptosis in primary open-angle glaucoma

Glaucoma is a chronic and progressive disease, which affects more than 60 million people worldwide. Primary open-angle glaucoma (POAG) is one of the most common forms of glaucoma. For example, about 2.71 million people in the USA had primary open-angle glaucoma in 2011. Currently POAG is a major cause of irreversible vision loss. In patients with treated open-angle glaucoma the risk of blindness reached to be about 27 %. It is known that the death of optic nerve cells can be triggered by mechanical stress caused by increased intraocular pressure, which induces neuronal apoptosis and is observed in patients with POAG. Currently, there is a large number of scientific publications describing proteins and genes involved in the pathogenesis of POAG, including neuronal apoptosis and the cell response to mechanical stress. However, the molecular- genetic mechanisms underlying the pathophysiology of POAG are still poorly understood. Reconstruction of associative networks describing the functional interactions between these genes/proteins, including biochemical reactions, regulatory interactions, transport, etc., requires the use of methods of automated knowledge extraction from texts of scientific publications. The aim of the work was the analysis of associative networks, describing the molecular-genetic interactions between proteins and genes involved in cell response to mechanical stress (CRMS), neuronal apoptosis and pathogenesis of POAG using ANDSystem, our previous development for automated text analysis. It was shown that genes associated with POAG are statistically significantly more often represented among the genes involved in the interactions between CRMS and neuronal apoptosis than it was expected by random reasons, which can be an explanation for the effect of POAG leading to the retinal ganglion cell death

Prioritization of potato genes involved in the formation of agronomically valuable traits using the SOLANUM TUBEROSUM knowledge base

The development of highly efficient technologies in genomics, transcriptomics, proteomics and metabolomics, as well as new technologies in agriculture has led to an “information explosion” in plant biology and crop production, including potato production. Only a small part of the information reaches formalized databases (for example, Uniprot, NCBI Gene, BioGRID, IntAct, etc.). One of the main sources of reliable biological data is the scientific literature. The well-known PubMed database contains more than 18 thousand abstracts of articles on potato. The effective use of knowledge presented in such a number of non-formalized documents in natural language requires the use of modern intellectual methods of analysis. However, in the literature, there is no evidence of a widespread use of intelligent methods for automatically extracting knowledge from scientific publications on cultures such as potatoes. Earlier we developed the SOLANUM TUBEROSUM knowledge base (http://www-bionet.sysbio.cytogen. ru/and/plant/). Integrated into the knowledge base information about the molecular genetic mechanisms underlying the selection of significant traits helps to accelerate the identification of candidate genes for the breeding characteristics of potatoes and the development of diagnostic markers for breeding. The article searches for new potential participants of the molecular genetic mechanisms of resistance to adverse factors in plants. Prioritizing candidate genes has shown that the PHYA, GF14, CNIH1, RCI1A, ABI5, CPK1, RGS1, NHL3, GRF8, and CYP21-4 genes are the most promising for further testing of their relationships with resistance to adverse factors. As a result of the analysis, it was shown that the molecular genetic relationships responsible for the formation of significant agricultural traits are complex and include many direct and indirect interactions. The construction of associative gene networks and their analysis using the SOLANUM TUBEROSUM knowledge base is the basis for searching for target genes for targeted mutagenesis and marker-oriented selection of potato varieties with valuable agricultural characteristics

The effect of composition and microstructure on hardness and toughness of Mo₂FeB₂ based cermets

Mo₂FeB₂ based cermets with various Ni, Cr and C concentrations were prepared. The effect of Ni, Cr and C on the phase composition and microstructure was investigated by scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDS) and X-ray diffraction (XRD). Hardness (HRA) and fracture toughness (K1c) were also measured. It was found that nickel alloying leads to formation of two-phase state represented by Mo₂FeB₂ boride and austenite. Chromium alloying results in austenite to ferrite transformation and M₂₃C₆ and M₆C carbide precipitation in the case of carbon doping. Also, it was found that chromium influences the borides mean siz

Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins

Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aber rant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. It has been shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicated in the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes, which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstrated that following the transcription factor inhibition caused by binding to viral proteins, the expression of a number of oncosuppressors (WT1, MGMT, SOCS1, P53) was suppressed, while the expression of others (RASF1, RUNX3, WIF1, DAPK1) was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influence not only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtained can be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC

THE SOLANUM TUBEROSUM KNOWLEDGE BASE: THE SECTION ON MOLECULAR-GENETIC REGULATION OF METABOLIC PATHWAYS

Rapid development of high-performance genomic, transcriptomic, proteomic and metabolic technologies led to an information explosion in the field of plant biology and agrobiology. To date, the number of scientific publications on only one of the most important agricultural crops of Solanum tuberosum L. (potato) has exceeded 1.5 million. Effective access to knowledge distributed over such a multitude of non-formalized natural language textual sources requires the use of special computer-assisted intelligent methods of data mining (text-mining). However, in the literature, there is no data on the application of intellectual methods of automatic knowledge extraction from publications on agricultural crops, such as potato. Previously we have developed a pilot version of the SOLANUM TUBEROSUM knowledge base. SOLANUM TUBEROSUM is a computer platform for complex intellectual processing of large data bodies, including (1) automatic analysis of scientific publications and databases for extraction of information on genetics, markers, breeding, diagnostics, protection and storage technologies for potato, (2) formalized representation of extracted information in the knowledge base, (3) user access to these data, (4) analysis and visualization of query results. The ontology of the SOLANUM TUBEROSUM knowledge base contains dictionaries of molecular genetic objects (proteins, genes, metabolites, microRNAs, biomarkers); phenotypic characteristics of potato varieties; potato diseases and pests; biotic/abiotic environmental factors; potato agrobiotechnologies. This article describes the current version of the SOLANUM TUBEROSUM knowledge base developed from an extensive analysis of scientific publications on the moleculargenetic regulation of metabolic pathways in potatoes, as well as model plant organisms (maize, rice, Arabidopsis  thaliana). In total, about 9,000 full-text articles and more than 130,000 abstracts of PubMed were analyzed. With the help of automatic analysis of scientific publications, more than 59,000 facts on molecular genetic interactions and genetic regulation were identified, and the analysis of factual databases revealed more than 380,000 such interactions in the examined organisms. It turned out that about 3 % of extracted facts about molecular genetic interactions and genetic regulation were related to Solanum tuberosum L. Thus, the inclusion of information on well-studied model species during the extraction of information on the molecular-genetic regulation of metabolic processes is important. It allows prediction of orthologous genes in potato and their further identification and analysis based on homology. An associative network of genetic regulation of starch biosynthesis in potatoes, including 33 metabolites, 36 proteins, 6 metabolic pathways and 132 interactions between them, 86 of which describe catalytic reactions, and the rest – regulatory events, was reconstructed. The reconstructed network is the basis for the search for target genes for directed mutagenesis and marker-oriented selection of potato varieties with specified starch properties. The trial version of the SOLANUM TUBEROSUM knowledge base is available at http://www-bionet.sysbio.cytogen.ru/and/ plant/