1,720,980 research outputs found
Comparative analysis of Rac1 binding efficiency with different classes of ligands: morpholines, flavonoids and imidazoles
No full textThe focal adhesion pathway has a great impact on cellular growth and survival. Its disregulation is correlated with the loss of cellular mechanical properties. Such modifications are, in many cases, associated with pathologies such as cancer and cardiovascular diseases. Actin remodeling is a critical reaction cascade embedded in focal adhesion pathway, and Rac1 is one of the proteins involved in actin remodeling. In order to design highly selective pharmacophores against this target, it is necessary to maximize the binding affinity of chemical entities against Rac1. To this purpose we propose an integrative chemo-bioinformatics tool to screen ligand specificity for a target protein. Our integrative workflow includes chemo-informatics data mining (Chemical System), structural bioinformatics and combined exploratory data analysis. We have applied this integrative chemo-bioinformatics workflow to a comparative analysis of three different classes of ligands (morpholines, flavonoids and imidazoles) against the Rac1 protein. Our analysis emphasizes the presence of several ligands that preferentially dock Rac1 in the domain that seems to be responsible for Rac1-phospholipase C gamma 1 interaction. Recent studies have highlighted the Rac1 and PLC interactions in platelet adhesion. Our study has highlighted the role of Rac1-PLC gamma1 interaction in cytoskeleton remodeling associated with cardiovascular diseases. Rac1 PLC interaction is Calcium dependent. This suggest that some of the analysed ligands, could be used to control the Calcium dependent cytoskeleton remodeling since they dock Rac1 in the switch 2 domain. Our results, in a nanotechnology perspective, also endorse the use Rac1's switch 2 domain suitable for new highly specific biosensors
SNP analysis of Rac1 For personalized ligand interaction
No full textThis paper addresses mutational events that give rise to differing response to drugs focusing on Rac1, a protein that has been recognized as a target for drug design for cardiovascular disease due its regulatory role of angiogenesis. Rac1 has been considered with reference to Single Nucleotide Polymorphism (SNP), which has become of great value for personalized medicine. We have considered four variation of Rac1 registered in UNIPROTKB. Two of these variations are due to the environmental or population factors and two are mutation that we have selected because they are located near the binding sites of Rac1. Rac1 has been modelled by Rosetta software and by i-Tasser web server. We have chosen i-Tasser based modelling because the Rac1 structure obtained was more closely resembling crystallography data. In silico model have been used as receptors for docking with a set of 20 morpholines. The results that have been obtained on SNPs shows that a single ligand can react very differently with a mutated structure. Our analysis shows that all mutations that have been considered change Rac1 conformation and increase the accessible surface of Rac1. Our analysis highlights the effect of two sources of genetic variability: single base variation and alternative splicing
Drug design for cardiovascular disease: The effect of solvation energy on Rac1-ligand interactions
No full text'OMICS' techniques have deeply changed the drug discovery process. The availability of many different potential druggable genes, generated by these new techniques, have exploited the complexity of new lead compounds screening. 'Virtual screening', based on the integration of different analytical tools on high performance hardware platforms, has speeded up the search for new chemical entities suitable for experimental validation. Docking is a key step in the screening process. The aim of this paper is the evaluation of binding differences due to solvation. We have compared two commonly used software, one of which takes into account solvation, on a set of small molecules (Morpholines, flavonoids and imidazoles) which are able to target the RAC1 protein--a cardiovascular target. We have evaluated the degree of agreement between the two different programs using a machine learning approach combined with statistical test. Our analysis, on a sample of small molecules, has pointed out that 35% of the molecules seem to be sensitive to solvation. This result, even though quite preliminary, stresses the need to combine different algorithms to obtain a more reliable filtered set of ligands
Biomedical, informatics and systems biology for the design of new drugs for cardiovascular disease
No full textToll-like receptor structural determinants: Variability analysis by digital signal processing methods
No full textIn silico screening of Rac1 ligand specificity
No full textMicrotubule (MT) destabilization promotes the formation of actin stress fibers and enhances the contractility of cells. The actin cytoskeleton is bound to each junction and controls the integrity of each through actin remodeling and these junctions can be disassembled or assembled to either increase or decrease cellular permeability. Mediators, such as thrombin, stimulate their respective receptor on endothelial cells to initiate signaling that increases cytosolic Ca2+ and activates myosin light chain kinase (MLCK), as well as monomeric GTPases RhoA, Rac1, and Cdc42. Ca2+ activation of MLCK and RhoA disrupts junctions, whereas Rac1 and Cdc42 promote junctional assembly. In order to develop formal systems biology model of actin remodelling it is necessary to investigate the reciprocal interactions between Rac1 and Cdc42 by using experimental selective inhibition. We have screened, by docking analysis, a new class of compounds for Rac1 and/or Cdc42 inhibition, the Morpholinos, that could be used as alternative tool to switch off a gene
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