Search results for "PHARMACOPHORE"
showing 10 items of 71 documents
A Definitive Pharmacophore Modelling Study on CDK2 ATP Pocket Binders: Tracing the Path of New Virtual High-Throughput Screenings
2020
Cyclin Dependent Kinases-2 (CDK2) are members of serine/threonine protein kinases family. They play an important role in the regulation events of the eukaryotic cell division cycle, especially during the G1 to S phase transition. Experimental evidence indicate that excessive expression of CDK2s should cause abnormal cell cycle regulation. Therefore, since a long time, CDK2s have been considered potential therapeutic targets for cancer therapy. In this work, onehundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket were submitted to short MD simulations (10ns) and free energy calculation. Comparison with experimental data (K<sub>i</sub>, K<sub>d</su…
Comparing molecular dynamics-derived pharmacophore models with docking: A study on CDK-2 inhibitors
2020
Abstract We compared the performance of molecular dynamics (MD)-derived pharmacophore modeling approaches, Common Hit Approach (CHA), and the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach, with semi-flexible constrained/unconstrained docking. The aim of this work is to enrich the hit-list of a virtual screening on CDK-2 known inhibitors as a case study. Cyclin-dependent kinases (CDKs) deregulation is associated with cancer growth. CDKs are an attractive target for anticancer agents. MD-derived pharmacophore models have been obtained with LigandScout 4.2.1. Docking analysis has been performed through Glide 7.6. The results highlighted the MYSHAPE approach has a better performanc…
Comparative analysis of virtual screening approaches in the search for novel EphA2 receptor antagonists
2015
The EphA2 receptor and its ephrin-A1 ligand form a key cell communication system, which has been found overexpressed in many cancer types and involved in tumor growth. Recent medicinal chemistry efforts have identified bile acid derivatives as low micromolar binders of the EphA2 receptor. However, these compounds suffer from poor physicochemical properties, hampering their use in vivo. The identification of compounds able to disrupt the EphA2-ephrin-A1 complex lacking the bile acid scaffold may lead to new pharmacological tools suitable for in vivo studies. To identify the most promising virtual screening (VS) protocol aimed at finding novel EphA2 antagonists, we investigated the ability of…
In silico prediction of central nervous system activity of compounds. Identification of potential pharmacophores by the TOPS–MODE approach
2004
The central nervous system (CNS) activity has been investigated by using a topological substructural molecular approach (TOPS-MODE). A discriminant analysis to classify CNS and non-CNS drugs was developed on a data set (302 compounds) of great structural variability where more than 81% (247/302) were well classified. Randic's orthogonalization procedures was carried out to allow the interpretation of the model and to avoid the collinearity among descriptors. The discriminant model was assessed by a leave-n-out (when n varies from 2 to 20) cross-validation procedure (79.94% of correct classification), an external prediction set composed by 78 CNS/non-CNS drugs (80.77% of correct classificati…
6-Amino-1-benzyl-4-(4-chloro-phen-yl)-3-(4-pyrid-yl)-1,4-dihydro-pyrano[2,3-c]pyrazole-5-carbonitrile.
2008
The crystal structure of the title compound, C25H18ClN5O, was determined in the course of our studies on the synthesis of 1,4-dihydropyrano[2,3-c]pyrazole as an inhibitor of the p38 mitogen-activated protein kinase (MAPK). The compound was prepared via a base-catalysed synthesis from 1-benzyl-3-(4-pyridyl)-1H-pyrazol-5(4H)-one with p-chloroaldehyde and malononitrile. The crystal data obtained were used to generate a three-dimensional pharmacophore model for in silico database screening. The phenyl ring is disordered over two positions, with site occupancy factors of 0.55 and 0.45. The dihedral angles between the 1,4-dihydropyrano[2,3-c]pyrazole unit and the chlorophenyl and pyridine rings a…
Efficiency of antidepressant drugs as monoamine reuptake inhibitors: analysis of the hydrophobicity influence using biopartitioning micellar chromato…
2004
The reuptake blockade of biogenic amines by antidepressants is related not only to their therapeutics effects, but also to their side effects and potential drug-drug interactions. As an alternative to classical quantitative structure-activity relationships studies, in this work we propose different quantitative retention-activity relationships (QRAR) models that are able to describe the monoamine reuptake inhibition by antidepressants. The retention of compounds is measured using a biopartitioning micellar chromatography (BMC) system that can simulate the same hydrophobic, electronic and steric molecular interactions as those that condition drug activity. Since all the compounds considered …
Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics
2021
To date, computational approaches have been recognized as a key component in drug design and discovery workflows. Developed to help researchers save time and reduce costs, several computational tools have been developed and implemented in the last twenty years. At present, they are routinely used to identify a therapeutic target, understand ligand–protein and protein–protein interactions, and identify orthosteric and allosteric binding sites, but their primary use remains the identification of hits through ligand-based and structure-based virtual screening and the optimization of lead compounds, followed by the estimation of the binding free energy. The repurposing of an old drug for the tr…
Dynamic-shared Pharmacophore Approach as Tool to Design New Allosteric PRC2 Inhibitors, Targeting EED Binding Pocket.
2020
Abstract: The Polycomb Repressive complex 2 (PRC2) maintains a repressive chromatin state and silences many genes, acting as methylase on histone tails. This enzyme was found overexpressed in many types of cancer. In this work, we have set up a Computer-Aided Drug Design approach based on the allosteric modulation of PRC2. In order to minimize the possible bias derived from using a single set of coordinates within the protein-ligand complex, a dynamic workflow was developed. In details, molecular dynamic was used as tool to identify the most significant ligand-protein interactions from several crystallized protein structures. The identified features were used for the creation of dynamic pha…
Reliability of Virtual Screening Methods in Prediction of PDE4Binhibitor Activity
2015
Identification of active ligands using computational methods is a challenging task. For example, molecular docking, pharmacophore modeling, and three dimensional quantitative structure-activity relationship models (3D-QSAR) are widely used methods to identify novel small molecules. However, all these methods have, in addition to advantages, also significant pitfalls. The aim of this study was to compare some commonly used computational methods to estimate their ability to separate highly active PDE4B-inhibitors from less active and inactive ones. Here, 152 molecules with pIC 50 -range of 3.4-10.5, originating from six original studies were used. High correlation coefficients by using dockin…
Bioactive pyrrole-based compounds with target selectivity
2020
The discovery of novel synthetic compounds with drug-like properties is an ongoing challenge in medicinal chemistry. Natural products have inspired the synthesis of compounds for pharmaceutical application, most of which are based on N-heterocyclic motifs. Among these, the pyrrole ring is one of the most explored heterocycles in drug discovery programs for several therapeutic areas, confirmed by the high number of pyrrole-based drugs reaching the market. In the present review, we focused on pyrrole and its hetero-fused derivatives with anticancer, antimicrobial, and antiviral activities, reported in the literature between 2015 and 2019, for which a specific target was identified, being resp…