Search results for "molecular model"
showing 10 items of 274 documents
New ligand-based approach for the discovery of antitrypanosomal compounds.
2005
The antitrypanosomal activity of 10 already synthesized compounds was in silico predicted as well as in vitro and in vivo explored against Trypanosoma cruzi. For the computational study, an approach based on non-stochastic linear fingerprints to the identification of potential antichagasic compounds is introduced. Molecular structures of 66 organic compounds, 28 with antitrypanosomal activity and 38 having other clinical uses, were parameterized by means of the TOMOCOMD-CARDD software. A linear classification function was derived allowing the discrimination between active and inactive compounds with a confidence of 95%. As predicted, seven compounds showed antitrypanosomal activity (%AE > 7…
Novel γ-turn mimetics with a reinforced hydrogen bond
1999
Abstract Pyridylmethylphenols 2 can mimic the geometry of γ-turns. Hydrogen bonding in 2 has been characterized by X-ray crystallography, IR and NMR spectroscopy, and molecular modeling.
Allosterism of Nautilus pompilius hemocyanin as deduced from 8 Å cryo-EM structures obtained under oxy and deoxy conditions
2008
Hemocyanins are the blue copper-containing respiratory proteins of many molluscs. Nautilus pompilius hemocyanin (NpH) is a cylindrical decamer composed of ten copies of a 350 kDa polypeptide subunit, in turn consisting of seven O2-binding functional units (FUs, termed NpH-a to NpH-g). Ten copies of the subunit segment NpH-a to NpH-f form the cylinder wall (ca. 35 nm in diameter), whereas the ten copies of NpH-g build the internal collar. Recently we published a 9A cryo-EM structure and molecular model of NpH that solved the principal architecture of this protein [1]. Hemocyanins are highly allosteric, and the cooperativity of oxygen binding should be transferred between functional units by …
Design of novel small molecule base-pair recognizers of toxic CUG RNA transcripts characteristics of DM1.
2020
Graphical abstract
On the impact of side methyl groups on the structure and vibrational properties of β-carotenoids. The case of butadiene and isoprene
2021
Abstract Theoretical consideration about the impact of methyl groups on the structure and vibrational properties of β-carotenoids, using medium size molecules of trans-butadiene and trans-isoprene, are reported. Density functional theory (DFT) calculations with correlation-consistent and polarization-consistent basis sets were applied to trans-1,3-butadiene and trans-isoprene as the smallest building bricks of β-carotenoids. Their structure and harmonic vibrations were estimated in the complete basis set limit (CBS) using the non-linear least square fit. Optimized geometries and harmonic frequencies, obtained with B3LYP and BLYP density functionals and large basis sets, were favorably repro…
Kramers potential study of the Rouse-like dynamics of short alkane chains.
1999
In this work we present a Kramers potential study of the orientational dynamics and shear viscosity of short chain alkanes. In this approach the determination of the orientational relaxation time is reduced to the calculation of static moments of single chain conformations. We study a chemically realistic alkane model that asymptotically produces Gaussian chain conformations by means of a Monte Carlo simulation. Our results are applicable to single chain descriptions of polymer melt dynamics and to the intrinsic viscosity of molecules in a Theta solvent. When we map the unknown time unit of our relaxation time result for one particular chain length and temperature to the value obtained for …
The human OR1G1 olfactory receptor is differentially activated by various sandalwood odorants. A joint approach combining in silico and in vitro expe…
2013
International audience; Sandalwood is a highly valuable component in perfumery. The action mode of sandalwood odorant molecules remains to be addressed. In fact, olfactory receptors involved in their perception have not yet been identified. The interaction of a human olfactory receptor, hOR1G1, with sandalwood odorants has been investigated. By means of cellular biology and functional tests experiments, we provide an additional insight to our atomic model of OR1G1 and our olfactophore approach performed on various odorants. The studied odorants cover a wide range of structures and sandalwood intensities. We experimentally show that beta-santalol is a strong agonist of hOR1G1, contrarily to …
Categorization of chlordecone potential transformation products to predict their environmental fate
2016
EABIOmE; Chlordecone (C10Cl10O; CAS number 143-50-0) has been used extensively as an organochlorine insecticide but is nowadays banned and listed on annex A in The Stockholm Convention on Persistent Organic Pollutants (POPs). Although experimental evidences of biodegradation of this compound are scarce, several dechlorination products have been proposed by Dolfing et al. (2012) using Gibbs free energy calculations to explore different potential transformation routes. We here present the results of an in silico classification (TyPol similar to Typology of Pollutants) of chlordecone transformation products (TPs) based on statistical analyses combining several environmental endpoints and struc…
3D-QSAR study of ligands for two human olfactory receptors
2008
International audience; All living organisms, including human beings, are able to detect and discriminate myriads of structurally diverse odorants through their interaction with olfactory receptors (ORs) (1). It is well accepted that the perception of thousands of odors by about 380 ORs results from a combinatorial coding, in which one OR recognizes multiple odorants and different odorants are recognized by different combinations of ORs (2). In a previous study (3), the functional characterization on two human ORs, called OR1G1 (class II) and OR52D1 (class I) have been performed using 95 odorant molecules. We used these previously obtained functional data (3) to perform a molecular modellin…
Phosphonic Acid Analogues of Phenylglycine as Inhibitors of Aminopeptidases: Comparison of Porcine Aminopeptidase N, Bovine Leucine Aminopeptidase, T…
2019
The inhibitory activity of 14 racemic phosphonic acid analogs of phenylglycine, substituted in aromatic rings, towards porcine aminopeptidase N (pAPN) and barley seed aminopeptidase was determined experimentally. The obtained patterns of the inhibitory activity against the two enzymes were similar. The obtained data served as a basis for studying the binding modes of these inhibitors by pAPN using molecular modeling. It was found that their aminophosphonate fragments were bound in a highly uniform manner and that the difference in their affinities most likely resulted from the mode of substitution of their phenyl rings. The obtained binding modes towards pAPN were compared, with these predi…