Biomedical subjects

Luigi Villa

Publications and source records attributed to Luigi Villa.

13 recordsLinked to original sources

PubMed2005

Solvent constraints on the property space of acetylcholine. 2. Ordered media.

The objective of this study was to investigate the conformational and property spaces of acetylcholine in hydrated octanol and in a membrane model. Molecular dynamics simulations of long duration (15 ns) were carried out, yielding 3000 conformers. For each, we calculated N(+)-C8 distance, solvent-accessible surface area (SAS), polar surface area (PSA), dipole moment, and lipophilicity (virtual logP). Their variations as a function of the dihedral angles tau(2) and tau(3) remained unexpectedly broad and comparable to those seen previously in a vacuum, in water, and in chloroform.(12) Thus, each of the seven conformational clusters was able to access a marked proportion of the lipophilicity space accessible to acetylcholine (0.40 in the logP scale). Histograms of logP distributions revealed two overlapping populations, namely more lipophilic and more hydrophilic. Their deconvolution into two Gaussian curves demonstrated solvent-mediated constraints on the lipophilicity space of acetylcholine, clearly showing how a polar medium favors polar conformers, whereas the opposite is true for media of low polarity.

Acetylcholine↗

PubMed2005

Range and sensitivity as descriptors of molecular property spaces in dynamic QSAR analyses.

In this paper, we report the first study aimed at correlating pharmacological properties with molecular parameters derived from the physicochemical property space of bioactive molecules. A dataset of 36 ligands of the alpha(1a)-, alpha(1b)-, and alpha(1d)-adrenoceptors as published by Bremner et al. (Bioorg. Med. Chem. 2000, 8, 201-214) was used. One thousand conformers were generated for each ligand by Monte Carlo conformational analysis, and four 3D-dependent physicochemical properties were computed for each conformer of each ligand, namely virtual lipophilicity (log P), dipole moment, polar surface area (PSA), and solvent-accessible surface area (SAS). Thus, a space of four physicochemical properties was obtained for each ligand. These spaces were assessed by two descriptors, namely their range and their sensitivity (i.e., the variation amplitude of a given physicochemical property for a given variation in molecular geometric properties). Little or no correlation was found to exist between the physicochemical properties and their range or sensitivity, indicating that the latter descriptors do not encode the same molecular information as the former properties. As expected, neither the range nor the sensitivity of any of the four physicochemical properties correlated with receptor affinities. In contrast, range and sensitivity showed promising correlations with deltapK(a-b) (i.e., the alpha(1a)/alpha(1b) selectivity) for the complete dataset. The correlations were lower for deltapK(a-d) (i.e., the alpha(1a)/alpha(1d) selectivity), whereas there was no correlation at all with deltapK(b-d). These results are consistent with the results of Bremner et al., which indicate that the alpha(1a)-AR ligands bind in an extended geometry, whereas the alpha(1b)-AR and alpha(1d)-AR ligands assume more folded conformations. Since the property space descriptors presented here take structural variability into account, their correlation with deltapK(a-b) and deltapK(a-d) indicates that these selectivities are indeed driven by differences in conformational behavior and hence in property spaces.

Chemical Phenomena↗

PubMed2005

QSAR study for a novel series of ortho monosubstituted phenoxy analogues of alpha1-adrenoceptor antagonist WB4101.

A number of (S)- and (R)-2-[(2-phenoxyethyl)aminomethyl]-1,4-benzodioxanes unsubstituted or ortho monosubstituted at the phenoxy moiety were synthesized and tested in binding assays on the alpha(1a)-AR, alpha(1b)-AR, alpha(1d)-AR and the 5-HT(1A) receptor. The affinity values of the new compounds 1-16 were compared with those of the enantiomers of the 2,6-dimethoxyphenoxy analogue, the well-known alpha(1) antagonist WB4101, finding that the unsubstituted derivative (S)-1 and the o-methyl, the o-t-butyl, the o-fluoro and the o-methoxy derivatives, (S)-2, (S)-4, (S)-8 and (S)-16, respectively, display a significantly specific 5-HT(1A) affinity, very close, with the exception of (S)-4, to the almost nanomolar one of (S)-WB4101. Otherwise, sensible affinity decreases were recorded for the three alpha(1)-AR subtypes. A classical quantitative structure-activity relationship (Hansch) analysis was successfully applied to compounds (S)-1 to (S)-16 and (S)-WB4101 to rationalize such binding data.

Adrenergic alpha-1 Receptor Antagonists↗

PubMed2005

Solvent constraints on the property space of acetylcholine. I. Isotropic solvents.

The objective of this study was, first, to examine the property space of a test molecule and, second, to assess solvent constraints. Acetylcholine was chosen as the object of study given its interesting molecular structure and major biological significance. Molecular dynamics simulations of long duration (30 ns) were carried out with acetylcholine in a vacuum or in a box of solvent (chloroform, water, water plus one chloride counterion). For each of the 6000 conformers stored during each run, various geometric and physicochemical properties were calculated, namely, N(+)-C8 distance, solvent-accessible surface area (SAS), polar surface area (PSA), dipole moment, and lipophilicity (virtual log P). The variations of these properties as a function of the dihedral angles tau(2) and tau(3) were unexpectedly broad for such a small molecule. Dipole moment and virtual log P were well correlated, and they varied in a complex manner with the dihedral angles. For example, each of the seven conformational clusters was able to access much of the lipophilicity space of acetylcholine. Solvent constraints on the property space clearly indicate that a polar medium tends to favor polar conformers, whereas the opposite is true for a solvent of low polarity.

Acetylcholine↗

PubMed2004

Synthesis and alpha4beta2 nicotinic affinity of 2-pyrrolidinylmethoxyimines and prolinal oxime ethers.

Homochiral E and Z isomers of N-methylprolinal O-isopropyloxime and (1-methyl-2-pyrrolidinyl)methoxyimines were synthesized as candidate bioisosteres of nicotine and its isoxazolic analogue ABT 418. Two of them, namely (S)-2-isopropylideneaminooxymethyl- and (Z)-(S)-2-ethylideneaminooxymethyl-1-methylpyrrolidine, proved to bind at alpha4beta2 nicotinic acetylcholine receptor with submicromolar affinity and remarkable selectivity over alpha7 and muscarinic receptors thus supporting the hypothesized bioisosteric relationship between their methyloxyimino group and the aromatic heterocycles of the reference ligands.

Animals↗

PubMed2004

Structure-affinity studies for a novel series of homochiral naphtho and tetrahydronaphtho analogues of alpha 1 antagonist WB-4101.

A number of enantiomeric pairs of naphthodioxane, tetrahydronaphthodioxane and naphthoxy analogues of WB-4101 (1) were designed and synthesized in order to improve the selectivity profile of the parent compound, hopefully in favour of the alpha(1a)-AR with respect to the other two alpha(1) subtypes and the 5-HT(1A) receptor. The new compounds 2-8 and, in addition, the two enantiomers of 1 were tested in binding assays on the alpha(1a)-AR, alpha(1b)-AR, alpha(1d)-AR, and the 5-HT(1A) receptor. Two of them, namely the naphtho- and tetrahydronaphthodioxane derivatives (S)-2 and (S)-3, showed lower, but significantly more specific alpha(1a) affinity than (S)-1, while the two enantiomers of the 2-methoxy-1-naphthoxy analogue 6 maintained most of the very high alpha(1a) affinity of (S)-1 and its alpha(1a) versus alpha(1b) selectivity slightly increasing the alpha(1a)/alpha(1d) and alpha(1a)/5HT(1A) affinity ratios. The SAR data were evaluated in the light of known alpha(1) subtype pharmacophores and of the alpha(1a)-AR binding mode of WB-4101 resultant from literature mutagenesis studies disclosing some interesting consonances with these models.

Adrenergic alpha-1 Receptor Antagonists↗

PubMed2004

Binding site analysis of full-length alpha1a adrenergic receptor using homology modeling and molecular docking.

The recent availability of crystal structure of bovine rhodopsin offers new opportunities in order to approach the construction of G protein coupled receptors. This study focuses the attention on the modeling of full-length alpha(1a) adrenergic receptor (alpha(1a)-AR) due to its biological role and significant implications in pharmacological treatment of benign prostate hyperplasia. This work could be considered made up by two main steps: (a) the construction of full structure of alpha(1a)-AR, through homology modeling methods; (b) the automated docking of an endogenous agonist, norepinephrine, and of an antagonist, WB-4101, using BioDock program. The obtained results highlight the key residues involved in binding sites of both agonists and antagonists, confirming the mutagenesis data and giving new suggestions for the rational design of selective ligands.

Amino Acid Sequence↗

PubMed2004

VEGA--an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming.

In this paper we present the expandability and flexibility features of the VEGA program (downloadable free of charge at http://www.ddl.unimi.it), for the development of custom applications, using it as a multipurpose graphical environment. VEGA can be customized using both plug-in architecture and script programming. The first is useful to add new features and functions, using homemade routines, written with the VEGA Plug-in Development Kit (SDK). With the second approach it is possible to design scripts in VEGA, using the REBOL language, in order to (1) add new functions or customize existing ones; (2) automate common procedures; and (3) allow network communications, by creating a bridge between VEGA and other applications (or other PCs) through the TCP/IP protocol.

Computational Biology↗

PubMed2003

Analysis of the full-length integrase-DNA complex by a modified approach for DNA docking.

A model of the full-length HIV-1 integrase dimer was constructed assembling the experimentally determined structures of the single domains. Subsequently, the three-domain protein-viral DNA complex was generated for the first time through an automated docking algorithm, obtained modifying the ESCHER program, a well-known method for protein-protein docking. A detailed study of the contacts established with DNA by the enzyme revealed that the predicted model reproduced the results of mutagenesis and cross-linking experiments, confirming the validity of our docking approach in predicting the base specificity in the DNA-protein interaction.

Base Sequence↗

PubMed2002

The solute-solvent system: solvent constraints on the conformational dynamics of acetylcholine.

The objective of this study was to determine if and how a solvent influences internal motions in a solute molecule. Acetylcholine was chosen as the object of study given its interesting molecular structure and major biological significance. Molecular dynamics simulations were carried out in the vacuum (10 ns), water (5 ns), methanol (5 ns), and octanol (1.5 ns). Seven clusters of conformers were identified, namely, +g+g, -g-g, +gt, -gt, t+g, t-g, and tt, where the gauche and trans labels refer to the dihedral angles tau(2) and tau(3), respectively. As expected, the relative proportion of these conformational clusters was highly solvent-dependent and corresponded to a progressive loss of conformational freedom with increasing molecular weight of the solvent. More importantly, the conformational clusters were used to calculate instantaneous and median angular velocity (omega and omega(M), respectively) and instantaneous and median angular acceleration (alpha and alpha(M), respectively). Angular velocity and angular acceleration were both found to decrease markedly with increasing molecular weight of the solvent, i.e., vacuum (epsilon = 1) > water > methanol > octanol. The decrease from the vacuum to octanol was approximately 40% for tau(2) and approximately 60% for tau(3). Such solvent-dependent constraints on a solute's internal motions may be biologically and pharmacologically relevant.

1-Octanol↗

PubMed2002

Modeling of binding modes and inhibition mechanism of some natural ligands of farnesyl transferase using molecular docking.

Several natural inhibitors of farnesyl transferase have been reported in the literature: some compounds are competitive with farnesyl pyrophosphate (FPP), whereas other ones are competitive with Ras proteins, even though it is usually hard to highlight their inhibition mechanism, which is still unknown for several natural compounds. The aim of this work is to show that the molecular docking analysis can be successfully used to underline the inhibition mechanism of these natural compounds. First, the selected compounds were subjected to a detailed docking analysis, by means of BioDock, a program able to reveal the most likely binding mode for each ligand. By comparing these results with the binding sites for the natural substrates, earlier determined, it was possible to highlight the site specificity and the inhibition mechanism of the selected compounds. In addition, it is possible to relate the binding mode of these molecules with their lipole values, which is appreciably less for peptidomimetics than for FPP mimetic and reveals a straightforward method to predict and to understand the inhibition mechanism of these natural derivatives.

Alkyl and Aryl Transferases↗

PubMed2002

VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs.

We here propose the program VEGA, that was developed to create a bridge between the most popular molecular software packages. In this tool some features are implemented some features to analyze, display and manage the three dimensional (3D) structure of the molecules. The most important features are (1) file format conversion (with assignment of the atom types and atomic charges), (2) surface calculation and (3) trajectory analysis. The executable and the source code can be free downloaded from [URL: see text].

Bacterial Toxins↗

PubMedDate not supplied

Uremic serum induces proatherogenic changes in human endothelial cells.

BACKGROUND: Cardiovascular complications are the main cause of death in uremic patients. Uremic angiopathy has been regarded as an accelerated form of atherosclerosis. However the mechanism leading to vessel wall injury is still unknown. We hypothesized that uremic serum affects endothelium inducing a proatherogenic state. METHODS: We studied the effects of uremic serum on human endothelial cells (HECs). Cell proliferation and adhesion of mononuclear cells to HEC monolayers were evaluated by cell counting, apoptosis and collagen production by ELISA, and nitric oxide (NO) by measuring the concentration of nitrite/nitrate in the cell supernatant. (alfa2)IV collagen, tissue inhibitor of metalloproteases-1 (TIMP-1) and transforming growth factor-beta (TGF-beta) mRNA levels were measured by reverse transcriptase polymerase chain reaction (RT-PCR). In some experiments cells were preincubated with anti-receptor for advanced glycation end product (anti-RAGE) blocking antibodies. RESULTS: Uremic serum did not modify HEC proliferation but induced apoptosis after 72 hours of incubation. Adhesion of mononuclear cells to HEC monolayers was significantly increased by uremic serum. In addition, uremic serum increased (alfa2)IV collagen, TIMP-1 and TGF-beta mRNA levels. There was no increase in nitric oxide concentration in ure-mic serum-treated endothelial cells, and the expression of TGF-beta was neither modified by L-NAME nor by anti-RAGE antibodies. CONCLUSIONS: Our results indicate that uremic serum affects HEC inducing a proatherogenic state that may be responsible for the accelerated atherosclerosis of uremic patients. Apparently uremic serum effect is not mediated by NO or by AGEs.

Antibodies, Monoclonal↗