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J Mestres

Publications and source records attributed to J Mestres.

11 recordsLinked to original sources
PubMed2002

Virtual screening: a real screening complement to high-throughput screening.

Virtual screening is being routinely used as an integral part of today's hit-identification strategies for, on one hand, prioritizing large corporate screening collections and, on the other hand, to extend the scope of screening to external databases. A brief description of the essential elements required for virtual screening and an application example to the identification of agonist hits for the oestrogen receptor subtype ER alpha are presented.

Drug Evaluation, Preclinical↗
PubMed2001

Mechanism of the addition reaction of alkyl azides to [60]fullerene and the subsequent N2 extrusion to form monoimino-[60]fullerenes.

The 1,3-dipolar cycloaddition of methyl azide to C60 and the subsequent nitrogen elimination from the formed triazoline intermediate to yield the aziridine adduct have been studied using semiempirical and density functional methods. The results obtained show that the addition of methyl azide to C60 takes place in the ring junction between two six-membered rings leading to a closed [6,6]-trizoline intermediate with an energy barrier of about 20 kcal mol-1 and an exothermicity of ca. 2 kcal mol-1 at the B3LYP/6-31G**//AM1 level of theory. The subsequent thermal loss of N2 takes place through a stepwise mechanism in which the cleavage of the N-N single bond precedes the breaking of the N-C bond, with a total activation energy of approximately 45 kcal mol-1. The N2 loss occurs simultaneously with the formation of the new N-C bond. During the process, the steric effects of the leaving N2 molecule prevent the addition of the nitrene substituent to the [6,6]-ring junction attacked initially and force the addition to an adjacent [5,6]-ring junction.

Journal Article↗
PubMed2001

Comparing protein structures: a Gaussian-based approach to the three-dimensional structural similarity of proteins.

This study describes a new method for comparing three-dimensional protein structures based on an optimal alignment of their steric fields. The method is based upon the use of spherical Gaussian functions located on individual atoms. This representation generates a flexible description of the underlying fold geometry of proteins that can be adjusted by changing the 'width' of the Gaussians. Reducing the width sharpens the representation and leads to a more 'atomlike' description; increasing the width creates a fuzzier representation that preserves the general shape features of the chain fold but with a consequent loss in atomic resolution. The width used in this study is based upon the features of individual atoms and provides a representation that is quite robust with respect to the variety of geometric features typically encountered in the alignment process. In addition, a post-alignment analysis is performed that generates sequence alignments from the corresponding structure alignments. An example, based on five mammalian and fungal matrix metalloproteinase crystal structures (human fibroblast collagenase, neutrophil collagenase, stromelysin, astacin, and adamalysin), illustrates a number of features of the Gaussian-based approach.

Amino Acid Sequence↗
PubMed2000

Similarity-driven flexible ligand docking.

A similarity-driven approach to flexible ligand docking is presented. Given a reference ligand or a pharmacophore positioned in the protein active site, the method allows inclusion of a similarity term during docking. Two different algorithms have been implemented, namely, a similarity-penalized docking (SP-DOCK) and a similarity-guided docking (SG-DOCK). The basic idea is to maximally exploit the structural information about the ligand binding mode present in cases where ligand-bound protein structures are available, information that is usually ignored in standard docking procedures. SP-DOCK and SG-DOCK have been derived as modified versions of the program DOCK 4.0, where the similarity program MIMIC acts as a module for the calculation of similarity indices that correct docking energy scores at certain steps of the calculation. SP-DOCK applies similarity corrections to the set of ligand orientations at the end of the ligand incremental construction process, penalizing the docking energy and, thus, having only an effect on the relative ordering of the final solutions. SG-DOCK applies similarity corrections throughout the entire ligand incremental construction process, thus affecting not only the relative ordering of solutions but also actively guiding the ligand docking. The performance of SP-DOCK and SG-DOCK for binding mode assessment and molecular database screening is discussed. When applied to a set of 32 thrombin ligands for which crystal structures are available, SG-DOCK improves the average RMSD by ca. 1 A when compared with DOCK. When those 32 thrombin ligands are included into a set of 1,000 diverse molecules from the ACD, DIV, and WDI databases, SP-DOCK significantly improves the retrieval of thrombin ligands within the first 10% of each of the three databases with respect to DOCK, with minimal additional computational cost. In all cases, comparison of SP-DOCK and SG-DOCK results with those obtained by DOCK and MIMIC is performed.

Crystallography, X-Ray↗
PubMed2000

A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching.

An analysis of the relationship among alignment solutions obtained from field-based matching of a representative set of rigid conformers of three non-nucleoside HIV-1 reverse transcriptase inhibitors and solutions obtained from flexible matching of the same conformers is presented. In some cases, different alignment solutions obtained from rigid matching converge to the same solution when conformational rigidity is relaxed, indicating that a reduced set of conformers per molecule may be sufficient in many field-based similarity studies. Furthermore, the results also indicate the importance of going beyond the pairwise similarity level to obtain consistent solutions in flexible-matching studies. In this respect, the best conformationally flexible multi-molecule alignment obtained is found to be in good agreement with the relative binding geometry and orientation found experimentally from protein-ligand crystal structures. The rms separation between corresponding atoms in computed and 'experimental' sets of three inhibitor structures is 0.94 A.

Acetamides↗
PubMed1999

A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors.

This article describes a molecular-field-based similarity method for aligning molecules by matching their steric and electrostatic fields and an application of the method to the alignment of three structurally diverse non-nucleoside HIV-1 reverse transcriptase inhibitors. A brief description of the method, as implemented in the program MIMIC, is presented, including a discussion of pairwise and multi-molecule similarity-based matching. The application provides an example that illustrates how relative binding orientations of molecules can be determined in the absence of detailed structural information on their target protein. In the particular system studied here, availability of the X-ray crystal structures of the respective ligand-protein complexes provides a means for constructing an 'experimental model' of the relative binding orientations of the three inhibitors. The experimental model is derived by using MIMIC to align the steric fields of the three protein P66 subunit main chains, producing an overlay with a 1.41 A average rms distance between the corresponding C alpha's in the three chains. The inter-chain residue similarities for the backbone structures show that the main-chain conformations are conserved in the region of the inhibitor-binding site, with the major deviations located primarily in the 'finger' and RNase H regions. The resulting inhibitor structure overlay provides an experimental-based model that can be used to evaluate the quality of the direct a priori inhibitor alignment obtained using MIMIC. It is found that the 'best' pairwise alignments do not always correspond to the experimental model alignments. Therefore, simply combining the best pairwise alignments will not necessarily produce the optimal multi-molecule alignment. However, the best simultaneous three-molecule alignment was found to reproduce the experimental inhibitor alignment model. A pairwise consistency index has been derived which gauges the quality of combining the pairwise alignments and aids in efficiently forming the optimal multi-molecule alignment analysis. Two post-alignment procedures are described that provide information on feature-based and field-based pharmacophoric patterns. The former corresponds to traditional pharmacophore models and is derived from the contribution of individual atoms to the total similarity. The latter is based on molecular regions rather than atoms and is constructed by computing the percent contribution to the similarity of individual points in a regular lattice surrounding the molecules, which when contoured and colored visually depict regions of highly conserved similarity. A discussion of how the information provided by each of the procedures is useful in drug design is also presented.

Crystallography, X-Ray↗
PubMed1997

A molecular field-based similarity approach to pharmacophoric pattern recognition.

The use of molecular field-based similarity approaches for obtaining quality molecular alignments and for identifying field-based patterns in bioactive molecules is described. In addition to pairwise similarities, computation of multimolecule similarities affords a means for determining consensus multimolecule alignments. These multimolecule alignments constitute the basis for developing models for the relative binding of bioactive molecules to common protein-binding sites and for the graphical portrayal of molecular field similarity surface plots that identify, visually, molecular regions possessing similar molecular field characteristics. The latter information can then be exploited in the design of molecules that mimic appropriate characteristics of these highly similar steric and electrostatic domains. Regions with low steric and electrostatic similarity in suitably aligned sets of bioactive molecules represent tolerant domains where new structural motifs can be incorporated without significant reductions in activity. To illustrate the potential applicability of the actual molecular field-based similarity approaches to the design of bioactive molecules, a study on a set of HIV-1 protease inhibitors is presented.

Carbamates↗
PubMed1997

Vitamin E serum levels in patients with leukemia, lymphoma and myeloma.

The serum alpha-tocopherol levels were determined in a group of 182 patients with hematological neoplasms: 87 lymphoid or myeloid leukemias, 65 lymphomas and 30 myelomas. The levels did not differ from those of controls, when compared either globally or for diagnosis. Low alpha-tocopherol serum levels were observed in 6 patients (3.3%).

Adolescent↗
PubMed1990

[Medical counseling, nursing counseling, and nicotine chewing gum for smoking cessation in primary care].

The 2-month results of a study designed to compare the effectiveness of three methods to encourage giving up smoking in primary health care are reported: individualized medical counseling (minimal intervention), counseling plus follow-up option by the nurse, and medical counseling plus nicotine chewing gum. Overall 425 smokers between 15 and 65 years of age were included in the study. In 349 of them (82%), short term follow-up was carried out by phone interview. The proportion who declared to have given up smoking, after adjustment for the estimated validity of the phone report of smoking status, was 10, 9%, 10.8% and 11.1%, respectively, without significant differences between the three groups. In the logistic regression analysis, only the existence of concomitant disease and the anticipated difficulty in giving up smoking appeared as predictive variables of abstention. The implications of the results for the strategies to control smoking are discussed.

Adolescent↗
PubMed1987

Plasma kallikrein-kinin system in patients with uncomplicated sepsis and septic shock--comparison with cardiogenic shock.

Alterations of the kallikrein-kinin system consistent with activation and increased consumption have been reported in septic patients and it has been suggested that this activation could contribute to the development of septic shock. The aim of this work was to confirm these alterations in septic patients and to investigate the possible existence of similar changes in subjects developing cardiogenic shock secondary to myocardial infarction as a model of non septic shock. Patients with septic shock, especially in fatal cases, showed a highly significant decrease in levels of factor XII, prekallikrein, high molecular weight kininogen (HMW-kininogen), alpha 2-macroglobulin (alpha 2-M) and antithrombin III (AT-III). C1-esterase inhibitor (C1-INH) activity was increased in uncomplicated sepsis but came back to normal or was slightly decreased in septic shock. Components and inhibitors of the kallikrein-kinin system were within normal limits in patients with cardiogenic shock. Our findings support the idea of a contribution of the kallikrein-kinin system to the development of septic shock though this system does not seem to play a significant role in the pathogenesis of cardiogenic shock or seem to be altered as a consequence of it.

Adolescent↗