Biomedical subjects

Anna Maria Ferrari

Publications and source records attributed to Anna Maria Ferrari.

9 recordsLinked to original sources

PubMed2006

An ab initio periodic study of NiO supported at the Pd(100) surface. Part 2: The nonstoichiometric Ni3O4 phase.

The present computational study describes the structure and properties of a substoichiometric 2D monatomic in the height phase of nickel oxide, c(4 x 2)-Ni(3)O(4), which has been newly found to epitaxially grow under special deposition conditions on the (100) face of palladium. A slab model is adopted where palladium is simulated by a thin film covered on both sides by epilayers, in combination with a DFT hybrid-exchange Hamiltonian; to make convergence of the SCF procedure easier, a thermal smearing technique is used, whose consequences on the results are critically analyzed. Three adsorbed systems are considered and characterized: (i) RH, that is, the c(4 x 2)-Ni(3)O(4) phase with a rhombic distribution of Ni vacancies, as is experimentally observed; SQ, or p(2 x 2)-Ni(3)O(4), which differs from the previous one for a square, instead of a rhombic distribution of vacancies; (iii) OX, or p(2 x 2)-O, that is, a surface oxidized phase of Pd(100) which is believed to be the precursor for the formation of RH. For a better understanding of the interaction of the metal with the adlayers, the isolated substoichiometric oxides, i-RH and i-SQ, have also been studied. It is shown that RH is more stable than SQ by a few tenths of electronvolts per Ni(3)O(4) unit, which justifies its preferential formation and that the surface reaction, OX + 3NiO(ads) --> RH, is thermodynamically possible. Special attention has been devoted to characterize RH from an energetic, geometric, electronic, and magnetic viewpoint. The strong bond which is formed between surface Pd and O ions in the adlayer is responsible for some peculiar aspects of the electronic and magnetic structures of that phase.

Journal Article↗

PubMed2006

An ab initio periodic study of NiO supported at the Pd(100) surface. Part 1: The perfect epitaxial monolayer.

The epitaxial monolayer of NiO on Pd(100) has been theoretically simulated using a hybrid-exchange GGA-DFT Hamiltonian and a slab model, periodic in two dimensions. This "perfect" system is an essential reference for the simulation of nonstoichiometric two-dimensional phases which are formed during the deposition of nickel on palladium in the presence of oxygen. The adequacy of the computational procedure is discussed, especially as concerns the use of a thermal smearing technique which has been adopted to improve the convergence properties of the SCF procedure and to prevent the onset of nonphysical spin-polarized solutions. The equilibrium configuration corresponds to antiferromagnetic order in the overlayer, with oxygens on top of the surface Pd atoms; the ad-film is slightly corrugated with Ni closer to the surface by 0.1 A with respect to O. The interaction energy is quite small, 0.20 eV/NiO unit (about 5 kcal mol(-1)); correspondingly, the electronic and magnetic properties of the Pd slab and the isolated NiO monolayer are only marginally affected by the interaction.

Journal Article↗

PubMed2004

Soft docking and multiple receptor conformations in virtual screening.

Protein conformational change is an important consideration in ligand-docking screens, but it is difficult to predict. A simple way to account for protein flexibility is to soften the criterion for steric fit between ligand and receptor. A more comprehensive but more expensive method would be to sample multiple receptor conformations explicitly. Here, these two approaches are compared. A "soft" scoring function was created by attenuating the repulsive term in the Lennard-Jones potential, allowing for a closer approach between ligand and protein. The standard, "hard" Lennard-Jones potential was used for docking to multiple receptor conformations. The Available Chemicals Directory (ACD) was screened against two cavity sites in the T4 lysozyme. These sites undergo small but significant conformational changes on ligand binding, making them good systems for soft docking. The ACD was also screened against the drug target aldose reductase, which can undergo large conformational changes on ligand binding. We evaluated the ability of the scoring functions to identify known ligands from among the over 200 000 decoy molecules in the database. The soft potential was always better at identifying known ligands than the hard scoring function when only a single receptor conformation was used. Conversely, the soft function was worse at identifying known leads than the hard function when multiple receptor conformations were used. This was true even for the cavity sites and was especially true for aldose reductase. To test the multiple-conformation method predictively, we screened the ACD for molecules that preferentially docked to the expanded conformation of aldose reductase, known to bind larger ligands. Six novel molecules that ranked among the top 0.66% of hits from the multiple-conformation calculation, but ranked relatively poorly in the soft docking calculation, were tested experimentally for enzyme inhibition. Four of these six inhibited the enzyme, the best with an IC(50) of 8 microM. Although ligands can get better scores in soft docking, the same is also true for decoys. The improved ranking of such decoys can come at the expense of true ligands.

Aldehyde Reductase↗

PubMed2004

Three-dimensional quantitative structure-activity relationship analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors using a pharmacophore generation approach.

A 3D pharmacophore model able to quantitatively predict inhibition constants was derived for a series of inhibitors of Plasmodium falciparum dihydrofolate reductase (PfDHFR), a validated target for antimalarial therapy. The data set included 52 inhibitors, with 23 of these comprising the training set and 29 an external test set. The activity range, expressed as Ki, of the training set molecules was from 0.3 to 11 300 nM. The 3D pharmacophore, generated with the HypoGen module of Catalyst 4.7, consisted of two hydrogen bond donors, one positive ionizable feature, one hydrophobic aliphatic feature, and one hydrophobic aromatic feature and provided a 3D-QSAR model with a correlation coefficient of 0.954. Importantly, the type and spatial location of the chemical features encoded in the pharmacophore were in full agreement with the key binding interactions of PfDHFR inhibitors as previously established by molecular modeling and crystallography of enzyme-inhibitor complexes. The model was validated using several techniques, namely, Fisher's randomization test using CatScramble, leave-one-out test to ensure that the QSAR model is not strictly dependent on one particular compound of the training set, and activity prediction in an external test set of compounds. In addition, the pharmacophore was able to correctly classify as active and inactive the dihydrofolate reductase and aldose reductase inhibitors extracted from the MDDR database, respectively. This test was performed in order to challenge the predictive ability of the pharmacophore with two classes of inhibitors that target very different binding sites. Molecular diversity of the data sets was finally estimated by means of the Tanimoto approach. The results obtained provide confidence for the utility of the pharmacophore in the virtual screening of libraries and databases of compounds to discover novel PfDHFR inhibitors.

Aldehyde Reductase↗

PubMed2003

Oxide/metal interface distance and epitaxial strain in the NiO/Ag(001) system.

Geometric parameters of NiO films epitaxially grown on Ag(001) were determined using two independent experimental techniques and ab initio simulations. Primary beam diffraction modulated electron emission experiments determined that the NiO films grow with O on top of Ag and that the oxide/metal interface distance is d=2.3+/-0.1 A. Polarization-dependent x-ray absorption, at the Ni-K edge, determined the tetragonal strain (r( parallel )=2.046+/-0.009 A, r( perpendicular )=2.12+/-0.02 A) and d=2.37+/-0.05 A. Periodic slab model results agree with the experiments (d=2.40, r( parallel )=2.07, r( perpendicular )=2.10 A; the O-on-top configuration is the most stable).

Journal Article↗

PubMed2003

Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors.

Plasmodium falciparum dihydrofolate reductase (PfDHFR) is an important target for antimalarial chemotherapy. Unfortunately, the emergence of resistant parasites has significantly reduced the efficiency of classical antifolate drugs such as cycloguanil and pyrimethamine. In this study, an approach toward molecular docking of the structures contained in the Available Chemicals Directory (ACD) database to search for novel inhibitors of PfDHFR is described. Instead of docking the whole ACD database, specific 3D pharmacophores were used to reduce the number of molecules in the database by excluding a priori molecules lacking essential requisites for the interaction with the enzyme and potentially unable to bind to resistant mutant PfDHFRs. The molecules in the resulting "focused" database were then evaluated with regard to their fit into the PfDHFR active site. Twelve new compounds whose structures are completely unrelated to known antifolates were identified and found to inhibit, at the micromolar level, the wild-type and resistant mutant PfDHFRs harboring A16V, S108T, A16V + S108T, C59R + S108N + I164L, and N51I + C59R + S108N + I164L mutations. Depending on the functional groups interacting with key active site residues of the enzyme, these inhibitors were classified as N-hydroxyamidine, hydrazine, urea, and thiourea derivatives. The structures of the complexes of the most active inhibitors, as refined by molecular mechanics and molecular dynamics, provided insight into how these inhibitors bind to the enzyme and suggested prospects for these novel derivatives as potential leads for antimalarial development.

Animals↗

PubMed2002

Binding of 1-benzopyran-4-one derivatives to aldose reductase: a free energy perturbation study.

The relative binding affinities to human aldose reductase (ALR2) of three new 7-hydroxy-2-benzyl-4H-1-benzopyran-4-one inhibitors were predicted by free energy perturbation (FEP) simulations. Molecular substitutions were specifically designed to investigate the role of hydrogen bonding at the active site of ALR2. Starting from the lead inhibitor 7-hydroxy-2-(4'-hydroxybenzyl)-4H-1-benzopyran-4-one, the 4'-hydroxyl was mutated to methyl and to trifluoromethyl, and an hydroxyl at position 8 was additionally introduced. Once synthesized and tested as inhibitors of ALR2, the compounds displayed variations of K(i) that were in qualitative to quantitative agreement with the calculated relative free energies of binding. The results, discussed in terms of balance between free energies of solvation and free energies of binding to ALR2, elucidate the importance of hydrogen bonding with Thr113 and with Trp111 and cofactor, and provide a rationale to the observed differences in binding affinities.

Aldehyde Reductase↗

PubMed2002

Discovery of new inhibitors of aldose reductase from molecular docking and database screening.

Aldose reductase (ALR2) is a target enzyme for the treatment of diabetic complications. Owing to the limited number of currently available drugs for the treatment of diabetic complications, the discovery of new inhibitors of ALR2 that can potentially be optimized as drugs appears highly desirable. In this study, a molecular docking analysis of the structures of more than 127,000 organic compounds contained in the National Cancer Institute database was performed to find and score molecules that are complementary to ALR2. Besides retrieving several carboxylic acid derivatives, which are known to generally inhibit aldose reductase, docking proposed other families of putative inhibitors such as sulfonic acids, nitro-derivatives, sulfonamides and carbonyl derivatives. Twenty-five compounds, chosen as the highest-scoring representatives of each of these families, were tested as aldose reductase inhibitors. Five of them were found to inhibit aldose reductase in the micromolar range. For these active compounds, selectivity with respect to the closely-related aldehyde reductase was determined by measuring the corresponding inhibitory activities. The structures of the complexes between the new lead inhibitors and aldose reductase, here refined with molecular mechanics and molecular dynamics calculations, suggest that new pharmacophoric groups can bind aldose reductase very efficiently. In the case of the family of the nitro-derivative inhibitors, a class of particularly interesting compounds, a round of optimizations was performed with the synthesis and biological evaluation of a series of derivatives aimed at testing the proposed binding mode and at improving interaction with active site residues. Starting from a hit compound having an IC(50) of 42 microM, the most potent compound synthesized showed a 10-fold increase in inhibitory activity and 10-fold selectivity with respect to ALR1, and structure--activity relationships of the designed compounds were in agreement with the proposed mode of binding at the active site.

Aldehyde Reductase↗

PubMed2002

Nitrophenyl derivatives as aldose reductase inhibitors.

Nitrophenyl derivatives were recently discovered as a new class of ALR2 inhibitors by means of docking and database screening of the National Cancer Institute database of organic molecules. The nitro group was predicted to bind to the Tyr48 and His110 active site residues of the enzyme, the site where acidic ALR2 inhibitors such as carboxylic acids bind in their anionic form. Given the novelty of these compounds, we decided to expand their structure-activity relationships by synthesizing and testing a series of derivatives and the corresponding compounds having a carboxylic group instead of the nitro moiety; the results obtained were rationalized by means of docking and molecular dynamics simulations. On the whole there is an agreement between inhibitory data and the results of molecular modeling experiments, supporting the hypothesized binding mode of these compounds.

Aldehyde Reductase↗