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Ismael Zamora

Publications and source records attributed to Ismael Zamora.

17 recordsLinked to original sources
PubMed2006

Contribution of solid-state properties to the aqueous solubility of drugs.

This study investigates the influence of the solid-state properties melting point (T(m)), enthalpy of melting (DeltaH(m)) and entropy of melting (DeltaS(m)) of a drug on its intrinsic solubility (S(0)). For this purpose, 26 chemically and structurally diverse drugs covering the oral drug space were selected and the S(0), T(m), DeltaH(m) and DeltaS(m) were determined experimentally. The influence of T(m), DeltaH(m) and DeltaS(m) on S(0) was studied using regression analysis. The overall improvement of the predictions were 0.3 log units, however, five compounds (astemizole, glyburide, fenbufen, gliclazide and griseofulvin) were improved by more than one log unit. T(m) and DeltaH(m) had a larger effect than DeltaS(m) on the solubility predictions. The well-known general solubility equation (GSE) and the Dannenfelser semi-empirical equation for the calculation of DeltaS(m) were evaluated using our data set. While predictions of drug solubility obtained using the GSE were acceptable, the use of the experimental DeltaS(m) values instead of the constant 56.5 J mol(-1)K(-1) improved the accuracy of the prediction. The Dannenfelser equation underestimated the DeltaS(m) for most compounds with on average 15 J mol(-1)K(-1). Our results show that solid-state properties should be considered for improved performance of future models for prediction of drug solubility. In addition our study provides accurate experimental data on intrinsic solubility for 26 compounds, supplying a useful external data set for validation of drug solubility models.

Entropy↗
PubMed2006

Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions.

Predictions of the metabolic sites for new chemical entities, synthesized or only virtual, are important in the early phase of drug discovery to guide chemistry efforts in the synthesis of new compounds with reduced metabolic liability. This information can now be obtained from in silico predictions, and therefore, a thorough and unbiased evaluation of the computational techniques available is needed. Several computational methods to predict the metabolic hot spots are emerging. In this study, metabolite identification using MetaSite and a docking methodology, GLUE, were compared. Moreover, the published CYP3A4 crystal structure and computed CYP3A4 homology models were compared for their usefulness in predicting metabolic sites. A total of 227 known CYP3A4 substrates reported to have one or more metabolites adding up to 325 metabolic pathways were analyzed. Distance-based fingerprints and four-point pharmacophore derived from GRID molecular interaction fields were used to characterize the substrate and protein in MetaSite and the docking methodology, respectively. The CYP3A4 crystal structure and homology model with the reactivity factor enabled achieved a similar prediction success (78%) using the MetaSite method. The docking method had a relatively lower prediction success (approximately 57% for the homology model), although it still may provide useful insights for interactions between ligand and protein, especially for uncommon reactions. The MetaSite methodology is automated, rapid, and has relatively accurate predictions compared with the docking methodology used in this study.

Binding Sites↗
PubMed2006

Impact of extracellular protein binding on passive and active drug transport across Caco-2 cells.

AIM: The objective of the study is to evaluate the mechanism behind alterations in passive and active transport of drugs in the presence of basolaterally applied extracellular protein using the Caco-2 cell model. METHODS: The permeation across Caco-2 monolayers of two groups of compounds, transported either solely by passive diffusion or partly also by active transport in the secretory direction, was studied at two donor concentrations in the absence or presence of bovine serum albumin (BSA, 0-4%). Each group contained compounds with high or low protein binding (PB) capabilities and high or low absorption in humans (fraction absorbed, f(a)). The unbound fraction (f(u)) of each compound was determined by ultrafiltration. RESULTS: The transport rate of the passively permeating compounds was the same in both apical-to-basolateral (absorptive) and basolateral-to-apical (secretory) directions in the absence of BSA. Basolaterally applied BSA increased the transport rate in the absorptive direction and decreased it in the secretory direction for all compounds, in direct proportion to the extent of PB. The efflux ratios for the actively transported compounds were reduced in the presence of BSA. CONCLUSIONS: Basolaterally applied BSA, which mimics in vivo PB, alters both passive and active drug transport in the Caco-2 cell model. Using C(u) in the calculations of transport rate allowed elucidation of the different mechanisms behind these alterations. Our data also suggest that active secretory transport for highly protein-bound compounds might have less effect in vivo than predicted from traditional Caco-2 cell models (without BSA).

Algorithms↗
PubMed2005

Anchor-GRIND: filling the gap between standard 3D QSAR and the GRid-INdependent descriptors.

The aim of this work is to present the anchor-GRIND methodology. Anchor-GRIND efficiently combines a priori chemical and biological knowledge about the studied compounds with alignment-independent molecular descriptors derived from molecular interaction fields. Such descriptors are particularly useful for series of ligands sharing a common scaffold but with very diverse substituents. The method uses a specific position of the molecular structure (the "anchor point") to compare the spatial distribution of the molecular interaction fields of the substituents. The descriptors produced are more detailed and specific than the original GRIND while still avoiding the bias introduced by the alignment. Three data sets have been studied to demonstrate the usefulness of the anchor-GRIND methodology for 3D-QSAR modeling. The two first data sets respectively include congeneric series of the hepatitis C virus NS3 protease and of the acetylcholinesterase inhibitors. The third data set discriminates between factor Xa inhibitors of high and low affinity. In all the series presented, the models obtained with the anchor-GRIND are statistically sound and easy to interpret.

Acetylcholinesterase↗
PubMed2005

pH-Dependent passive and active transport of acidic drugs across Caco-2 cell monolayers.

The aim of this study was to investigate pH-dependent passive and active transport of acidic drugs across Caco-2 cells. Therefore, the bidirectional pH-dependent transport of two acidic drugs, indomethacin and salicylic acid, across Caco-2 cells was studied in the physiological pH range of the gastrointestinal tract. The transport of both drugs decreased with increased pH, as expected from the pH-partition hypothesis. Net absorption occurred when the basolateral pH exceeded the apical pH. Concentration dependence and transporter inhibition studies indicated passive transport for indomethacin and a mixture of pH-dependent passive and active influx for salicylic acid. Unexpectedly, active and passive drug transport results were indistinguishable in temperature dependency studies. The transport of salicylic acid (apical pH 5.0; basolateral pH 7.4) was partly blocked by inhibitors of the proton-dependent transporters MCT1 (SLC16A1) and OATP-B (SLC21A9, SLCO2B1). This study shows that the asymmetry in bidirectional transport of acidic drugs is affected by both passive and active components in the presence of pH gradients across Caco-2 cells. Thus, combined studies of concentration-dependency and transport-inhibition are preferred when acidic drug transport is studied in a pH gradient. The findings of this in vitro study can be extrapolated to in vivo situations involving an acidic microclimate.

Biological Transport, Active↗
PubMed2004

Conformer- and alignment-independent model for predicting structurally diverse competitive CYP2C9 inhibitors.

A conformer- and alignment-independent three-dimensional structure-activity relationship (3D-QSAR) model has been derived that is based on flexible molecular interaction fields calculated in GRID and the subsequent description of these fields by use of alignment-independent descriptors derived in ALMOND. The training set consisted of 22 diverse and flexible competitive inhibitors of the drug-metabolizing enzyme CYP2C9 and generated a model with r(2) of 0.81 and q(2) of 0.62. The predicitive capacity of the model was externally evaluated with a test set of 12 competitive inhibitors and 11 out of 12 were predicted within 0.5 log unit. The most relevant points of interaction in the model correlated well to the amino acids involved in CYP2C9-substrate/inhibitor binding in the active site of a CYP2C9 homology model, further validating the mechanistic sense of our model. This approach offers the possibility to derive predicitve 3D-QSAR models without the need for an alignment rule for chemically diverse ligands and in the absence of target protein crystal structure information.

Amino Acids↗
PubMed2004

Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates.

A number of computational approaches are being proposed for an early optimization of ADME (absorption, distribution, metabolism and excretion) properties to increase the success rate in drug discovery. The present study describes the development of an in silico model able to estimate, from the three-dimensional structure of a molecule, the stability of a compound with respect to the human cytochrome P450 (CYP) 3A4 enzyme activity. Stability data were obtained by measuring the amount of unchanged compound remaining after a standardized incubation with human cDNA-expressed CYP3A4. The computational method transforms the three-dimensional molecular interaction fields (MIFs) generated from the molecular structure into descriptors (VolSurf and Almond procedures). The descriptors were correlated to the experimental metabolic stability classes by a partial least squares discriminant procedure. The model was trained using a set of 1800 compounds from the Pharmacia collection and was validated using two test sets: the first one including 825 compounds from the Pharmacia collection and the second one consisting of 20 known drugs. This model correctly predicted 75% of the first and 85% of the second test set and showed a precision above 86% to correctly select metabolically stable compounds. The model appears a valuable tool in the design of virtual libraries to bias the selection toward more stable compounds.

Cytochrome P-450 CYP3A↗
PubMed2004

Structural analysis of CYP2C9 and CYP2C5 and an evaluation of commonly used molecular modeling techniques.

This work had two separate aims: to evaluate different modeling techniques and to make a detailed structural characterization of CYP2C9. To achieve these goals, the consensus principal component analysis (CPCA) technique and distance measurements were used to explore available crystal structures, newly built homology models, and repeated molecular dynamics simulations. The CPCA was based on molecular interaction fields focused on the active site regions of the proteins and include detailed amino acid analysis. The comparison of the CYP2C9 and CYP2C5 crystal structures revealed differences in the flexible regions such as the B-C and F-G loop and the N and C termini. Cross homology models of CYP2C9 and CYP2C5, using their respective crystal structures as templates, indicated that such models were more similar to their templates than to their target proteins. Inclusion of multiple templates slightly improved the similarity to the crystal target in some cases and could be recommended even though it requires a careful manual alignment process. The application of molecular dynamics simulations to highly flexible proteins such as cytochromes P450 is also explored and the information is extracted by the CPCA. Advantages and drawbacks are presented for the different modeling techniques. Despite the varying modeling success, the models give insight and understanding by the mutual forming and discarding of hypotheses. This is a dynamic process since the crystal structures are improving with time and, therefore, the answers to the models are also changing accordingly.

Aryl Hydrocarbon Hydroxylases↗
PubMed2003

Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P450 2C9.

The aim of the present study is to develop a method for predicting the site at which molecules will be metabolized by CYP 2C9 (cytochrome P450 2C9) using a previously reported protein homology model of the enzyme. Such a method would be of great help in designing new compounds with a better pharmacokinetic profile, or in designing prodrugs where the compound needs to be metabolized in order to become active. The methodology is based on a comparison between alignment-independent descriptors derived from GRID Molecular Interaction Fields for the CYP 2C9 active site, and a distance-based representation of the substrate. The predicted site of metabolism is reported as a ranking list of all the hydrogen atoms of each substrate molecule. Eighty-seven CYP 2C9-catalyzed oxidative reactions reported in the literature have been analyzed. In more than 90% of these cases, the hydrogen atom ranked at the first, second, or third position was the experimentally reported site of oxidation.

Animals↗
PubMed2003

Surface descriptors for protein-ligand affinity prediction.

Molecular descriptors calculated by the VolSurf program have been extensively used to model pharmacokinetic properties, e.g., passive permeability through the gastrointestinal tract or through the blood-brain barrier. These descriptors quantify steric, hydrophobic, and hydrogen bond interactions between model compounds and different environments. Since these interactions are the same as those involved in the ligand-receptor binding, VolSurf descriptors could potentially be relevant in modeling this process as well. We obtained a significant model (r(2) = 0.85, q(2) = 0.75) using VolSurf descriptors derived from the ligand, the protein, and the ligand-protein complex for a diverse set of 38 structures previously used in the VALIDATE (ref 23) training set. Furthermore, a statistically significant model (r(2) = 0.94, q(2) = 0.89) was obtained using the same type of descriptors for a homogeneous set of glycogen phosphorylase inhibitors (ref 25). Using the VolSurf computational framework, both ligand-receptor binding and the ligand's pharmacokinetic behavior can be modeled simultaneously during the preclinical aspects of drug discovery.

Ligands↗
PubMed2003

pH-dependent bidirectional transport of weakly basic drugs across Caco-2 monolayers: implications for drug-drug interactions.

PURPOSE: The purpose of this study was to investigate the pH-dependent passive and active transport of weakly basic drugs across the human intestinal epithelium. METHODS: The bidirectional pH-dependent transport of weak bases was studied in Caco-2 cell monolayers in the physiologic pH range of the gastrointestinal tract. RESULTS: A net secretion of atenolol and metoprolol was observed when a pH gradient was applied. However, the bidirectional transport of both compounds was equal in the nongradient system. Hence, at lower apical than basolateral pH a change in passive transport caused by an imbalance in the concentration of the uncharged drug species resulted in a "false" asymmetry (efflux ratio). Furthermore, a mixture of pH-dependent passive and active efflux was found for the P-glycoprotein (P-gp, MDR1, ABCB1) substrates, talinolol and quinidine, but not for the neutral drug, digoxin. However, the clinically important digoxin-quinidine interaction depended on the presence of a pH gradient. Hence, the degree of interaction depends on the amount of quinidine available at the binding site of the P-gp. CONCLUSIONS: Active efflux of weak bases can only be accounted for when the fraction of unionized drug species is equal in all compartments because the transport is biased by a pH-dependent passive component. However, this component may take part in vivo and contribute to drug-drug interactions involving P-gp.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2002

Discriminant and quantitative PLS analysis of competitive CYP2C9 inhibitors versus non-inhibitors using alignment independent GRIND descriptors.

This study describes the use of alignment-independent descriptors for obtaining qualitative and quantitative predictions of the competitive inhibition of CYP2C9 on a serie of highly structurally diverse compounds. This was accomplished by calculating alignment independent descriptors in ALMOND. These GRid INdependent Descriptors (GRIND) represent the most important GRID-interactions as a function of the distance instead of the actual position of each grid-point. The experimental data was determined under uniform conditions. The inhibitor data set consists of 35 structurally diverse competitive stereospecific inhibitors of the cytochrome P450 2C9 and the non -inhibitor data set of 46 compounds. In a PLS discriminant analysis 21 inhibitors and 21 non-inhibitors (1 and 0 as activities) were analyzed using the ALMOND program obtaining a model with an r2 of 0.74 and a cross-validation value (q2) of 0.64. The model was externally validated with 39 compounds (14 inhibitors/25 non-inhibitors). 74% of the compounds were correctly predicted and an additional 13% was assigned to a borderline cluster. Thereafter, a model for quantitative predictions was generated by a PLS analysis of the GRIND descriptors using the experimental Ki-value for 21 of the competitive inhibitors (r2 = 0.77, q2 = 0.60). The model was externally validated using 12 compounds and predicted 11 out of 12 of the Ki-values within 0.5 log units. The discriminant model will be useful in screening for CYP2C9 inhibitors from large compound collections. The 3D-QSAR model will be used during lead optimization to avoid chemistry that result in inhibition of CYP2C9.

Aryl Hydrocarbon Hydroxylases↗
PubMedDate not supplied

Pharmacokinetically based mapping device for chemical space navigation.

ChemGPS, the chemical global positioning system, is a tool that combines rules (equivalent to dimensions) and objects (chemical structures) to provide a consistent chemical space map (Oprea, T. I.; Gottfries, J. J. Comb. Chem. 2001, 3, 157-166.). Rules included, initially, general properties such as size, lipophilicity, and hydrogen bond capacity, while objects include "satellites", intentionally placed outside the druglike space, as well as "core" objects, mostly orally available drugs. ChemGPS molecules (objects) were used in conjunction with the VolSurf (http://www.moldiscovery.com) descriptors (rules), which are relevant for ADME (absorption, distribution, metabolism, and excretion) properties. The combination of ChemGPS and VolSurf, GPSVS, was investigated with respect to the biopharmaceutics classification system, which is recommended by the Food and Drug Administration (FDA) (http://www.fda.gov/cder/OPS/BCS_guidance.htm), in particular with respect to permeability and solubility. The first GPSVS principal component correlates, with no further training, to passive transcellular permeability, as illustrated for the Caco-2, ghost erythrocyte, and blood-brain barrier datasets, respectively. The second GPSVS principal component correlates, without prior training, to solubility, as shown for the octanol-water partition and intrinsic solubility datasets, respectively. Although derived from principal component analysis, the two property axes rotate and form an angle of approximately 43 degrees, thus being no longer orthogonal. GPSVS can be used to map the chemical space with respect to permeability and solubility, as recommended by FDA's biopharmaceutics classification system.

Journal Article↗
PubMedDate not supplied

Virtual screening and scaffold hopping based on GRID molecular interaction fields.

In this study, a set of strategies for structure-based design using GRID molecular interaction fields (MIFs) to derive a pharmacophoric representation of a protein is reported. Thrombin, one of the key enzymes involved in the blood coagulation cascade, was chosen as the model system since abundant published experimental data are available related to both crystal structures and structurally diverse sets of inhibitors. First, a virtual screening methodology was developed either using a pharmacophore representation of the protein based on GRID MIFs or using GRID MIFs from the 3D structure of a set of chosen thrombin inhibitors. The search was done in a 3D multiconformation version of the Available Chemical Directory (ACD) database, which had been spiked with 262 known thrombin inhibitors (multiple conformers available per compound). The model managed to find 80% of the known thrombin inhibitors among the 74,291 conformers in the ACD by only searching 5% of the database; hence, a 15-fold enrichment of the library was achieved. Second, a scaffold hopping methodology was developed using GRID MIFs, giving the scaffold interaction pattern and the shape of the scaffold, together with the distance between the anchor points. The scaffolds reported by Dolle in the Journal of Combinatorial Chemistry summaries (2000 and 2001) and scaffolds built or derived from ligands cocomplexed with the thrombin enzyme were parameterized using a new set of descriptors and saved into a searchable database. The scaffold representation from the database was then compared to a template scaffold (from a thrombin crystal structure), and the thrombin-derived scaffolds included in the database were found among the top solutions. To validate the usefulness of the methodology to replace the template scaffold, the entire molecule was built (scaffold and side chains) and the resulting compounds were docked into the active site of thrombin. The docking solutions showed the same binding pattern as the cocomplexed compound, hence, showing that this method can be a valuable tool for medicinal chemists to select interchangeable core structures (scaffolds) in an easy manner and retaining the binding properties from the original ligand.

Binding Sites↗