RESUMO

BACE1 is an aspartyl protease with a very relevant role in medicinal chemistry related to Alzheimer Disease since it has demonstrated to be a promising therapeutic target for inhibition and possible control for the progress of the peptide accumulation characteristic of this pathology. The enzymatic activity of this protein is given by the aspartic dyad, Asp93 and Asp289, which can adopt several protonation states depending on the chemical nature of its inhibitors, this is, monoprotonated, diprotonated and di-deprotonated states. In the present study, the analysis of the population density, for a series of protein-inhibitor molecular dynamics simulations, was carried out to identify the most feasible protonation state adopted by the catalytic dyad in the presence of tertiary carbinamine (TC) transition state analog inhibitors. The results revealed that the monoprotonated Asp289i state, in which the Asp93 and Asp289 residue side chains are deprotonated and protonated on the inner oxygen, respectively, is the most preferred in the presence of TC family inhibitors. This result was obtained after evaluating, for all 9 possible protonation state configurations, the individual and combined population densities of a set of parameters sensitive to protonation state of the Aspartic dyad, using an X-ray experimental BACE1/TC crystallographic structure as reference. This case study demonstrates again the usefulness of the concept of population density as a quantitative tool to establish the most stable system settings, among all possible, by measuring the level of occurrence of simultaneous events obtained from a sampling over time. These results will help to clear the phenomena related to the TCs inhibitory pathway, as well as assist in the design of better TC inhibitors against Alzheimer's protease.

Assuntos

RESUMO

BACE1 is an aspartyl protease which is a therapeutic target for Alzheimer's disease (AD) because of its participation in the rate-limiting step in the production of Aß-peptide, the accumulation of which produces senile plaques and, in turn, the neurodegenerative effects associated with AD. The active site of this protease is composed in part by two aspartic residues (Asp93 and Asp289). Additionally, the catalytic site has been found to be covered by an antiparallel hairpin loop called the flap. The dynamics of this flap are fundamental to the catalytic function of the enzyme. When BACE1 is inactive (Apo), the flap adopts an open conformation, allowing a substrate or inhibitor to access the active site. Subsequent interaction with the ligand induces flap closure and the stabilization of the macromolecular complex. Further, the protonation state of the aspartic dyad is affected by the chemical nature of the species entering the active site, so that appropriate selection of protonation states for the ligand and the catalytic residues will permit the elucidation of the inhibitory pathway for BACE1. In the present study, comparative analysis of different combinations of protonation states for the BACE1-hydroxyethylamine (HEA) system is reported. HEAs are potent inhibitors of BACE1 with favorable pharmacological and kinetic properties, as well as oral bioavailability. The results of Molecular Dynamics (MD) simulations and population density calculations using 8 different parameters demonstrate that the LnAsp289 configuration (HEA with a neutral amine and the Asp289 residue protonated) is the only one which permits the expected conformational change in BACE1, from apo to closed form, after flap closure. Additionally, differences in their capacities to establish and maintain interactions with residues such as Asp93, Gly95, Thr133, Asp289, Gly291, and Asn294 during this step allow differentiation among the inhibitory activities of the HEAs. The results and methodology here reported will serve to elucidate the inhibitory pathway of other families of compounds that act as BACE1 inhibitors, as well as the design of better leader compounds for the treatment of AD.

Assuntos

RESUMO

BACE1 is an aspartyl protease of pharmacological interest for its direct participation in Alzheimer's disease (AD) through ß-amyloid peptide production. Two aspartic acid residues are present in the BACE1 catalytic region which can adopt multiple protonation states depending on the chemical nature of its inhibitors, i.e., monoprotonated, diprotonated and di-deprotonated states. In the present study a series of protein-ligand molecular dynamics (MD) simulations was carried out to identify the most feasible protonation state adopted by the catalytic dyad in the presence of hydroxyethylamine transition state analogue inhibitors. The MD trajectories revealed that the di-deprotonated state is most prefered in the presence of hydroxyethilamine (HEA) family inhibitors. This appears as a result after evaluating, for all 9 protonation state configurations during the simulation time, the deviations of a set of distances and dihedral angles measured on the ligand, protein and protein-ligand complex with reference to an X-ray experimental BACE1/HEA crystallographic structure. These results will help to clarify the phenomena related to the HEAs inhibitory pathway, and improve HEAs databases' virtual screening and ligand design processes targeting ß-secretase protein.

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RESUMO

The identification of BACE-1, a key enzyme in the production of Amyloid-ß (Aß) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of Aß peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus dispersion energies.

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RESUMO

Se realizó un estudio tridimensional cuantitativo de relación-estructura con nuevos análogos de la sulfonanilida que actúan como supresores de la expresión y actividad de la aromatasa en células de cáncer de mama, independientemente de la inhibición de la ciclooxigenasa-2 (COX-2). La superposición molecular de los ligandos en la plantilla fue llevada a cabo por el método Database Alignment. El mejor modelo estuvo constituido por la combinación de los campos estérico e hidrofóbico, los cuales arrojaron los siguientes parámetros: q² = 0,613 con siete componentes, R² no validado igual a 0,976, valor de F igual a 81,695; 0,347 y 0,047 para los errores estándar de predicción y estimación, respectivamente. Las contribuciones estérica e hidrofóbica fueron de 50,5 y 49,5% respectivamente. Los datos generados por el presente estudio podrían impulsar el diseño de nuevos y más potentes reguladores selectivos de la expresión de la aromatasa.

A three-dimensional quantitative structure-activity relationship study was performed with new Sulfonanilide analogue molecules acting as aromatase expression and activity suppressors in breast cancer cells independent of COX-2 inhibition. The molecular supression of the ligands in the grid was carried out by the DATA-BASE ALIGNMENT method. The best model formed by combining the esteric fields and hydrophobic fields yielded the following parameters: q² = 0.613 with seven components, not validated R² equal to 0.976, with an F value of 81.695, 0.347 and 0.047 for the standard errors of prediction and estimate, respectively. The contribution of esteric and hydrophobic fields was 50.5 and 49.5% respectively. data generated from this study may be used to design new and more potent selective aromatase expression regulators.

Assuntos