Homology modeling of the estrogen receptor subtype beta (ER-beta) and calculation of ligand binding affinities.

Estrogen is a steroid hormone playing critical roles in physiological processes such as sexual differentiation and development, female and male reproductive processes, and bone health. Numerous natural and synthetic environmental compounds have been shown capable of estrogenic effects. This area has been the focus of significant fundamental and applied research due both to the potential detrimental effects of these compounds upon normal physiological processes and to the potential beneficial effects of tissue-selective estrogen agonists/antagonists for the prevention and treatment of numerous diseases. Genomic effects of the active form of estrogen, 17beta-estradiol, are mediated through at least two members of the steroid hormone receptor superfamily, estrogen receptor subtype alpha (ER-alpha) and estrogen receptor subtype beta (ER-beta). At the time of this work, the X-ray crystal structure of the ER-alpha had been elucidated, however, coordinates of the ER-beta were not publicly available. Based upon the significant structural conservation across members of the steroid hormone receptor family, and the high sequence homology between ER-alpha and ER-beta (>60%), we have developed a homology model of the ER-beta structure. Using the crystal structure of ER-alpha and the homology model of ER-beta, we demonstrate a strong correlation between computed values of the binding-energy and published values of the observed relative binding affinity (RBA) for a variety of compounds for both receptors, as well as the ability to identify receptor subtype selective compounds. Furthermore, using the recently available crystal structure of ER-beta for comparison purposes, we show that not only is the predicted homology model structurally accurate, but that it can be used to assess ligand binding affinities.

Computational studies on HIV-1 protease inhibitors: influence of calculated inhibitor-enzyme binding affinities on the statistical quality of 3D-QSAR CoMFA models.

A theoretical study was performed on a set of 38 human immunodeficiency type 1 (HIV-1) protease inhibitors that are structurally similar to the AIDS drug Indinavir. Comparison between the computed binding energies and experimental activity data (pIC(50)) found a high degree of correlation (r(2)() = 0.82). Three-dimensional quantitative structure-activity relationship (3D-QSAR) models using comparative molecular field analysis (CoMFA) yielded predicted activities that were in excellent agreement with the corresponding experimentally determined values. Inclusion of the calculated enzyme-inhibitor binding energy as an additional descriptor in the CoMFA model yielded a significant improvement in the internal predictive ability of our model (q(2)() = 0.45 to q(2)() = 0.69). Separate CoMFA models were constructed to evaluate the influence of different alignment schemes (Atom Fit and Field Fit) and different partial atomic charge assignment schemes (Discover CVFF, Gasteiger-Marsili, and AM1-ESP) on the statistical quality of the models.

Aspartic protease inhibitors. An integrated approach for the design andsynthesis of diaminodiol-based peptidomimetics.

Aspartic proteases play key roles in a variety of pathologies, including acquired immunodeficiency syndrome. Peptidomimetic inhibitors can act as drugs to combat these pathologies. We have developed an integrated methodology for preparing human immunodeficiency virus (HIV)-1 aspartic protease diaminodiol inhibitors, based on a computational method that predicts the potential inhibitory activity of the designed structures in terms of calculated enzyme-inhibitor complexation energies. This is combined with a versatile synthetic strategy that couples a high degree of stereochemical control in the central diaminodiol module with complete flexibility in the choice of side chains in the core and in flanking residues. A series of 23 tetrameric, pentameric and hexameric inhibitors, with a wide range of calculated relative complexation energies (-47.2 to +117 kJ.mol-1) and predicted hydrophobicities (logPo/w = 1.8-8.4) was thus assembled from readily available amino acids and carboxylic acids. The IC50 values for these compounds ranged from 3.2 nM to 90 microM, allowing study of correlations between structure and activity, and individuation of factors other than calculated complexation energies that determine the inhibition potency. Multivariable regression analysis revealed the importance of side-chain bulkiness and rigidity at the P2, P2' positions, suggesting possible improvements for the prediction process used to select candidate structures.

A computational study of the resistance of HIV-1 aspartic protease to the inhibitors ABT-538 and VX-478 and design of new analogues.

Recent experimental findings with HIV-1 protease (HIV-1 PR) mutants containing variations at four residues, M46I, L63P, V82T and I84V, have shown that only mutants containing the latter two exhibit cross resistance to the inhibitors ABT-538 and VX-478. The V82T and I84V modifications in fact concern residues in the active site while the other two are in the flap (M46I) and hinge (L63P) domains of the enzyme. We have modelled the M46I/L63P, V82T/I84V and M46I/L63P/ V82T/I84V (4X) mutants of HIV-PR and computed their complexation energies with these two inhibitors. A good correlation was found between these complexation energies and the trend in published inhibition constants for these inhibitors. Reasons for the decrease in binding affinities with the two critical mutants (V82T/I84V and 4X) have also been elucidated in detail. Based on these findings, we have designed several analogues of ABT-538 and VX-478, some of which show a better calculated binding affinity towards both mutant and wild type PR.

Study of structure-activity relationships for neurotransmitters using molecular electric field mapping: histamine and some of its H2-receptor agonists.

Molecular electric field mapping has been carried out to study structure-activity relationships for neutral and cationic forms of histamine and some of its agonists which are thiazole derivatives. Optimised geometries and Mulliken charges at the atomic sites were obtained using the PM3 method. Electric field values near the N3-H bond in histamine and those near substituents at the C2 position in the agonists have been found to correlate reasonably well with observed activities. Electric fields near the sulphur atom in thiazoles indicate that involvement of this site in hydrogen bonding with the H2-receptor is unlikely.