1H, 13C NMR, X-ray and conformational studies of new 1-alkyl-3-benzoyl-pyrazole and 1-alkyl-3-benzoyl-pyrazoline derivatives.

The (1)H and (13)C NMR resonances of 22 1-alkyl-pyrazole and 25 1-alkyl-pyrazoline derivatives were assigned completely using the concerted application of one- and two-dimensional experiments (DEPT, gs-HMQC and gs-HMBC). Nuclear Overhauser enhancement (NOE) effects, conformational analysis and X-ray crystallography confirm the preferred conformation of those compounds.

Back door modulation of the farnesoid X receptor: design, synthesis, and biological evaluation of a series of side chain modified chenodeoxycholic acid derivatives.

Carbamate derivatives of bile acids were synthesized with the aim of systematically exploring the potential for farnesoid X receptor (FXR) modulation endowed with occupancy of the receptor's back door, localized between loops H1-H2 and H4-H5. Since it was previously shown that bile acids bind to FXR by projecting the carboxylic tail opposite the transactivation function 2 (AF-2, helix 12), functionalization of the side chain is not expected to interfere directly with the orientation of H12 but can result in a more indirect way of receptor modulation. The newly synthesized compounds were extensively characterized for their ability to modulate FXR function in a variety of assays, including the cell-free fluorescence resonance energy transfer (FRET) assay and the cell-based luciferase transactivation assay, and displayed a broad range of activity from full agonism to partial antagonism. Docking studies clearly indicate that the side chain of the new derivatives fits in a so far unexploited receptor cavity localized near the "back door" of FXR. We thus demonstrate the possibility of achieving a broad FXR modulation without directly affecting the H12 orientation.

Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding.

The dynamic changes which take place in the ligand binding domain (LBD) of farneosid X receptor (FXR) in response to agonist binding and in the presence of coactivator peptides were studied with nanosecond time-scale molecular dynamics. Four different systems were analyzed, including the holo-LBD complexed with 6ECDCA, the holo-LBD in the presence of two coactivator peptides, and two artificial apo forms, with and without coactivator peptides. Our results revealed a detailed picture of the differential micro- and macromodifications occurring in the LBD in the presence or not of the agonist molecule and the coactivator peptides. In the apo simulation a major conformational change took place in the crucial helix 12, while the holo-LBD was globally stabilized by the ligand. When the coactivator peptides were included in the simulation, a clear agonist-induced stabilization was observed for the canonical peptide. Interestingly, the second peptide was released from the holo-LBD while it was kept bound in the apo simulation. The present results provide a molecular basis for the understanding the role played by the bile acid agonist in receptor stabilization and enhanced cofactor recruitments.

New more polar symmetrical bipyridinic compounds: new strategy for the inhibition of choline kinase α1.

AIM: Research of the antitumor properties of biscationic compounds has received significant attention over the last few years. RESULTS: A novel family of 1,1'-([2,2'-bipyridine]-5,5'-diylbis(methylene))bis-substituted bromide (9a-k), containing two nitrogen atoms in the linker, considered as hypothetical hydrogen bond acceptors, were synthesized and evaluated as ChoK inhibitors and their antiproliferative activity against six cancer cell lines. CONCLUSION: The most promising compounds in this series are 1,1'-([2,2'-bipyridine]-5,5'-diylbis(methylene))bis(4-(methyl(phenyl)amino)-quinolinium bromide derivatives 9g-i (analogs to RSM932A), that significantly inhibit cancer cell growth at even submicromolar concentrations, especially against leukemia cells. Compounds 9g-i also inhibit the ChoKα1 with good or moderate values, as predicted by initial docking studies. In addition, the most active compound 9h remarkably induces apoptosis in two cell lines following the mitochondrial pathway.

Unbinding pathways from the glucocorticoid receptor shed light on the reduced sensitivity of glucocorticoid ligands to a naturally occurring, clinically relevant mutant receptor.

Glucocorticoids are endogenous steroid hormones that regulate essential biological functions, including metabolism, growth, and apoptosis. Glucocorticoids represent the most effective anti-inflammatory agents for the treatment of several inflammatory conditions. However, the clinical use of such drugs is hampered by severe side effects. Therefore, the development of novel glucocorticoid receptor (GR) modulators with an increased therapeutic index is impelling. Herein, using steered molecular dynamics (SMD) simulations, we provide a detailed picture of the unbinding process of three clinically relevant GR modulators from GR ligand binding domains. The SMD protocol described here can be used to prioritize the synthesis of structural analogues on the basis of their potentials of mean force and calculated unbinding energies. Moreover, our results are instrumental in explaining at atomic resolution the weakened ability of dexamethasone to activate the naturally occurring mutant I747M GR, which is implicated in rare familial glucocorticoid resistance, clinically characterized by glucocorticoid insensitivity.

Binding mode of 6ECDCA, a potent bile acid agonist of the farnesoid X receptor (FXR).

Based on the folding conservation across the nuclear receptor superfamily and the sequence homology with RAR-gamma, we report the construction of a three dimensional model of the ligand binding domain of FXR. The model is exploited for the elucidation of the binding mode of 6alpha-ethyl-chenodeoxycholic acid. The results of the docking experiments give quite clear indications that the bile acid derivative would bind the receptor in a mode significantly different than that observed for agonists of other nuclear receptor superfamily.