Molecular dynamics reveal binding mode of glutathionylspermidine by trypanothione synthetase.

The trypanothione synthetase (TryS) catalyses the two-step biosynthesis of trypanothione from spermidine and glutathione and is an attractive new drug target for the development of trypanocidal and antileishmanial drugs, especially since the structural information of TryS from Leishmania major has become available. Unfortunately, the TryS structure was solved without any of the substrates and lacks loop regions that are mechanistically important. This contribution describes docking and molecular dynamics simulations that led to further insights into trypanothione biosynthesis and, in particular, explains the binding modes of substrates for the second catalytic step. The structural model essentially confirm previously proposed binding sites for glutathione, ATP and two Mg(2+) ions, which appear identical for both catalytic steps. The analysis of an unsolved loop region near the proposed spermidine binding site revealed a new pocket that was demonstrated to bind glutathionylspermidine in an inverted orientation. For the second step of trypanothione synthesis glutathionylspermidine is bound in a way that preferentially allows N(1)-glutathionylation of N(8)-glutathionylspermidine, classifying N(8)-glutathionylspermidine as the favoured substrate. By inhibitor docking, the binding site for N(8)-glutathionylspermidine was characterised as druggable.

Induced fit simulations on nuclear receptors.

The large superfamily of nuclear receptors is a family of ligand-activated transcription factors involved in numerous fundamental processes and shows many common characteristics and behaviors. The comprehension of these roles is of fundamental importance to select the right target for receptor structure-based screening. Recently, during the last ten years, several crystallographic structures of nuclear receptors complexed with ligands have been registered in the Protein Data Bank, supplying a structural basis for computational simulations. The macroscopic flexibility of helix12 and local flexibility of some amino acids sidechains within cavities of the Ligand Binding Domain suggest a reason for the behavior of these receptors toward different ligands. Several approaches have been applied in trying to explain this flexibility and to predict how ligand binding can influence complex conformations. In this short review, we present an introduction to the structure and function of nuclear receptors, specifically the estrogen, androgen, glucorticoid, peroxisome proliferator, steroid, thyroid and vitamin D receptors, and a discussion of the state-of-the-art of induced fit approaches for the nuclear receptor family.

Theoretical prediction of hydrogen bond strength for use in molecular modeling.

Hybrid density functional theory calculations are used to investigate the strength of hydrogen bonds of structurally different molecules in complex with a standard donor and acceptor in vacuo. B3LYP/aug-cc-pVDZ calculations with one angle constraint lead to excellent correlations with experimental data (R(2) = 0.94, s(y) = 0.45 for acceptors and R(2) = 0.77, s(y) = 0.88 for donors). Substitutions of aromatic systems by electron donating and -withdrawing groups show a reinforcement of the interaction when substituting an acceptor with electron donating groups and weakening by substitution with electron withdrawing groups. For donor systems the opposite effect can be observed. Drug design of novel ligands will be able to profit from the predictive power of the method established, as hydrogen bonds between receptor and drug molecules are an important criterion for binding affinities.