Molecular dynamics analysis of the interaction between the human BCL6 BTB domain and its SMRT, NcoR and BCOR corepressors: the quest for a consensus dynamic pharmacophore.

Targeting the BCL6 protein is a promising therapeutic strategy for the treatment of B cell lymphomas. One approach to treat these diseases consists of finding drug candidates able to disrupt the interactions established between BCL6 and its corepressors. Thus, this work presents a thorough comparative analysis of the interactions between the BCL6 BTB (bric-a-brac tramtrack broad complex) protein domain and its SMRT, NcoR and BCOR corepressor BBDs (BCL6 binding domain) through molecular dynamics. Moreover, a theoretical structure is presented and checked for the BCL6(BTB)-NcoR(BBD) complex. Considering the BBDs to be composed of 17 amino acids, our analyses show the region involving residues 4-15 of these 17 to play a main role in the protein-corepressor interactions. Particularly SER(11) seems to have a high relevance as it establishes specific bonds with BCL6(BTB) and is one of the only two residues sequence equivalent for the three studied corepressors. From this study, 14 pharmacophoric points have been proposed divided in two groups which coincide with residues 4-11 and 11-15, being SER(11) a hinge point. This finding suggests the possibility of searching for 2 small molecule inhibitors, mimicking 8 and 7 pharmacophoric points, respectively, which could incorporate a hydrogen donor pharmacophoric point mimicking SER(11) in any or both molecules. In short, the present work aims to contribute further knowledge in the modeling of drugs mimicking BCL6(BTB)-corepressor complexes.

The role of disorder on the electronic structure of conjugated polymers. The case of poly-2,5-bis(phenylethynyl)-1,3,4-thiadiazole.

Insight into the electronic structure of disordered poly-2,5-bis(phenylethynyl)-1,3,4-thiadiazole in an amorphous region, in comparison to an ideal two-planar cofacial oligomer system, is pursued. The atomic structure of the amorphous polymer was obtained from classical molecular dynamics. It was subsequently used to calculate the electronic states and inter- and intrachain electronic coupling integrals using the density functional theory based charge patching method. The interchain electronic coupling integrals in the amorphous system were found to be an order of magnitude smaller than in the ordered system with similar distances between the chains. The results also suggest that the electronic structure of the whole system cannot be understood as a collection of the electronic structures of individual chains. The band gap of the whole system is significantly smaller than the band gaps of individual chains. This decrease originates from the disordered long range electrostatic potential created by the dipole moments of polymer repeat units, which should be minimized if one seeks good transport properties.

Recognition and discrimination of DNA quadruplexes by acridine-peptide conjugates.

We have explored a series of trisubstituted acridine-peptide conjugates for their ability to recognize and discriminate between DNA quadruplexes derived from the human telomere, and the c-kit and N-ras proto-oncogenes. Quadruplex affinity was measured as the peptide sequences were varied, together with their substitution position on the acridine, and the identity of the C-terminus (acid or amide). Surface plasmon resonance measurements revealed that all compounds bound to the human telomeric quadruplex with sub-micromolar affinity. Docking calculations from molecular modelling studies were used to model the effects of substituent orientation and peptide sequence. Modelling and experiment were in agreement that placement of the peptide over the face of the acridine is detrimental to binding affinity. The highest degrees of selectivity were observed towards the N-ras quadruplex by compounds capable of forming simultaneous contacts with their acridine and peptide moieties. The ligands that bound best displayed quadruplex affinities in the 1-5 nM range and at least 10-fold discrimination between the quadruplexes studied.