In this work, Halogen Bond (X‐bond) interactions formed by halogenated ligands (LX) at the Dopamine Receptor D2 (DRD2) binding pocket were studied by Molecular Dynamics (MD) and charge density analysis. The X‐bonds were contrasted with the Hydrogen Bond (H‐bond) interactions established by hydroxylated analogs (LOH, where X was replaced by OH). The ligands for this study were extracted from a dataset of compounds deposited in ZINC database that were active in binding assays to DRD2. This dataset was subjected to the filtering rules by employing cheminformatics tools to find the LX/LOH pairs that were then submitted to MD simulations. A homology model of DRD2 was employed for the simulations because no crystal structure is yet available for the receptor. To mimic the positive cap (σ‐hole) on the halogen atom, a massless, positive charged extra‐point was introduced in the force field. An analysis of the charge density (QTAIM) was performed on reduced models of simulated complexes to explain their binding differences. Results show that the halogen atom tends to form X‐bond with protein backbone oxygen atom. Two out of the four halogenated ligands studied form a specific X‐bond with the carbonyl oxygen of Ser193. This specific X‐bond decreases the inherent propensity of transmembrane 5 to unfolding. These results suggest a possible role of the X‐bond as a protein secondary structure modulator because of the ability of the halogen to interact with the protein backbone. Copyright © 2016 John Wiley & Sons, Ltd.

Trypanosoma cruzi, a flagellate protozoan parasite, is responsible for Chagas disease. The parasite major cysteine protease, cruzain (Cz), plays a vital role at every stage of its life cycle and the active-site region of the enzyme, similar to those of other members of the papain superfamily, is well characterized. Taking advantage of structural information available in public databases about Cz bound to known covalent inhibitors, along with their corresponding activity annotations, in this work, we performed a deep analysis of the molecular interactions at the Cz binding cleft, in order to investigate the enzyme inhibition mechanism. Our toolbox for performing this study consisted of the charge density topological analysis of the complexes to extract the molecular interactions and machine learning classification models to relate the interactions with biological activity. More precisely, such a combination was useful for the classification of molecular interactions as “active-like” or “inactive-like” according to whether they are prevalent in the most active or less active complexes, respectively. Further analysis of interactions with the help of unsupervised learning tools also allowed the understanding of how these interactions come into play together to trigger the enzyme into a particular conformational state. Most active inhibitors induce some conformational changes within the enzyme that lead to an overall better fit of the inhibitor into the binding cleft. Curiously, some of these conformational changes can be considered as a hallmark of the substrate recognition event, which means that most active inhibitors are likely recognized by the enzyme as if they were its own substrate so that the catalytic machinery is arranged as if it is about to break the substrate scissile bond. Overall, these results contribute to a better understanding of the enzyme inhibition mechanism. Moreover, the information about main interactions extracted through this work is already being used in our lab to guide docking solutions in ongoing prospective virtual screening campaigns to search for novel noncovalent cruzain inhibitors.

HIV-1 protease (HIV-PR) performs a vital step in the virus life cycle which makes it an excellent target for drug therapy. However, due to the error-prone of HIV reverse transcriptase, mutations in HIV-PR often occur, inducing drug-resistance to inhibitors. Some HIV-PR mutations can make the flaps of the enzyme more flexible thus increasing the flaps opening rate and inhibitor releasing. It has been shown that by targeting novel binding sites on HIV-PR with small molecules, it is possible to alter the equilibrium of flap conformational states. A previous fragment-based crystallographic screen have found two novel binding sites for small fragments in the inhibited, closed form of HIV-PR, termed flap and exo sites. While these experiments were performed in wild type HIV-PR, it still remains to be proven whether these small fragments can stabilize the closed conformation of flaps in resistant forms of the enzyme. Here we performed Molecular Dynamics simulations of wild type and mutant form of HIV-PR bound to inhibitor TL-3. Simulations show that on going from wild type to 6X mutant the equilibrium shifts from closed to semi-open conformation of flaps. However, when fragment Br6 is placed at flap site of mutant form, the enzyme is restored back to closed conformation. This finding supports the hypothesis that allosteric inhibitors, together with active site inhibitors could increase the number of point mutations necessary for appreciable clinical resistance to AIDS therapy.