Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket.

The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3.

Graphene and its derivatives: understanding the main chemical and medicinal chemistry roles for biomedical applications.

Over the past few years, there has been a growing potential use of graphene and its derivatives in several biomedical areas, such as drug delivery systems, biosensors, and imaging systems, especially for having excellent optical, electronic, thermal, and mechanical properties. Therefore, nanomaterials in the graphene family have shown promising results in several areas of science. The different physicochemical properties of graphene and its derivatives guide its biocompatibility and toxicity. Hence, further studies to explain the interactions of these nanomaterials with biological systems are fundamental. This review has shown the applicability of the graphene family in several biomedical modalities, with particular attention for cancer therapy and diagnosis, as a potent theranostic. This ability is derivative from the considerable number of forms that the graphene family can assume. The graphene-based materials biodistribution profile, clearance, toxicity, and cytotoxicity, interacting with biological systems, are discussed here, focusing on its synthesis methodology, physicochemical properties, and production quality. Despite the growing increase in the bioavailability and toxicity studies of graphene and its derivatives, there is still much to be unveiled to develop safe and effective formulations.