Oxazolidinone antibiotics bind to the highly conserved peptidyl transferase center in the ribosome. For developing selective antibiotics, a profound understanding of the selectivity determinants is required. We have performed for the first time technically challenging molecular dynamics simulations in combination with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations of the oxazolidinones linezolid and radezolid bound to the large ribosomal subunits of the eubacterium Deinococcus radiodurans and the archaeon Haloarcula marismortui. A remarkably good agreement of the computed relative binding free energy with selectivity data available from experiment for linezolid is found. On an atomic level, the analyses reveal an intricate interplay of structural, energetic, and dynamic determinants of the species selectivity of oxazolidinone antibiotics: A structural decomposition of free energy components identifies influences that originate from first and second shell nucleotides of the binding sites and lead to (opposing) contributions from interaction energies, solvation, and entropic factors. These findings add another layer of complexity to the current knowledge on structure-activity relationships of oxazolidinones binding to the ribosome and suggest that selectivity analyses solely based on structural information and qualitative arguments on interactions may not reach far enough. The computational analyses presented here should be of sufficient accuracy to fill this gap.

Glycogen Synthase (GS) Kinase-3 (GSK-3), a serine/threonine kinase, isolated and purified as an enzyme capable of phosphorylating and inactivating the enzyme GS is a fascinating enzyme with diverse biological actions in intracellular signaling pathways. A large body of evidence supports speculation that pharmacological inhibitors of GSK-3 could be used to treat several disorders including Alzheimers disease and other neurodegenerative diseases, bipolar affective disorder, diabetes, various types of cancer, and diseases caused by unicellular parasites that express GSK-3 homologues. In the present work, we have carried out a Quantitative Structure -Activity Relationship (QSAR) study on indirubin derivatives reported as potent GSK-3b inhibitors using molecular descriptors calculated by CODESSA and Molconn-Z. Also a novel ThreeDimensional QSAR (3D-QSAR) study based on the principle of the alignment of pharmacophoric features by PHASE module of Schrçdinger suite has been carried out on the same set of inhibitors. Statistically significant 2-D (R 2 ¼ 0.93) and 3-D (R 2 ¼ 0.97) QSAR models were generated using 36 molecules in the training set. The predictive ability of both models was determined using a randomly chosen test set of eight molecules which gave predictive correlation coefficients (R 2 pred ) of 0.6 and 0.91, respectively for 2-D and 3-D models, indicating good predictive power. The cocrystallographic data of GSK-3b with indirubin-3'-monoxime ligand allowed us to compare the PHASE pharmacophore model with experimental intermolecular interactions. The results of PHASE pharmacophore hypothesis AADDRR correspond very closely to the interactions recorded in the active site of the ligand bound complex. This relation between the crystallographic data and pharmacophore hypothesis allowed us to confirm the preferential binding mode of indirubins inside the active site. These studies showed that 3D-QSAR model is a better predictive model for the indirubins compared to 2D-QSAR model.

The emergence of multidrug-resistant pathogens will make current antibiotics ineffective. For linezolid, a member of the novel oxazolidinone class of antibiotics, 10 nucleotide mutations in the ribosome have been described conferring resistance. Hypotheses for how these mutations affect antibiotics binding have been derived based on comparative crystallographic studies. However, a detailed description at the atomistic level of how remote mutations exert long-distance effects has remained elusive. Here, we show that the G2032A-C2499A double mutation, located > 10 Å away from the antibiotic, confers linezolid resistance by a complex set of effects that percolate to the binding site. By molecular dynamics simulations and free energy calculations, we identify U2504 and C2452 as spearheads among binding site nucleotides that exert the most immediate effect on linezolid binding. Structural reorganizations within the ribosomal subunit due to the mutations are likely associated with mutually compensating changes in the effective energy. Furthermore, we suggest two main routes of information transfer from the mutation sites to U2504 and C2452. Between these, we observe cross-talk, which suggests that synergistic effects observed for the two mutations arise in an indirect manner. These results should be relevant for the development of oxazolidinone derivatives that are active against linezolid-resistant strains.

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