A Synthetic Substrate of DNA Polymerase Deviating from the Bases,Sugar, and Leaving Group of Canonical Deoxynucleoside Triphosphates

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Highlights? A highly modified nucleotide as substrate for polymerases ? The reversibility of the polymerase reaction at the template level ? Synthesis of a nucleoside with two anomeric centers     

The kalimantacin/batumin biosynthesis operon encodes a self-resistance isoform of the FabI bacterial target

BatG is a trans-2-enoyl-ACP reductase, encoded in?the kalimantacin/batumin (kal/bat) biosynthesis operon. It is not essential for the production of the kal/bat secondary metabolite. Instead, BatG is an isoform of FabI, conferring full resistance to target bacteria. It also complements FabI in its role in fatty acid biosynthesis. The identification of FabI as the antibacterial target is important to assess clinical potential of the kalimantacin/batumin antibiotics against Staphylococcus aureus.     

Base-base interactions in the minor groove of double-stranded DNA

A method has been developed for the synthesis of bisheaded nucleosides with thymine and adenine base moieties. We have demonstrated that, when incorporated in oligonucleotides, extrahelical A-T base interactions are possible when the bisheaded nucleosides are positioned in opposite strands of the duplex and are separated from each other by one regular base pair.     

Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance?

Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the \(\beta \) -ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.     

Polymorphism in pentacene

Pentacene, C₂₂H₁₄, crystallizes in different morphologies characterized by their d(001)‐spacings of 14.1, 14.5, 15.0 and 15.4 Å. We have studied the crystal structure of the 14.1 and 14.5 Åd‐spacing morphologies grown by vapour transport and from solution. We find a close correspondence between the 14.1 Å structure reported by Holmes, Kumaraswamy, Matzeger & Vollhardt [Chem. Eur. J. (1999), 5 , 3399–3412] and the 14.5 Å structure reported by Campbell, Monteath Robertson & Trotter [Acta Cryst. (1961), 14 , 705–711]. Single crystals commonly adopt the 14.1 Åd‐spacing morphology with an inversion centre on both mol­ecules in the unit cell. Thin films grown on SiO₂ substrates above 350 K preferentially adopt the 14.5 Åd‐spacing morphology, with a slightly smaller unit‐cell volume.