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000844311 1001_ $$0P:(DE-HGF)0$$aFranco-Ulloa, Sebastian$$b0
000844311 245__ $$aNovel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site
000844311 260__ $$aBasel$$bMolecular Diversity Preservation International$$c2018
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000844311 520__ $$aDNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase
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000844311 7001_ $$0P:(DE-HGF)0$$aLa Sala, Giuseppina$$b1
000844311 7001_ $$0P:(DE-HGF)0$$aMiscione, Gian$$b2$$eCorresponding author
000844311 7001_ $$00000-0003-4022-5661$$aDe Vivo, Marco$$b3$$eCorresponding author
000844311 773__ $$0PERI:(DE-600)2019364-6$$a10.3390/ijms19020453$$gVol. 19, no. 2, p. 453 -$$n2$$p453 -$$tInternational journal of molecular sciences$$v19$$x1422-0067$$y2018
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