Scorciapino Mariano Andrea, Acosta-Gutierrez Silvia, Benkerrou Dehbia, D'Agostino Tommaso, Malloci Giuliano, Samanta Susruta, Bodrenko Igor, Ceccarelli Matteo
Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700-09042 Monserrato (CA), Italy.
J Phys Condens Matter. 2017 Mar 22;29(11):113001. doi: 10.1088/1361-648X/aa543b. Epub 2017 Feb 3.
The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.
革兰氏阴性菌中抗生素耐药性水平不断上升，加上研发中的新型潜在药物支架匮乏，使得传染病问题成为现代医学面临的全球性挑战。革兰氏阴性菌特别具有挑战性的主要原因是存在外部细胞保护膜，而革兰氏阳性菌中不存在这种膜。这种不对称双层膜是极性分子的高效屏障。外膜中表达了几种蛋白质系统来控制营养物质和有害物质的内部浓度，特别是：（i）根据浓度梯度调节极性分子和离子渗透的充满水的通道，以及（ii）主动排出有毒化合物的外排泵。因此，除了表达用于药物降解的特定酶外，革兰氏阴性菌还可以通过调节抗生素的流入和流出，保持内部浓度较低来产生耐药性。然而，目前尚无直接且可靠的实验方法能够测量小分子的渗透性，因此严重限制了我们对最终控制抗生素透过外膜渗透的分子机制的了解。这是革兰氏阴性菌需要填补的创新空白。本综述聚焦于小分子通过孔蛋白的渗透，孔蛋白被认为是极性抗生素进入革兰氏阴性菌的主要途径。深入了解这些蛋白质如何过滤小分子是设计/优化具有改善渗透性的抗菌药物的先决条件。现代分子建模算法的复杂程度以及新计算机硬件的进步使得在分子水平上模拟此类复杂过程成为可能。在这项工作中，我们旨在分享在IMI-易位联盟多学科扩展合作背景下的经验和观点。结构数据、体外试验和计算机模拟的协同结合已被证明能为识别和描述调节渗透的物理化学性质提供新的见解。一旦确定了类似的一般规则，我们相信虚拟筛选技术的使用将非常有助于寻找具有增强渗透性的新分子支架，并且分子建模将对优化阶段提供重要帮助。
