Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome , 00185 Rome, Italy.
Medicinal Chemistry Unit, School of Pharmacy, University of Camerino , 62032 Camerino, MC, Italy.
J Med Chem. 2015 Oct 22;58(20):8269-84. doi: 10.1021/acs.jmedchem.5b01184. Epub 2015 Oct 12.
Cyclic di-GMP (c-di-GMP) is a widespread second messenger that plays a key role in bacterial biofilm formation. The compound's ability to assume multiple conformations allows it to interact with a diverse set of target macromolecules. Here, we analyzed the binding mode of c-di-GMP to the allosteric inhibitory site (I-site) of diguanylate cyclases (DGCs) and compared it to the conformation adopted in the catalytic site of the EAL phosphodiesterases (PDEs). An array of novel molecules has been designed and synthesized by simplifying the native c-di-GMP structure and replacing the charged phosphodiester backbone with an isosteric nonhydrolyzable 1,2,3-triazole moiety. We developed the first neutral small molecule able to selectively target DGCs discriminating between the I-site of DGCs and the active site of PDEs; this molecule represents a novel tool for mechanistic studies, particularly on those proteins bearing both DGC and PDE modules, and for future optimization studies to target DGCs in vivo.
环二鸟苷酸（c-di-GMP）是一种广泛存在的第二信使，在细菌生物膜形成中起着关键作用。该化合物能够采取多种构象，使其能够与多种靶大分子相互作用。在这里，我们分析了 c-di-GMP 与双鸟苷酸环化酶（DGCs）的别构抑制位点（I 位点）的结合模式，并将其与在 EAL 磷酸二酯酶（PDEs）的催化位点中采用的构象进行了比较。通过简化天然 c-di-GMP 结构并将带电荷的磷酸二酯骨架替换为等排的不可水解 1,2,3-三唑部分，我们设计和合成了一系列新的分子。我们开发了第一个能够选择性靶向 DGCs 的中性小分子，区分 DGCs 的 I 位点和 PDEs 的活性位点；该分子代表了一种用于机制研究的新型工具，特别是对于那些同时具有 DGC 和 PDE 模块的蛋白质，并且可以用于未来的优化研究，以在体内靶向 DGCs。
