Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche 86090, Italy.
Bioorg Chem. 2022 Jan;118:105480. doi: 10.1016/j.bioorg.2021.105480. Epub 2021 Nov 15.
A well-structured in silico workflow is here reported for disclosing structure-based pharmacophore models against bromodomain-containing protein 9 (BRD9), accelerating virtual screening campaigns and facilitating the identification of novel binders. Specifically, starting from 23 known ligands co-crystallized with BRD9, three-dimensional pharmacophore models, namely placed in a reference protein structure, were developed. Specifically, we here introduce a fragment-related pharmacophore model, useful for the identification of new promising small chemical probes targeting the protein region responsible of the acetyllysine recognition, and two further pharmacophore models useful for the selection of compounds featuring drug-like properties. A pharmacophore-driven virtual screening campaign was then performed to facilitate the selection of new selective BRD9 ligands, starting from a large library of commercially available molecules. The identification of a promising BRD9 binder (7) prompted us to re-iterate this computational workflow on a second focused in-house built library of synthesizable compounds and, eventually, three further novel BRD9 binders were disclosed (8-10). Moreover, all these compounds were tested among a panel comprising other nine bromodomains, showing a high selectivity for BRD9. Preclinical bioscreens for potential anticancer activity highlighted compound 7 as that showing the most promising biological effects, proving the reliability of this in silico pipeline and confirming the applicability of the here introduced structure-based three-dimensional (3D) pharmacophore models as straightforward tools for the selection of new BRD9 ligands.
本文报道了一种针对含溴结构域蛋白 9（BRD9）的基于结构的药效团模型的合理的计算机工作流程，旨在加速虚拟筛选活动并促进新型结合物的鉴定。具体来说，从与 BRD9 共结晶的 23 种已知配体出发，开发了三维药效团模型，即放置在参考蛋白结构中。具体而言，我们在这里引入了一种与片段相关的药效团模型，可用于鉴定新的有前途的小分子化学探针，这些探针可靶向负责乙酰赖氨酸识别的蛋白质区域，以及另外两种用于选择具有类药性特征的化合物的药效团模型。然后，我们进行了基于药效团的虚拟筛选活动，以从大量商业可得的分子库中选择新的选择性 BRD9 配体。鉴定出一种有前途的 BRD9 结合物（7）后，我们在第二个内部合成化合物库上重复了此计算工作流程，并最终揭示了另外三个新的 BRD9 结合物（8-10）。此外，所有这些化合物都在一个包含其他九个溴结构域的小组中进行了测试，结果显示它们对 BRD9 具有很高的选择性。潜在抗癌活性的临床前生物筛选突出了化合物 7，因为它显示出最有希望的生物学效应，证明了这种计算机管道的可靠性，并证实了这里介绍的基于结构的三维（3D）药效团模型作为新型 BRD9 配体选择的直接工具的适用性。
