Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States.
Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States.
J Chem Inf Model. 2023 Nov 13;63(21):6655-6666. doi: 10.1021/acs.jcim.3c00722. Epub 2023 Oct 17.
Protein-ligand interactions are essential to drug discovery and drug development efforts. Desirable on-target or multitarget interactions are the first step in finding an effective therapeutic, while undesirable off-target interactions are the first step in assessing safety. In this work, we introduce a novel ligand-based featurization and mapping of human protein pockets to identify closely related protein targets and to project novel drugs into a hybrid protein-ligand feature space to identify their likely protein interactions. Using structure-based template matches from PDB, protein pockets are featured by the ligands that bind to their best co-complex template matches. The simplicity and interpretability of this approach provide a granular characterization of the human proteome at the protein-pocket level instead of the traditional protein-level characterization by family, function, or pathway. We demonstrate the power of this featurization method by clustering a subset of the human proteome and evaluating the predicted cluster associations of over 7000 compounds.
蛋白质-配体相互作用对于药物发现和药物开发工作至关重要。理想的靶标或多靶标相互作用是寻找有效治疗方法的第一步,而不理想的脱靶相互作用是评估安全性的第一步。在这项工作中,我们引入了一种新的基于配体的特征化和映射人类蛋白质口袋的方法,以识别密切相关的蛋白质靶标,并将新型药物投射到混合蛋白质-配体特征空间中,以识别其可能的蛋白质相互作用。使用来自 PDB 的基于结构的模板匹配,通过与最佳共复合物模板匹配结合的配体来为蛋白质口袋加特征。这种方法的简单性和可解释性提供了一种在蛋白质口袋水平而不是传统的通过家族、功能或途径进行的蛋白质水平上对人类蛋白质组进行详细描述的方法。我们通过对人类蛋白质组的一个子集进行聚类并评估超过 7000 种化合物的预测聚类相关性来证明这种特征化方法的强大功能。