Identification of novel inhibitors targeting TIRAP interactions with BTK and PKCδ in inflammation through an in silico approach

Advanced computational tools focusing on protein–protein interaction (PPI) based drug development is a powerful platform to accelerate the therapeutic development of small lead molecules and repurposed drugs. Toll/interleukin-1 receptor (TIR) domain-containing adapter protein (TIRAP) and its interactions with other proteins in macrophages signalling are crucial components of severe or persistent inflammation. TIRAP activation through Bruton’s tyrosine kinase (BTK) and Protein Kinase C delta (PKCδ) is essential for downstream inflammatory signalling. We created homology-based structural models of BTK and PKCδ in MODELLER 9.24. TIRAP interactions with BTK and PKCδ in its non-phosphorylated and phosphorylated states were determined by multiple docking tools including HADDOCK 2.4, pyDockWEB and ClusPro 2.0. Food and Drug Administration (FDA)-approved drugs were virtually screened through Discovery Studio LibDock and Autodock Vina tools to target the common TIR domain residues of TIRAP, which interact with both BTK and PKC at the identified interfacial sites of the complexes. Four FDA-approved drugs were identified and found to have stable interactions over a range of 100 ns MD simulation timescales. These drugs block the interactions of both kinases with TIRAP in silico. Hence, these drugs have the potential to dampen downstream inflammatory signalling and inflammation-mediated disease.

聚焦于基于蛋白质-蛋白质相互作用（protein–protein interaction, PPI）的药物开发的先进计算工具，是加速小分子先导化合物与重定位药物研发的高效平台。Toll/白细胞介素-1受体（Toll/interleukin-1 receptor, TIR）结构域包含型适配蛋白（TIRAP）及其在巨噬细胞信号通路中与其他蛋白质的相互作用，是重度或持续性炎症的关键调控组分。由布鲁顿酪氨酸激酶（Bruton’s tyrosine kinase, BTK）与蛋白激酶Cδ（Protein Kinase C delta, PKCδ）介导的TIRAP激活，是下游炎症信号通路的必要环节。本研究借助MODELLER 9.24构建了BTK与PKCδ的同源建模结构模型。通过HADDOCK 2.4、pyDockWEB与ClusPro 2.0等多款分子对接工具，本研究解析了TIRAP在非磷酸化与磷酸化状态下与BTK、PKCδ的相互作用模式。本研究借助Discovery Studio LibDock与Autodock Vina工具，针对TIRAP的TIR结构域中与BTK、PKCδ在复合物已确定的界面结合位点存在相互作用的共有残基，对美国食品药品监督管理局（Food and Drug Administration, FDA）获批药物开展了虚拟筛选。最终筛选得到4种FDA获批药物，且经100纳秒分子动力学（Molecular Dynamics, MD）模拟验证，这些药物与靶标位点的结合状态在模拟时长内保持稳定。在计算机模拟环境中，此类药物可阻断两种激酶与TIRAP的相互作用。因此，这些药物具备抑制下游炎症信号通路、缓解炎症介导疾病的应用潜力。