Abstract：
BACKGROUND: Protein-protein interaction interfaces play a major role in cell signaling pathways. There is always a great interest in developing protein-protein interaction (PPI) inhibitors of kinases, as they are challenging due to their hydrophobicity, flat surface, specificity, potency, etc. 3 Phosphoinositide-dependent kinase-1 (PDK1), which is involved in the PI3K/PDK1/AKT pathway, is a cancer target that has gained insight for the past two decades. PDK1 possesses a protein interaction fragment (PIF) pocket, which is a well-known PPI that targets allosteric modulators. This work focusses on energy-based pharmacophore model development which on virtual screening could yield novel scaffolds towards the drug designing objective for the kind of PDK1 modulators. A novel pyrazolo pyridine molecule was identified as an allosteric modulator that binds to the PPI site. The metadynamics simulations with free energy profiles further revealed the conformational allosteric changes stimulated on the protein structure upon ligand binding. The cytotoxic activity (IC50-20 μM) of the identified compound against five different cancer cell lines and cell cycle analysis supported the anticancer activity of the identified compound.
METHODS: All the computational works were carried out by the most commonly used Schrodinger Suite software. The pharmacophore was validated by Receiver Operation Characteristics (ROC) and screening against allosteric Enamine database library. The Optimized Potential Liquid Simulations (OPLS-2005) was used to minimize the structures for molecular docking calculations, and inbuilt scoring method of ranking the compounds based on docking score and Glide energy was used. Molecular dynamics simulations were conducted by Desmond implemented in Maestro. The hit compound was purchased from Enamine and tested against different cancer cell lines by MTT assay, apoptosis by western blotting technique, and by flow cytometry analysis.
METHODS: All the computational works were carried out by the most commonly used Schrodinger Suite software. The pharmacophore was validated by Receiver Operation Characteristics (ROC) and screening against allosteric Enamine database library. The Optimized Potential Liquid Simulations (OPLS-2005) was used to minimize the structures for molecular docking calculations, and inbuilt scoring method of ranking the compounds based on docking score and Glide energy was used. Molecular dynamics simulations were conducted by Desmond implemented in Maestro. The hit compound was purchased from Enamine and tested against different cancer cell lines by MTT assay, apoptosis by western blotting technique, and by flow cytometry analysis.
摘要：
背景：蛋白质-蛋白质相互作用界面在细胞信号传导途径中起主要作用。人们总是对开发激酶的蛋白质-蛋白质相互作用（PPI）抑制剂非常感兴趣，因为它们的疏水性具有挑战性，平坦表面,特异性，效力，效力等。3磷酸肌醇依赖性激酶-1（PDK1），参与PI3K/PDK1/AKT通路，是过去二十年来获得洞察力的癌症靶标。PDK1具有蛋白质相互作用片段（PIF）口袋，这是一种众所周知的PPI，以变构调节剂为目标。这项工作专注于基于能量的药效团模型的开发，该模型在虚拟筛选上可以为PDK1调节剂的药物设计目标产生新型支架。一种新的吡唑并吡啶分子被鉴定为与PPI位点结合的变构调节剂。具有自由能曲线的元动力学模拟进一步揭示了配体结合后在蛋白质结构上刺激的构象变构变化。鉴定的化合物对五种不同癌细胞系的细胞毒性活性(IC50-20μM)和细胞周期分析支持鉴定的化合物的抗癌活性。
方法：所有计算工作均由最常用的SchrodingerSuite软件进行。通过接收器操作特征(ROC)和针对变构烯胺数据库文库的筛选来验证药效基团。优化潜在液体模拟（OPLS-2005）用于最小化分子对接计算的结构，并使用基于对接得分和Glide能量对化合物进行排名的内置评分方法。分子动力学模拟由在Maestro中实现的Desmond进行。命中化合物购自Enamine，并通过MTT测定法对不同的癌细胞系进行测试，通过蛋白质印迹技术进行细胞凋亡，并通过流式细胞术分析。
方法：所有计算工作均由最常用的SchrodingerSuite软件进行。通过接收器操作特征(ROC)和针对变构烯胺数据库文库的筛选来验证药效基团。优化潜在液体模拟（OPLS-2005）用于最小化分子对接计算的结构，并使用基于对接得分和Glide能量对化合物进行排名的内置评分方法。分子动力学模拟由在Maestro中实现的Desmond进行。命中化合物购自Enamine，并通过MTT测定法对不同的癌细胞系进行测试，通过蛋白质印迹技术进行细胞凋亡，并通过流式细胞术分析。
