肝醣合成酶激酶-3β抑制劑搜尋:分子嵌合計算和激酶抑制效果實驗

Abstract

Glycogen synthase kinase-3β（GSK-3β）為一種蛋白質激酶，當GSK-3β活性過高，過度磷酸化下游蛋白分子，而導致細胞訊息傳遞異常，會引發疾病，如癌症、發炎反應以及阿茲海默症等。本研究利用分子嵌合計算的方式，並加上激酶抑制效果實驗尋找GSK-3β抑制劑。首先，從蛋白質資料庫中挑選16個胺基酸序列100%相同的複合體結晶結構，並且研究其再現性。再來選擇10個再現性較佳的結構進行交叉分子嵌合，藉此研究不同結晶構型時，能否正確的再現出蛋白質與小分子之間的結合模式。接著選擇交叉分子嵌合中，表現最佳的構型作為單一嵌合的蛋白質結構；交叉分子嵌合中，表現前五名的構型作為多重嵌合的蛋白質結構；並利用Q-SiteFinder計算活性中心體積精確度最高的前五名作為多重嵌合的蛋白質結構，同時不同測試評分函數及不同氫鍵限制位置對計算結果的影響。我們從Binding Database中208個已知Ki的GSK-3β抑制劑，利用Discovery Studio挑選出21個結構不相似的GSK-3β活性分子，再利用ZINC網站產生其對應的decoys，共有759個decoys，建立一套GSK-3β專用的標準測試資料庫，篩選的效率以Enrichment Factor（EF）為主要指標，測試不同評分函數的表現及有無氫鍵限制對篩選效率的影響。由計算的結果得到，最好的氫鍵限制及評分函數提升Enrichment Factor至26倍。選用Kinase_ChemScore評分函數及在ASP133骨幹上的O原子與VAL135骨幹上的H原子設定氫鍵的組合為最佳設定。因此我們利用這個設定進行高速虛擬篩選，並在ZINC及烏克蘭資料庫中進行篩選，從中找出較有潛力的小分子化合物，並且將這些化合物進行激酶抑制效果實驗，確認小分子化合物是否有抑制效果。在測試的10個化合物中，有5個化合物有抑制效果，並且將有抑制效果的分子再進一步給生物學家進行後續的生物實驗。Glycogen synthase kinase-3β（GSK-3β）is an important protein target for treatment of several diseases. When the activity of GSK-3β is too high, it over-phosphorylates downstream proteins and causes some diseases such as cancer, inflammation, and Alzheimer’s Diseases. This study utilized docking computation and kinase assay to search new GSK-3β kinase inhibitors. First, we selected 16 crystal structures of GSK-3β kinase-ligand complexes which have 100% amino acid sequence homology in the Protein Data Bank to examine their reproducibility. Next, we chose 10 complexes which have good reproducibility to do cross docking, and investigate how ligand conformation can be regained when protein structures from different complexes were used. According to the result of cross docking, the best protein structure was used for later docking with single structure. The top five protein structures were used to do ensemble docking. In addition, the volume of binding sites were computed using Q-SiteFinder, and the top five protein structures which present high precision based on a volume computation criterion were chosen to do ensemble docking. Furthermore, we investigated how scoring functions and different H-bond constraints performed in our docking computation. For this purpose, we built a DUD-E benchmark set consisting of active and inactive compounds. For the former, Discovery Studio was used to selected 21 dissimilar compounds from the existing 208 active compounds with Ki values available in the Binding Database. Inactive decoy compounds of those 21 active compounds were generated using a ZINC program, which gave 759 decoy compounds. This compound set was used for benchmark based on the enrichment factor（EF）value for each docking protocol. The computed results showed that the best protocol is to use the scoring function: Kinase_ChemScore combined with the H-bond constraints on O atom of ASP133 and H atom of VAL135 on the backbone, which enhanced the EF up to 26. Moreover, we use this protocol to do high throughput virtual screening in the ZINC Database and the Enamine Database to find out some potential small molecular compounds, and suggested these compounds for kinase assay. Among the 10 compound undergone kinase assay, 5 compounds were identified to be active, and were recommended for further cell and animal assays.