桂枝中酚类提取物潜在作用靶点的探索
|
摘要
目的研究桂枝中酚类提取物木脂素的潜在作用靶点。方法在药效团模型数据库中筛选出与木脂素衍生物匹配值(FitValue)大于0.75的药效团模型;运用反向对接技术,从上述药效团模型所对应的靶点蛋白中挑选出与木脂素衍生物结合能最低的蛋白;以该靶蛋白已报道的抑制剂建立3D-QSAR药效团模型预测木脂素衍生物的活性,同时通过荧光偏振实验测试化合物1与Tankyrase 1蛋白的结合力,通过Western blot实验测试加入化合物1后细胞中Tankyrase 1蛋白的含量变化;最后用分子动力学模拟分析木脂素衍生物与该蛋白的作用模式。结果与木脂素衍生物匹配值大于0.75的药效团模型有17个,其中4个为神经保护类靶点,占比(24%)最大;反向对接结果显示该化合物与Tankyrase 1蛋白(PDB ID:4TOR)的结合能(E=-66 kcal/mol)最低;预测该化合物的活性为0.61μmol/L,荧光偏振实验测得化合物1与Tankyrase 1蛋白的结合力Ki=(0.15±0.01)μmol/L,属于中等抑制,Western blot表明在SW480细胞中化合物1使Tankyrase 1蛋白的表达下降;且分子动力学结果显示对接构象与该靶点已报道的抑制剂类似。结论经过对桂枝中酚类提取物木脂素衍生物的反向找靶,以及活性测试确定其对Tankyrase 1蛋白具有潜在的抑制活性。
OBJECTIVE To discovery the potential target of lignans, phenolic extracts from the twigs of Cinnamomum cassia. METHODS Firstly, hypothesis which matched the lignan derivative with the FitValue greater than 0.75 were selected from the pharmacophore model database. Secondly, the lignan derivative was inverse docked to the target proteins which these pharmacophore models selected from. Thirdly, the protein with the best docking result was chosen to build the 3 D-QSAR pharmacophore model using their reported inhibitors to predict the potency of the lignan derivative. The binding force of compound 1 with Tankyrase 1 was tested by fluorescence polarization. The content of Tankyrase 1 in cells after adding compound 1 was tested by Western blot. Finally, the interactions between the lignan derivative and target protein were obtained by molecular dynamics simulation. RESULTS Seventeen pharmacophore models matched the lignan derivative with the FitValue greater than 0.75. Four of them belonged to neuroprotective targets with a highest proportion up to 24%. Inverse docking results showed that the binding energy(E=-65 kcal/mol) between the lignan derivative and the Tankyrase 1 protein(PDB ID: 4 TOR) was the lowest. In addition, the predicted potency of the compound was 0.61 μmol/L, the Ki of compound and Tankyrase 1 protein was(0.15±0.01)μmol/L, a moderate inhibition. Western blot showed that compound 1 could decrease the expression of Tankyrase 1 protein in SW480 cells. Molecular dynamics results showed that the interactions between the lignan derivative and 4 TOR were similar to that between the reported inhibitor and 4 TOR. CONCLUSION After inverse targeting of the phenolic extracts from the Twigs Cinnamomum cassia lignan derivative and the activity test, lignan derivative potentially inhibited against Tankyrase 1.
OBJECTIVE To discovery the potential target of lignans, phenolic extracts from the twigs of Cinnamomum cassia. METHODS Firstly, hypothesis which matched the lignan derivative with the FitValue greater than 0.75 were selected from the pharmacophore model database. Secondly, the lignan derivative was inverse docked to the target proteins which these pharmacophore models selected from. Thirdly, the protein with the best docking result was chosen to build the 3 D-QSAR pharmacophore model using their reported inhibitors to predict the potency of the lignan derivative. The binding force of compound 1 with Tankyrase 1 was tested by fluorescence polarization. The content of Tankyrase 1 in cells after adding compound 1 was tested by Western blot. Finally, the interactions between the lignan derivative and target protein were obtained by molecular dynamics simulation. RESULTS Seventeen pharmacophore models matched the lignan derivative with the FitValue greater than 0.75. Four of them belonged to neuroprotective targets with a highest proportion up to 24%. Inverse docking results showed that the binding energy(E=-65 kcal/mol) between the lignan derivative and the Tankyrase 1 protein(PDB ID: 4 TOR) was the lowest. In addition, the predicted potency of the compound was 0.61 μmol/L, the Ki of compound and Tankyrase 1 protein was(0.15±0.01)μmol/L, a moderate inhibition. Western blot showed that compound 1 could decrease the expression of Tankyrase 1 protein in SW480 cells. Molecular dynamics results showed that the interactions between the lignan derivative and 4 TOR were similar to that between the reported inhibitor and 4 TOR. CONCLUSION After inverse targeting of the phenolic extracts from the Twigs Cinnamomum cassia lignan derivative and the activity test, lignan derivative potentially inhibited against Tankyrase 1.
引文
[1] 高洪义.桂枝的功效[J].天津药学,2002,14(2):43-44.
[2] LIU X,FU J,YAO XJ,et al.Phenolic constituents isolated from the twigs of Cinnamomum cassia and their potential neuroprotective effects[J].J Nat Prod,2018,81(6):1333-1342.
[3] CASSON RJ,CHIDLOW G,EBNETER A,et al.Translational neuroprotection research in glaucoma:a review of definitions and principles [J].Clin Exp Ophthalmol,2012,40(4):350-357.
[4] WIEDAU-PAZOS M,WONG E,SOLOMON E,et al.Wnt-pathway activation during the early stage of neurodegeneration in FTDP-17 mice[J].Neurobiol Aging,2009,30(1):14-21.
[5] XUE X,ZHAO NY,YU HT,et al.Discovery of novel inhibitors disrupting HIF-1α/von Hippel-Lindau interaction through shape-based screening and cascade docking[J].Peer J,2016,4:e2757.
[6] 章靓,严国鸿,江川,等.反向分子对接方法预测丹参酮Ⅱ_B抗血小板潜在作用靶标[J].中国现代应用药学,2017,34(2):221-224.
[7] EISEMANN T,MCCAULEY M,LANGELIER MF,et al.Tankyrase-1 ankyrin repeats form an adaptable binding platform for targets of ADP-ribose modification[J].Structure,2016,24(10):1679-1692.
[8] WOLBER G,LANGER T.LigandScout:3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters[J].J Chem Inf Model,2005,45(1):160-169.
[9] MESLAMANI J,LI J,SUTTER J,et al.Protein-ligand-based pharmacophores:Generation and utility assessment in computational ligand profiling[J].J Chem Inf Model,2012,52(4):943-955.
[10] KULAK O,CHEN H,HOLOHAN B,et al.Disruption of Wnt/β-catenin signaling and telomeric shortening are inextricable cnsequences of tankyrase inhibition in human cells[J].Mol Cell Biol,2015,35(14):2425-2435.
[11] QIN J,XIE P,VENTOCILLA C,et al.Identification of a novel family of BRAF(V600E) inhibitors[J].J Med Chem,2012,55(11):5220-5230.
[12] SYMERSKY J,OSOWSKI D,WALTERS DE,et al.Oligomycin frames a common drug-binding site in the ATP synthase[J].Proc Natl Acad Sci USA,2012,109(35):13961-13965.
[13] KERR G,SHELDON H,CHAIKUAD A,et al.A small molecule targeting ALK1 prevents Notch cooperativity and inhibits functional angiogenesis[J].Angiogenesis,2015,18(2):209-217.
[14] LU IL,MAHINDROO N,LIANG PH,et al.Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease[J].J Med Chem,2006,49(17):5154-5161.
[15] RD RT,GRANT JA,MOSYAK L,et al.A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction[J].J Med Chem,2005,48(5):1489-1495.
[16] BRENT MM,ANAND R,MARMORSTEIN R.Structural basis for DNA recognition by FoxO1 and its regulation by posttranslational modification[J].Structure,2008,16(9):1407-1416.
[17] STABEN ST,SIU M,GOLDSMITH R,et al.Structure-based design of thienobenzoxepin inhibitors of PI3-kinase[J].Bioorg Med Chem Lett,2011,21(13):4054-4058.
[18] CARD GL,ENGLAND BP,SUZUKI Y,et al.Structural basis for the activity of drugs that inhibit phosphodiesterases[J].Structure,2004,12(12):2233-2247.
[2] LIU X,FU J,YAO XJ,et al.Phenolic constituents isolated from the twigs of Cinnamomum cassia and their potential neuroprotective effects[J].J Nat Prod,2018,81(6):1333-1342.
[3] CASSON RJ,CHIDLOW G,EBNETER A,et al.Translational neuroprotection research in glaucoma:a review of definitions and principles [J].Clin Exp Ophthalmol,2012,40(4):350-357.
[4] WIEDAU-PAZOS M,WONG E,SOLOMON E,et al.Wnt-pathway activation during the early stage of neurodegeneration in FTDP-17 mice[J].Neurobiol Aging,2009,30(1):14-21.
[5] XUE X,ZHAO NY,YU HT,et al.Discovery of novel inhibitors disrupting HIF-1α/von Hippel-Lindau interaction through shape-based screening and cascade docking[J].Peer J,2016,4:e2757.
[6] 章靓,严国鸿,江川,等.反向分子对接方法预测丹参酮Ⅱ_B抗血小板潜在作用靶标[J].中国现代应用药学,2017,34(2):221-224.
[7] EISEMANN T,MCCAULEY M,LANGELIER MF,et al.Tankyrase-1 ankyrin repeats form an adaptable binding platform for targets of ADP-ribose modification[J].Structure,2016,24(10):1679-1692.
[8] WOLBER G,LANGER T.LigandScout:3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters[J].J Chem Inf Model,2005,45(1):160-169.
[9] MESLAMANI J,LI J,SUTTER J,et al.Protein-ligand-based pharmacophores:Generation and utility assessment in computational ligand profiling[J].J Chem Inf Model,2012,52(4):943-955.
[10] KULAK O,CHEN H,HOLOHAN B,et al.Disruption of Wnt/β-catenin signaling and telomeric shortening are inextricable cnsequences of tankyrase inhibition in human cells[J].Mol Cell Biol,2015,35(14):2425-2435.
[11] QIN J,XIE P,VENTOCILLA C,et al.Identification of a novel family of BRAF(V600E) inhibitors[J].J Med Chem,2012,55(11):5220-5230.
[12] SYMERSKY J,OSOWSKI D,WALTERS DE,et al.Oligomycin frames a common drug-binding site in the ATP synthase[J].Proc Natl Acad Sci USA,2012,109(35):13961-13965.
[13] KERR G,SHELDON H,CHAIKUAD A,et al.A small molecule targeting ALK1 prevents Notch cooperativity and inhibits functional angiogenesis[J].Angiogenesis,2015,18(2):209-217.
[14] LU IL,MAHINDROO N,LIANG PH,et al.Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease[J].J Med Chem,2006,49(17):5154-5161.
[15] RD RT,GRANT JA,MOSYAK L,et al.A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction[J].J Med Chem,2005,48(5):1489-1495.
[16] BRENT MM,ANAND R,MARMORSTEIN R.Structural basis for DNA recognition by FoxO1 and its regulation by posttranslational modification[J].Structure,2008,16(9):1407-1416.
[17] STABEN ST,SIU M,GOLDSMITH R,et al.Structure-based design of thienobenzoxepin inhibitors of PI3-kinase[J].Bioorg Med Chem Lett,2011,21(13):4054-4058.
[18] CARD GL,ENGLAND BP,SUZUKI Y,et al.Structural basis for the activity of drugs that inhibit phosphodiesterases[J].Structure,2004,12(12):2233-2247.