分子对接与核磁共振方法筛选人双特异性磷酸酶VHR抑制剂的研究
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摘要
本论文的工作重点是结合计算机虚拟筛选和核磁共振(NMR)技术筛选人双特异性蛋白质磷酸酶VHR的抑制剂，发现了一个结构新颖的强效抑制剂，并进一步研究了此抑制剂在细胞内的影响。VHR在调控MAPK级联途径中起重要作用，从而与许多人类疾病联系在一起，因而抑制剂的发现不仅有助于蛋白质酪氨酸磷酸酶生理功能的阐明，而且有作为药物先导物的前景。论文共分为以下四个部分：
第一章简介了计算机辅助药物设计和筛选，其中重点综述了利用分子对接方法虚拟筛选小分子化合物库的原理，以及一些常用分子对接程序的理论基础和筛选流程。虚拟筛选是创新药物研究的新方法和新技术，并且已经成为一种与高通量筛选互补的实用化工具，加入到了创新药物研究的工作流程中。随着结构生物学、结构基因组、功能基因组学及蛋白质组学的发展，越来越多的生物大分子三维结构被测定，虚拟筛选能够发挥更大的作用。分子对接是药物发现和设计中一种非常重要的方法，将会减少随机筛选的盲目性，大大加快药物发现的速度。
第二章主要综述了核磁共振(NMR)技术在药物筛选中的方法与应用。核磁共振(NMR)技术在方法学和硬件上的迅速发展，使其成为化学和结构生物学中最重要的波谱技术。特别是生物核磁共振技术在药物研发过程中，提供从药物设计结构信息到基于NMR技术进行配体的筛选的广泛应用，使得生物核磁共振技术在药物研究领域地位不断加强，成为药物研究的基础工具。核磁共振已经作为一个强大的筛选方法来识别和探测蛋白和配体的相互作用。药物公司也已经将NMR筛选平台纳入药物发现和药物设计部门。
NMR筛选可以被定义为通过观察当蛋白和配体相互作用时NMR参数的变化来识别靶蛋白的小分子配体。NMR筛选可以被分为基于探测大分子蛋白的参数变化和基于探测小分子配体的参数变化两大类。对于大分子，可观测的参数被限制只能是最典型的化学位移。对于小分子，可选择的参数就比较多。包括纵向，横向驰豫，扩散系数，分子间和分子内磁化转移。后者包括转移NOE(Nuclear Overhauser Effect)，NOE pumping和反向NOE pumping，WaterLOGSY实验。
第三章介绍了结合计算机虚拟筛选和核磁共振(NMR)技术筛选人双特异性蛋白质磷酸酶VHR的抑制剂的研究。首先对VHR的功能和结构，已发现的抑制剂进行了全面介绍。并进一步研究了抑制剂在细胞内的影响。双特异性蛋白质磷酸酶是参与促有丝分裂信号转导和细胞周期调控的主要酶类。既能从含有磷酸酪氨酸，又能从含有磷酸苏氨酸／丝氨酸的蛋白质中移去磷酸盐。VHR在调控MAPK级联途径中起重要作用，从而与许多人类疾病联系在一起。ZAP-70酪氨酸激酶和牛痘相关激酶VRK 3能通过不同方式增强VHR的活性，从而促进VHR对Erk2-Elk-1途径的抑制。VHR能够调节细胞周期而且能够调节自身的表达量．缺失VHR的细胞会在G1-S和G2-M期静息，并且有衰老迹象。
我们首先运用分子对接程序DOCK4.0对小分子库进行虚拟筛选，通过扩散编辑NMR方法评估所选小分子的结合能力，发现了4个能够结合VHR的配体。并以对硝基苯酚磷酸盐为底物测定计算了它们抑制VHR去磷酸的能力，发现其中一个小分子GATPT具有新颖的结构，强烈并且竞争性抑制VHR的酶活(IC_(50)=2.92μM)。AutoDock计算显示的复合物结构模型表明这个小分子和蛋白质活性口袋紧密结合。一系列实验结果显示抑制剂GATPT能够影响细胞内VHR的天然底物phosphor-ERK和phosphor-JNK的表达量。而且它对细胞周期的影响和RNA干扰细胞内VHR表达所导致的细胞周期变化一致。VHR的小分子抑制剂可以为研究蛋白质酪氨酸磷酸酶生理功能提供一种新的途径。
第四章首先对本工作的研究背景，即AF-6蛋白及PDZ结构域的功能和结构、Bcr蛋白的功能和结构进行了简单的介绍。AF-6基因最早是在急性淋巴性白血病人中作为ALL-1的融合配体被发现的。AF-6在细胞连接和信号转导中发挥双重作用。AF-6 PDZ结构域位于AF-6蛋白的C-端部分。在细胞中AF-6蛋白参与的很多蛋白质—蛋白质相互作用是由它的PDZ结构域介导的。细胞连接和肿瘤的浸润转移关系密切，上皮细胞向间质细胞的转化过程中细胞结构改变，失去极性，并且失去与邻近细胞的接触，获得运动性。因此抑制细胞黏附的小分子有可能发展成阻止肿瘤转移的药物。基于本组解出AF-6 PDZ结构域NMR溶液结构和AF-6蛋白质PDZ结构域与Bcr C-末端小肽的复合物NMR溶液结构，我们通过计算虚拟筛选化合物库和荧光标记蛋白来找出能够和AF-6 PDZ结构域的两个小分子，并希望以此为基础进一步优化增强小分子配体的结合能力，从而为研究AF-6蛋白质PDZ结构域在细胞内的功能提供一种途径。
Our work focuses on identifying the inhibitor of Human Vaccina H1 related protein (VHR), by using virtual screening and NMR method. One compound with novel structure was found to be a competitive and potent inhibitor of VHR. And the effects of this inhibitor in cells were also investigated. VHR is a dual-specific phosphatase (DSPs) playing an important role in the mitogen-activated protein (MAP) kinase cascades regulation. It is also a potential drug target for designing inhibitors against diseases related to the immune response. The inhibitor may be contribute to the clarification of physiological function of VHR, and may be a promising candidate for designing of more effective agents against VHR.
First chapter introduces and reviews the current docking methods in drug virtual screening. As a new method or technology for drug discovery, virtual screening has been involved into the pipeline of drug discovery and development as a practical tool. With the development of structural biology, structural genomics, functional genomics, and proteomics, more and more three dimensional structures of biologic molecule will be expressed, virtual screening would play a vital role which could accelerate the course of drug discovery.
The second chapter is the brief review of NMR screening techniques in drug discovery and drug design. Library about NMR screening design is also discussed. Pharmaceutical and academic nuclear magnetic resonance (NMR) groups have implemented NMR screening techniques as a powerful approach to identify and to investigate protein/ligand interactions. Pharmaceutical groups in particular have incorporated NMR screening strategies into their drug discovery and drug design programs. This stems from the fact that NMR screening is naturally synergistic with combinatorial or medicinal chemistry, high throughput screening (HTS), structure-based drug design, and genomics.
NMR screening can be defined as the identification of small molecule ligands for macromolecular targets by observation of a change in an NMR parameter that occurs upon their interaction. NMR screening methods can be divided into those that detect interactions by observation of either macromolecule NMR parameters or small molecule NMR parameters. In the case of macromolecules, the parameter that can be monitored is limited typically to chemical shifts. For small molecules, the choice of NMR parameters is more diverse. These include longitudinal, transverse; diffusion coefficients; and intermolecular and intramolecular magnetization transfer. The latter includes transferred NOE, NOE pumping and reverse NOE pumping, saturation transfer, and WaterLOGSY experiments.
In the third chapter, we described the work about identifying the potent inhibitor of VHR. Human Vaccinia H1-related phosphatase (VHR) is a dual-specific phosphatase (DSPs) playing an important role in the mitogen-activated protein (MAP) kinase cascades regulation. It is also a potential drug target for designing inhibitors against diseases related to the immune response. Combining virtual and NMR-based ligand screening strategy, we successfully identified four VHR inhibitors, of which GATPT (glucosamine-aminoethoxy-triphenyl-tin) can bind to VHR with a K_i value of 2.54μM. The putative binding mode of GATPT was constructed by molecular docking simulation to provide structural insights into the ligand binding mechanism. Furthermore, we found that this compound can significantly inhibit the dephosphorylation of the extracellular regulated kinases (ERKs) and c-Jun N-terminal kinases (JNKs) and block transition of G1-S phase in the cell cycle. Therefore, GATPT structure is a promising candidate for designing of more effective agents against VHR.
The fourth chapter introduced the work processed on identifying inhibitors of AF-6 PDZ domain. The human AF-6 gene was initially discovered as a fusion partner of the ALL-1 gene in acute lymphoblastic leukemia. The human AF-6, a scaffold protein between cell membrane-associated proteins and actin cytoskeleton, plays an important role in special cell-cell junctions and signal transduction. Molecules that can block cell adhesion may have value as therapeutic agents that prevent tumor metastasis. Therefore, the inhibitors of AF-6 PDZ domain may be a potential candidate for blocking cell adhesion and preventing tumor metastasis.
第一章简介了计算机辅助药物设计和筛选，其中重点综述了利用分子对接方法虚拟筛选小分子化合物库的原理，以及一些常用分子对接程序的理论基础和筛选流程。虚拟筛选是创新药物研究的新方法和新技术，并且已经成为一种与高通量筛选互补的实用化工具，加入到了创新药物研究的工作流程中。随着结构生物学、结构基因组、功能基因组学及蛋白质组学的发展，越来越多的生物大分子三维结构被测定，虚拟筛选能够发挥更大的作用。分子对接是药物发现和设计中一种非常重要的方法，将会减少随机筛选的盲目性，大大加快药物发现的速度。
第二章主要综述了核磁共振(NMR)技术在药物筛选中的方法与应用。核磁共振(NMR)技术在方法学和硬件上的迅速发展，使其成为化学和结构生物学中最重要的波谱技术。特别是生物核磁共振技术在药物研发过程中，提供从药物设计结构信息到基于NMR技术进行配体的筛选的广泛应用，使得生物核磁共振技术在药物研究领域地位不断加强，成为药物研究的基础工具。核磁共振已经作为一个强大的筛选方法来识别和探测蛋白和配体的相互作用。药物公司也已经将NMR筛选平台纳入药物发现和药物设计部门。
NMR筛选可以被定义为通过观察当蛋白和配体相互作用时NMR参数的变化来识别靶蛋白的小分子配体。NMR筛选可以被分为基于探测大分子蛋白的参数变化和基于探测小分子配体的参数变化两大类。对于大分子，可观测的参数被限制只能是最典型的化学位移。对于小分子，可选择的参数就比较多。包括纵向，横向驰豫，扩散系数，分子间和分子内磁化转移。后者包括转移NOE(Nuclear Overhauser Effect)，NOE pumping和反向NOE pumping，WaterLOGSY实验。
第三章介绍了结合计算机虚拟筛选和核磁共振(NMR)技术筛选人双特异性蛋白质磷酸酶VHR的抑制剂的研究。首先对VHR的功能和结构，已发现的抑制剂进行了全面介绍。并进一步研究了抑制剂在细胞内的影响。双特异性蛋白质磷酸酶是参与促有丝分裂信号转导和细胞周期调控的主要酶类。既能从含有磷酸酪氨酸，又能从含有磷酸苏氨酸／丝氨酸的蛋白质中移去磷酸盐。VHR在调控MAPK级联途径中起重要作用，从而与许多人类疾病联系在一起。ZAP-70酪氨酸激酶和牛痘相关激酶VRK 3能通过不同方式增强VHR的活性，从而促进VHR对Erk2-Elk-1途径的抑制。VHR能够调节细胞周期而且能够调节自身的表达量．缺失VHR的细胞会在G1-S和G2-M期静息，并且有衰老迹象。
我们首先运用分子对接程序DOCK4.0对小分子库进行虚拟筛选，通过扩散编辑NMR方法评估所选小分子的结合能力，发现了4个能够结合VHR的配体。并以对硝基苯酚磷酸盐为底物测定计算了它们抑制VHR去磷酸的能力，发现其中一个小分子GATPT具有新颖的结构，强烈并且竞争性抑制VHR的酶活(IC_(50)=2.92μM)。AutoDock计算显示的复合物结构模型表明这个小分子和蛋白质活性口袋紧密结合。一系列实验结果显示抑制剂GATPT能够影响细胞内VHR的天然底物phosphor-ERK和phosphor-JNK的表达量。而且它对细胞周期的影响和RNA干扰细胞内VHR表达所导致的细胞周期变化一致。VHR的小分子抑制剂可以为研究蛋白质酪氨酸磷酸酶生理功能提供一种新的途径。
第四章首先对本工作的研究背景，即AF-6蛋白及PDZ结构域的功能和结构、Bcr蛋白的功能和结构进行了简单的介绍。AF-6基因最早是在急性淋巴性白血病人中作为ALL-1的融合配体被发现的。AF-6在细胞连接和信号转导中发挥双重作用。AF-6 PDZ结构域位于AF-6蛋白的C-端部分。在细胞中AF-6蛋白参与的很多蛋白质—蛋白质相互作用是由它的PDZ结构域介导的。细胞连接和肿瘤的浸润转移关系密切，上皮细胞向间质细胞的转化过程中细胞结构改变，失去极性，并且失去与邻近细胞的接触，获得运动性。因此抑制细胞黏附的小分子有可能发展成阻止肿瘤转移的药物。基于本组解出AF-6 PDZ结构域NMR溶液结构和AF-6蛋白质PDZ结构域与Bcr C-末端小肽的复合物NMR溶液结构，我们通过计算虚拟筛选化合物库和荧光标记蛋白来找出能够和AF-6 PDZ结构域的两个小分子，并希望以此为基础进一步优化增强小分子配体的结合能力，从而为研究AF-6蛋白质PDZ结构域在细胞内的功能提供一种途径。
Our work focuses on identifying the inhibitor of Human Vaccina H1 related protein (VHR), by using virtual screening and NMR method. One compound with novel structure was found to be a competitive and potent inhibitor of VHR. And the effects of this inhibitor in cells were also investigated. VHR is a dual-specific phosphatase (DSPs) playing an important role in the mitogen-activated protein (MAP) kinase cascades regulation. It is also a potential drug target for designing inhibitors against diseases related to the immune response. The inhibitor may be contribute to the clarification of physiological function of VHR, and may be a promising candidate for designing of more effective agents against VHR.
First chapter introduces and reviews the current docking methods in drug virtual screening. As a new method or technology for drug discovery, virtual screening has been involved into the pipeline of drug discovery and development as a practical tool. With the development of structural biology, structural genomics, functional genomics, and proteomics, more and more three dimensional structures of biologic molecule will be expressed, virtual screening would play a vital role which could accelerate the course of drug discovery.
The second chapter is the brief review of NMR screening techniques in drug discovery and drug design. Library about NMR screening design is also discussed. Pharmaceutical and academic nuclear magnetic resonance (NMR) groups have implemented NMR screening techniques as a powerful approach to identify and to investigate protein/ligand interactions. Pharmaceutical groups in particular have incorporated NMR screening strategies into their drug discovery and drug design programs. This stems from the fact that NMR screening is naturally synergistic with combinatorial or medicinal chemistry, high throughput screening (HTS), structure-based drug design, and genomics.
NMR screening can be defined as the identification of small molecule ligands for macromolecular targets by observation of a change in an NMR parameter that occurs upon their interaction. NMR screening methods can be divided into those that detect interactions by observation of either macromolecule NMR parameters or small molecule NMR parameters. In the case of macromolecules, the parameter that can be monitored is limited typically to chemical shifts. For small molecules, the choice of NMR parameters is more diverse. These include longitudinal, transverse; diffusion coefficients; and intermolecular and intramolecular magnetization transfer. The latter includes transferred NOE, NOE pumping and reverse NOE pumping, saturation transfer, and WaterLOGSY experiments.
In the third chapter, we described the work about identifying the potent inhibitor of VHR. Human Vaccinia H1-related phosphatase (VHR) is a dual-specific phosphatase (DSPs) playing an important role in the mitogen-activated protein (MAP) kinase cascades regulation. It is also a potential drug target for designing inhibitors against diseases related to the immune response. Combining virtual and NMR-based ligand screening strategy, we successfully identified four VHR inhibitors, of which GATPT (glucosamine-aminoethoxy-triphenyl-tin) can bind to VHR with a K_i value of 2.54μM. The putative binding mode of GATPT was constructed by molecular docking simulation to provide structural insights into the ligand binding mechanism. Furthermore, we found that this compound can significantly inhibit the dephosphorylation of the extracellular regulated kinases (ERKs) and c-Jun N-terminal kinases (JNKs) and block transition of G1-S phase in the cell cycle. Therefore, GATPT structure is a promising candidate for designing of more effective agents against VHR.
The fourth chapter introduced the work processed on identifying inhibitors of AF-6 PDZ domain. The human AF-6 gene was initially discovered as a fusion partner of the ALL-1 gene in acute lymphoblastic leukemia. The human AF-6, a scaffold protein between cell membrane-associated proteins and actin cytoskeleton, plays an important role in special cell-cell junctions and signal transduction. Molecules that can block cell adhesion may have value as therapeutic agents that prevent tumor metastasis. Therefore, the inhibitors of AF-6 PDZ domain may be a potential candidate for blocking cell adhesion and preventing tumor metastasis.
引文
Abagyan, R., Totrov, M., 2001. High-throughput docking for lead generation. Curr Opin Chem Biol. 5, 375-82.
Arnold, J. R., et al, 2004. SitePrint: three-dimensional pharmacophore descriptors derived from protein binding sites for family based active site analysis, classification, and drug design. J Chem Inf Comput Sci. 44,2190-8.
Berman, H. M., et al., 2002. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 58, 899-907.
Brooijmans, N., Kuntz, I. D., 2003. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 32, 335-73.
Carlson, H. A., 2002a. Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol. 6, 447-52.
Carlson, H. A., 2002b. Protein Flexibility is an Important Component of Structure-Based Drug Discovery. Current Pharmaceutical Design. 8, 1571-1578.
Charifson, P. S., et al., 1999. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem. 42, 5100-9.
Chen, H. F., et al., 2003. Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking. SAR QSAR Environ Res. 14, 251-64.
Clark, R. D., et al., 2002. Consensus scoring for ligand/protein interactions. J Mol Graph Model. 20,281-95.
Davis, A. M., et al., 2003. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed Engl. 42, 2718-36.
Doman, T. N., et al., 2002. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine Phosphatase-1B. J Med Chem. 45, 2213-21.
Dror, O., et al., 2004. Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. Curr Med Chem. 11, 71-90.
Ferrara, P., et al., 2004. Assessing scoring functions for protein-ligand interactions. J Med Chem. 47, 3032-47.
Floyd, C. D., et al., 1999. Combinatorial chemistry as a tool for drug discovery. Prog Med Chem. 36,91-168.
Gohlke H, K. G, 2002. Approaches to the description and prediction of the binding affinity of small-molecule ligands to acromolecular receptors. Angew Chem Int Ed Engl. 41, 2644-2676.
Guner, O. F., 2002. History and evolution of the pharmacophore concept in computer-aided drug design. Curr Top Med Chem. 2, 1321-32.
Halperin, I., et al., 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 47,409-43.
Harriman, D. J., Deslongchamps, G, 2004. Reverse-docking as a computational tool for the study of asymmetric organocatalysis. J Comput Aided Mol Des. 18, 303-8.
Kellogg, G. E., Semus, S. F., 2003. 3D QSAR in modern drug design. Exs. 223-41.
Kitchen, D. B., et al., 2004. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 3, 935-49.
Kollman, P. A., 1993. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem Rev. 93, 2395-2417.
Kurogi, Y., Guner, O. F., 2001. Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr Med Chem. 8, 1035-55.
Laederach, A., Reilly, P. J., 2003. Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comput Chem. 24, 1748-57.
Lee, A., Breitenbucher, J. G, 2003. The impact of combinatorial chemistry on drug discovery. Curr Opin Drug Discov Devel. 6, 494-508.
McConkey BJ, et al., 2002. The performance of current methods in ligand-protein docking. Current Science. 83, 845-855.
Melese, T., Hieter, P., 2002. From genetics and genomics to drug discovery: yeast rises to the challenge. Trends Pharmacol Sci. 23, 544-7.
Murcko, M., Caron, P., 2002. Transforming the genome to drug discovery. Drug Discov Today. 7, 583-4.
Myers, S., Baker, A., 2001. Drug discovery--an operating model for a new era. Nat Biotechnol. 19, 727-30.
Oprea, T. I., Matter, H., 2004. Integrating virtual screening in lead discovery. Curt Opin Chem Biol. 8, 349-58.
Otto, S., 2003. Dynamic combinatorial chemistry: a new method for selection and preparation of synthetic receptors. Curr Opin Drug Discov Devel. 6, 509-20.
Plunkett, M. J., Ellman, J. A., 1997. Combinatorial chemistry and new drugs. Sci Am. 276, 68-73.
Raha, K., Merz, K. M., Jr., 2004. A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc. 126, 1020-1.
Richards, W. G., 2002. Virtual screening using grid computing: the screensaver project. Nat Rev Drug Discov. 1, 551-5.
Shen, J., et al., 2003. Virtual screening on natural products for discovering active compounds and target information. Curr Med Chem. 10, 2327-42.
Shoichet, B. K., 2004. Virtual screening of chemical libraries. Nature. 432, 862-5.
Simonson, T., et al., 2002. Free energy simulations come of age: protein-ligand recognition. Acc Chem Res. 35,430-7.
Teague, S. J., 2003. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov. 2, 527-41.
Waiters, W. P., Murcko, M. A., 2002. Prediction of'drug-likeness'. Adv Drug Deliv Rev. 54, 255-71.
Wei, B. Q., et al., 2004. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol, 337, 1161-82.
陈凯先；蒋华良；嵇汝运，2000．计算机辅助药物设计---原理、方法及应用．上海：上海科学技术出版社．
李洪林；沈建华；罗小民；沈旭；朱维良；王希诚；陈凯先；蒋华良，2005．虚拟筛选与新药发现．生命科学 17，(2)，125-131．
徐筱杰；侯廷军；乔学斌；章威，2004计算机辅助药物分子设计．化学工业出版社．
A. Fersht, 1985. Enzyme Structure and Mechanism, Freeman, New York,.
A. KμMar, P. K. M., 1996. Conc. Magn. Reson. 8, 139.
Balaram, P., et al., 1972. Negative nuclear Overhauser effects as probes of macromolecular structure. J Am Chem Soc. 94, 4015-7.
Bemis, G. W., Murcko, M. A., 1996. The properties of known drugs. 1. Molecular frameworks. J Med Chem. 39, 2887-93.
Benie, A. J., et al., 2003. Virus-ligand interactions: identification and characterization of ligand binding by NMR spectroscopy. J Am Chem Soc. 125, 14-5.
C. D. Brian J. Stockman, 2002. Progress in Nuclear Magnetic Resonance Spectroscopy. Prog. NMR Spectrosc. 41, 187-231.
C. Rossi, A. D., C. Bonechi, G. Corbini, R. Rappuoli, E. Dreassi, P. Corti,, 1997. Nuclear relaxation studies in ligand-macromolecule affinity index determination. Chem. Phys. Lett. . 264, 205-209.
C. Rossi, C. B., S. Martini, M. Ricci, G. Corbini, P. Corti, A. Donati, ,2001. Ligand-macromolecule complexes: affinity index determination by selective nuclear relaxation analysis Magn. Reson. Chem. . 39, 457.
C. Rossi, S. B., C. Bonechi, G. Corbini, P. Corti, A. Donati,, 1999. Ligand-Proteins Recognition Studies as Determined by Nuclear Relaxation Analysis. Chem. Phys. Lett. . 30,495-500.
Campbell, A. P., Sykes, B. D., 1993. The two-dimensional transferred nuclear Overhauser effect: theory and practice. Annu Rev Biophys Biomol Struct. 22, 99-122.
D.L. Rabenstein, T. N., G. Bigam,, 1979. A Pulse Sequence for the Measurement of Spin-Lattice Relaxation Times of Small Molecules in Protein Solutions. J. Magn. Reson. . 34, 669-674.
Dalvit, C, Bohlen, J. M., 1997. Analysis of biofluids and chemical mixtures in non-deuterated solvents with 1H diffusion-weighted PFG phase-sensitive double-quantum NMR spectroscopy. NMR Biomed. 10, 285-91.
Dalvit, C, et al., 2002. High-throughput NMR-based screening with competition binding experiments. J Am Chem Soc. 124, 7702-9.
Delfini , M., et al., 2000. 1H NMR relaxation investigation of inhibitors interacting with Torpedo californica acetylcholinesterase. J Magn Reson. 144, 129-33.
E. Gaggelli, G. V., K. Tamir, G. Navon,, 1992. Determination of absolute values of dipolar cross-relaxation rates for ligands bound to macromolecules using double-selective TI. Magn. Reson. Chem. . 30, 461-465.
E. MacNamara, T. H., G. Fisher, S. Williams, D. Raftery, 1999. Multiplex Sample NMR: An Approach to High-Throughput NMR using a Parallel Coil Probe. Anal. Chim. Acta 397, 9.
E.O. Stejskal, J. E. T., 1965. Spin diffusion measurements: spin echoes in the presence of. a time-dependent field gradient. J. Chem. Phys.. 42, 288-292.
F. Ni, 1994. Recent developments in transferrred NOE methods. Prog. NMR Spectrosc. . 26, 517-606.
Fejzo, J., et al., 1999. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem Biol. 6, 755-69.
G. Valensin, T. K., G.J. Navon,, 1982. Selective and Nonselective Proton Spin-Lattice Relaxation Studies of Enzyme-Substrate Interactions J. Magn. Reson. . 46, 23.
G.M. Clore, A. M. G., 1982. Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J. Magn. Reson.. 48, 402-417.
Hajduk, P. J., et al., 2000a. Identification of novel inhibitors of urokinase via NMR-based screening. J Med Chem. 43, 3862-6.
Hajduk, P. J., et al., 1997a. NMR-based discovery of lead inhibitors that block DNA binding of the human papillomavirus E2 protein. J Med Chem. 40, 3144-50.
Hajduk, P. J., et al., 1999. Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. J Med Chem. 42, 3852-9.
Hajduk, P. J., et al., 2000b. Design of adenosine kinase inhibitors from the NMR-based screening of fragments. J Med Chem. 43, 4781-6.
Hajduk, P. J., et al., 1997b. Discovering high-affinity ligands for proteins. Science. 278, 497,499.
J. Klein, R. M., M. Mayer, B. Meyer,, 1999. Detecting Binding Affinity to Immobilized Receptor Proteins in Compound Libraries by HR-MAS STD NMR J. Am. Chem. Soc. .121, 5336-5337.
J.E. Tanner, 1970. Use of the stimulated echo in NMR diffusion studies. J. Chem. Phys. . 52, 2523-2526.
J.Stockman, B., 1998. NMR spectroscopy as a tool for structure-based drug design Prog. NMR Spectrosc. . 33.
Jahnke, W., et al., 2001. Spin label enhanced NMR screening. J Am Chem Soc. 123, 3149-50.
Jeffrey W. Peng, J. M., Norzehan Abdul-Manan, 2004. NMR experiments for lead generation in drug discovery. Progress in Nuclear Magnetic Resonance Spectroscopy. 44, 225-256.
Jr., C. S. J., 1999. Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Progress in Nuclear Magnetic Resonance Spectroscopy. 34, 203-256.
L. Herfurth, T. W., T. Peters,, 2000. Application of 3D-TOCSY-trNOESY for the Assignment of Bioactive Ligands from Mixtures. Angew. Chem. Int. Ed. 39,2097-2099.
Lepre, C. A., 2001. Library design for NMR-based screening. Drug Discov Today. 6, 133-140.
Liu, J., et al., 1991. Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell. 66, 807-15.
M. Mayer, B. M., 1999. Characterization of Ligand Binding by Saturation Transfer Difference NMR Spectroscopy Angew. Chem. Int. Ed. 38, 1784-1788.
Mansfield, P., 1984. Spatial mapping of the chemical shift in NMR. Magn Reson Med. 1, 370-86.
Mayer, M., Meyer, B., 2001. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc. 123,6108-17.
Meyer, B., et al, 1997. Screening mixtures for biological activity by NMR. Eur J Biochem. 246, 705-9.
P. Stilbs, 1987. Fourier Transform Pulsed-Gradient Spin-Echo Studies of Molecular Diffusion. Prog. NMR Spectrosc. 19, 1.
P. J. Hajduk, E. T. O., S.W. Fesik,, 1997. One-Dimensional Relaxation- and Diffusion-Edited NMR Methods for Screening Compounds That Bind to Macromolecules J. Am. Chem. Soc. 119,12257-12261.
R. Freeman, H. D. W. H., 1971. Natural abundance carbon-13 relaxed Fourier Transform Nuclear Magnetic Resonance spectra of complex molecules. J. Chem. Phys. . 55, 189-198.
R. Meinecke, B. M., 2001. J. Am. Chem. Soc.. 44, 3059.
S. Forse'n, R. A. H., 1963. Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance. J. Chem. Phys. 39, 2892.
Scherf, T., Anglister, J., 1993. A T1 rho-filtered two-dimensional transferred NOE spectrum for studying antibody interactions with peptide antigens. Biophys J. 64, 754-61.
Serber, Z., et al., 2001. High-resolution macromolecular NMR spectroscopy inside living cells. J Am Chem Soc. 123, 2446-7.
Shapiro, M. J., Wareing, J. R., 1998. NMR methods in combinatorial chemistry. Curr Opin Chem Biol. 2,372-5.
Shuker, S. B., et al., 1996. Discovering high-affinity ligands for proteins: SAR by NMR. Science. 274,1531-4.
T.-L. Hwang, A. J. S., 1995. Water suppression that works. Excitation sculpting using arbitray waveforms and pulsed field gradients. J. Magn. Reson. Al 12, 275-279.
T.E. Bull, 1992. Relaxation in the rotating frame in liquids. Prog. NMR Spectrosc. 24, 377-410.
van Dongen, M. J., et al., 2002. Structure-based screening as applied to human FABP4: a highly efficient alternative to HTS for hit generation. J Am Chem Soc. 124, 11874-80.
Veglia, G., et al., 1998. 1H NMR studies on the interaction of beta-carboline derivatives with human serum albumin. J Magn Reson. 130, 281-6.
W. Jahnke, H. C. K., M.J.J. Blommers, J.L. Magnani, B. Ernst,, 1997. Comparison of the Bioactive Conformations of Sialyl LewisX and a Potent Sialyl LewisX Mimic. Angew. Chem. Int. Ed. . 36, 2603-2607.
W. Jahnke, L. B. P., C.G. Paris, A. Strauss, G. Fendrich, C.M. Nalin, 2000. Second-Site NMR Screening with a Spin-Labeled First Ligand J. Am. Chem. Soc. 122, 7394.
W.S. Price, P. W. K., 1991. Effect of nonrectangular field gradient pulses in the Stejskal and Tanner (diffusion) pulse sequence. J. Magn. Reson. . 94, 133-139.
Alonso, A., et al., 2003. Tyrosine phosphorylation of VHR Phosphatase by ZAP-70. Nat Immunol. 4, 44-8.
Barford, D., 1999. Colworth Medal Lecture. Structural studies of reversible protein phosphorylation and protein phosphatases. Biochem Soc Trans. 27, 751-66.
Barford, D., et al., 1994. Crystal structure of human protein tyrosine Phosphatase 1B. Science. 263, 1397-404.
Braham, R., et al, 2003. The effect of glucosamine supplementation on people experiencing regular knee pain. Br J Sports Med. 37, 45-9; discussion 49.
Brian J. Stockman, C. D., 2002. NMR screening techniques in drug discovery and drug design. Progress in Nuclear Magnetic Resonance Spectroscopy. 41, 187-231.
Canagarajah, B. J., et al., 1997. Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell. 90, 859-69.
Chen, L., et al., 1996. VHR and PTP1 protein phosphatases exhibit remarkably different active site specificities toward low molecular weight nonpeptidic substrates. Biochemistry. 35, 9349-54.
Cohen, P., 2000. The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem Sci. 25, 596-601.
D. S. G. Garrett, M. M., 1999. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 19.
Denu, J. M., Dixon, J. E., 1995. A catalytic mechanism for the dual-specific phosphatases. Proc Natl Acad Sci U S A. 92, 5910-4.
Denu, J. M., et al., 1996. Visualization of intermediate and transition-state structures in protein-tyrosine Phosphatase catalysis. Proc Natl Acad Sci U S A. 93, 2493-8.
Denu, J. M., et al., 1995. The catalytic role of aspartic acid-92 in a human dual-specific protein-tyrosine-phosphatase. Biochemistry. 34, 3396-403.
Drickamer, K., 1992. Engineering galactose-binding activity into a C-type mannose-binding protein. Nature. 360, 183-6.
Elchebly, M., et al., 1999. Increased insulin sensitivity and obesity resistance in mice lacking the protein tyrosine Phosphatase-1B gene. Science. 283, 1544-8.
Ewing TJ, M. S., Skillman AG, Kuntz ID.. 2001. Dock 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aid. Mol. Des. 15, 411-428.
Fauman, E. B., et al., 1996. The X-ray crystal structures of Yersinia tyrosine Phosphatase with bound tungstate and nitrate. Mechanistic implications. J Biol Chem. 271, 18780-8.
Garrett M. Morris, D. S. G, 1998. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry. 19, 1639-1662.
Gibbs, S. J., 1991. A PFG-NMR experiment for accurate diffusion and flow studies in the presence of eddy currents. J. Magn. Reson. 93, 395-402.
Guan, K. L, et al., 1991. A Tyr/Ser protein Phosphatase encoded by vaccinia virus. Nature. 350, 359-62.
Hamaguchi, T., et al., 1995. RK-682, a potent inhibitor of tyrosine Phosphatase, arrested the mammalian cell cycle progression at Glphase. FEBS Lett. 372, 54-8.
Hengge, A. C, et al., 1996. Transition-state structures for the native dual-specific Phosphatase VHR and D92N and S131A mutants. Contributions to the driving force for catalysis. Biochemistry. 35,7084-92.
Hoff, R. H., et al., 2000. Effects on general acid catalysis from mutations of the invariant tryptophan and arginine residues in the protein tyrosine Phosphatase from Yersinia. Biochemistry. 39, 46-54.
Hunter, T., Sefton, B. M., 1980. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci U S A. 77, 1311-5.
Ishibashi, T., et al., 1992. Expression cloning of a human dual-specificity Phosphatase. Proc Natl Acad Sci U S A. 89, 12170-4.
Jin-Hahn Kim, M.-H. H., and Myung-Un Choi, 2001. Mutational and Kinetic Evaluation of Conserved His-123 in Dual Specificity Protein-tyrosine Phosphatase Vaccinia H1-related Phosphatase. J Biol Chem. 276,27568.
Kang, T. H., Kim, K. T., 2006. Negative regulation of ERK activity by VRK3-mediated activation of VHR Phosphatase. Nat Cell Biol. 8, 863-9.
Keyse, S. M., 2000. Protein phosphatases and the regulation of mitogen-activated protein kinase signalling. Curr Opin Cell Biol. 12, 186-92.
Klaman, L. D., et al., 2000. Increased energy expenditure, decreased adiposity, and tissue-specific insulin sensitivity in protein-tyrosine Phosphatase IB-deficient mice. Mol Cell Biol. 20, 5479-89.
Lazo, J. S., et al., 2006. Novel benzofuran inhibitors of human mitogen-activated protein kinase Phosphatase-1. Bioorg Med Chem. 14, 5643-50.
Mengfen Lin, M. J. S., * and James R. Wareing 1997. Diffusion-Edited NMR-Affinity NMR for Direct Observation of Molecular Interactions J. Am. Chem. Soc. 119, 5249-5250.
Moriz Mayer, B. M., 2001. Group Epitope Mapping by Saturation Transfer Difference NMR To Identify Segments of a Ligand in Direct Contact with a Protein Receptor J. Am. Chem. Soc. 123.
Neel, B. G, Tonks, N. K., 1997. Protein tyrosine phosphatases in signal transduction. Curr Opin Cell Biol. 9, 193-204.
Peters, G H., et al., 1998. Electrostatic evaluation of the signature motif (H/V)CX5R(S/T) in protein-tyrosine phosphatases. Biochemistry. 37, 5383-93.
Rahmouni, S., et al, 2006. Loss of the VHR dual-specific Phosphatase causescell-cycle arrest and senescence. Nat Cell Biol. 8, 524-31.
Ruane, R., Griffiths, P., 2002. Glucosamine therapy compared to ibuprofen for joint pain. Br J Community Nurs. 7, 148-52.
Schubert, H. L., et al., 1995. A ligand-induced conformational change in the Yersinia protein tyrosine Phosphatase. Protein Sci. 4, 1904-13.
Sodeoka, M., et al., 2001. Synthesis of a tetronic acid library focused on inhibitors of tyrosine and dual-specificity protein phosphatases and its evaluation regarding VHR and cdc25B inhibition. J Med Chem. 44, 3216-22.
Todd, J. L., et al., 2002. Dual-specificity protein tyrosine Phosphatase VHR down-regulates c-Jun N-terminal kinase (JNK). Oncogene. 21,2573-83.
Todd, J. L., et al., 1999. Extracellular regulated kinases (ERK) 1 and ERK2 are authentic substrates for the dual-specificity protein-tyrosine Phosphatase VHR. A novel role in down-regulating the ERK pathway. J Biol Chem. 274, 13271-80.
Ueda, K., et al., 2002. 4-isoavenaciolide covalently binds and inhibits VHR, a dual-specificity Phosphatase. FEBS Lett. 525,48-52.
Usui, T., et al., 2001. Design and synthesis of a dimeric derivative of RK-682 with increased inhibitory activity against VHR, a dual-specificity ERK Phosphatase: implications for the molecular mechanism of the inhibition. Chem Biol. 8, 1209-20.
Van Vactor, D., et al., 1998. Genetic analysis of protein tyrosine phosphatases. Curr Opin Genet Dev. 8, 112-26.
Yuvaniyama, J., et al, 1996. Crystal structure of the dual specificity protein Phosphatase VHR. Science. 272, 1328-31.
Zhang, Z. Y., 1998. Protein-tyrosine phosphatases: biological function, structural characteristics, and mechanism of catalysis. Crit Rev Biochem Mol Biol. 33, 1-52.
Zhang, Z. Y., 2001. Protein tyrosine phosphatases: prospects for therapeutics. Curr Opin Chem Biol. 5,416-23.
Zhang, Z. Y, et al., 1995. Transition state and rate-limiting step of the reaction catalyzed by the human dual-specificity Phosphatase, VHR. Biochemistry. 34, 16088-96.
Zhou, G, et al., 1994. The catalytic role of Cysl24 in the dual specificity Phosphatase VHR. J Biol Chem. 269,28084-90.
Asakura, T., et al., 1999. Similar and differential behaviour between the nectin-afadin-ponsin and cadherin-catenin systems during the formation and disruption of the polarized junctional alignment in epithelial cells. Genes Cells. 4, 573-81.
Begay-Muller, V., et al, 2002. The LIM domain protein Lmo2 binds to AF6, a translocation partner of the MLL oncogene. FEBS Lett. 521, 36-8.
Boettner, B., et al., 2000. The junctional multidomain protein AF-6 is a binding partner of the RaplA GTPase and associates with the actin cytoskeletal regulator profilin. Proc Natl Acad Sci U S A. 97, 9064-9.
Chen, Q., et al., 2007. Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex. Protein Sci. 16, 1053-62.
Ferrara, P., et al., 2004. Assessing scoring functions for protein-ligand interactions. J Med Chem. 47, 3032-47.
Gasteiger, J., et al., 1990. Automatic Generation of 3D-Atomic Coordinates for Organic Molecules. . Tetrahedron Comp. Method. 3, 537-547.
Goodsell, D. S., et al., 1996. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit. 9, 1-5.
Halperin, I., et al., 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 47, 409-43.
Hillier, B. J., et al., 1999. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science. 284, 812-5.
Hofmann, K., Bucher, P., 1995. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem Sci. 20, 347-9.
Im, Y. J., et al., 2003. Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization. J Biol Chem. 278, 48099-104.
Kramer, B., et al., 1999. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins. 37, 228-41.
Krumrine, J., et al., 2003. Principles and methods of docking and ligand design. Methods Biochem Anal. 44, 443-76.
Kuntz, I. D., 1992. Structure-based strategies for drug design and discovery. Science. 257, 1078-82.
Kuntz, I. D., et al., 1982. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 161,269-88.
Kuriyama, M., et al., 1996. Identification of AF-6 and canoe as putative targets for Ras. J Biol Chem. 271,607-10.
Mandai, K., et al., 1997. Afadin: A novel actin filament-binding protein with one PDZ domain localized at cadherin-based cell-to-cell adherens junction. J Cell Biol. 139, 517-28.
Morris, G. M., et al., 1996. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des. 10, 293-304.
Oschkinat, H., 1999. A new type of PDZ domain recognition. Nat Struct Biol. 6, 408-10.
Ponting, C. P., 1995. AF-6/cno: neither a kinesin nor a myosin, but a bit of both. Trends Biochem Sci. 20, 265-6.
Ponting, C. P., Benjamin, D. R., 1996. A novel family of Ras-binding domains. Trends Biochem Sci. 21,422-5.
Prasad, R., et al., 1993. Cloning of the ALL-1 fusion partner, the AF-6 gene, involved in acute myeloid leukemias with the t(6;ll) chromosome translocation. Cancer Res. 53, 5624-8.
Radziwill, G., et al, 2003. The Bcr kinase downregulates Ras signaling by phosphorylating AF-6 and binding to its PDZ domain. Mol Cell Biol. 23, 4663-72.
Rarey, M., et al., 1997. Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des. 11, 369-84.
Rarey, M., et al., 1996. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des. 10, 41-54.
Su, L., et al., 2003. AF-6 controls integrin-mediated cell adhesion by regulating Rap1 activation through the specific recruitment of RaplGTP and SPA-1. J Biol Chem. 278, 15232-8.
Wang, R., et al., 2003. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem. 46,2287-303.
Yamamoto, T., et al., 1997. The Ras target AF-6 interacts with ZO-1 and serves as a peripheral component of tight junctions in epithelial cells. J Cell Biol. 139, 785-95.
Yamamoto, T., et al., 1999. In vivo interaction of AF-6 with activated Ras and ZO-1. Biochem Biophys Res Commun. 259, 103-7.
Yokoyama, S., et al., 2001. alpha-catenin-independent recruitment of ZO-1 to nectin-based cell-cell adhesion sites through afadin. Mol Biol Cell. 12, 1595-609.
Zhou, H., et al., 2005. Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr. J Biol Chem. 280, 13841-7.
Arnold, J. R., et al, 2004. SitePrint: three-dimensional pharmacophore descriptors derived from protein binding sites for family based active site analysis, classification, and drug design. J Chem Inf Comput Sci. 44,2190-8.
Berman, H. M., et al., 2002. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 58, 899-907.
Brooijmans, N., Kuntz, I. D., 2003. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 32, 335-73.
Carlson, H. A., 2002a. Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol. 6, 447-52.
Carlson, H. A., 2002b. Protein Flexibility is an Important Component of Structure-Based Drug Discovery. Current Pharmaceutical Design. 8, 1571-1578.
Charifson, P. S., et al., 1999. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem. 42, 5100-9.
Chen, H. F., et al., 2003. Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking. SAR QSAR Environ Res. 14, 251-64.
Clark, R. D., et al., 2002. Consensus scoring for ligand/protein interactions. J Mol Graph Model. 20,281-95.
Davis, A. M., et al., 2003. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed Engl. 42, 2718-36.
Doman, T. N., et al., 2002. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine Phosphatase-1B. J Med Chem. 45, 2213-21.
Dror, O., et al., 2004. Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. Curr Med Chem. 11, 71-90.
Ferrara, P., et al., 2004. Assessing scoring functions for protein-ligand interactions. J Med Chem. 47, 3032-47.
Floyd, C. D., et al., 1999. Combinatorial chemistry as a tool for drug discovery. Prog Med Chem. 36,91-168.
Gohlke H, K. G, 2002. Approaches to the description and prediction of the binding affinity of small-molecule ligands to acromolecular receptors. Angew Chem Int Ed Engl. 41, 2644-2676.
Guner, O. F., 2002. History and evolution of the pharmacophore concept in computer-aided drug design. Curr Top Med Chem. 2, 1321-32.
Halperin, I., et al., 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 47,409-43.
Harriman, D. J., Deslongchamps, G, 2004. Reverse-docking as a computational tool for the study of asymmetric organocatalysis. J Comput Aided Mol Des. 18, 303-8.
Kellogg, G. E., Semus, S. F., 2003. 3D QSAR in modern drug design. Exs. 223-41.
Kitchen, D. B., et al., 2004. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 3, 935-49.
Kollman, P. A., 1993. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem Rev. 93, 2395-2417.
Kurogi, Y., Guner, O. F., 2001. Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr Med Chem. 8, 1035-55.
Laederach, A., Reilly, P. J., 2003. Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comput Chem. 24, 1748-57.
Lee, A., Breitenbucher, J. G, 2003. The impact of combinatorial chemistry on drug discovery. Curr Opin Drug Discov Devel. 6, 494-508.
McConkey BJ, et al., 2002. The performance of current methods in ligand-protein docking. Current Science. 83, 845-855.
Melese, T., Hieter, P., 2002. From genetics and genomics to drug discovery: yeast rises to the challenge. Trends Pharmacol Sci. 23, 544-7.
Murcko, M., Caron, P., 2002. Transforming the genome to drug discovery. Drug Discov Today. 7, 583-4.
Myers, S., Baker, A., 2001. Drug discovery--an operating model for a new era. Nat Biotechnol. 19, 727-30.
Oprea, T. I., Matter, H., 2004. Integrating virtual screening in lead discovery. Curt Opin Chem Biol. 8, 349-58.
Otto, S., 2003. Dynamic combinatorial chemistry: a new method for selection and preparation of synthetic receptors. Curr Opin Drug Discov Devel. 6, 509-20.
Plunkett, M. J., Ellman, J. A., 1997. Combinatorial chemistry and new drugs. Sci Am. 276, 68-73.
Raha, K., Merz, K. M., Jr., 2004. A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc. 126, 1020-1.
Richards, W. G., 2002. Virtual screening using grid computing: the screensaver project. Nat Rev Drug Discov. 1, 551-5.
Shen, J., et al., 2003. Virtual screening on natural products for discovering active compounds and target information. Curr Med Chem. 10, 2327-42.
Shoichet, B. K., 2004. Virtual screening of chemical libraries. Nature. 432, 862-5.
Simonson, T., et al., 2002. Free energy simulations come of age: protein-ligand recognition. Acc Chem Res. 35,430-7.
Teague, S. J., 2003. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov. 2, 527-41.
Waiters, W. P., Murcko, M. A., 2002. Prediction of'drug-likeness'. Adv Drug Deliv Rev. 54, 255-71.
Wei, B. Q., et al., 2004. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol, 337, 1161-82.
陈凯先；蒋华良；嵇汝运，2000．计算机辅助药物设计---原理、方法及应用．上海：上海科学技术出版社．
李洪林；沈建华；罗小民；沈旭；朱维良；王希诚；陈凯先；蒋华良，2005．虚拟筛选与新药发现．生命科学 17，(2)，125-131．
徐筱杰；侯廷军；乔学斌；章威，2004计算机辅助药物分子设计．化学工业出版社．
A. Fersht, 1985. Enzyme Structure and Mechanism, Freeman, New York,.
A. KμMar, P. K. M., 1996. Conc. Magn. Reson. 8, 139.
Balaram, P., et al., 1972. Negative nuclear Overhauser effects as probes of macromolecular structure. J Am Chem Soc. 94, 4015-7.
Bemis, G. W., Murcko, M. A., 1996. The properties of known drugs. 1. Molecular frameworks. J Med Chem. 39, 2887-93.
Benie, A. J., et al., 2003. Virus-ligand interactions: identification and characterization of ligand binding by NMR spectroscopy. J Am Chem Soc. 125, 14-5.
C. D. Brian J. Stockman, 2002. Progress in Nuclear Magnetic Resonance Spectroscopy. Prog. NMR Spectrosc. 41, 187-231.
C. Rossi, A. D., C. Bonechi, G. Corbini, R. Rappuoli, E. Dreassi, P. Corti,, 1997. Nuclear relaxation studies in ligand-macromolecule affinity index determination. Chem. Phys. Lett. . 264, 205-209.
C. Rossi, C. B., S. Martini, M. Ricci, G. Corbini, P. Corti, A. Donati, ,2001. Ligand-macromolecule complexes: affinity index determination by selective nuclear relaxation analysis Magn. Reson. Chem. . 39, 457.
C. Rossi, S. B., C. Bonechi, G. Corbini, P. Corti, A. Donati,, 1999. Ligand-Proteins Recognition Studies as Determined by Nuclear Relaxation Analysis. Chem. Phys. Lett. . 30,495-500.
Campbell, A. P., Sykes, B. D., 1993. The two-dimensional transferred nuclear Overhauser effect: theory and practice. Annu Rev Biophys Biomol Struct. 22, 99-122.
D.L. Rabenstein, T. N., G. Bigam,, 1979. A Pulse Sequence for the Measurement of Spin-Lattice Relaxation Times of Small Molecules in Protein Solutions. J. Magn. Reson. . 34, 669-674.
Dalvit, C, Bohlen, J. M., 1997. Analysis of biofluids and chemical mixtures in non-deuterated solvents with 1H diffusion-weighted PFG phase-sensitive double-quantum NMR spectroscopy. NMR Biomed. 10, 285-91.
Dalvit, C, et al., 2002. High-throughput NMR-based screening with competition binding experiments. J Am Chem Soc. 124, 7702-9.
Delfini , M., et al., 2000. 1H NMR relaxation investigation of inhibitors interacting with Torpedo californica acetylcholinesterase. J Magn Reson. 144, 129-33.
E. Gaggelli, G. V., K. Tamir, G. Navon,, 1992. Determination of absolute values of dipolar cross-relaxation rates for ligands bound to macromolecules using double-selective TI. Magn. Reson. Chem. . 30, 461-465.
E. MacNamara, T. H., G. Fisher, S. Williams, D. Raftery, 1999. Multiplex Sample NMR: An Approach to High-Throughput NMR using a Parallel Coil Probe. Anal. Chim. Acta 397, 9.
E.O. Stejskal, J. E. T., 1965. Spin diffusion measurements: spin echoes in the presence of. a time-dependent field gradient. J. Chem. Phys.. 42, 288-292.
F. Ni, 1994. Recent developments in transferrred NOE methods. Prog. NMR Spectrosc. . 26, 517-606.
Fejzo, J., et al., 1999. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem Biol. 6, 755-69.
G. Valensin, T. K., G.J. Navon,, 1982. Selective and Nonselective Proton Spin-Lattice Relaxation Studies of Enzyme-Substrate Interactions J. Magn. Reson. . 46, 23.
G.M. Clore, A. M. G., 1982. Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J. Magn. Reson.. 48, 402-417.
Hajduk, P. J., et al., 2000a. Identification of novel inhibitors of urokinase via NMR-based screening. J Med Chem. 43, 3862-6.
Hajduk, P. J., et al., 1997a. NMR-based discovery of lead inhibitors that block DNA binding of the human papillomavirus E2 protein. J Med Chem. 40, 3144-50.
Hajduk, P. J., et al., 1999. Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. J Med Chem. 42, 3852-9.
Hajduk, P. J., et al., 2000b. Design of adenosine kinase inhibitors from the NMR-based screening of fragments. J Med Chem. 43, 4781-6.
Hajduk, P. J., et al., 1997b. Discovering high-affinity ligands for proteins. Science. 278, 497,499.
J. Klein, R. M., M. Mayer, B. Meyer,, 1999. Detecting Binding Affinity to Immobilized Receptor Proteins in Compound Libraries by HR-MAS STD NMR J. Am. Chem. Soc. .121, 5336-5337.
J.E. Tanner, 1970. Use of the stimulated echo in NMR diffusion studies. J. Chem. Phys. . 52, 2523-2526.
J.Stockman, B., 1998. NMR spectroscopy as a tool for structure-based drug design Prog. NMR Spectrosc. . 33.
Jahnke, W., et al., 2001. Spin label enhanced NMR screening. J Am Chem Soc. 123, 3149-50.
Jeffrey W. Peng, J. M., Norzehan Abdul-Manan, 2004. NMR experiments for lead generation in drug discovery. Progress in Nuclear Magnetic Resonance Spectroscopy. 44, 225-256.
Jr., C. S. J., 1999. Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Progress in Nuclear Magnetic Resonance Spectroscopy. 34, 203-256.
L. Herfurth, T. W., T. Peters,, 2000. Application of 3D-TOCSY-trNOESY for the Assignment of Bioactive Ligands from Mixtures. Angew. Chem. Int. Ed. 39,2097-2099.
Lepre, C. A., 2001. Library design for NMR-based screening. Drug Discov Today. 6, 133-140.
Liu, J., et al., 1991. Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell. 66, 807-15.
M. Mayer, B. M., 1999. Characterization of Ligand Binding by Saturation Transfer Difference NMR Spectroscopy Angew. Chem. Int. Ed. 38, 1784-1788.
Mansfield, P., 1984. Spatial mapping of the chemical shift in NMR. Magn Reson Med. 1, 370-86.
Mayer, M., Meyer, B., 2001. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc. 123,6108-17.
Meyer, B., et al, 1997. Screening mixtures for biological activity by NMR. Eur J Biochem. 246, 705-9.
P. Stilbs, 1987. Fourier Transform Pulsed-Gradient Spin-Echo Studies of Molecular Diffusion. Prog. NMR Spectrosc. 19, 1.
P. J. Hajduk, E. T. O., S.W. Fesik,, 1997. One-Dimensional Relaxation- and Diffusion-Edited NMR Methods for Screening Compounds That Bind to Macromolecules J. Am. Chem. Soc. 119,12257-12261.
R. Freeman, H. D. W. H., 1971. Natural abundance carbon-13 relaxed Fourier Transform Nuclear Magnetic Resonance spectra of complex molecules. J. Chem. Phys. . 55, 189-198.
R. Meinecke, B. M., 2001. J. Am. Chem. Soc.. 44, 3059.
S. Forse'n, R. A. H., 1963. Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance. J. Chem. Phys. 39, 2892.
Scherf, T., Anglister, J., 1993. A T1 rho-filtered two-dimensional transferred NOE spectrum for studying antibody interactions with peptide antigens. Biophys J. 64, 754-61.
Serber, Z., et al., 2001. High-resolution macromolecular NMR spectroscopy inside living cells. J Am Chem Soc. 123, 2446-7.
Shapiro, M. J., Wareing, J. R., 1998. NMR methods in combinatorial chemistry. Curr Opin Chem Biol. 2,372-5.
Shuker, S. B., et al., 1996. Discovering high-affinity ligands for proteins: SAR by NMR. Science. 274,1531-4.
T.-L. Hwang, A. J. S., 1995. Water suppression that works. Excitation sculpting using arbitray waveforms and pulsed field gradients. J. Magn. Reson. Al 12, 275-279.
T.E. Bull, 1992. Relaxation in the rotating frame in liquids. Prog. NMR Spectrosc. 24, 377-410.
van Dongen, M. J., et al., 2002. Structure-based screening as applied to human FABP4: a highly efficient alternative to HTS for hit generation. J Am Chem Soc. 124, 11874-80.
Veglia, G., et al., 1998. 1H NMR studies on the interaction of beta-carboline derivatives with human serum albumin. J Magn Reson. 130, 281-6.
W. Jahnke, H. C. K., M.J.J. Blommers, J.L. Magnani, B. Ernst,, 1997. Comparison of the Bioactive Conformations of Sialyl LewisX and a Potent Sialyl LewisX Mimic. Angew. Chem. Int. Ed. . 36, 2603-2607.
W. Jahnke, L. B. P., C.G. Paris, A. Strauss, G. Fendrich, C.M. Nalin, 2000. Second-Site NMR Screening with a Spin-Labeled First Ligand J. Am. Chem. Soc. 122, 7394.
W.S. Price, P. W. K., 1991. Effect of nonrectangular field gradient pulses in the Stejskal and Tanner (diffusion) pulse sequence. J. Magn. Reson. . 94, 133-139.
Alonso, A., et al., 2003. Tyrosine phosphorylation of VHR Phosphatase by ZAP-70. Nat Immunol. 4, 44-8.
Barford, D., 1999. Colworth Medal Lecture. Structural studies of reversible protein phosphorylation and protein phosphatases. Biochem Soc Trans. 27, 751-66.
Barford, D., et al., 1994. Crystal structure of human protein tyrosine Phosphatase 1B. Science. 263, 1397-404.
Braham, R., et al, 2003. The effect of glucosamine supplementation on people experiencing regular knee pain. Br J Sports Med. 37, 45-9; discussion 49.
Brian J. Stockman, C. D., 2002. NMR screening techniques in drug discovery and drug design. Progress in Nuclear Magnetic Resonance Spectroscopy. 41, 187-231.
Canagarajah, B. J., et al., 1997. Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell. 90, 859-69.
Chen, L., et al., 1996. VHR and PTP1 protein phosphatases exhibit remarkably different active site specificities toward low molecular weight nonpeptidic substrates. Biochemistry. 35, 9349-54.
Cohen, P., 2000. The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem Sci. 25, 596-601.
D. S. G. Garrett, M. M., 1999. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 19.
Denu, J. M., Dixon, J. E., 1995. A catalytic mechanism for the dual-specific phosphatases. Proc Natl Acad Sci U S A. 92, 5910-4.
Denu, J. M., et al., 1996. Visualization of intermediate and transition-state structures in protein-tyrosine Phosphatase catalysis. Proc Natl Acad Sci U S A. 93, 2493-8.
Denu, J. M., et al., 1995. The catalytic role of aspartic acid-92 in a human dual-specific protein-tyrosine-phosphatase. Biochemistry. 34, 3396-403.
Drickamer, K., 1992. Engineering galactose-binding activity into a C-type mannose-binding protein. Nature. 360, 183-6.
Elchebly, M., et al., 1999. Increased insulin sensitivity and obesity resistance in mice lacking the protein tyrosine Phosphatase-1B gene. Science. 283, 1544-8.
Ewing TJ, M. S., Skillman AG, Kuntz ID.. 2001. Dock 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aid. Mol. Des. 15, 411-428.
Fauman, E. B., et al., 1996. The X-ray crystal structures of Yersinia tyrosine Phosphatase with bound tungstate and nitrate. Mechanistic implications. J Biol Chem. 271, 18780-8.
Garrett M. Morris, D. S. G, 1998. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry. 19, 1639-1662.
Gibbs, S. J., 1991. A PFG-NMR experiment for accurate diffusion and flow studies in the presence of eddy currents. J. Magn. Reson. 93, 395-402.
Guan, K. L, et al., 1991. A Tyr/Ser protein Phosphatase encoded by vaccinia virus. Nature. 350, 359-62.
Hamaguchi, T., et al., 1995. RK-682, a potent inhibitor of tyrosine Phosphatase, arrested the mammalian cell cycle progression at Glphase. FEBS Lett. 372, 54-8.
Hengge, A. C, et al., 1996. Transition-state structures for the native dual-specific Phosphatase VHR and D92N and S131A mutants. Contributions to the driving force for catalysis. Biochemistry. 35,7084-92.
Hoff, R. H., et al., 2000. Effects on general acid catalysis from mutations of the invariant tryptophan and arginine residues in the protein tyrosine Phosphatase from Yersinia. Biochemistry. 39, 46-54.
Hunter, T., Sefton, B. M., 1980. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci U S A. 77, 1311-5.
Ishibashi, T., et al., 1992. Expression cloning of a human dual-specificity Phosphatase. Proc Natl Acad Sci U S A. 89, 12170-4.
Jin-Hahn Kim, M.-H. H., and Myung-Un Choi, 2001. Mutational and Kinetic Evaluation of Conserved His-123 in Dual Specificity Protein-tyrosine Phosphatase Vaccinia H1-related Phosphatase. J Biol Chem. 276,27568.
Kang, T. H., Kim, K. T., 2006. Negative regulation of ERK activity by VRK3-mediated activation of VHR Phosphatase. Nat Cell Biol. 8, 863-9.
Keyse, S. M., 2000. Protein phosphatases and the regulation of mitogen-activated protein kinase signalling. Curr Opin Cell Biol. 12, 186-92.
Klaman, L. D., et al., 2000. Increased energy expenditure, decreased adiposity, and tissue-specific insulin sensitivity in protein-tyrosine Phosphatase IB-deficient mice. Mol Cell Biol. 20, 5479-89.
Lazo, J. S., et al., 2006. Novel benzofuran inhibitors of human mitogen-activated protein kinase Phosphatase-1. Bioorg Med Chem. 14, 5643-50.
Mengfen Lin, M. J. S., * and James R. Wareing 1997. Diffusion-Edited NMR-Affinity NMR for Direct Observation of Molecular Interactions J. Am. Chem. Soc. 119, 5249-5250.
Moriz Mayer, B. M., 2001. Group Epitope Mapping by Saturation Transfer Difference NMR To Identify Segments of a Ligand in Direct Contact with a Protein Receptor J. Am. Chem. Soc. 123.
Neel, B. G, Tonks, N. K., 1997. Protein tyrosine phosphatases in signal transduction. Curr Opin Cell Biol. 9, 193-204.
Peters, G H., et al., 1998. Electrostatic evaluation of the signature motif (H/V)CX5R(S/T) in protein-tyrosine phosphatases. Biochemistry. 37, 5383-93.
Rahmouni, S., et al, 2006. Loss of the VHR dual-specific Phosphatase causescell-cycle arrest and senescence. Nat Cell Biol. 8, 524-31.
Ruane, R., Griffiths, P., 2002. Glucosamine therapy compared to ibuprofen for joint pain. Br J Community Nurs. 7, 148-52.
Schubert, H. L., et al., 1995. A ligand-induced conformational change in the Yersinia protein tyrosine Phosphatase. Protein Sci. 4, 1904-13.
Sodeoka, M., et al., 2001. Synthesis of a tetronic acid library focused on inhibitors of tyrosine and dual-specificity protein phosphatases and its evaluation regarding VHR and cdc25B inhibition. J Med Chem. 44, 3216-22.
Todd, J. L., et al., 2002. Dual-specificity protein tyrosine Phosphatase VHR down-regulates c-Jun N-terminal kinase (JNK). Oncogene. 21,2573-83.
Todd, J. L., et al., 1999. Extracellular regulated kinases (ERK) 1 and ERK2 are authentic substrates for the dual-specificity protein-tyrosine Phosphatase VHR. A novel role in down-regulating the ERK pathway. J Biol Chem. 274, 13271-80.
Ueda, K., et al., 2002. 4-isoavenaciolide covalently binds and inhibits VHR, a dual-specificity Phosphatase. FEBS Lett. 525,48-52.
Usui, T., et al., 2001. Design and synthesis of a dimeric derivative of RK-682 with increased inhibitory activity against VHR, a dual-specificity ERK Phosphatase: implications for the molecular mechanism of the inhibition. Chem Biol. 8, 1209-20.
Van Vactor, D., et al., 1998. Genetic analysis of protein tyrosine phosphatases. Curr Opin Genet Dev. 8, 112-26.
Yuvaniyama, J., et al, 1996. Crystal structure of the dual specificity protein Phosphatase VHR. Science. 272, 1328-31.
Zhang, Z. Y., 1998. Protein-tyrosine phosphatases: biological function, structural characteristics, and mechanism of catalysis. Crit Rev Biochem Mol Biol. 33, 1-52.
Zhang, Z. Y., 2001. Protein tyrosine phosphatases: prospects for therapeutics. Curr Opin Chem Biol. 5,416-23.
Zhang, Z. Y, et al., 1995. Transition state and rate-limiting step of the reaction catalyzed by the human dual-specificity Phosphatase, VHR. Biochemistry. 34, 16088-96.
Zhou, G, et al., 1994. The catalytic role of Cysl24 in the dual specificity Phosphatase VHR. J Biol Chem. 269,28084-90.
Asakura, T., et al., 1999. Similar and differential behaviour between the nectin-afadin-ponsin and cadherin-catenin systems during the formation and disruption of the polarized junctional alignment in epithelial cells. Genes Cells. 4, 573-81.
Begay-Muller, V., et al, 2002. The LIM domain protein Lmo2 binds to AF6, a translocation partner of the MLL oncogene. FEBS Lett. 521, 36-8.
Boettner, B., et al., 2000. The junctional multidomain protein AF-6 is a binding partner of the RaplA GTPase and associates with the actin cytoskeletal regulator profilin. Proc Natl Acad Sci U S A. 97, 9064-9.
Chen, Q., et al., 2007. Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex. Protein Sci. 16, 1053-62.
Ferrara, P., et al., 2004. Assessing scoring functions for protein-ligand interactions. J Med Chem. 47, 3032-47.
Gasteiger, J., et al., 1990. Automatic Generation of 3D-Atomic Coordinates for Organic Molecules. . Tetrahedron Comp. Method. 3, 537-547.
Goodsell, D. S., et al., 1996. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit. 9, 1-5.
Halperin, I., et al., 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 47, 409-43.
Hillier, B. J., et al., 1999. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science. 284, 812-5.
Hofmann, K., Bucher, P., 1995. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem Sci. 20, 347-9.
Im, Y. J., et al., 2003. Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization. J Biol Chem. 278, 48099-104.
Kramer, B., et al., 1999. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins. 37, 228-41.
Krumrine, J., et al., 2003. Principles and methods of docking and ligand design. Methods Biochem Anal. 44, 443-76.
Kuntz, I. D., 1992. Structure-based strategies for drug design and discovery. Science. 257, 1078-82.
Kuntz, I. D., et al., 1982. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 161,269-88.
Kuriyama, M., et al., 1996. Identification of AF-6 and canoe as putative targets for Ras. J Biol Chem. 271,607-10.
Mandai, K., et al., 1997. Afadin: A novel actin filament-binding protein with one PDZ domain localized at cadherin-based cell-to-cell adherens junction. J Cell Biol. 139, 517-28.
Morris, G. M., et al., 1996. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des. 10, 293-304.
Oschkinat, H., 1999. A new type of PDZ domain recognition. Nat Struct Biol. 6, 408-10.
Ponting, C. P., 1995. AF-6/cno: neither a kinesin nor a myosin, but a bit of both. Trends Biochem Sci. 20, 265-6.
Ponting, C. P., Benjamin, D. R., 1996. A novel family of Ras-binding domains. Trends Biochem Sci. 21,422-5.
Prasad, R., et al., 1993. Cloning of the ALL-1 fusion partner, the AF-6 gene, involved in acute myeloid leukemias with the t(6;ll) chromosome translocation. Cancer Res. 53, 5624-8.
Radziwill, G., et al, 2003. The Bcr kinase downregulates Ras signaling by phosphorylating AF-6 and binding to its PDZ domain. Mol Cell Biol. 23, 4663-72.
Rarey, M., et al., 1997. Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des. 11, 369-84.
Rarey, M., et al., 1996. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des. 10, 41-54.
Su, L., et al., 2003. AF-6 controls integrin-mediated cell adhesion by regulating Rap1 activation through the specific recruitment of RaplGTP and SPA-1. J Biol Chem. 278, 15232-8.
Wang, R., et al., 2003. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem. 46,2287-303.
Yamamoto, T., et al., 1997. The Ras target AF-6 interacts with ZO-1 and serves as a peripheral component of tight junctions in epithelial cells. J Cell Biol. 139, 785-95.
Yamamoto, T., et al., 1999. In vivo interaction of AF-6 with activated Ras and ZO-1. Biochem Biophys Res Commun. 259, 103-7.
Yokoyama, S., et al., 2001. alpha-catenin-independent recruitment of ZO-1 to nectin-based cell-cell adhesion sites through afadin. Mol Biol Cell. 12, 1595-609.
Zhou, H., et al., 2005. Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr. J Biol Chem. 280, 13841-7.