标题: 抑制剂-磷酸化酵素-生化途径-疾病交互作用网络应用于癌症机制探讨与新型抑制剂开发
Inhibitor-kinase-pathway-disease network for cancer mechanisms and new-type inhibitors
作者: 杨进木 
国立交通大学生物科技研究所 
关键字: 抑制剂-蛋白质激酶-生化途径-疾病交互作用网络;新型激酶抑制剂;多标靶激酶抑制剂;副作用;抗药性;癌症治疗 ;inhibitor-kinase-pathway-disease network;new types (type-C and type-S) of kinase inhibitors;multi-target kinase inhibitors;side-effects;drug resistance;cancer treatments 
公开日期: 2016
摘要: 本计画研究领域为“1-3 Development of novel therapeutics (small molecule drugs) in cancer development, progression and metastasis”,我们将探讨蛋白质激酶(Protein kinase)及与其交互作用的 蛋白质、新型激酶抑制剂,以及其在癌症生化途径中所扮演的角色。蛋白质激酶在生物体中扮演 关键的角色,由于常在许多疾病中过度表现,因此常作为治疗疾病之药物标靶。在先前执行的国 卫院计画中,我们提出“分子间药理作用介面家族(Molecular Pharma-interface Family)”以及“蛋白质 激酶-抑制剂-疾病家族地图(Kinase-Inhibitor-Disease Family Map; KIDFamMap)”的创新概念,用来 探讨激酶-分子结合机制以及开发激酶抑制剂,根据这些结果我们已发表了6 篇论文(致谢栏中载明国卫院经费补助)在相关重要的期刊上,如Nucleic Acids Research、Scientific Reports, PLoS Computational Biology、BMC Genomics、及PLoS ONE 等,并有2 项申请中的专利,另有一项正 与马偕纪念医院人体试验委员会申请中的临床试验。 本计画将延伸先前计画来达到两项目的:(1)建立抑制剂-蛋白质激酶-生化途径-疾病交互 作用网络;(2)发展新型激酶抑制剂(Type-C 及Type-S)。本计画的这二项目标,是针对目前癌症 标靶药物产生的抗药性(如gefitinib 对EGFR)及专一性不足造成副作用的急迫性议题,提出突破性 的策略。针对特定疾病(如癌症)我们提出NetPharma 的概念,结合计算系统生物及HomoPharama 建立抑制剂-蛋白质激酶-生化途径-疾病交互作用网络的多标靶药物(目标ㄧ) ,此网络囊括蛋 白质激酶与其他蛋白质之交互作用、和抑制剂间之关联性,以及其在癌症生化途径中所扮演的角 色。另外,我们利用前期国卫院计画的成果(KIDFamMap),分析约300 种蛋白质激酶-抑制剂家 族,发现蛋白质激酶的选择性结合部位,发展新型激酶抑制剂(Type-C 及Type-S) (目标二)。Type- C 抑制剂结合于C 端铰链部位附近的特定位点,而Type-S 抑制剂则同时结合于ATP 结合位置及 蛋白质受质识别位点,由于这些位点距离ATP 结合位置远,因此新型抑制剂具有较高选择性。目 前人类共有约518 蛋白质激酶,每一激酶依特定生物功能及结合特性,催化特定蛋白质 (substrate),我们发展的Type-S 抑制剂就是依此特性针对特定激酶设计的高专ㄧ性小分子抑制 剂。我们已经累积了丰富经验及优势来达到计画目的:1) 我们是全球第一个提出分子介面家族的 团队;2)提出区域官能基地图(site-moiety map),透过官能基偏好(moiety preference)以及结合位的 物化特性来研究蛋白质的结合机制,并应用于药物设计;3)提出了全面性的分子交互作用网络来 探讨蛋白质交互作用;4)设计了知名且广为所用的分子嵌合软体GEMDOCK,可用于探讨结合机 制及设计药物。 在初步结果中,我们已建立了与肺癌及乳癌相关激酶(如EGFR、ALK、KIT 和AURKA)及与 其交互作用之蛋白质网络。我们将透过分析446 份正常组织以及711 份肿瘤组织之微阵列晶片资 料来探索更多与癌症相关之激酶,以期建构出更全面之疾病交互作用网络。此外,我们初步建立 了肺癌、淋巴癌和乳癌三组激酶NetPharma,并且合成了3 个Type-C 抑制剂及9 个type-S 抑制 剂,实验结果显示,Type-C 及Type-S 抑制剂具有较高之选择性及较不受抗药性影响之特性。如 Type-C 抑制剂中的 RA-D1 能同时抑制野生型及抗药型EGFR,并能降低乳癌细胞的侵袭能力; Type-S 抑制剂中的STU-Trp(Boc) 在40 个受测激酶中仅抑制1 个,具有高选择性; STU-Glu (Type-S)由于能同时抑制多个参与肺癌生化途径的激酶,包含INSR、KDR 及FGFR1 (IC50 < 500 nM),而具有治疗肺癌之潜力。我们相信藉由抑制剂-蛋白质激酶-生化途径-疾病交互作用网 络,能协助我们针对特定疾病生化途径上的多个标靶激酶设计出高专一性之Type-C 及Type-S 抑 制剂。我们正致力于合成开发出具有高活性之Type-C 及Type-S 抑制剂,将具有应用至临床研究 之潜力。我们相信此网络及新型激酶抑制剂对于基本机制的了解及在癌症治疗中克服抗药性及选 择性提供有效的解决方案。 
The primary focus of our project will be "1-3 Development of novel therapeutics (small molecule drugs) in cancer development, progression and metastasis". We will focus on protein kinases to discover their interacting proteins, inhibitors, and their playing roles in cancer pathways. Protein kinases regulate various biological processes. Their overexpressions in many cancers have led them to be considered as promising drug targets. In our previous NHRI project, we have proposed novel concepts "molecular pharma-interface family" and "Kinase-Inhibitor-Disease Family Map (KIDFamMap)" to study molecular binding mechanisms and discover kinase inhibitors. Based on these results, we have published 6 papers with acknowledgements for the support of NHRI on some journals, such as Nucleic Acids Research, Scientific Reports, PLoS Computational Biology, BMC Genomics、and PLoS ONE. One paper won the Best Paper Award at International Conference on Bioinformatics. In addition, we are applying for two USA patents. One of our lead compounds is currently applying for an IRB approval at Mackay Memorial Hospital (马偕医院) for clinical trials. In this project, we will focus on two issues: (1) Establishing the inhibitor-kinase-pathway-disease network; and (2) Developing new types (type-C and type-S) of kinase inhibitors. Currently, there are two major issues in designing kinase inhibitors for cancer treatment: low selectivity and drug resistance. For example, the anti-cancer drug gefitinib has 64 kinase targets in 356 tested kinases, which results in side effects, such as diarrhae or live damage. In addition, gefitinib loses its efficacy for T790M/L858R mutant EGFR. Here, we propose a new concept, namely "NetPharma", to address these two issues. This concept will be used to establish the inhibitor-kinase-pathway-disease network by combining systems biology approaches and HomoPharama (Aim 1). The network will consist of relationships between protein kinases, their interacting proteins, new types of kinase inhibitors, and their roles in cancer pathways. In addition, we will apply and extend KIDFamMap to analyze ~300 protein-inhibitor families for the development of type-C and type-S kinase inhibitors (Aim 2). Type-C inhibitors bind a specific pocket located near the C-terminal hinge region of kinases, while type-S inhibitors occupy the protein substrate recognition site. The new type inhibitors have higher selectivity, because these two regions are located far from the conserved ATP-binding site. Protein kinases regulate biological functions by selectively interacting with physico-chemical properties of protein substrates. Type-S inhibitors are designed by attaching moieties that mimic physico-chemical properties of protein substrates of a protein kinase; therefore, type-S inhibitors have high selectivity. We have accumulated extensive experiences and advantages to address the two issues: 1) We are the first team that propose molecular-interface families; 2) We have established the statistical biophysics methods to infer site-moiety maps (hotspots) of proteins for protein-ligand binding mechanisms and drug discovery; 3) We have proposed the comprehensive molecular interaction networks to study interactomes; and 4) We have developed GEMDOCK, which is a world-wide used docking programs. In our preliminary results, we have established a network containing cancer-relevant kinases (e.g., EGFR and AURKA) and their interacting proteins (substrates) for cancers. We will improve the scope of this network by analyzing microarray data of 446 normal and 711 tumor tissue samples, which can lead to identify cancer-relevant kinases and explore the mechanisms. We have identified three NetPharma kinase groups for lung cancer, lymphoma, and breast cancer and synthesized 3 type-C inhibitors and 9 type-S inhibitors. Our kinase profiling results showed that these inhibitors are selective for certain kinases and are less susceptible to drug resistance. For example, a type-C inhibitor, RA-D1, can maintain activities for drug-resistant EGFR and decrease the invasion of breast cancer cells. STU-Trp(Boc), a type-S inhibitor, only inhibits 1 kinase out of 40 kinases tested. STU-Glu (type-S) has potential for treating lung cancer because it inhibits multiple kinases involved in lung cancer pathways, such as INSR, KDR, and FGFR1 (IC50 < 500 nM). By using the inhibitor-kinase-pathway-disease network, we can design type-C and type- S inhibitors that specifically target multiple kinases that participate in a specific disease pathway. We are working to discover and synthesize type-C and type-S kinase inhibitors with high potency. We believe that the network and the new types of kinase inhibitors are useful to understand basic mechanism and overcome drug resistance and kinase selectivity during cancer treatments. 
官方说明文件#: NHRI-EX105-10504PI  
URI: https://www.grb.gov.tw/search/planDetail?id=11735366&docId=481257
http://hdl.handle.net/11536/131733
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