网络构建技术在药物重定位研究中的应用
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摘要
药物重定位就是老药新用,是指对已知的药物发掘其新的药效。对已知的药物重定位是研发药物策略中风险最低、效益最好的策略之一,也是解决新药开发中存在的投入高、成功率低问题的有效方法之一。老药新用的研究方法不断完善、不断推陈出新,并且计算机技术的飞速发展,推动了药物重定位的研究进入一个新的发展阶段。到目前为止,计算预测分析和实验筛选过程是老药新用研究的主要的2大方面,其中计算预测分析方法又分为3种主要的重定位方法:网络模型、小分子和药物靶标。在老药新用研究中越来越受关注的是网络模型。疾病关联网络、药物关联网络和蛋白质互作网络是网络模型中主要应用的3大网络,针对网络模型中3大网络的构建进行综述。
Drug repositioning is a new use of old drugs, which refers to the discovery of new effects on known drugs. A known drug relocation is one of the least risky and most effective strategies in the development of drug strategies, and it is also one of the effective methods to solve the problems of high investment and low success rate in the development of new drugs. The research methods for the new use of old drugs have been continuously improved, and new innovations have been made, and the rapid development of computer technology has pushed the research of drug relocation into a new stage of development. So far, the calculation of predictive analysis and experimental screening process are the two major aspects of the new drug research, and the computational prediction analysis method is divided into three main relocation methods: network model, small molecule and drug target. More and more researchers pay attention to the network model in the study of new drug use. The disease association network, drug association network and protein interaction network are the three major networks in the network model, and the construction of the three networks in the network model is reviewed.
Drug repositioning is a new use of old drugs, which refers to the discovery of new effects on known drugs. A known drug relocation is one of the least risky and most effective strategies in the development of drug strategies, and it is also one of the effective methods to solve the problems of high investment and low success rate in the development of new drugs. The research methods for the new use of old drugs have been continuously improved, and new innovations have been made, and the rapid development of computer technology has pushed the research of drug relocation into a new stage of development. So far, the calculation of predictive analysis and experimental screening process are the two major aspects of the new drug research, and the computational prediction analysis method is divided into three main relocation methods: network model, small molecule and drug target. More and more researchers pay attention to the network model in the study of new drug use. The disease association network, drug association network and protein interaction network are the three major networks in the network model, and the construction of the three networks in the network model is reviewed.
引文
[ 1 ]徐艳,邓颖.药物重定位研究策略[J].中国新药杂志,2017(11):1253-1258.
[ 2 ]谢达菲,李鹏,李非,等.药物重定位的计算分析方法[J].生物化学与生物物理学进展,2012,39(11):1029-1036.
[ 3 ]欧阳玉梅.基因表达数据聚类分析技术及其软件应用[J].生物信息学,2010(6):104-109.
[ 4 ]ASHBURN T T,THOR K B.Drug repositioning:identifying and developing new uses for existing drugs[J].Nat Rev Drug Discov,2004,3(8):673-683.
[ 5 ]KEISER M J,SETOLA V,IRWIN J J,et al.Predicting new molecular targets for known drugs[J].Nature,2009,462:175-181.
[ 6 ]KEISER M J,ROTH B L,ARMBRUSTER B N,et al.Relating protein pharmacology by ligand chemistry[J].Nat Biotechnol,2007,25(2):197-206.
[ 7 ]ALEJANDRO S P,KLEANDROVA V V,FENG L,et al.Multi-target inhibitors for proteins associated with alzheimer:in silico discovery using fragment-based descriptors[J].Current Alzheimer Research,2013,10:117-124.
[ 8 ]VINA D,URIARTE E,ORALLO F,et al.Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors[J].Mol Pharm,2009,6(3):825-835.
[ 9 ]LI X,EVANGELIDIS T,LEI X,et al.Drug discovery using chemical systems biology:weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir[J].PLoS Comput,Biol,2011,7(4):e1002037.
[10]LI H,GAO Z,KANG L,et al.TarFisDock:a web server for identifying drug targets with docking approach[J].Nucleic Acids Research,2006,34:W219-W224.
[11]YANG L,WANG K,CHEN J,et al.Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome-clozapine-induced agranulocytosis as a case study[J].PLoS Computation Biology,2011,7(3):1002016.
[12]YAMANISHI Y,ARAKI M,GUTTERIDAGE A,et al.Prediction of drug-target interaction networks from the integration of chemical and genomic spaces[J].Bioinformatics,2008,24(13):i232-i240.
[13]YAMANISHI Y,KOTERA M,KANEHISA M,et al.Drug-target interaction prediction from chemical,gen-omic and pharmacological data in an integrated framework[J].Bioinformatics,2010,26(12):i246-i254.
[14]HE Z Z,ZHANG J,SHI X H,et al.Predicting drug-target interaction networks based on functional groups and biological features[J].PLoS One,2010,5(3):e9603.
[15]张菁.基于表型及通路的药物重定位研究[D].西安:西安电子科技大学,2015.
[16]PARK S,LEE D G,SHIN H.Network mirroring for drug repositioning[J].BMC Medical Informatics and Decision Making,2017,17(S1):55.
[17]LIANG X,LI H,LI S.A novel network pharmacology approach to analyse traditional herbal formulae:the Liu-Wei-Di-Huang pill as a case study[J].Molecular BioSystems,2014,10(5):934-1212.
[18]ALI I S J,THANGAMANI M.Prediction of novel drugs and diseases for hepatocellular carcinoma based on multi-source simulated annealing based random walk[J].Medical Systems,2018,42(10):188.
[19]HIDALGO C A,BLUMM N,BARABASI A L,et al.A dynamic network approach for the study of human phenotypes[J].PLoS Computational Biology,2009,5(4):e1000353.
[20]SUN K,GONCALVES J P,LARMINIE C,et al.Predicting disease associations via biological network analysis[J].BMC Bioinformatics,2014,15(1):304.
[21]GARCIA ALBORNOZ M,NIELSEN J.Finding directionality and gene-disease predictions in disease associations[J].BMC Systems Biology,2015,9(1):35.
[22]CAMPILLOS M,KUHN M,GAVIN A C,et al.Drug target identification using side-effect similarity[J].Science,2008,321:263-266.
[23]HU G,AGARWAL P.Human disease-drug network based on genomic expression profiles[J].PLoS One,2009,4(8):e6536.
[24]LIU H,SONG Y,GUAN J,et al.Inferring new indications for approved drugs via random walk on drug-disease heterogenous networks[J].BMC Bioinformatics,2016,17:269-277.
[25]赵晋.基于网络模型的药物重定位研究[D].西安:西安电子科技大学,2017.
[26]CHEN X,LIU M X,YAN G Y.Drug-target interaction prediction by random walk on the heterogeneous network[J].Molecular BioSystems,2012,8(7):1970-1978.
[27]LYU Y N,LI S X,ZHAI K F,et al.Network pharmacology-based prediction and verification of the molecular targets and pathways for schisandrin against cerebrovascular disease[J].Chin J Nat Med,2014,12(4):251-258.
[28]SHI J Y,YIU S M,LI Y M,et al.Predicting drug-target interaction for new drugs using enhanced similarity measures and super-arget clustering[C]//IEEE International Conference on Bioinformatics & Biomedicine.IEEE,2015.
[29]ZHANG T T,WANG X N,et al.Network-based drug repositioning:A novel strategy for discovering potential antidepressants and their mode of action[J].European Neuropsy chophar macology,2018,12:1137-1150.
[30]JEONG H.Lethality and centrality in protein networks[J].Nature,2001,411:41-42.
[31]BARABASI A L,BONABEAN E.Scale-free network[J].Scientific American,2003,288(5):60-69.
[32]HAN J D J,BERTIN N,HAO T,et al.Evidence for dynamically organized modularity in the yeast protein-protein interaction network[J].Nature,2004,430:88-93.
[33]YOOK S H,OLTVAI,Z N.Functional and topological characterization of protein interaction networks[J].Proteomics,2004,4(4):928-942.
[34]LIM J,HAO T,SHAW C,et al.A protein-protein interaction network for human inherited ataxias and disorgers of purkinje cell degeneration[J].Cell,2006,125:801-814.
[35]HUANG H,JEDYNAK B M,BADER J S.Where have all the interaction gone?Estimating the coverage of two-hybrid protein interaction maps[J].PLoS Computational Biology,2007,3(11):2155-2174.
[36]SHENORR S,MILO R,MANGAN S,et al.Network motifs in the transcriptional regulation network of Escherichia coli[J].Nature Genetics,2002,31(1):64-68.
[37]MILO R,SHENORR S,ITZKOVITZ S,et al.Network motifs:simple building blocks of complex networks[J].Science,2002,298:824-827.
[38]SAID M R,BEGLEY T J,OPPENHEIM A V,et al.Global network analysis of phenotypic effects:protein net-work and toxicity modulation in Saccharomyces cerevisiae[J].Proc Natl Acad Sci U S A,2004,101(52):18006-18011.
[39]XIA K,XUE H,DONG D,et al.Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms[J].PLoS Computational Biology,2006,2(11):1482-1497.
[40]HWANG S,SON S W,KIM S C,et al.A protein interaction network associated with asthma[J].Journal of Theoretical Biology,2008,252(4):722-731.
[41]邹亚鹏.基于模块距离与多源随机游走的药物重定位研究[D].西安:西安电子科技大学,2015.
[42]杨光.生物数学教学改革初探[J].沈阳师范大学学报(自然科学版),2012,30(3):427-429.
[ 2 ]谢达菲,李鹏,李非,等.药物重定位的计算分析方法[J].生物化学与生物物理学进展,2012,39(11):1029-1036.
[ 3 ]欧阳玉梅.基因表达数据聚类分析技术及其软件应用[J].生物信息学,2010(6):104-109.
[ 4 ]ASHBURN T T,THOR K B.Drug repositioning:identifying and developing new uses for existing drugs[J].Nat Rev Drug Discov,2004,3(8):673-683.
[ 5 ]KEISER M J,SETOLA V,IRWIN J J,et al.Predicting new molecular targets for known drugs[J].Nature,2009,462:175-181.
[ 6 ]KEISER M J,ROTH B L,ARMBRUSTER B N,et al.Relating protein pharmacology by ligand chemistry[J].Nat Biotechnol,2007,25(2):197-206.
[ 7 ]ALEJANDRO S P,KLEANDROVA V V,FENG L,et al.Multi-target inhibitors for proteins associated with alzheimer:in silico discovery using fragment-based descriptors[J].Current Alzheimer Research,2013,10:117-124.
[ 8 ]VINA D,URIARTE E,ORALLO F,et al.Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors[J].Mol Pharm,2009,6(3):825-835.
[ 9 ]LI X,EVANGELIDIS T,LEI X,et al.Drug discovery using chemical systems biology:weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir[J].PLoS Comput,Biol,2011,7(4):e1002037.
[10]LI H,GAO Z,KANG L,et al.TarFisDock:a web server for identifying drug targets with docking approach[J].Nucleic Acids Research,2006,34:W219-W224.
[11]YANG L,WANG K,CHEN J,et al.Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome-clozapine-induced agranulocytosis as a case study[J].PLoS Computation Biology,2011,7(3):1002016.
[12]YAMANISHI Y,ARAKI M,GUTTERIDAGE A,et al.Prediction of drug-target interaction networks from the integration of chemical and genomic spaces[J].Bioinformatics,2008,24(13):i232-i240.
[13]YAMANISHI Y,KOTERA M,KANEHISA M,et al.Drug-target interaction prediction from chemical,gen-omic and pharmacological data in an integrated framework[J].Bioinformatics,2010,26(12):i246-i254.
[14]HE Z Z,ZHANG J,SHI X H,et al.Predicting drug-target interaction networks based on functional groups and biological features[J].PLoS One,2010,5(3):e9603.
[15]张菁.基于表型及通路的药物重定位研究[D].西安:西安电子科技大学,2015.
[16]PARK S,LEE D G,SHIN H.Network mirroring for drug repositioning[J].BMC Medical Informatics and Decision Making,2017,17(S1):55.
[17]LIANG X,LI H,LI S.A novel network pharmacology approach to analyse traditional herbal formulae:the Liu-Wei-Di-Huang pill as a case study[J].Molecular BioSystems,2014,10(5):934-1212.
[18]ALI I S J,THANGAMANI M.Prediction of novel drugs and diseases for hepatocellular carcinoma based on multi-source simulated annealing based random walk[J].Medical Systems,2018,42(10):188.
[19]HIDALGO C A,BLUMM N,BARABASI A L,et al.A dynamic network approach for the study of human phenotypes[J].PLoS Computational Biology,2009,5(4):e1000353.
[20]SUN K,GONCALVES J P,LARMINIE C,et al.Predicting disease associations via biological network analysis[J].BMC Bioinformatics,2014,15(1):304.
[21]GARCIA ALBORNOZ M,NIELSEN J.Finding directionality and gene-disease predictions in disease associations[J].BMC Systems Biology,2015,9(1):35.
[22]CAMPILLOS M,KUHN M,GAVIN A C,et al.Drug target identification using side-effect similarity[J].Science,2008,321:263-266.
[23]HU G,AGARWAL P.Human disease-drug network based on genomic expression profiles[J].PLoS One,2009,4(8):e6536.
[24]LIU H,SONG Y,GUAN J,et al.Inferring new indications for approved drugs via random walk on drug-disease heterogenous networks[J].BMC Bioinformatics,2016,17:269-277.
[25]赵晋.基于网络模型的药物重定位研究[D].西安:西安电子科技大学,2017.
[26]CHEN X,LIU M X,YAN G Y.Drug-target interaction prediction by random walk on the heterogeneous network[J].Molecular BioSystems,2012,8(7):1970-1978.
[27]LYU Y N,LI S X,ZHAI K F,et al.Network pharmacology-based prediction and verification of the molecular targets and pathways for schisandrin against cerebrovascular disease[J].Chin J Nat Med,2014,12(4):251-258.
[28]SHI J Y,YIU S M,LI Y M,et al.Predicting drug-target interaction for new drugs using enhanced similarity measures and super-arget clustering[C]//IEEE International Conference on Bioinformatics & Biomedicine.IEEE,2015.
[29]ZHANG T T,WANG X N,et al.Network-based drug repositioning:A novel strategy for discovering potential antidepressants and their mode of action[J].European Neuropsy chophar macology,2018,12:1137-1150.
[30]JEONG H.Lethality and centrality in protein networks[J].Nature,2001,411:41-42.
[31]BARABASI A L,BONABEAN E.Scale-free network[J].Scientific American,2003,288(5):60-69.
[32]HAN J D J,BERTIN N,HAO T,et al.Evidence for dynamically organized modularity in the yeast protein-protein interaction network[J].Nature,2004,430:88-93.
[33]YOOK S H,OLTVAI,Z N.Functional and topological characterization of protein interaction networks[J].Proteomics,2004,4(4):928-942.
[34]LIM J,HAO T,SHAW C,et al.A protein-protein interaction network for human inherited ataxias and disorgers of purkinje cell degeneration[J].Cell,2006,125:801-814.
[35]HUANG H,JEDYNAK B M,BADER J S.Where have all the interaction gone?Estimating the coverage of two-hybrid protein interaction maps[J].PLoS Computational Biology,2007,3(11):2155-2174.
[36]SHENORR S,MILO R,MANGAN S,et al.Network motifs in the transcriptional regulation network of Escherichia coli[J].Nature Genetics,2002,31(1):64-68.
[37]MILO R,SHENORR S,ITZKOVITZ S,et al.Network motifs:simple building blocks of complex networks[J].Science,2002,298:824-827.
[38]SAID M R,BEGLEY T J,OPPENHEIM A V,et al.Global network analysis of phenotypic effects:protein net-work and toxicity modulation in Saccharomyces cerevisiae[J].Proc Natl Acad Sci U S A,2004,101(52):18006-18011.
[39]XIA K,XUE H,DONG D,et al.Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms[J].PLoS Computational Biology,2006,2(11):1482-1497.
[40]HWANG S,SON S W,KIM S C,et al.A protein interaction network associated with asthma[J].Journal of Theoretical Biology,2008,252(4):722-731.
[41]邹亚鹏.基于模块距离与多源随机游走的药物重定位研究[D].西安:西安电子科技大学,2015.
[42]杨光.生物数学教学改革初探[J].沈阳师范大学学报(自然科学版),2012,30(3):427-429.