Topological network measures for drug repositioning

被引:41
作者
Badkas, Apurva [1 ]
De Landtsheer, Sebastien [2 ]
Sauter, Thomas [2 ]
机构
[1] Univ Luxembourg, Syst Biol Grp, Esch Sur Alzette, Luxembourg
[2] Univ Luxembourg, Syst Biol, Esch Sur Alzette, Luxembourg
关键词
drug repositioning; networks; topological network measures; topology; computational methods; CENTRALITY MEASURES; CLINICAL-TRIALS; DISCOVERY; TARGETS; OPPORTUNITIES; ROBUSTNESS; STABILITY; THERAPY; MODE;
D O I
10.1093/bib/bbaa357
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Drug repositioning has received increased attention since the past decade as several blockbuster drugs have come out of repositioning. Computational approaches are significantly contributing to these efforts, of which, network-based methods play a key role. Various structural (topological) network measures have thereby contributed to uncovering unintuitive functional relationships and repositioning candidates in drug-disease and other networks. This review gives a broad overview of the topic, and offers perspectives on the application of topological measures for network analysis. It also discusses unexplored measures, and draws attention to a wider scope of application efforts, especially in drug repositioning.
引用
收藏
页数:13
相关论文
共 110 条
[1]   Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks [J].
Abdolhosseini, Farzad ;
Azarkhalili, Behrooz ;
Maazallahi, Abbas ;
Kamal, Aryan ;
Motahari, Seyed Abolfazi ;
Sharifi-Zarchi, Ali ;
Chitsaz, Hamidreza .
SCIENTIFIC REPORTS, 2019, 9 (1)
[2]  
Akhondzadeh Shahin, 2016, Avicenna Journal of Medical Biotechnology, V8, P151
[3]   A systematic survey of centrality measures for protein-protein interaction networks [J].
Ashtiani, Minoo ;
Salehzadeh-Yazdi, Ali ;
Razaghi-Moghadam, Zahra ;
Hennig, Holger ;
Wolkenhauer, Olaf ;
Mirzaie, Mehdi ;
Jafari, Mohieddin .
BMC SYSTEMS BIOLOGY, 2018, 12
[4]   Complex networks: Structure and dynamics [J].
Boccaletti, S. ;
Latora, V. ;
Moreno, Y. ;
Chavez, M. ;
Hwang, D. -U. .
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 2006, 424 (4-5) :175-308
[5]   Unveiling the Kinomes of Leishmania infantum and L. braziliensis Empowers the Discovery of New Kinase Targets and Antileishmanial Compounds [J].
Borba, Joyce V. B. ;
Silva, Arthur C. ;
Ramos, Pablo I. P. ;
Grazzia, Nathalia ;
Miguel, Danilo C. ;
Muratov, Eugene N. ;
Furnham, Nicholas ;
Andrade, Carolina H. .
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2019, 17 :352-361
[6]   On the robustness of centrality measures under conditions of imperfect data [J].
Borgatti, SP ;
Carley, KM ;
Krackhardt, D .
SOCIAL NETWORKS, 2006, 28 (02) :124-136
[7]   Informed walks: whispering hints to gene hunters inside networks' jungle [J].
Bourdakou, Marilena M. ;
Spyrou, George M. .
BMC SYSTEMS BIOLOGY, 2017, 11
[8]   What Do Centrality Measures Measure in Psychological Networks? [J].
Bringmann, Laura F. ;
Elmer, Timon ;
Epskamp, Sacha ;
Krause, Robert W. ;
Schoch, David ;
Wichers, Marieke ;
Wigman, Johanna T. W. ;
Snippe, Evelien .
JOURNAL OF ABNORMAL PSYCHOLOGY, 2019, 128 (08) :892-903
[9]   Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis [J].
Carrella, Diego ;
Napolitano, Francesco ;
Rispoli, Rossella ;
Miglietta, Mario ;
Carissimo, Annamaria ;
Cutillo, Luisa ;
Sirci, Francesco ;
Gregoretti, Francesco ;
Di Bernardo, Diego .
BIOINFORMATICS, 2014, 30 (12) :1787-1788
[10]   Drug repurposing from the perspective of pharmaceutical companies [J].
Cha, Y. ;
Erez, T. ;
Reynolds, I. J. ;
Kumar, D. ;
Ross, J. ;
Koytiger, G. ;
Kusko, R. ;
Zeskind, B. ;
Risso, S. ;
Kagan, E. ;
Papapetropoulos, S. ;
Grossman, I. ;
Laifenfeld, D. .
BRITISH JOURNAL OF PHARMACOLOGY, 2018, 175 (02) :168-180