In Silico Identification of Novel Cancer Drugs with 3D Interaction Profiling

• Main Author: Salentin, Sebastian
• Other Authors: Technische Universität Dresden, Fakultät Informatik
• Format: Doctoral Thesis
• Language: English
• Published: Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden 2018
• Subjects: Protein-Ligand Interaktionen; Interaktionsmuster; Drug Repositioning; Krebs; Virtuelles Screening; Fingerprinting; PDB; protein-ligand interactions; interaction patterns; drug repositioning; BVDU; cancer; virtual screening; fingerprinting; ddc:540; rvk:VS 9107
• Online Access: http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-226435; http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-226435; http://www.qucosa.de/fileadmin/data/qucosa/documents/22643/Dissertation_Salentin_Qucosa.pdf

Cancer is a leading cause of death worldwide. Development of new cancer drugs is increasingly costly and time-consuming. By exploiting massive amounts of biological data, computational repositioning proposes new uses for old drugs to reduce these development hurdles. A promising approach is the systematic analysis of structural data for identification of shared binding pockets and modes of action. In this thesis, I developed the Protein-Ligand Interaction Profiler (PLIP), which characterizes and indexes protein-ligand interactions to enable comparative analyses and searching in all available structures. Following, I applied PLIP to identify new treatment options in cancer: the heat shock protein Hsp27 confers resistance to drugs in cancer cells and is therefore an attractive target with a postulated drug binding site. Starting from Hsp27, I used PLIP to define an interaction profile to screen all structures from the Protein Data Bank (PDB). The top prediction was experimentally validated in vitro. It inhibits Hsp27 and significantly reduces resistance of multiple myeloma cells against the chemotherapeutic agent bortezomib. Besides computational repositioning, PLIP is used in docking, binding mode analysis, quantification of interactions and many other applications as evidenced by over 12,000 users so far. PLIP is provided to the community online and as open source.