Unit:
Κατεύθυνση ΒιοπληροφορικήLibrary of the School of Science
Supervisors info:
Ι. Τρουγκάκος, Καθηγητής, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Β. Οικονομίδου, Αναπληρώτρια Καθηγήτρια, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Δρ. Μαρία Ζερβού, Κύρια Ερευνήτρια , Ινστιτούτο Χημικής Βιολογίας (IXB/ΕΙΕ)
Original Title:
«Επιλεκτικοί αναστολείς της ογκοπρωτεΐνης BRAFV600E μέσω ανάλυσης χημικής ομοιότητας, in silico μελέτες πρόσδεσης και in vitro έλεγχο»
Translated title:
Identification of new selective inhibitors of the BRAFV600E mutant oncoprotein, using similarity methods, in silico docking and in vitro testing
Summary:
BRAF protein is a member of RAF family proteins and is an important component of the RAS-RAF-MEK-ERK (MAPK) signaling pathway which controls cell growth, differentiation, and proliferation.
BRAF mutation plays a major role in the development of many human tumors such as melanoma (>50%), colon cancer (5-10%), hairy cell leukemia (100%). It is also often present in thyroid carcinomas (25%-45%) and less commonly in lung and ovarian cancers. The most common mutation is the BRAF V600E which is a hyperactivating point mutation leading to uncontrolled cell growth and survival.
Vemurafenib and Dabrafenib are two FDA approved drugs targeting specifically the BRAF V600E oncogenic mutation, which have significantly improved the survival of patients that suffer from metastatic melanoma.
Despite the initial response the disease often progresses in less than a year, due to acquired resistance. Furthermore, cancers like colon cancer are primary resistant to BRAF inhibitors. Notably, secondary skin cancers are often developed after months of monotherapy treatment because the inhibitors paradoxically activate the MAPK signaling pathway in WT-BRAF cells. Thus, there is an urgent need towards the discovery of new selective and potent mutated BRAF inhibitors.
Research efforts to overcome paradoxical activation have led to so-called paradox breakers (PLX7904 and PLX8394 with the latter currently in clinical trials). The new inhibitors have an advantage over approved drugs as they suppress mutant BRAF cells without paradoxically activating the MAPK pathway in WT-BRAF cells and, in addition, they seem to be effective against several resistance mechanisms.
The first part of the current thesis includes in silico approaches towards the identification of novel specific BRAFV600E inhibitors. Previous studies of the Molecular Analysis Team, of the Institute of Chemical Biology of NHRF, led to the discovery of a lead compound (hit713) with low μΜ inhibitory activity against BRAFV600E. In the current thesis, Mcule database was exhaustively screened for structures similar to hit713 by applying molecular similarity algorithms. The retrieved structures were evaluated for their in silico binding to the active site of the mutant protein using the paradox breaker PLX7904 crystal complex.
In the context of our collaboration with the Organic & Organometallic Chemistry Team of ICB/NHRF (PI: Dr. I. Costas) and within the frame of an ongoing doctoral thesis, a lead optimization process is currently in progress comprising the design and synthesis of new modified analogs.
In the second part of the current thesis, hit 713 and the most active new synthesized analogs (according to their inhibitory effect as measured at the kinase assay) were evaluated in vitro against melanoma cell lines homozygous or heterozygous for the BRAFV600E mutation or wtBRAF cell lines bearing RAS mutation. The XTT Cell Viability Test was applied. The in vitro experiments were performed under the supervision of Dr. P. Georgiadis, Research Group "Environment and Health", ICB / NHRF.
Main subject category:
Science
Keywords:
BRAFV600E inhibitors, similarity methods, in silico docking, in vitro testing
