Ιn silico library scanning for identification of new mutant inhibitors of BRAFV600E oncoprotein

Postgraduate Thesis uoadl:2800183 82 Read counter

Unit:
Κατεύθυνση Βιοπληροφορική
Library of the School of Science
Deposit date:
2018-10-01
Year:
2018
Author:
Lafazanidi Foteini
Supervisors info:
Κωνσταντίνος Βοργιάς,Καθηγητής,Τμήμα Bιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Μαρία Ζερβού,Δόκτωρ,Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Θεοδώρα Καλογεροπούλου,Δόκτωρ,Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Original Title:
Εικονική σάρωση βιβλιοθηκών για τον προσδιορισμό νέων αναστολέων της μεταλλαγμένης ογκοπρωτεϊνης BRAFV600E
Languages:
Greek
Translated title:
Ιn silico library scanning for identification of new mutant inhibitors of BRAFV600E oncoprotein
Summary:
BRAF belongs to the class of serine-threonine kinases and plays an important role in the RAS / RAF / MEK / ERK (MAKK) signaling pathway. The role of this intracellular pathway consists of transducing signals from the extracellular environment to the cell nucleus. These signals activate the pathway by controlling the processing of critical cell functions such as proliferation, survival, differentiation and apoptosis. Many types of cancer, such as melanoma, thyroid, colon, liver, ovarian cancer have been associated with BRAF mutations with the V600E mutation being the most common. This mutation results in the BRAF protein being permanently activated and consequently in the MAPK signaling pathway, resulting in proliferation and survival in cancer cells. Vemurafenib and Dabrafenib are the approved medicines for the treatment of metastatic or non-operable melanoma bearing the BRAFV600E mutation, but their efficacy is limited due to the development of resistance and the paradoxical activation of the MAPK pathway in wt-BRAF cells, leading in tumorgenesis. PLX7904 and PLX8394 (Paradox breakers) are the last generation of mutant oncoprotein that appear to escape the side effects of authorized drugs, with the latter being currently in clinical trials.

The aim of this diploma thesis is to identify potential new inhibitors of the oncoprotein BRAFV600E. A virtual scanning protocol based on the structure of the protein target was applied. Specifically, the online Ambinter database (3.5 million molecules) was screened by applying in silico molecular binding to the catalytic center of the receptor using the crystalline structure of the BRAFV600E: PLX7904 complex. The workflow was implemented in the Knime data management platform environment by integrating filtering, modeling, and lashing control nodes. The library was initially filtered for the physicochemical properties of the molecules and based on expanded Lipinski criteria, and the higher throughput (HTVS), SPV (Standard Precision) and IFD (Induced Fit Docking Protocol) GLIDE of the Schrödinger suite. The most promising compounds were selected based on the calibration of their binding to the protein target and the desired interactions with critical amino acids of the active site.
The theoretical prediction of their physicochemical properties with the QikProp software of the Schrodinger Suite further prioritized the compounds, while six compounds with satisfactory ADME properties were selected to be purchased and tested in vitro for the selective inhibition of BRAFv600e enzyme.

The diploma thesis was conducted during the academic year 2017-2018 at the Institute of Biology, Pharmacy Chemistry and Biotechnology of the National Research Foundation.
Main subject category:
Science
Keywords:
oncoprotein ,tumorgenesis,interactions ,inhibition ,enzyme
Index:
No
Number of index pages:
0
Contains images:
Yes
Number of references:
49
Number of pages:
80

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