IN SILICO SCREENING FOR THE DISCOVERY OF NEW INHIBITORS FOR THE MUTATED PROTEIN BRAF

Postgraduate Thesis uoadl:2726020 136 Read counter

Unit:
Κατεύθυνση Βιοπληροφορική
Library of the School of Science
Deposit date:
2018-03-30
Year:
2018
Author:
Evgeniou Michail
Supervisors info:
Καθ. Δρ. Κωνσταντίνος Βοργιάς, ΕΚΠΑ
Δρ. Μάρια Ζερβού, Ερευνήτρια Β΄ΕΙΕ
Δρ. Θεοδώρα Καλογεροπούλου Ερευνήτρια Α΄ΕΙΕ
Original Title:
In sillico μελέτες αναστολέων της μεταλλαγμένης ογκοπρωτεΐνης BRAFV600E
Languages:
Greek
Translated title:
IN SILICO SCREENING FOR THE DISCOVERY OF NEW INHIBITORS FOR THE MUTATED PROTEIN BRAF
Summary:
The mitogen-activated protein kinase (MAPK) signaling pathway which affects cell proliferation, apoptosis, migration and differentiation has attracted the attention of anticancer research since abnormal activation of the pathway components is often identified in human cancers. BRAF belongs to the RAF family of serine/threonine protein kinases which are key regulators of the MAPK cascade. Activating BRAF mutations are harbored in certain cancers as in melanoma (50%), thyroid cancer (35-70%), colorectal cancer (5-20%), liver cancer (~14%) and ovarian cancer (~30%). BRAF-V600E is the most frequent mutation leading to multiple and uncontrolled amplification of downstream signal with tumorigenesis as a result. Two selective BRAFV600E inhibitors, Vemurafenib (Zelboraf) and Dabrafenib (Tafinlar), have been already approved for the treatment of unresectable and metastatic BRAF mutated melanoma. However, their efficacy is limited due to intrinsic resistance or the development of acquired resistance. Besides, in the context of wild-type BRAF cells bearing upstream activation (RAS, receptor tyrosine kinase), treatment with BRAF-V600E inhibitors leads to the paradoxical enhancement of MAPK signaling, resulting in enhancement of wt-tumour growth and adverse effects. For that reason combined treatments are being tested with very good clinical outcomes. A new generation of BRAF V600E inhibitors (PLX7904 and PLX8394), being capable of overcoming the MAPK paradoxical activation, has been discovered recently and are currently in clinical investigations.
In this thesis, we have conducted a virtual screening approach ,utilizing structure based pharmacophore modeling and in silico docking, towards the identification of novel, selective BRAFV600E inhibitors which potentially could be less prone to resistance and avoid the paradox enhancement of MAPK pathway in wt-BRAF cells. Pharmacophore model generation was based on the top-ranked features extracted from the respective models originated from the crystal complexes of BRAFV600E with the paradox breaker PLX7904 (pdb: 4xv1) and Dabrafenib (pdb: 4xv2). We validated our models by utilizing a library of actives and inactives recovered by ChEMBL database. ZINC database (12M compounds) was queried against the generated pharmacophore models and the selected compounds based on the pharmacophore fit score we refiltered according to a defined set of physicochemical properties. . The filtered compounds were evaluated for their in silico binding at the BRAFV600E active site using Glide HTVS and SP and Induced Fit Docking protocol.The best ranked molecules were further analysed for their drug-likeness properties.
The process qualified a final dataset of molecules capable of developing strong interactions with the crucial amino acids of the binding site,and predicted to bear a satisfactory ADME profile.
Our future plans include the purchase of the qualified molecules and the in vitro assessment of their inhibitory activity and selectivity against BRAFV600E.
Main subject category:
Science
Keywords:
BRAF, inhibitors, protein, cancer, melanoma, in sillico drug design, pharmacophore, modeling, dabrafenib, vemurafenib, virtual screening, in sillico docking
Index:
Yes
Number of index pages:
2
Contains images:
Yes
Number of references:
62
Number of pages:
113

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