Open Access

ARTICLE

Computational high-throughput screening and in vitro approaches identify CB-006-3; A novel PI3K-BRAF^V600E dual targeted inhibitor against melanoma

FAISAL HASSAN TOBEIGEI¹, REEM M. GAHTANI², AHMAD SHAIKH², AMER AL ALI³, NADER KAMELI^4,5, HOSSAM KAMLI², PRASANNA RAJAGOPALAN^2,6,*

1 Department of Dermatology, College of Medicine, King Khalid University, Abha, Saudi Arabia
2 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
3 Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Bisha, Al Nakhil, Bisha, Saudi Arabia
4 Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
5 Medical Research Center, Jazan University, Jazan, Saudi Arabia
6 Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia

* Corresponding Author: PRASANNA RAJAGOPALAN. Email:

Oncology Research 2021, 29(5), 305-318. https://doi.org/10.32604/or.2022.025187

Received 27 June 2022; Accepted 31 August 2022; Issue published 10 October 2022

Abstract

Malignant melanoma is characterized by both genetic and molecular alterations that activate phosphoinositide 3-kinase (PI3K), and RAS/BRAF pathways. In this work, through diversity-based high-throughput virtual screening we identified a lead molecule that selectively targets PI3K and BRAF^V600E kinases. Computational screening, Molecular dynamics simulation and MMPBSA calculations were performed. PI3K and BRAF^V600E kinase inhibition was done. A375 and G-361 cells were used for in vitro cellular analysis to determine antiproliferative effects, annexin V binding, nuclear fragmentation and cell cycle analysis. Computational screening of small molecules indicates compound CB-006-3 selectively targets PI3KCG (gamma subunit), PI3KCD (delta subunit) and BRAF^V600E. Molecular dynamics simulation and MMPBSA bases binding free energy calculations predict a stable binding of CB-006-3 to the active sites of PI3K and BRAF^V600E. The compound effectively inhibited PI3KCG, PI3KCD and BRAF^V600E kinases with respective IC₅₀ values of 75.80, 160.10 and 70.84 nM. CB-006-3 controlled the proliferation of A375 and G-361 cells with GI₅₀ values of 223.3 and 143.6 nM, respectively. A dose dependent increase in apoptotic cell population and sub G₀/G₁ phase of cell cycle were also observed with the compound treatment in addition to observed nuclear fragmentation in these cells. Furthermore, CB-006-3 inhibited BRAF^V600E, PI3KCD and PI3KCG in both melanoma cells. Collectively, based on the computational modeling and in vitro validations, we propose CB-006-3 as a lead candidate for selectively targeting PI3K and mutant BRAF^V600E to inhibit melanoma cell proliferation. Further experimental validations, including pharmacokinetic evaluations in mouse models will identify the druggability of the proposed lead candidate for further development as a therapeutic agent for treating melanoma.

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