Development of a novel class of B-RafV600E-selective inhibitors through virtual screening and hierarchical hit optimization

Abstract

Oncogenic mutations in critical nodes of cellular signaling pathways have been associated with tumorigenesis and progression. The B-Raf protein kinase, a key hub in the canonical MAPK signaling cascade, is mutated in a broad range of human cancers and especially in malignant melanoma. The most prevalent B-RafV600E mutant exhibits elevated kinase activity and results in constitutive activation of the MAPK pathway, thus making it a promising drug target for cancer therapy. Herein, we described the development of novel B-RafV600E selective inhibitors via multi-step virtual screening and hierarchical hit optimization. Nine hit compounds with low micromolar IC50 values were identified as B-RafV600E inhibitors through virtual screening. Subsequent scaffold-based analogue searching and medicinal chemistry efforts significantly improved both the inhibitor potency and oncogene selectivity. In particular, compounds 22f and 22q possess nanomolar IC50 values with selectivity for B-RafV600E in vitro and exclusive cytotoxicity against B-RafV600E harboring cancer cells.

Identification and synthesis of N-(thiophen-2-yl) benzamide derivatives as BRAFV600E inhibitors

“…19–21 In our previous work, a series of 2-phenyl-5-vinylfuran derivatives were identified as potent novel BRAF V600E inhibitors based on SBVS and chemical optimization. 22 In the present study, N -(thiophen-2-yl) benzamide derivatives are reported as another series of BRAF V600E selective inhibitors. In particular, compounds b40 and b47 in this series exhibit submicromolar inhibitory activities against the BRAF V600E kinase.…”

“…Finally, 30 compounds from 38 manually classified groups were purchased and evaluated for their ability to inhibit the enzymatic activity of BRAF V600E . An ELISA-based MEK phosphorylation assay, which was performed according to our previous work, 22 revealed that the N -(thiophen-2-yl) benzamide derivative, a1, was the most potent BRAF V600E kinase inhibitor with an IC 50 value of about 2.01 μM (Table 1). Since few studies demonstrated that N -(thiophen-2-yl) benzamide derivatives were potential BRAF V600E kinase inhibitors.…”

“…To better understand the molecular mechanism of BRAF V600E inhibition by these compounds, the most potent inhibitor ( a6 ) was docked to the active site of BRAF V600E 22 . The docking results suggest that a hydrophobic interaction may occur between the ethoxy group of the phenyl ring of a6 and the hydrophobic pocket formed by S535, F583, and C532 of BRAF V600E (Figure 1).…”

Integrating docking scores and key interaction profiles to improve the accuracy of molecular docking: towards novel B-RafV600E inhibitors

“…1 The frequency of B-RAF mutations varies widely in human cancers, with a particularly high frequency found in malignant melanoma (60-70%), thyroid (30-50%), ovarian (∼30%) and colorectal carcinomas (5-20%). 2,3 Among the detected activated mutations in B-Raf, B-Raf V600E , a glutamic acid for valine substitution at residue 600, represents one of the most commonly mutated proto-oncogenes. Furthermore, the isoform plays a significant role in the development of numerous cancers of high clinical impact.…”

Insight into molecular dynamics simulation of BRAF(V600E) and potent novel inhibitors for malignant melanoma

“…In this study, we tried to identify if there was any compound better than the existing or experimental BRAF inhibitors by virtual screening from the large traditional Chinese medicine (TCM) compound database. [39][40][41][42] ligand-based quantitative structureactivity relationship (Qsar) models…”