BRAF Inhibitory Activity Research Articles

Molecular Modeling Unveils the Effective Interaction of B-RAF Inhibitors with Rare B-RAF Insertion Variants.

The Food and Drug Administration (FDA) has approved MAPK inhibitors as a treatment for melanoma patients carrying a mutation in codon V600 of the BRAF gene exclusively. However, BRAF mutations outside the V600 codon may occur in a small percentage of melanomas. Although these rare variants may cause B-RAF activation, their predictive response to B-RAF inhibitor treatments is still poorly understood. We exploited an integrated approach for mutation detection, tumor evolution tracking, and assessment of response to treatment in a metastatic melanoma patient carrying the rare p.T599dup B-RAF mutation. He was addressed to Dabrafenib/Trametinib targeted therapy, showing an initial dramatic response. In parallel, in-silico ligand-based homology modeling was set up and performed on this and an additional B-RAF rare variant (p.A598_T599insV) to unveil and justify the success of the B-RAF inhibitory activity of Dabrafenib, showing that it could adeptly bind both these variants in a similar manner to how it binds and inhibits the V600E mutant. These findings open up the possibility of broadening the spectrum of BRAF inhibitor-sensitive mutations beyond mutations at codon V600, suggesting that B-RAF V600 WT melanomas should undergo more specific investigations before ruling out the possibility of targeted therapy.

Integrated computational approach for in silico design of new purinyl pyridine derivatives as B-Raf kinase inhibitors

B-Raf is one among the most frequently mutating proto-oncogene which is associated with the serine/threonine Raf kinase family involved in the RAS-RAF-MEK-ERK pathway, which is the most deregulated pathway in human cancers. Mutant B-Raf V600E got an excellent scope for investigation in cancer as a potential therapeutic target. Formerly B-RafV600E is considered the molecular target for numerous antitumor compounds like purinyl pyridine and pyrimidine derivatives. In the current research work using molecular docking approach of Schrodinger Glide 5.6 version, ligand docking, pharmacophore-based virtual screening, binding free energy calculations of a series of 2-amino purinyl pyridine and pyrimidine derivatives were modeled, their docking values were predicted, that were considered to be potent against B-Raf V600E. A five-point hypothesis accompanied by a hydrogen bond acceptor(A), two hydrogen bond donors(D), and two aromatic rings (R) was built with a justifiable R2 value of 0.91 and a Q2 value of 0.64. Then by using Asinex Elite Synergy database, virtual screening was performed, and identified several potential hits. Subsequently, the molecules which had interactions with the target B-Raf kinase were determined by subjecting the obtained hits for SP and XP docking processes. Finally, for the top leads obtained, binding free energies were accomplished. About 16 new purinyl pyridine molecules were also designed. Almost nine molecules manifested crucial ligand interactions and binding free energies. At the outset, this research paved the way for us in spotting new molecules with B-Raf inhibitory activity, which can further be explored to design molecules with enhanced pharmacokinetic profiles.

Design, synthesis and molecular modeling of phenyl dihydropyridazinone derivatives as B-Raf inhibitors with anticancer activity

Three new series of phenyl dihydropyridazinone derivatives 4b–8i have been designed, synthesized and evaluated for their anticancer activity against different cancer cell lines. Nine compounds showed strong inhibitory activity, among which compound 8b exhibited potent activity against PC-3 cell line with IC50 value of 7.83 µM in comparison to sorafenib (IC50 11.53 µM). Compounds 6a, 6c, 7f-h and 8a-d were further screened for their B-Raf inhibitory activity where seven compounds 7f-h and 8a-d showed high B-Raf inhibition with ranges of IC50 values 70.65–84.14 nM and 24.97–44.60 nM, respectively when compared to sorafenib (IC50 44.05 nM). Among the tested compounds, 8b was the most potent B-Raf inhibitor with IC50 value of 24.79 nM. Cell cycle analysis of MCF-7 cells treated with 8b showed cell cycle arrest at G2-M phase with significant apoptotic effect. Molecular modeling study was performed to understand the binding mode of the most active synthesized compounds with B-Raf enzyme.

Design, Synthesis and Antiproliferative Evaluation of Novel 1,2,4-Triazole/Schiff Base Hybrids with EGFR and B-RAF Inhibitory Activities.

1,2,4-triazoles possess a broad spectrum of biological activities such as analgesic, antimicrobial, antitubercular, anti-inflammatory and antineoplastic activities. This heterocycle and their derivatives were included into a wide variety of therapeutically interesting drugs. Hence, it is of great interest to explore new 1,2,4-triazoles as cytotoxic agents targeting EGFR, B-Raf kinases. The final compounds 9a-b, 10a-b, 11a-b, 12a-b, 13a-b and 14a-f were prepared by refluxing a mixture of triazole 3a-b and 7a-d with the corresponding benzaldehyde derivatives 8a-d in absolute ethanol to afford the target final compounds in good yields. The newly synthesized triazole-containing compounds were assessed according to standard protocols for their in vitro antiproliferative activity against four human cancer cell lines including human pancreas cancer cell line (Panc-1), pancreatic carcinoma cells (PaCa-2), colon cancer cells (HT-29) and lung cancer cells (H-460) using the propidium iodide (PI) fluorescence assay. Compounds 9a and 13a were evaluated against EGFR, B-Raf and Tubulin anticancer targets. Compounds 9a, 9b, 10a, 11a, 12a, 13a and 13b showed remarkable antiproliferative activity against the tested cell lines with IC50 range of 1.3-5.9µM. Compounds 9a and 13a with the least IC50 values in the anticancer screening assay were tested against three known anticancer targets including EGFR, B-Raf kinase and Tubulin. The results revealed that compound 13a showed the highest potency against B-Raf and EGFR kinases with IC50 = 0.7 and 1.9 µM, respectively. 1,2,4-triazoles reported herein are potent EGFR, B-Raf inhibitors. These lead compounds will be subjected to more detailed mechanistic studies.

Design and biological evaluation of novel triaryl pyrazoline derivatives with dioxane moiety for selective BRAFV600E inhibition

A series of novel selective BRAFV600E inhibitory agents (Compound 1–16) 5-(2,3-dihydrobenzo[b][1,4]dioxane-6-yl)-N,3-diaryl-4,5-dihydro-1H-pyrazole-1-carbothioamides have been designed and synthesized. Their anti-proliferation and BRAF inhibitory activities were evaluated. Though 15, 4 and 12 all displayed comparable activity with the positive control Vemurafenib, only 12 indicated fine selectivity on BRAFV600E (IC50 = 0.06 μM for BRAFV600E; GI50 = 0.52 μM for A375) over BRAFWT at both kinase and cell levels. This result satisfied the designing concept of improving activity and introducing selectivity. Flow cytometry analysis and western blot convinced the apoptosis induction and kinase inhibitory activity. Docking simulation inferred the differences in binding patterns of BRAFV600E and BRAFWT, pointing out that the future orientation might be seeking for outer space binding of BRAFV600E and avoiding interactions with HIS573 of BRAFWT. These results brought potent BRAF inhibitors one step further to selective agents, enhancing the potential for safe medication.

Design, synthesis and anticancer evaluation of novel spirobenzo[h]chromene and spirochromane derivatives with dual EGFR and B-RAF inhibitory activities

A novel series of spirobenzo[h]chromene and spirochromane derivatives was designed, synthesized and evaluated as potential anticancer agents against MCF-7 (human breast carcinoma), HT-29 (human colorectal adenocarcinoma) and A549 (human lung carcinoma) cell lines using MTT assay. Eight compounds 7, 8e, 13a-e and 16 showed a better anticancer activity than that of sorafenib, the multi-kinase inhibitor with IC50 values between 1.78 and 5.47 μM or erlotinib with IC50 values over 20 μM. Representative compounds 8e, 13c and 16 were selected for further mechanistic investigation via EGFR, B-RAF and tubulin polymerization assays. Compound 16 was the most potent EGFR inhibitor (IC50 = 1.2 μM), yet compounds 8e, 13c and 16 displayed moderate tubulin polymerization inhibition effects. Molecular docking studies of those compounds revealed their possible binding modes into the active sites of both EGFR and B-RAF kinases. The newly developed compounds represent a therapeutically promising approach for the treatment of different types of cancer.

Novel 1,2,4-triazole derivatives as potential anticancer agents: Design, synthesis, molecular docking and mechanistic studies

A series of novel compounds carrying 1,2,4-triazole scaffold was synthesized and evaluated for their anticancer activity against a panel of cancer cell lines using MTT assay. Compounds 8a, 8b, 8c, 8d, 10b, 10e, and 10 g showed remarkable antiproliferative activity against the tested cell lines. Compounds 8a, 8b, 8c, 8d, 10b, 10e, and 10 g with the least IC50 values in MTT assay were tested against three known anticancer targets including EGFR, BRAF and Tubulin. The results revealed that compounds 8c and 8d showed almost same BRAF inhibitory activity and were discovered to be potent inhibitors of cancer cell proliferation and were also observed to be strong Tubulin inhibitors. Moreover, 8c also showed the best EGFR inhibition with IC50 = 3.6 μM. Finally molecular modeling studies were performed to explore the binding mode of the most active compounds to the target enzymes.

Abstract 5475: Interrogation of NCI-60 patterns of growth inhibition in conjunction with investigational oncology agents kinase profiling for the elucidation of mechanistic targets

Abstract As oncology treatment moves toward personalized targeted therapeutic agents, the NCI-60 human tumor cell line panel is an ideal community-wide tool to further understanding of the disease and molecular targets of new agents. The panel includes cell lines from nine tumor types, and is extremely well characterized at the molecular level, enabling interrogation of patterns of growth inhibition by a set of targeted investigational oncology agents looking for characteristics of the cell lines that determine sensitivity. We have used a number of online tools to enable data analysis, including COMPARE (http://dtp.nci.nih.gov/compare/), which provided the identification of compounds and/or genes that have highly correlated response patterns for any selected ‘seed’ compound. These data enable comparisons between drug sensitivity profiles that lead to the elucidation of common mechanistic targets or pathways, associations with potential response biomarkers, the confirmation of mechanism of action or identification of novel mechanisms, and the uncovering of unexpected “off-target” activities. For example, using the allosteric Akt inhibitor MK-2206 as the seed compound, response patterns for the ATP-competitive Akt inhibitors PF-4173640 (0.84), GDC-0068 (0.80), AZD-5363 (0.83), GSK-690693 (0.67), and CCT-128930 (0.69) are highly correlated. In addition, examination of the response profile for vandetinib produced a set of highly correlative agents including the corresponding EGFR inhibitors sapatinib (0.81) and AEE-788 (0.83), as well as the recently FDA-approved BTK inhibitor, ibrutinib (0.72) and the SRC inhibitor, AZD-0530 (0.74). Not surprisingly, kinase profiling of these 5 agents (0.5 uM) showed >90% inhibition of EGFR in all cases. In a third example, the BRAF V600E mutated cell lines were found to be sensitive to the bcr-abl inhibitors bafetinib and rebastinib, similarly to vemurafenib. This association suggested BRAF inhibitory activity for the former agents, which was confirmed through kinase profiling. Moreover, the NCI-60 response pattern for the androgen receptor modulator AZD-3514 has a high correlation with the BET bromodomain inhibitors JQ-1 (0.77), I-Bet-151 (0.80), and I-Bet-762 (0.78), suggesting a commonality of target/pathway for these compounds. Further correlations, associations and hypotheses generated from interrogating the compound response patterns, gene expression profiles, mutations and other characteristics will be presented. Funded by NCI Contract No. HHSN261200800001E. Citation Format: Joel Morris, Mark Kunkel, Eric Polley, Susan Holbeck, Anne Monks, David Evans, Annamaria Rapisarda, Jerry Collins, Beverly Teicher. Interrogation of NCI-60 patterns of growth inhibition in conjunction with investigational oncology agents kinase profiling for the elucidation of mechanistic targets. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5475. doi:10.1158/1538-7445.AM2014-5475

Novel pyrazoline derivatives as bi-inhibitor of COX-2 and B-Raf in treating cervical carcinoma

Twenty four pyrazoline derivatives modified from Celecoxib were designed and synthesized as bi-inhibitor of COX-2 and B-Raf. They were evaluated for their COX-1/COX-2/B-Raf inhibitory and anti-proliferation activities. Compound A3 displayed the most potent activity against COX-2 and HeLa cell line (IC50=0.008μM; GI50=19.86μM) and showed superb COX-1/COX-2 selectivity (>500), being more potent and selective than positive control Celecoxib or 5-fluorouracil. Compounds A5 and B5 were introduced best B-Raf inhibitory activities (IC50=0.15μM and 0.12μM, respectively). Compound A4 retained superb bioactivity against COX-2 and HeLa cell line (IC50=0.015μM; GI50=23.82μM) and displayed moderate B-Raf inhibitory activity (IC50=3.84μM). Docking simulation was conducted to give binding patterns. QSAR models were built using bioactivity data and optimized conformations to provide a future modification of COX-2/B-Raf inhibitors.

Modification, biological evaluation and 3D QSAR studies of novel 2-(1,3-diaryl- 4,5-dihydro-1H-pyrazol-5-yl)phenol derivatives as inhibitors of B-Raf kinase.

A series of novel 2-(1,3-diaryl- 4,5-dihydro-1H-pyrazol-5-yl)phenol derivatives (C1–C24) have been synthesized. The B-Raf inhibitory activity and anti-proliferation activity of these compounds have been tested. Compound C6 displayed the most potent biological activity against B-RafV600E (IC50 = 0.15 µM) and WM266.4 human melanoma cell line (GI50 = 1.75 µM), being comparable with the positive control (Vemurafenib and Erlotinib) and more potent than our previous best compounds. The docking simulation was performed to analyze the probable binding models and poses while the QSAR model was built to check the previous work as well as to introduce new directions. This work aimed at seeking more potent inhibitors as well as discussing some previous findings. As a result, the introduction of ortho-hydroxyl group on 4,5-dihydro-1H-pyrazole skeleton did reinforce the anti-tumor activity while enlarging the group on N-1 of pyrazoline was also helpful.

Models for Prediction of V600EBRAF and Melanoma Cells Growth Inhibitory Activities of Pyridoimidazolones

Targeted inhibition of activated BRAF mutation has emerged as a most promising and putative therapeutic approach for the anticancer drug development. In the present study, an in-silico approach using decision tree and moving average analysis has been applied to a data set comprising of 43 analogues of pyridoimidazolones for development of models for prediction of both (V)600(E)BRAF and melanoma cells (BRAF WM266.4) growth inhibitory activities. A decision tree was mainly employed for determining the importance of molecular descriptors (n=46). The value of majority of these descriptors for each analogue in the dataset was computed using E-Dragon software (version 1.0). The decision tree learned the information from the input data with an accuracy of 98% and correctly predicted the cross-validated (10-fold) data with accuracy up to 79%. A total of three non-correlating descriptors, identified best by the decision tree analysis, were subsequently utilized for development of suitable models using moving average analysis. These proposed models resulted in the prediction of (V)600(E)BRAF inhibitory activity (IC50) and melanoma cells growth (SRB GI50) inhibitory activity with an overall accuracy of ≥90%. The statistical significance of models/descriptors was assessed through intercorrelation analysis, sensitivity, specificity and Matthew's correlation coefficient.

Azine-carboxamides as anticancer agents

Despite disappointing results with the Raf inhibitor ZM 336372, AstraZeneca claims new B-Raf kinase inhibitors with the same m-phenylenediamine core structure. The new bisamides have two distinct linker groups attached. One is a substituted aromatic carboxylic acid group that constitutes the lipophilic part of the molecule, and the other is usually a pyrimidine carboxylic acid. The new molecules are part of a series of m-phenylenediamine bisamides. The compounds are expected to have anticancer activity due to their B-Raf inhibitory activity. B-Raf is mutated in a number of cancers into a constitutively active enzyme.