High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carcinoma

Shahrani, Mesfer Al; Abohassan, Mohammad; Alshahrani, Mohammad Y.; Hakami, Abdulrahim R.; Rajagopalan, Prasanna

doi:10.1007/s10822-021-00426-1

Cited by 6 publications

(4 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Using previously established diversity-based high-throughput virtual screen technology (D-HTVS), around 0.75 million compounds were screened from the ChemBridge database. Autodock-vina software from SiBioLead LLP was used for the high-throughput virtual screening [ 29 ]. D-HTVS of ChemBridge library identified top candidates having high binding affinity for EGFR at the kinase site in its active conformation.…”

Section: Resultsmentioning

confidence: 99%

High-throughput computational screening and <i>in vitro</i> evaluation identifies 5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione (C3), as a novel EGFR—HER2 dual inhibitor in gastric tumors

SHAHRANI,

GAHTANI,

ABOHASSAN

et al. 2024

View full text Add to dashboard Cite

Gastric cancers are caused primarily due to the activation and amplification of the EGFR or HER2 kinases resulting in cell proliferation, adhesion, angiogenesis, and metastasis. Conventional therapies are ineffective due to the intra-tumoral heterogeneity and concomitant genetic mutations. Hence, dual inhibition strategies are recommended to increase potency and reduce cytotoxicity. In this study, we have conducted computational high-throughput screening of the ChemBridge library followed by in vitro assays and identified novel selective inhibitors that have a dual impediment of EGFR/HER2 kinase activities. Diversity-based High-throughput Virtual Screening (D-HTVS) was used to screen the whole ChemBridge small molecular library against EGFR and HER2. The atomistic molecular dynamic simulation was conducted to understand the dynamics and stability of the protein-ligand complexes. EGFR/HER2 kinase enzymes, KATOIII, and Snu-5 cells were used for in vitro validations. The atomistic Molecular Dynamics simulations followed by solvent-based Gibbs binding free energy calculation of top molecules, identified compound C3 (5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione) to have a good affinity for both EGFR and HER2. The predicted compound, C3, was promising with better binding energy, good binding pose, and optimum interactions with the EGFR and HER2 residues. C3 inhibited EGFR and HER2 kinases with IC 50 values of 37.24 and 45.83 nM, respectively. The GI 50 values of C3 to inhibit KATOIII and Snu-5 cells were 84.76 and 48.26 nM, respectively. Based on these findings, we conclude that the identified compound C3 showed a conceivable dual inhibitory activity on EGFR/HER2 kinase, and therefore can be considered as a plausible lead-like molecule for treating gastric cancers with minimal side effects, though testing in higher models with pharmacokinetic approach is required.

show abstract

Section: Resultsmentioning

confidence: 99%

High-throughput computational screening and <i>in vitro</i> evaluation identifies 5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione (C3), as a novel EGFR—HER2 dual inhibitor in gastric tumors

SHAHRANI,

GAHTANI,

ABOHASSAN

et al. 2024

View full text Add to dashboard Cite

show abstract

“…High-throughput virtual screening of ChemBridge library identify novel PI3K/BRAF V600E binding compounds In order to identify novel compounds that specifically targets PI3KCG, PI3KCD, and BRAF V600E kinases, we first performed high-throughput virtual screening of ChemBridge compounds, having molecular weight between 350 to 750 kDa, using a diversity-based high-throughput virtual screening technique (see methods for detailed protocol) [14]. We first screened the ChemBridge library against the PI3KCG subunit and identified top compounds with high affinity (stage I screening) for PI3KCG subunit.…”

Section: Resultsmentioning

confidence: 99%

“…B-Raf V600E inhibition assay B-Raf V600E was performed using a luminescence-kinase assay kit as per the manufacturer's instructions as described elsewhere [14]. In brief, master mix that had 500 µM ATP, Raf substrate, and water were added to 96 well plate with DMSO or test compounds in different concentrations followed by addition of enzyme to initiate reaction.…”

Section: Pi3k Enzyme Inhibition Assaysmentioning

confidence: 99%

Computational High-throughput screening and In vitro approaches identify CB-006-3; A novel PI3K-BRAFV600E dual targeted inhibitor against melanoma

TOBEIGEI¹,

Gahtani²,

SHAIKH³

et al. 2021

Oncology Research

Self Cite

View full text Add to dashboard Cite

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 IC 50 values of 75.80, 160.10 and 70.84 nM. CB-006-3 controlled the proliferation of A375 and G-361 cells with GI 50 values of 223.3 and 143.6 nM, respectively. A dose dependent increase in apoptotic cell population and sub G 0 /G 1 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.

show abstract

“…In RBL-2H3 cells, IgE-degranulation was analyzed by following the protocol stated previously by Naal et al [ 25 ]. RBL-2H3 cells were seeded at a concentration of 2 × 10 5 cells/mL in 24-well plates.…”

Section: Methodsmentioning

confidence: 99%

Computational and Preclinical Analysis of 2-(4-Methyl)benzylidene-4,7-dimethyl Indan-1-one (IPX-18): A Novel Arylidene Indanone Small Molecule with Anti-Inflammatory Activity via NF-κB and Nrf2 Signaling

2023

View full text Add to dashboard Cite

Background: The adverse effects of anti-inflammatory drugs urges the search for new anti-inflammatory agents. This study aims at the preclinical analysis of the in-house synthesized small molecule IPX-18. Human whole blood (HWB), peripheral blood mononuclear cells (PBMCs), and neutrophils were used. Rat basophil cells (RBL-2H3) were used to assess degranulation. Binding stability to NF-κB-p50 was predicted using computational docking and molecular dynamic simulations. Essential signaling proteins were evaluated through flow cytometry. Results: IPX-18 inhibited the release of TNF-α with an IC50 value of 298.8 nM and 96.29 nM in the HWB and PBMCs, respectively. The compound depicted an IC50 value of 217.6 nM in the HWB and of 103.7 nM in the PBMCs for IFN-γ inhibition. IL-2 release and IL-8 release were inhibited by IPX-18 in the HWB and PBMCs. The compound controlled the migration of and the elastase in the activated neutrophils. The IC50 value for basophil activation through the FcεRI receptor assay was found to be 91.63 nM. IPX-18 inhibited RBL-2H3-degranulation with an IC50 value of 98.52 nM. The computational docking analysis predicted that IPX-18 would effectively bind NF-κB-p50. NF-κB-phosphorylation in the activated RBL-2H3 cells was decreased, and the levels of nuclear factor erythroid 2-related factor 2 (Nrf2) were increased with IPX-18 treatment. Conclusions: IPX-18 demonstrated efficacy in mediating the effector cells’ inflammatory responses through NF-κB/Nrf2 signaling.

show abstract

High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carcinoma

Cited by 6 publications

References 31 publications

High-throughput computational screening and <i>in vitro</i> evaluation identifies 5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione (C3), as a novel EGFR—HER2 dual inhibitor in gastric tumors

High-throughput computational screening and <i>in vitro</i> evaluation identifies 5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione (C3), as a novel EGFR—HER2 dual inhibitor in gastric tumors

Computational High-throughput screening and In vitro approaches identify CB-006-3; A novel PI3K-BRAFV600E dual targeted inhibitor against melanoma

Computational and Preclinical Analysis of 2-(4-Methyl)benzylidene-4,7-dimethyl Indan-1-one (IPX-18): A Novel Arylidene Indanone Small Molecule with Anti-Inflammatory Activity via NF-κB and Nrf2 Signaling

Contact Info

Product

Resources

About