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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

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Abstract

Paradoxical Raf activation via Raf dimerization is a major drawback of wild/mutant B-Raf inhibitors. Herein, we report that CB-1 a novel, potent B-Raf/c-Raf dual inhibitor, effective against colon cancer cells, irrespective of their genetic status. High-throughput virtual screening of the ChemBridge library against wild B-Raf (B-RafWT), mutant B-Raf (B-RafV600E), and c-Raf was performed using an automated protocol with the AutoDock-VINA. Caco-2 and HT-29 cells were used. Of the 23,365 compounds screened computationally, CB-1 showed the highest binding energy towards B-RafWT with a ΔGbinding score of − 13.0 kcal/mol. The compound was also predicted to be effective against B-RafV600E and c-Raf molecules with ΔGbinding energies of − 10.6 and − 10.1 kcal/mol, respectively. The compound inhibited B-RafWT, B-RafV600E and c-Raf kinases with IC50 values of 27.13, 51.70, and 40.23 nM, respectively. The GI50 value of CB-1 was 247.9 nM in B-RafWT-expressing Caco-2 cells and 352.4 nM in B-RafV600E-expressing HT-29 cells. Dose-dependent increases in total apoptosis and G1 cell cycle phase arrest was observed in CB-1-treated colon cancer cells. The compound decreased B-Raf expression in both wild and mutant colon cancer cells. CB-1, a novel, potent dual B-Raf/c-Raf inhibitor was effective against colon cancer cells bearing wild-type and mutant variants of B-Raf expression.

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All data used in manuscript and is available with corresponding author upon reasonable request for non-commercial purposes.

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Acknowledgements

Authors express their gratitude to SiBIOLEAD, Chennai, Tamil Nadu, India and SMARTBIO LABS, Chennai, Tamil Nadu, India, for the help rendered in this study.

Funding

The author extend appreciation to the Deanship of Scientific Research at King Khalid University, Abha, Saudi Arabia, for funding this work through Grant No. R.G.P.1/228/42.

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Authors and Affiliations

  1. Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia

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

  2. Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia

    Mesfer Al Shahrani & Prasanna Rajagopalan

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  1. Mesfer Al Shahrani
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  2. Mohammad Abohassan
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  4. Abdulrahim R. Hakami
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Contributions

MAS—funding acquisition, experimental, plan execution, data curing manuscript drafting. MA—experimental, data analysis, statistical, manuscript drafting. MAS—supervision, data analysis, manuscript preparation, validation. ARH—Technical guidance, data collection, interpretation of results. PR—conceptual and experimental design, supervision, data analysis, manuscript finalization and communication.

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Correspondence to Prasanna Rajagopalan.

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Al Shahrani, M., Abohassan, M., Y. Alshahrani, M. et al. 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. J Comput Aided Mol Des 35, 1165–1176 (2021). https://doi.org/10.1007/s10822-021-00426-1

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