Identification of the potential compounds for inhibition CD44 target of human breast cancer stem cells by docking method
Main Article Content
Abstract
In a recent cell-based assay, it has been demonstrated that the F-19848A compound inhibits the binding of hyaluronan to the CD44 receptor, which is a cell-surface glycoprotein and a receptor for hyaluronan, a major component of the tumor extracellular matrix. The interaction between CD44 and hyaluronan has been shown to promote breast cancer metastasis according to evidence. In this study, the PubChem database contains more than 112 million compounds. This data is inputted for virtual screening find out top hits by combining Lipinski’s rule and docking method. With 20 configurations obtained by docking method, the lowest binding affinity ΔEbind achieved in the best docking mode was chosen as a scoring function for picking out top ligands. For inhibition the CD44 target, the top-leads compounds with binding energy less than -9.0 kcal.mol-1 and F-19848A have selected. By docking method, the binding site and other quantities were determined such as the number of hydrogen bonds (HB), non-bond contacts (NBC) of top ligands with CD44 target. Besides, the results also showed that the non-bonded contacts dominate over hydrogen bonds in the interaction between top ligands with CD44 target.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
References
Berendsen, H. J., Postma, J. P., van Gunsteren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In Intermolecular forces (pp. 331-342). Springer.
Bolton, E. E., Wang, Y., Thiessen, P. A., & Bryant, S. H. (2008). PubChem: integrated platform of small molecules and biological activities. Annu Rep Comput Chem, 4, 217-241.
Gökmen-Polar, Y., Nakshatri, H., & Badve, S. (2011). Biomarkers for breast cancer stem cells: the challenges ahead. Biomarkers in medicine, 5(5), 661-671.
Hortobagyi, G. N., de la Garza Salazar, J., Pritchard, K., Amadori, D., Haidinger, R., Hudis, C. A., . . . Namer, M. (2005). The global breast cancer burden: variations in epidemiology and survival. Clinical breast cancer, 6(5), 391-401.
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev., 64, 4-17.
Liu, L.-K., & Finzel, B. C. (2014). Fragment-based identification of an inducible binding site on cell surface receptor CD44 for the design of protein–carbohydrate interaction inhibitors. Journal of medicinal chemistry, 57(6), 2714-2725.
Naor, D., Nedvetzki, S., Golan, I., Melnik, L., & Faitelson, Y. (2002). CD44 in cancer. Critical reviews in clinical laboratory sciences, 39(6), 527-579.
Sanner, M. F. (1999). Python: a programming language for software integration and development. J. Mol. Graph. Model., 17(1), 57-61.
Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 31(2), 455-461.
Most read articles by the same author(s)
- TS Quoc Tuan Tran, TS Van Hoang Ong, TS Thi Thu Cuc Nguyen, Trong Dung Nguyen, Effects of factors on the structure and crystallization process of Cu1-xAux alloy (x=0.25; 0.5; 0.75) by molecular dynamics simulation method , Dong Thap University Journal of Science: Vol. 13 No. 2 (2024): Natural Sciences Issue (Vietnamese)
- Thi Ngoc Thanh Huynh, Quoc Thai Nguyen, Van Thang Bui, Studying the interaction of CID 16040294 compound with beta amyloid by docking method , Dong Thap University Journal of Science: Vol. 12 No. 2 (2023): Natural Sciences Issue (Vietnamese)
- Thi Ngoc Thanh Huynh, Thi Thanh Thu Tran, Thi My Hanh Pham, Kha Quang Quach, Study on the interaction mechanism of penciclovir drug on 3CLpro of SAR-CoV-2 by simulation methods , Dong Thap University Journal of Science: Vol. 12 No. 5 (2023): Natural Sciences Issue (English)
- Thanh Tung Ha, Vinh Phuc Huynh, Thi Ngoc Tu Le, Influence of preparation methods on the performance efficiency of quantum dot sensitized solar cell , Dong Thap University Journal of Science: Vol. 11 No. 2 (2022): Natural Sciences Issue (Vietnamese)
- Thi Hoa Le, Ngoc Bich Tran, Ngoc Hieu Nguyen, Thi Ngoc Tu Le, Vinh Phuc Huynh, Dirac electron in gapped graphene under exponentially decaying magnetic field , Dong Thap University Journal of Science: Vol. 11 No. 5 (2022): Natural Sciences Issue (English)
- Ngoc Bich Tran, Ngoc Hieu Nguyen, Thi Tho Ta, Thi Ngoc Tu Le, Vinh Phuc Huynh, Linear and nonlinear refractive index changes in monolayer MoSe2 , Dong Thap University Journal of Science: Vol. 10 No. 5 (2021): Natural Sciences Issue (English)
- Thi Ngoc Thanh Huynh, Quoc Thai Nguyen, Minh Tri Pham, Identifying potential drugs for inhibition the M2 protein channel of influenza A by steered molecular dynamics , Dong Thap University Journal of Science: Vol. 11 No. 5 (2022): Natural Sciences Issue (English)
- Master Thi Ngoc Thanh Huynh, Bachelor Minh Nhan Kieu, Bachelor Nhat Ha Kieu, TS. Thai Nguyen Quoc, Molecular mechanism of Ensitrelvir and its similarity inhibiting SARS-CoV-2 main protease by molecular dynamics simulation , Dong Thap University Journal of Science: Vol. 13 No. 5 (2024): Natural Sciences Issue (English)