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Open AccessArticle

Identification of High-Affinity Inhibitors of Cyclin-Dependent Kinase 2 Towards Anticancer Therapy

1
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
2
Amity Institute of Biotechnology, Amity University Rajasthan, Rajasthan 303002, India
3
Department of Family Medicine, Yonsei University College of Medicine, Gangnam Severance Hospital, 211 Eonju-Ro, Gangnam-Gu, Seoul 06273, Korea
4
Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80141, Jeddah 21589, Saudi Arabia
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Bartosz Tylkowski
Molecules 2019, 24(24), 4589; https://doi.org/10.3390/molecules24244589
Received: 19 November 2019 / Revised: 12 December 2019 / Accepted: 13 December 2019 / Published: 15 December 2019
(This article belongs to the Special Issue Anticancer Drug Discovery and Development)
Cyclin-dependent kinase 2 (CDK2) is an essential protein kinase involved in the cell cycle regulation. The abnormal activity of CDK2 is associated with cancer progression and metastasis. Here, we have performed structure-based virtual screening of the PubChem database to identify potent CDK2 inhibitors. First, we retrieved all compounds from the PubChem database having at least 90% structural similarity with the known CDK2 inhibitors. The selected compounds were subjected to structure-based molecular docking studies to investigate their pattern of interaction and estimate their binding affinities with CDK2. Selected compounds were further filtered out based on their physicochemical and ADMET properties. Detailed interaction analysis revealed that selected compounds interact with the functionally important residues of the active site pocket of CDK2. All-atom molecular dynamics simulation was performed to evaluate conformational changes, stability and the interaction mechanism of CDK2 in-complex with the selected compound. We found that binding of 6-N,6-N-dimethyl-9-(2-phenylethyl)purine-2,6-diamine stabilizes the structure of CDK2 and causes minimal conformational change. Finally, we suggest that the compound (PubChem ID 101874157) would be a promising scaffold to be further exploited as a potential inhibitor of CDK2 for therapeutic management of cancer after required validation. View Full-Text
Keywords: cyclin-dependent kinase 2; molecular docking; drug-likeness; drug design and discovery; molecular dynamics simulation; kinase inhibitor; cancer cyclin-dependent kinase 2; molecular docking; drug-likeness; drug design and discovery; molecular dynamics simulation; kinase inhibitor; cancer
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MDPI and ACS Style

Mohammad, T.; Batra, S.; Dahiya, R.; Baig, M.H.; Rather, I.A.; Dong, J.-J.; Hassan, I. Identification of High-Affinity Inhibitors of Cyclin-Dependent Kinase 2 Towards Anticancer Therapy. Molecules 2019, 24, 4589.

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