Design, Synthesis, and Evaluation of Novel 7-(2-hydrazineyl-2-oxoethoxy)-5-hydroxyflavone Derivatives as CDK9 Inhibitors for Targeted Breast Cancer Therapy

Abstract

Introduction: Across the globe, women face a common adversary in the realm of health: breast cancer, the leading cause of cancer-related deaths among them. Cyclin-dependent Kinase 9 (CDK9) stands at the forefront of gene transcription regulation, playing a pivotal role in the progression of cancerous activities, especially in the difficult-to-treat triple-negative breast cancer (TNBC) subtype. The current research emphasizes the critical demand for better treatments for breast cancer, concentrating on the development and testing of new inhibitors targeting CDK9.

Objectives: In our research, we developed a range of new Flavone-based compounds, focusing on modifications at the C7 position. These compounds feature a variety of pharmacophoric groups, such as dimethyl-pyrazol, mercapto-oxadiazol, mercapto-triazol, and side chains with thiazolidin rings. This approach was aimed at exploring the potential therapeutic effects of these modified Flavone derivatives. These modifications were aimed at enhancing binding affinity to the glycine-rich loop of CDK9, a crucial interaction point in the ATP-binding pocket of the kinase.

Methods: In our study, we advanced the synthesis of novel Flavone derivatives by first converting chrysin into 7-(2-hydrazineyl-2-oxoethoxy)-5-hydroxyflavone, which then underwent cyclo-condensation and Schiff’s base reactions. These reactions produced diverse compounds, including dimethyl-pyrazol, mercapto-oxadiazol, and mercapto-triazol derivatives, and a compound with a thiazolidin ring. To evaluate the anticancer properties of these Flavone derivatives, cytotoxicity tests were conducted on two different breast cancer cell lines. We used two types of breast cancer cells for this: one kind that depends on estrogen, known as MCF-7, and another kind that doesn't, known as MDA-MB-231.

Results: The structural characterization of these compounds was confirmed through IR and NMR spectroscopy, revealing the successful incorporation of the intended functional groups and confirming their molecular frameworks. Compounds 4a, 4b, and 4c exhibited potent cytotoxicity against MCF-7 cells, with compounds 4b and 4c also demonstrating significant activity against MDA-MB-231 cells. Molecular docking studies compounds exhibited low root-mean-square displacement (RMSD) values and favorable grid scores, particularly compounds 4b and 4c, indicating efficient binding and stable conformations. The interaction of these derivatives with essential amino acid residues located within the active site of CDK9, especially through hydrogen bonding with CYS 106 was highlighted as a key aspect of their mechanism of action.

Conclusions: Overall, this research contributes to the advancement of breast cancer therapeutics by identifying novel 7-(2-hydrazineyl-2-oxoethoxy)-5-hydroxyflavone-based CDK9 inhibitors with promising anticancer activities. The insights gained from this study hold significant potential for the development of new treatments, particularly for patients with TNBC.