Rational Design of Coumarin Derivatives as CK2 Inhibitors by Improving the Interaction with the Hinge Region

Machine Learning Models for the Classification of CK2 Natural Products Inhibitors with Molecular Fingerprint Descriptors

Casein kinase 2 (CK2) is considered an important target for anti-cancer drugs. Given the structural diversity and broad spectrum of pharmaceutical activities of natural products, numerous studies have been performed to prove them as valuable sources of drugs. However, there has been little study relevant to identifying structural factors responsible for their inhibitory activity against CK2 with machine learning methods. In this study, classification studies were conducted on 115 natural products as CK2 inhibitors. Seven machine learning methods along with six molecular fingerprints were employed to develop qualitative classification models. The performances of all models were evaluated by cross-validation and test set. By taking predictive accuracy(CA), the area under receiver operating characteristic (AUC), and (MCC)as three performance indicators, the optimal models with high reliability and predictive ability were obtained, including the Extended Fingerprint-Logistic Regression model (CA = 0.859, AUC = 0.826, MCC = 0.520) for training test andPubChem fingerprint along with the artificial neural model (CA = 0.826, AUC = 0.933, MCC = 0.628) for test set. Meanwhile, the privileged substructures responsible for their inhibitory activity against CK2 were also identified through a combination of frequency analysis and information gain. The results are expected to provide useful information for the further utilization of natural products and the discovery of novel CK2 inhibitors.

Structure-based identification of novel CK2 inhibitors with a linear 2-propenone scaffold as anti-cancer agents

Protein kinase CK2 has emerged as an attractive cancer therapeutic target. Previous studies have highlighted the challenge of optimizing CK2 ATP-competitive inhibitors that have low druggability due to their polycyclic ring scaffolds. Therefore the development of novel inhibitors with non-polycyclic scaffolds emerges as a promising strategy for drug discovery targeting CK2. In this current study, based on the similar predicted binding poses of the linear 2-propenone scaffold of isoliquiritigenin with that of the polycyclic inhibitor CX-4945, a series of 2-propenone derivatives containing an amine-substituted five-membered heterocycle and a benzoic acid were designed, synthesized and evaluated for their in vitro CK2 inhibition and anti-cancer activity. Compound 8b was found to be the most potent CK2 inhibitor (IC₅₀ = 0.6 μM) with the anti-proliferative activity on HepG2 cancer cells (IC₅₀ = 14 μM), compared to the activity of isoliquiritigenin (IC₅₀ = 17 μM and 51 μM, respectively). Molecular docking was performed to understand the binding modes of the newly designed 2-propenone derivatives with CK2. Compound 8b formed the most favorable network of hydrogen bonds with both the hinge region and positive area. Our results indicate that CK2 derivatives with a linear 2-propenone scaffold are promising candidates for anti-cancer drug discovery.

Coumarin: A Natural, Privileged and Versatile Scaffold for Bioactive Compounds

Many naturally occurring substances, traditionally used in popular medicines around the world, contain the coumarin moiety. Coumarin represents a privileged scaffold for medicinal chemists, because of its peculiar physicochemical features, and the versatile and easy synthetic transformation into a large variety of functionalized coumarins. As a consequence, a huge number of coumarin derivatives have been designed, synthesized, and tested to address many pharmacological targets in a selective way, e.g., selective enzyme inhibitors, and more recently, a number of selected targets (multitarget ligands) involved in multifactorial diseases, such as Alzheimer's and Parkinson's diseases. In this review an overview of the most recent synthetic pathways leading to mono- and polyfunctionalized coumarins will be presented, along with the main biological pathways of their biosynthesis and metabolic transformations. The many existing and recent reviews in the field prompted us to make some drastic selections, and therefore, the review is focused on monoamine oxidase, cholinesterase, and aromatase inhibitors, and on multitarget coumarins acting on selected targets of neurodegenerative diseases.

Exploring the Pivotal Role of the CK2 Hinge Region Sub-Pocket in Binding with Tricyclic Quinolone Analogues by Computational Analysis

Protein kinase CK2 has been considered as an attractive therapeutic target of cancer therapy. The tricyclic quinoline compound CX-4945 is the first representative of CK2 inhibitors used in human clinical trials. The binding of non-2,6-naphtyridine substituted compounds 27e (IC₅₀ > 500 nM) and 27h (IC₅₀ > 1000 nM) to CK2 is abolished. However, the unbinding mechanisms due to the key pharmacophore group replacement of compounds 27e and 27h are unveiled. In the present work, combined computational analysis was performed to investigate the underlying structural basis of the low-affinity of two systems. As indicated in the results, the loss of hydrogen bonds between the non-2,6-naphtyridine and the hinge region destroyed the proper recognition of the two complexes. Besides, the allosteric mechanisms between the deviated ligands and the changed regions (G-loop, C-loop and β4/β5 loop) are proposed. Furthermore, energetic analysis was evaluated by detailed energy calculation and residue-based energy decomposition. More importantly, the summary of known polar pharmacophore groups elucidates the pivotal roles of hinge region sub-pocket in the binding of CK2 inhibitors. These results provide rational clues to the fragment-based design of more potent CK2 inhibitors.

Recent developments of C-4 substituted coumarin derivatives as anticancer agents

Cancer is a prominent cause of death in global. Currently, the numbers of drugs that are in clinical practice are having a high prevalence of side effect and multidrug resistance. Researchers have made an attempt to expand a suitable anticancer drug that has no MDR and side effect. Coumarin scaffold became an attractive subject due to their broad spectrum of pharmacological activities. Coumarin derivatives extensively explored for anticancer activities as it possesses minimum side effect along with multi-drug reversal activity. Coumarin derivatives can act by various mechanisms on different tumor cell lines depending on substitution pattern of the core structure of coumarin. Substitution on coumarin nucleus leads to the search for more potent compounds. In this review, we have made an effort to give a synthetic strategy for the preparation of C-4 substituted coumarin derivatives as anticancer agents based on their mechanism of action and also discuss the SAR of the most active compound.