Coumarin as Attractive Casein Kinase 2 (CK2) Inhibitor Scaffold: An Integrate Approach To Elucidate the Putative Binding Motif and Explain Structure–Activity Relationships

CK2: The master regulator in tumor immune-microenvironment - A crucial target in oncotherapy

A constitutively active serine/threonine kinase, casein kinase 2 (CK2) is involved in several physiological functions, such as DNA repair, apoptosis, and cell cycle control. New research emphasizes how critical CK2 is to the immune system's dysregulation in the tumor immune-microenvironment (TIME). The inhibition of immunological responses, including the downregulation of immune effector cells and the elevation of immunosuppressive proteins that aid in the development of tumor and immune evasion, has been linked to CK2 overexpression. CK2 maintains an immunosuppressive milieu that impedes anti-tumor immunity by encouraging the expressions and activities of immune checkpoint markers, regulating cytokines release, and boosting immune-suppressive cells such as regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs) to maintain immune evasion. It is a promising target for cancer treatment due to its complex role in immune regulation and oncogenic pathways. In this study, we address the therapeutic perspectives of targeting CK2 in oncotherapy and investigate the mechanisms by which it controls immunological responses in the TME. This review, comprehending the function of CK2 in immune suppression can facilitate the creation of innovative treatment approaches aimed at augmenting anti-tumor immunity and enhancing immunotherapy effectiveness.

Characterization, multivariate analysis and bioactivity evaluation of coumarins in the bark of Fraxinus mandshurica

The bark of Fraxinus mandshurica is a traditional folk herb used to clear heat and dry dampness. To investigate the differences in coumarins content in the bark of F. mandshurica, 24 batches of samples from four origins were collected and analyzed. Eight coumarins were obtained by traditional natural product extraction, isolation and identification techniques and quantified by high performance liquid chromatography-photodiode array (HPLC-DAD). The quantitative results showed that the overall content of compound 30 (Fraxinol) was higher at 100.23 mg/g, while the overall content of compound 23 (Cichoriin) was lower, which may be related to environmental factors in different regions. The method validation showed that the linear range of the eight standards was between 10 and 2500 μg/mL with correlation coefficient (R2) values >0.9991; the relative standard deviation (RSD, %) values of intra-day precision were between 0.35 and 1.38, while the RSD values of inter-day precision were between 0. 29-1.78; the RSD (%) values for the reproducibility experiments ranged from 0.29 to 1.87, while the RSD (%) values for the stability experiments ranged from 0.22 to 2.33; the spiked recovery of the samples ranged from 98.65 to 101.34%, and the RSD (%) values ranged from 0.22 to 1.96. The method validation results showed that the instrument used for the analysis had good precision, the reproducibility and stability of the samples were good, and the accuracy of the experimental method was high. In addition, a total of 54 chemical components were identified from F. mandshurica bark by ultra performance liquid chromatography-electrospray quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS). Based on this, fingerprinting, heatmap and multivariate analysis, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), were established for 24 batches of samples, and four marker compounds that could be used to distinguish different origins of F. mandshurica were screened. To further investigate the bioactivities of the eight coumarins, in vitro enzyme activity inhibition studies were performed, and the results showed that they all exhibited different degrees of inhibition of acetylcholinesterase, tyrosinase and α-glucosidase, thus having potential applications in the treatment of Alzheimer's disease, blemish whitening and anti-diabetes, and becoming a new source of natural enzyme activity inhibitors. This study established an identification and evaluation method applicable to plants of different origins, which provides a strong reference for quality control, origin evaluation and clinical application of traditional medicinal plants.

7-Methoxy-4-methylcoumarin: Standard Molar Enthalpy of Formation Prediction in the Gas Phase Using Machine Learning and Its Comparison to the Experimental Data

Experimentally, the standard molar enthalpy of formation in the crystalline phase at 298.15 K, ΔfHm°(cr) for 7-methoxy-4-methylcoumarin (7M4MC) was calculated by traditional linear regression, which was obtained by combustion calorimetry. Similarly, the standard molar enthalpy of sublimation was determined through the standard molar enthalpy of fusion and by the standard molar enthalpy of vaporization, from differential scanning calorimetry and thermogravimetry, respectively; lately using these results, the standard molar enthalpy of formation in the gas phase was calculated at 298.15 K, ΔfHm°(g). In addition ML was used to predict the standard molar enthalpy of formation in the gas phase for the 7M4MC, constructing an experimental data set containing three kinds of functional groups: esters, coumarins, and aromatic compounds. The procedure was performed by using multiple linear regression algorithms and stochastic gradient descent with a R2 of 0.99. The obtained models were used to compare those predicted values versus experimental for coumarins, resulting in an average error rate of 9.0%. Likewise, four homodesmic reactions were proposed and predicted with the multiple linear regression algorithm of ML obtaining good results.

Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC₅₀ ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC₅₀ = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC₅₀ 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.

Structure-guided discovery of adenosine triphosphate-competitive casein kinase 2 inhibitors

Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic serine-threonine kinase. CK2 has been identified as a potential drug target for the treatment of cancer and related disorders. Several adenosine triphosphate-competitive CK2 inhibitors have been identified and have progressed at different levels of clinical trials. This review presents details of CK2 protein, structural insights into adenosine triphosphate binding pocket, current clinical trial candidates and their analogues. Further, it includes the emerging structure-based drug design approaches, chemistry, structure-activity relationship and biological screening of potent and selective CK2 inhibitors. The authors tabulated the details of CK2 co-crystal structures because these co-crystal structures facilitated the structure-guided discovery of CK2 inhibitors. The narrow hinge pocket compared with related kinases provides useful insights into the discovery of CK2 inhibitors.

Strategies of Targeting CK2 in Drug Discovery: Challenges, Opportunities, and Emerging Prospects

CK2 (casein kinase 2) is a serine/threonine protein kinase that is ubiquitous in eukaryotic cells and plays important roles in a variety of cellular functions, including cell growth, apoptosis, circadian rhythms, DNA damage repair, transcription, and translation. CK2 is involved in cancer pathogenesis and the occurrence of many diseases. Therefore, targeting CK2 is a promising therapeutic strategy. Although many CK2-specific small-molecule inhibitors have been developed, only CX-4945 has progressed to clinical trials. In recent years, novel CK2 inhibitors have gradually become a research hotspot, which is expected to overcome the limitations of traditional inhibitors. Herein, we summarize the structure, biological functions, and disease relevance of CK2 and emphatically analyze the structure-activity relationship (SAR) and binding modes of small-molecule CK2 inhibitors. We also discuss the latest progress of novel strategies, providing insights into new drugs targeting CK2 for clinical practice.

Pharmacokinetics of Novel Furoxan/Coumarin Hybrids in Rats Using LC-MS/MS Method and Physiologically Based Pharmacokinetic Model

Novel furoxan/coumarin hybrids were synthesized, and pharmacologic studies showed that the compounds displayed potent antiproliferation activities via downregulating both the phosphatidylinositide 3-kinase (PI3K) pathway and the mitogen-activated protein kinase (MAPK) pathway. To investigate the preclinical pharmacokinetic (PK) properties of three candidate compounds (CY-14S-4A83, CY-16S-4A43, and CY-16S-4A93), liquid chromatography, in tandem with the mass spectrometry LC-MS/MS method, was developed and validated for the simultaneous determination of these compounds. The absorption, distribution, metabolism, and excretion (ADME) properties were investigated in in vitro studies and in rats. Meanwhile, physiologically based pharmacokinetic (PBPK) models were constructed using only in vitro data to obtain detailed PK information. Good linearity was observed over the concentration range of 0.01−1.0 μg/mL. The free drug fraction (fu) values of the compounds were less than 3%, and the clearance (CL) values were 414.5 ± 145.7 mL/h/kg, 2624.6 ± 648.4 mL/h/kg, and 500.6 ± 195.2 mL/h/kg, respectively. The predicted peak plasma concentration (Cmax) and the area under the concentration-time curve (AUC) were overestimated for the CY-16S-4A43 PBPK model compared with the experimental ones (fold error > 2), suggesting that tissue accumulation and additional elimination pathways may exist. In conclusion, the LC-MS/MS method was successively applied in the preclinical PK studies, and the detailed information from PBPK modeling may improve decision-making in subsequent new drug development.

Structure prediction of eukaryotic elongation factor-2 kinase and identification of the binding mechanisms of its inhibitors: homology modeling, molecular docking, and molecular dynamics simulation

Protein kinases emerged as one of the most successful families of drug targets due to their increased activity and involvement in mediating critical signal transduction pathways in cancer cells. Recent evidence suggests that eukaryotic elongation factor 2 kinase (eEF-2K) is a potential therapeutic target for treating some highly aggressive solid cancers, including lung, pancreatic and triple-negative breast cancers. Thus, several compounds have been developed for the inhibition of the enzyme activity, but they are not sufficiently specific and potent. Besides, the crystal structure of this kinase remains unknown. Hence, the functional organization and regulation of eEF-2K remain poorly characterized. For this purpose, we constructed a homology model of eEF-2K and then used docking methodology to better understanding the binding mechanism of eEF-2K with 58 compounds that have been proposed as existing inhibitors. The results of this analysis were compared with the experimental results and the compounds effective against eEF-2K were determined against eEF-2K as a result of both studies. And finally, molecular dynamics (MD) simulations were performed for the stability of eEF-2K with these compounds. According to these study defined that the binding mechanism of eEF-2K with inhibitors at the molecular level and elucidated the residues of eEF-2K that play an important role in enzyme selectivity and ligand affinity. This information may lead to new selective and potential drug molecules to be for inhibition of eEF-2K.Communicated by Ramaswamy H. Sarma.

Synthesis, docking studies, biological activity of carbon monoxide release molecules based on coumarin derivatives

In the present work, we synthesized seven complexes. All complexes were identified by ESI-HRMS, ¹H-NMR, ¹⁹F-NMR and ¹³C-NMR spectroscopies. The synthesized complexes were tested for their anticancer activities in vitro against three different human cell lines, including breast MDAMB231, cervical Hela, liver HepG2. IC₅₀ values of complexes 1-7 were 34.98–667.35 µM. Complex 5 revealed higher sensitivity towards MDAMB231 cells with IC₅₀ values 34.98 μM in comparison to 5-FU as positive control. Moreover, complex 5 caused a decrease of mitochondrial membrane potential and effectively induced ROS production against MDAMB231 cells. Western blot analysis showed that complex 5 could up-regulate the expression of Bax protein and down-regulate the expression of Bcl-2, activate Caspase-3, slightly down-regulate the expression of HO-1. The docking studies showed that complex 5 could be interacted with Bcl-2 protein through hydrophobic interactions, hydrogen bonds and salt bridges to enhance the binding affinity. All the analyzed coumarins obeyed the Lipinski’s rule of five for orally administered drugs. Based on the aforementioned results, it suggests that the complex induced apoptosis cell via mitochondria pathways. Collectively, complex 5 could be considered as a promising hit for new anti-breast cancer agents. Carbonyl cobalt CORMs, as potential anticancer therapeutic agents, provided a new idea for the development of metal anticancer drugs.

A novel phenolic derivative inhibits AHL-dependent quorum sensing signaling in Pseudomonas aeruginosa

Increasing antibiotic resistance and the decline in the pharmaceutical industry’s investments have amplified the need for novel treatments for multidrug-resistant bacteria. Quorum sensing (QS) inhibitors reduce pathogens’ virulence without selective pressure on bacteria and provide an alternative to conventional antibiotic-based therapies. P. aeruginosa uses complex QS signaling to control virulence and biofilm formation. We aimed to identify inhibitors of P. aeruginosa QS acting on acyl-homoserine lactones (AHL)-mediated circuits. Bioluminescence and qRT-PCR assays were employed to screen a library of 81 small phenolic derivatives to reduce AHL-dependent signaling. We identified GM-50 as the most active compound inhibiting the expression of AHL-regulated genes but devoid of cytotoxic activity in human epithelial cells and biocidal effects on bacteria. GM-50 reduces virulence factors such as rhamnolipids, pyocyanin, elastase secretion, and swarming motility in P. aeruginosa PAO1 laboratory strain. By molecular docking, we provide evidence that GM-50 highly interacts with RhlR. GM-50 significantly improved aztreonam-mediated biofilm disruption. Moreover, GM-50 prevents adhesion of PAO1 and inflammatory damage in the human A549 cell line and protects Galleria mellonella from PAO1-mediated killing. GM-50 significantly reduces virulence factors in 20 P. aeruginosa clinical isolates from patients with respiratory tract infections. In conclusion, GM-50 inhibits AHL-signaling, reduces virulence factors, enhances the anti-biofilm activity of aztreonam, and protects G. mellonella larvae from damage induced by P. aeruginosa. Since GM-50 is active on clinical strains, it represents a starting point for identifying and developing new phenolic derivatives acting as QS-inhibitors in P. aeruginosa infections.

Diverse and efficient catalytic applications of new cockscomb flower-like Fe3O4@SiO2@KCC-1@MPTMS@CuII mesoporous nanocomposite in the environmentally benign reduction and reductive acetylation of nitroarenes and one-pot synthesis of some coumarin compounds

In this research, Fe3O4@SiO2@KCC-1@MPTMS@CuII as a new cockscomb flower-like mesoporous nanocomposite was prepared and characterized by various techniques including Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), SEM-based energy-dispersive X-ray (EDX) spectroscopy, inductively coupled plasma-optical emission spectrometry (ICP-OES), thermogravimetric analysis/differential thermal analysis (TGA/DTA), vibrating sample magnetometry (VSM), UV-Vis spectroscopy, and Brunauer-Emmett-Teller (BET) and Barrett-Joyner-Halenda (BJH) analyses. The as-prepared Fe3O4@SiO2@KCC-1@MPTMS@CuII mesoporous nanocomposite exhibited satisfactory catalytic activity in the reduction and reductive acetylation of nitroarenes in a water medium and solvent-free one-pot synthesis of some coumarin compounds including 3,3'-(arylmethylene)bis(4-hydroxy-2H-chromen-2-ones) (namely, bis-coumarins) (3a-n) and 2-amino-4-aryl-7,7-dimethyl-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitriles (6a-n) along with acceptable turnover numbers (TONs) and turnover frequencies (TOFs). Furthermore, the mentioned CuII-containing mesoporous nanocatalyst was conveniently recovered by a magnet from reaction environments and reused for at least seven cycles without any significant loss in activity, which confirms its good stability.

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.

Therapeutic Journey and Recent Advances in the Synthesis of Coumarin Derivatives

BACKGROUND

Coumarin is an oxygen-containing compound in medicinal chemistry. Coumarin plays an important role in both natural systems like plants and also in synthetic medicinal applications as drug molecules. Many structurally different coumarin compounds were found to show a big range of similarity with the vital molecular targets for their pharmacological action and small modifications in their structures resulted insignificant changes in their biological activities.

OBJECTIVE

This review gives detailed information about the studies of the recent advances in various pharmacological aspects of coumarins.

METHOD

Various oxygen-containing heterocyclic compounds represented remarkable biological significances. The fused aromatic oxygen-heterocyclic nucleus is able to change its electron density; thus changing the chemical, physical and biological properties respectively due to its multiple binding modes with the receptors, which play crucial role in pharmacological screening of drugs. A number of heterocyclic compounds have been synthesized which have their nucleus derived from various plants and animals. In coumarins, benzene ring is fused with pyrone nucleus which provides stability to the nucleus. Coumarins have shown a wide range of pharmacological activities such as anti-tumour, anti-coagulant, anti-inflammatory, anti-oxidant, antiviral, anti-malarial, anti-HIV and antimicrobial activity etc. Results: Reactive oxygen species like superoxide anion, hydroxyl radical and hydrogen peroxide are a type of unstable molecule that contains oxygen, which reacts with other molecules in the cell during the metabolism process but it may produce cytotoxicity when reactive oxygen species increase in number, by the damage of biological macromolecules. Hydroxyl radical (˙OH), is a strong oxidizing agent and it is responsible for the cytotoxicity by oxygen in different plants, animals and other microbes. coumarin is the oldest and effective compound having antimicrobial activity, anti-inflammatory, antioxidant, antidepressant activity, analgesic, anticonvulsant activity, etc. Naturally existing coumarin compounds act against SARS-CoV-2 by preventing viral replication through the targeting on active site against the Mpro target protein.

CONCLUSION

This review highlights the different biological activities of coumarin derivatives. In this review we provide an updated summary of the researches which are related to recent advances in biological activities of coumarins analogue and their most recent activities against COVID -19. Natural compounds act as a rich resource for novel drug development against various SARS-CoV-2 viral strains including viruses like herpes simplex virus, influenza virus, human immunodeficiency virus, hepatitis B and C viruses, middle east respiratory syndrome and severe acute respiratory syndrome.

Synthesis and Biological Activity Evaluation of Coumarin-3-Carboxamide Derivatives

A series of novel coumarin-3-carboxamide derivatives were designed and synthesized to evaluate their biological activities. The compounds showed little to no activity against gram-positive and gram-negative bacteria but specifically showed potential to inhibit the growth of cancer cells. In particular, among the tested compounds, 4-fluoro and 2,5-difluoro benzamide derivatives (14b and 14e, respectively) were found to be the most potent derivatives against HepG2 cancer cell lines (IC₅₀ = 2.62-4.85 μM) and HeLa cancer cell lines (IC₅₀ = 0.39-0.75 μM). The activities of these two compounds were comparable to that of the positive control doxorubicin; especially, 4-flurobenzamide derivative (14b) exhibited low cytotoxic activity against LLC-MK2 normal cell lines, with IC₅₀ more than 100 μM. The molecular docking study of the synthesized compounds revealed the binding to the active site of the CK2 enzyme, indicating that the presence of the benzamide functionality is an important feature for anticancer activity.

Protein kinase CK2 inhibition as a pharmacological strategy

CK2 is a constitutively active Ser/Thr protein kinase which phosphorylates hundreds of substrates. Since they are primarily related to survival and proliferation pathways, the best-known pathological roles of CK2 are in cancer, where its targeting is currently being considered as a possible therapy. However, CK2 activity has been found instrumental in many other human pathologies, and its inhibition will expectably be extended to different purposes in the near future. Here, after a description of CK2 features and implications in diseases, we analyze the different inhibitors and strategies available to target CK2, and update the results so far obtained by their in vivo application.

Chemical Manipulation of Abscisic Acid Signaling: A New Approach to Abiotic and Biotic Stress Management in Agriculture

The phytohormone abscisic acid (ABA) is the best-known stress signaling molecule in plants. ABA protects sessile land plants from biotic and abiotic stresses. The conserved pyrabactin resistance/pyrabactin resistance-like/regulatory component of ABA receptors (PYR/PYL/RCAR) perceives ABA and triggers a cascade of signaling events. A thorough knowledge of the sequential steps of ABA signaling will be necessary for the development of chemicals that control plant stress responses. The core components of the ABA signaling pathway have been identified with adequate characterization. The information available concerning ABA biosynthesis, transport, perception, and metabolism has enabled detailed functional studies on how the protective ability of ABA in plants might be modified to increase plant resistance to stress. Some of the significant contributions to chemical manipulation include ABA biosynthesis inhibitors, and ABA receptor agonists and antagonists. Chemical manipulation of key control points in ABA signaling is important for abiotic and biotic stress management in agriculture. However, a comprehensive review of the current knowledge of chemical manipulation of ABA signaling is lacking. Here, a thorough analysis of recent reports on small-molecule modulation of ABA signaling is provided. The challenges and prospects in the chemical manipulation of ABA signaling for the development of ABA-based agrochemicals are also discussed.

Flavone inspired discovery of benzylidenebenzofuran-3(2H)-ones (aurones) as potent inhibitors of human protein kinase CK2

In this work, we describe the design, synthesis and SAR studies of 2-benzylidenebenzofuran-3-ones (aurones), a new family of potent inhibitors of CK2. A series of aurones have been synthesized. These compounds are structurally related to the synthetic flavones and showed nanomolar activities towards CK2. Biochemical tests revealed that 20 newly synthesized compounds inhibited CK2 with IC₅₀ values in the nanomolar range. Further property-based optimization of aurones was performed, yielding a series of CK2 inhibitors with enhanced lipophilic efficiency. The most potent compound 12m (BFO13) has CLipE = 4.94 (CLogP = 3.5; IC₅₀ = 3.6 nM) commensurable with the best known inhibitors of CK2.

Molecular dynamics and computational study of Mannich-based coumarin derivatives: potent tyrosine kinase inhibitor

The manifestation of bacterial UTI (Urinary Tract Infection) has been predominantly endemic, globally; eventually, the development of new UTI antibacterial agent(s) remains the call of the day. Herein, two series of Mannich-based 4-hydroxy coumarin derivatives, 7a-m and 8a-m were designed by suitable heterocyclic amines condensed with aldehydes. The synthesised molecules were interpreted by ¹H-NMR and ¹³C-NMR spectral analyses with in vitro antibacterial studies. The compound, 4-hydroxy-3-((4-hydroxy-3-methoxyphenyl)(morpholino)methyl)-2H-chromen-2-one 8l was the significant derivative against pathogenic bacteria Staphylococcus aureus and Escherichia coli with MIC values 12.50 and 25 µM, respectively. Computational assessments with the Lipinski's rule of five, ADMET properties and molecular docking studies revealed that analogues, 7f, 7l, 8d, 8j and 8k could be potent druggable molecules with significant binding affinity towards bacterial tyrosine kinase, as target. To understand the mode of binding and intrinsic stabilities of potent receptor-ligand complexes, each system was subjected molecular dynamics simulations for 100 ns. Inter-molecular contact analysis and intrinsic hydrogen-bond stability portrayed the analogues 8l form a number of non-bonded contacts with the receptor tyrosine kinase being mostly dominated by electrostatic and hydrophobic contacts. The results from the present structure-based designing approach might be a valuable tool towards identification of a new antibacterial drug candidate(s) against UTI in near future.Abbreviations4-HC4-hydroxy coumarinADMETabsorption, distribution, metabolism, excretion, toxicityDCE1,2-dichloroethaneDCMdichloromethaneDMSOdimethyl sulfoxideMDmolecular dynamicsMICminimum inhibitory concentrationNMRnuclear magnetic resonanceNPTisothermal isobaric ensemblesNVTcanonical ensemblesPCAprincipal component analysisPDBprotein data bankRgradius gyrationRMSFroot-mean-square fluctuationsRSMDroot-mean-square deviationUTIurinary Tract InfectionCommunicated by Ramaswamy H. Sarma.

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.

Synthesis and Biological Evaluation of Novel Triazoles Linked 7-hydroxycoumarin as Potent Cytotoxic Agents

Background:

BacCancer is regarded as second leading cause of death worldwide. Therefore, there is a high demand for the discovery, development and improvement of novel anti-cancer agents which could efficiently prevent proliferative pathways and clonal expansion of cells.

Objective:

In view of this, a new series of bioactive scaffolds viz triazoles linked 7-hydroxycoumarin (1) were synthesized using click chemistry approach.

Method:

All the synthesized compounds were screened for cytotoxicity against a panel of seven different human cancer cell lines viz. Colon (Colo-205 and HCT-116), breast (MCF-7), lung (NCI-H322 and A549), prostate (PC-3) and skin (A-431) using 3-(4,5-Dimethylthiazol-yl)-diphenyl tetrazoliumbromide (MTT) assay.

Results:

Among all tested analogs, compound 5, displayed better cytotoxic activity as compared to the parent 7- hydroxycoumarin (1) with IC50 of 5.1, 22.7, 14.3 and 10.2 µM against breast (MCF-7), lung (NCI- H322), prostate (PC-3) and skin (A-431) cancer cell lines, respectively; the compound 5 was 8-fold more sensitive against MCF-7 than the parent 7-hydroxycoumarin. Moreover, Compound 5 induced both cytotoxic as well as cytostatic effects via induction of apoptosis and G1 phase arrest, respectively in breast cancer cells (MCF-7). The apoptotic cell population enhanced to 18.8% at 8 µM of 5 from 9.8% in case of negative control, while G1 phase arrest increased to 54.4% at 8 µM compared to negative control of 48.1%. Moreover, Compound 5 also exhibited a remarkable decrease in mitochondrial membrane potential (ΛΨm) leading to apoptosis of cancer cells used.

Conclusion:

The structure-activity relationship study revealed that the derivatives bearing electron-withdrawing substituents were more effective. The present study resulted in identification of the compounds demonstrating broad spectrum cytotoxic activity.

An efficient, mild and metal free l-proline catalyzed construction of fused pyrimidines under microwave conditions in water

One-pot condensation of 4-hydroxy coumarins, aldehydes and urea/thiourea to build C-C and C-N bonds is described. Fused pyrimidines have been synthesized under mild reaction conditions using l-proline. The protocol has been performed rapidly and efficiently in water under metal free conditions. Heterocyclic derivatives have been synthesized using the present methodology and avoid the use of hazardous solvents over conventional organic solvents. A proposed mechanism could be established for three component reactions. The present study reveals the first case in which l-proline has been explored as a homogeneous catalyst in the synthesis of fused pyrimidines in water under microwave irradiation. This synthesis involves simple workup and acceptable efficiency. The most notable feature of this protocol is the ability of the catalyst to influence asymmetric induction in the reaction.

A Network Pharmacology-Based Approach to Investigate the Novel TCM Formula against Huntington's Disease and Validated by Support Vector Machine Model

Several pathways are crucial in Huntington's disease (HD). Based on the concept of multitargets, network pharmacology-based analysis was employed to find out related proteins in disease network. The network target method aims to find out related mechanism of efficacy substances in rational design way. Traditional Chinese medicine prescriptions would be used for research and development against HD. Virtual screening was performed to obtain drug molecules with high binding capacity from traditional Chinese medicine (TCM) database@Taiwan. Quantitative structure-activity relationship (QSAR) models were conducted by MLR, SVM, CoMFA, and CoMSIA, constructed to predict the bioactivities of candidates. The compounds with high-dock score were further analyzed compared with control. Traditional Chinese medicine reported in the literature could be the training set provided for constructing novel formula by SVM model. We tried to find a novel formula that can bind well with these targets at the same time, which indicates our design could be highly related to the HD. Additionally, the candidates would validate by a long-term molecular dynamics (MD) simulation, 5 microseconds. Thus, we suggested the herbs Brucea javanica, Holarrhena antidysenterica, Dichroa febrifuga, Erythrophleum guineense, etc. which contained active compounds might be a novel medicine formula toward Huntington's disease.

Metal-Free Construction of Fused Pyrimidines via Consecutive C-C and C-N Bond Formation in Water

A facile and efficient protocol has been developed for mild construction of fused pyrimidines via l-proline-catalyzed reaction of 4-hydroxy coumarins, aldehydes, and 2-aminobenzothiazoles/urea. The reaction has been carried out rapidly and efficiently in water under mild and metal-free conditions. Current etiquette has efficiently synthesized the heterocycles and avoids the use of hazardous solvents over conventional organic solvents. A plausible reaction mechanism has been established in this study. This study represents the first case in which l-proline as a homogeneous catalyst has been explored in the synthesis of fused pyrimidines in water in view of simple procedure and acceptable efficiency. This method gives the target product in excellent yield with ease of workup.

Synthesis and Biological Evaluation of Novel Osthol Derivatives as Potent Cytotoxic Agents

BACKGROUND

Natural product, osthol has been found to have important biological and pharmacological roles particularly having inhibitory effect on multiple types of cancer.

OBJECTIVE

The unmet needs in cancer therapeutics make its derivatization an important and exciting field of research. Keeping this in view, a whole new series of diverse analogues of osthol (1) were synthesized.

METHOD

All the newly synthesized compounds were made through modification in the lactone ring as well as in the side chain of the osthol molecule and were subjected to anti-proliferative screening through 3-(4,5-Dimethylthiazol-yl)-diphenyl tetrazoliumbromide (MTT) against four different human cancers of diverse origins viz. Colon (Colo-205), lung (A549), Leukemia (THP- 1) and breast (MCF-7) including SV40 transformed normal breast epithelial cell (fR-2).

RESULTS

Interestingly, among the tested molecules, most of the analogs displayed better antiproliferative activity than the parent Osthol 1. However, among all the tested analogs, compound 28 exhibited the best results against leukemia (THP1) cell line with IC50 of 5µM.Compound 28 induced potent apoptotic effects and G1 phase arrest in leukemia cancer cells (THP1). The population of apoptotic cells increased from 13.8% in negative control to 26.9% at 8μM concentration of 28. Compound 28 also induced a remarkable decrease in mitochondrial membrane potential (ΛΨm) leading to apoptosis of the cancer cells.

CONCLUSION

A novel series of molecules derived from natural product osthol were synthesized, wherein compound 28 was found to be most effective against leukemia and with 10 fold less toxicity against normal cells. The compound induced cancer inhibition mainly through apoptosis and thus has a potential in cancer therapeutics.

Discovery of 2,6-disubstituted pyrazine derivatives as inhibitors of CK2 and PIM kinases

The design and synthesis of a novel series of 2,6-disubstituted pyrazine derivatives as CK2 kinase inhibitors is described. Structure-guided optimization of a 5-substituted-3-thiophene carboxylic acid screening hit (3a) led to the development of a lead compound (12b), which shows inhibition in both enzymatic and cellular assays. Subsequent design and hybridization efforts also led to the unexpected identification of analogs with potent PIM kinase activity (14f).

A hybrid of coumarin and phenylsulfonylfuroxan induces caspase-dependent apoptosis and cytoprotective autophagy in lung adenocarcinoma cells

BACKGROUND

Lung adenocarcinoma is the most primary histologic subtype of non-small cell lung cancer (NSCLC). Compound 8b, a novel coumarin derivative with phenylsulfonylfuroxan group, shows significant antiproliferation activity against lung adenocarcinoma cell with low toxicity.

PURPOSE

This study aims to uncover the potential of compound 8b in relation to apoptosis as well as autophagy induction in lung adenocarcinoma cells.

STUDY DESIGN

The cytotoxicity and apoptosis of A549 and H1299 cells induced by compound 8b were detected by MTT, microscope and western blot analysis. Autophagy was determined by TEM, confocal microscopy and western blot analysis. Akt/mTOR and Erk signaling pathway were also examined by western blot analysis.

RESULTS

First, significant growth inhibition and caspase-dependent apoptosis were observed in compound 8b-treated A549 and H1299 cells. Then, we confirmed compound 8b-induced autophagy by autophagosomes formation, upregulated expression of autophagy-related protein LC3-II and autophagic flux. Importantly, abolishing autophagy using inhibitors and ATG5 siRNA enhanced the cytotoxicity of compound 8b, indicating the cytoprotective role of autophagy in lung adenocarcinoma. Further mechanistic investigations suggested that Akt/mTOR and Erk signaling pathways contributed to autophagy induction by compound 8b.

CONCLUSION

This results demonstrate that compound 8b induces caspase-dependent apoptosis as well as cytoprotective autophagy in lung adenocarcinoma cells, which may provide scientific evidence for developing this furoxan-based NO-releasing coumarin derivative as a potential anti-lung adenocarcinoma therapeutic agents.

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.

The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design

Casein kinase II (CK2) is an ubiquitous and pleiotropic serine/threonine protein kinase able to phosphorylate hundreds of substrates. Being implicated in several human diseases, from neurodegeneration to cancer, the biological roles of CK2 have been intensively studied. Upregulation of CK2 has been shown to be critical to tumor progression, making this kinase an attractive target for cancer therapy. Several CK2 inhibitors have been developed so far, the first being discovered by "trial and error testing". In the last decade, the development of in silico rational drug design has prompted the discovery, de novo design and optimization of several CK2 inhibitors, active in the low nanomolar range. The screening of big chemical libraries and the optimization of hit compounds by Structure Based Drug Design (SBDD) provide telling examples of a fruitful application of rational drug design to the development of CK2 inhibitors. Ligand Based Drug Design (LBDD) models have been also applied to CK2 drug discovery, however they were mainly focused on methodology improvements rather than being critical for de novo design and optimization. This manuscript provides detailed description of in silico methodologies whose applications to the design and development of CK2 inhibitors proved successful and promising.

Synthesis and Cytotoxic Evaluation of Pyran, Dihydropyridine and Thiophene Derivatives of 3-Acetylcoumarin

A series of coumarin analogues bearing 4H-pyran rings 2a-d, 11a-d and 1,4-dihydropyridine rings 3a-d, 12a-d at position 3 were synthesized starting from either 3-acetyl coumarin (1) or the coumarin acetohydrazide derivative 4. Condensation of 3-acetylcoumarin (1) with 2-cyanoacetohydrazide afforded 2-cyano-N'-{1-[2-oxo-2H-chromen-3-yl]ethylidene}acetohydrazide (4). Reaction of compound 4 with elemental sulfur and either malononitrile or ethyl cyanoacetate afforded the thiophene derivatives 8 and 9, respectively. The structures of the newly synthesized compounds were confirmed on the basis of their spectral data and elemental analyses. All synthesized compounds were screened for their in vitro anticancer activity against six human cancer cell lines and normal fibroblasts. Several compounds showed potent inhibition with an IC50 value of ˂870 nM. Compound 3d exhibited equivalent cytotoxic effect as the standard CHS 828 against a breast cancer cell line (IC50 value=18 nM). Normal fibroblast cells (WI38) were affected to a much lesser extent (IC50 value >10000 nM).

Discovery of new protein kinase CK2 inhibitors with 1,3-dioxo-2,3-dihydro-1H-indene core

Protein kinase CK2 (CK2) serves as an attractive anticancer target. Herein new CK2 inhibitors with a 1,3-dioxo-2,3-dihydro-1H-indene core are reported.

Eco-friendly grinding synthesis of a double-layered nanomaterial and the correlation between its basicity, calcination and catalytic activity in the green synthesis of novel fused pyrimidines

The synthesis of hydrotalcite using Al : Mg molar ratios of 1.0 : 3.0 by a grinding method at room temperature is reported.

Design and synthesis of coumarin–glyoxal hybrids for spermicidal and antimicrobial actions: a dual approach to contraception

Today there is an urgent need for safe and effective dual-purpose contraceptive agents, which can simultaneously prevent unintended pregnancies and sexually transmitted infections (STI).