Human Cyclin-dependent Kinase Research Articles

New AIEgens based on thieno[2,3-d]pyrimidine derivatives: Synthesis, DFT calculations, and molecular docking

In this paper, new thieno[2,3-d]pyrimidine analogs have been synthesized and characterized through different spectroscopic techniques. The photophysical properties of the molecules (7b-7f) and the quantum chemical calculations have been investigated. These molecules exhibited aggregation-induced emission behavior and showed efficient emission in both solid and solution states. A shift toward shorter wavelengths (hypsochromic shift) was observed when transitioning from the solution to the solid state, which could be explained by photoinduced intramolecular charge transfer (ICT) processes. DFT calculations confirmed that the diverse behavior of the thieno[2,3-d]pyrimidine analogs could be attributed to variations in molecular packing and rigidity. This study illustrates how luminophores aggregation can occur without significantly impacting the excited state, emphasizing the unconventional behavior resulting from minor alterations in terminal substituents. These findings hold implications for the advancement of luminescent materials. Additionally, theoretical calculations were conducted to compare the excitations and emissions of the new AIEgens with practical observations. Furthermore, a molecular docking study of the five AIEgens suggested their potential utility as anticancer drugs. Compound 7c exhibited a high affinity for human cyclin-dependent kinase 2 (CDK-2) protein, with a binding energy of 9.6 kcal/mol, indicating its potential as an inhibitor for this specific protein.

413 (PB401): Comprehensive characterization of CDK inhibitors using a complete panel of all 20 human cyclin-dependent kinases

413 (PB401): Comprehensive characterization of CDK inhibitors using a complete panel of all 20 human cyclin-dependent kinases

Phytochemical investigation and spectral characterization of isolated compounds from Pyracantha crenulata (D. Don) M. Roem (syn. Crataegus crenulata Roxb) leaves: evaluation of antioxidant activity and molecular docking analysis

Pyracantha crenulata (D. Don) M. Roem (syn. Crataegus crenulata Roxb.) is an evergreen shrub in the Rosaceae family, notable for its chemical diversity and biological potential. This study isolates and characterises six compounds (Cc-1 to Cc-6), including four new ones, using repeated column chromatography. Structural elucidation employed IR, UV-vis, 1H and 13 C NMR, and mass spectrometry. The DPPH assay was used to test the antioxidant activity in vitro. Compounds Cc-4, Cc-2, Cc-1, and Cc-5 had IC50 values of 15.734 μg/ml, 51.422 μg/ml, 62.864 μg/ml, and 71.622 μg/ml, in that order. Quantitative phytochemical analysis revealed flavonoid content (22.81 mg/g), tannin content (385.15 mg/g), and total phenolic content (128.78 mg/g). Human cyclin-dependent kinase 2 (CDK2) (PDB ID: 1hck) docked with compound Cc-4, which demonstrated strong antioxidant activity and revealed significant non-bonding interactions. The pkCSM and SwissADME analyses suggested promising drug-like properties for Cc-4, supported by BOILED-Egg diagrams highlighting its therapeutic potential.

Eco-friendly Synthesis of Indole Conjugated Chromeno[d]Pyrimidines as Anti-cancer Agents and their Molecular Modelling Studies

Introduction: Many medicinally active new chemical entities depend on indole conjugated chromeno[d]pyrimidine derivatives as a building block. The synthesis of 4-(1H-indol-3-yl)-3,4- dihydro-1H-chromeno[4,3-d]pyrimidine-2,5-dione 4 were achieved in the current study by treating 4- hydroxy-2H-chromen-2-one 1, indole aldehydes 2, and urea/thiourea 3 in the presence of L-proline. Methods: By adopting the above protocol, we were able to synthesize eight compounds, i.e. 4-(1Hindol- 3-yl)-3,4-dihydro-1H-chromeno[4,3-d]pyrimidine-2,5-diones (4a-4h), in the presence of Lproline as a catalyst in ethanol as solvent for 2-3 hours at 70-75°C with decent yields of 80-85%, and their structures were ascertained by various spectral techniques. They were further screened for their potentiality to inhibit cancer growth in HepG2 and MDA-MD-231 cells. Results: The scope of the synthesis of biological relevant Indole conjugated Chromeno[ d]Pyrimidines by three-component reaction (MCRs) process was investigated. The most optimised conditions obtained were 0.3 eq of L-proline for 2 hours at 70-75°C which gave the best yield (85%). The few advantages of this newly developed method are excellent yields, no metal catalyst, less toxic solvents, simple workup no chromatographic column purifications. On further screening for their anticancer activities, out of all, the compound 4b displayed noteworthy cytotoxicity with IC50 values of 8.1 and 9.2 μM against HepG2 and MDA-MD-231, respectively. Additionally, in silico studies also supported that compound 4b had favourable binding energy (-7.8 kcal/mol) when compared to the co-crystal ligand (LS5) in inhibiting the human cyclin-dependent kinase 2 (CDK2) protein. Conclusion: In conclusion, we have developed a simple, convenient, and efficient method for the synthesis of structurally diverse indole conjugated chromeno[d]pyrimidine analogues in the presence of L-proline as catalyst in ethanol as solvent with good yields. Further, the in vitro cytotoxic studies against HepG2 and MDA-MD-231 cells demonstrated that the synthesized compounds had good to reasonable activity, except for compound 4d.

Genomic Discovery and Structure-Activity Exploration of a Novel Family of Enzyme-Activated Covalent Cyclin-Dependent Kinase Inhibitors.

Fungi have historically been the source of numerous important medicinal compounds, but full exploitation of their genetic potential for drug development has been hampered in traditional discovery paradigms. Here we describe a radically different approach, top-down drug discovery (TD3), starting with a massive digital search through a database of over 100,000 fully genomicized fungi to identify loci encoding molecules with a predetermined human target. We exemplify TD3 by the selection of cyclin-dependent kinases (CDKs) as targets and the discovery of two molecules, 1 and 2, which inhibit therapeutically important human CDKs. 1 and 2 exhibit a remarkable mechanism, forming a site-selective covalent bond to the CDK active site Lys. We explored the structure-activity relationship via semi- and total synthesis, generating an analog, 43, with improved kinase selectivity, bioavailability, and efficacy. This work highlights the power of TD3 to identify mechanistically and structurally novel molecules for the development of new medicines.

Cytotoxic flavone-C-glycosides from the leaves of Dypsis pembana (H.E.Moore) Beentje & J.Dransf., Arecaceae: in vitro and molecular docking studies

BackgroundCancer poses a health threat, with an increased incidence worldwide. Thus, it is essential to develop new natural anticancer agents. Dypsis pembana (H.E.Moore) Beentje & J.Dransf (DP) is an ornamental plant belonging to the family Arecaceae. This study aimed to isolate and identify phytoconstituents from the leaves of this plant and evaluate their in vitro cytotoxic activities.MethodsDifferent chromatographic techniques were applied to fractionate the hydro-alcoholic extract of DP and separate the major phytoconstituents. The isolated compounds were structurally elucidated based on their physical and spectroscopic data. The in vitro cytotoxic activities of the crude extract and fractions thereof were evaluated against human colon carcinoma (HCT-116), human breast carcinoma (MCF-7), and human hepatocellular carcinoma (HepG-2) cell lines via MTT assay. Moreover, selected isolates were tested against HepG-2 cell line. Molecular docking analysis was performed to investigate the interactions of these compounds with two potential targets, the human topoisomerase IIα and cyclin-dependent kinase 2 enzymes.ResultsThirteen diverse compounds were reported for the first time from DP, providing significant chemotaxonomic biomarkers. Among tested compounds, vicenin-II (7) was the most cytotoxic against HepG-2 cell line, with an IC50 value of 14.38 µg/mL, followed by isovitexin (13) (IC50 of 15.39 µg/mL). These experimental findings were complemented by molecular docking, which demonstrated that vicenin-II exhibited superior enzyme-binding affinities to the studied vital targets and shed light on the structure–activity relationships among the investigated flavone-C-glycosides members.ConclusionThe phytochemical profile of DP was characterized for the first time, reflecting chemotaxonomic data about the concerned species, genus, or even the family. Biological and computational findings revealed that vicenin-II and isovitexin are possible lead structures as inhibitors of the human topoisomerase IIα and cyclin-dependent kinase 2 enzymes.

Therapeutic potential of CDK11 in cancer.

Human cyclin-dependent kinases (CDKs) direct the progression of the cell cycle and transcription. They are deregulated in tumours, and despite their involvement in the regulation of basic cellular processes, many CDKs are promising targets for cancer therapy. CDK11 is an essential gene for the growth of many malignancies; however, its primary cellular function has been obscure, and the mode-of-action of OTS964, the first CDK11 inhibitor and antiproliferative compound, has been unknown. A recent study has shown that OTS964 prevents spliceosome activation, revealing a key role of CDK11 in the regulation of pre-mRNA splicing. In light of these findings, we discuss the therapeutic potential of CDK11 in cancer.

Immortalized Canine Adipose-Derived Mesenchymal Stem Cells as a Novel Candidate Cell Source for Mesenchymal Stem Cell Therapy.

Mesenchymal stem cells are expected to be a cell source for stem cell therapy of various diseases in veterinary medicine. However, donor-dependent cell heterogenicity has been a cause of inconsistent therapeutic efficiency. Therefore, we established immortalized cells from canine adipose tissue-derived mesenchymal stem cells (ADSCs) to minimize cellular heterogeneity by reducing the number of donors, evaluated their properties, and compared them to the primary cells with RNA-sequencing. Immortalized canine ADSCs were established by transduction with combinations of the R24C mutation of human cyclin-dependent kinase 4 (CDKR24C), canine cyclin D1, and canine TERT. The ADSCs transduced with CDK4R24C, cyclin D1, and TERT (ADSC-K4DT) or with CDK4R24C and cyclin D1 (ADSC-K4D) showed a dramatic increase in proliferation (population doubling level >100) without cellular senescence compared to the primary ADSCs. The cell surface markers, except for CD90 of the ADSC-K4DT and ADSC-K4D cells, were similar to those of the primary ADSCs. The ADSC-K4DT and ADSC-K4D cells maintained their trilineage differentiation capacity and chromosome condition, and did not have a tumorigenic development. The ability to inhibit lymphocyte proliferation by the ADSC-K4D cells was enhanced compared with the primary ADSCs and ADSC-K4DT cells. The pathway analysis based on RNA-sequencing revealed changes in the pathways mainly related to the cell cycle and telomerase. The ADSC-K4DT and ADSC-K4D cells had decreased CD90 expression, but there were no obvious defects associated with the decreased CD90 expression in this study. Our results suggest that ADSC-K4DT and ADSC-K4D cells are a potential novel cell source for mesenchymal stem cell therapy.

Synthesis, crystal structure, DFT, Hirshfeld surface analysis, energy framework, docking and molecular dynamic simulations of (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one as anticancer agent

In this work, a novel crystal, (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one (E-BSP) was synthesized via Knoevenagel condensation of benzaldehyde and (E)-6-(4-methoxystyryl)-4,5-dihydropyridazin-3(2H)-one. The molecular structure of E-BSP was confirmed by using FT-IR, 1H-NMR, 13C-NMR, UV-vis, ESI-MS, TGA/DTA thermal analyses and single crystal X-ray diffraction. The DFT/B3LYP methods with the 6-311++G(d,p) basis set were used to determine the vibrational modes over the optimized structure. Potential energy distribution (PED) and the VEDA 4 software were used to establish the theoretical mode assignments. The same approach was used to compute the energies of frontier molecular orbitals (HOMO-LUMO), global reactivity descriptors, and molecular electrostatic potential (MEP). Additionally, experimental and computed UV spectral parameters were determined in methanol and the obtained outputs were supported by FMO analysis. Molecular docking and molecular dynamics (MD) simulation analyses of the E-BSP against six proteins obtained from different cancer pathways were carried out. The proteins include; epidermal growth factor receptor (EGFR), Estrogen receptor (ERα), Mammalian target of rapamycin (mTOR), Progesterone receptor (PR) (Breast cancer), Human cyclin-dependent kinase 2 (CDK2) (Colorectal cancer), and Survivin (Squamous cell carcinoma/Non-small cell lung cancer). The results of the analyses showed that the compound had less binding energies ranging between −6.30 to −9.09 kcal/mol and formed stable complexes at the substrate-binding site of the proteins after the 50 ns MD simulation. Therefore, E-BSP was considered a potential inhibitor of different cancer pathways and should be used for the treatment of cancer after experimental validation and clinical trial. Communicated by Ramaswamy H. Sarma

Anticancer Potential of Rhychosia beddomei: An In vitro and In silico Study

Rhychosia beddomei is widely distributed in tropical and subtropical regions around the world. Traditionally this plant has been used as a medicine for multiple ailments including cancer. The present study addresses the evaluation of In vitro anticancer activity by using MTT Assay of methanolic extracts of whole plant of Rhychosia beddomei in Human Hepatocellular Carcinoma (HepG2) cell line in comparison with standard drug doxorubicin as well as In silico analysis. Doxorubicin acts in the cancer cell by intercalation into DNA and disruption of topoisomerase-II-mediated DNA repair and generation of free radicals and their damage to cellular membranes, DNA and proteins. Cytotoxicity studies have indicated that the phytoconstituents of Rhychosia beddomei have the ability to selectively target cancer, whereas minimal or negligible cytotoxic effects were observed on normal cells. The molecular docking approach was employed to check binding conformations of phytochemicals against human cyclin-dependent kinase 2, CDK-2 and Topoisomerase-2, Topo-II proteins (Protein Data bank-ID: 1DI8 and 1ZXM) through Mcule online molecular modelling tool. The docking revealed an encouraging binding score with a maximum score of -11.5 and -10.4 kCal/mol with CDK-2 and Topo-II respectively and all the selected ligands indicate promising anticancer activity. Molecular docking studies using the phytoconstituents were performed in order to gain a better understanding of the putative mechanisms of action leading to the development of improved and affordable therapies. This study paves a way to better understand the integration of molecular docking and in vitro studies can accelerate cancer drug discovery showing a good consistency of anticancer therapeutic drug potentials of Rhychosia beddomei by In vitro and In silico approaches.

Synthetic beidellite clay as nanocarrier for delivery of antitumor oxindolimine-metal complexes

Studies on the immobilization of oxindolimine‑copper(II) or zinc(II) complexes [ML] in synthetic beidellite (BDL) clay were developed to obtain a suitable inorganic carrier capable of promoting the modified-release of metallopharmaceuticals. Previous investigations have shown that the studied metal complexes are promising antitumor agents, targeting DNA, mitochondria, and some proteins. They can bind to DNA, causing oxidative damage via formation of reactive oxygen species (ROS). In mitochondria they lead to a decrease in membrane potential, acting as decoupling agents, and therefore efficiently inducing apoptosis. Additionally, they inhibit human topoisomerase IB and cyclin dependent kinases, proteins involved in the cell cycle. BDL clays in the sodium form were synthesized under hydrothermal conditions and characterized by a set of physicochemical techniques while the BDL-[ML] hybrid materials were prepared by ion exchange method. The characterization of pristine clay and the obtained hybrids were performed by Infrared, Raman, electron paramagnetic resonance and energy dispersive X-ray spectroscopies, thermogravimetric analysis, scanning electron microscopy, X-ray powder diffraction, specific surface area, zeta potential and surface ionic charge measurements. The [ML] release assays under the same cell incubation conditions were performed monitoring metals by X-ray fluorescence. The BDL-[CuL] hybrid materials were stable and able to derail tumor HeLa cells, with corresponding IC50 values in the 0.11–0.41 mg mL−1 range. By contrast, the analogous hybrid samples of zinc(II) and the pristine BDL proved to be non-toxic facing the same cells. These results indicate a promising possibility of using synthetic beidellite as a carrier of such antitumor metal complexes.

Design, Synthesis, Docking Studies and Biological Evaluation of Novel Benzochromenopyrimidines via Silica Sulfuric Acid Catalyzed Reaction on Apoptosis in Human Cancer Cells

Via one-pot reaction of 2-naphthol, thiobarbituric acid and aldehyde in the presence of silica sulfuric acid (SSA) as a catalyst to synthesis benzochromenopyrimidines derivatives. Then we studied the reaction of benzochromenopyrimidines derivatives with bromoacetic acid to obtain benzo[5,6]chromeno[2,3-d]thiazolo[3,2-a]pyrimidine-11,13(10H,14H)-dione derivatives. Meanwhile, dichloroethane was reacted with 12-(4-fluorophenyl)-9-thioxo-9,10-dihydro-8H-benzo[5,6]chromeno[2,3-d]pyrimidin-11(12H)-one to form 14-(4-fluorophenyl)-10,11-dihydrobenzo[5,6]chromeno[2,3-d]thiazolo[3,2-a]pyrimidin-13(14H)-one. All new products structure was elucidated based on analytical and spectroscopic analyses. Anti-cancer activity of newly synthesized structures was investigated. Cancer cells (MDA-MB-231 and HepG2) were used to evaluate the anti-cancer activity of tested compounds using neutral red uptake assay. Treatment of MDA-MB-231 and HepG2 cells with tested compound 6h revealed more inhibitory influence after 48 h. The expression levels of BCL2, BAX, Caspase3, Survivin and P53 genes were investigated using QRT-PCR. This study exhibited that compound 6h revealed significant pro-apoptotic effect via down regulation of BCL2 and Survivin genes and up-regulation of BAX, Caspase3 and P53 genes when treated with MDA-MB-231 and HepG2 cells as compared to control values. The biological studies of these compounds were proved through molecular docking studies with human cyclin-dependent kinase 2 (PDB code: 2A4L) and compound 6h showed low binding energy and shortage bond length with different amino acids. Noteworthy, the tested compound 6h exhibited the most pronounced effect in this respect.

Synthesis, Antioxidant, and Cytotoxic Activities of New 1,3,4-Thiadiazoldiazenylacrylonitrile Derivatives

To develop potent anticancer agents, a series of novel 1,3,4-thiadiazoldiazenylacrylonitrile derivatives 2–16 were designed and synthesized using (1,3,4-thiadiazol-2-yl) carbonohydrazonoyl dicyanide (2) as starting material. The radical scavenging activity of the synthesized compounds was evaluated, and it was observed that the compounds have radical scavenging properties. For studying the radical scavenging activity of the synthesized compounds, the 1,1-diphenyl-2-picrylhydrazyl (DPPH) method was applied. It was found that compounds 12–16 are the most potent antioxidant compounds compared to the results of ascorbic acid (reference drug). Cytotoxicity studies of the newly synthesized compounds were performed against two mammalian cancer cell lines, HepG2, and MCF-7 cells. Compound 15 showed an IC50 value (11.5 ± 0.6 µM) that is very similar to DOX as a standard for the two used cell lines. The most promising values were observed from compounds 5 and 12–16 (very strong activity). Histopathology of liver tissues treated with compound 15 confirmed its anticancer activity. Molecular docking (MD) simulations were run to evaluate the putative binding ability of the most promising anti-cancer synthesized compounds 5 and 12–16 with the human cyclin-dependent kinase 2 (CDK2). Based on MD results as well as physicochemical and pharmacokinetic (ADMET) predictions, the compounds under investigation are promising candidates for the future development of novel anticancer agents targeting CDK2.

Serine 13 of the human cytomegalovirus viral cyclin-dependent kinase UL97 is required for regulatory protein 14-3-3 binding and UL97 stability

The human cytomegalovirus (HCMV) UL97 protein is a conserved herpesvirus protein kinase (CHPK) and a viral cyclin-dependent kinase (v-CDK). However, mechanisms regulating its activity in the context of infection are unknown. Here, we identified several cellular regulatory 14-3-3 proteins as UL97-interacting partners that promote UL97 stability. Humans are known to encode seven isoforms of 14-3-3 proteins (β, ε, η, γ, σ, θ, and ζ) that bind phosphoserines or phosphothreonines to impact protein structure, stability, activity, and localization. Our proteomic analysis of UL97 identified 49 interacting partners, including 14-3-3 isoforms β, η, and γ. Furthermore, coimmunoprecipitation with Western blotting assays demonstrated that UL97 interaction with 14-3-3 isoforms β, ε, η, γ, and θ occurs in a kinase activity-dependent manner. Using mutational analysis, we determined the serine residue at amino acid 13 of UL97 is crucial for 14-3-3 interaction. We demonstrate UL97 S13A (serine to alanine substitution at residue 13) retains kinase activity but the mutant protein accumulated at lower levels than WT UL97. Finally, we show both laboratory (AD169) and clinical (TB40/E) strains of HCMV encoding UL97 S13A replicated with WT kinetics in fibroblasts but showed decreased UL97 accumulation. Taken together, we conclude that 14-3-3 proteins interact with and stabilize UL97 during HCMV infection.

Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3

Human cyclin-dependent kinase inhibitor 3 (CDKN3) is a known oncogene in hepatocellular carcinoma (HCC) and its expression is promoted during tumor development. CDKN3 serves as a cell cycle regulator and its dysregulation is considered to be a causal factor for tumor progression. However, the molecular basis of the regulation of CDKN3 expression remains largely elusive. Using in silico approach, we identified CDKN3SE, a super enhancer (SE), and enhancer RNA (eRNA) candidates transcribed from this SE. Among the eRNA candidates, the expression of CDKN3eRNA was detected in the human HCC model cell line HepG2, and was found to facilitate the expression of CDKN3 without affecting the cell proliferation rate. In silico screening revealed two DNA-binding transcription factors, upstream stimulatory factor (USF) 1 and 2, involved in the regulation of CDKN3eRNA expression on CDKN3SE. A knock-down of USF1/USF2 expression in the HepG2 cells did not affect CDKN3eRNA expression, while the expression of CDKN3 was down-regulated. In a USF2 dominant negative HepG2 cell line generated by genome editing, a drastically altered cell shape and lowered cell proliferation rate were found; however, the expression of CDKN3eRNA appeared unaffected. Thus, the present study illustrated two regulators for CDKN3 expression: USF2, as a cell cycle-associated protein regulator, and CDKN3eRNA, as a cell cycle-unassociated RNA regulator.

Abstract 2304: Comprehensive characterization of CDK inhibitors using a complete panel of all 20 human cyclin-dependent kinases

Abstract The family of human Cyclin dependent kinases (CDKs) comprises 20 different CDKs that play critical roles in the regulation of cell cycle progression, gene transcription and neuronal function. Deregulation of different CDKs is frequently observed in human cancer. Enzymatic kinase activity of CDKs is dependent on the binding of a member of the Cyclin protein family. So far more than 15 Cyclins have been described most of them can bind and activate different CDKs. Current data suggest the physiological relevance of at least 50 different CDK/Cyclin complexes. Since the 20 CDKs share significant structural homology and regulate different function in cell growth and development, selectivity of compounds within the CDK family is of critical importance. Approval of a first CDK inhibitor (Palbociclib) targeting CDK4/6 for the treatment of ER+/HER+- breast cancer served as a clinical proof that targeting specific members of the CDK protein kinase family is a versatile approach to treat cancer. The approval of the first CDK inhibitor sparked the research and development of other inhibitors targeting different members of the CDK-family. Currently, four additional CDK4/6 inhibitors have been approved and more than 15 CDK inhibitors with limited selectivity are in different preclinical or clinical development phases. However, the critical importance of selectivity within the CDK family is underlined by the fact that the clinical development of four CDK9 inhibitors has been stopped due to the lack of selectivity and high toxicity. Different approaches (including inhibition by covalent binding) have resulted in more selective inhibitors, especially against CDKs like CDK7, CDK9 and CDK12. Although several biochemical activity assays for different CDKs have been set up and used for selectivity testing, so far no panel covering all 20 human CDKs using one assay technology has been described. We report here the setup of a biochemical in-vitro activity assay panel of 32 CDK/Cyclins complexes generated recombinantly in insect cells covering the complete set of all 20 human CDKs. For all 32 complexes a radiometric biochemical activity assay has successfully been established allowing to characterize inhibitors with respect to their biochemical selectivity applying the same assay technology. Using the comprehensive CDK panel we determined the IC50 values of more than 15 CDK inhibitors that have been either approved or are in different preclinical and clinical development phases. Results will be presented showing the selectivity of these inhibitors not only for all 20 CDKs but also for specific CDKs forming active complexes with two or more different cyclins. This CDK screening panel allows the generation of comparative data on compound selectivity early in development, thereby helping to reduce the risk of designing compounds with suboptimal target selectivity. Citation Format: Daniel Müller, Frank Totzke, Thomas Weber, Andreas Gericke, Diane Krämer, Carolin Heidemann-Dinger, Constance Ketterer, Michael H. Kubbutat. Comprehensive characterization of CDK inhibitors using a complete panel of all 20 human cyclin-dependent kinases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2304.

Naringenin as a potential inhibitor of human cyclin-dependent kinase 6: Molecular and structural insights into anti-cancer therapeutics

Cancer is one of the major causes of global deaths and needs immediate therapeutic development. So far, several strategies have been undertaken to prevent cancer, including kinase targeting by small-molecule inhibitors. Cyclin dependent kinase 6 (CDK6) plays an essential role in cancer progression and development as its overexpression is associated with tumor development and progression. The present study demonstrated that Naringenin (NAG) binds strongly to CDK6 with a binding affinity of −7.51 kcal/mol. ATPase assay of CDK6 in the presence of NAG shows that it inhibits CDK6 with an IC50 = 3.13 μM. Fluorescence and isothermal titration calorimetry studies demonstrated that NAG binds to CDK6 with the binding constant (K) values of 3.55 × 106 M−1 and 7.06 ± 2.70 × 106 M−1, respectively. The cell-based functional studies showed that NAG decreases the cell viability of human cancer cell lines, induces apoptosis, and reduces their colonization ability. Outcomes of the present in silico and in vitro studies highlighted the significance of NAG for the development of anti-cancer leads in terms of CDK6 inhibitors and provided future implications for combinatorial anti-cancer therapies.

The emerging roles of the CDK/cyclin complexes in antiviral innate immunity.

More than 20 members of the human cyclin-dependent kinases (CDKs) family share the feature of being activated by cyclins. CDKs have been involved in diverse biological processes, such as cell cycle, transcription, DNA damage response, and apoptosis. If CDKs are not properly regulated, they can cause diseases like cancer. CDKs are Ser/Thr kinases that work with cyclins to control cell cycle progression. Various CDK-cyclin complexes phosphorylate particular target proteins and drive different cell cycle stages. Accumulating evidence demonstrated that CDKs play an essential role in the cell cycle; however, their roles in antiviral innate immunity are just emerging. This minireview summarizes how CDKs play their roles in antiviral innate immunity. Our goal is to draw attention to the involvement of CDKs in antiviral innate immunity, whether as separate entities or as components of CDK/cyclin complexes that have gotten less attention in the past.

Biocompatible silver(I) complexes with heterocyclic thioamide ligands for selective killing of cancer cells and high antimicrobial activity – A combined in vitro and in silico study

A series of heteroleptic Ag(I) complexes bearing 4,6-dimethyl-2-pyrimidinethiol (dmp2SH), i.e., [AgCl(dmp2SH)(PPh3)2] (1), [Ag(dmp2SH)(PPh3)2]NO3 (2), [Ag(dmp2SΗ)(xantphos)]NO3 (3), [Ag(μ-dmp2S)(PPh3)]2 (4), [Ag(dmp2S)(xantphos)] (5), [Ag(μ-dmp2S)(DPEphos)]2 (6) (xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene and DPEPhos = bis[(2-diphenylphosphino)phenyl]ether) were synthesized. The complexes display systematic variation of particular structural characteristics which were proved to have a significant impact on their in vitro cytotoxicity and antimicrobial properties. A moderate-to-high potential for bacteria growth inhibition was observed for all complexes, with 2, 3 and 5 being particularly effective against Gram-(+) bacteria (IC50 = 1.6–4.5 μM). The three complexes exhibit high in vitro cytotoxicity against HeLa and MCF-7 cancer cells (IC50 = 0.32–3.00 μΜ), suggesting the importance of coordination unsaturation and cationic charge for effective bioactivity. A very low cytotoxicity against HDFa normal cells was observed, revealing a high degree of selectivity (selectivity index ~10) and, hence, biocompatibility. Fluorescence microscopy using 2 showed effective targeting on the membrane of the HeLa cancer cells, subsequently inducing cell death. Binding of the complexes to serum albumin proteins is reasonably strong for potential uptake and subsequent release to target sites. A moderate in vitro antioxidant capacity for free radicals scavenging was observed and a low potential to destroy the double-strand structure of calf-thymus DNA by intercalation, suggesting likely implication of these properties in the bioactivity mechanisms of these complexes. Further insight into possible mechanisms of bioactivity was obtained by molecular modeling calculations, by exploring their ability to act as potential inhibitors of DNA-gyrase, human estrogen receptor alpha, human cyclin-dependent kinase 6, and human papillomavirus E6 oncoprotein.

Evaluation of The Antioxidant, Antimicrobial, and Anticancer Activities of Dicliptera bupleuroides Isolated Compounds Using In Vitro and In Silico Studies.

Phytochemical investigation of chloroform fraction (DBC) and ethyl acetate fraction (DBE) of D. bupleuroides (Acanthaceae) resulted in the isolation of β-sitosterol (1) from DBC and vanillic acid (2) from DBE, which were first to be isolated from D. bupleuroides. β-Sitosterol (1) exhibited substantial antioxidant activity (IC50 = 198.87 µg/mL), whereas vanillic acid (2) showed significant antioxidant power (IC50 = 92.68 µg/mL) employing 1,1-diphenyl-2-picrylhydrazyl (DPPH*) radical scavenging capacity assay. Both compounds showed pronounced antimicrobial activity using the agar disc diffusion method, particularly against fungi showing MIC values of 0.182 and 0.02 concerning Candida albicans, respectively, and 0.001 mg/mL regarding Penicillium notatum. They revealed considerable antibacterial activity with MIC values ranging between 0.467 and 0.809 mg/mL. Vanillic acid (2) exhibited substantial anticancer potential displaying 48.67% cell viability at a concentration of 100 μg/mL using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-Diphenyl-2H-Tetrazolium Bromide) assay concerning HepG2 cell lines. These results were further consolidated by in silico studies on different enzymes, where vanillic acid displayed a high fitting score in the active pockets of DNA-gyrase, dihydrofolate reductase, aminoglycoside nucleotidyltransferase, and β-lactamase. It also inhibited human cyclin-dependent kinase 2 (CDK-2) and DNA topoisomerase II, as revealed by the in silico studies. ADME/TOPKAT (absorption, distribution, metabolism, excretion, and toxicity) prediction showed that vanillic acid exhibited reasonable pharmacodynamic, pharmacokinetic, and toxicity properties and, thus, could perfectly together with D. bupleuroides crude extract be incorporated in pharmaceutical preparations to counteract cancer and microbial invasion, as well as oxidative stress. Thus, it is concluded that D. bupleroides could be a potential source of therapeutically active compounds, which would be helpful for the discovery of clinically effective and safe drugs.