Inhibition mechanism of CDK-2 and GSK-3β by a sulfamoylphenyl derivative of indoline-a molecular dynamics study

Design, synthesis, antineoplastic activity of new pyrazolo[3,4-d]pyrimidine derivatives as dual CDK2/GSK3β kinase inhibitors; molecular docking study, and ADME prediction

In the current study, novel pyrazolo[3,4-d]pyrimidine derivatives 5a-h were designed and synthesized as targeted anti-cancer agents through dual CDK2/GSK-3β inhibition. The designed compounds demonstrated moderate to potent activity on the evaluated cancer cell lines (MCF-7 and T-47D). Compounds 5c and 5 g showed the most promising cytotoxic activity against the tested cell lines surpassing that of the used reference standard; staurosporine. On the other hand, both compounds showed good safety and tolerability on normal fibroblast cell line (MCR5). The final compounds 5c and 5 g showed a promising dual CDK2/GSK-3β inhibitory activity with IC50 of 0.244 and 0.128 μM, respectively, against CDK2, and IC50 of 0.317 and 0.160 μM, respectively, against GSK-3β. Investigating the effect of compounds 5c and 5 g on CDK2 and GSK-3β downstream cascades showed that they reduced the relative cellular content of phosphorylated RB1 and β-catenin compared to that in the untreated MCF-7 cells. Moreover, compounds 5c and 5 g showed a reasonable selective inhibition against the target kinases CDK2/GSK-3β in comparison to a set of seven off-target kinases. Furthermore, the most potent compound 5 g caused cell cycle arrest at the S phase in MCF-7 cells preventing the cells' progression to G2/M phase inducing cell apoptosis. Molecular docking studies showed that the final pyrazolo[3,4-d]pyrimidine derivatives have analogous binding modes in the target kinases interacting with the hinge region key amino acids. Molecular dynamics simulations confirmed the predicted binding mode by molecular docking. Moreover, in silico predictions indicated their favorable physicochemical and pharmacokinetic properties in addition to their promising cytotoxic activity.

Molecular docking and dynamics simulations revealed the potential inhibitory activity of honey-iQfood ingredients against GSK-3β and CDK5 protein targets for brain health

Honey-iQfood is an herbal supplement made of a mixture of polyherbal extracts and wild honey. The mixture is traditionally claimed to improve various conditions related to brain cells and functions including dementia and Alzheimer's disease. Glycogen synthase kinase-3 beta (GSK-3β) and cyclin-dependent kinase 5 (CDK5) have been identified as being involved in the pathological hyperphosphorylation of tau proteins, which leads to the formation of neurofibrillary tangles and causes Alzheimer's disease. Therefore, this study was conducted to confirm the traditional claims by detection of active compounds, namely curcumin, gallic acid, catechin, rosmarinic acid, and andrographolide in the raw materials of Honey-iQfood through HPLC analysis, molecular docking, and dynamic simulations. Two potential compounds, andrographolide, and rosmarinic acid, produced the best binding affinities following the molecular docking of the active compounds against the GSK-3β and CDK5 targets. Andrographolide binds with GSK-3β at -8.2 kcal/mol, whereas rosmarinic acid binds to CDK5 targets at -8.6 kcal/mol. Molecular dynamics was further carried out to confirm the docking results and clarify their dynamic properties such as RMSD, RMSF, rGyr, SASA, PSA, and binding free energy. CDK5-andrographolide complexes had the best MM-GBSA score (-83.63 kcal/mol) compared to other complexes, indicating the better interaction profile and stability of the complex. These findings warrant further research into andrographolide and rosmarinic acid as efficient inhibitors of tau protein hyperphosphorylation to verify their therapeutic potential in brain-related illnesses.Communicated by Ramaswamy H. Sarma.

A Computational Study of the Immobilization of New 5-Nitroisatine Derivatives with the Use of C60-Based Functionalized Nanocarriers

Isatin-based compounds are a large group of drugs used as competitive inhibitors of ATP. The 5-nitroisatin derivatives studied in this work are inhibitors of the CDK2 enzyme, which can be used in the development of new anti-cancer therapies. One of the basic activities that often allows for an increase in biological activity while reducing the undesirable effects associated with the toxicity of medicinal substances is immobilization based on carriers. In this work, fifty nanocarriers derived from C60 fullerene, containing a bound phenyl ring on their surfaces, were used in the process of the immobilization of isatin derivatives. Based on flexible docking methods, the binding capacities of the drugs under consideration were determined using a wide range of nanocarriers containing symmetric and asymmetric modifications of the phenyl ring, providing various types of interactions. Based on the data collected for each of the tested drugs, including the binding affinity and the structure and stability of complexes, the best candidates were selected in terms of the type of substituent that modified the nanoparticle and its location. Among the systems with the highest affinity are the dominant complexes created by functionalized fullerenes containing substituents with a symmetrical location, such as R2-R6 and R3-R5. Based on the collected data, nanocarriers with a high potential for immobilization and use in the development of targeted therapies were selected for each of the tested drugs.

Novel oxindole/benzofuran hybrids as potential dual CDK2/GSK-3β inhibitors targeting breast cancer: design, synthesis, biological evaluation, and in silico studies

The serine/threonine protein kinases CDK2 and GSK-3β are key oncotargets in breast cancer cell lines, therefore, in the present study three series of oxindole-benzofuran hybrids were designed and synthesised as dual CDK2/GSK-3β inhibitors targeting breast cancer (5a-g, 7a-h, and 13a-b). The N1 -unsubstituted oxindole derivatives, series 5, showed moderate to potent activity on both MCF-7 and T-47D breast cancer cell lines. Compounds 5d-f showed the most potent cytotoxic activity with IC50 of 3.41, 3.45 and 2.27 μM, respectively, on MCF-7 and of 3.82, 4.53 and 7.80 μM, respectively, on T-47D cell lines, in comparison to the used reference standard (staurosporine) IC50 of 4.81 and 4.34 μM, respectively. On the other hand, the N1 -substituted oxindole derivatives, series 7 and 13, showed moderate to weak cytotoxic activity on both breast cancer cell lines. CDK2 and GSK-3β enzyme inhibition assay of series 5 revealed that compounds 5d and 5f are showing potent dual CDK2/GSK-3β inhibitory activity with IC50 of 37.77 and 52.75 nM, respectively, on CDK2 and 32.09 and 40.13 nM, respectively, on GSK-3β. The most potent compounds 5d-f caused cell cycle arrest in the G2/M phase in MCF-7 cells inducing cell apoptosis because of the CDK2/GSK-3β inhibition. Molecular docking studies showed that the newly synthesised N1 -unsubstituted oxindole hybrids have comparable binding patterns in both CDK2 and GSK-3β. The oxindole ring is accommodated in the hinge region interacting through hydrogen bonding with the backbone CO and NH of the key amino acids Glu81 and Leu83, respectively, in CDK2 and Asp133 and Val135, respectively, in GSK-3β. Whereas, in series 7 and 13, the N1 -substitutions on the oxindole nucleus hinder the compounds from achieving these key interactions with hinge region amino acids what rationalises their moderate to low anti-proliferative activity.

Inhibition of GSK_3β by Iridoid Glycosides of Snowberry (Symphoricarpos albus) Effective in the Treatment of Alzheimer's Disease Using Computational Drug Design Methods

The inhibition of glycogen synthase kinase-3β (GSK-3β) activity prevents tau hyperphosphorylation and binds it to the microtubule network. Therefore, a GSK-3β inhibitor may be a recommended drug for Alzheimer's treatment. In silico methods are currently considered as one of the fastest and most cost-effective available alternatives for drug/design discovery in the field of treatment. In this study, computational drug design was conducted to introduce compounds that play an effective role in inhibiting the GSK-3β enzyme by molecular docking and molecular dynamics simulation. The iridoid glycosides of the common snowberry (Symphoricarpos albus), including loganin, secologanin, and loganetin, are compounds that have an effect on improving memory and cognitive impairment and the results of which on Alzheimer's have been studied as well. In this study, in the molecular docking phase, loganin was considered a more potent inhibitor of this protein by establishing a hydrogen bond with the ATP-binding site of GSK-3β protein and the most negative binding energy to secologanin and loganetin. Moreover, by molecular dynamics simulation of these ligands and GSK-3β protein, all structures were found to be stable during the simulation. In addition, the protein structure represented no change and remained stable by binding ligands to GSK-3β protein. Furthermore, loganin and loganetin have higher binding free energy than secologanin; thus, these compounds could effectively bind to the active site of GSK-3β protein. Hence, loganin and loganetin as iridoid glycosides can be effective in Alzheimer's prevention and treatment, and thus, further in vitro and in vivo studies can focus on these iridoid glycosides as an alternative treatment.

The Oxindole Derivatives, New Promising GSK-3β Inhibitors as One of the Potential Treatments for Alzheimer's Disease-A Molecular Dynamics Approach

Simple Summary

Enzymatic overexpression is a determinant of the development of many diseases. Increased activity of the GSK-3β enzyme is a factor that manifests itself in the development of numerous disease entities such as Alzheimer’s disease, schizophrenia, diabetes and cancers. An important medical procedure in such cases is the inhibition of enzyme activity. Based on the comprehensive use of computational chemistry methods, a group of new compounds derived from 2-oxindole was designed. The conducted research allowed the assessment of the conformational properties of the ligand molecules in the GSK-3β active site, the dynamic stability of the obtained complexes and their exact energetic characteristics. Taking into account the obtained data, a narrow group of derivatives showing an affinity for the active site of the GSK-3β enzyme was selected. The comparison of binding properties of selected 2-oxindole derivatives with an inhibitor with confirmed pharmacological activity indicates the high application potential of the newly developed compounds.

Abstract

The glycogen synthase kinase 3β (GSK-3β) is a protein kinase involved in regulating numerous physiological processes such as embryonic development, transcription, insulin action, cell division cycle and multiple neuronal functions. The overexpression of this enzyme is related to many diseases such as schizophrenia, Alzheimer’s disease, diabetes and cancer. One of the basic methods of treatment in these cases is the usage of ATP-competitive inhibitors. A significant group of such compounds are indirubin and its analogs, e.g., oxindole derivatives. The compounds considered in this work are 112 newly designed oxindole derivatives. In the first stage, such molecular properties of considered compounds as toxicity and LogP were estimated. The preliminary analysis of the binding capabilities of considered compounds towards the GSK-3β active site was conducted with the use of the docking procedure. Based on obtained molecular properties and docking simulations, a selected group of complexes that were analyzed in the molecular dynamics stage was nominated. The proposed procedure allowed for the identification of compounds such as Oxind_4_9 and Oxind_13_10, which create stable complexes with GSK-3β enzyme and are characterized by the highest values of binding affinity. The key interactions responsible for stabilization of considered ligand–protein complexes were identified, and their dynamic stability was also determined. Comparative analysis including analyzed compounds and reference molecule 3a, which is also an oxindole derivative with a confirmed inhibitory potential towards GSK3B protein, clearly indicates that the proposed compounds exhibit an analogous binding mechanism, and the obtained binding enthalpy values indicate a slightly higher binding potential than the reference molecule.

The Immobilization of ChEMBL474807 Molecules Using Different Classes of Nanostructures

Indirubin derivatives and analogues are a large group of compounds which are widely and successfully used in treatment of many cancer diseases. In particular, the ChEMBL474807 molecule, which has confirmed inhibiting abilities against CDK2 and GSK3B enzymes, can be included in this group. The immobilization of inhibitors with the use of nanocarriers is an often used strategy in creation of targeted therapies. Evaluations were made of the possibility of immobilizing ligand molecules on different types of nanocarrier, such as carbon nanotubes (CNT), functionalized fullerene C60 derivatives (FF_X), and functionalized cube rhombellanes, via the use of docking methods. All results were compared with a reference system, namely C60 fullerene. The realized calculations allowed indication of a group of compounds that exhibited significant binding affinity relative to the ligand molecule. Obtained data shows that structural modifications, such as those related to the addition of functional groups or changes of structure symmetry, realized in particular types of considered nanostructures, can contribute to increases of their binding capabilities. The analysis of all obtained nano complexes clearly shows that the dominant role in stabilization of such systems is played by stacking and hydrophobic interactions. The realized research allowed identification of potential nanostructures that, together with the ChEMBL474807 molecule, enable the creation of targeted therapy.

Investigation of the Inhibition Potential of New Oxindole Derivatives and Assessment of Their Usefulness for Targeted Therapy

Oxindole derivatives are a large group of compounds that can play the role of Adenosine triphosphate (ATP) competitive inhibitors. The possibility of modification of such compounds by addition of active groups to both cyclic systems of oxindole allows the obtaining of derivatives showing significant affinity toward cyclin-dependent kinase (CDK) proteins. Overexpression of that enzyme is observed in the case of most cancers. The discovery of new efficient inhibitors, which could be used in the development of targeted therapies, is one of the current goals setting trends in recent research. In this research, an oxindole molecular core was used, which was modified by the addition of different substituents to both side chains. The realized procedure allowed the creation of a set of oxindole derivatives characterized by binding affinity values and molecular descriptors evaluated during docking procedures and QSAR calculations. The most promising structures characterized by best sets of parameters were used during the molecular dynamics stage. The analysis of structural and energetic properties of systems obtained during this stage of computation gives an indication of inhibitors creating the most stable complexes, characterized by the highest affinity. During this stage, two structures were selected, where affinity towards potential nanocarriers was evaluated. Realized calculations confirmed a significant role of stacking interactions in the stabilization of ligand complexes with fullerene molecules. Obtained data indicates that complexes of oxindole derivatives and considered nanocarriers exhibit significant potential in the creation of immobilized drugs, and can be used in the development of targeted therapies.

The Immobilization of Oxindole Derivatives with Use of Cube Rhombellane Homeomorphs

A key aspect of modern drug research is the development of delivery methods that ensure the possibility of implementing targeted therapy for a specific biological target. The use of nanocarriers enables to achieve this objective, also allowing to reduce the toxicity of used substances and often extending their bioavailability. Through the application of docking methods, the possibility of using cube rhombellanes as potential carriers for two oxindole derivatives was analyzed. In the studies, compounds identified as inhibitors of the CDK2 enzyme and a set of nanostructures proposed by the Topo Cluj Group were used. The popular fullerene molecule C60 was used as the reference system. The estimated binding affinities and structures of obtained complexes show that use of functionalized cube rhombellanes containing hydrogen bond donors and acceptors in their external molecular shell significantly increases ligand affinity toward considered nanocariers, compared to classic fullerenes. The presented values also allow to state that an important factor determining the mutual affinity of the tested ligands and nanostructures is the symmetry of the analyzed nanocarriers and its influence on the distribution of binding groups (aromatic systems, donors and acceptors of hydrogen bonds) on the surface of nanoparticles.