Structural basis for the GSK-3beta binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5-dialkylaminomethyl-1H-[1,2,3] triazole-4-carboxylic acid derivatives

Discovery of novel and highly potential inhibitors of glycogen synthase kinase 3-beta (GSK-3β) through structure-based pharmacophore modeling, virtual computational screening, docking and in silico ADMET analysis

The protein Glycogen Synthase Kinase 3-Beta (GSK-3β), is a promising therapeutic target for treating various diseases such as neurodegenerative disorders, diabetes, inflammation and cancer. This study aims to investigate the potential of compounds targeting inflammation or carbohydrate metabolism to selectively inhibit GSK3β by binding to its ATP site. To achieve this goal, we filtered a database of 49367 molecules involved in carbohydrate metabolism or targeting inflammation using various computational analyses, including pharmacophore modeling, molecular docking, dynamic simulation, prime MM-GBSA calculation, and in silico ADME studies. We generated a pharmacophore model (hypo S: AADDHRR) using two different crystallographic complexes of GSK3β and evaluated the model's performance in identifying hits using various parameters, including EF, GH, ROC, AUC and BEDROC. Subsequently, we performed various dockings (HTVS, SP, XP and IFD) for the retrieved hits and found that, 5 out of the top 10 ranked compounds had the scaffold of pyrazolidine 3,5-dione, which has never been reported to inhibit kinases. We also conducted ADMET studies to and concluded that compound N6 exhibited the best pharmacokinetic profile passing the blood-brain barrier, possessing high lipophilicity and a high coefficient of skin permeability in the intestines, along with good bioavailability and low toxicity risk assessment. Dynamic simulation were also performed indicating that compounds N6 derived from pyrazolidine 3,5-dione demonstrated better binding potential for GSK3β during the simulation period. Therefore, we propose that compounds derived from pyrazolidine-3,5-dione, which modulate the activity of lysosomal alpha-glucosidase could serve as a novel scaffold for the selective inhibition of GSK-3β.Communicated by Ramaswamy H. Sarma.

Angular Regioselective Synthesis of Varied Functionalized Hexahydro-1,2,4-triazolo[4,3-a]quinazolin-9-ones and Their Antiproliferative Action

New 2-thioxopyrimidin-4-ones capable of participating in regioselective reactions with functionally diverse hydrazonoyl chlorides towards angular regioisomers, rather than linear ones, were designed and synthesized to form stereoisomeric cis- and trans-hexahydro [1,2,4]triazolo[4,3-a]quinazolin-9-ones to be tested as antitumor candidates. The angular regiochemistry of the products was verified through crystallographic experiments and NMR studies. In addition, the regioselectivity of the reaction was found to be independent of the stereochemistry of the used 2-thioxopyrimidin-4-one. Only compound 4c demonstrated satisfactory growth inhibition against all the cancer cells used among all the produced drugs.

Bioactivities and Mode of Actions of Dibutyl Phthalates and Nocardamine from Streptomyces sp. H11809

Dibutyl phthalate (DBP) produced by Streptomyces sp. H11809 exerted inhibitory activity against human GSK-3β (Hs GSK-3β) and Plasmodiumfalciparum 3D7 (Pf 3D7) malaria parasites. The current study aimed to determine DBP’s plausible mode of action against Hs GSK-3β and Pf 3D7. Molecular docking analysis indicated that DBP has a higher binding affinity to the substrate-binding site (pocket 2; −6.9 kcal/mol) than the ATP-binding site (pocket 1; −6.1 kcal/mol) of Hs GSK-3β. It was suggested that the esters of DBP play a pivotal role in the inhibition of Hs GSK-3β through the formation of hydrogen bonds with Arg96/Glu97 amino acid residues in pocket 2. Subsequently, an in vitro Hs GSK-3β enzymatic assay revealed that DBP inhibits the activity of Hs GSK-3β via mixed inhibition inhibitory mechanisms, with a moderate IC₅₀ of 2.0 µM. Furthermore, the decrease in K_m value with an increasing DBP concentration suggested that DBP favors binding on free Hs GSK-3β over its substrate-bound state. However, the antimalarial mode of action of DBP remains unknown since the generation of a Pf 3D7 DBP-resistant clone was not successful. Thus, the molecular target of DBP might be indispensable for Pf survival. We also identified nocardamine as another active compound from Streptomyces sp. H11809 chloroform extract. It showed potent antimalarial activity with an IC₅₀ of 1.5 μM, which is ~10-fold more potent than DBP, but with no effect on Hs GSK-3β. The addition of ≥12.5 µM ferric ions into the Pf culture reduced nocardamine antimalarial activity by 90% under in vitro settings. Hence, the iron-chelating ability of nocardamine was shown to starve the parasites from their iron source, eventually inhibiting their growth.

Comprehensive investigation of selectivity landscape of glycogen synthase kinase-3 inhibitors

Interaction signatures of drug candidates are characteristic to off-target (neutral) and antitarget (negative) effects, inferring reduced efficiency, side-effects and high attrition rate. Today's retroactive scaled-down virtual screening (VS) experiments relying on benchmarking datasets are extensively involved to assess ligand enrichment in the real-world problem. In recent years, unbiased benchmarking sets turned into a tremendous need to assist virtual screening methodologies for emerging drug targets. To date, the benchmarking datasets are quite limited, whereas glycogen synthase kinase-3 (GSK-3) is not included into directories of benchmarking datasets such as DUD-e, MUV, etc. Herein we introduced our in-house algorithm to build an unbiased benchmarking dataset, including highly selective, moderately selective and nonselective inhibitors for a significant therapeutic target - GSK-3, suitable for both ligand-based and structure-based VS approaches. These datasets are unbiased in terms of physico-chemical properties and topological descriptors, as resulted from mean(ROC-AUC) leave-one-out cross-validation (LOO CV). and additional 2 D similarity search. Moreover, we investigated the gradual selectivity dataset by application of multiple 2 D similarity coefficients and distances, 3 D similarity and docking. Besides the resulted links between the enrichment of selective GSK-3 inhibitors and their chemical structures, a database of compounds and their 3 D similarity signatures including cut-off thresholds for enhanced selectivity was generated. 2 D similarity space analysis revealed that selectivity problem cannot be evaluated appropriately with 2 D similarity searching alone. The current analysis provided useful, comprehensive insights, which may facilitate the knowledge-based identification of novel selective GSK-3 inhibitors.Communicated by Ramaswamy H. Sarma.

CoFe2O4/Cu(OH)2 magnetic nanocomposite: an efficient and reusable heterogeneous catalyst for one-pot synthesis of β-hydroxy-1,4-disubstituted-1,2,3-triazoles from epoxides

A magnetically separable CoFe₂O₄/Cu(OH)₂ nanocomposite was prepared and characterized by various techniques such as FESEM, EDS, TEM, XRD, VSM and FT-IR. This novel composite was used as a heterogeneous catalyst for the regioselective synthesis of β-hydroxy-1,4-disubstituted-1,2,3-triazoles from sodium azide, terminal alkynes and structurally different epoxides in water at 60 °C. The formation of the product proceeds in one pot through a mechanism that involves an in situ generated organic azide intermediate, followed by rapid ring closure with the alkyne component. The simple procedure, short reaction times, perfect regioselectivity, high product yields, and use of a benign solvent and nontoxic catalyst are among the considerable advantages of this protocol. Furthermore, the catalyst was easily separated using an external magnet and reused several times without any significant loss of catalytic activity or magnetic properties.

Magnetically separable CoFe₂O₄/Cu(OH)₂ nanocomposite was prepared and used as a novel heterogeneous catalyst for synthesis of β-hydroxy-1,4-disubstituted-1,2,3-triazoles from epoxides.

Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors

The current study was conducted to elaborate a novel pharmacophore model to accurately map selective glycogen synthase kinase-3 (GSK-3) inhibitors, and perform virtual screening and drug repurposing. Pharmacophore modeling was developed using PHASE on a data set of 203 maleimides. Two benchmarking validation data sets with focus on selectivity were assembled using ChEMBL and PubChem GSK-3 confirmatory assays. A drug repurposing experiment linking pharmacophore matching with drug information originating from multiple data sources was performed. A five-point pharmacophore model was built consisting of a hydrogen bond acceptor (A), hydrogen bond donor (D), hydrophobic (H), and two rings (RR). An atom-based 3D quantitative structure-activity relationship (QSAR) model showed good correlative and satisfactory predictive abilities (training set [Formula: see text]; test set: [Formula: see text]; whole data set: stability [Formula: see text]). Virtual screening experiments revealed that selective GSK-3 inhibitors are ranked preferentially by Hypo-1, but fail to retrieve nonselective compounds. The pharmacophore and 3D QSAR models can provide assistance to design novel, potential GSK-3 inhibitors with high potency and selectivity pattern, with potential application for the treatment of GSK-3-driven diseases. A class of purine nucleoside antileukemic drugs was identified as potential inhibitor of GSK-3, suggesting the reassessment of the target range of these drugs.

Theoretical studies on the selective mechanisms of GSK3β and CDK2 by molecular dynamics simulations and free energy calculations

Glycogen synthase kinase 3 (GSK3) is a serine/threonine protein kinase which is widely involved in cell signaling and controls a broad number of cellular functions. GSK3 contains α and β isoforms, and GSK3β has received more attention and becomes an attractive drug target for the treatment of several diseases. The binding pocket of cyclin-dependent kinase 2 (CDK2) shares high sequence identity to that of GSK3β, and therefore, the design of highly selective inhibitors toward GSK3β remains a big challenge. In this study, a computational strategy, which combines molecular docking, molecular dynamics simulations, free energy calculations, and umbrella sampling simulations, was employed to explore the binding mechanisms of two selective inhibitors to GSK3β and CDK2. The simulation results highlighted the key residues critical for GSK3β selectivity. It was observed that although GSK3β and CDK2 share the conserved ATP-binding pockets, some different residues have significant contributions to protein selectivity. This study provides valuable information for understanding the GSK3β-selective binding mechanisms and the rational design of selective GSK3β inhibitors.

Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: understanding the factors contributing to selectivity

Glycogen synthase kinase-3 is a constitutively acting, multifunctional serine threonine kinase, the role of which has been implicated in several physiological pathways and has emerged as a promising target for the treatment of type-II diabetes and Alzheimer's disease. In order to provide a detailed understanding of the origin of selectivity determinants of ATP competitive inhibitors, molecular dynamics simulations in combination with MM-PBSA binding energy calculations were performed using crystal structures of GSK-3β and CDK-2 in complex with 12 ATP competitive inhibitors. Analysis of energy contributions indicate that electrostatic interaction energy dictates the selectivity of ATP competitive inhibitors against CDK-2. Key interactions as well as residues that potentially make a major contribution to the binding free energy were identified at the ATP binding site. This analysis stresses the need for the inhibitors to interact with Lys85, Thr138, and Arg141 in the binding site of GSK-3β to show selectivity. The residue-wise energy decomposition analysis further suggested the additional role of Gln185 in determining the selectivity of maleimides. The results obtained in this study can be utilized to design new selective GSK-3 ATP competitive inhibitors.

1,2,3-Triazoles from carbonyl azides and alkynes: filling the gap

Electron deficient azides are challenging substrates in CuAAC reactions. Particularly, when N-carbonyl azides are applied the formation of N-carbonyl triazoles has not yet been observed. We report herein the first example of this class of reaction, with a copper-based system that efficiently enables the synthesis of N-carbamoyl 1,2,3-triazoles by [3+2] cycloaddition of N-carbamoyl azides and alkynes.

Synthesis and cytotoxicity evaluation of some novel thiazoles, thiadiazoles, and pyrido[2,3-d][1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-ones incorporating triazole moiety

Reactions of hydrazonoyl halides and each of methyl 2-(1-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)ethylidene)hydrazine-1-carbodithioate and 2-(1-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)ethylidene)hydrazine-1-carbothioamide afforded 2-(1-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)ethylidene)hydrazono)-3-phenyl-5-substituted-2,3-dihydro-1,3,4-thiadiazoles and 5-(4-substituted)diazenyl)-2-(2-(1-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)ethylidene)hydrazinyl)-4-arylthiazoles, respectively. Analogously, the reactions of hydrazonoyl halides with 7-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)-5-phenyl-2-thioxo-2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-one gave 3-(4-substituted)-8-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)-6-phenyl-1-arylpyrido[2,3-d]-[1,2,4]-triazolo-[4,3-a]pyrimidin- 5(1H)-ones in a good yield. The structures of the newly synthesized were elucidated via elemental analysis, spectral data and alternative synthesis routes whenever possible. Twelve of the newly synthesized compounds have been evaluated for their antitumor activity against human breast carcinoma (MCF-7) and human hepatocellular carcinoma (HepG2) cell lines. Their structure activity relationships (SAR) were also studied. The 1,3,4-thiadiazole derivative 9b (IC50 = 2.94 µM) has promising antitumor activity against the human hepatocellular carcinoma cell line and the thiazole derivative 12a has promising inhibitory activity against both the human hepatocellular carcinoma cell line and the breast carcinoma cell line (IC50 = 1.19, and 3.4 µM, respectively).

Investigation of the flexibility of protein kinases implicated in the pathology of Alzheimer's disease

The pathological characteristics of Alzheimer’s Disease (AD) have been linked to the activity of three particular kinases—Glycogen Synthase Kinase 3β (GSK3β), Cyclin-Dependent Kinase 5 (CDK5) and Extracellular-signal Regulated Kinase 2 (ERK2). As a consequence, the design of selective, potent and drug-like inhibitors of these kinases is of particular interest. Structure-based design methods are well-established in the development of kinase inhibitors. However, progress in this field is limited by the difficulty in obtaining X-ray crystal structures suitable for drug design and by the inability of this method to resolve highly flexible regions of the protein that are crucial for ligand binding. To address this issue, we have undertaken a study of human protein kinases CDK5/p25, CDK5, ERK2 and GSK3β using both conventional molecular dynamics (MD) and the new Active Site Pressurisation (ASP) methodology, to look for kinase-specific patterns of flexibility that could be leveraged for the design of selective inhibitors. ASP was used to examine the intrinsic flexibility of the ATP-binding pocket for CDK5/p25, CDK5 and GSK3β where it is shown to be capable of inducing significant conformational changes when compared with X-ray crystal structures. The results from these experiments were used to quantify the dynamics of each protein, which supported the observations made from the conventional MD simulations. Additional information was also derived from the ASP simulations, including the shape of the ATP-binding site and the rigidity of the ATP-binding pocket. These observations may be exploited in the design of selective inhibitors of GSK3β, CDK5 and ERK2.

Small-Molecule Inhibitors of GSK-3: Structural Insights and Their Application to Alzheimer's Disease Models

The world health organization (WHO) estimated that 18 million people are struck by Alzheimer's disease (AD). The USA, France, Germany, and other countries launched major programmes targeting the identification of risk factors, the improvement of caretaking, and fundamental research aiming to postpone the onset of AD. The glycogen synthase kinase 3 (GSK-3) is implicated in multiple cellular processes and has been linked to the pathogenesis of several diseases including diabetes mellitus, cancer, and AD. Inhibition of GSK-3 leads to neuroprotective effects, decreased β-amyloid production, and a reduction in tau hyperphosphorylation, which are all associated with AD. Various classes of small molecule GSK-3 inhibitors have been published in patents and original publications. Herein, we present a comprehensive summary of small molecules reported to interact with GSK-3. We illustrate the interactions of the inhibitors with the active site. Furthermore, we refer to the biological characterisation in terms of activity and selectivity for GSK-3, elucidate in vivo studies and pre-/clinical trials.

Transition-metal-catalyzed denitrogenative transannulation: converting triazoles into other heterocyclic systems

Transition metal catalyzed denitrogenative transannulation of a triazole ring has recently received considerable attention as a new concept for the construction of diverse nitrogen-containing heterocyclic cores. This method allows a single-step synthesis of complex nitrogen heterocycles from easily available and cheap triazole precursors. In this Minireview, recent progress of the transition metal catalyzed denitrogenative transannulation of a triazole ring, which was discovered in 2007, is discussed.

Studying synergism of methyl linked cyclohexyl thiophenes with triazole: synthesis and their cdk5/p25 inhibition activity

A novel clubbed triazolyl thiophene series of cdk5/p25 inhibitors, potentially useful for the treatment of Alzheimer's disease, is disclosed. Evaluation of the SAR of substitution within these series has allowed the identification of a range of compounds which significantly reduce brain cdk5/p25 and thus have potential as possible treatments for Alzheimer's disease.

Synthesis of chiral 1,4-disubstituted-1,2,3-triazole derivatives from amino acids

A versatile method for the synthesis of chiral 1,4-disubstituted-1,2,3-triazole derivatives starting from easily accessible naturally occurring D-or L-amino acids as chiral synthons is described. The amino acids were converted into azido alcohols, followed by copper catalyzed [3+2] cycloaddition reactions between the azido alcohols and methyl propiolate and subsequent ester aminolysis with primary and secondary amines furnished the target compounds, which were obtained in excellent yields with no racemization. Docking of selected target compounds shows that the chiral 1,4-disubstituted-1,2,3-triazoles derivatives has the potential of mimicking the binding mode of known purine analogues.

QSAR models for predicting the similarity in binding profiles for pairs of protein kinases and the variation of models between experimental data sets

We propose a direct QSAR methodology to predict how similar the inhibitor-binding profiles of two protein kinases are likely to be, based on the properties of the residues surrounding the ATP-binding site. We produce a random forest model for each of five data sets (one in-house, four from the literature) where multiple compounds are tested on many kinases. Each model is self-consistent by cross-validation, and all models point to only a few residues in the active site controlling the binding profiles. While all models include the "gatekeeper" as one of the important residues, consistent with previous literature, some models suggest other residues as being more important. We apply each model to predict the similarity in binding profile to all pairs in a set of 411 kinases from the human genome and get very different predictions from each model. This turns out not to be an issue with model-building but with the fact that the experimental data sets disagree about which kinases are similar to which others. It is possible to build a model combining all the data from the five data sets that is reasonably self-consistent but not surprisingly, given the disagreement between data sets, less self-consistent than the individual models.

Synthesis of new triazole-based trifluoromethyl scaffolds

Trifluoromethyl propargylamines react with various azide derivatives to afford 1,4-disubstituted 1,2,3-triazoles through a Huisgen 1,3-dipolar cycloaddition. The reaction is catalyzed by a Cu(I) species in acetonitrile, and the corresponding products are obtained in good yields. This process thus offers an entry to new trifluoromethyl peptidomimetics as interesting scaffolds.

Exploiting glycogen synthase kinase 3beta flexibility in molecular recognition

GSK3beta (glycogen synthase kinase 3beta) is involved in the phosphorylation of various important regulatory proteins. Pharmacological inhibition of this enzyme could yield treatments for a variety of diseases including diabetes and Alzheimer's disease. The understanding of events involved in the molecular recognition of inhibitors by the active site of this enzyme is key in structure-based design strategies. The present study deals with the dynamic nature of GSK3beta and highlights the importance of studying protein plasticity in structure-based drug design, exemplified by our method called ASP (active-site pressurization).