Synthesis and evaluation of indenopyrazoles as cyclin-dependent kinase inhibitors. Part 4: Heterocycles at C3

Identification of Novel PI3Kα Inhibitor Against Gastric Cancer: QSAR-, Molecular Docking-, and Molecular Dynamics Simulation-Based Analysis

Gastric cancer (GC) is a malignant tumor with global incidence and death ranking fifth and fourth, respectively. GC patients nevertheless have a poor prognosis despite the effectiveness of more advanced chemotherapy and surgical treatment options. The second most frequently mutated gene in GC is PI3Kalpha, a confirmed oncogene that results in abnormal PI3K/AKT/mTOR signaling, causing enhanced translation, proliferation, and survival, and is mutated in 7-25% of GC patients. The protein PI3Kalpha was targeted in the present study by utilizing machine learning (ML), molecular docking, and simulation. A total of 9214 molecules from the DrugBank database were chosen for the first screening. A training set for 6770 compounds tested against PI3Kalpha was assessed to create a quantitative structure-activity relationship-based machine learning model using five different classification algorithms: random forest, random tree, J48 pruned tree, decision stump, and REPTree. Furthermore, consideration was given to the random forest classifier for screening based on its performance index (Kappa statistics, ROC, and MCC). Overall, 1539 of the 9214 drug bank compounds were predicted to be active. Thereafter, three pharmacological filters, Lipinski's rule, Ghose filter, and Veber rule, were applied to test the drug-like properties of the screened compounds. Twenty-six of 1593 compounds showed excellent drug-like properties and were further considered for molecular docking. Thereafter, two compounds were screened as hits because they possessed the molecular docked position with the lowest binding energy and an excellent bonding profile. The binding stability of the selected compounds was further assessed through molecular dynamics simulations for up to 100 ns. Furthermore, compound 1-(3-(2,4-dimethylthiazol-5-YL)-4-oxo-2,4-dihydroindeno[1,2-C]pyrazol-5-YL)-3-(4-methylpiperazin-1-YL) urea was selected as a potential hit in the final screening by analyzing a number of parameters, including the Rg, RMSD, RMSF, H bonding, and SASA profile. Therefore, we conclude that compound 1-(3-(2, 4-dimethylthiazol-5-YL)-4-oxo-2,4-dihydroindeno[1,2-C]pyrazol-5-YL)-3-(4-methylpiperazin-1-YL) urea has efficient inhibitory potential against PI3Kalpha protein and could be utilized for the development of effective drugs against GC.

High-throughput virtual screening followed by in vitro investigation to identify new lead inhibitors of Cyclin Dependent Kinase 4

In the family of serine/threonine kinases, Cyclin Dependent Kinase 4 (CDK4), is an important regulator in numerous signal transduction pathways. The cell cycle is dysregulated in human breast adenocarcinoma (MCF-7). A set of various categorical QSAR models were generated and validated in the current examination. A recursive partition model, with predictive ability shown by an accuracy of greater than 0.90, was used for virtual screening of 500,000 molecules. Following a consecutive series of molecular docking procedures, followed by pharmacokinetic analysis of 49759 molecules predicted to have pIC50 greater than 7.39, 25 molecules displayed properties that could be described as drug-like. We selected the lead molecules in the MCF-7 cell line based on its ability to promote cell cycle progression.

A facile and metal-free domino reaction of TsDAM and 2-alkenylarylaldehyde: An easy access to 8-hydroxy-2,8-dihydro indeno [2,1-c]pyrazoles

An efficient straightforward metal free domino approach was developed for the synthesis of various 8-hydroxy-2,8-dihydroindeno[2,1-c]pyrazoles via [3 + 2] cycloaddition of substituted alkenes and TsDAM (TosylDiAzoMethane). The salient features of this protocol include high efficiency, mild reaction conditions, greener solvent, metal-free reaction, scalability and broad substrate scope along with high regioselectivity and yields.

Recent Progress on Anticancer Agents Incorporating Pyrazole Scaffold

The search of new anticancer agents is considered as a dynamic field of medicinal chemistry. In recent years, the synthesis of compounds with anticancer potential has increased and a large number of structurally varied compounds displaying potent anticancer activities have been published. Pyrazole is an important biologically active scaffold that possessed nearly all types of biological activities. The aim of this review is to collate literature work reported by researchers to provide an overview on in vivo and in vitro anticancer activities of pyrazole based derivatives among the diverse biological activities displayed by them and also presents recent efforts made on this heterocyclic moiety regarding anticancer activities. This review has been driven from the increasing number of publications, on this issue, which have been reported in the literature since the ending of the 20th century (from 1995-to date).

Fusion of Structure and Ligand Based Methods for Identification of Novel CDK2 Inhibitors

Cyclin dependent kinases play a central role in cell cycle regulation which makes them a promising target with multifarious therapeutic potential. CDK2 regulates various events of the eukaryotic cell division cycle, and the pharmacological evidence indicates that overexpression of CDK2 causes abnormal cell-cycle regulation, which is directly associated with hyperproliferation of cancer cells. Therefore, CDK2 is regarded as a potential target molecule for anticancer medication. Thus, to decline CDK2 activity by potential lead compounds has proved to be an effective treatment for cancer. The availability of a large number of X-ray crystal structures and known inhibitors of CDK2 provides a gateway to perform efficient computational studies on this target. With the aim to identify new chemical entities from commercial libraries, with increased inhibitory potency for CDK2, ligand and structure based computational drug designing approaches were applied. A druglike library of 50,000 compounds from ChemDiv and ChemBridge databases was screened against CDK2, and 110 compounds were identified using the parallel application of these models. On in vitro evaluation of 40 compounds, seven compounds were found to have more than 50% inhibition at 10 μM. MD studies of the hits revealed the stability of these inhibitors and pivotal role of Glu81 and Leu83 for binding with CDK2. The overall study resulted in the identification of four new chemical entities possessing CDK2 inhibitory activity.

Discovery of nitroaryl urea derivatives with antiproliferative properties

A series of urea derivatives bearing nitroaryl moiety has been synthesized and assayed for their potential antiproliferative activities. Some of the tested compounds displayed activity in RK33 laryngeal cancer cells and TE671 rhabdomyosarcoma cells while being generally less toxic to healthy HSF human fibroblasts cells. One compound was demonstrated to be a moderate CDK2 inhibitor with IC50 = 14.3 µM. Its structure was solved by an X-ray crystallography and molecular modelling was performed to determine structure-activity relationship. Obtained compounds constitute novel structures and generally demonstrated greater cytotoxicity in comparison to cisplatin. This study offers new structural motifs with potential for further development.

Selective Amidation of 2,6-Dihalogenopurines: Application to the Synthesis of New 2,6,9-Trisubstituted Purines

We report herein the palladium(0)/Xantphos-catalyzed cross-coupling of various amides with 2,6-dihalogenopurines, with substituent-dependent regioselectivity. Furthermore, subjecting the same 2,6-dihalogenopurines to SNAr conditions with amide/NaH in DMF leads to inverted regioselectivity albeit in lower yield. These methodologies allow the two-step synthesis of new 2,6,9-trisubstituted purines from readily available 2,6-dihalogenopurines.

3D-QSAR CoMFA study on indenopyrazole derivatives as cyclin dependent kinase 4 (CDK4) and cyclin dependent kinase 2 (CDK2) inhibitors

Cyclin dependent kinases (CDKs) have appeared as an important drug targets over the years with diverse therapeutic potentials. With the objective of designing new chemical entities with enhanced inhibitory potencies against CDK 2 (CDK2) and CDK 4 (CDK4), the 3D-QSAR CoMFA study carried out on indenopyrazole derivatives as inhibitors of these kinases is presented here. The developed model showed a strong correlative and predictive capability having a cross validated correlation co-efficient of 0.747 for CDK4 and 0.755 for CDK2 inhibitions. The conventional and predictive correlation co-efficients were, respectively, found to be 0.913 and 0.760 for CDK4, 0.941 and 0.765 for CDK2. The models could be employed to design ligands with enhanced inhibitory potencies and/or to predict the potencies of analogues to guide synthesis.

Loop Flexibility and Solvent Dynamics as Determinants for the Selective Inhibition of Cyclin-Dependent Kinase 4: Comparative Molecular Dynamics Simulation Studies of CDK2 and CDK4

The design and discovery of selective cyclin-dependent kinase 4 (CDK4) inhibitors have been actively pursued in order to develop therapeutic cancer treatments. By means of a consecutive computational protocol involving homology modeling, docking experiments, and molecular dynamics simulations, we examine the characteristic structural and dynamic properties that distinguish CDK4 from CDK2 in its complexation with selective inhibitors. The results for all three CDK4-selective inhibitors under investigation show that the large-amplitude motion of a disordered loop of CDK4 is damped out in the presence of the inhibitors whereas their binding in the CDK2 active site has little effect on the loop flexibility. It is also found that the binding preference of CDK4- selective inhibitors for CDK4 over CDK2 stems from the reduced solvent accessibility in the active site of the former due to the formation of a stable hydrogen-bond triad by the Asp99, Arg101, and Thr102 side chains at the top of the active-site gorge. Besides the differences in loop flexibility and solvent accessibility, the dynamic stabilities of the hydrogen bonds between the inhibitors and the side chain of the lysine residue at the bottom of the active site also correlate well with the relative binding affinities of the inhibitors for the two CDKs. These results highlight the usefulness of this computational approach in evaluating the selectivity of a CDK inhibitor, and demonstrate the necessity of considering protein flexibility and solvent effects in designing new selective CDK4-selective inhibitors.