Evaluation and Comparison of 3D-QSAR CoMSIA Models for CDK1, CDK5, and GSK-3 Inhibition by Paullones

New tetrahydroisoquinoline-4-carbonitrile derivatives as potent agents against cyclin-dependent kinases, crystal structures, and computational studies

The synthesis of two new hexahydroisoquinoline-4-carbonitrile derivatives (3a and 3b) is reported along with spectroscopic data and their crystal structures. In compound 3a, the intramolecular O-H···O hydrogen bond constraints the acetyl and hydroxyl groups to be syn. In the crystal, inversion dimers are generated by C-H···O hydrogen bonds and are connected into layers parallel to (10-1) by additional C-H···O hydrogen bonds. The layers are stacked with Cl···S contacts 0.17 Å less than the sum of the respective van der Waals radii. The conformation of the compound 3b is partially determined by the intramolecular O-H···O hydrogen bond. A puckering analysis of the tetrahydroisoquinoline unit was performed. In the crystal, O-H···O and C-H···O hydrogen bonds together with C-H···π(ring) interactions form layers parallel to (01-1) which pack with normal van der Waals interactions. To understand the binding efficiency and stability of the title molecules, molecular docking, and 100 ns dynamic simulation analyses were performed with CDK5A1. To rationalize their structure-activity relationship(s), a DFT study at the B3LYP/6-311++G** theoretical level was also done. The 3D Hirshfled surfaces were also taken to investigate the crystal packings of both compounds. In addition, their ADMET properties were explored.Communicated by Ramaswamy H. Sarma.

Structure‐Based Approaches for the Prediction of Alzheimer's Disease Inhibitors: Comparative Interactions Analysis, Pharmacophore Modeling and Molecular Dynamics Simulations

Due to its significant role in neurodegeneration, Cyclin‐dependent kinase 5 (CDK5) has emerged as a potential target for addressing neuropathological disorders, including Alzheimer's disease (AD). The application of CDK5 inhibitors has demonstrated promise in the treatment of AD. This prompted us to model this interesting target using a computational workflow named Docking‐based Comparative Intermolecular Contacts Analysis (dbCICA). Approaches including 3D‐QSAR, genetic algorithm, and pharmacophore modeling were employed to discover new CDK inhibitors.

An Effective Synthesis of Previously Unknown 7-Aryl Substituted Paullones

A straightforward three-step procedure affording a wide range of novel 7-aryl substituted paullone derivatives was developed. This scaffold is structurally similar to 2-(1H-indol-3-yl)acetamides-promising antitumor agents-hence, could be useful for the development of a new class of anticancer drugs.

Latonduine-1-Amino-Hydantoin Hybrid, Triazole-Fused Latonduine Schiff Bases and Their Metal Complexes: Synthesis, X-ray and Electron Diffraction, Molecular Docking Studies and Antiproliferative Activity

A series of latonduine derivatives, namely 11-nitro-indolo[2,3-d]benzazepine-7-(1-amino-hydantoin) (B), triazole-fused indolo[2,3-d]benzazepine-based Schiff bases HL1 and HL2 and metal complexes [M(p-cymene)(HL1)Cl]Cl, where M = Ru (1), Os (2), and [Cu(HL2)Cl2] (3) were synthesized and characterized by spectroscopic techniques (UV–vis, 1H, 13C, 15N–1H HSQC NMR) and ESI mass spectrometry. The molecular structures of B and HL1 were confirmed by single-crystal X-ray diffraction, while that of 3 by electron diffraction of nanometer size crystalline sample. Molecular docking calculations of species B in the binding pocket of PIM-1 enzyme revealed that the 1-amino-hydantoin moiety is not involved in any hydrogen-bonding interactions, even though a good accommodation of the host molecule in the ATP binding pocket of the enzyme was found. The antiproliferative activity of organic compounds B, HL1 and HL2, as well as complexes 1–3 was investigated in lung adenocarcinoma A549, colon adenocarcinoma LS-174 and triple-negative breast adenocarcinoma MDA-MB-231 cells and normal human lung fibroblast cells MRC-5 by MTT assays; then, the results are discussed.

Development of inhibitors targeting glycogen synthase kinase-3β for human diseases: Strategies to improve selectivity

Glycogen synthase kinase-3β (GSK-3β) is a conserved serine/threonine kinase that participates in the transmission of multiple signaling pathways and plays an important role in the occurrence and development of human diseases, such as metabolic diseases, neurological diseases and cancer, making it to be a potential and promising drug target. To date, copious GSK-3β inhibitors have been synthesized, but only few have entered clinical trials. Most of them exerts poor selectivity, concomitant off-target effects and side effects. This review summarizes the structural characteristics, biological functions and relationship with diseases of GSK-3β, as well as the selectivity profile and therapeutic potential of different categories of GSK-3β inhibitors. Strategies for increasing selectivity and reducing adverse effects are proposed for the future design of GSK-3β inhibitors.

A Practical Strategy for Exploring the Pharmacological Mechanism of Luteolin Against COVID-19/Asthma Comorbidity: Findings of System Pharmacology and Bioinformatics Analysis

Asthma patients may increase their susceptibility to SARS-CoV-2 infection and the poor prognosis of coronavirus disease 2019 (COVID-19). However, anti-COVID-19/asthma comorbidity approaches are restricted on condition. Existing evidence indicates that luteolin has antiviral, anti-inflammatory, and immune regulation capabilities. We aimed to evaluate the possibility of luteolin evolving into an ideal drug and explore the underlying molecular mechanisms of luteolin against COVID-19/asthma comorbidity. We used system pharmacology and bioinformatics analysis to assess the physicochemical properties and biological activities of luteolin and further analyze the binding activities, targets, biological functions, and mechanisms of luteolin against COVID-19/asthma comorbidity. We found that luteolin may exert ideal physicochemical properties and bioactivity, and molecular docking analysis confirmed that luteolin performed effective binding activities in COVID-19/asthma comorbidity. Furthermore, a protein–protein interaction network of 538 common targets between drug and disease was constructed and 264 hub targets were obtained. Then, the top 6 hub targets of luteolin against COVID-19/asthma comorbidity were identified, namely, TP53, AKT1, ALB, IL-6, TNF, and VEGFA. Furthermore, the enrichment analysis suggested that luteolin may exert effects on virus defense, regulation of inflammation, cell growth and cell replication, and immune responses, reducing oxidative stress and regulating blood circulation through the Toll-like receptor; MAPK, TNF, AGE/RAGE, EGFR, ErbB, HIF-1, and PI3K–AKT signaling pathways; PD-L1 expression; and PD-1 checkpoint pathway in cancer. The possible “dangerous liaison” between COVID-19 and asthma is still a potential threat to world health. This research is the first to explore whether luteolin could evolve into a drug candidate for COVID-19/asthma comorbidity. This study indicated that luteolin with superior drug likeness and bioactivity has great potential to be used for treating COVID-19/asthma comorbidity, but the predicted results still need to be rigorously verified by experiments.

Highly Antiproliferative Latonduine and Indolo[2,3-c]quinoline Derivatives: Complex Formation with Copper(II) Markedly Changes the Kinase Inhibitory Profile

A series of latonduine and indoloquinoline derivatives HL¹–HL⁸ and their copper(II) complexes (1–8) were synthesized and comprehensively characterized. The structures of five compounds (HL⁶, [CuCl(L¹)(DMF)]·DMF, [CuCl(L²)(CH₃OH)], [CuCl(L³)]·0.5H₂O, and [CuCl₂(H₂L⁵)]Cl·2DMF) were elucidated by single crystal X-ray diffraction. The copper(II) complexes revealed low micro- to sub-micromolar IC₅₀ values with promising selectivity toward human colon adenocarcinoma multidrug-resistant Colo320 cancer cells as compared to the doxorubicin-sensitive Colo205 cell line. The lead compounds HL⁴ and 4 as well as HL⁸ and 8 induced apoptosis efficiently in Colo320 cells. In addition, the copper(II) complexes had higher affinity to DNA than their metal-free ligands. HL⁸ showed selective inhibition for the PIM-1 enzyme, while 8 revealed strong inhibition of five other enzymes, i.e., SGK-1, PKA, CaMK-1, GSK3β, and MSK1, from a panel of 50 kinases. Furthermore, molecular modeling of the ligands and complexes showed a good fit to the binding pockets of these targets.

When Good Kinases Go Rogue: GSK3, p38 MAPK and CDKs as Therapeutic Targets for Alzheimer's and Huntington's Disease

Alzheimer's disease (AD) is a mostly sporadic brain disorder characterized by cognitive decline resulting from selective neurodegeneration in the hippocampus and cerebral cortex whereas Huntington's disease (HD) is a monogenic inherited disorder characterized by motor abnormalities and psychiatric disturbances resulting from selective neurodegeneration in the striatum. Although there have been numerous clinical trials for these diseases, they have been unsuccessful. Research conducted over the past three decades by a large number of laboratories has demonstrated that abnormal actions of common kinases play a key role in the pathogenesis of both AD and HD as well as several other neurodegenerative diseases. Prominent among these kinases are glycogen synthase kinase (GSK3), p38 mitogen-activated protein kinase (MAPK) and some of the cyclin-dependent kinases (CDKs). After a brief summary of the molecular and cell biology of AD and HD this review covers what is known about the role of these three groups of kinases in the brain and in the pathogenesis of the two neurodegenerative disorders. The potential of targeting GSK3, p38 MAPK and CDKS as effective therapeutics is also discussed as is a brief discussion on the utilization of recently developed drugs that simultaneously target two or all three of these groups of kinases. Multi-kinase inhibitors either by themselves or in combination with strategies currently being used such as immunotherapy or secretase inhibitors for AD and knockdown for HD could represent a more effective therapeutic approach for these fatal neurodegenerative diseases.

Role of the base Cs2CO3 on the palladium-catalyzed intramolecular cyclization of two bromoindole derivatives to yield paullone-type products

Reactions for the palladium-catalyzed intramolecular cyclization of the o-bromoindole and the o-bromo-N-methyl-indole derivatives in the presence and absence of base (Cs₂CO₃) were explored through DFT calculations. For the base-free reactions, the palladium atom firstly interacts with the aromatic rings of the indole molecule to yield a stable adduct. Once this adduct has been formed, reaction proceeds readily to the oxidative addition intermediate that arises from the insertion of the metal atom into the C-Br bond of the organic fragment. Further steps leading to the paullone (or dimethyl paullone) product, mainly those involving the metalation and deprotonation of the inserted intermediate, are not energetically viable for these reactions. When the effect of the base on the metalation-deprotonation steps is modeled by replacing the bromide ion with CO₃^2- in the metal-inserted structure, a feasible pathway connecting the oxidative addition intermediate with the paullone-type product was located for each of the investigated reactions. The results emerging from this study suggest that palladium can insert into the C-Br bond of the indole derivatives to yield the oxidative addition intermediate (without participation of the base). However, the metalation and deprotonation steps that evolve to the paullone-type product take place via a concerted action involving both the metal and the base. Metalation and deprotonation steps that evolve to the paullone-type product take place via a concerted action involving both the metal and the base.

Mechanistic and biological characterisation of novel N5-substituted paullones targeting the biosynthesis of trypanothione in Leishmania

Trypanothione synthetase (TryS) produces N¹,N⁸-bis(glutathionyl)spermidine (or trypanothione) at the expense of ATP. Trypanothione is a metabolite unique and essential for survival and drug-resistance of trypanosomatid parasites. In this study, we report the mechanistic and biological characterisation of optimised N⁵-substituted paullone analogues with anti-TryS activity. Several of the new derivatives retained submicromolar IC₅₀ against leishmanial TryS. The binding mode to TryS of the most potent paullones has been revealed by means of kinetic, biophysical and molecular modelling approaches. A subset of analogues showed an improved potency (EC₅₀ 0.5–10 µM) and selectivity (20–35) against the clinically relevant stage of Leishmania braziliensis (mucocutaneous leishmaniasis) and L. infantum (visceral leishmaniasis). For a selected derivative, the mode of action involved intracellular depletion of trypanothione. Our findings shed light on the molecular interaction of TryS with rationally designed inhibitors and disclose a new set of compounds with on-target activity against different Leishmania species.

Stereocontrolled addition of Grignard reagents to oxa-bridged benzazepines: highly efficient synthesis of functionalized benzazepine scaffolds

An efficient and highly diastereoselective synthesis of 2-substituted benzo[b]azepin-5-ol via stereocontrolled addition of Grignard reagents to oxa-bridged benzazepines has been developed. The reaction proceeds efficiently starting from versatile skeletons with mild reaction conditions as well as simple operation. Furthermore, 2-substituted benzazepinones could been obtained by simple Dess–Martin oxidation in excellent yields.

An efficient and highly diastereoselective synthesis of 2-substituted benzo[b]azepin-5-ol via stereocontrolled addition of Grignard reagents to oxa-bridged benzazepines has been developed.

Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder and characterized by brain cell death, memory loss and is the most common form of dementia. Although AD has devastating effects, however, drugs which can treat the AD remain limited. The cyclin-dependent kinase 5 (CDK5) has been recognized as being involved in the pathological hyperphosphorylation of tau protein, which leads to the formation of neurofibrillary tangles (NFTs). We utilized the structure-based virtual screening (SBVS) approach to find the potential inhibitors against HsCDK5. The natural compound subset from the ZINC database (n = 167,741) was retrieved and screened by using SBVS method. From here, we have predicted 297 potent inhibitors. These 297 compounds were evaluated through their pharmacokinetic properties by ADMET (absorption, distribution, metabolism, elimination/excretion and toxicity) descriptors. Finally, 17 compounds were selected and used for re-docking. After the refinement by molecular docking and by using drug-likeness analysis, we have identified four potential inhibitors (ZINC85877721, ZINC96114862, ZINC96115616 and ZINC96116231). All these four ligands were employed for 100 ns MDS study. From the root mean square deviation (RMSD), root mean square fluctuation (RMSF), Rg, number of hydrogen bonds, solvent accessible surface area (SASA), principal component analysis (PCA) and binding free energy analysis we have found that out of four inhibitors ZINC85877721 and ZINC96116231 showed good binding free energy of -198.84 and -159.32 kJ.mol^-1, respectively, and also good in other structural analyses. Both compounds displayed excellent pharmacological and structural properties to be the drug candidates. Collectively, these findings recommend that two compounds have great potential to be a promising agent against AD to reduce the CDK5 induced hyperphosphorylation and could be considered as therapeutic agents for the AD.Communicated by Ramaswamy H. Sarma.

2D-QSAR and 3D-QSAR simulations for the reaction rate constants of organic compounds in ozone-hydrogen peroxide oxidation

Synergistic oxidation of ozone (O₃) and hydrogen peroxide (H₂O₂) is an effective water treatment for the elimination of organic pollutants. In this study, 23 organic compounds were conducted to study the reaction rate constants during O₃-H₂O₂ oxidation. Then, two- and three-dimensional quantitative structure-activity relationship (QSAR) models were established to investigate the factors influencing the reaction rate constants by using multiple linear regression method and comparative molecular similarity index analysis (CoMSIA) method, respectively. Both of the two models showed good performance on predicting the reaction rate constants, the associated statistical indices of 2D-QSAR and 3D-QSAR models were R² = 0.898 and 0.952, q² = 0.841 and 0.951, Q_ext² = 0.968 and 0.970, respectively. But varied in the influence factors, as for the 2D-QSAR model, three quantum chemical parameters, included dipole moment, the largest change of charge in each atom during the nucleophilic attack, the maximum positive partial charge on a hydrogen atom linked with a carbon atom affected the reaction rate. While in the 3D-QSAR model, the electrostatic field played the most important role in evaluating the reaction rate with the contribution of 35.8%, followed by hydrogen bond acceptor and hydrophobic fields with the contribution of 24.9% and 23.2%, respectively. These two models provided predictive tools to study the influencing factors for the degradation of organics and might potentially be applied for estimating the removal properties of unknown organics in O₃-H₂O₂ oxidation process.

Indole-fused azepines and analogues as anticancer lead molecules: Privileged findings and future directions

The search for new lead compounds of simple structure, displaying highest quality anti-tumor potency with new mechanisms of action and least adverse effects is the major intention of cancer drug discovery now a days. For the time being, indole-fused azepines emerged as a simple class of compounds prolifically designed with strong pharmacological significances in particular of cancer protecting ability. In the recent years from the efforts of our research group, indole-fused heteroazepines, a simple structural class achieved by fusion of indole with oxygen, sulphur and nitrogen containing heteroazepine rings, have known for its superior outcomes in cancer treatment. Surprisingly, the chemistry and biology of these unique families with an amazing role in cancer drug discovery has remained broadly unexplored. This short review is consequently an endeavor to highlight the preliminary ideas over this structural class and to draw the medical attention towards future development of indole-fused azepines and analogues for their promising function in cancer drug discovery.

A simple and efficient method for constructing azepino[4,5-b]indole derivatives via acid catalysis

A new and efficient synthetic methodology has been developed to prepare azepino[4,5-b]indole derivatives under Brønsted acid catalysis.

Binding mechanism of CDK5 with roscovitine derivatives based on molecular dynamics simulations and MM/PBSA methods

Roscovitine derivatives are potent inhibitors of cyclin-dependent kinase 5 (CDK5), but they exhibit different activities, which has not been understood clearly up to now. On the other hand, the task of drug design is difficult because of the fuzzy binding mechanism. In this context, the methods of molecular docking, molecular dynamics (MD) simulation, and binding free energy analysis are applied to investigate and reveal the detailed binding mechanism of four roscovitine derivatives with CDK5. The electrostatic and van der Waals interactions of the four inhibitors with CDK5 are analyzed and discussed. The calculated binding free energies in terms of MM-PBSA method are consistent with experimental ranking of inhibitor effectiveness for the four inhibitors. The hydrogen bonds of the inhibitors with Cys83 and Lys33 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the pivotal contacts with Ile10 and Leu133 have larger contributions to the binding free energy and play critical roles in distinguishing the variant bioactivity of four inhibitors. In terms of binding mechanism of the four inhibitors with CDK5 and energy contribution of fragments of each inhibitor, two new CDK5 inhibitors are designed and have stronger inhibitory potency.

Molecular docking and 3D-QSAR studies on the glucocorticoid receptor antagonistic activity of hydroxylated polychlorinated biphenyls

The glucocorticoid receptor (GR) antagonistic activities of hydroxylated polychlorinated biphenyls (HO-PCBs) were recently characterised. To further explore the interactions between HO-PCBs and the GR, and to elucidate structural characteristics that influence the GR antagonistic activity of HO-PCBs, molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed. Comparative molecular similarity indices analysis (CoMSIA) was performed using both ligand- and receptor-based alignment schemes. Results generated from the receptor-based model were found to be more satisfactory, with q(2) of 0.632 and r(2) of 0.931 compared with those from the ligand-based model. Some internal validation strategies (e.g. cross-validation analysis, bootstrapping analysis and Y-randomisation) and an external validation method were used respectively to further assess the stability and predictive ability of the derived model. Graphical interpretation of the model provided some insights into the structural features that affected the GR antagonistic activity of HO-PCBs. Molecular docking studies revealed that some key residues were critical for ligand-receptor interactions by forming hydrogen bonds (Glu540) and hydrophobic interactions with ligands (Ile539, Val543 and Trp577). Although CoMSIA sometimes depends on the alignment of the molecules, the information provided is beneficial for predicting the GR antagonistic activities of HO-PCB homologues and is helpful for understanding the binding mechanisms of HO-PCBs to GR.

Design for carbon–carbon bond forming reactions under ambient conditions

The carbon–carbon (C–C) bond forms the ‘backbone’ of nearly every organic molecule, and lies at the heart of the chemical sciences! Let us explore designing of carbon–carbon frameworks at ambient conditions.

10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acids are selective inhibitors of DYRK1A

The protein kinase DYRK1A has been suggested to act as one of the intracellular regulators contributing to neurological alterations found in individuals with Down syndrome. For an assessment of the role of DYRK1A, selective synthetic inhibitors are valuable pharmacological tools. However, the DYRK1A inhibitors described in the literature so far either are not sufficiently selective or have not been tested against closely related kinases from the DYRK and the CLK protein kinase families. The aim of this study was the identification of DYRK1A inhibitors exhibiting selectivity versus the structurally and functionally closely related DYRK and CLK isoforms. Structure modification of the screening hit 11H-indolo[3,2-c]quinoline-6-carboxylic acid revealed structure-activity relationships for kinase inhibition and enabled the design of 10-iodo-substituted derivatives as very potent DYRK1A inhibitors with considerable selectivity against CLKs. X-ray structure determination of three 11H-indolo[3,2-c]quinoline-6-carboxylic acids cocrystallized with DYRK1A confirmed the predicted binding mode within the ATP binding site.

9- and 11-Substituted 4-azapaullones are potent and selective inhibitors of African trypanosoma

Trypanosomes from the "brucei" complex are pathogenic parasites endemic in sub-Saharan Africa and causative agents of severe diseases in humans and livestock. In order to identify new antitrypanosomal chemotypes against African trypanosomes, 4-azapaullones carrying α,β-unsaturated carbonyl chains in 9- or 11-position were synthesized employing a procedure with a Heck reaction as key step. Among the so prepared compounds, 5a and 5e proved to be potent antiparasitic agents with antitrypanosomal activity in the submicromolar range.

3D-QSAR and molecular docking studies on 3-anilino-4-arylmaleimide derivatives as glycogen synthase kinase-3β inhibitors

Glycogen synthase kinase-3, a serine/threonine kinase, is a fascinating enzyme with diverse biological actions in intracellular signaling systems, making it an emerging target for diseases such as diabetes mellitus, cancer, chronic inflammation, bipolar disorders, and Alzheimer's disease. It is important to inhibit glycogen synthase kinase-3 selectively, and the net effect of the glycogen synthase kinase-3 inhibitors thus should be target specific, over other phylogenetically related kinases such as CDK-2. In the present work, we have carried out three-dimensional quantitative structure-activity relationship studies on novel class of 3-anilino-4-arylmaleimide derivatives to have improved cellular activity. Docked conformation of the most active molecule in the series, which shows desirable interactions in the receptor, was taken as template for the alignment of the molecules. Statistically significant CoMSIA (r2(cv)=0.614, r2(ncv)=0.948) and comparative molecular field analysis (r2(cv) =0.652, r2(ncv)=0.958) models were generated using 57 molecules in training set. The predictive ability of CoMSIA and comparative molecular field analysis models was determined using a test set of 17 molecules, which gave predictive correlation coefficients (r2(pred)) of 0.87 and 0.82, respectively, indicating good predictive power. Based on the information derived from CoMSIA and comparative molecular field analysis contour maps, we have identified some key features that explain the observed variance in the activity and have been used to design new anilinoarylmaleimide derivatives. The designed molecules showed better binding affinity in terms of estimated docking scores with respect to the already reported systems, hence suggesting that newly designed molecules can be more potent and selective toward glycogen synthase kinase-3β inhibition.

Structural investigations of anthranilimide derivatives by CoMFA and CoMSIA 3D-QSAR studies reveal novel insight into their structures toward glycogen phosphorylase inhibition

In the present work, three-dimensional quantitative structure-activity relationship (3-D QSAR) studies on a set of 70 anthranilimide compounds has been performed using docking-based as well as substructure-based molecular alignments. This resulted in the selection of more statistically relevant substructure-based alignment for further studies. Further, molecular models with good predictive power were derived using CoMFA (r² = 0.997; Q² = 0.578) and CoMSIA (r² = 0.976; Q² = 0.506), for predicting the biological activity of new compounds. The so-developed contour plots identified several key features of the compounds explaining wide activity ranges. Based on the information derived from the CoMFA contour maps, novel leads were proposed which showed better predicted activity with respect to the already reported systems. Thus, the present study not only offers a highly significant predictive QSAR model for anthranilimide derivatives as glycogen phosphorylase (GP) inhibitors which can eventually assist and complement the rational drug-design attempts, but also proposes a highly predictive pharmacophore model as a guide for further development of selective and more potent GP inhibitors as anti-diabetic agents.

A new protocol for predicting novel GSK-3β ATP competitive inhibitors

Glycogen synthase kinase 3β (GSK-3β) is a potential therapeutic target for cancer, type-2 diabetes, and Alzheimer's disease. This paper proposes a new lead identification protocol that predicts new GSK-3β ATP competitive inhibitors with topologically diverse scaffolds. First, three-dimensional quantitative structure-activity relationship (3D QSAR) models were built and validated. These models are based upon known GSK-3β inhibitors, benzofuran-3-yl-(indol-3-yl) maleimides, by means of comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Second, 28 826 maleimide derivatives were selected from the PubChem database. After filtration via Lipinski's rules, 10 429 maleimide derivatives were left. Third, the FlexX-dock program was employed to virtually screen the 10 429 compounds against GSK-3β. This resulted in 617 virtual hits. Fourth, the 3D QSAR models predicted that from the 617 virtual hits, 93 compounds would have GSK-3β inhibition values of less than 15 nM. Finally, from the 93 predicted active hits, 23 compounds were confirmed as GSK-3β inhibitors from literatures; their GSK-3β inhibition ranged from 1.3 to 480 nM. Therefore, the hits rate of our virtual screening protocol is greater than 25%. The protocol combines ligand- and structure-based approaches and therefore validates both approaches and is capable of identifying new hits with topologically diverse scaffolds.

Ruthenium- and Osmium-Arene Complexes of 2-Substituted Indolo[3,2-c]quinolines: Synthesis, Structure, Spectroscopic Properties, and Antiproliferative Activity

The synthesis of new modified indolo[3,2-c]quinoline ligands L¹−L⁸ with metal-binding sites is reported. By coordination to ruthenium− and osmium−arene moieties 16 complexes of the type [(η⁶-p-cymene)M(L)Cl]Cl (1a,b−8a,b), where M is Ru^II or Os^II and L is L¹−L⁸, have been prepared. All compounds were comprehensively characterized by elemental analysis, electrospray ionization mass spectrometry, IR, UV−vis, and NMR spectroscopy, thermogravimetric analysis, and single-crystal X-ray diffraction (2a, 4a, 4b, 5a, 7a, and 7b). The complexes were tested for antiproliferative activity in vitro in three human cancer cell lines, namely, CH1 (ovarian carcinoma), SW480 (colon adenocarcinoma), and A549 (non-small-cell lung cancer), yielding IC₅₀ values in the submicromolar or low micromolar range.

Concise synthesis and CDK/GSK inhibitory activity of the missing 9-azapaullones

A remarkably concise, chromatography-free route to the parent compound of the paullone family of cyclin-dependent kinase (CDK) inhibitors is reported. A similar strategy allowed the synthesis of the hitherto missing 9-azapaullone and its protonated, N-oxidised and N-alkylated derivatives. Screening studies identified an active and strongly selective inhibitor of CDK9/cyclin T.

Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors

Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3beta (GSK-3beta) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) are used for the 3D-QSAR of 51 substituted benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors. Two binding modes of the inhibitors to the binding site of GSK-3beta are investigated. The binding mode 1 yielded better 3D-QSAR correlations using both CoMFA and CoMSIA methodologies. The three-component CoMFA model from the steric and electrostatic fields for the experimentally determined pIC(50) values has the following statistics: R(2)(cv) = 0.386 nd SE(cv) = 0.854 for the cross-validation, and R(2) = 0.811 and SE = 0.474 for the fitted correlation. F (3,47) = 67.034, and probability of R(2) = 0 (3,47) = 0.000. The binding mode suggested by the results of this study is consistent with the preliminary results of X-ray crystal structures of inhibitor-bound GSK-3beta. The 3D-QSAR models were used for the estimation of the inhibitory potency of two additional compounds.

Synthesis and cytotoxic activity of new azepino[3',4':4,5]pyrrolo[2,1-a]isoquinolin-12-ones

A series of azepino[3',4':4,5]pyrrolo[2,1-a]isoquinolin-12-ones (3a-f), that were conformationally restricted analogs of lead compound 2, were designed as potential cytotoxic compounds and synthesized using a radical oxidative aromatic substitution reaction as the key step. Compounds 3a-f were tested on five tumor cell lines to determine the conformational requirements for biological activity of compound 2. The results show that conformational restrictions on compound 2, generating the derivatives 3a-f, do not appreciably reduce the cytotoxic activity of 2, although compound 3d (R=Br) showed good activity against U-251 cells. Preliminary structure-activity relationship studies with these compounds revealed the importance of halogens bonded to the isoquinoline moiety. Additionally, derivatives 3f (R=NO(2)) and 3b (R=F) were cytotoxic to PC-3 and K-562 cells. However, none of the azepino[3',4':4,5]pyrrolo[2,1-a]isoquinolinones inhibited the enzymatic activity of CDK1/cyclin B, CDK5/p25, or GSK-3.

Synthesis and evaluation of the antiproliferative activity of novel thiazoloquinazolinone kinases inhibitors

The microwave-assisted synthesis of a family of 2,8-substituted thiazoloquinazolinones is described. The preliminary evaluation of the antiproliferative activity and the capacity of these molecules to inhibit CDKs and GSK-3 are reported. A lead compound was identified, constituting a scaffold from which more potent inhibitors could be designed.

Receptor guided 3D-QSAR: a useful approach for designing of IGF-1R inhibitors

Research by other investigators has established that insulin-like growth factor‐1 receptor (IGF-1R) is a key oncological target, and that derivatives of 1, 3-disubstituted-imidazo[1,5-α] pyrazine are potent IGF-1R inhibitors. In this paper, we report on our three-dimensional quantitative structure activity relationship (3D-QSAR) studies for this series of compounds. We validated the 3D-QSAR models by the comparison of two major alignment schemes, namely, ligand-based (LB) and receptor-guided (RG) alignment schemes. The latter scheme yielded better 3D-QSAR models for both comparative molecular field analysis (CoMFA) (q² = 0.35, r² = 0.95) and comparative molecular similarity indices analysis (CoMSIA) (q² = 0.51, r² = 0.86). We submit that this might arise from the more accurate inhibitor alignment that results from using the structural information of the active site. We conclude that the receptor-guided 3D-QSAR may be helpful to design more potent IGF-1R inhibitors, as well as to understand their binding affinity with the receptor.

9-cyano-1-azapaullone (cazpaullone), a glycogen synthase kinase-3 (GSK-3) inhibitor activating pancreatic beta cell protection and replication

Recently, the serine/threonine kinase glycogen synthase kinase-3 (GSK-3) emerged as a regulator of pancreatic beta cell growth and survival. On the basis of the previous observation that GSK-3 inhibitors like 1-azakenpaullone promote beta cell protection and replication, paullone derivatives were synthesized including 1-aza-, 2-aza-, and 12-oxapaullone scaffolds. In enzymatic assays distinct 1-azapaullones were found to exhibit selective GSK-3 inhibitory activity. Within the series of 1-azapaullones, three derivatives stimulated INS-1E beta cell replication and protected INS-1E cells against glucolipotoxicity induced cell death. Cazpaullone (9-cyano-1-azapaullone), the most active compound in the protection assays, also stimulated the replication of primary beta cells in isolated rat islets. Furthermore, cazpaullone showed a pronounced transient stimulation of the mRNA expression of the beta cell transcription factor Pax4, an important regulator of beta cell development and growth. These features distinguish cazpaullone as a unique starting point for the development of beta cell regenerative agents which might be useful in the treatment of diabetes.