Assessing the Target Differentiation Potential of Imidazole-Based Protein Kinase Inhibitors

Controllable Site-Selective Construction of 4- and 5-Hydroxyalkyl-Substituted Imidazoles from Amidines, Ynals, and Water

The first example of controllable site-selective pathways to construct 4- and 5-hydroxyalkyl-substituted imidazoles through a three-component reaction of amidines, ynals, and water has been documented. Particularly, the high regioselectivity of the reaction was simply switched by changing the additives. In addition, further ¹⁸O-labeled experiments to probe a plausible mechanism and the gram-scale synthesis were studied.

QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping

An affinity fingerprint is the vector consisting of compound’s affinity or potency against the reference panel of protein targets. Here, we present the QAFFP fingerprint, 440 elements long in silico QSAR-based affinity fingerprint, components of which are predicted by Random Forest regression models trained on bioactivity data from the ChEMBL database. Both real-valued (rv-QAFFP) and binary (b-QAFFP) versions of the QAFFP fingerprint were implemented and their performance in similarity searching, biological activity classification and scaffold hopping was assessed and compared to that of the 1024 bits long Morgan2 fingerprint (the RDKit implementation of the ECFP4 fingerprint). In both similarity searching and biological activity classification, the QAFFP fingerprint yields retrieval rates, measured by AUC (~ 0.65 and ~ 0.70 for similarity searching depending on data sets, and ~ 0.85 for classification) and EF5 (~ 4.67 and ~ 5.82 for similarity searching depending on data sets, and ~ 2.10 for classification), comparable to that of the Morgan2 fingerprint (similarity searching AUC of ~ 0.57 and ~ 0.66, and EF5 of ~ 4.09 and ~ 6.41, depending on data sets, classification AUC of ~ 0.87, and EF5 of ~ 2.16). However, the QAFFP fingerprint outperforms the Morgan2 fingerprint in scaffold hopping as it is able to retrieve 1146 out of existing 1749 scaffolds, while the Morgan2 fingerprint reveals only 864 scaffolds.

Synthesis and biological activity of new bisbenzofuran-imidazolium salts

A series of novel bisbenzofuran-imidazolium salts were designed and prepared. The in vitro antitumor activity of these derivatives was evaluated against a panel of human tumor cell lines (A549, HL-60, MCF-7, SMMC-7721 and SW480). Results demonstrated that 2-methyl-benzimidazole ring and substitution of the imidazolyl-3-position with a 4-methoxyphenacyl or 2-naphthylacyl substituent were important for promoting cytotoxic activity. Notably, compound 23 was found to be the most potent compound with IC₅₀ values of 0.64-1.47 μM against five human tumor cell lines, and exhibited higher selectivity to MCF-7 and SW-480 cell lines with IC₅₀ values 15.3-fold and 9.1-fold lower than DDP.

A dynamic and electrostatic potential prediction of the prototropic tautomerism between imidazole 3-oxide and 1-hydroxyimidazole in external electric field

In order to obtain an optimum scheme for separating the proton-transfer tautomer, a dynamic investigation into the effect of the external electric field on the proton-transfer tautomeric conversion in imidazole 3-oxide and 1-hydroxyimidazole was carried out at the M06-2X/6-311++G** and CCSD(T)/6-311++G(2d,p) level, accompanied by the analysis of the surface electrostatic potentials. The results show that, for both the forward reaction "imidazole 3-oxide → N-hydroxyimidazole free radical → 1-hydroxyimidazole" and its reverse reaction processes, the fields parallel to the N→O or N-OH bond axis affect the barrier heights and rate constants considerably more than those parallel to the other orientations. As the field strength is increased along the orientation from the O to N atom, the chemical equilibrium moves toward the direction for the formation of 1-hydroxyimidazole, while the amount of imidazole 3-oxide is increased with the increased field strength along the opposite orientation. In the fields along the orientation consistent with the dipole moment, the electrostatic potentials and their variances "abnormally" increase for the transition states with the N→O bond in comparison with those in no field (they decrease generally), which enhances the nucleophilicity of the coordination O atom and the electrophilicity of the activated H atom. The analyses of the AIM (atoms in molecules) and NICS (nucleus-independent chemical shift) were used to explain the above anomaly. Graphical Abstract Electrostatic potentials and their variances "abnormally" increase in the external electric field, which greatly affects tautomeric conversion.

Discovery and synthesis of 2-amino-1-methyl-1H-imidazol-4(5H)-ones as GPCR ligands; an approach to develop breast cancer drugs via GPCR associated PAR1 and PI3Kinase inhibition mechanism

Efforts were taken to synthesis and characterize 2-amino-1-methyl-1H-imidazole-4(5H)-one derivatives (4a-u) through a four-step reaction. The achieved compounds in remarkable yield have characterized through standard analytical techniques such as FTIR, LC-MS, NMR, HRMS, and elemental analysis. Present study mainly aimed to evaluate 4a-u as G protein-coupled receptors (GPCR). In the mechanism, stimulation of phosphoinositide 3-kinase (PI3K) and Akt (protein kinase B) is a general reaction activated by a series of membrane-bound receptors such as GPCR. Protease-activated receptor-1 (PAR1) is a subfamily of related GPCR, which triggered by the division of fragment of its extracellular domain. Therefore, molecular docking is done to ensure the inhibition of PAR1 and PI3Kinase. PI3Kinase is a chief enzyme in the development of breast cancer via the Akt/mTOR pathway. Thus, in vitro PI3Kinase inhibition and anti-breast cancer studies has also done to screen medicinally important compounds among (4a-u). Based on the best binding affinity, in vitro relative % activity and IC₅₀ values, compounds 4a, 4g, 4i, 4n, and 4u were screened for further preclinical studies in animal model evaluations.

Prototropic Tautomerism and Some Features of the IR Spectra of 2-(3-Chromenyl)-1-hydroxyimidazoles

Prototropic tautomerism of 2-(3-chromenyl)-1-hydroxyimidazoles with various substituents in the chromenyl moiety (1-hydroxyimidazole – imidazole N-oxide) was studied by means of 1H NMR and IR spectroscopies. It was demonstrated that in d6-DMSO solution, the substituents in the chromenyl ring have no influence on the equilibrium shift: the prevalence of the N-oxide tautomeric form is caused by the possibility of stabilization of the planar structure with the help of the carbonyl group in position 5 of the imidazole ring. In contrast, in the solid state the general effect of the chromenyl substituent in position 2 of imidazole plays the leading role. The increase in general electron-withdrawing effect of the chromenyl moiety leads to the prevalence of the imidazole N-oxide tautomer.

Introduction of a methodology for visualization and graphical interpretation of Bayesian classification models

Supervised machine learning models are widely used in chemoinformatics, especially for the prediction of new active compounds or targets of known actives. Bayesian classification methods are among the most popular machine learning approaches for the prediction of activity from chemical structure. Much work has focused on predicting structure-activity relationships (SARs) on the basis of experimental training data. By contrast, only a few efforts have thus far been made to rationalize the performance of Bayesian or other supervised machine learning models and better understand why they might succeed or fail. In this study, we introduce an intuitive approach for the visualization and graphical interpretation of naïve Bayesian classification models. Parameters derived during supervised learning are visualized and interactively analyzed to gain insights into model performance and identify features that determine predictions. The methodology is introduced in detail and applied to assess Bayesian modeling efforts and predictions on compound data sets of varying structural complexity. Different classification models and features determining their performance are characterized in detail. A prototypic implementation of the approach is provided.

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets.

Synthesis, biological evaluation, and molecular docking studies of novel 2-styryl-5-nitroimidazole derivatives containing 1,4-benzodioxan moiety as FAK inhibitors with anticancer activity

A series of 2-styryl-5-nitroimidazole derivatives containing 1,4-benzodioxan moiety (3a-3r) has been designed, synthesized and their biological activities were also evaluated as potential antiproliferation and focal adhesion kinase (FAK) inhibitors. Among all the compounds, 3p showed the most potent activity in vitro which inhibited the growth of A549 with IC50 value of 3.11 μM and Hela with IC50 value of 2.54 μM respectively. Compound 3p also exhibited significant FAK inhibitory activity (IC50=0.45 μM). Docking simulation was performed for compound 3p into the FAK structure active site to determine the probable binding model.

Ni(ii)–salt catalyzed activation of primary amine-sp3Cα–H and cyclization with 1,2-diketone to tetrasubstituted imidazoles

NiCl₂·6H₂O and Ni(OAc)₂·4H₂O were found as efficient catalysts for C–H activation of benzyl and aliphatic amines for an unprecedented multi C–N bond forming cyclization with 1,2-diketones under refluxing toluene to furnish highly substituted and polycyclic imidazoles.

Comprehensive review in current developments of imidazole-based medicinal chemistry

Imidazole ring is an important five-membered aromatic heterocycle widely present in natural products and synthetic molecules. The unique structural feature of imidazole ring with desirable electron-rich characteristic is beneficial for imidazole derivatives to readily bind with a variety of enzymes and receptors in biological systems through diverse weak interactions, thereby exhibiting broad bioactivities. The related research and developments of imidazole-based medicinal chemistry have become a rapidly developing and increasingly active topic. Particularly, numerous imidazole-based compounds as clinical drugs have been extensively used in the clinic to treat various types of diseases with high therapeutic potency, which have shown the enormous development value. This work systematically gives a comprehensive review in current developments of imidazole-based compounds in the whole range of medicinal chemistry as anticancer, antifungal, antibacterial, antitubercular, anti-inflammatory, antineuropathic, antihypertensive, antihistaminic, antiparasitic, antiobesity, antiviral, and other medicinal agents, together with their potential applications in diagnostics and pathology. It is hoped that this review will be helpful for new thoughts in the quest for rational designs of more active and less toxic imidazole-based medicinal drugs, as well as more effective diagnostic agents and pathologic probes.