Synthesis, pharmacology and molecular modeling of N-substituted 2-phenyl-indoles and benzimidazoles as potent GABAA agonists

Integrated workflow for the identification of new GABAA R positive allosteric modulators based on the in silico screening with further in vitro validation. Case study using Enamine's stock chemical space

Numerous studies reported an association between GABAA R subunit genes and epilepsy, eating disorders, autism spectrum disorders, neurodevelopmental disorders, and bipolar disorders. This study was aimed to find some potential positive allosteric modulators and was performed by combining the in silico approach with further in vitro evaluation of its real activity. We started from the GABAA R-diazepam complexes and assembled a lipid embedded protein ensemble to refine it via molecular dynamics (MD) simulation. Then we focused on the interaction of α1β2γ2 with some Z-drugs (non-benzodiazepine compounds) using an Induced Fit Docking (IFD) into the relaxed binding site to generate a pharmacophore model. The pharmacophore model was validated with a reference set and applied to decrease the pre-filtered Enamine database before the main docking procedure. Finally, we succeeded in identifying a set of compounds, which met all features of the docking model. The aqueous solubility and stability of these compounds in mouse plasma were assessed. Then they were tested for the biological activity using the rat Purkinje neurons and CHO cells with heterologously expressed human α1β2γ2 GABAA receptors. Whole-cell patch clamp recordings were used to reveal the GABA induced currents. Our study represents a convenient and tunable model for the discovery of novel positive allosteric modulators of GABAA receptors. A High-throughput virtual screening of the largest available database of chemical compounds resulted in the selection of 23 compounds. Further electrophysiological tests allowed us to determine a set of 3 the most outstanding active compounds. Considering the structural features of leader compounds, the study can develop into the MedChem project soon.

Exploring cyclin-dependent kinase inhibitors: a comprehensive study in search of CDK-6 inhibitors using a pharmacophore modelling and dynamics approach

Cancer prevalence and resistance issues in cancer treatment are a significant public health concern globally. Among the existing strategies in cancer therapy, targeting cyclin-dependent kinases (CDKs), especially CDK-6 is found to be one of the most promising targets, as this enzyme plays a pivotal role in cell cycle stages and cell proliferation. Cell proliferation is the characteristic feature of cancer giving rise to solid tumours. Our research focuses on creating novel compounds, specifically, pyrazolopyrimidine fused azetidinones, using a groundbreaking molecular hybridization approach to target CDK-6. Through computational investigations, ligand-based pharmacophore modelling, pharmacokinetic studies (ADMET), molecular docking, and dynamics simulations, we identified 18 promising compounds. The pharmacophore model featured one aromatic hydrophobic centre (F1: Aro/Hyd) and two H-bond acceptors (F2 and F3: Acc). Molecular docking results showed favourable binding energies (-6.5 to -8.0 kcal mol-1) and effective hydrogen bonds and hydrophobic interactions. The designed compounds demonstrated good ADMET profiles. Specifically, B6 and B18 showed low energy conformation (-7.8 kcal and -7.6 kcal), providing insights into target inhibition compared to the standard drug Palbociclib. Extensive molecular dynamics simulations confirmed the stability of these derivatives. Throughout the 100 ns simulation, the ligand-protein complexes maintained structural stability, with acceptable RMSD values. These compounds hold promise as potential leads in cancer therapy.

2-(4-Fluorophenyl)-1H-benzo[d]imidazole as a Promising Template for the Development of Metabolically Robust, α1β2γ2GABA-A Receptor-Positive Allosteric Modulators

Modulation of α1β2γ2GABA-A receptor subpopulation expressed in the basal ganglia region is a conceptually novel mode of pharmacological strategy that offers prospects to tackle a variety of neurological dysfunction. Although clinical findings provided compelling evidence for the validity of this strategy, the current chemical space of molecules able to modulate the α1/γ2 interface of the GABA-A receptor is limited to imidazo[1,2-a]pyridine derivatives that undergo rapid biotransformation. In response to a deficiency in the chemical repertoire of GABA-A receptors, we identified a series of 2-(4-fluorophenyl)-1H-benzo[d]imidazoles as positive allosteric modulators (PAMs) with improved metabolic stability and reduced potential for hepatotoxicity, where lead molecules 9 and 23 displayed interesting features in a preliminary investigation. We further disclose that the identified scaffold shows a preference for interaction with the α1/γ2 interface of the GABA-A receptor, delivering several PAMs of the GABA-A receptor. The present work provides useful chemical templates to further explore the therapeutic potential of GABA-A receptor ligands and enriches the chemical space of molecules suitable for the interaction with the α1/γ2 interface.

Research progress on the structure and biological diversities of 2-phenylindole derivatives in recent 20 years

The privileged structure binds to multiple receptors with high affinity, which is helpful to the development of new bioactive compounds. Indole is classified as a privileged structure, which may be one of the most important structural categories in drug discovery. As a special subset of indole compounds, 2-phenylindole seems to be one of most promising forerunners of drug development. In this paper, 106 articles were referenced to review the structural changes, biological activities and structure-activity relationship of compounds in recent 20 years, and classified them according to their pharmacological activities, from several aspects, including anticancer, antibacterial, anti-inflammatory, analgesic, antiviral, anti-parasite, the biological activities target to central nervous system, et al. It also points out the importance of artificial intelligence (AI) technology in discovery of new 2-phenylindole compounds in a broader prospect. This review will provide some ideas for researchers to develop new indole drugs.

Hypervalent iodine(iii) promoted C–H/C–H amination/annulation tandem reactions: synthesis of benzimidazoles from simple anilines and aldehydes

A novel hypervalent iodine mediated cascade transformation of anilines and aldehydes to benzimidazoles was developed.

Pyrazolopyrimidines as anticancer agents: A review on structural and target-based approaches

Pyrazolopyrimidine scaffold is one of the privileged heterocycles in drug discovery. This scaffold produced numerous biological activities in which anticancer is important one. Previous studies showed its importance in interactions with various receptors such as growth factor receptor, TGFBR2 gene, CDK2/cyclin E and Abl kinase, adenosine receptor, calcium-dependent Protein Kinase, Pim-1 kinase, Potent Janus kinase 2, BTK kinase, P21-activated kinase 1, extracellular signal-regulated kinase 2, histone lysine demethylase and Human Kinesin-5. However, there is a need of numerous studies for the discovery of target based potential compounds. The structure activity relationship studies may help to explore the generation of potential compounds in short time period. Therefore, in the present review we tried to explore the structural aspects of Pyrazolopyrimidine with their structure activity relationship against various targets for the development of potential compounds. The current review is the compilation of significant advances made on Pyrazolopyrimidines reported between 2015 and 2020.

tert-Amino Effect-Promoted Rearrangement of Aryl Isothiocyanate: A Versatile Approach to Benzimidazothiazepines and Benzimidazothioethers

A general and practical approach to benzimidazothiazepine and benzimidazothioether derivatives via an intramolecular nucleophilic addition/ring expansion rearrangement of aryl isothiocyanates promoted by the tert-amino effect has been developed. This reaction is catalyzed by low-cost camphorsulfonic acid and tolerates a broad substrate scope with complete atom economy. Structurally intriguing benzimidazothiazepine and benzimidazothioether products could be easily obtained by a simple operation in good to excellent yield (up to 98%).

1,2-Disubstituted Benzimidazoles by the Iron Catalyzed Cross-Dehydrogenative Coupling of Isomeric o-Phenylenediamine Substrates

Benzimidazoles are common in nature, medicines, and materials. Numerous strategies for preparing 2-arylbenzimidazoles exist. In this work, 1,2-disubstituted benzimidazoles were prepared from various mono- and disubstituted ortho-phenylenediamines (OPD) by iron-catalyzed oxidative coupling. Specifically, O₂ and FeCl₃·6H₂O catalyzed the cross-dehydrogenative coupling and aromatization of diarylmethyl and dialkyl benzimidazole precursors. N,N'-Disubstituted-OPD substrates were significantly more reactive than their N,N-disubstituted isomers, which appears to be relative to their propensity for complexation and charge transfer with Fe³⁺. The reaction also converted N-monosubstituted OPD substrates to 2-substituted benzimidazoles; however, electron-poor substrates produce 1,2-disubstituted benzimidazoles by intermolecular imino-transfer. Kinetic, reagent, and spectroscopic (UV-vis and EPR) studies suggest a mechanism involving metal-substrate complexation, charge transfer, and aerobic turnover, involving high-valent Fe(IV) intermediates. Overall, comparative strategies for the relatively sustainable and efficient synthesis of 1,2-disubstituted benzimidazoles are demonstrated.

Molecular docking, 3D-QSAR, molecular dynamics, synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors

A therapeutic rationale is proposed by selectively targeting tyrosine kinase 2 (TYK 2) to obtain potent TYK 2 inhibitors by molecular modeling studies. In the present study, we have taken tyrosine kinase (TYK 2) inhibitors and carried out molecular docking, 3 D quantitative structure-activity relationship (3D-QSAR) analysis and molecular dynamics (MD). Based on the 3D-QSAR results thirteen new compounds (R-1 to R-13) were designed and synthesized in good yields. The synthesized molecules were evaluated for their in vitro anticancer activity against LnCap and A549 cell lines. The molecules R-1, R-3, R-5, R-7, and R-10 exhibited considerable anti cancer activity.

Cobalt-catalyzed C2α-acyloxylation of 2-substituted indoles with tert-butyl peresters

An efficient cobalt-catalyzed C2α selective C(sp3)-H acyloxylation of 2-substituted indoles with tert-butyl peresters to synthesize diverse 2α-acyloxylated indole derivatives is described. This newly developed method exhibits mild conditions, low-cost catalyst, and high functional group compatibility. In addition, the effectiveness of this chemistry is illuminated by a late-stage modification of methylated indomethacin.

Antimicrobial potential of 1H-benzo[d]imidazole scaffold: a review

Background

Benzimidazole is a heterocyclic moiety whose derivatives are present in many of the bioactive compounds and posses diverse biological and clinical applications. Benzimidazole agents are the vital pharmacophore and privileged sub-structures in chemistry of medicine. They have received much interest in drug discovery because benzimidazoles exhibited enormous significance. So attempts have been made to create repository of molecules and evaluate them for prospective inherent activity. They are extremely effective both with respect to their inhibitory activity and favorable selectivity ratio.

Conclusion

Benzimidazole is most promising category of bioactive heterocyclic compound that exhibit a wide variety of biological activities in medicinal field. The present review only focus on antimicrobial activity of reported benzimidazole derivatives may serve as valuable source of information for researchers who wish to synthesize new molecules of benzimidazole nucleus which have immense potential to be investigated for newer therapeutic possibilities.

Bimetallic Cu–Mn B spinel oxide catalyzed oxidative synthesis of 1,2-disubstituted benzimidazoles from benzyl bromides

Cu–Mn B (a heterogeneous catalyst) catalyzed synthesis of 1-benzyl-2-phenyl-1H-benzo[d]imidazoles is reported.

Synthesis, Spectroscopic Characterization and Antimicrobial Potential of Certain New Isatin-Indole Molecular Hybrids

Molecular hybridization has a wide application in medicinal chemistry to obtain new biologically active compounds. New isatin-indole molecular hybrids 5a-n have been synthesized and characterized by various spectroscopic tools. The in vitro antimicrobial potential of the prepared compounds 5a-n was assessed using diameter of the inhibition zone (DIZ) and minimum inhibitory concentration (MIC) assays against a panel of Gram-negative bacteria, Gram-positive bacteria and fungi. Most of the synthesized compounds 5a-n showed weak activities against Gram-negative bacteria while compounds 5b and 5c exhibited good activities against Gram-positive bacteria. On the other hand, compound 5j emerged as the most active compound towards Candida albicans (C. albicans), with an MIC value of 3.9 µg/mL, and compound 5g as the most active congener towards Asperagillus niger (A. niger), with an MIC value of 15.6 µg/mL. Moreover, compound 5h manifested the best anti-P. notatum effect, with an MIC value of 7.8 µg/mL, making it equipotent with compound 5g.

Gold(i)-catalyzed synthesis of 2-substituted indoles from 2-alkynylnitroarenes with diboron as reductant

An efficient method for the synthesis of 2-substituted indoles via a diboron/base promoted tandem reductive cyclization of o-alkynylnitroarene under Au catalysis conditions has been disclosed.

Synthesis of 1,2-disubstituted benzimidazoles using an aza-Wittig-equivalent process

Based on an aza-Wittig-equivalent process, a novel synthetic approach for 1,2-disubstituted benzimidazoles has been successfully designed, which provides mild reaction conditions and excellent yields.

The therapeutic journey of benzimidazoles: a review

Presence of benzimidazole nucleus in numerous categories of therapeutic agents such as antimicrobials, antivirals, antiparasites, anticancer, anti-inflammatory, antioxidants, proton pump inhibitors, antihypertensives, anticoagulants, immunomodulators, hormone modulators, CNS stimulants as well as depressants, lipid level modulators, antidiabetics, etc. has made it an indispensable anchor for development of new therapeutic agents. Varied substitutents around the benzimidazole nucleus have provided a wide spectrum of biological activities. Importance of this nucleus in some activities like, Angiotensin I (AT(1)) receptor antagonism and proton-pump inhibition is reviewed separately in literature. Even some very short reviews on biological importance of this nucleus are also known in literature. However, owing to fast development of new drugs possessing benzimidazole nucleus many research reports are generated in short span of time. So, there is a need to couple the latest information with the earlier information to understand the current status of benzimidazole nucleus in medicinal chemistry research. In the present review, various derivatives of benzimidazole with different pharmacological activities are described on the basis of substitution pattern around the nucleus with an aim to help medicinal chemists for developing an SAR on benzimidazole derived compounds for each activity. This discussion will further help in the development of novel benzimidazole compounds.

A Clean Method for the Synthesis of 1,2-Disubstituted Benzimidazoles through a Redox Reaction of o-Phenylenediamine and Aldehydes

The reactions of o-phenylenediamine with aromatic aldehydes gave 1,2-disubstituted benzimidazoles in good to excellent yields under mild reaction conditions by using water as the reaction medium in the presence of 20 mol% FeCl3.

Synthesis, characterization, and biological evaluation of benzimidazole derivatives as potential anxiolytics

The synthesized benzimidazoles compounds were prepared from the condensation reaction between o-Phenylenediamine and various carbonyl compounds, in the presence of ammonium chloride as a catalyst. Ammonium chloride is a commercial and environmentally benign catalyst. The yield of all benzimidazole derivatives was found to be in the range of 75 - 94%. The purity of the compounds was ascertained by melting point and TLC. The synthesized compounds were characterized by using IR,(1)H NMR, and MASS spectral data together with elemental analysis. The synthesized benzimidazole compounds were screened for acute and chronic anti-anxiety activity in Wistar rats by using an elevated plus maze model with standard Diazepam. The synthesized compounds Z(B), Z(E), Z(F), Z(G), and Z(H) showed potent anti-anxiety activity when compared to the standard Diazepam. The compound Z(H) exhibited a higher anti-anxiety activity when compared to other prepared benzimidazoles. The results were subjected to statistical analysis by using one-way ANOVA followed by the Tukey-Kramer test, to calculate the significance.

A facile, mild and efficient one-pot synthesis of 2-substituted indole derivatives catalyzed by Pd(PPh3)2Cl2

2-Phenylindoles were prepared by heteroannulation of 2-haloaniline derivatives and phenylacetylene under mild conditions in a one-pot reaction catalyzed by Pd(PPh3)2Cl2.