Imidazo[1,2-a]pyrimidines as functionally selective and orally bioavailable GABA(A)alpha2/alpha3 binding site agonists for the treatment of anxiety disorders

Design and synthesis of imidazo[1,2-a]pyridine-chalcone conjugates as antikinetoplastid agents

A library of imidazo[1,2-a]pyridine-appended chalcones were synthesized and characterized using 1 H NMR, 13 C NMR and HRMS. The synthesized analogues were screened for their antikinetoplastid activity against Trypanosoma cruzi, Trypanosoma brucei brucei, Trypanosoma brucei rhodesiense and Leishmania infantum. The analogues were also tested for their cytotoxicity activity against human lung fibroblasts and primary mouse macrophages. Among all screened derivatives, 7f was found to be the most active against T. cruzi and T. b. brucei exhibiting IC50 values of 8.5 and 1.35 μM, respectively. Against T. b. rhodesiense, 7e was found to be the most active with an IC50 value of 1.13 μM. All synthesized active analogues were found to be non-cytotoxic against MRC-5 and PMM with selectivity indices of up to more than 50.

Metal-free C-3 selective C(sp2)-C(sp3) heteroarylation of anilines with imidazo[1,2-a]pyridine derivatives via cross-dehydrogenative coupling

A general and straightforward method for the regioselective construction of C-3 heteroaryl-containing imidazo[1,2-a]pyridines via cross-dehydrogenative coupling under transition-metal-free conditions has been reported, utilizing N,N-dimethylaniline as the methylenation source and furnishing the C(sp²)-C(sp³) functionalized products in good to excellent yields. Mechanism studies indicate that a radical pathway is responsible for this transformation.

The pyridazine heterocycle in molecular recognition and drug discovery

The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization.

Graphical Abstract

A novel pan-selective bromodomain inhibitor for epigenetic drug design

For a long time, the development of bromodomain (BD) inhibitors (BDi) was almost exclusively related to the BET family. More recently, BDi for BDs outside the BET family have also been developed. Here we present a novel pan-BDi with micromolar affinities to various BDs, and nanomolar affinities to representatives of BD families I, II (Bromodomain and Extra-Terminal Domain (BET) family), III, and IV. The inhibitor shows a broad activity profile with nanomolar growth inhibition (GI50) values on various cancer cell lines. Subsequently, we were able to control the selectivity of the inhibitor by simple modifications and turned it into a highly selective BRD9 inhibitor.

A Convenient Cascade Strategy Towards the Synthesis of Novel Substituted Morpholinopyrimidines and Pyrimidooxazapines

Abstract:

A simple and novel protocol for the facile synthesis of bicyclic hybrid molecular framework of morpholinopyrimidines having six-membered pyrimidine ring fused with the morpholine unit is established. The method has been successfully employed to synthesize both regioisomers of the morpholinopyrimidine derivatives in good to high yields. The strategy is further extended successfully to synthesize bicyclic pyrimidooxazapine derivatives bearing the six-membered aromatic pyrimidine unit fused with seven-membered aliphatic oxazapine fragment.

Design, synthesis and anticancer activity of sulfenylated imidazo-fused heterocycles

We report herein, the design, synthesis and study of anticancer properties of sulfenylated 2-phenylimidazo[1,2-a]pyridines and their analogues. A set of twenty sulfenylated imidazo[1, 2-a]pyridine derivatives were synthesized. Whereby elusive amendments to the imidazo[1,2-a]pyridine motif confer dramatic changes in functional affinity of a novel action to modulate anticancer activity in seven different human cancer cell lines i.e.: MDA MB 231 (breast), HepG2 (liver), Hela (cervical), A549 (lung), U87MG (glioblastoma), SKMEL-28 (skin melanoma) and DU-145 (prostate) by employing MTT assay. Among the series, compounds 4e (naphthalene), 4f (styrene) and 4h (thiomethyl) showed potent activity towards human liver cancer cells HepG2. Cell cycle analysis results revealed that these compounds arrested the cell cycle at G2/M phase and induced apoptosis in human liver cancer cells HepG2. It was further confirmed by Hoechst staining, Measurement of mitochondrial membrane potential (ΔΨm) and Annexin V-FITC assay.

Hydromagnesite sheets impregnated with cobalt-ferrite magnetic nanoparticles as heterogeneous catalytic system for the synthesis of imidazo[1,2-a]pyridine scaffolds

This paper manifests an A³-coupling strategy assisted by novel hydromagnesite sheets impregnated with cobalt ferrite (CoFe₂O₄-HMS) magnetic nanoparticles (MNPs) as an environmentally benign nanocomposite to synthesize imidazo[1,2-a]pyridine scaffolds under ultrasonication. The synthesis of these biologically active derivatives was achieved through A³-coupling employing 2-aminopyridines derivatives, pertinent aryl aldehydes, and phenylacetylene in the presence of polyethylene glycol 400 (PEG 400) as a green solvent under aerobic conditions. Based on its high product yield (up to 94%) in a short reaction time, with a modest catalyst loading, excellent catalyst, and solvent recyclability without substantial loss of operation (up to five synthetic cycles), as demonstrated by the high ecological compatibility and sustainability factors, this strategy follows the principles of green chemistry. The synthesized nanocomposite was characterized via several spectroanalytical techniques, including PXRD, FE-SEM, HR-TEM, EDAX, ICP-AES, FT-IR, Raman spectroscopy, CO₂-TPD, TGA-DTA-DTG analyses, magnetic studies, and nitrogen porosimetry. Furthermore, the structures of synthesized compounds were confirmed based on FT-IR, ¹H NMR, ¹³C NMR, mass spectroscopy, and elemental analysis data.

Sustainable synthesis of imidazo[1,2-a]pyridine scaffolds assisted by hydromagnesite sheets impregnated with cobalt–ferrite (CoFe₂O₄-HMS) magnetic nanoparticles (MNPs).

Novel pyrimidine-benzimidazole hybrids with antibacterial and antifungal properties and potential inhibition of SARS-CoV-2 main protease and spike glycoprotein

Objective

The study aimed to synthesize and characterize pyrimidine-linked benzimidazole hybrids, define their antimicrobial and antifungal activities in vitro, and determine their ability to inhibit the main protease and spike glycoprotein of SARS-CoV-2.

Methods

The ability of the synthesized compounds to inhibit the main protease and spike glycoprotein inhibitory of SARS-CoV-2 was investigated by assessing their mode of binding to the allosteric site of the enzyme using molecular docking. The structures of pyrimidine-linked benzimidazole derivatives synthesized with microwave assistance were confirmed by spectral analysis. Antibacterial and antifungal activities were determined by broth dilution.

Results

Gram-negative bateria (Escherichia coli and Pseudomonas aeruginosa) were more sensitive than gram-positive bateria (Staphylococcus aureus and Streptococcus pyogenes) to the derivatives. Candida albicans was sensitive to the derivatives at a minimal inhibitory concentration (MIC) of 250 μg/mL. The novel derivatives had better binding affinity (kcal/mol) than nelfinavir, lopinavir, ivermectin, remdesivir, and favipiravir, which are under investigation as treatment for SARS-CoV-2 infection. Compounds 2c, 2e, and 2g formed four hydrogen bonds with the active cavity of the main protease. Many derivatives had good binding affinity for the RBD of the of SARS-CoV-2 spike glycoprotein with the formation of up to four hydrogen bonds.

Conclusion

We synthesized novel pyrimidine-linked benzi-midazole derivatives that were potent antimicrobial agents with ability to inhibit the SARS-CoV-2 spike glycoprotein. Understanding the pharmacophore features of the main protease and spike glycoprotein offers much scope for the development of more potent agents. We plan to optimize the properties of the derivatives using models in vivo and in vitro so that they will serve as more effective therapeutic options against bacterial and SARS-CoV-2 infections.

Ferrocene-Functionalized Dithiocarbamate Zinc(II) Complexes as Efficient Bifunctional Catalysts for the One-Pot Synthesis of Chromene and Imidazopyrimidine Derivatives via Knoevenagel Condensation Reaction

Four new mononuclear/coordination polymeric (CP) zinc(II) complexes (1-4) of ferrocenyl/pyridyl-functionalized dithiocarbamate ligands, N-ferrocenylmethyl-N-butyl dithiocarbamate (L1), N-ferrocenylmethyl-N-ethylmorpholine dithiocarbamate (L2), N-ferrocenylmethyl-N-2-(diethylamino)ethylamine dithiocarbamate (L3), and N-4-methoxybenzyl-N-3-methylpyridyl dithiocarbamate (L4), have been synthesized and characterized by elemental analyses, IR, UV-vis, and ¹H and ¹³C{¹H} NMR spectroscopic techniques. The solid-state structures of complexes 1, 3, and 4 have been determined by single-crystal X-ray crystallography as well as powder X-ray diffraction. Single-crystal X-ray crystallography revealed a monomeric structure for complex 1 but 1D polymeric structures for complexes 3 and 4. In all complexes, dithiocarbamate ligands are bonded to the Zn(II) metal ion in a S^S chelating mode, and in the CPs, N atoms on the 2-(diethylamino)ethylamine and 3-pyridyl functionalities in the ligands on the neighboring molecules are also bonded to metal centers, leading to the formation of either a discrete tetrahedral molecule in 1 or 1D CP structures in 3 and 4. The Zn(II) metal centers in the polymeric structures exhibited either square-pyramidal or octahedral geometries. The supramolecular structures in these complexes are sustained via C-H···π (ZnCS₂, chelate; 3 and 4), C-H···π, and H···H interactions. The catalytic performances of complexes have also been assessed in the Knoevenagel condensation and one-pot multicomponent reactions. Catalysis results showed that the CP 3 acts as a heterogeneous bifunctional catalyst with excellent transformation efficiency at low catalyst loading.

Synthesis of indole-tethered [1,3,4]thiadiazolo and [1,3,4]oxadiazolo[3,2-a]pyrimidin-5-one hybrids as anti-pancreatic cancer agents

New indole-tethered [1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one (8a-j) and [1,3,4]oxadiazolo[3,2-a]pyrimidin-5-one hybrids (9a-e) were synthesized using [4+2] cycloaddition reactions of functionalized 1,3-diazabuta-1,3-dienes with indole-ketenes. All molecular hybrids were structurally characterized by spectroscopic techniques (IR, NMR, and HRMS) and screened for their anti-pancreatic cancer activity in vitro. The [1,3,4]oxadiazolo[3,2-a]pyrimidin-5-one hybrids (9a-e) showed stronger anti-pancreatic cancer activity than the [1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one hybrids (8a-j) against the PANC-1 cell line. Compound 9d bearing an ortho-chlorophenyl moiety emerged as the most potent anti-pancreatic cancer agent with an IC₅₀ value of 7.7 ± 0.4 µM, much superior to the standard drug Gemcitabine (IC₅₀ > 500 µM). The discovery of these [1,3,4]thiadiazolo and [1,3,4]oxadiazolo[3,2-a]pyrimidin-5-one hybrids elicits their potentials as pursuable candidates for pancreatic cancer chemotherapy.

Novel magnetic propylsulfonic acid-anchored isocyanurate-based periodic mesoporous organosilica (Iron oxide@PMO-ICS-PrSO3H) as a highly efficient and reusable nanoreactor for the sustainable synthesis of imidazopyrimidine derivatives

In this study, preparation and characterization of a new magnetic propylsulfonic acid-anchored isocyanurate bridging periodic mesoporous organosilica (Iron oxide@PMO-ICS-PrSO3H) is described. The iron oxide@PMO-ICS-PrSO3H nanomaterials were characterized by Fourier transform infrared spectroscopy, energy-dispersive X-ray spectroscopy and field emission scanning electron microscopy as well as thermogravimetric analysis, N2 adsorption-desorption isotherms and vibrating sample magnetometer techniques. Indeed, the new obtained materials are the first example of the magnetic thermally stable isocyanurate-based mesoporous organosilica solid acid. Furthermore, the catalytic activity of the Iron oxide@PMO-ICS-PrSO3H nanomaterials, as a novel and highly efficient recoverable nanoreactor, was investigated for the sustainable heteroannulation synthesis of imidazopyrimidine derivatives through the Traube-Schwarz multicomponent reaction of 2-aminobenzoimidazole, C‒H acids and diverse aromatic aldehydes. The advantages of this green protocol are low catalyst loading, high to quantitative yields, short reaction times and the catalyst recyclability for at least four consecutive runs.

Regioselective synthesis of ortho-iodobiphenylboronic acid derivatives: a superior catalyst for carboxylic acid activation

Efficient and versatile synthesis of ortho-iodobiphenylboronic acids with remarkable catalytic and microbial activities.

Visible light promoted C–H functionalization of imidazoheterocycles

The present review summarizes the visible light mediated direct C–H functionalizations of pharmacologically active imidazo[1,2-a]pyridines and other related heterocycles.

Development of 1,3-thiazole analogues of imidazopyridines as potent positive allosteric modulators of GABAA receptors

Structure-activity relationship studies were conducted in the search for 1,3-thiazole isosteric analogs of imidazopyridine drugs (Zolpidem, Alpidem). Three series of novel γ-aminobutyric acid receptor (GABA_AR) ligands belonging to imidazo[2,1-b]thiazoles, imidazo[2,1-b][1,3,4]thiadiazoles, and benzo[d]imidazo[2,1-b]thiazoles were synthesized and characterized as active agents against GABA_AR benzodiazepine-binding site. In each of these series, potent compounds were discovered using a radioligand competition binding assay. The functional properties of highest-affinity compounds 28 and 37 as GABA_AR positive allosteric modulators (PAMs) were determined by electrophysiological measurements. In vivo studies on zebrafish demonstrated their potential for the further development of anxiolytics. Using the OECD "Fish, Acute Toxicity Test" active compounds were found safe and non-toxic. Structural bases for activity of benzo[d]imidazo[2,1-b]thiazoles were proposed using molecular docking studies. The isosteric replacement of the pyridine nuclei by 1,3-thiazole, 1,3,4-thiadiazole, or 1,3-benzothiazole in the ring-fused imidazole class of GABA_AR PAMs was shown to be promising for the development of novel hypnotics, anxiolytics, anticonvulsants, and sedatives drug-candidates.

Efficient synthesis and preliminary biological evaluations of trifluoromethylated imidazo[1,2-a]pyrimidines and benzimidazo[1,2-a]pyrimidines

Fluoromethylated imidazo[1,2-a]pyrimidines and benzimidazo[1,2-a]pyrimidines were synthesized through Michael addition/intramolecular cyclization reaction by condensation of 2-amino imidazole derivatives with ethyl 4,4,4-trifluorobut-2-ynate and using C–O bond activation.

Metal-free C–H arylation of imidazoheterocycles with aryl hydrazines

Metal-free C–H arylation of imidazo[1,2-a]pyridines at C-3 position with arylhydrazines in presence of DBU has been developed at room temperature under ambient air.

Sonochemical rate enhanced by a new nanomagnetic embedded core/shell nanoparticles and catalytic performance in the multicomponent synthesis of pyridoimidazoisoquinolines

A sonochemical approach for the one-pot three-component synthesis of pyridoimidazoisoquinolines via by using phthalaldehyde, trimethylsilylcyanide and aminopyridines the presence of a catalytic amount of a new nanomagnetic catalyst Fe₃O₄@SiO₂-CO-C₆H₄-NH₂ is described. The characterization of the nanocatalyst and the product was done by various methods, such as FT-IR, SEM, EDX, TGA/DTA, NMR, MS and CHN analyses. This is the first design, preparation, characterization and application of the present core/shell nanomaterial and also the first ultrasound irradiated synthesis of the biologically and pharmaceutically important fused polycyclic compounds in ethanol as a green solvent. This novel protocol offers several advantages such as high yields, short reaction times, environmentally-friendly reaction media, easily isolation of the products, simple preparation and recoverability of the nanocatalyst by an external magnet and reusing several times without significant decrease in catalytic activity.

Visible-light-mediated C3-azolylation of imidazo[1,2-a]pyridines with 2-bromoazoles

3-Heterocycle-substituted imidazo[1,2-a]pyridines were produced by a visible-light-mediated coupling reaction of imidazo[1,2-a]pyridines with 2-bromoazoles.

A facile I2-catalyzed synthesis of imidazo[1,2-a]pyridines via sp3 C–H functionalization of azaarenes and evaluation of anticancer activity

A three component synthetic protocol has been developed for the synthesis of medicinally important imidazo[1,2-a]pyridines via the iodine-catalyzed oxidative amination of benzylic C–H bonds of azaarenes. The synthesized compounds were evaluated for their anti-cancer activity.

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Background

Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields. For instance, the chemical classification of a compound could help predict its metabolic fate in humans, its druggability or potential hazards associated with it, among others. However, the sheer number (tens of millions of compounds) and complexity of chemical structures is such that any manual classification effort would prove to be near impossible.

Results

We have developed a comprehensive, flexible, and computable, purely structure-based chemical taxonomy (ChemOnt), along with a computer program (ClassyFire) that uses only chemical structures and structural features to automatically assign all known chemical compounds to a taxonomy consisting of >4800 different categories. This new chemical taxonomy consists of up to 11 different levels (Kingdom, SuperClass, Class, SubClass, etc.) with each of the categories defined by unambiguous, computable structural rules. Furthermore each category is named using a consensus-based nomenclature and described (in English) based on the characteristic common structural properties of the compounds it contains. The ClassyFire webserver is freely accessible at http://classyfire.wishartlab.com/. Moreover, a Ruby API version is available at https://bitbucket.org/wishartlab/classyfire_api, which provides programmatic access to the ClassyFire server and database. ClassyFire has been used to annotate over 77 million compounds and has already been integrated into other software packages to automatically generate textual descriptions for, and/or infer biological properties of over 100,000 compounds. Additional examples and applications are provided in this paper.

Conclusion

ClassyFire, in combination with ChemOnt (ClassyFire’s comprehensive chemical taxonomy), now allows chemists and cheminformaticians to perform large-scale, rapid and automated chemical classification. Moreover, a freely accessible API allows easy access to more than 77 million “ClassyFire” classified compounds. The results can be used to help annotate well studied, as well as lesser-known compounds. In addition, these chemical classifications can be used as input for data integration, and many other cheminformatics-related tasks.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-016-0174-y) contains supplementary material, which is available to authorized users.

An unprecedented Pd-catalyzed decarboxylative coupling reaction of aromatic carboxylic acids in aqueous medium under air: synthesis of 3-aryl-imidazo[1,2-a]pyridines from aryl chlorides

An efficient and practical protocol for palladium-catalyzed decarboxylative arylation of imidazo[1,2-a]pyridine-3-carboxylic acids with aryl chlorides has been developed. Note that the reaction could proceed smoothly without an additive in aqueous medium under an ambient atmosphere, and the addition of H2O could effectively promote the decarboxylative arylation. Particularly noteworthy is that these results represent the first examples of Pd-catalyzed decarboxylative coupling reactions of (hetero) aromatic carboxylic acids in aqueous medium under air, and the first successful examples of the synthesis of 3-aryl-imidazo[1,2-a]pyridines using cheap, diverse aryl chlorides and heteroaryl chlorides as the starting materials.

A novel approach for the synthesis of imidazo and triazolopyridines from dithioesters

Various imidazo- and triazolo-pyridines were synthesised by the intramolecular cyclization of pyridine 2-methylamine and dithioesters under mild conditions.

Ligand-free Pd-catalysed decarboxylative arylation of imidazo[1,2-a]pyridine-3-carboxylic acids with aryl bromides

A facile ligand-free method for Pd(OAc)₂ catalysed decarboxylative arylation of imidazo[1,2-a]pyridine-3-carboxylic acids with hetero(aryl) bromides has been developed.

Computer aided drug discovery of highly ligand efficient, low molecular weight imidazopyridine analogs as FLT3 inhibitors

The FLT3 kinase represents an attractive target to effectively treat AML. Unfortunately, no FLT3 targeted therapeutic is currently approved. In line with our continued interests in treating kinase related disease for anti-FLT3 mutant activity, we utilized pioneering synthetic methodology in combination with computer aided drug discovery and identified low molecular weight, highly ligand efficient, FLT3 kinase inhibitors. Compounds were analyzed for biochemical inhibition, their ability to selectively inhibit cell proliferation, for FLT3 mutant activity, and preliminary aqueous solubility. Validated hits were discovered that can serve as starting platforms for lead candidates.

Copper-mediated three-component synthesis of 3-cyanoimidazo[1,2-a]pyridines

A copper-mediated three-component approach towards the synthesis of 3-cyanoimidazo[1,2-a]pyridines from 2-aminopyridines, acetophenones and benzyl cyanide was developed. This cascade reaction proceeds through a copper-mediated oxidative release of cyanide from benzyl cyanide, a copper-mediated Ortoleva–King reaction, and a copper-catalyzed cyanation.

Palladium(0)-catalyzed direct C–H hetero-arylation of 2-arylimidazo [1,2-a]pyridines with (E)-1-(5-bromothiophen-2-yl)-3-arylprop-2-en-1-ones and their anticancer activity

An efficient palladium(0)-catalyzed direct hetero-arylation of imidazo[1,2-a]pyridines at the C-3 position of the imidazole ring has been described.

A copper-catalyzed multi-component reaction accessing fused imidazo-heterocycles via C–H functionalization

An efficient synthesis of fused imidazo-heterocycles is described using Cu(OTf)₂ in [bmim]BF₄ by the multi-component reaction of pyridin-2(1H)-one or thiazol/benzo[d]thiazol-2(3H)-ones with O-tosylhydroxyl amine and acetophenones under microwave irradiation.

Advances in direct C–H arylation of 5,5- 6,5- and 6,6-fused-heterocycles containing heteroatoms (N, O, S)

This report aims to review the advances made in C–H arylation of 5,6, 6,6 and 5,5 fused-heterocyclic systems.