Microwave-assisted synthesis, antioxidant activity, docking simulation, and DFT analysis of different heterocyclic compounds

Molecular docking studies, DFT, and ADMET calculations of some flavonoids and their characteristic structural features involved in inhibition of pro-inflammatory enzymes

Inflammation is an immune system response triggered by pathogens, damaged cells, or stimuli. Some regulatory enzymes, such as phosphodiesterase, hyaluronidase, collagenase, and lipoxygenase, play an essential role in the inflammatory process. Polyphenolic compounds, such as flavonoids, are active suppressors of inflammatory cytokines, modulators of transcription factors, and inflammation-related pathways. A set of flavonoid structures was screened and docked against inflammation pathway enzymes. Amentoflavone has been shown to cause interactions with phosphodiesterase enzymes, while Bilobetin and Silibinin demonstrated an increase in binding energy with collagenase enzymes. The retrieved compounds from the docking study were subjected to DFT theory. The results showed that the LUMO orbital is located on the flavonoid part. The thermochemical parameters indicated that Silibinin is more stable than other compounds. The ADMET profile predicted that Silibinin can be used orally among the compounds. Silibinin can be introduced as a promising anti-inflammatory agent demonstrating phosphodiesterase and collagenase inhibitory properties.

Synthesis and characterization of new hexahydroquinoline derivatives and evaluation of their cytotoxicity, intracellular ROS production, and inhibitory effects on inflammatory mediators

Inflammation is a response to injury and infection in an organism. It can be categorized as acute or chronic. Chronic inflammation is the underlying cause of many diseases such as Alzheimer disease, diabetes, rheumatoid arthritis, atherosclerosis, and cardiovascular diseases. Recent studies have proven the antiinflammatory properties of 1,4-dihydropyridines (1,4-DHPs) and their derivatives, which have many biological activities including the blocking of calcium channels. In this study, 15 compounds that are condensed derivatives of 1,4-DHPs, with the general structure of hexahydroquinoline-3-carboxylate, were synthesized. These compounds, expected to show inhibitory activity against inflammatory mediators, were obtained by the reaction of 4-(difluoromethoxy)benzaldehyde, substituted/nonsubstituted 1,3-cyclohexanedione derivatives, and appropriate alkyl acetoacetate compounds in the presence of ammonium acetate as a nitrogen source according to the Hantzsch synthesis method. The structures of the synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, and HRMS methods. The cytotoxic properties of the compounds were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in the 3T3 cell line. Among the 15 compounds, the three compounds with the lowest levels of cytotoxic effects were selected for further experiments. Inflammation was induced by lipoxygenase and the effects of the selected compounds on the levels of reactive oxygen species, cytokines, and complement C3 and C9 regulatory proteins were investigated. It was found that the three selected compounds decreased the levels of transforming growth factor-beta 1 (TGF-β1). Among these compounds, compound 3e provided the most significant decrease in this cytokine. Moreover, 3e increased both C3 and C9 levels. Molecular modeling studies also showed that 3e had better affinity for TGF-β1. When the binding modes of these compounds in the active site of TGF-β1 were analyzed, it was found that compound 3e had hydrophobic interactions with amino acids Leu142, Tyr84, and Ile13; halogen bond interactions with Asp92; and hydrogen bond interactions with Ser89, Gly88, and Gly14 in the active binding site. Further in vitro and in vivo studies are needed to show the possible mechanism of action of compound 3e.

Computational studies on a selection of phosphite esters as antioxidants for polymeric materials

CONTEXT

Phosphite esters, a class of organo-phosphorus compounds, are widely used as non-discolouring antioxidants in many polymeric products. Apart from normal radical scavenging, they prevent the splitting of hydroperoxides (ROOH), one of the initial products of autoxidation, from forming extremely reactive free radicals such as alkoxy (RO.) and hydroxy (.OH) radicals. The inherent molecular properties of antioxidants and the chemistry of their action are essential for researchers working in this field of science. Four organo-phosphorous compounds well-known for their antioxidant activity are selected here for theoretical analysis: Tri(m-methylphenyl) phosphite (m-TMPP), Tri(4-methyl-2,6-di-tert-butylphenyl) phosphite (TMdtBPP), Tri(allylphenyl) phosphite (TAPP) and Tri(mercaptobenzothiazoyl) thiophosphate (TMBTTP). The antioxidant activity exhibited by these compounds is theoretically verified, and the results are consistent with the available experimental data. Such theoretical predictions offer advantages in scientific research, particularly when researchers need to select certain molecules as antioxidants for experiments from a pool of molecular systems.

METHODS

The chemical computations presented in this report are done in Gaussian 16 program package. The procedure of density functional theory (DFT) with the model chemistry B3LYP/6-31G(d,p) is used to generate computational data. Global reactivity indices, thermochemical data, Fukui functions, molecular electrostatic potential and NMR spectra are computed for the chosen molecular systems from their optimized geometries.

Exploring isoindolin-1-ones as potential CDK7 inhibitors using cheminformatic tools

In women who die from cancer, breast cancer is the most common cause of death. The development of small molecular scaffolds as specific Cyclin-dependent kinase (CDK) inhibitors is a promising strategy in the discovery of anti-breast cancer drugs. Isoindolin-1-ones are heterocyclic compounds with useful therapeutic properties. In this study, a library of 48 isoindolinones has been virtually screened by molecular docking that showed high binding affinity up to - 10.1 kcal/mol and conventional hydrogen bonding interactions with active amino acid residues of CDK7. The molecular dynamics simulation (MDS), fragment molecular orbital (FMO), density functional theory (DFT), and pharmacokinetics studies of the best two docked scored ligands 7 and 14 have been studied. Examining the ligand root mean square deviation and hydrogen bonding occupancy of the 100 ns MDS trajectory, both ligands 7 and 14 showed docked pose stability. FMO calculations displayed that LYS139 and LYS41 are majorly contributing to the binding interactions with ligands 7 and 14 in the docked poses. DFT studies of ligands 7 and 14 showed high values of global softness and low values of global hardness and chemical potential thus displaying chemically reactive soft molecules and this influences their anti-cancer activity. Our hits exhibited superior qualities to known CDK7 inhibitors, according to the comprehensive pharmacokinetic parameters that were predicted. The results indicate that isoindolin-1-one moieties are good candidates for anti-cancer action and could serve as effective CDK7 inhibitors.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00225-0.

Novel pyrazole and imidazolone compounds: synthesis, X-ray crystal structure with theoretical investigation of new pyrazole and imidazolone compounds anticipated insecticide's activities against targeting Plodia interpunctella and nilaparvata lugens

In this study, we synthesized (2-propoxyphenyl)(3-(p-tolyl)oxiran-2-yl)methanone through oxidizing the double bond of the respective chalcone via the Weitz-Scheffer epoxidation reaction. Additionally, the chalcone with an oxirane ring served as a fundamental building block for the synthesis of various pyrazole and imidazole derivatives, employing diverse nitrogen nucleophiles. All synthesized compounds were confirmed via analytical and spectroscopic analysis, such as FT-IR, 1H NMR, 13C NMR, and mass spectroscopy. Furthermore, all these nitrogen heterocycles were optimized via the DFT/B3LYP/6-31G(d,p) basis set and their physical descriptors were identified. Compound 11 was further confirmed using single-crystal X-ray diffraction with Hirshfeld analysis, and the results were correlated with the optimized structure by comparing their bond length and bond angle, which provided excellent correlation. Additionally, the insecticidal activities of the newly synthesized compounds were tested against P. interpunctella and Nilaparvata lugens. The heterocyclic compounds exhibited remarkable activity compared to the standard reference thiamethoxam. These findings were further confirmed through docking simulation with different proteins, namely PDBID 3aqy and 3wyw. The compounds interacted effectively within the protein pockets, displaying a higher binding energy with amino acids.

Designing a green poly(β-amino ester) for the delivery of nicotinamide drugs with biological activities and conducting a DFT investigation

The environmentally friendly polymerization process was carried out using microwave irradiation without additional solvents or catalysts to produce poly(β-amino ester) (PβAE) which served as a drug delivery system. PβAE was synthesized through Michael addition polymerization of 1,4-butane diol diacrylate and piperazine. Swelling and biodegradation studies were conducted in various solvents and phosphate-buffered saline (PBS, pH 7.4) at 37 °C to evaluate the properties of the polymeric gel. The PβAE matrix demonstrated solubility enhancement for hydrophobic antimicrobial and antitumor-active nicotinamide derivatives (TEINH, APTAT, and MOAPM), controlling their release over 10 days in (PBS). The successful formation of free and loaded PβAE with nicotinamide active materials was confirmed by spectroscopic analysis including Fourier-transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). Optimization and physical descriptor determination via the DFT/B3LYP-631(G) basis set were performed to aid in the biological evaluation of these compounds with elucidation of their physical and chemical interaction between poly(β-amino ester) and nicotinamide drugs.

Exploring the Antioxidant Potency of New Naphthalene-Based Chalcone Derivatives: Design, Synthesis, Antioxidant Evaluation, Docking Study, DFT Calculations

Naphthalene-based chalcone derivative was successfully synthesized through the condensation of 2,4-dichlorobenzaldehyde with 2-acetylnaphthalene. This chalcone, denoted as compound 1, demonstrated a versatile reactivity upon treatment with both nitrogen and carbon nucleophiles, and yielded diverse heterocyclic scaffolds such as pyrazoline, thiazole, pyrimidine, pyran, and pyridine derivatives. The pyrazoline aldehyde derivative 7 was further derivatized to produce the hydrazide-hydrazone 13, namely, (1H-pyrazol-1-yl)methylene)acetohydrazide, which was exploited to synthesize derivatives of 2-oxo-2H-chromene-3-carbohydrazide 14, 2-(4-oxo-4,5-dihydrothiazol-2-yl)acetohydrazide 15, and 3-(4-nitrophenyl)acrylohydrazide 16. All the newly synthesized compounds were characterized by melting point, elemental analysis, as well as FT-IR, 1 H-NMR and mass spectroscopy. Furthermore, these heterocyclic derivatives were screened for their antioxidant capacities using the DPPH radical assay. The results showed that compounds 5 and 10 are the most potent antioxidants with IC50 values 178, 177(μM), respectively. comparable to that of ascorbic acid which has IC50 value 148. Meanwhile, compounds 2, 12, 13, 14, 15, and 16 exhibited moderate antioxidant activities with IC50 values ranged from 266 to 291(μM). Thus, these heterocycles could emerge as promising antioxidant drugs for the treatment of oxidative stress-related diseases. Finally, molecular docking was conducted to study the binding affinity for the most potent antioxidant compounds 5, 10, and ascorbic acid inside the active pocket of Human Peroxiredoxin 5 (1HD2). DFT calculations and global descriptors were calculated for the most potent compounds to correlate the relation between chemical structure and reactivity.

Assessment of the synthesis method of Fe3O4 nanocatalysts and its effectiveness in viscosity reduction and heavy oil upgrading

In this research, Fe3O4 nanocatalysts were synthesized systematically microwave-assisted. The effectiveness of the synthesized nanocatalysts in reducing viscosity and upgrading heavy oil was evaluated. The nanocatalysts were investigated for their magnetic and electromagnetic properties. The impact of microwave radiation's time and power on the size and purity of nanocatalysts was investigated. The purities in the crystal network of Fe3O4 nanocatalysts expanded as a result of reducing microwave radiation time and power due to less heat production. Increased temperature leads to dope NH4Cl into the Fe3O4 nanocatalysts crystal network. At: 1 min and power of 400 watts the most satisfactory results in the size and purity of nanocatalysts. The electromagnetic properties, size, and effectiveness of the synthesized Fe3O4 nanocatalysts have been examined to determine the effect of the synthesis method. The performance of Fe3O4 nanocatalysts synthesized by co-precipitation and microwave-assisted viscosity reduction and heavy oil upgrading was evaluated and compared. The crystallite size of the Fe3O4 nanocatalysts synthesized by microwave-assisted was smaller than that synthesized using co-precipitation. Fe3O4 nanocatalysts synthesized by microwave-assisted and the co-precipitation method decreased viscosity by 28% and 23%, respectively. Moreover, Fe3O4 nanocatalysts synthesized by microwave-assisted reduced the sulfoxide index and aromatic index considerably more than the co-precipitation synthesized Fe3O4 (90% against. 48% and 13% vs. 7%, respectively).

Benzimidazole-Triazole Hybrids as Antimicrobial and Antiviral Agents: A Systematic Review

Bacterial infections have attracted the attention of researchers in recent decades, especially due to the special problems they have faced, such as their increasing diversity and resistance to antibiotic treatment. The emergence and development of the SARS-CoV-2 infection stimulated even more research to find new structures with antimicrobial and antiviral properties. Among the heterocyclic compounds with remarkable therapeutic properties, benzimidazoles, and triazoles stand out, possessing antimicrobial, antiviral, antitumor, anti-Alzheimer, anti-inflammatory, analgesic, antidiabetic, or anti-ulcer activities. In addition, the literature of the last decade reports benzimidazole-triazole hybrids with improved biological properties compared to the properties of simple mono-heterocyclic compounds. This review aims to provide an update on the synthesis methods of these hybrids, along with their antimicrobial and antiviral activities, as well as the structure-activity relationship reported in the literature. It was found that the presence of certain groups grafted onto the benzimidazole and/or triazole nuclei (-F, -Cl, -Br, -CF₃, -NO₂, -CN, -CHO, -OH, OCH₃, COOCH₃), as well as the presence of some heterocycles (pyridine, pyrimidine, thiazole, indole, isoxazole, thiadiazole, coumarin) increases the antimicrobial activity of benzimidazole-triazole hybrids. Also, the presence of the oxygen or sulfur atom in the bridge connecting the benzimidazole and triazole rings generally increases the antimicrobial activity of the hybrids. The literature mentions only benzimidazole-1,2,3-triazole hybrids with antiviral properties. Both for antimicrobial and antiviral hybrids, the presence of an additional triazole ring increases their biological activity, which is in agreement with the three-dimensional binding mode of compounds. This review summarizes the advances of benzimidazole triazole derivatives as potential antimicrobial and antiviral agents covering articles published from 2000 to 2023.

Copper Catalyzed Synthesis of Heterocyclic Molecules via C-N and C-O Bond Formation under Microwaves: A Mini-Review

Heterocyclic moieties play a significant role in the field of drug discovery. C-N and C-O bond formation reactions are the primary synthetic sequence for the generation of heterocyclic molecules. The generation of C-N and C-O bonds involves the use of mostly Pd or Cu catalysts although other transition metal catalyst's are also involved. However, in C-N and C-O bond formation reactions, several problems were faced such as catalytic systems containing costly ligands, lack of substrate scope, lots of waste generation, and high temperature conditions. So it is imperative to uncover new eco-friendly synthetic strategies. In view of enormous drawbacks, it is important to develop an alternate microwave-assisted synthesis of heterocycles via C-N and C-O bond formation, which provides a short reaction time, tolerance for functional groups, and less waste production. Numerous chemical reactions have been accelerated using microwave irradiation which provides a cleaner reaction profile, lower energy consumption, and higher yields. This review article highlights a comprehensive overview on the potential application of microwave assisted synthetic routes for the synthesis of diverse heterocycles via mechanistic pathways covering the year ranges from 2014 to 2023, along with possible biological interests.

Making a new bromo-containing cellulosic dye with antibacterial properties for use on various fabrics using computational research

The reaction of cyanoethyl cellulose with para-bromo diazonium chloride resulted in the creation of a novel bromo-containing cellulosic (MCPT). The dispersion stability of MCPT has been improved by its dispersion into 1% waterborne polyurethane acrylate (WPUA). TEM, particle size, and zeta potential were used to track the dispersion stability of aqueous MCPT and MCPT in 1% WPUA and particle size. The prepared MCPT has been utilized as a unique green colorant (dye) for the printing of cotton, polyester, and cotton/polyester blend fabrics using a silkscreen printing technique through a single printing step and one color system. Color improvement has been achieved by printing different fabrics with a printing paste of MCPT dispersed in 1% WPUA. The MCPT and MCPT in 1% WPUA printed fabrics were evaluated for rubbing, light, washing, and perspiration fastness, UV blocking activity, and antibacterial activity. These findings were established through structural optimization at the DFT/B3LYP/6-31 (G) level and simulations involving several proteins.

Antioxidant activity of novel nitrogen scaffold with docking investigation and correlation of DFT stimulation

Heterocyclic scaffolds are frequently employed in drug development to treat a variety of conditions, including cancers. These substances have the ability to engage covalently or non-covalently with particular residues in the target proteins, inhibiting them. In this study, the formation of N-, S-, and O-containing heterocycles by the interaction of chalcone with nitrogen-containing nucleophiles such as hydrazine, hydroxyl amine, guanidine, urea, and aminothiourea was explored. FT-IR, UV-visible, NMR, and mass spectrometric studies were used to confirm the heterocyclic compounds that were produced. These substances were tested for their antioxidant activity by their capacity to scavenge the artificial radicals 2,2-diphenyl-1-picrylhydrazyl (DPPH). The strongest antioxidant activity was demonstrated by compound 3 (IC50 = 93.4 μM), whereas compound 8 (IC50 = 448.70 μM) had the lowest activity when compared to vitamin C (IC50 141.9 μM). Also, the experimental findings and the docking estimation of these heterocyclic compounds with PDBID:3RP8 were in agreement. Additionally, the compounds' global reactivity characteristics, such as HOMO-LUMO gaps, electronic hardness, chemical potential, electrophilicity index, and Mulliken charges, were identified using DFT/B3LYP/6-31G(d,p) basis sets. The two chemicals that displayed the best antioxidant activity also had their molecular electrostatic potential (MEP) ascertained using DFT simulations.