De novo antioxidant peptide design via machine learning and DFT studies

Antioxidant peptides (AOPs) are highly valued in food and pharmaceutical industries due to their significant role in human function. This study introduces a novel approach to identifying robust AOPs using a deep generative model based on sequence representation. Through filtration with a deep-learning classification model and subsequent clustering via the Butina cluster algorithm, twelve peptides (GP1-GP12) with potential antioxidant capacity were predicted. Density functional theory (DFT) calculations guided the selection of six peptides for synthesis and biological experiments. Molecular orbital representations revealed that the HOMO for these peptides is primarily localized on the indole segment, underscoring its pivotal role in antioxidant activity. All six synthesized peptides exhibited antioxidant activity in the DPPH assay, while the hydroxyl radical test showed suboptimal results. A hemolysis assay confirmed the non-hemolytic nature of the generated peptides. Additionally, an in silico investigation explored the potential inhibitory interaction between the peptides and the Keap1 protein. Analysis revealed that ligands GP3, GP4, and GP12 induced significant structural changes in proteins, affecting their stability and flexibility. These findings highlight the capability of machine learning approaches in generating novel antioxidant peptides.

Magnet-responsive choline carbomer ionogels as a versatile and recyclable catalyst for one-pot synthesis of benzopyran in water

Ionogels are gaining popularity as a potential replacement for volatile organic solvents in various processes, such as catalysts, electrochemistry, spectroscopy, and medicinal chemistry, due to their low toxicity, high thermal stability, and good solubility. Magnet-responsive ion gels with high magnetic susceptibility are promising and can be used as catalysts, sensors, and MRI contrast agents. Herein, we fabricated simple and novel magnet choline carbomer ionogels using a precipitation-deposition method with carbomers and choline hydroxide. The morphology and structure of the resulting ionogels were analyzed using various characterization techniques, including FTIR, EDX, TGA, and SEM spectroscopy. These magnet ionogels were effective catalysts for a one-pot, three-component synthesis of benzopyran derivatives, providing mild reaction conditions, environmental friendliness, and good to excellent (78-96%) yields within a short reaction time (1-2 h). Additionally, the magnet ionogels were easily recyclable, and they could be reused up to five times without catalytic deactivation.

Electron ionization mass spectrometry fragmentation routes of Chemical Weapons Convention-related organoarsenic compounds: Electron ionization and density functional theory studies

RATIONALE

For unambiguous identification of Chemical Weapons Convention (CWC)-related chemicals in environmental and biological samples, access to mass spectra and expertise in spectral interpretation is required. As of today, there is no mass spectrum available for dialkyl alkylarsonodithioites in the literature. Therefore, it is essential to obtain spectral information about these compounds.

METHODS

CWC-related organoarsenic compounds were synthesized and analyzed by gas chromatography combined with mass spectrometry (MS), and their retention index (RI) was calculated by Van Den Dool's method. The relationship between RI and density functional theory (DFT)-calculated polarizability (⍺) and molecular weight was also studied. Electron ionization (EI) mode was used to investigate the general fragmentation patterns of the synthesized compounds. A DFT analysis of some major fragment ions was performed in order to confirm the fragmentation pathways.

RESULTS

A linear relationship between RI and ⍺ is observed. The mass spectra of compounds 5-7 are affected by alkyl groups on sulfur and arsenic atoms. The molecular ions of compounds 5-7 can be observed in their EI-MS spectra with relatively good abundance. EI-MS studies revealed some interesting fragmentation pathways, such as the formation of arsenic analogue of benzylic and tropylium cations in EI-MS of chemicals 6.

CONCLUSIONS

By analyzing the mass spectra and RI values, it is possible to detect CWC-related chemicals in aqueous, blood and urine samples during an on-site or off-site inspection.

Design and optimization various formulations of PEGylated niosomal nanoparticles loaded with phytochemical agents: potential anti-cancer effects against human lung cancer cells

BACKGROUND

Phytochemicals and their derivatives are good options to improve treatment efficiency in cancer patients. Artemisinin (ART) and metformin (MET) are widely used phytochemicals to treat various types of cancers. However, their application because of their dose-dependent side effects, and poor bioavailability brings several challenges. Niosome is a novel nanocarrier that is the best choice to encapsulate both lipophilic and hydrophilic drugs. In this study, we synthesized and characterized various formulations of PEGylated (polyethylene glycol) niosomal nanoparticles co-loaded with ART-MET and evaluated their anticancer effect on A549 lung cancer cells.

METHODS

Various formulations of PEGylated noisome were prepared by the thin-film hydration method and characterized in size, morphology, release pattern, and physicochemical structure. The cytotoxic effect of the free ART-MET and optimized PEGylated niosomal nanoparticles loaded with ART-MET on A549 cells were evaluated by MTT assay. Furthermore, the Real-time PCR (RT-PCR) technique used to evaluate apoptotic and anti-apoptotic gene expression.

RESULTS

The size, encapsulation efficiency (EE), and polydispersity index (PDI) of the optimized nanoparticles are 256 nm, 95%, and 0.202, respectively. Additionally, due to the PEGylation hydrophilic character, there is a major consideration of the high impact of PEGylation on reducing niosome size. According to the results of the MTT assay, free ART-MET and ART-MET-loaded niosomal nanoparticles showed dose-dependent toxicity and inhibits the growth of A549 lung cancer cells. Furthermore, the RT-PCR results indicated that ART-MET-loaded niosomal nanoparticles have a higher anti-proliferative effect by inhibiting anti-apoptotic and inducing apoptotic gene expression in A549 lung cancer cells.

CONCLUSIONS

Our study revealed that the simultaneous use of ART and MET in the optimized PEGylated niosomal nanoparticles delivery system could be an appropriate approach to improve the effectiveness of lung cancer treatment.

Aromaticity enhancement of cyclopentadiene in piperidine derivatives: A DFT study on combination anomeric effect and Schleyer hyperconjugative aromaticity

Schleyer introduced hyperconjugative aromaticity and antiaromaticity in 5-substituted cyclopentadienes. In this study, the cyclopentadiene hyperconjugative aromaticity on anomeric carbon of piperidine derivatives were computationally investigated through structural, electronic, energetic and...

Nitriles with High Gas-Phase Basicity-Part II Transmission of the Push-Pull Effect through Methylenecyclopropene and Cyclopropenimine Scaffolds Intercalated between Different Electron Donor(s) and the Cyano N-Protonation Site

This work extends our earlier quantum chemical studies on the gas-phase basicity of very strong N-bases to two series of nitriles containing the methylenecyclopropene and cyclopropenimine scaffolds with dissymmetrical substitution by one or two electron-donating substituents such as Me, NR2, N=C (NR2)2, and N=P (NR2)3, the last three being strong donors. For a proper prediction of their gas-phase base properties, all potential isomeric phenomena and reasonable potential protonation sites are considered to avoid possible inconsistencies when evaluating the energetic parameters and associated protonation or deprotonation equilibria B + H+ = BH+. More than 250 new isomeric structures for neutral and protonated forms are analyzed. The stable structures are selected and the favored ones identified. The microscopic (kinetic) gas-phase basicity parameters (PA and GB) corresponding to N sites (cyano and imino in the cyclopropenimine or in the substituents) in each isomer are calculated. The macroscopic (thermodynamic) PAs and GBs, referring to the isomeric mixtures of favored isomers, are also estimated. The total (pushing) substituent effects are analyzed for monosubstituted and disubstituted derivatives containing two identical or two different substituents. Electron delocalization is examined in the two π-π conjugated transmitters, the methylenecyclopropene and cyclopropenimine scaffolds. The aromatic character of the three-membered ring is also discussed.

Structural characterization of Chemical Weapons Convention-related phosphonoselenoates by electron ionization and electrospray ionization mass spectrometry

RATIONALE

Organophosphorus compounds with phosphorus atom bonded to one methyl, ethyl or propyl (normal or iso) group are listed in Schedule 2 of the Chemical Weapons Convention (CWC). Selenophosphorus compounds, listed in Schedule 2.B.4, have very limited representation in mass spectral libraries and the open literature.

METHODS

Members of a new category of selenophosphorus compounds were prepared via microsynthetic protocols and their fragmentation pathways were investigated using electron ionization (EI) and positive electrospray ionization (ESI) mass spectrometry. The EI and ESI fragmentation pathways were suggested and supported by acquired fragment ions of deuterated analogs and density functional theory calculations.

RESULTS

Mass spectrometric investigations showed some interesting fragmentation pathways, such as McLafferty-type, selenono-selenolo rearrangements, intramolecular electrophilic aromatic substitution reaction and α-cleavage.

CONCLUSIONS

Efficient microsynthesis was conducted, and EI-MS spectra and ESI-MS/MS spectra of a series of selenophosphorus compounds were collected and studied with the purpose of identifying CWC-related chemicals during on-site inspection and/or off-site analysis.

Novel edaravone-based azo dyes: efficient synthesis, characterization, antibacterial activity, DFT calculations and comprehensive investigation of the solvent effect on the absorption spectra

The present study deals with designing and synthesizing novel dyes using the drug combination of edaravone and azo compounds which can be used as an indicator for anions and cations. The desired product synthesis was accomplished via a two-step process involving diazotizing the aromatic amines followed by the resultant salts coupling with edaravone. The resulting dyes were obtained with high yields under mild conditions. The structures of the dyes were identified with UV-vis, FT-IR, ¹H NMR and ¹³C NMR spectra and CHN analysis. To investigate the solvatochromism effect, the interaction of different solvents with the selected dyes was evaluated using several parameters including the dielectric constant, refractive index, hydrogen bond donating ability, hydrogen bond accepting ability and dipolarity/polarizability scale. To achieve deep understanding about the stability and geometrical characteristics of the azo–hydrazo tautomers of the synthesized dyes and their UV-visible spectra prediction, some DFT calculations were also carried out on the synthesized dyes. The antibacterial activities of some synthesized compounds were also evaluated using the disk diffusion method. The results revealed different activity of the selected synthesized dyes for antibacterial tests against selected Gram positive and Gram negative bacteria.

The present study deals with designing and synthesizing novel dyes using the drug combination of edaravone and azo compounds which can be used as an indicator for anions and cations.

Anion recognition by urea metal-organic frameworks: remarkable sensitivity for arsenate and fluoride ions

Functionalized metal-organic frameworks (F-MOFs) are known as a promising chemical sensors since they have specific merits like fixed functionalized ligands projecting into the pores which can be utilized to enhance sensitivity and selectivity. Due to the important role of anions in biological process and environmental systems, there is an increasing interest in synthesis and design of new receptors for anions. Urea groups can operate as a hydrogen bond donating site with hydrogen bond acceptor molecules. Strong and directional hydrogen-bonding between the positive urea groups and anions could reduce vibrational quenching and enhance the fluorescence intensity. In this study, two luminescent porous urea decorated MOFs have been successfully assembled and structurally characterized. Luminescence studies of these MOFs toward anions revealed that these F-MOFs exhibit high sensitivity and selectivity toward H₂AsO₄^- and F^- anions as two major ground water pollutants. Moreover, the proposed materials have been applied for the removal of arsenate and nitrate in contaminant well water samples. Graphical abstract.

Engineering non-ionic carbon super- and hyperbases by a computational DFT approach: substituted allenes have unprecedented cation affinities

DFT calculations reveal that allenes substituted by a cyclopropene or a methylenecyclopropene group, offer suitable scaffolds for tailoring powerful carbon bases. The protonation at C(sp) site provide superbases with PAs = 879–1218 kJ mol⁻¹.

Preparation and characterization of polycaprolactone nanocapsules containing pretilachlor as a herbicide nanocarrier

Polycaprolactone nanocapsules (PCL) containing pretilachlor were prepared, and Fourier transform infrared spectroscopy, atomic force microscopy, and transmission electron microscopy were used for their structural and morphological investigations. The results revealed that the nanocapsules had irregular shape and their particles size was in the range of 70-200 nm. The encapsulation efficiency of pretilachlor was measured as 99.5 ± 1.3% using high-performance liquid chromatography analysis. The physicochemical stability studies over 60 days showed that the nanocapsules were stable in the suspension without any aggregation. The herbicide activity was examined in a pre-emergence manner using barnyard grass as a target plant and rice as a non-target plant. The nanoformulation had no negative effect on rice plant. However, its effect on barnyard grass was significant. The cytotoxicity analysis indicated that the nanocapsulated herbicide is less toxic rather than the commercial formulation. Therefore, encapsulation of pretilachlor in PCL nanocapsules can be used effectively to construct environmentally friendly PCL-herbicide systems in agriculture.