Analysis of temperature effect in the CO2 absorption using a deep eutectic solvent: An in silico approach.

The excess level of carbon dioxide in the atmosphere has contributed a lot to global warming, occasioning several damages to the planet. Therefore, it is urgent to find ways to capture this gas. Then, the present work analyzed the temperature effect in CO2 absorption through deep eutectic solvents (DESs) based on urea and choline chloride using an in silico approach. The Molecular Dynamics (MD) simulations indicated that the increased temperature reduced the interaction potential of carbon dioxide molecules with the DESs components, indicating that the absorption process is more favorable at 303 K. On the other hand, the Noncovalent Interactions (NCI) simulations suggest that the increased temperature reduced the strong attractions and increased repulsive interactions between the carbon dioxide molecules with the solvent analyzed. Therefore, both in silico approaches suggest that the carbon dioxide absorption is more indicated at 303 K.

A mechanistic insight for the biosynthesis of N,N-dimethyltryptamine: An ONIOM theoretical approach.

Psychoactive natural products are potent serotonergic agonists capable of modulating brain functions such as memory and cognition. These substances have shown therapeutic potential for treating various mental disorders. The fact that N,N-dimethyltryptamine (DMT) is produced endogenously in several plants and animals, including humans, makes it particularly attractive. As an amino acid-derived alkaloid, the DMT biosynthetic pathway is part of the L-tryptophan biochemical cascade and can be divided into the decarboxylation by an aromatic L-amino acid decarboxylase (AADC) for tryptamine formation and the subsequent double-methylation by the indolethylamine-N-methyltransferase (INMT) through the cofactor S-adenosyl-L-methionine (SAM), a methyl donor. Unlike the decarboxylation mechanism of L-tryptophan, the molecular details of the double methylation of tryptamine have not been elucidated. Therefore, we propose an in silico model using molecular dynamics (MD), non-covalent interaction index (NCI) and density functional theory (DFT) calculations with the ONIOM QM:MM B3LYP/6-31+G(d,p):MM/UFF level of theory. Based on the obtained energetic data, the potential energy surface (PES) indicates an SN2 mechanism profile, with the second methylation energy barrier being the rate-limiting step with δG‡=60kJ∙mol-1 larger than the previous methylation, following the NCI analysis showing more repulsive interactions for the second transition state. In addition, the hybridization information of each reaction step provides geometric details about the double-methylation.

Prospecting native and analogous peptides with anti-SARS-CoV-2 potential derived from the trypsin inhibitor purified from tamarind seeds.

The study aimed to prospect in silico native and analogous peptides with anti-SARS-CoV-2 potential derived from the trypsin inhibitor purified from tamarind seeds (TTIp). From the most stable theoretical model of TTIp (TTIp 56/287), in silico cleavage was performed for the theoretical identification of native peptides and generation of analogous peptides. The anti-SARS-CoV-2 potential was investigated through molecular dynamics (MD) simulation between the peptides and binding sites of transmembrane serine protease 2 (TMPRSS2), responsible for the entry of SARS-CoV-2 into the host cell. Five native and analogous peptides were obtained and validated through chemical and physical parameters. The best interaction potential energy (IPE) occurred between TMPRSS2 and one of the native peptides obtained by cleavage with trypsin and its analogous peptide. Thus, both peptides showed many hydrophobic residues, a common physical-chemical property among the peptides that inhibit the entry of enveloped viruses, such as SARS-CoV-2, present in specific drugs to treat COVID-19.

Prospecting in silico antibacterial activity of a peptide from trypsin inhibitor isolated from tamarind seed.

Bacterial infections have become a global concern, stimulating the growing demand for natural and biologically safe therapeutic agents with antibacterial action. This study was evaluated the genotoxicity of the trypsin inhibitor isolated from tamarind seeds (TTI) and the antibacterial effect of TTI theoric model, number 56, and conformation number 287 (TTIp 56/287) and derived peptides in silico. TTI (0.3 and 0.6 mg.mL-1) did not cause genotoxicity in cells (p > 0.05). In silico, a greater interaction of TTIp 56/287 with the Gram-positive membrane (GP) was observed, with an interaction potential energy (IPE) of -1094.97 kcal.mol-1. In the TTIp 56/287-GP interaction, the Arginine, Threonine (Thr), and Lysine residues presented lower IPE. In molecular dynamics (MD), Peptidotrychyme59 (TVSQTPIDIPIGLPVR) showed an IPE of -518.08 kcal.mol-1 with the membrane of GP bacteria, and the Thr and Arginine residues showed the greater IPE. The results highlight new perspectives on TTI and its derived peptides antibacterial activity.

Antioxidant activity of eugenol and its acetyl and nitroderivatives: the role of quinone intermediates-a DFT approach of DPPH test.

This work investigated the antioxidant potential of acetylated and nitrated eugenol derivatives through structural analysis and the mechanism of hydrogen atomic transfer (HAT) by density functional theory (DFT). The structures were optimized by the hybrid functional M06-2X with basis set 6-31 + G(d,p), and the HAT mechanism was evaluated with HO, HOO, CH3O, DPPH radicals. In agreement with experimental data from previous studies, two steps of hydrogen transfer were tested. The thermodynamic data showed the need for two hydrogen atomic transfer steps from antioxidants, followed by the formation of p-quinomethanes (27, 28, and 29) to make the reaction spontaneous with DPPH. Furthermore, theoretical kinetic data showed that the preferred antioxidant site depends on the instability of the attacking radical and confirmed the antioxidant profile for eugenol (1, 4-allylbenzene-1,2-diol), and nitro-derivative 7 (5-allyl-3-nitrobenzene-1,2-diol) in the DPPH assay. Finally, this study showed that nitro compound 6 (4-allyl-2-methoxy-6-nitrophenol) also has anti-radical activity with smaller radicals but is not observed in the experiment due to structural characteristics and chemoselectivity of DPPH.

Electrochemical and theoretical investigation on the behavior of the Co2+ ion in three eutectic solvents.

Deep eutectic solvents (DESs) have many advantages, making them a promising alternative in replacing ionic liquids and organic solvents. Besides, DESs have received much prominence due to their diverse applications: Electrodeposition of metals, organic synthesis, gas adsorption, and biodiesel production. Therefore, this work analyzed the effect of the temperature increase (298 K-353 K) on the behavior of the Co2+ ions in three eutectic solvents through electrochemical techniques and computational simulations. From the electrochemical analysis realized, the increase in temperature caused a reduction in specific mass and an increase in the diffusion coefficient. Besides, the activation energy values were of 15.3, 29.9, and 55.2 kJ mol-1 for 1ChCl:2 EG, 1ChCl:2U, and 1ChCl:2G, respectively. The computational simulations indicate that the increased temperature effect caused the replacement of HBD molecules by anions chloride around Co2+ ions for the SDW1 and SDW3 systems between the temperatures of 298 K-353 K, except for the SDW2 system that the replaced occurred in the interval of 313 K-353 K. Besides, the increase of temperature occasioned the increase of strength for Co-Cl interaction and weakened the interactions between the Co2+ ions with the oxygen of HBD molecules.

Structural insights and molecular dynamics into the inhibitory mechanism of a Kunitz-type trypsin inhibitor from Tamarindus indica L.

Trypsin inhibitors from tamarind seed have been studied in vitro and in preclinical studies for the treatment of obesity, its complications and associated comorbidities. It is still necessary to fully understand the structure and behaviour of these molecules. We purifed this inhibitor, sequenced de novo by MALDI-TOF/TOF, performed its homology modelling, and assessed the interaction with the trypsin enzyme through molecular dynamics (MD) simulation under physiological conditions. We identified additional 75 amino acid residues, reaching approximately 72% of total coverage. The four best conformations of the best homology modelling were submitted to the MD. The conformation n°287 was selected considering the RMSD analysis and interaction energy (-301.0128 kcal.mol-1). Residues Ile (54), Pro (57), Arg (59), Arg (63), and Glu (78) of pTTI presented the highest interactions with trypsin, and arginine residues were mainly involved in its binding mechanism. The results favour bioprospecting of this protein for pharmaceutical health applications.