Phytoscreening of Vochysiaceae species: Molecular identification by HPLC-ESI-MS/MS and evaluating of their antioxidant activity and inhibitory potential against human α-amylase and protein glycation.

Scientific research based on medicinal plants has been highlighted as a complementary treatment to T2DM, stand out the Vochysiaceae family, which have been widely used in folk medicine by traditional South American communities to treat some diseases. Our study aimed to investigate the antioxidant and antiglycation activities of ethanol extracts of leaves (LF) and stem barks (SB) of Vochysiaceae species, evaluated their capacities to inhibit glycoside and lipid hydrolases related to T2DM and molecular identification by HPLC-ESI-MS/MS. Our main findings indicate that the ethanolic extract of four of eight analyzed plants such as LF and SB of Q. grandiflora, Q. parviflora, V. elliptica and Calisthene major exhibited, respectively, potential of α-amylase inhibition (IC50 of LF: 5.7 ±â€¯0.6, 4.1 ±â€¯0.5, 5.8 ±â€¯0.5, 3.2 ±â€¯0.6 and IC50 of SB: 3.3 ±â€¯0.7, 6.2 ±â€¯2.0, 121.0 ±â€¯8.6 and 11.2 ±â€¯2.8 µg/mL), capacities of antioxidant (ORAC of LF: 516.2 ±â€¯0.1, 547.6 ±â€¯4.9, 544.3 ±â€¯6.1, 442.6 ±â€¯2.4 and ORAC of SB: 593.6 ±â€¯22.3, 497.7 ±â€¯0.8, 578 ±â€¯12.3, 593.6 ±â€¯19.5 µmol trolox eq/g; FRAP of LF: 796.1 ±â€¯0.9, 427.7 ±â€¯22.0, 81.0 ±â€¯1.9, 685 ±â€¯37.9 and FRAP of SB: 947.4 ±â€¯24.9, 738.6 ±â€¯24.3, 98.8 ±â€¯7.9, 970.8 ±â€¯13.9 µmol trolox eq/g; DPPH IC50 of LF: 14.2 ±â€¯1.8, 36.3 ±â€¯6.9, 11.8 ±â€¯1.9, 13.3 ±â€¯1.2 and DPPH IC50 of SB: 16.0 ±â€¯3.0, 15.5 ±â€¯1.9, 126.1 ±â€¯23. 6, 5.3 ±â€¯0.3 µg/mL, respectively) and antiglycation (BSA/Frutose IC50 of LF: 43.1 ±â€¯3.4, 52.1 ±â€¯6.0, 175.5 ±â€¯32, 8, 111.8 ±â€¯14.7 and BSA/Frutose IC50 of SB:, 40.1 ±â€¯11.9, 51.2 ±â€¯16. 7, 46.6 ±â€¯5.7, 53.5 ±â€¯13.6 µg/mL) and presence of polyphenols, such as flavonoids and condensed tannins. The extracts presented low ability to inhibit α-glycosidase and lipase enzymes in the initial assays, with values below 40% of inhibition. In BSA/methylglyoxal, only Q. grandiflora SB, V. eliptica LF and V. tucanorum LF showed activity (IC50: 655.5 ±â€¯208.5, 401.9 ±â€¯135.2 and 617.1 ±â€¯80.6 µg/mL, respectively) and only C. major LF and SB, in Arg/methylglyoxal (IC50: 485.1 ±â€¯130.8 and 468.0 ±â€¯150.5 µg/ml, respectively). This study presented new findings about the biological and pharmacological potential of some species of Vochysiaceae family, contributing to the understanding of the action and efficacy in use of these plants, in their management of postprandial hyperglycemia and in glycation and oxidative processes that contribute to managing diabetes mellitus.

On the characterization of energy networks of proteins.

The construction of a realistic theoretical model of proteins is determinant for improving the computational simulations of their structural and functional aspects. Modeling proteins as a network of non-covalent connections between the atoms of amino acid residues has shown valuable insights into these macromolecules. The energy-related properties of protein structures are known to be very important in molecular dynamics. However, these same properties have been neglected when the protein structures are modeled as networks of atoms and amino acid residues. A new approach for the construction of protein models based on a network of atoms is presented. This method, based on interatomic interaction, takes into account the energy and geometric aspects of the protein structures that were not employed before, such as atomic occlusion inside the protein, the use of solvation, protein modeling and analysis, and the use of energy potentials to estimate the energies of interatomic non-covalent contacts. As a result, we achieved a more realistic network model of proteins. This model has the virtue of being more robust in face of different unknown variables that usually are arbitrarily estimated. We were able to determine the most connected residues of all the proteins studied, so that we are now in a better condition to study their structural role.

On the characterization of energy networks of proteins

The construction of a realistic theoretical model of proteins is determinant for improving the computational simulations of their structural and functional aspects. Modeling proteins as a network of non-covalent connections between the atoms of amino acid residues has shown valuable insights into these macromolecules. The energy-related properties of protein structures are known to be very important in molecular dynamics. However, these same properties have been neglected when the protein structures are modeled as networks of atoms and amino acid residues. A new approach for the construction of protein models based on a network of atoms is presented. This method, based on interatomic interaction, takes into account the energy and geometric aspects of the protein structures that were not employed before, such as atomic occlusion inside the protein, the use of solvation, protein modeling and analysis, and the use of energy potentials to estimate the energies of interatomic non-covalent contacts. As a result, we achieved a more realistic network model of proteins. This model has the virtue of being more robust in face of different unknown variables that usually are arbitrarily estimated. We were able to determine the most connected residues of all the proteins studied, so that we are now in a better condition to study their structural role.

Thermodynamic evaluation and modeling of proton and water exchange associated with benzamidine and berenil binding to beta-trypsin.

Serine-proteases are involved in vital processes in virtually all species. They are important targets for researchers studying the relationships between protein structure and activity, for the rational design of new pharmaceuticals. Trypsin was used as a model to assess a possible differential contribution of hydration water to the binding of two synthetic inhibitors. Thermodynamic parameters for the association of bovine beta-trypsin (homogeneous material, observed 23,294.4 +/- 0.2 Da, theoretical 23,292.5 Da) with the inhibitors benzamidine and berenil at pH 8.0, 25 degrees C and with 25 mM CaCl2, were determined using isothermal titration calorimetry and the osmotic stress method. The association constant for berenil was about 12 times higher compared to the one for benzamidine (binding constants are K = 596,599 +/- 25,057 and 49,513 +/- 2,732 M(-1), respectively; the number of binding sites is the same for both ligands, N = 0.99 +/- 0.05). Apparently the driving force responsible for this large difference of affinity is not due to hydrophobic interactions because the variation in heat capacity (DeltaCp), a characteristic signature of these interactions, was similar in both systems tested (-464.7 +/- 23.9 and -477.1 +/- 86.8 J K(-1) mol(-1) for berenil and benzamidine, respectively). The results also indicated that the enzyme has a net gain of about 21 water molecules regardless of the inhibitor tested. It was shown that the difference in affinity could be due to a larger number of interactions between berenil and the enzyme based on computational modeling. The data support the view that pharmaceuticals derived from benzamidine that enable hydrogen bond formation outside the catalytic binding pocket of beta-trypsin may result in more effective inhibitors.

Thermodynamic evaluation and modeling of proton and water exchange associated with benzamidine and berenil binding to ß-trypsin

Serine-proteases are involved in vital processes in virtually all species. They are important targets for researchers studying the relationships between protein structure and activity, for the rational design of new pharmaceuticals. Trypsin was used as a model to assess a possible differential contribution of hydration water to the binding of two synthetic inhibitors. Thermodynamic parameters for the association of bovine ß-trypsin (homogeneous material, observed 23,294.4 ± 0.2 Da, theoretical 23,292.5 Da) with the inhibitors benzamidine and berenil at pH 8.0, 25°C and with 25 mM CaCl2, were determined using isothermal titration calorimetry and the osmotic stress method. The association constant for berenil was about 12 times higher compared to the one for benzamidine (binding constants are K = 596,599 ± 25,057 and 49,513 ± 2,732 M-1, respectively; the number of binding sites is the same for both ligands, N = 0.99 ± 0.05). Apparently the driving force responsible for this large difference of affinity is not due to hydrophobic interactions because the variation in heat capacity (DCp), a characteristic signature of these interactions, was similar in both systems tested (-464.7 ± 23.9 and -477.1 ± 86.8 J K-1 mol-1 for berenil and benzamidine, respectively). The results also indicated that the enzyme has a net gain of about 21 water molecules regardless of the inhibitor tested. It was shown that the difference in affinity could be due to a larger number of interactions between berenil and the enzyme based on computational modeling. The data support the view that pharmaceuticals derived from benzamidine that enable hydrogen bond formation outside the catalytic binding pocket of ß-trypsin may result in more effective inhibitors.