Table_1_Conceptual DFT Study of the Local Chemical Reactivity of the Colored BISARG Melanoidin and Its Protonated Derivative.pdf

<p>This computational study assessed eight fixed RSH (range-separated hybrid) density functionals that include CAM-B3LYP, LC-ωPBE, M11, MN12SX, N12SX, ωB97, ωB97X, and ωB97XD related to the Def2TZVP basis sets together with the SMD solvation model in the calculation the molecular structure and reactivity properties of the BISARG intermediate melanoidin pigment (5-(2-(E)-(Z)-5-[(2-furyl)methylidene]-3-(4-acetylamino-4-carboxybutyl)-2-imino-1,3-dihydroimidazol-4-ylideneamino(E)-4-[(2-furyl)methylidene]-5-oxo-1H-imidazol-1-yl)-2-acetylaminovaleric acid) and its protonated derivative, BISARG(p). The chemical reactivity descriptors for the systems were calculated via the Conceptual Density Functional Theory. The choice of active sites applicable to nucleophilic, electrophilic as well as radical attacks were made by linking them with Fukui functions indices, electrophilic and nucleophilic Parr functions, and the condensed Dual Descriptor Δf(r). The study found the MN12SX and N12SX density functionals to be the most appropriate in predicting the chemical reactivity of the molecular systems under study starting from the knowledge of the HOMO, LUMO, and HOMO-LUMO gap energies.</p

MOESM1 of A conceptual DFT study of the molecular properties of glycating carbonyl compounds

Additional file 1. Additional tables

Permeability of antioxidants through a lipid bilayer model with coarse-grained simulations

Oxidative stress caused by pollution and lifestyle changes causes an excess of free radicals that react chemically with cell constituents leading to irreversible damage. There are molecules known as antioxidants that reduce the levels of free radicals. Some pigments of fruits and vegetables known as anthocyanins have antioxidant properties. Their interaction with the cell membrane becomes a crucial step in studying these substances. In this research, molecular dynamics simulations, particularly, coarse-grained molecular dynamics (CGMD) were used. This technique aims to replace functional groups with corresponding beads that represent their level of polarity and affinities to other chemical groups. Also, umbrella sampling was carried out to obtain free energy profiles that describe well the orientation and location of antioxidants in a membrane considering Trolox, Cyanidin, Gallic Acid, and Resveratrol molecules to study the structural effects they cause on it. It was concluded in this study that an antioxidant when crossing the membrane does not cause either damage to the structural properties or the loss of packing and stratification of phospholipids. it was also observed that the most reactive part of the molecules could easily approach area A prone to lipid oxidation, which can describe the antioxidant capacity of these molecules. Communicated by Ramaswamy H. Sarma</p

Data_Sheet_1_Interaction of Tamoxifen Analogs With the Pocket Site of Some Hormone Receptors. A Molecular Docking and Density Functional Theory Study.pdf

<p>In this paper, the antiestrogenic properties of Tamoxifen analogs have been investigated and a theoretical report of its analogs interaction with the pocket site of some hormone receptors are presented. Analogs were generated by modification of the hydrophilic functional group of Tamoxifen by hydroxyl, amide, carboxyl, and sulfhydryl functional groups, in an attempt to improve their activity and selectivity. The analogs exhibit a negative binding energy in the estrogen and progesterone receptors, which indicates a spontaneous interaction between the analogs and the pocket site in the hormone receptors. The values of the molecular polar surface area indicate that the analogs have good permeability and are strong electrophiles. The couplings showed electrostatic interactions such as hydrogen bond and π-π interactions. According with the Lipinsky Rule of Five, the four analogs presented a good biodistribution, permeability, and pharmacological action on the hormone receptors. The analysis of the charge transfer suggests a limited enhanced oxidative damage in the estrogen receptor that not takes place with the progesterone receptor.</p

Z-score for the model of the structure of multiple proteins generated by ProSA web tool.

Z-score for the model of the structure of multiple proteins generated by ProSA web tool.</p

Graphical representation of the dual descriptor DD of Ashwangandhanolide.

Top: DD > 0, Bottom: DD < 0.</p

3D X-Ray crystallographic structures of the selected breast cancer target protein receptors and extended and detailed version of the materials and methodology employed including additional references.

(PDF)</p

Interaction of human TOP2A (PDB: 5GWK) with Ashwagandhanolide and Withanolide sulfoxide.

Three-dimensional (3D) illustration shows the interaction of ligands with human TOP2A structure and two-dimensional (2D) diagram displays the interactions of the ligand with the specific amino acid residues in the active site of the protein.</p

Ramachandran plot for the model of the structure of ERα (PDB: 6CBZ) and human 17β-HSD1 (PDB: 1FDW) proteins generated by PROCHECK.

The red color region denotes residues of the protein in the most favored regions; the brown color denotes residues in the additional allowed regions and the yellow indicates residues in the generously allowed regions.</p

Analysis of RMSD (A), Rg (B), SASA (C) and Hydrogen (D) graphs of TOP2A (PDB: 5GWK) in complex with Ashwagandhanolide (Back color indicating protein alone and Red indicating protein-ligand complex).

Analysis of RMSD (A), Rg (B), SASA (C) and Hydrogen (D) graphs of TOP2A (PDB: 5GWK) in complex with Ashwagandhanolide (Back color indicating protein alone and Red indicating protein-ligand complex).</p