Analysis of Pleurotin binding to human thioredoxin reductase using docking and molecular dynamics simulation.

Thioredoxin reductase (TrxR) has been considered a potential target for cancer chemotherapy. It acts by controlling the redox homeostasis of human cells and, therefore, interfering in its function may trigger apoptosis, which is a crucial tumor suppression mechanism. Despite the great effort in the search for TrxR inhibitors, none was approved for human therapy. In the present study a virtual screening for natural organic compounds is discussed for a set of 72 compounds with known IC-50 for TrxR inhibition. The results suggest the Pleurotin, a naphthoquinone obtained from Hohenbuehelia grisea fungus, as a potential TrxR inhibitor, which acts by binding to the active site of the enzyme, between the N- and C-terminal domains. The presence of the ligand blocks the approximation of the C-terminal arm to the N-terminal, which is an essential step of the enzyme function. Besides, the two equivalent binding sites of TrxR were explored, by docking two ligands simultaneously. The results indicate that both sites have an allosteric correlation and, the presence of the ligand in one site may interfere, or even prevent, the binding of the second ligand at the other site. All these findings are quantitatively discussed based on the analysis of long molecular dynamics trajectories, which provides a full description of the ligand-receptor binding modes, average binding energies and conformational changes.Communicated by Ramaswamy H. Sarma.

Antivirals virtual screening to SARS-CoV-2 non-structural proteins.

In March 2020, the World Health Organization (WHO) declared coronavirus disease-19 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a pandemic. Since then, the search for a vaccine or drug for COVID-19 treatment has started worldwide. In this regard, a fast approach is the repurposing of drugs, primarily antiviral drugs. Herein, we performed a virtual screening using 22 antiviral drugs retrieved from the DrugBank repository, azithromycin (antibiotic), ivermectin (antinematode), and seven non-structural proteins (Nsps) of SARS-CoV-2, which are considered important targets for drugs, via molecular docking and molecular dynamics simulations. Drug-receptor binding energy was employed as the main descriptor. Based on the results, paritaprevir was predicted as a promising multi-target drug that favorably bound to all tested Nsps, mainly adipose differentiation-related protein (ADRP) (-36.2 kcal mol-1) and coronavirus main proteinase (Mpro) (-32.2 kcal mol-1). Moreover, the results suggest that simeprevir is a strong inhibitor of Mpro (-37.2 kcal mol-1), which is an interesting finding because Mpro plays an important role in viral replication. In addition to drug-receptor affinity, hot spot residues were characterized to facilitate the design of new drug derivatives with improved biological responses.

Inclusion complex thermodynamics: The ß-cyclodextrin and sertraline complex example.

Thermodynamic properties for ß-cyclodextrin-Sertraline inclusion process was calculated at the density functional theory (DFT) level using the PBE0 functional with 6-31G(d,p), 6-31++G(d,p) and 6-311++G(2df,p) basis sets. Electron correlation was evaluated through Møller-Plesset second-order perturbation theory (MP2). The standard statistical thermodynamic approach was used to assess the entropic contribution to the Gibbs free energy value. According to our results, inclusion of hydration waters to describe the reactants and products in the complex formation reaction model is crucial in order to reproduce the experimental data and seems very coherent with basics thermodynamics yielding good agreement with experiment.

Assessing the quantum mechanical level of theory for prediction of linear and nonlinear optical properties of push-pull organic molecules.

In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (µ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (ßt) were calculated for a set of benzene, styrene, biphenyl and stilbene derivatives using HF, MP2 and DFT (31 different functionals) levels and over 71 distinct basis sets. In addition, we propose two new basis sets, NLO-V and aNLO-V, for NLO properties calculations. As the main outcomes it is shown that long-range corrected DFT functionals such as M062X, ωB97, cam-B3LYP, LC-BLYP and LC-ωPBE work satisfactorily for NLO properties when appropriate basis sets such as those proposed here (NLO-V or aNLO-V) are used. For most molecules with ß ranging from 0 to 190 esu, the average absolute deviation was 13.2 esu for NLO-V basis sets, compared to 27.2 esu for the standard 6-31 G(2d) basis set. Therefore, we conclude that the new basis sets proposed here (NLO-V and aNLO-V), together with the cam-B3LYP functional, make an affordable calculation scheme to predict NLO properties of large organic molecules.

Ab Initio Highly Correlated Conformational Analysis of 1,2-Difluorethane and 1,2-Dichloroethane.

Temperature-dependent conformational population calculations for anti and gauche forms of 1,2-dichloroethane and 1,2-difluorethane were carried out at a highly correlated level of theory (MP4(SDTQ) and CCSD(T)) employing good quality basis sets (6-311++G(3df,3pd) and aug-cc-pVQZ) for the determination of gas relative conformational energies, making use of the statistical thermodynamics formalism for the evaluation of the thermal energy correction at the MP2/6-311++G(3df,3pd) and MP2/aug-cc-pVTZ levels. In addition to the standard calculation of thermodynamic partition functions, a treatment of the lowest-frequency vibrational mode as hindered rotation and anharmonic correction to vibrational frequencies was also included. We found a good agreement between ab initio calculated conformational population values and experimental gas-phase electron diffraction data for the 1,2-dicloroethane. However, for the 1,2-difluorethane species, a reasonable agreement with the experimental anti/gauche population ratio obtained from the analysis of gas-phase far-infrared (50-370 cm(-1)) and low-frequency Raman (70-300 cm(-1)) spectra was not obtained. The results reported here indicate that, for 1,2-difluorethane, and probably other substituted alkanes where the gauche effect is of relevance, a more appropriated treatment of the low-frequency modes must be pursued in order to reproduce experimental conformational population data.