Molecular dynamics and free energy calculations of clozapine bound to D2 and H1 receptors reveal a cardiometabolic mitigated derivative

Most atypical antipsychotics derive from a high dropout of drug treatments due to adverse cardiometabolic side effects. These side effects are caused, in part, by the H1 receptor blockade. The current work sought a clozapine derivative with a reduced affinity for the H1 receptor while maintaining its therapeutic effect linked to D2 receptor binding. Explicit molecular dynamics simulations and end-point free energy calculations of clozapine in complex with the D2 and H1 receptors embedded in cholesterol-rich lipid bilayers were performed to analyze the intermolecular interactions and address the relevance of clozapine-functional groups. Based on that, free energy perturbation calculations were performed to measure the change in free energy of clozapine structural modifications. Our results indicate the best clozapine derivative is the iodine atom substitution for chlorine. The latter is mainly due to electrostatic interaction loss for the H1 receptor, while the halogen orientation out of the D2 active site reduces the impact on the affinity.Communicated by Ramaswamy H. Sarma.

Application of Molecular Dynamics Simulations to Determine Interactions between Canary Seed (Phalaris canariensis L.) Bioactive Peptides and Skin-Aging Enzymes

Food bioactive peptides are well recognized for their health benefits such as antimicrobial, antioxidant, and antihypertensive benefits, among others. Their drug-like behavior has led to their potential use in targeting skin-related aging factors like the inhibition of enzymes related with the skin-aging process. In this study, canary seed peptides (CSP) after simulated gastrointestinal digestion (<3 kDa) were fractioned by RP-HPLC and their enzyme-inhibition activity towards elastase and tyrosinase was evaluated in vitro. CSP inhibited elastase (IC50 = 6.2 mg/mL) and tyrosinase (IC50 = 6.1 mg/mL), while the hydrophobic fraction-VI (0.2 mg/mL) showed the highest inhibition towards elastase (93%) and tyrosinase (67%). The peptide fraction with the highest inhibition was further characterized by a multilevel in silico workflow, including physicochemical descriptor calculations, antioxidant activity predictions, and molecular dynamics-ensemble docking towards elastase and tyrosinase. To gain insights into the skin permeation process during molecular dynamics simulations, based on their docking scores, five peptides (GGWH, VPPH, EGLEPNHRVE, FLPH, and RPVNKYTPPQ) were identified to have favorable intermolecular interactions, such as hydrogen bonding of polar residues (W, H, and K) to lipid polar groups and 2-3 Å van der Waals close contact of hydrophobic aliphatic residues (P, V, and L). These interactions can play a critical role for the passive insertion of peptides into stratum corneum model skin-membranes, suggesting a promising application of CSP for skin-aging treatments.

Laccase catalytic activity shielded by SiO2 nanostructured materials: an in vitro and in silico approach

This study investigates the enhancement of enzymatic catalytic performance by immobilizing laccase on various nanostructured mesoporous silica materials (SBA-15, MCF, and MSU-F). The activity of immobilized laccase was evaluated under different hydrothermal, pH, and solvent conditions, with laccase@MSU-F showing a three-fold increase in stability. Laccase immobilized on these materials demonstrated stability in a pH range of 4.5 to 10.0, while free laccase was inactivated at pH higher than 7. Molecular dynamics simulations revealed that electrostatic interactions and protective confinement effects contribute to the improved stability of immobilized laccase. Overall, the findings suggest that nanomaterials can enhance the operational stability and recovery of enzymes.Communicated by Ramaswamy H. Sarma.

Synthesis, insecticidal activity, and ensembled docking of nitroguanidines bearing S- and R-proline

BACKGROUND

The amino acids R- and S-proline were used to synthesize novel neonicotinoid derivatives that, after being characterized by ¹ H, DEPTQ 135, and HRMS-QTOF, were evaluated for use as insecticides against Galleria mellonella (caterpillar), Sitophilus zeamais, Xylosandrus morigerus, Xyleborus affinis, and Xyleborus ferrugineus.

RESULTS

Comparisons of biological activity and absolute configuration showed that the R enantiomer had excellent and outstanding insecticidal activity against the insects tested, with up to 100% mortality after 12 h compared with dinotefuran at the same concentration.

CONCLUSIONS

The results suggest that compound R6 is an excellent lead enantiopure insecticide for future development in the field of crop protection. Furthermore, intermolecular interactions between nicotinic acetylcholine receptors and the R enantiomer displays a lower score which mean a higher affinity to the nAChR receptor and the π-π interactions are more stable than the S derivative. © 2023 Society of Chemical Industry.

Use of simplified models for theoretical prediction of the interactions between available antibodies and the receptor-binding domain of SARS-CoV-2 spike protein

The negative impact of infectious diseases like COVID-19 on public health and the global economy is evident. This pandemic represents a significant challenge for the scientific community to develop new practical analytical methods for accurately diagnosing emerging cases. Due to their selectivity and sensitivity, new methodologies based on antigen/antibody interactions to detect COVID-19 biomarkers are necessary. In this context, the theoretical, computational modeling reduces experimental efforts and saves resources for rational biosensor design. This study proposes using molecular dynamics to predict the interactions between the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein simplified model and a set of highly characterized antibodies. The binding free energy of the antigen/antibody complexes was calculated for the simplified models and compared against the complete SARS-CoV-2 ectodomain to validate the methodology. The structural data derived from our molecular dynamics and end-point free energy calculations showed a positive correlation between both approximations, with a 0.82 Pearson correlation coefficient; t = 3.661, df = 3, p-value = 0.03522, with a 95% confident interval. Furthermore, we identified the interfacial residues that could generate covalent bonds with a specific chemical surface without perturbing the binding dynamics to develop highly sensitive and specific diagnostic devices. Communicated by Ramaswamy H. Sarma.

Nutricosmetics: A new frontier in bioactive peptides' research toward skin aging

Food derived bioactive peptides are small protein fragments (2-20 amino acids long) that can exhibit health benefits, beyond basic nutrition. For example, food bioactive peptides can act as physiological modulators with hormone or drug-like activities including anti-inflammatory, antimicrobial, antioxidant, and the ability to inhibit enzymes related to chronic disease metabolism. Recently, bioactive peptides have been studied for their potential role as nutricosmetics. For example, bioactive peptides can impart skin-aging protection toward extrinsic (i.e., environmental and sun UV-ray damage) and intrinsic (i.e., natural cell or chronological aging) factors. Specifically, bioactive peptides have demonstrated antioxidant and antimicrobial activates toward reactive oxygen species (ROS) and pathogenic bacteria associated with skin diseases, respectively. The anti-inflammatory properties of bioactive peptides using in vivo models has also been reported, where peptides have shown to decreased the expression of IL-6, TNF-α, IL-1β, interferon-γ (INF-γ), and interleukin-17 (IL-17) in mice models. This chapter will discuss the main factors that trigger skin-aging processes, as well as provide examples of in vitro, in vivo, and in silico applications of bioactive peptides in relation to nutricosmetic applications.

Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.

Structure-Based Virtual Screening of Sterols and Triterpenoids Isolated from Ganoderma (Agaricomycetes) Medicinal Mushrooms Shows Differences in Their Affinity for Human Glucocorticoid and Mineralocorticoid Receptors

An extensive database of sterols and triterpenoids isolated from Ganoderma mushrooms was evaluated by in silico structure-based virtual screening to determine their respective ligand affinities for the glucocorticoid or mineralocorticoid receptor (GCR or MNR). The main ligands for GCR in our database were ergosta-7,22-dien-3-one (compound 1) and ganodermaside B (compound 2), while the best ligands for MNR were 2β,3α,9α-trihydroxyergosta-7,22-diene (compound 8) and 5α-ergosta-7,22-dien-3β-ol (compound 3). The binding free energy (BFE) values calculated for such metabolites were similar to those of the natural ligands for each receptor (i.e., dexamethasone for GCR and aldosterone for MNR). Moreover, the differences between mean BFE values calculated for both receptors suggest that ergosta-7,22-dien-3-one (compound 1), ganodermaside B (compound 2), fungisterol (compound 5), ganoderic acid Ma (compound 9), and cerevisterol (compound 10) might be used as specific ligands for GCR, with a significantly lower affinity for MNR. Finally, it is worth noting that even though this work is exclusively theoretical, the reported bioactivities (either pro- or anti-inflammatory) for those metabolites that were previously studied are consistent with our findings, suggesting that the well-known immunomodulatory effect of Ganoderma triterpenoids and sterols might be attributed, at least partially, to their ability to act as specific GCR ligands.

Ergosterol exerts a differential effect on AR-dependent LNCaP and AR-independent DU-145 cancer cells

Androgen-dependent LNCaP and androgen-independent DU-145 cells, were treated with different concentrations of ergosterol (15 µM and 25 µM) and its respective cell viability was measured by MTT bioassay. While ergosterol showed an antiproliferative effect on LNCaP, on DU-145 promoted cell proliferation. This differential effect suggests that the effect of ergosterol might be related to its ability to act as an Androgen Receptor ligand. In silico Molecular Dynamics simulations were performed to analyze the interaction mechanism between androgen receptor and ergosterol, in comparison with natural ligands, 5α-dihydrotestosterone and testosterone. Our model suggests that the binding of androgen receptor with ergosterol is thermodinamically feasible, which is concordant with our experimental results.

In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy

The transmembrane glycoprotein mucin 1 (MUC1) is an attractive tumor marker for cancer therapy and diagnosis. The nine amino acid extracellular epitope APDTRPAPG of this protein is selectively recognized by the S2.2 single-stranded DNA anti-MUC1 aptamer, which has emerged as a promising template for designing novel targeting agents for MUC1-directed therapy. In this work, 100 ns molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, and conformational analysis were employed to propose a novel prospective anti-MUC1 aptamer with increased affinity toward the MUC1 epitope resulting from the double mutation of the T11 and T12 residues with PSU and U nucleosides, respectively. The double mutant aptamer exhibits a tight interaction with the MUC1 epitope and adopts a groove conformation that structurally favors the intermolecular contact with the epitope through the intermediate T11-A18 region leaving the 3' and 5' ends free for further chemical conjugation with a nanocarrier or pharmaceutical. These results are valuable to gain understanding about the molecular features governing aptamer-epitope interactions and constitute a first key step for the design of novel aptamer-based nanocarriers for MUC1-targeted cancer therapy.

Molecular modeling simulation studies reveal new potential inhibitors against HPV E6 protein

High-risk strains of human papillomavirus (HPV) have been identified as the etiologic agent of some anogenital tract, head, and neck cancers. Although prophylactic HPV vaccines have been approved; it is still necessary a drug-based treatment against the infection and its oncogenic effects. The E6 oncoprotein is one of the most studied therapeutic targets of HPV, it has been identified as a key factor in cell immortalization and tumor progression in HPV-positive cells. E6 can promote the degradation of p53, a tumor suppressor protein, through the interaction with the cellular ubiquitin ligase E6AP. Therefore, preventing the formation of the E6-E6AP complex is one of the main strategies to inhibit the viability and proliferation of infected cells. Herein, we propose an in silico pipeline to identify small-molecule inhibitors of the E6-E6AP interaction. Virtual screening was carried out by predicting the ADME properties of the molecules and performing ensemble-based docking simulations to E6 protein followed by binding free energy estimation through MM/PB(GB)SA methods. Finally, the top-three compounds were selected, and their stability in the E6 docked complex and their effect in the inhibition of the E6-E6AP interaction was corroborated by molecular dynamics simulation. Therefore, this pipeline and the identified molecules represent a new starting point in the development of anti-HPV drugs.