In silico analysis of marine natural product from sponge (Clathria Sp.) for their activity as inhibitor of SARS-CoV-2 Main Protease

Predicting anti-COVID-19 potential: in silico analysis of Mauritine compound from Ziziphus-spina christi as a promising papain-like protease (PLpro) inhibitor

The COVID-19 pandemic caused by the SARS-CoV-2 virus, recognized by the World Health Organization (WHO), has led to 164,523,894 confirmed cases and 3,412,032 deaths globally as of May 20, 2021. SARS-CoV-2 encodes crucial proteases for its replication cycle, including the papain-like protease (PLpro), presenting a potential target for developing COVID-19 treatments. Mauritine, a cyclopeptide alkaloid found in the Ziziphus-spina christi plant, exhibits antiviral properties and was investigated for its affinity and toxicity towards PLpro using molecular docking through MGLTools 1.5.6 with Autodock Tools 4.2. Preceding this, toxicity and ADME prediction were performed via Toxtree 3.1.0 software and SwissADME servers. Results from molecular docking revealed free binding energy values of -8.58; -7.73; -8.36; -6.07; -6.67; -7.83; -7.67; -7.40; and -6.87 Kcal/mol for Mauritine-A, Mauritine-B, Mauritine-C, Mauritine-D, Mauritine-F, Mauritine-H, Mauritine-J, Mauritine-L, and Mauritine-M, respectively. Correspondingly, inhibition constants were 0.51724; 2.14; 0.7398; 35.43; 12.95; 1.83; 2.38; 3.80; and 9.17 µM, respectively. Interactions observed included hydrogen bonds, hydrophobic interactions, and electrostatic interactions between the Mauritine compounds and the receptor. Mauritine-A and Mauritine-C emerged as a promising anti-COVID-19 candidate due to its superior affinity compared to other derivatives, as indicated by research findings. Interestingly, Mauritine-A and Mauritine-C exhibits notable stability as depicted by the RMSD and RMSF graphs, along with a considerable MM-PBSA binding free energy value of -162.431 and -137.500 kJ/mol, respectively.Communicated by Ramaswamy H. Sarma.

Effectiveness of sesquiterpene derivatives from Cinnamomum genus in nicotine replacement therapy through blocking acetylcholine nicotinate: a computational analysis

Cigarette smoking poses various health risks, such as increasing the susceptibility to respiratory infections, contributing to osteoporosis, causing reproductive issues, delaying postoperative recovery, promoting ulcer formation and heightening the risk of diabetes. While many harmful effects of smoking are attributed to other cigarette components, it is nicotine's pharmacological effects that underlie tobacco addiction. Nicotine replacement therapy (NRT) aims to alleviate the urge to smoke and mitigate physiological and psychomotor withdrawal symptoms by delivering nicotine. This study explores the potential of sesquiterpene derivative compounds derived from the Cinnamomum genus using computational techniques. The research incorporates molecular docking analyses, Lipinski's rule of five filtration for drug-likeness, pharmacokinetic and toxicity predictions to assess safety profiles and molecular dynamics (MD) simulations to gauge interaction stability. The findings reveal that all sesquiterpene derivative compounds from the Cinnamomum genus can potentially inhibit nicotinic acetylcholine receptors (nAChRs), particularly nAChRÿ7. However, only abscisic acid exhibit active inhibition, along with suitable drug properties, pharmacokinetics and toxicity profiles. MD studies confirm the stability of interactions between abscisic acid with nAChRÿ7. Consequently, abscisic acid, as sesquiterpene derivatives from the Cinnamomum genus, holds substantial promise for further investigation as nAChRÿ7 inhibitors.Communicated by Ramaswamy H. Sarma.

Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach

The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor.

Anthocyanin-Containing Purple Sweet Potato (Ipomoea batatas L.) Synbiotic Yogurt Inhibited 3T3-L1 Adipogenesis by Suppressing White Adipocyte-Specific Genes

Purpose

We unravel the effect of anthocyanin-containing purple sweet potato synbiotic yogurt (PSPY) on 3T3-L1 adipocyte differentiation and its fundamental molecular mechanisms.

Methods

Molecular docking simulation was performed to observe and identify the affinity and interaction between bioactive compounds and targeted proteins. MDI (isobutylmethylxanthine, dexamethasone, and insulin)-containing medium, a cocktail that stimulates adipogenesis, was used in this study. The toxic effect possibility of the yogurt product was evaluated using 3-[4, 5-dimethylthiazol-2-yl]-2.5 diphenyl tetrazolium bromide (MTT) assay. A 0.25%, 0.5%, 1%, and 5% (v/v) plain or purple sweet potato yogurt supernatant was given to 3T3-L1 preadipocyte culture medium from 24 h after seeding until day 11 of MDI-induced differentiation. The mRNA expression and lipid accumulation were analyzed using RT-qPCR and Oil red O staining, respectively, on day 11 after differentiation induction.

Results

In silico study suggested that anthocyanin-derived compounds have the potential to inhibit peroxisome proliferator activated receptor gamma (PPAR-γ), a master regulator for white adipogenesis. Anthocyanin-containing PSPY significantly suppressed the expression of Pparg, Adipoq, Slc2a4, and Pgc1a. PSPY significantly suppressed Pparg with 1% and 5% concentrations, while with a concentration of 0.25%, PSPY significantly suppressed Adipoq expression as compared to control. Significant inhibition of Slc2a4 and Pgc1a was observed starting from a 0.25% concentration of PSPY. The suppression of adipogenic genes was also observed with the treatment of plain yogurt; however, the effects were relatively lower than the PSPY. The group treated with 1% and 5% of PSPY also showed inhibition effects on lipid accumulation.

Conclusion

This study demonstrated PSPY inhibition effect on white adipocyte differentiation through suppression of Pparg and its downstream genes, Adipoq and Slc2a4, indicating the potential of this yogurt as a functional food for obesity management and prevention.

Screening for Neuroprotective and Rapid Antidepressant-like Effects of 20 Essential Oils

Depression is a serious psychiatric disorder with high prevalence, and the delayed onset of antidepressant effects remains a limitation in the treatment of depression. This study aimed to screen essential oils that have the potential for rapid-acting antidepressant development. PC12 and BV2 cells were used to identify essential oils with neuroprotective effects at doses of 0.1 and 1 µg/mL. The resulting candidates were treated intranasally (25 mg/kg) to ICR mice, followed by a tail suspension test (TST) and an elevated plus maze (EPM) after 30 min. In each effective essential oil, five main compounds were computationally analyzed, targeting glutamate receptor subunits. As a result, 19 essential oils significantly abolished corticosterone (CORT)-induced cell death and lactate dehydrogenase (LDH) leakage, and 13 reduced lipopolysaccharide (LPS)-induced tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). From in vivo experiments, six essential oils decreased the immobility time of mice in the TST, in which Chrysanthemum morifolium Ramat. and Myristica fragrans Houtt. also increased time and entries into the open arms of the EPM. Four compounds including atractylon, α-curcumene, α-farnesene, and selina-4(14),7(11)-dien-8-one had an affinity toward GluN1, GluN2B, and Glu2A receptor subunits surpassed that of the reference compound ketamine. Overall, Atractylodes lancea (Thunb.) DC and Chrysanthemum morifolium Ramat essential oils are worthy of further research for fast-acting antidepressants through interactions with glutamate receptors, and their main compounds (atractylon, α-curcumene, α-farnesene, and selina-4(14),7(11)-dien-8-one) are predicted to underlie the fast-acting effect.

In Vitro, In Vivo, and In Silico Analyses of Molecular Anti-Pigmentation Mechanisms of Selected Thai Rejuvenating Remedy and Bioactive Metabolites

Thai rejuvenating remedies are mixed herbal formulas promoting longevity. Due to the complexity, the biological activities of these remedies are minimal. Therefore, in this study, the authors evaluated the anti-pigmentation effect at the molecular level of the selected Thai rejuvenating remedy to fulfill the knowledge gap. First, the authors found that the selected remedy showed promising activity against the tyrosinase enzyme with an IC₅₀ value of 9.41 µg/mL. In the comparison, kojic acid (positive control) exhibited an IC₅₀ value of 3.92 µg/mL against the same enzyme. Later, the authors identified glabridin as a bioactive molecule against tyrosinase with an IC₅₀ value of 0.08 µg/mL. However, ethyl p-methoxycinnamate was the most abundant metabolite found in the remedy. The authors also found that the selected remedy and glabridin reduced the melanin content in the cell-based assay (B16F1) but not in the zebrafish larvae experiment. Finally, the authors conducted a computational investigation through molecular docking proposing a theoretical molecular interplay between glabridin, ethyl p-methoxycinnamate, and target proteins (tyrosinase and melanocortin-1 receptor, MC1R). Hence, in this study, the authors reported the molecular anti-pigmentation mechanism of the selected Thai rejuvenating remedy for the first time by combining the results from in silico, in vitro, and in vivo experiments.

Fused Tricyclic Guanidine Alkaloids: Insights into Their Structure, Synthesis and Bioactivity

A marine natural product possesses a diverse and unique scaffold that contributes to a vast array of bioactivities. Tricyclic guanidine alkaloids are a type of scaffold found only in marine natural products. These rare skeletons exhibit a wide range of biological applications, but their synthetic approaches are still limited. Various stereochemical assignments of the compounds remain unresolved. Batzelladine and ptilocaulins are an area of high interest in research on tricyclic guanidine alkaloids. In addition, mirabilins and netamines are among the other tricyclic guanidine alkaloids that contain the ptilocaulin skeleton. Due to the different structural configurations of batzelladine and ptilocaulin, these two main skeletons are afforded attention in many reports. These two main skeletons exhibit different kinds of compounds by varying their ester chain and sidechain. The synthetic approaches to tricyclic guanidine alkaloids, especially the batzelladine and ptilocaulin skeletons, are discussed. Moreover, this review compiles the first and latest research on the synthesis of these compounds and their bioactivities, dating from the 1980s to 2022.