Molecular Modeling and In Vitro Evaluation of Piplartine Analogs against Oral Squamous Cell Carcinoma.

Cancer is a principal cause of death in the world, and providing a better quality of life and reducing mortality through effective pharmacological treatment remains a challenge. Among malignant tumor types, squamous cell carcinoma-esophageal cancer (EC) is usually located in the mouth, with approximately 90% located mainly on the tongue and floor of the mouth. Piplartine is an alkamide found in certain species of the genus Piper and presents many pharmacological properties including antitumor activity. In the present study, the cytotoxic potential of a collection of piplartine analogs against human oral SCC9 carcinoma cells was evaluated. The analogs were prepared via Fischer esterification reactions, alkyl and aryl halide esterification, and a coupling reaction with PyBOP using the natural compound 3,4,5-trimethoxybenzoic acid as a starting material. The products were structurally characterized using 1H and 13C nuclear magnetic resonance, infrared spectroscopy, and high-resolution mass spectrometry for the unpublished compounds. The compound 4-methoxy-benzyl 3,4,5-trimethoxybenzoate (9) presented an IC50 of 46.21 µM, high selectively (SI > 16), and caused apoptosis in SCC9 cancer cells. The molecular modeling study suggested a multi-target mechanism of action for the antitumor activity of compound 9 with CRM1 as the main target receptor.

Cinnamomum sp. and Pelargonium odoratissimum as the Main Contributors to the Antibacterial Activity of the Medicinal Drink Horchata: A Study Based on the Antibacterial and Chemical Analysis of 21 Plants.

Horchata, a herbal infusion drink from Ecuador containing a mixture of medicinal plants, has been reported to exhibit anti-inflammatory, analgesic, diuretic, and antioxidant activity. The antibacterial activity of each of the plants contained in the horchata mixture has not been fully evaluated. Thus, in this study, we analysed the antibacterial activity of 21 plants used in horchata, collected from the Ecuadorian Andes region, against bacterial strains of clinical importance. The methanolic extract of Cinnamomum sp. showed minimal inhibitory concentration (MIC) values of 250 µg/mL against Staphylococcus aureus ATCC25923 and Methicillin-resistant S. aureus (MRSA), while Pelargonium odoratissimum exhibited a MIC value of 500 µg/mL towards S. aureus ATCC25923. The high-performance liquid chromatography-diode array detector-tandem mass spectrometry (HPLC-DAD-MS/MS) analyses identified in Cinnamomum sp. epicatechin tannins, cinnamaldehyde, and prehelminthosporol molecules, whereas in P. odoratissimum, gallocatechin and epigallocatechin tannins, some flavonoids, and gallic acid and derivatives were identified. Finally, Cinnamomum sp. and P. odoratissimum showed partial inhibition of biofilm formation of S. aureus ATCC25923 and MRSA. Overall, our findings revealed which of the plants used in horchata are responsible for the antibacterial activity attributed to this herbal drink and exhibit the potential for Cinnamomum sp. and P. odoratissimum secondary metabolites to be explored as scaffolds in drug development.

Critical Review of Plant-Derived Compounds as Possible Inhibitors of SARS-CoV-2 Proteases: A Comparison with Experimentally Validated Molecules.

Ever since coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, was declared a pandemic on March 11, 2020, by the WHO, a concerted effort has been made to find compounds capable of acting on the virus and preventing its replication. In this context, researchers have refocused part of their attention on certain natural compounds that have shown promising effects on the virus. Considering the importance of this topic in the current context, this study aimed to present a critical review and analysis of the main reports of plant-derived compounds as possible inhibitors of the two SARS-CoV-2 proteases: main protease (Mpro) and Papain-like protease (PLpro). From the search in the PubMed database, a total of 165 published articles were found that met the search patterns. A total of 590 unique molecules were identified from a total of 122 articles as potential protease inhibitors. At the same time, 114 molecules reported as natural products and with annotation of theoretical support and antiviral effects were extracted from the COVID-19 Help database. After combining the molecules extracted from articles and those obtained from the database, we identified 648 unique molecules predicted as potential inhibitors of Mpro and/or PLpro. According to our results, several of the predicted compounds with higher theoretical confidence are present in many plants used in traditional medicine and even food, such as flavonoids, carboxylic acids, phenolic acids, triterpenes, terpenes phytosterols, and triterpenoids. These are potential inhibitors of Mpro and PLpro. Although the predictions of several molecules against SARS-CoV-2 are promising, little experimental information was found regarding certain families of compounds. Only 45 out of the 648 unique molecules have experimental data validating them as inhibitors of Mpro or PLpro, with the most frequent scaffold present in these 45 compounds being the flavone. The novelty of this work lies in the analysis of the structural diversity of the chemical space among the molecules predicted as inhibitors of SARS-CoV-2 Mpro and PLpro proteases and the comparison to those molecules experimentally validated. This work emphasizes the need for experimental validation of certain families of compounds, preferentially combining classical enzymatic assays with interaction-based methods. Furthermore, we recommend checking the presence of Pan-Assay Interference Compounds (PAINS) and the presence of molecules previously reported as inhibitors of Mpro or PLpro to optimize resources and time in the discovery of new SARS-CoV-2 antivirals from plant-derived molecules.

Metabolomic profile and computational analysis for the identification of the potential anti-inflammatory mechanisms of action of the traditional medicinal plants Ocimum basilicum and Ocimum tenuiflorum.

Ocimum basilicum and Ocimum tenuiflorum are two basil species widely used medicinally as an anti-inflammatory, antimicrobial and cardioprotective agent. This study focuses on the chemical characterization of the majoritarian compounds of both species and their anti-inflammatory potential. Up to 22 compounds such as various types of salvianolic acids, derivatives of rosmaniric acid and flavones were identified in both plants. The identified compounds were very similar between both plants and are consistent with previous finding in other studies in Portugal and Italy. Based on the identified molecules a consensus target prediction was carried out. Among the main predicted target proteins, we found a high representation of the carbonic anhydrase family (CA2, CA7 and CA12) and several key proteins from the arachidonic pathway (LOX5, PLA2, COX1 and COX2). Both pathways are well related to inflammation. The interaction between the compounds and these targets were explored through molecular docking and molecular dynamics simulation. Our results suggest that some molecules present in both plants can induce an anti-inflammatory response through a non-steroidal mechanism of action connected to the carbon dioxide metabolism.

Computational modeling predicts potential effects of the herbal infusion "horchata" against COVID-19.

Bioactive plant-derived molecules have emerged as therapeutic alternatives in the fight against the COVID-19 pandemic. In this investigation, principal bioactive compounds of the herbal infusion "horchata" from Ecuador were studied as potential novel inhibitors of the SARS-CoV-2 virus. The chemical composition of horchata was determined through a HPLC-DAD/ESI-MSn and GC-MS analysis while the inhibitory potential of the compounds on SARS-CoV-2 was determined by a computational prediction using various strategies, such as molecular docking and molecular dynamics simulations. Up to 51 different compounds were identified. The computational analysis of predicted targets reveals the compounds' possible anti-inflammatory (no steroidal) and antioxidant effects. Three compounds were identified as candidates for Mpro inhibition: benzoic acid, 2-(ethylthio)-ethyl ester, l-Leucine-N-isobutoxycarbonyl-N-methyl-heptyl and isorhamnetin and for PLpro: isorhamnetin-3-O-(6-Orhamnosyl-galactoside), dihydroxy-methoxyflavanone and dihydroxyphenyl)-5-hydroxy-4-oxochromen-7-yl]oxy-3,4,5-trihydroxyoxane-2-carboxylic acid. Our results suggest the potential of Ecuadorian horchata infusion as a starting scaffold for the development of new inhibitors of the SARS-CoV-2 Mpro and PLpro enzymes.

Protective effect of the medicinal herb infusion "horchata" against oxidative damage in cigarette smokers: An ex vivo study.

Cigarette smoking has been associated with an increase in oxidative stress (OS) and is considered a predisposing factor to chronic noncommunicable diseases, whilst dietary antioxidants has been proposed as an alternative to cope with this oxidative stress. In this study, 20 smokers and 20 non-smokers were studied with the aim of determining their antioxidant status, as well as the ability of an infusion of 23 medicinal plants, to counteract the damage caused by OS. The plasma, red blood cells (RBCs) and polymorphonuclear cells (PBMCs) of both groups were incubated or not with the horchata infusion extract and then the OS markers, genotoxicity, nanostructure of RBCs membrane and genes related to oxidative responses and cellular functionality were evaluated. Up to 33 different compounds, mainly quercetin glycosides, were identified in the extract. A significant deterioration in the antioxidant status in smokers compared to non-smokers was found. The horchata infusion extract improved the nanostructure of RBCs and DNA damage, as well as the activity of the endogenous antioxidant enzymes and markers of oxidative damage to lipid, and proteins in plasma, RBCs and PBMCs in both groups, whilst no significant changes were found in the expression of different genes related to OS response.

Anti-inflammatory effect of the medicinal herbal mixture infusion, Horchata, from southern Ecuador against LPS-induced cytotoxic damage in RAW 264.7 macrophages.

The phytochemical composition and the antioxidant and anti-inflammatory activities of a mixture of 23 plants, named Horchata, traditionally consumed in Ecuador, have been evaluated. The study was carried out using the hydroalcoholic extract (HHext) and infusion (IHext) of the horchata plant mixture. It was verified that thermal treatment affected the contents of vitamin C and carotenoids, but hardly those of polyphenols, which would be the main bioactive compounds in the infusion, the common form of preparation of horchata for consumption. Among phenolic compounds, caffeoylquinic acids, flavones and flavonols (mostly quercetin glycosides) were prominent. Both HHext and IHext extracts managed to protect RAW 264.7 macrophages against LPS-induced cytotoxic damage, increasing the levels of endogenous antioxidant enzymes and modulating the production of pro-inflammatory and anti-inflammatory cytokines. Greater protective effects were obtained for HHext compared to IHext, which was in agreement with its higher content of phenolic compounds favoured by a more efficient extraction in the hydroalcoholic medium. Nonetheless, the infusion still maintained a significant antioxidant and anti-inflammatory activity, which would support the protective effects on health traditionally attributed to its consumption by the population.

Ligand-Based Virtual Screening Using Tailored Ensembles: A Prioritization Tool for Dual A2AAdenosine Receptor Antagonists / Monoamine Oxidase B Inhibitors.

BACKGROUND: Virtual Screening methodologies have emerged as efficient alternatives for the discovery of new drug candidates. At the same time, ensemble methods are nowadays frequently used to overcome the limitations of employing a single model in ligand-based drug design. However, many applications of ensemble methods to this area do not consider important aspects related to both virtual screening and the modeling process. During the application of ensemble methods to virtual screening the proper validation of the models in virtual screening conditions is often neglected. No analysis of the diversity of the ensemble members is performed frequently or no considerations regarding the applicability domain of the base models are being made. METHODS: In this research, we review basic concepts and definitions related to virtual screening. We comment recent applications of ensemble methods to ligand-based virtual screening and highlight their advantages and limitations. RESULTS: Next, we propose a method based on genetic algorithms optimization for the generation of virtual screening tailored ensembles which address the previously identified problems in the current applications of ensemble methods to virtual screening. CONCLUSION: Finally, the proposed methodology is successfully applied to the generation of ensemble models for the ligand-based virtual screening of dual target A2A adenosine receptor antagonists and MAO-B inhibitors as potential Parkinson's disease therapeutics.

Harmonization of QSAR Best Practices and Molecular Docking Provides an Efficient Virtual Screening Tool for Discovering New G-Quadruplex Ligands.

Telomeres and telomerase are key players in tumorogenesis. Among the various strategies proposed for telomerase inhibition or telomere uncapping, the stabilization of telomeric G-quadruplex (G4) structures is a very promising one. Additionally, G4 stabilizing ligands also act over tumors mediated by the alternative elongation of telomeres. Accordingly, the discovery of novel compounds able to act on telomeres and/or inhibit the telomerase enzyme by stabilizing DNA telomeric G4 structures as well as the development of approaches efficiently prioritizing such compounds constitute active areas of research in computational medicinal chemistry and anticancer drug discovery. In this direction, we applied a virtual screening strategy based on the rigorous application of QSAR best practices and its harmonized integration with structure-based methods. More than 600,000 compounds from commercial databases were screened, the first 99 compounds were prioritized, and 21 commercially available and structurally diverse candidates were purchased and submitted to experimental assays. Such strategy proved to be highly efficient in the prioritization of G4 stabilizer hits, with a hit rate of 23.5%. The best G4 stabilizer hit found exhibited a shift in melting temperature from FRET assay of +7.3 °C at 5 µM, while three other candidates also exhibited a promising stabilizing profile. The two most promising candidates also exhibited a good telomerase inhibitory ability and a mild inhibition of HeLa cells growth. None of these candidates showed antiproliferative effects in normal fibroblasts. Finally, the proposed virtual screening strategy proved to be a practical and reliable tool for the discovery of novel G4 ligands which can be used as starting points of further optimization campaigns.

NAPL migration and ecotoxicity of conventional and renewable fuels in accidental spill scenarios.

Fuels derived from non-petroleum renewable resources have raised interest due to their potential in replacing petroleum-based fuels, but information on their fate and effects in the terrestrial and aquatic environments in accidental spill scenario is limited. In this study, migration of four fuels (conventional diesel, conventional gasoline, renewable diesel NExBTL, and ethanol-blended gasoline RE85 containing maximum 85% ethanol) as non-aqueous phase liquids (NAPL) in soil was demonstrated in a laboratory-scale experiment. Ecotoxicity data was produced for the same fuels. There was no significant difference in migration of conventional and renewable diesel, but gasoline migrated 1.5 times deeper and 7-9 times faster in sand than diesel. RE85 spread horizontally wider but not as deep (p < 0.05) as conventional gasoline. Conventional gasoline was the most toxic (lethal concentration [LC50] 20 mg/kg total hydrocarbon content [THC]) among the studied fuels in soil toxicity test with earthworm Eisenia fetida followed by ethanol-blended gasoline (LC50 1,643 mg/kg THC) and conventional diesel (LC50 2,432 mg/kg THC), although gasoline evaporated fast from soil. For comparison, the toxicity of the water-accommodated fractions (WAF) of the fuels was tested with water flea Daphnia magna and Vibrio fischeri, also demonstrating groundwater toxicity. The WAF of conventional gasoline and RE85 showed almost similar toxicity to both the aquatic test species. EC50 values of 1:10 (by volume) WAF were 9.9 %WAF (gasoline) and 9.3 %WAF (RE85) to D. magna and 9.3 %WAF (gasoline) and 12.3 %WAF (RE85) to V. fischeri. Low solubility decreased toxicity potential of conventional diesel in aquatic environment, but direct physical effects of oil phase pose a threat to organisms in nature. Renewable diesel NExBTL did not show clear toxicity to any test species.

Desirability-based multi-objective QSAR in drug discovery.

The adjustment of multiple criteria in hit-to-lead identification and lead optimization is a major advance in drug discovery. Thus, the development of approaches able to handle additional criteria for the early simultaneous treatment of the most important properties determining the pharmaceutical profile of a drug candidate is an emergent issue in this area. In this paper, we review a desirability-based multi-objective QSAR method allowing the joint handling of multiple properties of interest in drug discovery: the MOOP-DESIRE methodology. This methodology adapts desirability theory concepts allowing the holistic modeling of the many and conflicting biological properties determining the therapeutic utility of a drug candidate. Here we survey their suitability for key tasks involving the use of chemoinformatics methods in medicinal chemistry and drug discovery.