Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB.

The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.

Decentralized approach toward organic pollutants removal using UV radiation in combination with H2O2-based electrochemical water technologies.

The current literature lacks a comprehensive discussion on the trade-off between pollutant degradation/mineralization and treatment time costs in utilizing UV light in combination with H2O2-based electrochemical advanced oxidation processes (EAOPs). The present study sheds light on the benefits of using the photoelectro-Fenton (PEF) process with UVA or UVC for methylparaben (MetP) degradation in real drinking water. Although light boosts the photodegradation of refractory Fe(III) complexes and the photolysis of H2O2 (with UVC only), the energy-intensive nature of light-based treatments is acknowledged. To help tackle the high energy consumption issue, a novel approach was employed: partial application of UVA or UVC light after a predetermined electro-Fenton electrolysis time. The proposed treatment approach yielded satisfactory comparable results to those obtained from the application of PEF/UVA or PEF/UVC in terms of total organic carbon removal (ca. 100%), with notably lower energy consumption (ca. 50%). The study delves into the combined method's feasibility, analyzing pollutant degradation/mineralization process and overall energy consumption. The research identifies possible degradation routes based on intermediate detection and radical quenching experiments. Finally, toxicological assessments evaluate the toxicity levels of MetP and its intermediates. The findings of this study bring meaningful contributions to the fore and point to the highly promising potential of the proposed approach, in terms of sustainability and cost-effectiveness, when applied for decentralized water treatment.

PeruNPDB: the Peruvian Natural Products Database for in silico drug screening.

Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 natural products. Access to PeruNPDB is available for free ( https://perunpdb.com.pe/ ). The PeruNPDB's collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.

Highly porous seeding-free boron-doped ultrananocrystalline diamond used as high-performance anode for electrochemical removal of carbaryl from water.

Boron-doped diamond (BDD) electrodes are regarded as the most promising catalytic materials that are highly efficient and suitable for application in advanced electrochemical oxidation processes targeted at the removal of recalcitrant contaminants in different water matrices. Improving the synthesis of these electrodes through the enhancement of their morphology, structure and stability has become the goal of the material scientists. The present work reports the use of an ultranano-diamond electrode with a highly porous structure (B-UNCDWS/TDNT/Ti) for the treatment of water containing carbaryl. The application of the proposed electrode at current density of 75 mA cm-2 led to the complete removal of the pollutant (carbaryl) from the synthetic medium in 30 min of electrolysis with an electric energy per order of 4.01 kWh m-3 order-1. The results obtained from the time-course analysis of the carboxylic acids and nitrogen-based ions present in the solution showed that the concentrations of nitrogen-based ions were within the established maximum levels for human consumption. Under optimal operating conditions, the proposed electrode was successfully employed for the complete removal of carbaryl in real water. Thus, the findings of this study show that the unique, easy-to-prepare BDD-based electrode proposed in this study is a highly efficient tool which has excellent application potential for the removal of recalcitrant pollutants in water.

Structural and Energetic Affinity of Annocatacin B with ND1 Subunit of the Human Mitochondrial Respiratory Complex I as a Potential Inhibitor: An In Silico Comparison Study with the Known Inhibitor Rotenone.

ND1 subunit possesses the majority of the inhibitor binding domain of the human mitochondrial respiratory complex I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, that some metabolites from Annona muricata called acetogenins have important biological activities, such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine mitochondrial respiratory complex I by bis-tetrahydrofurans acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human mitochondrial respiratory complex I. In this work, we evaluate the in silico molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, quantum mechanical optimizations, molecular dynamics simulations and the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known mitochondrial respiratory complex I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger binding free energy compared to the rotenone complex. Detailed analysis of the binding free energy shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of the mitochondrial respiratory complex I.

Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations.

The effect of pH on the supramolecular structure of Helicobacter pylori urease was studied by means of molecular dynamics simulations at seven different pHs. Appropriate urease charge distributions were calculated using a semi-grand canonical Monte Carlo (SGCMC) procedure that assigns each residue's charge state depending on the assigned individual pKa obtained by PROPKA. The effect of pH on protein stability has been analyzed through root-mean-square deviation (RMSD), radius of gyration (RG), solvent-accessible surface area (SASA), hydrogen bonds (HB) and salt bridges (SB). Urease catalyses the hydrolysis of urea in 12 active sites that are covered by mobile regions that act like flaps. The mobility of these flaps is increased at acidic pHs. However, extreme acidic conditions cause urease to have the least number of stabilizing interactions. This initiates the process of denaturalization, wherein the four (αß)3 subunits of the global structure ((αß)3)4 of urease start to separate.

Fuzzy partitioning of clinical data for DMT2 patients.

The present study represents an original approach to data interpretation of clinical data for patients with diagnosis diabetes mellitus type 2 (DMT2) using fuzzy clustering as a tool for intelligent data analysis. Fuzzy clustering is often used in classification and interpretation of medical data (including in medical diagnosis studies) but in this study it is applied with a different goal: to separate a group of 100 patients with DMT2 from a control group of healthy volunteers and, further, to reveal three different patterns of similarity between the patients. Each pattern is described by specific descriptors (variables), which ensure pattern interpretation by appearance of underling disease to DMT2.

Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis.

Heat treatment can modify the allergenic potential, reducing allergenicity in specific proteins. Profilins are one of the important hazelnut allergens; these proteins are considered panallergens due to their high capacity for cross-reactivity with other allergens. In the present work, we evaluated the thermostability of hazelnut profilin, combining molecular dynamics simulation and immunoinformatic techniques. This approach helped us to have reliable results in immunogenicity studies. We modeled Cor a 2 profilin and applied annealing simulation, equilibrium, and production simulation at constant temperatures ranging from 300 to 500 K using Gromacs software. Despite the hazelnut profilins being able to withstand temperatures of up to 400 K, this does not seem to reduce its allergenicity. We have found that profilin subjected to temperatures of 450 and 500 K could generate cross-reactivity with other food allergens. In conclusion, we note a remarkable thermostability of Cor a 2 at 400 K which avoids its structural unfolding.

Vibrational Analysis of Manganese(II) Oxalates Hydrates: An In Silico Statistical Approach.

The experimental and computational vibrational study for three different manganese(II) oxalates hydrates was explored. The elucidation of IR and Raman spectra were discussed based on their structural singularity; in the same way, they establish some interesting relations between them in the field of computational and statistical approaches. The density functional theory (DFT) computational approach was conducted for accurate prediction and interpretation of the intermolecular effects based on experimental and calculated IR and Raman spectra in the solid-state data in combination with multivariate statistical technique. The proposed computational scheme was also explored for the case of the isolated-molecule model. The goals of the study were to access the accuracy of the proposed procedure for solid-state calculations along with electron calculations for the isolated molecules and to reveal the similarities within the groups of objects by the cluster analysis (CA) techniques and two-way CA for the data. The presented simulation procedure should be very valuable for exploring and to classify other oxalate compounds.

Amyloid beta oligomers: how pH influences over trimer and pentamer structures?

The aggregation of proteins in the brain is one of the main features of neurodegenerative diseases. In Alzheimer's disease, the abnormal aggregation of Aß-42 is due to intrinsic and extrinsic factors. The latter is due to variations in the environment, such as temperature, salt concentration, and pH. We evaluated the effect of protonation/deprotonation of residues that are part of trimeric and pentameric oligomers at pH 5, pH 6, and pH 7. Molecular dynamics simulation at 200 ns in the canonical ensemble was implemented. The results have revealed that histidine, glutamic acid, and aspartic acid residues showed a protonation/deprotonation effect in oligomers. The root mean square deviation analysis was used to analyze the structural stability at different pHs. We found an increase in hydrophobicity in the side chains of the trimer, while in the pentamer, the structural instability of a compact structure at pH 5 caused the hydrophobic core to open, revealing the hydrophobic region to the environment. At this point, we believe that conformational changes mediated by pH are essential in the aggregation of Aß-42 oligomers.

Theoretical study of the antioxidant capacity of the flavonoids present in the Annona muricata (Soursop) leaves.

A theoretical approach was used to evaluate the antioxidant capacity of 20 flavonoids reported in Annona muricata leaves. The theoretical study was at the GGA level using the wB97XD functional and the cc-pvtz basis set. The calculations were performed in gas phase and implicit solvent phase. The flavonol robinetin (03c) and the flavanol gallocatechin (01c) are species that exhibited the best antioxidant capacity in the HAT, SEPT, and SPLET mechanisms. On the other hand, in the SET I mechanism, flavonol quercetin (03b) was the best, and in the SET II mechanism, the most favored species is the flavanol catechin (01a). However, these species do not achieve to overcome the antioxidant capacity presented by the Trolox.

Nanoformulation for potential topical delivery of Vismodegib in skin cancer treatment.

Vismodegib (Erivedge®, Genentech) is a first-in-class inhibitor of the hedgehog signaling pathway for the treatment of basal cell carcinoma (BCC). The treatment currently consists of the oral administration of Erivedge® capsules. Although it has shown therapeutic efficacy in clinical trials, there are many side effects related to its systemic distribution. In this work, we have incorporated vismodegib to ultradeformable liposomes in order to obtain a nano-drug delivery system via topical route, which could be useful to reduce systemic distribution -and consequently side effects- while achieving a viable epidermis-specific target where neoplastic events of BCC develop. Vismodegib was loaded into liposomes composed of soy phosphatidylcholine and sodium cholate, and the obtained formulation was characterized by different techniques, both experimental and computational. Several analyses were performed,with a special focus on the interaction of the drug with the liposomal membrane. Additionally, the penetration of Vismodegib delivered by ultradeformable liposomes was assessed on human skin explants. This is one of the first works that propose the topical route for Vismodegib and the first, to our knowledge, in stabilizing this active into a nano-drug delivery system specifically designed for penetrating the stratum corneum impermeable barrier.