Latin American Natural Product Database (LANaPDB): An Update.

Natural product (NP) databases are crucial tools in computer-aided drug design (CADD). Over the past decade, there has been a worldwide effort to assemble information regarding natural products (NPs) isolated and characterized in certain geographical regions. In 2023, it was published LANaPDB, and to our knowledge, this is the first attempt to gather and standardize all the NP databases of Latin America.

CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance.

Effective management of emerging diseases relies on timely pathogen identification and monitoring. The emergence of COVID-19 in December 2019, rapidly evolved into a global pandemic, with millions of cases and deaths reported worldwide. The accumulation of SARS-CoV-2 genomes provided unprecedented opportunities for studying the virus's evolutionary dynamics, understanding the impact of mutations, and identifying emerging Variants of Interest (VOIs) and Variants of Concern (VOCs).

Updating and profiling the natural product-likeness of Latin American compound libraries.

Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB.

Critical Assessment of pH-Dependent Lipophilicity Profiles of Small Molecules: Which One Should We Use and In Which Cases?

The front cover artwork is provided by CBio Laboratory and Computational Toxicology and Artificial Intelligence Laboratory (LaToxCIA) both at the University of Costa Rica. The image shows the formalisms commonly used to determine the pH-dependent lipophilicity profile of ionizable compounds. Herein, for 4-phenylbutylamine it is accurately predicted when the apparent ion pair partitioning is considered.

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.

Critical Assessment of pH-Dependent Lipophilicity Profiles of Small Molecules: Which One Should We Use and In Which Cases?

Lipophilicity is a physicochemical property with wide relevance in drug design, computational biology, food, environmental and medicinal chemistry. Lipophilicity is commonly expressed as the partition coefficient for neutral molecules, whereas for molecules with ionizable groups, the distribution coefficient (D) at a given pH is used. The logD is usually predicted using a pH correction over the logP using the pK of ionizable molecules, while often ignoring the apparent ion pair partitioning .

Prediction of toluene/water partition coefficients in the SAMPL9 blind challenge: assessment of machine learning and IEF-PCM/MST continuum solvation models.

In recent years the use of partition systems other than the widely used biphasic -octanol/water has received increased attention to gain insight into the molecular features that dictate the lipophilicity of compounds. Thus, the difference between -octanol/water and toluene/water partition coefficients has proven to be a valuable descriptor to study the propensity of molecules to form intramolecular hydrogen bonds and exhibit chameleon-like properties that modulate solubility and permeability. In this context, this study reports the experimental toluene/water partition coefficients (log ) for a series of 16 drugs that were selected as an external test set in the framework of the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) blind challenge.

Antibiotic Resistance and Food Safety: Perspectives on New Technologies and Molecules for Microbial Control in the Food Industry.

Antibiotic resistance (ABR) has direct and indirect repercussions on public health and threatens to decrease the therapeutic effect of antibiotic treatments and lead to more infection-related deaths. There are several mechanisms by which ABR can be transferred from one microorganism to another. The risk of transfer is often related to environmental factors.

ASGARD+: A New Modular Platform for Bacterial Antibiotic-Resistant Analysis.

ASGARD+ (Accelerated Sequential Genome-analysis and Antibiotic Resistance Detection) is a command-line platform for automatic identification of antibiotic-resistance genes in bacterial genomes, providing an easy-to-use interface to process big batches of sequence files from whole genome sequencing, with minimal configuration. It also provides a CPU-optimization algorithm that reduces the processing time. This tool consists of two main protocols.

Phylogeographic and Phylogenomic Structure of the Quarantine Plant Pathogen , Including New Reports in the United States.

Global agricultural trade has accelerated the emergence and re-emergence of new plant pathogens. In the United States, the fungal pathogen is still considered a foreign quarantine pathogen that affects ornamental plants (i.e.

Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9).

In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations.

Molecular characteristics of several drugs evaluated from solvent/water partition measurements: Solvation parameters and intramolecular hydrogen bond indicator.

A wide set of well-known drugs, most of them included in the Abraham´s reference database, covering a wide variety of chemical structures and therapeutical functionalities were chosen in order to determine some molecular properties from solvent/water partition measurements. Partition data from aqueous solutions and four different solvents (n-dodecane, toluene, chloroform and n-octanol) were measured and reported. From them, Abraham´s molecular descriptors of selected compounds (A, B and S, accounting for hydrogen bond donor, hydrogen bond acceptor and dipolarity/polaritzability, respectively) were estimated.

Anchovy powder enrichment in brown rice-based instant cereal: a process optimization study using Response Surface Methodology (RSM).

There is a need for expanding the utilization of small fish as they constitute an undervalued and important source of protein and micronutrients in many developing countries suffering from micronutrient deficiencies. One way to increase consumption and health benefits is to add nutrient-rich fish meal into staple food ingredients. In this study, Response Surface Methodology (RSM) was applied to optimize the processing of an instant rice-based cereal enriched with anchovy powder.

Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge.

A multiple linear regression model called MLR-3 is used for predicting the experimental n-octanol/water partition coefficient (log P) of 22 N-sulfonamides proposed by the organizers of the SAMPL7 blind challenge. The MLR-3 method was trained with 82 molecules including drug-like sulfonamides and small organic molecules, which resembled the main functional groups present in the challenge dataset. Our model, submitted as "TFE-MLR", presented a root-mean-square error of 0.

Prediction of n-octanol/water partition coefficients and acidity constants (pK) in the SAMPL7 blind challenge with the IEFPCM-MST model.

Within the scope of SAMPL7 challenge for predicting physical properties, the Integral Equation Formalism of the Miertus-Scrocco-Tomasi (IEFPCM/MST) continuum solvation model has been used for the blind prediction of n-octanol/water partition coefficients and acidity constants of a set of 22 and 20 sulfonamide-containing compounds, respectively. The log P and pK were computed using the B3LPYP/6-31G(d) parametrized version of the IEFPCM/MST model. The performance of our method for partition coefficients yielded a root-mean square error of 1.

Simulation-based evaluation of school reopening strategies during COVID-19: A case study of São Paulo, Brazil.

During the coronavirus disease 2019 (COVID-19) pandemic, many countries opted for strict public health measures, including closing schools. After some time, they have started relaxing some of those restrictions. To avoid overwhelming health systems, predictions for the number of new COVID-19 cases need to be considered when choosing a school reopening strategy.

The proinflammatory cytokines TNF-α and IL-6 in lumpfish (Cyclopterus lumpus L.) -identification, molecular characterization, phylogeny and gene expression analyses.

The proinflammatory cytokines TNF-α and IL-6 are important mediators of inflammatory reactions and orchestrators of the immune system in vertebrate. In this study, we have identified TNF-α and IL-6 in lumpfish, molecular characterized them at mRNA and gene level, performed homology modelling and measured their gene expression in different tissues and upon in vitro stimulation. A comprehensive phylogenetic analysis of TNF-α teleost sequences give novel insight into the TNF -α biology.

Effects of Two Sublethal Concentrations of Mercury Chloride on the Morphology and Metallothionein Activity in the Liver of Zebrafish (Danio rerio).

Mercury (Hg) is a highly hazardous pollutant widely used in industrial, pharmaceutical and agricultural fields. Mercury is found in the environment in several forms, elemental, inorganic (iHg) and organic, all of which are toxic. Considering that the liver is the organ primarily involved in the regulation of metabolic pathways, homeostasis and detoxification we investigated the morphological and ultrastructural effects in Danio rerio liver after 96 h exposure to two low HgCl₂ concentrations (7.

Insect glycerol transporters evolved by functional co-option and gene replacement.

Transmembrane glycerol transport is typically facilitated by aquaglyceroporins in Prokaryota and Eukaryota. In holometabolan insects however, aquaglyceroporins are absent, yet several species possess polyol permeable aquaporins. It thus remains unknown how glycerol transport evolved in the Holometabola.

Big bubble deep anterior lamellar keratoplasty: the collagen layer in the wall of the big bubble is unique.

Purpose: In big bubble (BB), deep anterior lamellar keratoplasty intracorneal injection of air separates Descemet's membrane (DM) and the pre-Descemet's layer (Dua's layer [DL]) to create a type 1 BB. We tested the hypothesis that air injection after excision or ablation of DL will fail to produce a BB.

Methods: Nine human sclero-corneal discs were used.

Immunoglobulin isotypes in Atlantic salmon, Salmo salar.

There are three major immunoglobulin (Ig) isotypes in salmonid fish: IgM, IgD and IgT, defined by the heavy chains μ, δ and τ, respectively. As a result of whole genome duplication in the ancestor of the salmonid fish family, Atlantic salmon (Salmo salar) possess two highly similar Ig heavy chain gene complexes (A and B), comprising two μ genes, two δ genes, three intact τ genes and five τ pseudogenes. The μA and μB genes correspond to two distinct sub-populations of serum IgM.

Flow cytometry detection of infectious pancreatic necrosis virus (IPNV) within subpopulations of Atlantic salmon (Salmo salar L.) leucocytes after vaccination and during the time course of experimental infection.

In the present study, intracellular infectious pancreatic necrosis virus (IPNV) in salmon leucocytes was detected by flow cytometry after experimental cohabitant challenge. IPNV vaccinated, non-vaccinated and intraperitoneally (i.p.

Flow cytometry assay for intracellular detection of Infectious Pancreatic Necrosis virus (IPNV) in Atlantic salmon (Salmo salar L.) leucocytes.

Infectious Pancreatic Necrosis virus (IPNV) is traditionally detected in adherent leucocytes using immunofluorescence labelled specific antibodies, PCR or by further cultivation of infected cell material in cell lines. We present a flow cytometry (FCM) assay for detection of intracellular IPNV in salmon leucocytes, where each single cell is analysed for presence of virus. The method is established using in vitro challenge of salmon leucocytes and CHSE-214 cells.

Analysis of polymeric immunoglobulin receptor- and CD300-like molecules from Atlantic salmon.

The polymeric immunoglobulin receptor (pIgR) plays a pivotal role in mucosal immune protection by transporting secretory immunoglobulins to mucosal epithelia, and protecting them from proteolytic degradation. It has been reported that a homolog of the pIgR has a similar role in teleost fish. Considering the role pIgR has in mucosal defenses, this study was initiated to characterize a possible pIgR homolog in Atlantic salmon (Salmo salar) and its relatedness to pIgR of other vertebrates and similar molecules.