Visualizing and Analyzing the Chemical Space of Natural Product Databases for Drug Discovery.

Chemical space is a multidimensional descriptor space that encloses all possible molecules, and at least 1 x 1060 organic substances with a molecular weight below 500 Da are thought to be potentially relevant for drug discovery. Natural products have been the primary source of the new pharmacological entities marketed during the past forty years and continue to be one of the most productive sources for the creation of innovative medications. Chemoinformatics-based computational tools accelerate the drug development process for natural products. Methods including estimating bioactivities, safety profiles, ADME, and natural product likeness measurement have been used. Here, we go over recent developments in chemoinformatic tools designed to visualize, characterize, and expand the chemical space of natural compound data sets using various molecular representations, create visual representations of such spaces, and investigate structure-property relationships within chemical spaces. With an emphasis on drug discovery applications, we evaluate the open-source databases BIOFACQUIM and PeruNPDB as proof of concept.

Does the diversity of vegetation and diatoms correlate with soil and water factors in a tropical cloud forest's complex land use/land cover scenario?

Soil and water characteristics in micro basins with different land uses/land cover (LULC) can influence riparian vegetation diversity, stream water quality, and benthic diatom diversity. We analyzed 18 streams in the upper part of the La Antigua River basin, México, surrounded by cloud forests, livestock pastures, and coffee plantations. Concentrations of P, C, and N were elevated in the humus of forested streams compared to other land uses. In contrast, cations, ammonium, and total suspended solids (TSS) of water streams were higher in pastures and coffee plantations. These results indicate that LULC affects stream chemistry differently across land uses. Vegetation richness was highest (86-133 spp.) in forest streams and lowest in pastures (46-102), whereas pasture streams had the greatest richness of diatoms (9-24), likely due to higher light and temperatures. Some soil and water characteristics correlated with both true diversity and taxonomic diversity; soil carbon exchange capacity (CEC) correlated with vegetation diversity (r = 0.60), while water temperature correlated negatively (r = - 0.68). Diatom diversity was related to soil aluminum (r = - 0.59), magnesium (r = 0.57), water phosphorus (r = 0.88), and chlorophyll (r = 0.75). These findings suggest that land use affects riparian vegetation, while physical and chemical changes influence diatom diversity in stream water and soil. The lack of correlation between vegetation and diatom diversity indicates that one cannot predict the other. This research is an essential first step in understanding how land use changes impact vegetation and diatom diversity in mountain landscapes, providing valuable insights for environmental monitoring and conservation efforts in tropical cloud forests.

Novel Clinical, Immunological, and Metabolic Features Associated with Persistent Post-Acute COVID-19 Syndrome.

The coronavirus disease 2019 (COVID-19) survivors are frequently observed to present persistent symptoms constituting what has been called "post-acute COVID-19 syndrome" (PACS) or "long COVID-19". Some clinical risk factors have been identified to be associated with PACS development; however, specific mechanisms responsible for PACS pathology remain unknown. This study investigates clinical, immunological, and metabolomic risk factors associated with post-acute COVID-19 syndrome (PACS) in 51 patients, assessed 7-19 months after acute infection. Among the participants, 62.7% were male and 37.2% were female, with an average age of 47.8 years. At the follow-up, 37.2% met the criteria for PACS, revealing significant differences in immunological and metabolomic profiles at the time of acute infection. Patients with PACS were characterized by elevated levels of mature low-density granulocytes (LDGs), interleukin-8 (IL-8), pyruvate, pseudouridine, and cystine. Baseline multivariate analysis showed increased pyruvate and decreased alpha tocopherol levels. At follow-up, there was a decrease in absolute B lymphocytes and an increase in non-classical monocytes and 3-hydroxyisovaleric acid levels. These findings suggest that specific immunological and metabolomic markers during acute infection can help identify patients at higher risk of developing persistent PACS.

Chemoinformatic Characterization of NAPROC-13: A Database for Natural Product 13C NMR Dereplication.

Natural products (NPs) are secondary metabolites of natural origin with broad applications across various human activities, particularly the discovery of bioactive compounds. Structural elucidation of new NPs entails significant cost and effort. On the other hand, the dereplication of known compounds is crucial for the early exclusion of irrelevant compounds in contemporary pharmaceutical research. NAPROC-13 stands out as a publicly accessible database, providing structural and 13C NMR spectroscopic information for over 25 000 compounds, rendering it a pivotal resource in natural product (NP) research, favoring open science. This study seeks to quantitatively analyze the chemical content, structural diversity, and chemical space coverage of NPs within NAPROC-13, compared to FDA-approved drugs and a very diverse subset of NPs, UNPD-A. Findings indicated that NPs in NAPROC-13 exhibit properties comparable to those in UNPD-A, albeit showcasing a notably diverse array of structural content, scaffolds, ring systems of pharmaceutical interest, and molecular fragments. NAPROC-13 covers a specific region of the chemical multiverse (a generalization of the chemical space from different chemical representations) regarding physicochemical properties and a region as broad as UNPD-A in terms of the structural features represented by fingerprints.

FIRST RECORDS OF AEDES TORMENTOR AND CULEX PANOCOSSA AS A RESULT OF VECTOR SURVEILLANCE ACTIVITIES CONDUCTED DURING THE CHARACTERIZATION OF FOCI OF EASTERN EQUINE ENCEPHALITIS IN TAMAULIPAS, MEXICO.

We report the 1st records of Aedes tormentor and Culex panocossa throughout vector surveillance events carried out in putative foci of eastern equine encephalitis in Tamaulipas, Mexico. Formerly, Ae. tormentor had been reported in, at least, 2 Central American countries and Mexico. In Mexico, reports were from the states of Campeche, Chiapas, Quintana Roo, and Veracruz. Records of Ae. tormentor in these 4 Neotropical states were recently reviewed and eliminated; thus, the southernmost geographic distribution for this species is considered to be the state of Tamaulipas Mexico in its neotropical zone. Further, Cx. panocossa had been collected in Guerrero, Tabasco, and Veracruz. In Tamaulipas, there are 82 species of mosquitoes, being the 4th state accounting for the highest mosquito species diversity of 11 states in which comprehensive studies have been conducted on the subject of mosquito distribution.

Neglected Tropical Diseases: A Chemoinformatics Approach for the Use of Biodiversity in Anti-Trypanosomatid Drug Discovery.

The development of new treatments for neglected tropical diseases (NTDs) remains a major challenge in the 21st century. In most cases, the available drugs are obsolete and have limitations in terms of efficacy and safety. The situation becomes even more complex when considering the low number of new chemical entities (NCEs) currently in use in advanced clinical trials for most of these diseases. Natural products (NPs) are valuable sources of hits and lead compounds with privileged scaffolds for the discovery of new bioactive molecules. Considering the relevance of biodiversity for drug discovery, a chemoinformatics analysis was conducted on a compound dataset of NPs with anti-trypanosomatid activity reported in 497 research articles from 2019 to 2024. Structures corresponding to different metabolic classes were identified, including terpenoids, benzoic acids, benzenoids, steroids, alkaloids, phenylpropanoids, peptides, flavonoids, polyketides, lignans, cytochalasins, and naphthoquinones. This unique collection of NPs occupies regions of the chemical space with drug-like properties that are relevant to anti-trypanosomatid drug discovery. The gathered information greatly enhanced our understanding of biologically relevant chemical classes, structural features, and physicochemical properties. These results can be useful in guiding future medicinal chemistry efforts for the development of NP-inspired NCEs to treat NTDs caused by trypanosomatid parasites.

Validation of the delirium diagnostic tool-provisional (DDT-Pro) in geriatric medical inpatients with diagnostic permutations of the 3Ds with and without delirium.

OBJECTIVE: Validations of brief delirium tools have not included analysis of psychiatric disorders comorbidities or control groups. We validated the Delirium Diagnostic Tool-Provisional (DDT-Pro) in 422 geriatric inpatients with high incidence of depression and/or dementia. METHODS: Cross-sectional study using two delirium reference standards, DSM-5-TR and Delirium Rating Scale-Revised-98 (DRS-R98). We assessed concurrent and construct DDT-Pro validity too. RESULTS: There were 117 (27.7%) delirium cases using DDT-Pro, 104 (24.6%) per DSM-5-TR and 93 (22.0%) per DRS-R98; 133 patients (31.5%) had depression and 105 (24.9%) dementia, some comorbid with delirium. DDT-Pro accuracy (AUC under ROC curve) ranges were 88.3-95.9% vs DSM-5-TR and 92.7-95.0% vs DRS-R98 for whole sample and four diagnostic groups, without statistical differences. DDT-Pro ≤6 had the most balanced sensitivity-specificity for delirium diagnosis against both DSM-5-TR and DRS-R98 with similar specificity but higher sensitivity for DRS-R98 than DSM-5-TR delirium, with the highest values in patients with depression and dementia (≥92% sensitivity, ≥81% specificity). Positive and negative likelihood ratios support diagnostic strength. Concurrent validity was high reflected by significant correlations (p < 0.001) of DDT-Pro total and item scores with DRS-R98 and Delirium Frontal Index scores, highest in groups with comorbid depression and/or dementia. The DDT-Pro represented a single construct for delirium demonstrated by one factor with high item loadings and high internal consistency reliability of its items. CONCLUSIONS: The DDT-Pro demonstrated strong performance metrics in general hospital elderly inpatients with preexisting depression and/or dementia, which is unique among brief delirium tools. Its optimized cutoff score was the same as in other populations.

Exploring the persistence of the fluorinated thiolate 2,3,5,6-S(C6F4H-4) motif to establish πF-πF stacking in metal complexes: a crystal engineering perspective.

π-π stacking interactions are versatile because they are involved in many processes, such as protein folding, DNA stacking, and drug recognition. However, from the point of view of crystal engineering, there is an incipient knowledge of its exploitation. A comparison of these interactions with hydrogen bonds shows a huge difference in their employment as a reliable non-covalent interaction. And different reasons can be listed to explain why hydrogen bonding can be considered a more robust interaction than π-π stacking. For instance, hydrogen bonds encompass a wide energy range (25-40 kJ mol-1). From this, these interactions can be classified as strong, moderate, and weak. Hence, the first two can be considered highly to moderately directional to be exploited in crystal engineering. This aspect is relevant for them to be used in a relatively reliably way in this area of supramolecular chemistry. On the other hand, in the case of π-π stacking, the energy range is 0-10 kJ mol-1, thus implying that hydrogen bonds or any other energetically more robust contact would predominate in the competition for establishing packing interactions in a given arrangement. In this sense, if stacking is pretended to be exploited from the point of view of crystal engineering, one of the points that must be ensured is that this interaction will be the one energetically predominant. However, although there are other factors to consider, it seems that energetics is the dominant one. In this line, our research group has obtained and studied many single-crystalline structures of coordination and organometallic compounds containing fluorinated thiolates. This being particularly true in the case of the thiolate 2,3,5,6-S(C6F4H-4) bound to different metals, where it has been observed that they preferentially tend to establish πF-πF stacking interactions, results that have been reported in several papers. Thus, from this perspective, we have explored, using ConQuest (CCDC) a number of structures to observe how feasible is to find stacking in coordination and organometallic compounds containing the thiolate 2,3,5,6-S(C6F4H-4).

Valorization of Kraft Lignins from Different Poplar Genotypes as Vegetable Oil Structuring Agents via Electrospinning for Biolubricant Applications.

This work explores the use of Kraft lignins sourced from different poplar genotypes (Populus alba L. "PO-10-10-20" and Populus × canadensis "Ballotino") isolated by selective acid precipitation (at pHs 5 and 2.5) to produce electrospun nanostructures that can be further employed for structuring vegetable oils. This approach offers a new avenue for converting these waste materials into high-value-added ingredients of eco-friendly structured lubricants. Electrospinning of poplar Kraft lignin (PKL)/cellulose acetate (CA) solutions yielded homogeneous beaded nanofiber mats that were able to generate stable dispersions when they were blended with different vegetable oils (castor, soybean, and high-oleic sunflower oils). Electrospun PKL/CA nanofiber mats with larger average fiber diameters were achieved using the lignins isolated at pH 5. Dispersions of PKL/CA nanofibers in vegetable oils presented gel-like viscoelastic characteristics and shear-thinning flow behavior, which slightly differ depending on the nanofiber morphological properties and can be tuned by selecting the poplar lignin genotype and precipitation pH. The rheological properties and tribological performance of PKL/CA nanofibers suitably dispersed in vegetable oils were found to be comparable to those obtained for conventional lubricating greases. Additionally, lignin nanofibers confer suitable oxidative stability to the ultimate formulations to different extents depending on the vegetable oil used.

Effectiveness of mass trapping interventions using autocidal gravid ovitraps (AGO) for the control of the dengue vector, Aedes (Stegomyia) aegypti, in Northern Mexico.

BACKGROUND: Mosquito-borne diseases, such as malaria, dengue, Zika and chikungunya, pose significant public health threats in tropical and subtropical regions worldwide. To mitigate the impact of these diseases on human health, effective vector surveillance and control strategies are necessary. Traditional vector control methods, which rely on chemical agents such as insecticides and larvicides, face challenges such as resistance and environmental concerns. Consequently, there has been a push to explore novel surveillance and control tools. Mass trapping interventions have emerged as a promising and environmentally friendly approach to reducing the burden of mosquito-borne diseases. This study assessed mass-trapping interventions using autocidal gravid ovitraps (AGOs) on Aedes aegypti populations in Reynosa, Tamaulipas, Mexico. METHODS: Four neighborhoods were selected to evaluate the effects of three treatments: AGO mass-trapping, integrated vector control (IVC), which included source reduction and the application of chemical larvicide and adulticide, and AGO + IVC on Ae. aegypti populations. A control area with no interventions was also included. The effectiveness of the interventions was evaluated by comparing Ae. aegypti abundance between the pre-treatment period (9 weeks) and the post-treatment period (11 weeks) for each treatment. RESULTS: Only treatment using AGO mass trapping with an 84% coverage significantly reduced Ae. aegypti female populations by 47%, from 3.75 ± 0.32 to 1.96 ± 0.15 females/trap/week. As expected, the abundance of Ae. aegypti in the control area did not differ from the pre- and post-treatment period (range of 4.97 ± 0.59 to 5.78 ± 0.53); Ae. aegypti abundance in the IVC treatment was 3.47 ± 0.30 before and 4.13 ± 0.35 after, which was not significantly different. However, Ae. aegypti abundance in the AGO + IVC treatment increased from 1.43 ± 0.21 before to 2.11 ± 0.20 after interventions; this increase may be explained in part by the low AGO (56%) coverage. CONCLUSIONS: This is the first report to our knowledge on the effectiveness of mass-trapping interventions with AGOs in Mexico, establishing AGOs as a potential tool for controlling Ae. aegypti in Northeastern Mexico when deployed with sufficient coverage.

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. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.

Predicting Rail Corrugation Based on Convolutional Neural Networks Using Vehicle's Acceleration Measurements.

This paper presents a deep learning approach for predicting rail corrugation based on on-board rolling-stock vertical acceleration and forward velocity measurements using One-Dimensional Convolutional Neural Networks (CNN-1D). The model's performance is examined in a 1:10 scale railway system at two different forward velocities. During both the training and test stages, the CNN-1D produced results with mean absolute percentage errors of less than 5% for both forward velocities, confirming its ability to reproduce the corrugation profile based on real-time acceleration and forward velocity measurements. Moreover, by using a Gradient-weighted Class Activation Mapping (Grad-CAM) technique, it is shown that the CNN-1D can distinguish various regions, including the transition from damaged to undamaged regions and one-sided or two-sided corrugated regions, while predicting corrugation. In summary, the results of this study reveal the potential of data-driven techniques such as CNN-1D in predicting rails' corrugation using online data from the dynamics of the rolling-stock, which can lead to more reliable and efficient maintenance and repair of railways.

Synthesis, biosimulation and pharmacological evaluation of benzimidazole derivatives with antihypertensive multitarget effect.

In this study, we synthesized a series of seven benzimidazole derivatives incorporating the structural acidic framework of angiotensin II (Ang II) type 1 receptor (AT1R) antagonists (ARA-II) employing a three-step reaction sequence. The chemical structures were confirmed by 1H NMR, 13C NMR and mass spectral data. Through biosimulation, compounds 1-7 were identified as computational safe hits, thus, best candidates underwent ex vivo testing against two distinct mechanisms implicated in hypertension: antagonism of the Ang II type 1 receptor and the blockade of calcium channel. Molecular docking studies helped to understand at the molecular level the dual vasorelaxant effects with the recognition sites of the AT1R and the L-type calcium channel. In an in vivo spontaneously hypertensive rat model (SHR), intraperitoneally administration of compound 1 at 20 mg/kg resulted in a 25 % reduction in systolic blood pressure, demonstrating both ex vivo vasorelaxant action and in vivo antihypertensive multitarget efficacy. ©2024 Elsevier.

De Novo Design of Inhibitors of DNA Methyltransferase 1: A Critical Comparison of Ligand- and Structure-Based Approaches.

Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy that was used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and warrants further exploration. This study aimed to continue exploring the potential of de novo design to build epigenetic-focused libraries targeted toward DNMT1. Herein, we report the results of an in-depth and critical comparison of ligand- and structure-based de novo design of screening libraries focused on DNMT1. The newly designed chemical libraries focused on DNMT1 are freely available on GitHub.

Domestic Dog Infection with Trypanosoma cruzi from Northern and Southern Regions of Mexico.

Background: Chagas disease or American trypanosomiasis, caused by Trypanosoma cruzi and vectored by triatomines, affects millions of people worldwide. In endemic countries including Mexico, infections in domestic animals, such as dogs, may affect the risk of human disease when they serve as a source of infection to vectors that subsequently infect humans. Materials and Methods: We conducted a cross-sectional study of 296 dogs from two cities near the northern and southern borders of Mexico: Reynosa, Tamaulipas, and Tuxtla Gutierrez, Chiapas. Infection was measured based on testing of blood using T. cruzi quantitative PCR (qPCR) and up to three antibody detection assays. The StatPak immunochromatographic assay was used to screen samples and the indirect fluorescent antibody (IFA) and multiplex microsphere immunoassay (MIA) tests were used as secondary tests on all samples that screened positive and a subset of negatives. Serologic positivity was defined based on reactivity on at least two independent tests. Results: Of the 280 samples tested for parasite DNA, two (0.7%) were positive, one of which (0.4%) was confirmed as T. cruzi discrete typing unit TcIV. Overall, 72 (24.3%) samples were reactive for T. cruzi antibodies via StatPak of which 8 were also positive using MIA and 2 were also positive using IFA (including one of the PCR-positive dogs). Overall, nine dogs (3.4%) met study criteria of positivity based on either/both serology or PCR tests. Positive dogs were found in both regions of Mexico; five (2.7%) from Reynosa and four (3.6%) from Tuxtla Gutierrez. We found no association between infection status and state of origin, sex, age group, breed group, neighborhood, and whether other pets lived in the home. Conclusion: Our results re-emphasize dogs' utility as sentinels for T. cruzi in Mexico and underscore the need for improved veterinary diagnostic tests and parasite surveillance at the household level in endemic countries.

Autoantibodies Neutralizing GM-CSF in HIV-Negative Colombian Patients Infected with Cryptococcus gattii and C. neoformans.

BACKGROUND: Cryptococcosis is a life-threatening disease caused by Cryptococcus neoformans or C. gattii. Neutralizing autoantibodies (auto-Abs) against granulocyte-macrophage colony-stimulating factor (GM-CSF) in otherwise healthy adults with cryptococcal meningitis have been described since 2013. We searched for neutralizing auto-Abs in sera collected from Colombian patients with non-HIV-associated cryptococcosis in a retrospective national cohort from 1997 to 2016. METHODS: We reviewed clinical and laboratory records and assessed the presence of neutralizing auto-Abs against GM-CSF in 30 HIV negative adults with cryptococcosis (13 caused by C. gattii and 17 caused by C. neoformans). RESULTS: We detected neutralizing auto-Abs against GM-CSF in the sera of 10 out of 13 (77%) patients infected with C. gattii and one out of 17 (6%) patients infected with C. neoformans. CONCLUSIONS: We report eleven Colombian patients diagnosed with cryptococcosis who had auto-Abs that neutralize GM-CSF. Among these patients, ten were infected with C. gattii and only one with C. neoformans.

Food Chemicals and Epigenetic Targets: An Epi Food Chemical Database.

There is increasing awareness of epigenetics's importance in understanding disease etiologies and developing novel therapeutics. An increasing number of publications in the past few years reflect the renewed interest in epigenetic processes and their relationship with food chemicals. However, there needs to be a recent study that accounts for the most recent advances in the area by associating the chemical structures of food and natural product components with their biological activity. Here, we analyze the status of food chemicals and their intersection with natural products in epigenetic research. Using chemoinformatics tools, we compared quantitatively the chemical contents, structural diversity, and coverage in the chemical space of food chemicals with reported epigenetic activity. As part of this work, we built and curated a compound database of food and natural product chemicals annotated with structural information, an epigenetic target activity profile, and the main source of the food chemical or natural product, among other relevant features. The compounds are cross-linked with identifiers from other major public databases such as FooDB and the collection of open natural products, COCONUT. The compound database, the "Epi Food Chemical Database", is accessible in HTML and CSV formats at https://github.com/DIFACQUIM/Epi_food_Chemical_Database.

Putative mechanism of a multivitamin treatment against insulin resistance.

Insulin resistance is caused by the abnormal secretion of proinflammatory cytokines in adipose tissue, which is induced by an increase in lipid accumulation in adipocytes, hepatocytes, and myocytes. The inflammatory pathway involves multiple targets such as nuclear factor kappa B, inhibitor of nuclear factor κ-B kinase, and mitogen-activated protein kinase. Vitamins are micronutrients with anti-inflammatory activities that have unclear mechanisms. The present study aimed to describe the putative mechanisms of vitamins involved in the inflammatory pathway of insulin resistance. The strategy to achieve this goal was to integrate data mining and analysis, target prediction, and molecular docking simulation calculations to support our hypotheses. Our results suggest that the multitarget activity of vitamins A, B1, B2, B3, B5, B6, B7, B12, C, D3, and E inhibits nuclear factor kappa B and mitogen-activated protein kinase, in addition to vitamins A and B12 against inhibitor of nuclear factor κ-B kinase. The findings of this study highlight the pharmacological potential of using an anti-inflammatory and multitarget treatment based on vitamins and open new perspectives to evaluate the inhibitory activity of vitamins against nuclear factor kappa B, mitogen-activated protein kinase, and inhibitor of nuclear factor κ-B kinase in an insulin-resistant context.