The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods.

ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 and 2019 Nucleic Acids Research Database Issues. Since its introduction in 2009, ChEMBL's content has changed dramatically in size and diversity of data types. Through incorporation of multiple new datasets from depositors since the 2019 update, ChEMBL now contains slightly more bioactivity data from deposited data vs data extracted from literature. In collaboration with the EUbOPEN consortium, chemical probe data is now regularly deposited into ChEMBL. Release 27 made curated data available for compounds screened for potential anti-SARS-CoV-2 activity from several large-scale drug repurposing screens. In addition, new patent bioactivity data have been added to the latest ChEMBL releases, and various new features have been incorporated, including a Natural Product likeness score, updated flags for Natural Products, a new flag for Chemical Probes, and the initial annotation of the action type for ∼270 000 bioactivity measurements.

Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs.

The safety of marketed drugs is an ongoing concern, with some of the more frequently prescribed medicines resulting in serious or life-threatening adverse effects in some patients. Safety-related information for approved drugs has been curated to include the assignment of toxicity class(es) based on their withdrawn status and/or black box warning information described on medicinal product labels. The ChEMBL resource contains a wide range of bioactivity data types, from early "Discovery" stage preclinical data for individual compounds through to postclinical data on marketed drugs; the inclusion of the curated drug safety data set within this framework can support a wide range of safety-related drug discovery questions. The curated drug safety data set will be made freely available through ChEMBL and updated in future database releases.

ChEMBL: towards direct deposition of bioassay data.

ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.

BET 1: Intravenous tranexamic acid in the treatment of acute epistaxis.

A short-cut review was carried out to establish whether intravenous tranexamic acid is beneficial in managing acute epistaxis. Seven papers were found in Medline, Embase and the Cochrane Library using the reported searches, but none presented any evidence to answer the clinical question. It is concluded that there is no evidence to support or refute the use of intravenous tranexamic acid in acute epistaxis and that local advice should be followed.

A checklist of the 67 mosquito species of Ontario, Canada.

We provide an updated checklist of 67 endemic mosquito species known from Ontario, Canada. Nine endemic species are added to the checklist found in Darsie and Ward (2005) : Aedes cantator, Ae. churchillensis, Ae. nigripes, Ae. pullatus, Anopheles perplexens, An. crucians, An. smaragdinus, Culex erraticus, and Cx. salinarius. Only 4 specimens of Ae. albopictus have been recorded in Ontario since 2001 despite concerted efforts to find this species; therefore, it is considered an "accidental" species and is excluded from the checklist.

Towards evidence based emergency medicine: Best BETs from the Manchester Royal Infirmary. BET 1: Emergency physician performed 2-point bedside compression ultrasound for deep venous thrombosis.

A short cut review was carried out to establish the diagnostic utility of Emergency Physician performed ultrasound in confirming or refuting the diagnosis of deep vein thrombosis compared with a radiology scan. A systematic review incorporating 16 studies and two studies published subsequently were found to be relevant to the question. The clinical bottom line was that some studies demonstrated high sensitivity and specificity compared with the reference standard but this finding was not universal.

Towards evidence-based emergency medicine: best BETs from the Manchester Royal Infirmary. BET 3: Management of paediatric minor head injuries: safe discharge?

A short-cut review was carried out to establish whether the finding of a normal cranial CT scan, in a child with a history of minor head injury, a Glasgow coma scale (GCS) score of 15 and normal neurological examination could facilitate safe discharge from hospital. Ninety-eight articles were found using the reported search and a further two papers were found from the references of selected papers. A total of 11 trials were included with one prospective cohort study including 13,543 patients. The authors, date and country of publication, patient group studied, study type, relevant outcomes, results and study weaknesses of these papers are tabulated (table 3). It is concluded that in the absence of any coagulation problems, a child who presents following a minor head injury with a GCS of 15, normal neurological examination and a normal CT scan can be safely discharged to the care of a capable parent.

School of cheminformatics in Latin America.

We report the major highlights of the School of Cheminformatics in Latin America, Mexico City, November 24-25, 2022. Six lectures, one workshop, and one roundtable with four editors were presented during an online public event with speakers from academia, big pharma, and public research institutions. One thousand one hundred eighty-one students and academics from seventy-nine countries registered for the meeting. As part of the meeting, advances in enumeration and visualization of chemical space, applications in natural product-based drug discovery, drug discovery for neglected diseases, toxicity prediction, and general guidelines for data analysis were discussed. Experts from ChEMBL presented a workshop on how to use the resources of this major compounds database used in cheminformatics. The school also included a round table with editors of cheminformatics journals. The full program of the meeting and the recordings of the sessions are publicly available at https://www.youtube.com/@SchoolChemInfLA/featured .

Malaria in highlands of Ecuador since 1900.

A recent epidemic of malaria in the highlands of Bolivia and establishment of multiple Anopheles species mosquitoes in the highlands of Ecuador highlights the reemergence of malaria in the Andes Mountains in South America. Because malaria was endemic to many highland valleys at the beginning of the 20th century, this review outlines the 20th century history of malaria in the highlands of Ecuador, and focuses on its incidence (e.g., geographic distribution) and elimination from the northern highland valleys of Pichincha and Imbabura and the role of the Guayaquil to Quito railway in creating highland larval habitat and inadvertently promoting transportation of the vector and parasite. Involvement of control organizations in combating malaria in Ecuador is also outlined in a historical context.

Zika Virus Replication in a Mast Cell Model is Augmented by Dengue Virus Antibody-Dependent Enhancement and Features a Selective Immune Mediator Secretory Profile.

Zika virus and dengue virus are evolutionarily related and structurally similar mosquito-borne Flaviviruses. These congruencies can lead to cross-reactive antibody binding, whereby antibodies generated from previous dengue virus immunity can augment Zika virus replication in vitro. This phenomenon, termed antibody-dependent enhancement, may participate in the clinical manifestations detected in areas with Flavivirus cocirculations where Zika virus is endemic; however, a causal relationship has yet to be determined. The KU812 mast cell/basophil line was integral in identifying the first Flavivirus infection in mast cells and serves as an effective in vitro model to study dengue virus antibody-dependent enhancement. Mast cells, sentinel white blood cells intrinsic in coordinating early immune defenses, are characteristically situated in the intradermal space and are therefore among the first immune cells interfaced with blood-feeding mosquitoes. Here, we tested whether KU812 cells were permissive to Zika virus, how previous dengue virus immunity might augment Zika virus infection, and whether either condition induces an immunological response. We report an antibody-dependent enhancement effect of Zika virus infection in KU812 cells across multiple time points (48, 72, and 96 hours postinfection [hpi]) and a range of multiplicities of infection (4.0 × 10-3 to 4) using various concentrations of cross-reactive dengue virus monoclonal antibodies (D11C and 1.6D). This antigen-specific antibody-mediated infection was selectively coupled to chemokine ligand 5 (CCL5), interleukin 1ß (IL-1ß), and C-X-C motif chemokine ligand 10 (CXCL10) secretion and a reduction in granzyme B (GrB) release. Therefore, mast cells and/or basophils may significantly augment Zika virus infection in the context of preexisting dengue virus immunity. IMPORTANCE Antibodies generated against one dengue serotype can enhance infection of another by a phenomenon called antibody-dependent enhancement (ADE). Additionally, antigenic similarities between Zika and dengue viruses can promote Zika virus infection by way of ADE in vitro using these very same anti-dengue antibodies. We used the KU812 cell line to demonstrate for the first time that anti-dengue antibodies enhanced infectious Zika virus replication in a mast cell model and specifically increased CCL5, CXCL10, and IL-1ß, while also impairing granzyme B secretion. Furthermore, enhanced Zika virus infection and selective mediator release were mechanistically dependent on fragment crystallizable gamma receptor II (FcγRII). These findings establish a new model for Zika virus research and a new subcategory of immune cells previously unexplored in the context of Zika virus enhancement while being some of the very first immune cells likely to meet a blood-feeding infected mosquito.

New highland distribution records of multiple Anopheles species in the Ecuadorian Andes.

BACKGROUND: Several recent climate change reviews have stressed the possibility of some malaria vectors occupying regions of higher altitudes than previously recorded. Indeed, highland malaria has been observed in several African nations, possibly attributable to changes in land use, vector control and local climate. This study attempts to expand the current knowledge of the distribution of common Anopheles species in Ecuador, with particular attention to highland regions (> 500 m) of the Andes. METHODS: Extensive field collections of larvae were undertaken in 2008, 2009 and 2010 throughout all regions of Ecuador (except the lower-altitude Amazonian plain) and compared to historical distribution maps reproduced from the 1940s. Larvae were identified using both a morphological key and sequencing of the 800 bp region of the CO1 mitochondrial gene. In addition, spatial statistics (Getis-Ord Hotspot Analysis: Gi*) were used to determine high and low-density clusters of each species in Ecuador. RESULTS: Distributions have been updated for five species of Anopheles in Ecuador: Anopheles albimanus, Anopheles pseudopunctipennis, Anopheles punctimacula, Anopheles eiseni and Anopheles oswaldoi s.l.. Historical maps indicate that An. pseudopunctipennis used to be widespread in highland Andean valleys, while other species were completely restricted to lowland areas. By comparison, updated maps for the other four collected species show higher maximum elevations and/or more widespread distributions in highland regions than previously recorded. Gi* analysis determined some highland hot spots for An. albimanus, but only cold spots for all other species. CONCLUSIONS: This study documents the establishment of multiple anopheline species in high altitude regions of Ecuador, often in areas where malaria eradication programs are not focused.

A modified Centers for Disease Control and Prevention gravid trap for easier mosquito collection.

The original Centers for Disease Control and Prevention (CDC) gravid trap, with its mesh collection bag, can cause considerable damage to the captured mosquitoes. In an effort to reduce this damage and keep costs at a minimum, we modified our existing CDC gravid traps to accept a collection cup from a CDC light trap. This modification allowed for easier transport, freezing, storage, and removal of the mosquitoes. Modifying the CDC gravid traps takes little expertise or resources and can be completed quickly.

Network integration and modelling of dynamic drug responses at multi-omics levels.

Uncovering cellular responses from heterogeneous genomic data is crucial for molecular medicine in particular for drug safety. This can be realized by integrating the molecular activities in networks of interacting proteins. As proof-of-concept we challenge network modeling with time-resolved proteome, transcriptome and methylome measurements in iPSC-derived human 3D cardiac microtissues to elucidate adverse mechanisms of anthracycline cardiotoxicity measured with four different drugs (doxorubicin, epirubicin, idarubicin and daunorubicin). Dynamic molecular analysis at in vivo drug exposure levels reveal a network of 175 disease-associated proteins and identify common modules of anthracycline cardiotoxicity in vitro, related to mitochondrial and sarcomere function as well as remodeling of extracellular matrix. These in vitro-identified modules are transferable and are evaluated with biopsies of cardiomyopathy patients. This to our knowledge most comprehensive study on anthracycline cardiotoxicity demonstrates a reproducible workflow for molecular medicine and serves as a template for detecting adverse drug responses from complex omics data.

Geospatial Analysis and Seasonal Distribution of West Nile Virus Vectors (Diptera: Culicidae) in Southern Ontario, Canada.

The purpose of this study was to establish geospatial and seasonal distributions of West Nile virus vectors in southern Ontario, Canada using historical surveillance data from 2002 to 2014. We set out to produce mosquito abundance prediction surfaces for each of Ontario's thirteen West Nile virus vectors. We also set out to determine whether elevation and proximity to conservation areas and provincial parks, wetlands, and population centres could be used to improve our model. Our results indicated that the data sets for Anopheles quadrimaculatus, Anopheles punctipennis, Anopheles walkeri, Culex salinarius, Culex tarsalis, Ochlerotatus stimulans, and Ochlerotatus triseriatus were not suitable for geospatial modelling because they are randomly distributed throughout Ontario. Spatial prediction surfaces were created for Aedes japonicus and proximity to wetlands, Aedes vexans and proximity to population centres, Culex pipiens/restuans and proximity to population centres, Ochlerotatus canadensis and elevation, and Ochlerotatus trivittatus and proximity to population centres using kriging. Seasonal distributions are presented for all thirteen species. We have identified both when and where vector species are most abundant in southern Ontario. These data have the potential to contribute to a more efficient and focused larvicide program and West Nile virus awareness campaigns.

A large-scale dataset of in vivo pharmacology assay results.

ChEMBL is a large-scale, open-access drug discovery resource containing bioactivity information primarily extracted from scientific literature. A substantial dataset of more than 135,000 in vivo assays has been collated as a key resource of animal models for translational medicine within drug discovery. To improve the utility of the in vivo data, an extensive data curation task has been undertaken that allows the assays to be grouped by animal disease model or phenotypic endpoint. The dataset contains previously unavailable information about compounds or drugs tested in animal models and, in conjunction with assay data on protein targets or cell- or tissue- based systems, allows the investigation of the effects of compounds at differing levels of biological complexity. Equally, it enables researchers to identify compounds that have been investigated for a group of disease-, pharmacology- or toxicity-relevant assays.

West Nile virus in Ontario, Canada: A twelve-year analysis of human case prevalence, mosquito surveillance, and climate data.

West Nile Virus (WNV) first arrived in Ontario, Canada in 2001 and has since spread throughout most of the province, causing disease in humans. The provincial government established a province-wide surveillance program to monitor WNV transmission throughout the 36 regional health units. Here we have acquired records of WNV human and mosquito surveillance from 2002 to 2013 to describe seasonal and geographic trends in WNV activity in southern Ontario. Additionally, we obtained climate data from seven municipalities to investigate how temperature and precipitation affect WNV transmission dynamics. We identified a strong quadratic relationship between the number of confirmed human cases and positive Culex mosquito pools recorded at the end of each year (R2 = 0.9783, p < 0.001). Using Spearman rank correlation tests, we identified that the minimum infection rate of Culex pipiens/restuans pools are the strongest predictor of human cases at a 1 week lag period. We also identified positive correlations between minimum infection rates, temperature, vector abundance, and cumulative precipitation. Global Moran's I index indicates strong positive autocorrelation and clustering of positive Culex pool counts in southern Ontario. Local indicators of spatial association tests revealed a total of 44 high-high and 1 high-low trap locations (n = 680). In the current work we have identified when and where hot spots of WNV activity have occurred in southern Ontario. The municipalities surrounding the western shore of the Lake Ontario and Windsor-Essex County have the largest records of positive mosquitoes and human cases. We identified that positive mosquitoes are a strong indicator of human cases to follow in the coming weeks. An epidemic action threshold of cumulative positive Culex pools was established, allowing Ontario public health officials to predict an epidemic at epidemiological week 34 (rho = 0.90, p < 0.001). These data have the potential to contribute to more efficient larvicide programs and awareness campaigns for the public.

Genic capture and the genetic basis of sexually selected traits in the zebra finch.

The lek paradox, in which female choice erodes genetic variation in male sexually selected traits, is a fundamental issue in sexual selection. If females gain only genetic benefits from preferentially having their ova fertilized by males with particular traits, what maintains variation in these traits? Under strong directional selection mediated through mate choice, the alleles for beneficial male traits are expected to go to fixation and exhibit little variation. A theoretical solution to the lek paradox is the genic capture hypothesis which states that: costly male traits subject to female choice are condition dependent, that male condition is dependent on genes at many loci and exhibits additive genetic variance, and that positive genetic correlations exist between sexually selected traits and condition. Using a captive population of the zebra finch Taeniopygia guttata, we tested two key predictions from this model: (1) that genetic variance exists in beak color which is a sexually selected trait, but also in condition and immune function, and (2) that positive genetic correlations exist between condition and beak color, and between beak color, condition, and immune function. Genetic parameters were estimated from a large breeding experiment involving 81 sires, 972 offspring, a pedigree of 1526 individuals, using the animal model. We employed the following index of body condition: residuals from a log-log plot of body mass on tarsus length following a standardized and extended period of exercise, in which residual mass is known to reflect fat and protein reserves. Our results were broadly consistent with the genic capture hypothesis because we found (1) additive genetic variation in beak color and immune function and condition, and (2) positive genetic correlations between condition and beak color, and between condition, beak color, and several assays of immune responsiveness. However, both of these results need qualification. In the first case we identified an important general problem in estimating the coefficient of additive genetic variance (CVA) in body condition. In the second case, although most of the genetic correlations were positive as predicted, only some were statistically significant, possibly due to our relatively small sample sizes, because genetic correlations typically have large standard errors and therefore require very large samples to be statistically significant. The statistically significant, positive genetic correlations included those between beak color and immune function (response to tetanus), and between immune function (response to tetanus) and condition, both of which indicate that females gain good genes from mating with males in good condition and/or with a redder beak color. We discuss the implications of our results for devising more rigorous but pragmatic tests of the genic capture hypothesis.

Establishment of Ochlerotatus japonicus (Diptera: Culicidae) in Ontario, Canada.

Ochlerotatus (Finlaya) japonicus (Theobold) is newly established in Ontario, Canada. It was first discovered in 2001 during the province-wide West Nile virus mosquito surveillance program implemented by the Ontario Ministry of Health and Long Term Care. Although the numbers of adults trapped in CDC light traps were low in 2001 and 2002, they increased during the 2003 and 2004 surveillance seasons. Oc. japonicus larvae also have been collected in large numbers in the Niagara Peninsula in a variety of natural and artificial containers. The number of health units with records for Oc. japonicus has increased over the 4 yr of surveillance, illustrating the ability of this species to rapidly extend its range. As a potential arboviral bridge vector, its establishment in Ontario requires further study and should be considered a public health concern.

Zika Virus: Quantification, Propagation, Detection, and Storage.

Zika virus (ZIKV), belonging to the family Flaviviridae, genus Flavivirus, is an arthropod-borne virus that was first discovered from the Zika forest in Uganda in 1947. Recent outbreaks in South America have linked ZIKV to cases of microcephaly and Guillain-Barré syndrome in humans. With the increased interest in ZIKV, protocols must be established to facilitate proper research. Here we describe the laboratory techniques required to quantify, propagate, and store ZIVK. We also review the proper safety protocol for the handling of ZIKV, which is classified as a Biosafety Level 2 pathogen by the United States Centers for Disease Control and Prevention. © 2016 by John Wiley & Sons, Inc.