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1.
Nucleic Acids Res ; 51(D1): D1276-D1287, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36484092

RESUMO

DrugCentral monitors new drug approvals and standardizes drug information. The current update contains 285 drugs (131 for human use). New additions include: (i) the integration of veterinary drugs (154 for animal use only), (ii) the addition of 66 documented off-label uses and iii) the identification of adverse drug events from pharmacovigilance data for pediatric and geriatric patients. Additional enhancements include chemical substructure searching using SMILES and 'Target Cards' based on UniProt accession codes. Statistics of interests include the following: (i) 60% of the covered drugs are on-market drugs with expired patent and exclusivity coverage, 17% are off-market, and 23% are on-market drugs with active patents and exclusivity coverage; (ii) 59% of the drugs are oral, 33% are parenteral and 18% topical, at the level of the active ingredients; (iii) only 3% of all drugs are for animal use only; however, 61% of the veterinary drugs are also approved for human use; (iv) dogs, cats and horses are by far the most represented target species for veterinary drugs; (v) the physicochemical property profile of animal drugs is very similar to that of human drugs. Use cases include azaperone, the only sedative approved for swine, and ruxolitinib, a Janus kinase inhibitor.


Assuntos
Aprovação de Drogas , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Drogas Veterinárias , Animais , Humanos , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/veterinária , Drogas Veterinárias/administração & dosagem , Drogas Veterinárias/efeitos adversos , Uso Off-Label/veterinária
2.
Nucleic Acids Res ; 51(D1): D1405-D1416, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36624666

RESUMO

The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for fusers to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.


Assuntos
Bases de Dados Factuais , Terapia de Alvo Molecular , Proteoma , Humanos , Produtos Biológicos , Descoberta de Drogas , Internet , Proteoma/efeitos dos fármacos
3.
Nucleic Acids Res ; 49(D1): D1160-D1169, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33151287

RESUMO

DrugCentral is a public resource (http://drugcentral.org) that serves the scientific community by providing up-to-date drug information, as described in previous papers. The current release includes 109 newly approved (October 2018 through March 2020) active pharmaceutical ingredients in the US, Europe, Japan and other countries; and two molecular entities (e.g. mefuparib) of interest for COVID19. New additions include a set of pharmacokinetic properties for ∼1000 drugs, and a sex-based separation of side effects, processed from FAERS (FDA Adverse Event Reporting System); as well as a drug repositioning prioritization scheme based on the market availability and intellectual property rights forFDA approved drugs. In the context of the COVID19 pandemic, we also incorporated REDIAL-2020, a machine learning platform that estimates anti-SARS-CoV-2 activities, as well as the 'drugs in news' feature offers a brief enumeration of the most interesting drugs at the present moment. The full database dump and data files are available for download from the DrugCentral web portal.


Assuntos
Antivirais/uso terapêutico , Tratamento Farmacológico da COVID-19 , Bases de Dados de Produtos Farmacêuticos/estatística & dados numéricos , Aprovação de Drogas/estatística & dados numéricos , Descoberta de Drogas/estatística & dados numéricos , Reposicionamento de Medicamentos/estatística & dados numéricos , SARS-CoV-2/efeitos dos fármacos , Antivirais/efeitos adversos , Antivirais/farmacocinética , COVID-19/epidemiologia , COVID-19/virologia , Aprovação de Drogas/métodos , Descoberta de Drogas/métodos , Reposicionamento de Medicamentos/métodos , Epidemias , Europa (Continente) , Humanos , Armazenamento e Recuperação da Informação/métodos , Internet , Japão , SARS-CoV-2/fisiologia , Estados Unidos
4.
Nucleic Acids Res ; 49(D1): D1334-D1346, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33156327

RESUMO

In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.


Assuntos
Bases de Dados Factuais , Genoma Humano , Doenças Neurodegenerativas/genética , Proteômica/métodos , Software , Viroses/genética , Animais , Anticonvulsivantes/química , Anticonvulsivantes/uso terapêutico , Antivirais/química , Antivirais/uso terapêutico , Produtos Biológicos/química , Produtos Biológicos/uso terapêutico , Mineração de Dados/estatística & dados numéricos , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Interações Hospedeiro-Patógeno/genética , Humanos , Internet , Aprendizado de Máquina/estatística & dados numéricos , Camundongos , Camundongos Knockout , Terapia de Alvo Molecular/métodos , Doenças Neurodegenerativas/classificação , Doenças Neurodegenerativas/tratamento farmacológico , Doenças Neurodegenerativas/virologia , Mapeamento de Interação de Proteínas , Proteoma/agonistas , Proteoma/antagonistas & inibidores , Proteoma/genética , Proteoma/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/uso terapêutico , Viroses/classificação , Viroses/tratamento farmacológico , Viroses/virologia
5.
Bioinformatics ; 37(21): 3865-3873, 2021 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-34086846

RESUMO

MOTIVATION: Genome-wide association studies can reveal important genotype-phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study. RESULTS: Here, we describe rational ranking, filtering and interpretation of inferred gene-trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene-trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene-trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists. AVAILABILITY AND IMPLEMENTATION: Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Estudo de Associação Genômica Ampla , Iluminação , Genótipo , Polimorfismo de Nucleotídeo Único , Fenótipo
6.
BMC Med Res Methodol ; 21(1): 151, 2021 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-34303362

RESUMO

BACKGROUND: Converting electronic health record (EHR) entries to useful clinical inferences requires one to address the poor scalability of existing implementations of Generalized Linear Mixed Models (GLMM) for repeated measures. The major computational bottleneck concerns the numerical evaluation of multivariable integrals, which even for the simplest EHR analyses may involve millions of dimensions (one for each patient). The hierarchical likelihood (h-lik) approach to GLMMs is a methodologically rigorous framework for the estimation of GLMMs that is based on the Laplace Approximation (LA), which replaces integration with numerical optimization, and thus scales very well with dimensionality. METHODS: We present a high-performance, direct implementation of the h-lik for GLMMs in the R package TMB. Using this approach, we examined the relation of repeated serum potassium measurements and survival in the Cerner Real World Data (CRWD) EHR database. Analyzing this data requires the evaluation of an integral in over 3 million dimensions, putting this problem beyond the reach of conventional approaches. We also assessed the scalability and accuracy of LA in smaller samples of 1 and 10% size of the full dataset that were analyzed via the a) original, interconnected Generalized Linear Models (iGLM), approach to h-lik, b) Adaptive Gaussian Hermite (AGH) and c) the gold standard for multivariate integration Markov Chain Monte Carlo (MCMC). RESULTS: Random effects estimates generated by the LA were within 10% of the values obtained by the iGLMs, AGH and MCMC techniques. The H-lik approach was 4-30 times faster than AGH and nearly 800 times faster than MCMC. The major clinical inferences in this problem are the establishment of the non-linear relationship between the potassium level and the risk of mortality, as well as estimates of the individual and health care facility sources of variations for mortality risk in CRWD. CONCLUSIONS: We found that the direct implementation of the h-lik offers a computationally efficient, numerically accurate approach for the analysis of extremely large, real world repeated measures data via the h-lik approach to GLMMs. The clinical inference from our analysis may guide choices of treatment thresholds for treating potassium disorders in the clinic.


Assuntos
Registros Eletrônicos de Saúde , Potássio , Teorema de Bayes , Humanos , Modelos Lineares , Cadeias de Markov , Método de Monte Carlo , Valores de Referência
7.
Nucleic Acids Res ; 47(D1): D963-D970, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30371892

RESUMO

DrugCentral is a drug information resource (http://drugcentral.org) open to the public since 2016 and previously described in the 2017 Nucleic Acids Research Database issue. Since the 2016 release, 103 new approved drugs were updated. The following new data sources have been included: Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS), FDA Orange Book information, L1000 gene perturbation profile distance/similarity matrices and estimated protonation constants. New and existing entries have been updated with the latest information from scientific literature, drug labels and external databases. The web interface has been updated to display and query new data. The full database dump and data files are available for download from the DrugCentral website.


Assuntos
Bases de Dados de Produtos Farmacêuticos , Aprovação de Drogas/estatística & dados numéricos , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Expressão Gênica/efeitos dos fármacos , Preparações Farmacêuticas/classificação , Proteínas/classificação
8.
Nucleic Acids Res ; 45(D1): D932-D939, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27789690

RESUMO

DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.


Assuntos
Bases de Dados de Produtos Farmacêuticos , Ferramenta de Busca , Navegador , Aprovação de Drogas , Composição de Medicamentos , Interações Medicamentosas , Rotulagem de Medicamentos , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Humanos , Preparações Farmacêuticas/química , Estados Unidos , United States Food and Drug Administration
9.
Bioinformatics ; 33(16): 2601-2603, 2017 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-28398460

RESUMO

MOTIVATION: The increasing amount of peer-reviewed manuscripts requires the development of specific mining tools to facilitate the visual exploration of evidence linking diseases and proteins. RESULTS: We developed TIN-X, the Target Importance and Novelty eXplorer, to visualize the association between proteins and diseases, based on text mining data processed from scientific literature. In the current implementation, TIN-X supports exploration of data for G-protein coupled receptors, kinases, ion channels, and nuclear receptors. TIN-X supports browsing and navigating across proteins and diseases based on ontology classes, and displays a scatter plot with two proposed new bibliometric statistics: Importance and Novelty. AVAILABILITY AND IMPLEMENTATION: http://www.newdrugtargets.org. CONTACT: cbologa@salud.unm.edu.


Assuntos
Mineração de Dados/métodos , Doença/etiologia , Software , Ontologias Biológicas , Gráficos por Computador , Humanos , Canais Iônicos/metabolismo , Fosfotransferases/metabolismo , Receptores Citoplasmáticos e Nucleares/metabolismo , Receptores Acoplados a Proteínas G/metabolismo
10.
Proc Natl Acad Sci U S A ; 112(8): 2521-6, 2015 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-25659743

RESUMO

Metastasis is the most lethal step of cancer progression in patients with invasive melanoma. In most human cancers, including melanoma, tumor dissemination through the lymphatic vasculature provides a major route for tumor metastasis. Unfortunately, molecular mechanisms that facilitate interactions between melanoma cells and lymphatic vessels are unknown. Here, we developed an unbiased approach based on molecular mimicry to identify specific receptors that mediate lymphatic endothelial-melanoma cell interactions and metastasis. By screening combinatorial peptide libraries directly on afferent lymphatic vessels resected from melanoma patients during sentinel lymphatic mapping and lymph node biopsies, we identified a significant cohort of melanoma and lymphatic surface binding peptide sequences. The screening approach was designed so that lymphatic endothelium binding peptides mimic cell surface proteins on tumor cells. Therefore, relevant metastasis and lymphatic markers were biochemically identified, and a comprehensive molecular profile of the lymphatic endothelium during melanoma metastasis was generated. Our results identified expression of the phosphatase 2 regulatory subunit A, α-isoform (PPP2R1A) on the cell surfaces of both melanoma cells and lymphatic endothelial cells. Validation experiments showed that PPP2R1A is expressed on the cell surfaces of both melanoma and lymphatic endothelial cells in vitro as well as independent melanoma patient samples. More importantly, PPP2R1A-PPP2R1A homodimers occur at the cellular level to mediate cell-cell interactions at the lymphatic-tumor interface. Our results revealed that PPP2R1A is a new biomarker for melanoma metastasis and show, for the first time to our knowledge, an active interaction between the lymphatic vasculature and melanoma cells during tumor progression.


Assuntos
Metástase Linfática/patologia , Vasos Linfáticos/patologia , Melanoma/patologia , Sequência de Aminoácidos , Animais , Biópsia , Comunicação Celular/imunologia , Membrana Celular/metabolismo , Células Endoteliais/metabolismo , Células Endoteliais/patologia , Endotélio Linfático/patologia , Humanos , Ligantes , Camundongos Nus , Mimetismo Molecular , Dados de Sequência Molecular , Peptídeos/química , Peptídeos/imunologia , Proteína Fosfatase 2/metabolismo , Reprodutibilidade dos Testes , Neoplasias Cutâneas , Resultado do Tratamento , Melanoma Maligno Cutâneo
11.
Rev Roum Chim ; 60(2-3): 219-226, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26346852

RESUMO

Computational toxicology is a new discipline in the area of computational molecular sciences, which is rapidly developing as a result of the public interest stirred by several European and US initiatives. Here, we report the use of primary high throughput screening (HTS) data as biological descriptors to complement the chemical descriptors for the modelling of the acute toxicity. The combination of biological and chemical descriptors was performed on the median lethal dose following oral administration in rats (rat LD50). The hybrid model developed based on chemical and biological descriptors is superior to models based on the chemical or biological description alone. Using this model, besides the accurately prediction of a compound's toxicity we also identified molecular fragments whose presence may contribute to increase or decrease of the toxicity.

12.
PeerJ ; 12: e17470, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38948230

RESUMO

TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X's predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user's web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins.


Assuntos
Interface Usuário-Computador , Humanos , Processamento de Linguagem Natural , PubMed , Software
13.
Anal Biochem ; 437(1): 77-87, 2013 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-23470221

RESUMO

ATP binding cassette (ABC) transmembrane efflux pumps such as P-glycoprotein (ABCB1), multidrug resistance protein 1 (ABCC1), and breast cancer resistance protein (ABCG2) play an important role in anticancer drug resistance. A large number of structurally and functionally diverse compounds act as substrates or modulators of these pumps. In vitro assessment of the affinity of drug candidates for multidrug resistance proteins is central to predict in vivo pharmacokinetics and drug-drug interactions. The objective of this study was to identify and characterize new substrates for these transporters. As part of a collaborative project with Life Technologies, 102 fluorescent probes were investigated in a flow cytometric screen of ABC transporters. The primary screen compared substrate efflux activity in parental cell lines with their corresponding highly expressing resistant counterparts. The fluorescent compound library included a range of excitation/emission profiles and required dual laser excitation as well as multiple fluorescence detection channels. A total of 31 substrates with active efflux in one or more pumps and practical fluorescence response ranges were identified and tested for interaction with eight known inhibitors. This screening approach provides an efficient tool for identification and characterization of new fluorescent substrates for ABCB1, ABCC1, and ABCG2.


Assuntos
Transportadores de Cassetes de Ligação de ATP/antagonistas & inibidores , Transportadores de Cassetes de Ligação de ATP/metabolismo , Citometria de Fluxo/métodos , Corantes Fluorescentes/metabolismo , Subfamília B de Transportador de Cassetes de Ligação de ATP , Membro 1 da Subfamília B de Cassetes de Ligação de ATP/antagonistas & inibidores , Membro 1 da Subfamília B de Cassetes de Ligação de ATP/genética , Membro 1 da Subfamília B de Cassetes de Ligação de ATP/metabolismo , Membro 2 da Subfamília G de Transportadores de Cassetes de Ligação de ATP , Transportadores de Cassetes de Ligação de ATP/genética , Linhagem Celular , Humanos , Proteínas Associadas à Resistência a Múltiplos Medicamentos/antagonistas & inibidores , Proteínas Associadas à Resistência a Múltiplos Medicamentos/genética , Proteínas Associadas à Resistência a Múltiplos Medicamentos/metabolismo , Proteínas de Neoplasias/antagonistas & inibidores , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Ligação Proteica
14.
Clin J Am Soc Nephrol ; 18(11): 1396-1407, 2023 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-37722368

RESUMO

BACKGROUND: Hospital-acquired hypernatremia is highly prevalent, overlooked, and associated with unfavorable consequences. There are limited studies examining the outcomes and discharge dispositions of various levels of hospital-acquired hypernatremia in patients with or without CKD. METHODS: We conducted an observational retrospective cohort study, and we analyzed the data of 1,728,141 patients extracted from the Cerner Health Facts database (January 1, 2000, to June 30, 2018). In this report, we investigated the association between hospital-acquired hypernatremia (serum sodium [Na] levels >145 mEq/L) and in-hospital mortality or discharge dispositions with kidney function status at admission using adjusted multinomial regression models. RESULTS: Of all hospitalized patients, 6% developed hypernatremia after hospital admission. The incidence of in-hospital mortality was 12% and 1% in patients with hypernatremia and normonatremia, respectively. The risk of all outcomes was significantly greater for serum Na >145 mEq/L compared with the reference interval (serum Na, 135-145 mEq/L). In patients with hypernatremia, odds ratios (95% confidence interval) for in-hospital mortality, discharge to hospice, and discharge to nursing facilities were 14.04 (13.71 to 14.38), 4.35 (4.14 to 4.57), and 3.88 (3.82 to 3.94), respectively ( P < 0.001, for all). Patients with eGFR (Chronic Kidney Disease Epidemiology Collaboration) 60-89 ml/min per 1.73 m 2 and normonatremia had the lowest odds ratio for in-hospital mortality (1.60 [1.52 to 1.70]). CONCLUSIONS: Hospital-acquired hypernatremia is associated with in-hospital mortality and discharge to hospice or to nursing facilities in all stages of CKD.


Assuntos
Hipernatremia , Hiponatremia , Insuficiência Renal Crônica , Humanos , Hipernatremia/epidemiologia , Hipernatremia/terapia , Estudos Retrospectivos , Sódio , Mortalidade Hospitalar , Insuficiência Renal Crônica/epidemiologia , Insuficiência Renal Crônica/terapia , Insuficiência Renal Crônica/complicações , Hospitais
15.
Commun Med (Lond) ; 3(1): 98, 2023 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-37460679

RESUMO

BACKGROUND: Birth defects are functional and structural abnormalities that impact about 1 in 33 births in the United States. They have been attributed to genetic and other factors such as drugs, cosmetics, food, and environmental pollutants during pregnancy, but for most birth defects there are no known causes. METHODS: To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes. Specifically, we gathered data from drug/birth-defect associations from co-mentions in published abstracts, gene/birth-defect associations from genetic studies, drug- and preclinical-compound-induced gene expression changes in cell lines, known drug targets, genetic burden scores for human genes, and placental crossing scores for small molecules. RESULTS: Using ReproTox-KG and semi-supervised learning (SSL), we scored >30,000 preclinical small molecules for their potential to cross the placenta and induce birth defects, and identified >500 birth-defect/gene/drug cliques that can be used to explain molecular mechanisms for drug-induced birth defects. The ReproTox-KG can be accessed via a web-based user interface available at https://maayanlab.cloud/reprotox-kg . This site enables users to explore the associations between birth defects, approved and preclinical drugs, and all human genes. CONCLUSIONS: ReproTox-KG provides a resource for exploring knowledge about the molecular mechanisms of birth defects with the potential of predicting the likelihood of genes and preclinical small molecules to induce birth defects.


While birth defects are common, for most birth defects there are no known causes. During pregnancy, developing babies are exposed to drugs, cosmetics, food, and environmental pollutants that may cause birth defects. However, exactly how these environmental factors are involved in producing birth defects is difficult to discern. Also, birth defects can be a consequence of the genes inherited from the parents. We combined general data about human genes and drugs with specific data previously implicating genes and drugs in inducing birth defects to create a knowledge graph representation that connects genes, drugs, and birth defects. This knowledge graph can be used to explore new links that may explain why birth defects occur, particularly those that result from a combination of inherited and environmental influences.

16.
J Comput Aided Mol Des ; 26(1): 107-12, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22207193

RESUMO

For over a decade, cheminformatics has contributed to a wide array of scientific tasks from analytical chemistry and biochemistry to pharmacology and drug discovery; and although its contributions to decision making are recognized, the challenge is how it would contribute to faster development of novel, better products. Here we address the future of cheminformatics with primary focus on innovation. Cheminformatics developers often need to choose between "mainstream" (i.e., accepted, expected) and novel, leading-edge tools, with an increasing trend for open science. Possible futures for cheminformatics include the worst case scenario (lack of funding, no creative usage), as well as the best case scenario (complete integration, from systems biology to virtual physiology). As "-omics" technologies advance, and computer hardware improves, compounds will no longer be profiled at the molecular level, but also in terms of genetic and clinical effects. Among potentially novel tools, we anticipate machine learning models based on free text processing, an increased performance in environmental cheminformatics, significant decision-making support, as well as the emergence of robot scientists conducting automated drug discovery research. Furthermore, cheminformatics is anticipated to expand the frontiers of knowledge and evolve in an open-ended, extensible manner, allowing us to explore multiple research scenarios in order to avoid epistemological "local information minimum trap".


Assuntos
Inteligência Artificial , Química/tendências , Informática/tendências , Descoberta de Drogas/tendências , Genômica/tendências , Humanos , Biologia de Sistemas
17.
Kidney360 ; 3(7): 1144-1157, 2022 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-35919520

RESUMO

Background: Hypernatremia is a frequently encountered electrolyte disorder in hospitalized patients. Controversies still exist over the relationship between hypernatremia and its outcomes in hospitalized patients. This study examines the relationship of hypernatremia to outcomes among hospitalized patients and the extent to which this relationship varies by kidney function and age. Methods: We conducted an observational study to investigate the association between hypernatremia, eGFR, and age at hospital admission and in-hospital mortality, and discharge dispositions. We analyzed the data of 1.9 million patients extracted from the Cerner Health Facts databases (2000-2018). Adjusted multinomial regression models were used to estimate the relationship of hypernatremia to outcomes of hospitalized patients. Results: Of all hospitalized patients, 3% had serum sodium (Na) >145 mEq/L at hospital admission. Incidence of in-hospital mortality was 12% and 2% in hyper- and normonatremic patients, respectively. The risk of all outcomes increased significantly for Na >155 mEq/L compared with the reference interval of Na=135-145 mEq/L. Odds ratios (95% confidence intervals) for in-hospital mortality and discharge to a hospice or nursing facility were 34.41 (30.59-38.71), 21.14 (17.53-25.5), and 12.21 (10.95-13.61), respectively (all P<0.001). In adjusted models, we found that the association between Na and disposition was modified by eGFR (P<0.001) and by age (P<0.001). Sensitivity analyses were performed using the eGFR equation without race as a covariate, and the inferences did not substantially change. In all hypernatremic groups, patients aged 76-89 and ≥90 had higher odds of in-hospital mortality compared with younger patients (all P<0.001). Conclusions: Hypernatremia was significantly associated with in-hospital mortality and discharge to a hospice or nursing facility. The risk of in-hospital mortality and other outcomes was highest among those with Na >155 mEq/L. This work demonstrates that hypernatremia is an important factor related to discharge disposition and supports the need to study whether protocolized treatment of hypernatremia improves outcomes.


Assuntos
Hipernatremia , Mortalidade Hospitalar , Hospitalização , Humanos , Hipernatremia/epidemiologia , Alta do Paciente , Sódio
18.
Curr Protoc ; 2(1): e355, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-35085427

RESUMO

The Illuminating the Druggable Genome (IDG) consortium is a National Institutes of Health (NIH) Common Fund program designed to enhance our knowledge of under-studied proteins, more specifically, proteins unannotated within the three most commonly drug-targeted protein families: G-protein coupled receptors, ion channels, and protein kinases. Since 2014, the IDG Knowledge Management Center (IDG-KMC) has generated several open-access datasets and resources that jointly serve as a highly translational machine-learning-ready knowledgebase focused on human protein-coding genes and their products. The goal of the IDG-KMC is to develop comprehensive integrated knowledge for the druggable genome to illuminate the uncharacterized or poorly annotated portion of the druggable genome. The tools derived from the IDG-KMC provide either user-friendly visualizations or ways to impute the knowledge about potential targets using machine learning strategies. In the following protocols, we describe how to use each web-based tool to accelerate illumination in under-studied proteins. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Interacting with the Pharos user interface Basic Protocol 2: Accessing the data in Harmonizome Basic Protocol 3: The ARCHS4 resource Basic Protocol 4: Making predictions about gene function with PrismExp Basic Protocol 5: Using Geneshot to illuminate knowledge about under-studied targets Basic Protocol 6: Exploring under-studied targets with TIN-X Basic Protocol 7: Interacting with the DrugCentral user interface Basic Protocol 8: Estimating Anti-SARS-CoV-2 activities with DrugCentral REDIAL-2020 Basic Protocol 9: Drug Set Enrichment Analysis using Drugmonizome Basic Protocol 10: The Drugmonizome-ML Appyter Basic Protocol 11: The Harmonizome-ML Appyter Basic Protocol 12: GWAS target illumination with TIGA Basic Protocol 13: Prioritizing kinases for lists of proteins and phosphoproteins with KEA3 Basic Protocol 14: Converting PubMed searches to drug sets with the DrugShot Appyter.


Assuntos
Bases de Dados Genéticas , Genoma , COVID-19 , Humanos , Aprendizado de Máquina , Proteínas , SARS-CoV-2
19.
Nat Rev Chem ; 6(4): 287-295, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35783295

RESUMO

One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available, and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared, and openly published. CACHE will launch 3 new benchmarking exercises every year. The outcomes will be better prediction methods, new small molecule binders for target proteins of importance for fundamental biology or drug discovery, and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins.

20.
JMIR Med Educ ; 8(1): e23845, 2022 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-35142625

RESUMO

BACKGROUND: On March 11, 2020, the New Mexico Governor declared a public health emergency in response to the COVID-19 pandemic. The New Mexico medical advisory team contacted University of New Mexico (UNM) faculty to form a team to consolidate growing information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its disease to facilitate New Mexico's pandemic management. Thus, faculty, physicians, staff, graduate students, and medical students created the "UNM Global Health COVID-19 Intelligence Briefing." OBJECTIVE: In this paper, we sought to (1) share how to create an informative briefing to guide public policy and medical practice and manage information overload with rapidly evolving scientific evidence; (2) determine the qualitative usefulness of the briefing to its readers; and (3) determine the qualitative effect this project has had on virtual medical education. METHODS: Microsoft Teams was used for manual and automated capture of COVID-19 articles and composition of briefings. Multilevel triaging saved impactful articles to be reviewed, and priority was placed on randomized controlled studies, meta-analyses, systematic reviews, practice guidelines, and information on health care and policy response to COVID-19. The finalized briefing was disseminated by email, a listserv, and posted on the UNM digital repository. A survey was sent to readers to determine briefing usefulness and whether it led to policy or medical practice changes. Medical students, unable to partake in direct patient care, proposed to the School of Medicine that involvement in the briefing should count as course credit, which was approved. The maintenance of medical student involvement in the briefings as well as this publication was led by medical students. RESULTS: An average of 456 articles were assessed daily. The briefings reached approximately 1000 people by email and listserv directly, with an unknown amount of forwarding. Digital repository tracking showed 5047 downloads across 116 countries as of July 5, 2020. The survey found 108 (95%) of 114 participants gained relevant knowledge, 90 (79%) believed it decreased misinformation, 27 (24%) used the briefing as their primary source of information, and 90 (79%) forwarded it to colleagues. Specific and impactful public policy decisions were informed based on the briefing. Medical students reported that the project allowed them to improve on their scientific literature assessment, stay current on the pandemic, and serve their community. CONCLUSIONS: The COVID-19 briefings succeeded in informing and guiding New Mexico policy and clinical practice. The project received positive feedback from the community and was shown to decrease information burden and misinformation. The virtual platforms allowed for the continuation of medical education. Variability in subject matter expertise was addressed with training, standardized article selection criteria, and collaborative editing led by faculty.

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