RESUMEN
Well-characterized small molecules are essential tools for studying the biology and therapeutic relevance of a target protein. However, many compounds reported in the literature and routinely studied in biomedical research lack the potency and selectivity required for mechanistic cellular studies on the function of a given protein. Furthermore, commercially available compounds often do not include useful tools developed by industry as part of their research and development efforts, as they frequently remain proprietary. The freely available donated chemical probe (DCP) library, fueled by generous donations of compounds from industry and academia, enables easy access to a steadily growing collection of these valuable and well-characterized tools. Here, we provide a systematic description of the current DCP library collection and their associated comprehensive characterization data, including a variety of in vitro and cellular assays. Of note, we characterized the set in relevant human primary models by employing hepatotoxicity screening in primary human liver spheroids and viability screening in patient-derived colorectal cancer organoids and matched normal-adjacent epithelium. Taken together, the DCP library represents a well-annotated, openly available collection of tool compounds for studying a wide range of targets, including kinases, G-protein-coupled receptors, and ion channels. As such, it represents a unique resource for the biomedical research community.
Asunto(s)
Sondas Moleculares , Neoplasias , Bibliotecas de Moléculas Pequeñas , Humanos , Hígado , Sistemas Microfisiológicos , Neoplasias/metabolismo , Organoides/metabolismo , Organoides/patología , Proteínas/metabolismo , Bibliotecas de Moléculas Pequeñas/clasificación , Sondas Moleculares/química , Sondas Moleculares/farmacologíaRESUMEN
At several stages of drug discovery, bioisosteric replacement is a common and efficient practice to find new bioactive chemotypes or to optimize series of molecules toward drug candidates. The critical steps consisting in selecting which molecular moiety should be replaced by which other chemical fragment is often relying on the expertise of specialists. Nowadays, valuable support can be obtained through the wealth of dedicated structural and knowledge data. The present article details the update of SwissBioisostere, a database of >25 millions of unique molecular replacements with data on bioactivity, physicochemistry, chemical and biological contexts extracted from the literature and related resources. The content of the database together with analysis and visualization capacities is freely available at www.swissbioisostere.ch.
Asunto(s)
Química Computacional/tendencias , Bases de Datos Factuales , Descubrimiento de Drogas/tendencias , Bibliotecas de Moléculas Pequeñas/química , Humanos , Bibliotecas de Moléculas Pequeñas/clasificación , Interfaz Usuario-ComputadorRESUMEN
Interrogation of cellular metabolism with high-throughput screening approaches can unravel contextual biology and identify cancer-specific metabolic vulnerabilities. To systematically study the consequences of distinct metabolic perturbations, we assemble a comprehensive metabolic drug library (CeMM Library of Metabolic Drugs; CLIMET) covering 243 compounds. We, next, characterize it phenotypically in a diverse panel of myeloid leukemia cell lines and primary patient cells. Analysis of the drug response profiles reveals that 77 drugs affect cell viability, with the top effective compounds targeting nucleic acid synthesis, oxidative stress, and the PI3K/mTOR pathway. Clustering of individual drug response profiles stratifies the cell lines into five functional groups, which link to specific molecular and metabolic features. Mechanistic characterization of selective responses to the PI3K inhibitor pictilisib, the fatty acid synthase inhibitor GSK2194069, and the SLC16A1 inhibitor AZD3965, bring forth biomarkers of drug response. Phenotypic screening using CLIMET represents a valuable tool to probe cellular metabolism and identify metabolic dependencies at large.
Asunto(s)
Leucemia Mieloide/metabolismo , Bibliotecas de Moléculas Pequeñas/metabolismo , Bibliotecas de Moléculas Pequeñas/farmacología , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Supervivencia Celular/efectos de los fármacos , Análisis por Conglomerados , Ácidos Grasos/biosíntesis , Genotipo , Humanos , Leucemia Mieloide/genética , Leucemia Mieloide/patología , Transportadores de Ácidos Monocarboxílicos/genética , Fenotipo , Fosfatidilinositol 3-Quinasa/metabolismo , Inhibidores de las Quinasa Fosfoinosítidos-3/metabolismo , Inhibidores de las Quinasa Fosfoinosítidos-3/farmacología , Pirimidinonas/metabolismo , Pirimidinonas/farmacología , Pirrolidinas/metabolismo , Pirrolidinas/farmacología , Transducción de Señal , Bibliotecas de Moléculas Pequeñas/clasificación , Simportadores/genética , Análisis de Sistemas , Tiofenos/metabolismo , Tiofenos/farmacología , Triazoles/metabolismo , Triazoles/farmacología , Células Tumorales CultivadasRESUMEN
Epithelial cells lining mucosal surfaces distinctively express the inflammatory bowel disease risk gene INAVA. We previously found that INAVA has dual and competing functions: one at lateral membranes where it affects mucosal barrier function and the other in the cytosol where INAVA enhances IL-1ß signal transduction and protein ubiquitination and forms puncta. We now find that IL-1ß-induced INAVA puncta are biomolecular condensates that rapidly assemble and physiologically resolve. The condensates contain ubiquitin and the E3 ligase ßTrCP2, and their formation correlates with amplified ubiquitination, suggesting function in regulation of cellular proteostasis. Accordingly, a small-molecule screen identified ROS inducers, proteasome inhibitors, and inhibitors of the protein folding chaperone HSP90 as potent agonists for INAVA condensate formation. Notably, inhibitors of the p38α and mTOR pathways enhanced resolution of the condensates, and inhibitors of the Rho-ROCK pathway induced INAVA's competing function by recruiting INAVA to newly assembled intercellular junctions in cells where none existed before.
Asunto(s)
Proteínas Portadoras/genética , Proteínas Activadoras de GTPasa/genética , Regulación de la Expresión Génica/efectos de los fármacos , Uniones Intercelulares/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Proteínas con Repetición de beta-Transducina/genética , Células CACO-2 , Proteínas Portadoras/metabolismo , Línea Celular Tumoral , Proteínas Activadoras de GTPasa/metabolismo , Células HEK293 , Proteínas HSP90 de Choque Térmico/genética , Proteínas HSP90 de Choque Térmico/metabolismo , Células HeLa , Humanos , Uniones Intercelulares/metabolismo , Uniones Intercelulares/ultraestructura , Interleucina-1beta/genética , Interleucina-1beta/metabolismo , Péptidos y Proteínas de Señalización Intracelular/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Proteína Quinasa 14 Activada por Mitógenos/genética , Proteína Quinasa 14 Activada por Mitógenos/metabolismo , FN-kappa B/genética , FN-kappa B/metabolismo , Proteína Adaptadora de Señalización NOD2/genética , Proteína Adaptadora de Señalización NOD2/metabolismo , Proteostasis/efectos de los fármacos , Proteostasis/genética , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Transducción de Señal , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/clasificación , Serina-Treonina Quinasas TOR/genética , Serina-Treonina Quinasas TOR/metabolismo , Proteínas con Repetición de beta-Transducina/metabolismoRESUMEN
With increasing prevalence of antimicrobial resistance, a fundamental goal of antibiotic discovery is to uncover new small molecules that prevent growth of pathogenic bacteria through diverse mechanisms of action. This goal is particularly pertinent for tuberculosis, caused by Mycobacterium tuberculosis. In this chapter, we describe the application of a chemical-genetic method, PROSPECT (primary screening of strains to prioritize expanded chemistry and targets), for sensitively detecting small molecule bioactivity using a pooled panel of hypomorphs (strains depleted in a particular essential gene) of M. tuberculosis. We describe statistical and heuristic approaches to assign small molecule mechanism of action from the resulting chemical-genetic interaction profiles.
Asunto(s)
Antituberculosos/clasificación , Antituberculosos/aislamiento & purificación , Proteínas Bacterianas/metabolismo , Descubrimiento de Drogas , Genes Esenciales , Mycobacterium tuberculosis/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Antituberculosos/farmacología , Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana Múltiple , Humanos , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/crecimiento & desarrollo , Mycobacterium tuberculosis/metabolismo , Bibliotecas de Moléculas Pequeñas/clasificación , Bibliotecas de Moléculas Pequeñas/aislamiento & purificación , Especificidad por SustratoRESUMEN
A global pandemic has emerged following the appearance of the new severe acute respiratory virus whose official name is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), strongly affecting the health sector as well as the world economy. Indeed, following the emergence of this new virus, despite the existence of a few approved and known effective vaccines at the time of writing this original study, a sense of urgency has emerged worldwide to discover new technical tools and new drugs as soon as possible. In this context, many studies and researches are currently underway to develop new tools and therapies against SARS CoV-2 and other viruses, using different approaches. The 3-chymotrypsin (3CL) protease, which is directly involved in the cotranslational and posttranslational modifications of viral polyproteins essential for the existence and replication of the virus in the host, is one of the coronavirus target proteins that has been the subject of these extensive studies. Currently, the majority of these studies are aimed at repurposing already known and clinically approved drugs against this new virus, but this approach is not really successful. Recently, different studies have successfully demonstrated the effectiveness of artificial intelligence-based techniques to understand existing chemical spaces and generate new small molecules that are both effective and efficient. In this framework and for our study, we combined a generative recurrent neural network model with transfer learning methods and active learning-based algorithms to design novel small molecules capable of effectively inhibiting the 3CL protease in human cells. We then analyze these small molecules to find the correct binding site that matches the structure of the 3CL protease of our target virus as well as other analyses performed in this study. Based on these screening results, some molecules have achieved a good binding score close to -18 kcal/mol, which we can consider as good potential candidates for further synthesis and testing against SARS-CoV-2.
Asunto(s)
Antivirales/química , Productos Biológicos/química , Proteasas 3C de Coronavirus/antagonistas & inhibidores , Redes Neurales de la Computación , Inhibidores de Proteasas/química , SARS-CoV-2/química , Bibliotecas de Moléculas Pequeñas/química , Antivirales/clasificación , Antivirales/farmacología , Productos Biológicos/clasificación , Productos Biológicos/farmacología , Dominio Catalítico , Proteasas 3C de Coronavirus/química , Proteasas 3C de Coronavirus/genética , Proteasas 3C de Coronavirus/metabolismo , Diseño de Fármacos , Expresión Génica , Humanos , Cinética , Simulación del Acoplamiento Molecular , Inhibidores de Proteasas/clasificación , Inhibidores de Proteasas/farmacología , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/enzimología , Bibliotecas de Moléculas Pequeñas/clasificación , Bibliotecas de Moléculas Pequeñas/farmacología , Especificidad por Sustrato , Termodinámica , Tratamiento Farmacológico de COVID-19RESUMEN
Organoids allow the recapitulation of intestinal homeostasis and cancerogenesis in vitro; however, RNA sequencing (RNA-seq)-based methods for drug screens are missing. We develop targeted organoid sequencing (TORNADO-seq), a high-throughput, high-content drug discovery platform that uses targeted RNA-seq to monitor the expression of large gene signatures for the detailed evaluation of cellular phenotypes in organoids. TORNADO-seq is a fast, highly reproducible time- and cost-effective ($5 per sample) method that can probe cell mixtures and their differentiation state in the intestinal system. We apply this method to isolate drugs that enrich for differentiated cell phenotypes and show that these drugs are highly efficacious against cancer compared to wild-type organoids. Furthermore, TORNADO-seq facilitates in-depth insight into the mode of action of these drugs. Our technology can easily be adapted to many other systems and will allow for more systematic, large-scale, and quantitative approaches to study the biology of complex cellular systems.
Asunto(s)
Antineoplásicos/farmacología , Detección Precoz del Cáncer/métodos , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Organoides/efectos de los fármacos , Medicamentos bajo Prescripción/farmacología , Bibliotecas de Moléculas Pequeñas/farmacología , Antineoplásicos/química , Antineoplásicos/clasificación , Diferenciación Celular/efectos de los fármacos , Neoplasias Colorrectales/tratamiento farmacológico , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Neoplasias Colorrectales/patología , Descubrimiento de Drogas/métodos , Reposicionamiento de Medicamentos , Enterocitos/efectos de los fármacos , Enterocitos/metabolismo , Enterocitos/patología , Redes Reguladoras de Genes , Células Caliciformes/efectos de los fármacos , Células Caliciformes/metabolismo , Células Caliciformes/patología , Ensayos Analíticos de Alto Rendimiento , Humanos , Proteínas de Neoplasias/antagonistas & inhibidores , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Células Madre Neoplásicas/efectos de los fármacos , Células Madre Neoplásicas/metabolismo , Células Madre Neoplásicas/patología , Organoides/metabolismo , Organoides/patología , Células de Paneth/efectos de los fármacos , Células de Paneth/metabolismo , Células de Paneth/patología , Medicamentos bajo Prescripción/química , Medicamentos bajo Prescripción/clasificación , RNA-Seq , Análisis de Secuencia de ARN , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/clasificaciónRESUMEN
The US Food and Drug Administration (FDA) and the National Center for Advancing Translational Sciences (NCATS) have collaborated to publish rigorous scientific descriptions of substances relevant to regulated products. The FDA has adopted the global ISO 11238 data standard for the identification of substances in medicinal products and has populated a database to organize the agency's regulatory submissions and marketed products data. NCATS has worked with FDA to develop the Global Substance Registration System (GSRS) and produce a non-proprietary version of the database for public benefit. In 2019, more than half of all new drugs in clinical development were proteins, nucleic acid therapeutics, polymer products, structurally diverse natural products or cellular therapies. While multiple databases of small molecule chemical structures are available, this resource is unique in its application of regulatory standards for the identification of medicinal substances and its robust support for other substances in addition to small molecules. This public, manually curated dataset provides unique ingredient identifiers (UNIIs) and detailed descriptions for over 100 000 substances that are particularly relevant to medicine and translational research. The dataset can be accessed and queried at https://gsrs.ncats.nih.gov/app/substances.
Asunto(s)
Bases de Datos de Compuestos Químicos , Bases de Datos Factuales , Bases de Datos Farmacéuticas , Salud Pública/legislación & jurisprudencia , Productos Biológicos/química , Productos Biológicos/clasificación , Conjuntos de Datos como Asunto , Drogas en Investigación/química , Drogas en Investigación/clasificación , Humanos , Internet , Ácidos Nucleicos/química , Ácidos Nucleicos/clasificación , Polímeros/química , Polímeros/clasificación , Medicamentos bajo Prescripción/química , Medicamentos bajo Prescripción/clasificación , Proteínas/química , Proteínas/clasificación , Salud Pública/métodos , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/clasificación , Programas Informáticos , Estados Unidos , United States Food and Drug Administration , Xenobióticos/química , Xenobióticos/clasificaciónRESUMEN
Proteolysis-targeting chimeras (PROTACs), which selectively degrade targeted proteins by the ubiquitin-proteasome system, have emerged as a novel therapeutic technology with potential advantages over traditional inhibition strategies. In the past few years, this technology has achieved substantial progress and two PROTACs have been advanced into phase I clinical trials. However, this technology is still maturing and the design of PROTACs remains a great challenge. In order to promote the rational design of PROTACs, we present PROTAC-DB, a web-based open-access database that integrates structural information and experimental data of PROTACs. Currently, PROTAC-DB consists of 1662 PROTACs, 202 warheads (small molecules that target the proteins of interest), 65 E3 ligands (small molecules capable of recruiting E3 ligases) and 806 linkers, as well as their chemical structures, biological activities, and physicochemical properties. Except the biological activities of warheads and E3 ligands, PROTAC-DB also provides the degradation capacities, binding affinities and cellular activities for PROTACs. PROTAC-DB can be queried with two general searching approaches: text-based (target name, compound name or ID) and structure-based. In addition, for the convenience of users, a filtering tool for the searching results based on the physicochemical properties of compounds is also offered. PROTAC-DB is freely accessible at http://cadd.zju.edu.cn/protacdb/.
Asunto(s)
Bases de Datos de Compuestos Químicos , Sistemas de Liberación de Medicamentos/métodos , Preparaciones Farmacéuticas/química , Complejo de la Endopetidasa Proteasomal/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/química , Programas Informáticos , Sitios de Unión , Descubrimiento de Drogas , Humanos , Internet , Ligandos , Preparaciones Farmacéuticas/clasificación , Unión Proteica , Proteolisis/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/clasificación , Bibliotecas de Moléculas Pequeñas/farmacología , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , Ubiquitinación/efectos de los fármacosRESUMEN
The compatibility of free boronic acid building blocks in multicomponent reactions to readily create large libraries of diverse and complex small molecules was investigated. Traditionally, boronic acid synthesis is sequential, synthetically demanding, and time-consuming, which leads to high target synthesis times and low coverage of the boronic acid chemical space. We have performed the synthesis of large libraries of boronic acid derivatives based on multiple chemistries and building blocks using acoustic dispensing technology. The synthesis was performed on a nanomole scale with high synthesis success rates. The discovery of a protease inhibitor underscores the usefulness of the approach. Our acoustic dispensing-enabled chemistry paves the way to highly accelerated synthesis and miniaturized reaction scouting, allowing access to unprecedented boronic acid libraries.
Asunto(s)
Ácidos Borónicos/química , Estructura Molecular , Bibliotecas de Moléculas Pequeñas/química , Ácidos Borónicos/síntesis química , Ácidos Borónicos/clasificación , Cianuros/síntesis química , Cianuros/química , Espectrometría de Masas/métodos , Microondas , Bibliotecas de Moléculas Pequeñas/síntesis química , Bibliotecas de Moléculas Pequeñas/clasificaciónRESUMEN
New antibiotics are needed to combat rising levels of resistance, with new Mycobacterium tuberculosis (Mtb) drugs having the highest priority. However, conventional whole-cell and biochemical antibiotic screens have failed. Here we develop a strategy termed PROSPECT (primary screening of strains to prioritize expanded chemistry and targets), in which we screen compounds against pools of strains depleted of essential bacterial targets. We engineered strains that target 474 essential Mtb genes and screened pools of 100-150 strains against activity-enriched and unbiased compound libraries, probing more than 8.5 million chemical-genetic interactions. Primary screens identified over tenfold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insights. We identified over 40 compounds that target DNA gyrase, the cell wall, tryptophan, folate biosynthesis and RNA polymerase, as well as inhibitors that target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating the ability of PROSPECT to yield inhibitors against targets that would have eluded conventional drug discovery.
Asunto(s)
Antituberculosos/clasificación , Antituberculosos/aislamiento & purificación , Descubrimiento de Drogas/métodos , Eliminación de Gen , Pruebas de Sensibilidad Microbiana/métodos , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/genética , Bibliotecas de Moléculas Pequeñas/farmacología , Antituberculosos/farmacología , Girasa de ADN/metabolismo , Farmacorresistencia Microbiana , Ácido Fólico/biosíntesis , Terapia Molecular Dirigida , Mycobacterium tuberculosis/citología , Mycobacterium tuberculosis/enzimología , Ácidos Micólicos/metabolismo , Reproducibilidad de los Resultados , Bibliotecas de Moléculas Pequeñas/clasificación , Bibliotecas de Moléculas Pequeñas/aislamiento & purificación , Especificidad por Sustrato , Inhibidores de Topoisomerasa II/aislamiento & purificación , Inhibidores de Topoisomerasa II/farmacología , Triptófano/biosíntesis , Tuberculosis/tratamiento farmacológico , Tuberculosis/microbiologíaRESUMEN
Self-renewal and multipotential differentiation are two important features of hematopoietic stem/progenitor cells (HS/PCs) that make them as an ideal source of stem cells for treatment of many hematologic disorders and cancers. Regarding the limited number of cord blood HS/PCs, proper ex vivo expansion can significantly increase the clinical use of cord blood stem cells. Meanwhile, expansion of HS/PCs will be feasible through bypassing the quiescent state of HS/PCs and simultaneously enhancing their proliferative potential and survival while delaying the terminal differentiation and exhaustion. Previous investigations have demonstrated that defined sets of exogenous hematopoietic cytokines/growth factors such as stem cell factor, Flt-3 ligand, and thrombopoietin are able to expand HS/PCs. However, in recent years, small molecule compounds (SMCs) have emerged as a powerful tool for the effective expansion of HS/PCs by modulating multiple cellular processes including different signaling pathways and epigenetics. In this review, recent progress toward the use of SMCs in HS cell research is presented. We focus on the significant applications of SMCs related to HS/PC expansion and discuss the associated mechanism. At the end we present a list of those SMCs which enter to clinical trials.
Asunto(s)
Diferenciación Celular/efectos de los fármacos , Proliferación Celular/efectos de los fármacos , Células Madre Hematopoyéticas/citología , Bibliotecas de Moléculas Pequeñas/farmacología , Ciclo Celular/efectos de los fármacos , Ciclo Celular/genética , Diferenciación Celular/genética , División Celular/efectos de los fármacos , División Celular/genética , Proliferación Celular/genética , Células Cultivadas , Expresión Génica/efectos de los fármacos , Células Madre Hematopoyéticas/metabolismo , Humanos , Transducción de Señal/efectos de los fármacos , Transducción de Señal/genética , Bibliotecas de Moléculas Pequeñas/clasificaciónRESUMEN
Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates.
Asunto(s)
Productos Biológicos/química , Estructura Molecular , Bibliotecas de Moléculas Pequeñas/química , Algoritmos , Productos Biológicos/clasificación , Descubrimiento de Drogas , Modelos Moleculares , Relación Estructura-Actividad Cuantitativa , Bibliotecas de Moléculas Pequeñas/clasificación , Bibliotecas de Moléculas Pequeñas/uso terapéuticoRESUMEN
Cytotoxicity is a commonly used in vitro endpoint for evaluating chemical toxicity. In support of the U.S. Tox21 screening program, the cytotoxicity of ~10K chemicals was interrogated at 0, 8, 16, 24, 32, & 40 hours of exposure in a concentration dependent fashion in two cell lines (HEK293, HepG2) using two multiplexed, real-time assay technologies. One technology measures the metabolic activity of cells (i.e., cell viability, glo) while the other evaluates cell membrane integrity (i.e., cell death, flor). Using glo technology, more actives and greater temporal variations were seen in HEK293 cells, while results for the flor technology were more similar across the two cell types. Chemicals were grouped into classes based on their cytotoxicity kinetics profiles and these classes were evaluated for their associations with activity in the Tox21 nuclear receptor and stress response pathway assays. Some pathways, such as the activation of H2AX, were associated with the fast-responding cytotoxicity classes, while others, such as activation of TP53, were associated with the slow-responding cytotoxicity classes. By clustering pathways based on their degree of association to the different cytotoxicity kinetics labels, we identified clusters of pathways where active chemicals presented similar kinetics of cytotoxicity. Such linkages could be due to shared underlying biological processes between pathways, for example, activation of H2AX and heat shock factor. Others involving nuclear receptor activity are likely due to shared chemical structures rather than pathway level interactions. Based on the linkage between androgen receptor antagonism and Nrf2 activity, we surmise that a subclass of androgen receptor antagonists cause cytotoxicity via oxidative stress that is associated with Nrf2 activation. In summary, the real-time cytotoxicity screen provides informative chemical cytotoxicity kinetics data related to their cytotoxicity mechanisms, and with our analysis, it is possible to formulate mechanism-based hypotheses on the cytotoxic properties of the tested chemicals.
Asunto(s)
Contaminantes Ambientales/toxicidad , Histonas/metabolismo , Bibliotecas de Moléculas Pequeñas/clasificación , Bibliotecas de Moléculas Pequeñas/farmacología , Proteína p53 Supresora de Tumor/metabolismo , Membrana Celular/efectos de los fármacos , Proliferación Celular/efectos de los fármacos , Supervivencia Celular/efectos de los fármacos , Análisis por Conglomerados , Bases de Datos de Compuestos Químicos , Regulación de la Expresión Génica , Células HEK293 , Células Hep G2 , Humanos , Estrés Oxidativo , Transducción de Señal/efectos de los fármacos , Relación Estructura-Actividad , Pruebas de ToxicidadRESUMEN
The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.
Asunto(s)
Transportadoras de Casetes de Unión a ATP/antagonistas & inhibidores , Bibliotecas de Moléculas Pequeñas/química , Miembro 11 de la Subfamilia B de Transportador de Casetes de Unión al ATP , Transportadoras de Casetes de Unión a ATP/química , Animales , Sitios de Unión , Transporte Biológico , Enfermedad Hepática Inducida por Sustancias y Drogas/tratamiento farmacológico , Simulación por Computador , Bases de Datos de Compuestos Químicos , Humanos , Ligandos , Aprendizaje Automático , Ratones , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica , Homología de Secuencia de Aminoácido , Bibliotecas de Moléculas Pequeñas/clasificaciónRESUMEN
Various small molecules present in biological systems can assist protein folding in vitro and are known as chemical chaperones. De novo design of chemical chaperones with higher activity than currently known examples is desirable to ameliorate protein misfolding and aggregation in multiple contexts. However, this development has been hindered by limited knowledge of their activities. It is thought that chemical chaperones are typically poor solvents for a protein backbone and hence facilitate native structure formation. However, it is unknown if different chemical chaperones can act differently to modulate folding energy landscapes. Using a model slow folding protein, double-mutant Maltose-binding protein (DM-MBP), we show that a canonical chemical chaperone, trimethylamine-N-oxide (TMAO), accelerates refolding by decreasing the flexibility of the refolding intermediate (RI). Among a number of small molecules that chaperone DM-MBP folding, proline and serine stabilize the transition state (TS) enthalpically, while trehalose behaves like TMAO and increases the rate of barrier crossing through nonenthalpic processes. We propose a two-group classification of chemical chaperones based upon their thermodynamic effect on RI and TS, which is also supported by single molecule Förster resonance energy transfer (smFRET) studies. Interestingly, for a different test protein, the molecular mechanisms of the two groups of chaperones are not conserved. This provides a glimpse into the complexity of chemical chaperoning activity of osmolytes. Future work would allow us to engineer synergism between the two classes to design more efficient chemical chaperones to ameliorate protein misfolding and aggregation problems.
Asunto(s)
Proteínas de Unión a Maltosa/química , Metilaminas/química , Prolina/química , Serina/química , Bibliotecas de Moléculas Pequeñas/química , Trehalosa/química , Bacterias/química , Transferencia Resonante de Energía de Fluorescencia , Cinética , Modelos Moleculares , Unión Proteica , Pliegue de Proteína , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Proteínas Recombinantes/química , Bibliotecas de Moléculas Pequeñas/clasificación , TermodinámicaRESUMEN
The European REACH regulation requires information on ready biodegradation, which is a screening test to assess the biodegradability of chemicals. At the same time REACH encourages the use of alternatives to animal testing which includes predictions from quantitative structure-activity relationship (QSAR) models. The aim of this study was to build QSAR models to predict ready biodegradation of chemicals by using different modeling methods and types of molecular descriptors. Particular attention was given to data screening and validation procedures in order to build predictive models. Experimental values of 1055 chemicals were collected from the webpage of the National Institute of Technology and Evaluation of Japan (NITE): 837 and 218 molecules were used for calibration and testing purposes, respectively. In addition, models were further evaluated using an external validation set consisting of 670 molecules. Classification models were produced in order to discriminate biodegradable and nonbiodegradable chemicals by means of different mathematical methods: k nearest neighbors, partial least squares discriminant analysis, and support vector machines, as well as their consensus models. The proposed models and the derived consensus analysis demonstrated good classification performances with respect to already published QSAR models on biodegradation. Relationships between the molecular descriptors selected in each QSAR model and biodegradability were evaluated.
Asunto(s)
Modelos Estadísticos , Bibliotecas de Moléculas Pequeñas/metabolismo , Biodegradación Ambiental , Bases de Datos de Compuestos Químicos , Estructura Molecular , Relación Estructura-Actividad Cuantitativa , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/clasificaciónRESUMEN
G-protein coupled receptors (GPCR(s)) are a large family of membrane-bound receptors that mediate a wide range of physiologic responses to hormones, neurotransmitters and dietary lipids, which represent an important class of drug targets. Significant chemical space regions have been explored both in the academia and by pharmaceutical companies, in the quest for new GPCR modulators as potential therapeutic agents. This accumulated body of evidence provides new opportunities to evaluate potential features of GPCR agonists and antagonists, and how to distinguish them. In this study, the chemical space covered within the WOMBAT database by GPCRs modulators was investigated with the aim of identifying specific molecular determinants that distinguish GPCR agonists from antagonists. While instrumental to get insights into the design strategies of GPCRs modulators, the results of this study provide novel clues on the molecular mechanisms that underlie the complexity of GPCR modulation.
Asunto(s)
Algoritmos , Receptores Acoplados a Proteínas G/agonistas , Receptores Acoplados a Proteínas G/antagonistas & inhibidores , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/clasificación , Sitios de Unión , Bases de Datos Farmacéuticas , Árboles de Decisión , Diseño de Fármacos , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Unión Proteica , Receptores Acoplados a Proteínas G/química , Electricidad Estática , Relación Estructura-ActividadRESUMEN
In ligand-based screening, retrosynthesis, and other chemoinformatics applications, one often seeks to search large databases of molecules in order to retrieve molecules that are similar to a given query. With the expanding size of molecular databases, the efficiency and scalability of data structures and algorithms for chemical searches are becoming increasingly important. Remarkably, both the chemoinformatics and information retrieval communities have converged on similar solutions whereby molecules or documents are represented by binary vectors, or fingerprints, indexing their substructures such as labeled paths for molecules and n-grams for text, with the same Jaccard-Tanimoto similarity measure. As a result, similarity search methods from one field can be adapted to the other. Here we adapt recent, state-of-the-art, inverted index methods from information retrieval to speed up similarity searches in chemoinformatics. Our results show a several-fold speed-up improvement over previous methods for both threshold searches and top-K searches. We also provide a mathematical analysis that allows one to predict the level of pruning achieved by the inverted index approach and validate the quality of these predictions through simulation experiments. All results can be replicated using data freely downloadable from http://cdb.ics.uci.edu/ .
Asunto(s)
Algoritmos , Bases de Datos de Compuestos Químicos , Informática/estadística & datos numéricos , Bibliotecas de Moléculas Pequeñas/química , Interfaz Usuario-Computador , Ensayos Analíticos de Alto Rendimiento , Informática/métodos , Funciones de Verosimilitud , Estructura Molecular , Bibliotecas de Moléculas Pequeñas/clasificaciónRESUMEN
A modified version of the CORAL software (http://www.insilico.eu/coral) allows building up the classification model for the case of the Yes/No data on the anti-sarcoma activity of organic compounds. Three random splits into the sub-training, calibration, and test sets of the data for 3017 compounds were examined. The performance of the proposed approach is satisfactory. The average values of the statistical characteristics for external test set on three random splits are as follows: n=1173-1234, sensitivity = 0.8903±0.0390, specificity = 0.9869±0.0013, and accuracy = 0.9759±0.0043. Mechanistic interpretation of the suggested model is discussed.