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Bromodomains (BDs) are small protein modules that interact with acetylated marks in histones. These posttranslational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here, we combine extensive molecular dynamics simulations, Markov state modeling, and available structural data to reveal a transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the αA helix, opening a cryptic pocket that partially occludes the one associated to histone binding. By analyzing more than 1,900 experimental structures, we unveil just two adopting the hidden state, explaining why it has been previously unnoticed and providing direct structural evidence for its existence. Our results suggest that this state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA-binding mode.
Assuntos
Proteínas de Ciclo Celular/química , Proteínas Correpressoras/química , Proteínas de Ligação a DNA/química , Histona Acetiltransferases/química , Peptídeos e Proteínas de Sinalização Intracelular/química , Fatores Genéricos de Transcrição/química , Fatores de Transcrição/química , Proteína 28 com Motivo Tripartido/química , Sequência de Aminoácidos , Sítios de Ligação , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Proteínas Correpressoras/genética , Proteínas Correpressoras/metabolismo , Cristalografia por Raios X , DNA/química , DNA/genética , DNA/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Regulação da Expressão Gênica , Histona Acetiltransferases/genética , Histona Acetiltransferases/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Cadeias de Markov , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Termodinâmica , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Fatores Genéricos de Transcrição/genética , Fatores Genéricos de Transcrição/metabolismo , Proteína 28 com Motivo Tripartido/genética , Proteína 28 com Motivo Tripartido/metabolismoRESUMO
Inhibition of intracellular nicotinamide phosphoribosyltransferase (NAMPT) represents a new mode of action for cancer-targeting antibody-drug conjugates (ADCs) with activity also in slowly proliferating cells. To extend the repertoire of available effector chemistries, we have developed a novel structural class of NAMPT inhibitors as ADC payloads. A structure-activity relationship-driven approach supported by protein structural information was pursued to identify a suitable attachment point for the linker to connect the NAMPT inhibitor with the antibody. Optimization of scaffolds and linker structures led to highly potent effector chemistries which were conjugated to antibodies targeting C4.4a (LYPD3), HER2 (c-erbB2), or B7H3 (CD276) and tested on antigen-positive and -negative cancer cell lines. Pharmacokinetic studies, including metabolite profiling, were performed to optimize the stability and selectivity of the ADCs and to evaluate potential bystander effects. Optimized NAMPTi-ADCs demonstrated potent in vivo antitumor efficacy in target antigen-expressing xenograft mouse models. This led to the development of highly potent NAMPT inhibitor ADCs with a very good selectivity profile compared with the corresponding isotype control ADCs. Moreover, we demonstrateâto our knowledge for the first timeâthe generation of NAMPTi payload metabolites from the NAMPTi-ADCs in vitro and in vivo. In conclusion, NAMPTi-ADCs represent an attractive new payload class designed for use in ADCs for the treatment of solid and hematological cancers.
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Antineoplásicos , Imunoconjugados , Neoplasias , Nicotinamida Fosforribosiltransferase , Animais , Antineoplásicos/química , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Antígenos B7 , Linhagem Celular Tumoral , Humanos , Imunoconjugados/química , Imunoconjugados/farmacologia , Camundongos , Neoplasias/tratamento farmacológico , Neoplasias/enzimologia , Nicotinamida Fosforribosiltransferase/antagonistas & inibidores , Nicotinamida Fosforribosiltransferase/química , Relação Estrutura-Atividade , Ensaios Antitumorais Modelo de XenoenxertoRESUMO
High-quality, up-to-date, systematic reviews comprehensively summarize the evidence from clinical studies for a focused clinical question. A meta-analyses is a quantitative summary of results from individual studies and often part of a systematic review. Important features of a systematic review are a focused research question, a comprehensive, reproducible search for primary studies, selection of studies using clear and transparent eligibility criteria, and a standardized critical appraisal of the methodological quality of included studies.
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Medicina Baseada em Evidências , Metanálise como Assunto , Literatura de Revisão como Assunto , Pesquisa Biomédica , HumanosRESUMO
Valid systematic reviews are essential for a safe navigation through the existing literature on a specific clinical topic. In the second part of our training to "Reviews, systematic reviews and meta-analyses", we explain how the results of systematic reviews and meta-analyses should be presented and how they should be interpreted. We describe the forest plot, with which you can get a quick overview of the results of numerous studies, the funnel plot, which can be useful for identifying a publication bias, and report on sensitivity and subgroup analyses, which are of great importance to discover the source of heterogeneity between individual studies. Finally, at the end of our article series, we hopefully convinced you of the importance to make up your own mind about the interpretation of the results of aggregated evidence.
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Medicina Baseada em Evidências , Metanálise como Assunto , Literatura de Revisão como Assunto , Humanos , Viés de PublicaçãoRESUMO
Results of clinical trials are presented in different expressions of risks: baseline risk, relative risk (RR), relative risk reduction (RRR), absolute risk reduction (ARR), or risk difference (RD). In this article of our series about the basics of evidence-based medicine we show how results of clinical trials are calculated based on the 2 x 2-table. The 2 x 2-table usually contains all information needed to calculate the main study results. Adequate interpretation of the results/treatment effects is the basis for evidence-based advices in pharmaceutical practice.
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Ensaios Clínicos como Assunto/estatística & dados numéricos , Interpretação Estatística de Dados , Medicina Baseada em Evidências , Humanos , Matemática , Farmácia/normas , Medição de Risco , Comportamento de Redução do RiscoRESUMO
In the last article, you learned about the interpretation of survival curves. This article is about the comparison of "survival" - or the time to any defined event. Two survival curves can be summarized with the hazard ratio, which is discussed in more detail in this article. In order to compare the "survival"of two treatment groups - particularly in non-randomised studies - additional variables (potential confounders) must be taken into account. This is done using a regression model, the so-called Cox-regression. After reading this article, hopefully these terms are more familiar to you.
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Modelos Estatísticos , Análise de Regressão , Análise de Sobrevida , Ensaios Clínicos como Assunto , HumanosRESUMO
In clinical trials data of individuals are collected, who are subjected to different treatments under controlled conditions. These studies investigate differences between interventions, and their results--provide the basis for clinical decision making in individuals or for policy decisions concerning entire patient populations. This requires reliable results. How confident a result of the study actually is, is illustrated by using various statistical parameters: p-value or confidence interval. What these parameters are and how to interpret them, is the objective of this article.
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Intervalos de Confiança , Interpretação Estatística de Dados , Ensaios Clínicos Controlados Aleatórios como Assunto , Resultado do Tratamento , HumanosRESUMO
In our previous articles we introduced the relative and absolute expressions of risk: baseline risk, relative risk (RR), relative risk reduction (RRR), absolute risk reduction (ARR), or risk difference (RD). The "number needed to xy" is another concept to describe the results of a clinical trial. Depending on the investigated problem the "number needed to xy" is the "number needed to treat", the "number needed to harm", the "number needed to vaccinate", or the "number needed to screen". In this article of our series we introduce the number needed to treat (NNT) and the number needed to harm (NNH) as a method to characterize the difference of two compared therapy options. As the other effect sizes the NNT and NNH can be used to inform patients about the expected benefit (or harm) of different therapy options.
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Ensaios Clínicos como Assunto/estatística & dados numéricos , Humanos , Números Necessários para Tratar , Projetos de Pesquisa , Medição de Risco , Comportamento de Redução do RiscoRESUMO
Survival curves plot percent survival as a function of time. Results of clinical trials are often presented as survival curves. However, the purpose of survival analysis is not, as the name suggests, limited to "survival". Rather, it can concern the time to any defined event, desired or undesired. The me- thod behind these curves may be tricky; "reading" of the curves, however, is simple and intuitive. And with a few basic skills misinterpretations can usually be avoided.
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Estimativa de Kaplan-Meier , Análise de Sobrevida , HumanosRESUMO
In addition to relative risk, relative risk reduction and absolute risk reduction there circulates another effect size for binary endpoints in the scientific medical literature: the odds ratio. Relative risk and odds ratio are alternative ways of reflecting study results. Both, relative risk (RR) and odds ratio (OR), can easily be calculated from the "2 x 2-table". Advantage of OR: odds ratios can be calculated in every type of controlled study design, including retrospective studies. Furthermore, odds ratios--the biostatisticians are swarming--offer beautiful mathematical properties and therefore are often used in meta-analysis as an effect size for calculating a pooled estimate of the results of different studies with the same clinical question. Disadvantage of OR: In clinical studies the presentation of the results as "odds ratios" may result in an overestimation of the intervention effect. This article shows the difference between ""chance" and "risk" and how odds ratio and relative risk are associated.
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Matemática , Medição de Risco , Bioestatística , Humanos , Razão de Chances , Projetos de Pesquisa , Estudos RetrospectivosRESUMO
Over the centuries some individual scientists have challenged their knowledge, believes and behaviour. The common knowledge developed very fast, but the challenge still remains to ask the question "what do we really know"? And "what is the basis of our decisions and recommendations?" The scattered individual efforts finally advanced to a consolidated methodology--known as "evidence based medicine". This is the first article of a series to get German speaking pharmacists familiar with the basic concepts of evidence based methodology. The series gives some examples how the concept of evidence based medicine can be implemented in pharmaceutical practice.
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Medicina Baseada em Evidências , Conhecimentos, Atitudes e Prática em Saúde , Disseminação de Informação , Interpretação Estatística de Dados , HumanosRESUMO
We live in the modern information society. "To be informed" has a crucial impact on the personal, professional, economic and social development. The knowledge of things and their relationships is essential for acute decisions as well as for long-term planning. And at no time it was easier to get the information required within shorter time periods--no matter to whatsoever. The offer of information of the World Wide Web is inexhaustible. This also applies to information about all possible therapeutic and pharmaceutical issues. But is the information found reliable, too? And are easily accessible sources credible? Can we deal with the information overload at these days or do we actually risk paddling only on the surface of the "information-sea", without ever perceiving the actual information depth and width, less to use it? How can we protect being taken in by marketing strategies? The present article describes a structured proceed when seeking literature to find useful medical and pharmaceutical information in a time saving manner.
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Educação em Saúde/tendências , Internet , HumanosRESUMO
The critical appraisal of a study publication includes several steps: quality inspection of the study methodology, examination of the results, assessments of benefit and harm for the individual patient. If the first step of the "critical appraisal" determines, that different sources of bias were successfully eliminated or minimized in the study conduct, it is worthwhile to work through the article completely. In the second step, the size and confidence of the study results have to be examined in detail. Different outcome measures are used to describe the effect of an intervention in clinical trials. However, not all endpoints studied, or differences that are found between treatment groups, are important for the decision making of a patient. In the last step, the study results are interpreted for the individual patient in terms of the expected ben- efits and possible harms. While the control of methodical quality and the effect size of study outcomes may be based on formal criteria, professional value judgement is necessary for the transfer of study results to an individual patient, by which a recommendation can be made, adapted to the individual circumstances, needs and expectations of the patient.
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Pesquisa Biomédica/tendências , Medicina Baseada em Evidências/tendências , Assistência Farmacêutica/organização & administração , Assistência Farmacêutica/tendências , Tratamento Farmacológico/tendências , Humanos , FarmáciaRESUMO
In a unique collaboration between Simulations Plus and several industrial partners, we were able to develop a new version 11.0 of the previously published in silico pKa model, S+pKa, with considerably improved prediction accuracy. The model's training set was vastly expanded by large amounts of experimental data obtained from F. Hoffmann-La Roche AG, Genentech Inc., and the Crop Science division of Bayer AG. The previous v7.0 of S+pKa was trained on data from public sources and the Pharmaceutical division of Bayer AG. The model has shown dramatic improvements in predictive accuracy when externally validated on three new contributor compound sets. Less expected was v11.0's improvement in prediction on new compounds developed at Bayer Pharma after v7.0 was released (2013-2023), even without contributing additional data to v11.0. We illustrate chemical space coverage by chemistries encountered in the five domains, public and industrial, outline model construction, and discuss factors contributing to model's success.
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Interleukin-1 receptor-associated kinase 4 (IRAK4) plays a critical role in innate inflammatory processes. Here, we describe the discovery of two clinical candidate IRAK4 inhibitors, BAY1834845 (zabedosertib) and BAY1830839, starting from a high-throughput screening hit derived from Bayer's compound library. By exploiting binding site features distinct to IRAK4 using an in-house docking model, liabilities of the original hit could surprisingly be overcome to confer both candidates with a unique combination of good potency and selectivity. Favorable DMPK profiles and activity in animal inflammation models led to the selection of these two compounds for clinical development in patients.
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Ensaios de Triagem em Larga Escala , Indazóis , Quinases Associadas a Receptores de Interleucina-1 , Piridinas , Animais , Humanos , Sítios de Ligação , InflamaçãoRESUMO
The Structural Genomics Consortium is an international open science research organization with a focus on accelerating early-stage drug discovery, namely hit discovery and optimization. We, as many others, believe that artificial intelligence (AI) is poised to be a main accelerator in the field. The question is then how to best benefit from recent advances in AI and how to generate, format and disseminate data to enable future breakthroughs in AI-guided drug discovery. We present here the recommendations of a working group composed of experts from both the public and private sectors. Robust data management requires precise ontologies and standardized vocabulary while a centralized database architecture across laboratories facilitates data integration into high-value datasets. Lab automation and opening electronic lab notebooks to data mining push the boundaries of data sharing and data modeling. Important considerations for building robust machine-learning models include transparent and reproducible data processing, choosing the most relevant data representation, defining the right training and test sets, and estimating prediction uncertainty. Beyond data-sharing, cloud-based computing can be harnessed to build and disseminate machine-learning models. Important vectors of acceleration for hit and chemical probe discovery will be (1) the real-time integration of experimental data generation and modeling workflows within design-make-test-analyze (DMTA) cycles openly, and at scale and (2) the adoption of a mindset where data scientists and experimentalists work as a unified team, and where data science is incorporated into the experimental design.
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Ciência de Dados , Descoberta de Drogas , Aprendizado de Máquina , Descoberta de Drogas/métodos , Ciência de Dados/métodos , Humanos , Inteligência Artificial , Disseminação de Informação/métodos , Mineração de Dados/métodos , Computação em Nuvem , Bases de Dados FactuaisRESUMO
BACKGROUND: Pelargonium sidoides (P. sidoides), also known as Umckaloabo, is a herbal remedy thought to be effective in the treatment of acute respiratory infections (ARIs). OBJECTIVES: To assess the efficacy and safety of P. sidoides for the treatment of ARIs in children and adults. SEARCH METHODS: In April 2013 we searched MEDLINE, Journals@Ovid, The Cochrane Library, Biosis Previews, Web of Science, CINAHL, CCMed, XToxline, Global Health, AMED, Derwent Drug File and Backfile, IPA, ISTPB + ISTP/ISSHP, EMBASE, Cambase, LILACS, PubMed component "Supplied by Publisher", TRIPdatabase, the publisher databases: Deutsches Ärzteblatt, Thieme, Springer, ScienceDirect from Elsevier. We conducted a cited reference search (forward) in Web of Science of relevant papers for inclusion. In addition we searched the study registries ClinicalTrials.gov, Deutsches Register klinischer Studien DRKS (German Clinical Trials Register), International Clinical Trials Registry Platform (ICTRP) - WHO ICTRP, Current Controlled Trials and EU Clinical Trials Register. SELECTION CRITERIA: Double-blind, randomized controlled trials (RCTs) examining the efficacy of P. sidoides preparations in ARIs compared to placebo or any other treatment. Complete resolution of all symptoms was defined as the primary outcome; in addition, we examined resolution of predefined key symptoms. DATA COLLECTION AND ANALYSIS: At least two review authors (AT, JG, WK) independently extracted and quality scored the data. We performed separate analyses by age group and disease entity. Subanalysis considered type of preparation (liquid, tablets). We examined heterogeneity using the I(2) statistic. We calculated pooled risk ratios (RR) using a fixed-effect model if heterogeneity was absent (I(2) < 5%; P > 0.1), or a random-effects model in the presence of heterogeneity. If heterogeneity was substantial (I(2) > 50%; P < 0.10), a pooled effect was not calculated. MAIN RESULTS: Of 10 eligible studies eight were included in the analyses; two were of insufficient quality. Three trials (746 patients, low quality of evidence) of efficacy in acute bronchitis in adults showed effectiveness for most outcomes in the liquid preparation but not for tablets. Three other trials (819 children, low quality of evidence) showed similar results for acute bronchitis in children. For both meta-analyses, we did not pool sub totals due to relevant heterogeneity induced by type of preparation.One study in patients with sinusitis (n = 103 adults, very low quality of evidence) showed significant treatment effects (complete resolution at day 21; RR 0.43, 95% confidence interval (CI) 0.30 to 0.62). One study in the common cold demonstrated efficacy after 10 days, but not five days (very low quality of evidence). We rated the study quality as moderate for all studies (unvalidated outcome assessment, minor attrition problems, investigator-initiated trials only). Based on the funnel plot there was suspicion of publication bias.There were no valid data for the treatment of other acute respiratory tract infections. Adverse events were more common with P. sidoides, but none were serious. AUTHORS' CONCLUSIONS: P. sidoides may be effective in alleviating symptoms of acute rhinosinusitis and the common cold in adults, but doubt exists. It may be effective in relieving symptoms in acute bronchitis in adults and children, and sinusitis in adults. The overall quality of the evidence was considered low for main outcomes in acute bronchitis in children and adults, and very low for acute sinusitis and the common cold. Reliable data on treatment for other ARIs were not identified.
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Pelargonium/química , Fitoterapia/métodos , Extratos Vegetais/uso terapêutico , Infecções Respiratórias/tratamento farmacológico , Doença Aguda , Adulto , Bronquite/tratamento farmacológico , Criança , Resfriado Comum/tratamento farmacológico , Humanos , Ensaios Clínicos Controlados Aleatórios como Assunto , Sinusite/tratamento farmacológicoRESUMO
AIMS: Objectives of this study were to examine the administrative incidence of urinary incontinence in children and to assess related outpatient health services utilization in this cohort. METHODS: Data of a statutory health insurance company were analyzed and outpatients from 1 to 18 years of age with a first recorded ICD-10 code for non-organic urinary incontinence during a 1-year-period (2007) were identified. For this cohort, the prescription of desmopressin, antispasmodics, non-selective monoamine reuptake inhibitors, alarm devices, and incontinence pads in the quarter of the first diagnosis and in the following one (i.e., 6 months) was evaluated with respect to age and gender. RESULTS: 3,188 patients (59.4% male; mean age 6.8 years) matched the inclusion criteria, of whom 25.4% were under 5 years old. 7.9% were prescribed desmopressin, 7.4% received urinary antispasmodics, and 7.0% were treated with alarm devices. For 77.9% of patients, no specific incontinence-related treatments were prescribed. We found considerable differences in treatment patterns between age groups, with patients ≥ 7 years receiving desmopressin more frequently than alarm devices. Regarding gender differences, the proportion of males treated with alarm devices (prevalence ratio [PR] 1.46; 95% confidence interval [95%CI] 1.11-1.92) and at least one specific treatment (PR 1.19; 95%CI 1.04-1.35) remained statistically significantly higher, even after adjusting for age. CONCLUSIONS: In our study, we found evidence that treatment modalities only partly comply with the current guidelines for treatment of children and adolescents with non-organic urinary incontinence. Therefore, the dissemination of current guidelines remains a major educational goal.
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Fidelidade a Diretrizes , Pacientes Ambulatoriais , Padrões de Prática Médica , Incontinência Urinária/epidemiologia , Incontinência Urinária/terapia , Adolescente , Fatores Etários , Antidiuréticos/uso terapêutico , Criança , Pré-Escolar , Alarmes Clínicos , Estudos de Coortes , Desamino Arginina Vasopressina/uso terapêutico , Feminino , Alemanha/epidemiologia , Humanos , Incidência , Tampões Absorventes para a Incontinência Urinária , Lactente , Masculino , Parassimpatolíticos/uso terapêutico , Estudos Retrospectivos , Fatores Sexuais , Resultado do TratamentoRESUMO
Mitochondria are key regulators of energy supply and cell death. Generation of ATP within mitochondria occurs through oxidative phosphorylation (OXPHOS), a process which utilizes the four complexes (complex I-IV) of the electron transport chain and ATP synthase. Certain oncogenic mutations (e.g., LKB1 or mIDH) can further enhance the reliance of cancer cells on OXPHOS for their energetic requirements, rendering cells sensitive to complex I inhibition and highlighting the potential value of complex I as a therapeutic target. Herein, we describe the discovery of a potent, selective, and species cross-reactive complex I inhibitor. A high-throughput screen of the Bayer compound library followed by hit triaging and initial hit-to-lead activities led to a lead structure which was further optimized in a comprehensive lead optimization campaign. Focusing on balancing potency and metabolic stability, this program resulted in the identification of BAY-179, an excellent in vivo suitable tool with which to probe the biological relevance of complex I inhibition in cancer indications.
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The branched-chain amino acid transaminases (BCATs) are enzymes that catalyze the first reaction of catabolism of the essential branched-chain amino acids to branched-chain keto acids to form glutamate. They are known to play a key role in different cancer types. Here, we report a new structural class of BCAT1/2 inhibitors, (trifluoromethyl)pyrimidinediones, identified by a high-throughput screening campaign and subsequent optimization guided by a series of X-ray crystal structures. Our potent dual BCAT1/2 inhibitor BAY-069 displays high cellular activity and very good selectivity. Along with a negative control (BAY-771), BAY-069 was donated as a chemical probe to the Structural Genomics Consortium.