688 research outputs found

    Characterization and Bioanalysis of Protein-Based Biopharmaceuticals, Peptides and Amino Acids by Liquid Chromatography and Mass Spectrometry

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    Biopharmazeutika sind zu einer essenziellen Klasse von Therapeutika geworden und werden für verschiedene medizinische Indikationen wie Diabetes, Krebs, entzündliche Erkrankungen und Infektionskrankheiten eingesetzt. Monoklonale Antikörper (mAbs) haben innerhalb der Biopharmazeutika den größten Anteil bezogen auf die Zulassungszahlen. Den Vorteilen bezüglich hoher Spezifität und Effektivität stehen jedoch Nachteile durch hohe Kosten und erhöhter Komplexität gegenüber. Die Komplexität ergibt sich einerseits aufgrund des hohen Molekulargewichts und anderseits aufgrund der strukturellen Heterogenität, wodurch die analytische Charakterisierung und Qualitätskontrolle von mAbs und anderer Biopharmazeutika zu einer Herausforderung wird. Neben diesen protein-basierten Biopharmazeutika ist auch die Aufklärung der absoluten Konfiguration von therapeutischen und natürlichen (Lipo)peptiden von besonderem Interesse für die Wirkstoffforschung. Zur Bewältigung dieser Herausforderungen wurden in der hier präsentierten Arbeit flüssigchromatographische (LC) und massenspektrometrische (MS) Methoden für die umfassende Analyse eingesetzt. Die erste Publikation dieser Dissertation bezog sich auf die Analyse von Ladungsvarianten von mAbs, welche wichtige Qualitätsmerkmale darstellen und die Sicherheit und Wirksamkeit des Arzneimittels beeinflussen können. Zur Charakterisierung der Ladungsvarianten wurden die mAbs auf Ebene des intakten Proteins als auch auf Fragmentebene nach begrenztem Verdau und Reduzierung der Disulfidbrücken mittels starker Kationenaustauschflüssigkeitschromatographie (SCX) analysiert. Die SCX-Methode wurde systematisch mittels statistischer Versuchsplanung (DoE) dahingehend optimiert, die höchstmögliche Anzahl an Ladungsvarianten zu trennen. Die mobile Phase der optimierten SCX-Methode enthielt jedoch eine hohe Konzentration an nicht-flüchtigen Salzen, wodurch sie nicht mit MS Detektion kompatibel ist, welche wiederum entscheidend für die Identifikation der Ladungsvarianten ist. Um dieser Herausforderung zu begegnen, wurde erfolgreich eine online zweidimensionale flüssigchromatographische (2D-LC) Methode entwickelt, bei der SCX in der ersten Trenndimension und Umkehrphasenflüssigchromatographie (RP-LC) in der zweiten Trenndimension zur Entsalzung vor der MS Detektion verwendet wurde. Die Entwicklung einer extrem kurzen (≤ 1 min) RP-LC Methode war unabdingbar zur Etablierung einer umfassenden 2D-LC Methode. Dazu wurde eine Säulenvergleichsstudie mit monolithischen und oberflächlich porösen Partikelsäulen (SPP-Säulen) durchgeführt und die Trenneffizienz sowie die Analysengeschwindigkeit untersucht. Eine noch umfassendere Säulenvergleichsstudie mit Fokus auf das kinetische Leistungsvermögen wurde in der zweiten Arbeit dieser Dissertation durchgeführt. Eine Auswahl von 13 RP-Proteintrennsäulen inklusive monolithischer, SPP und vollporöser Partikelsäulen (FPP-Säulen) wurde hinsichtlich ihrer Fähigkeit, Peaks in der kürzest möglichen Zeit zu trennen, untersucht. Es konnte gezeigt werden, dass SPP-Säulen mit einer Porengröße von etwa 400 Å und einer dünnen, porösen Schicht die beste Performance insbesondere für größere Proteinen besitzen. Proteine selbst können auch potenzielle Ziele für Arzneistoffe sein, wie z.B. das Tumorsuppressorprotein p53, welches in der dritten Publikation dieser Arbeit untersucht wurde. Intakte Protein LC-MS wurde erfolgreich verwendet, um die Bindungseffizienz und -spezifität des kovalenten Inhibitors an p53 nachzuweisen. Aminosäuren sind die Bausteine von Proteinen und Peptiden und die Mehrheit dieser Aminosäuren sind chiral. Die biologische Aktivität ist in der Regel abhängig von der absoluten Konfiguration der Aminosäuren, wodurch die enantiomerenselektive Analyse von höchster Wichtigkeit für die Strukturaufklärung und zur Qualitätskontrolle ist. Daher war die Entwicklung schneller und umfassender Trennmethoden zur Analyse von Aminosäuren, deren Enantiomeren, Diastereomeren und konstitutionellen Isomeren ein Ziel dieser Arbeit. Dieses konnte durch Derivatisierung mittels 6-Aminochinolyl-N-hydroxysuccinimidylcarbamat (AQC) und anschließender Analyse durch enantioselektiver flüssigchromatographischer Ionenmobilitäts-Massenspektrometrie (LC-IM-MS) erreicht werden. Eine sehr schnelle dreiminütige Analysenmethode konnte entwickelt und zur Strukturaufklärung von therapeutischen Peptiden und eines natürlichen Lipopeptides eingesetzt werden. Die absolute Konfiguration eines Tetrapeptides als Bestandteil des natürlichen, antimikrobiellen Peptidpolyens‘ Epifadin konnte mittels chiraler LC-MS bestimmt werden, was wiederum entscheidend für die Strukturaufklärung war. In dieser Arbeit konnten alle acht Enantiomerenpaare erfolgreich getrennt werden und die Diastereomerentrennung wurde optimiert.Biopharmaceuticals have become an essential class of therapeutics and are used for different medical indications such as diabetes, cancer, inflammatory diseases, and infectious diseases. Monoclonal antibodies (mAbs) have the biggest share within the biopharmaceuticals regarding the drug approval numbers. However, the benefits in terms of high specificity and efficacy come with the drawback of higher cost and higher complexity. This complexity arises from the high molecular weight on the one hand and high structural heterogeneity on the other hand, making the analytical characterization and quality control of mAbs and other biopharmaceuticals a significant challenge. In addition to these protein-based biopharmaceuticals, the elucidation of the absolute configuration of therapeutic peptides and natural (lipo)peptides is also of particular interest for drug discovery. To address these challenges, different liquid chromatography (LC) and mass spectrometric (MS) methods were used for the more comprehensive analysis in the presented work. The first publication of this dissertation was dedicated to the analysis of charge variants of mAbs, which is an important quality attribute that might affect safety and efficacy of the drug product. To characterize the charge variants, the mAbs were analysed at the intact protein level and the subunit level after limited digestion and disulphide reduction using strong cation-exchange chromatography (SCX). The SCX method was systematically optimized to enable the separation of the maximum number of charge variants using a design of experiments (DoE) approach. The optimized SCX mobile phase, however, contains high concentrations of non-volatile salt in the mobile phase, which is incompatible with MS detection. On the other hand, MS analysis is essential for the identification of the charge variants. To overcome this limitation, an online two-dimensional liquid chromatographic (2D-LC) method was successfully developed, which uses SCX in the first separation dimension and reversed-phase (RP) LC in the second separation dimension, which can be used for de-salting prior MS analysis. An ultra-short analysis time (≤ 1 min) of the second dimension RP method was essential to establish a full comprehensive 2D-LC analysis. For this purpose, a column comparison study was performed using a set of monolithic and superficially porous particle (SPP) columns, and the separation efficiency and analysis speed were investigated. An even more comprehensive column comparison study focusing on the kinetic performance was done for the second work presented in this dissertation. A set of 13 RP protein separation columns including monolithic, SPP, and fully porous particle (FPP) columns was investigated regarding their capability to separate peaks in the shortest possible time. It could be demonstrated that SPP columns with a pore size of 400 Å and a thin, porous shell provided the best performance especially for large proteins such as mAbs. Proteins themselves can also be the potential targets of drug products such as the tumour suppressor protein p53 studied in publication III. Intact protein LC-MS was successfully used to investigate the binding efficiency and specificity of covalent inhibitors. Amino acids are the building blocks of proteins and peptides and most of these amino acids are chiral. As the biological activity is usually dependent on the absolute configuration of the amino acids, the enantioselective analysis is of utmost importance for structural elucidation and quality control. Therefore, one goal of the presented work was to develop a fast and comprehensive method to separate amino acids, their enantiomers, diastereomers, and constitutional isomers. This was achieved by derivatization using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) and subsequent analysis by enantioselective liquid chromatography ion mobility-mass spectrometry (LC-IM-MS). A very fast three minutes short analysis method could be developed and was applied for the successful structure elucidation of a therapeutic peptide and a natural lipopeptide. The absolute configuration of a tetrapeptide originating from the natural antimicrobial peptide-polyene epifadin could be determined using chiral LC-MS, which was crucial for the structure elucidation. In this work, all eight enantiomer peak pairs could be successfully separated and the separation of the diastereomers was optimized

    De novo drug design through artificial intelligence: an introduction

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    Developing new drugs is a complex and formidable challenge, intensified by rapidly evolving global health needs. De novo drug design is a promising strategy to accelerate and refine this process. The recent introduction of Generative Artificial Intelligence (AI) algorithms has brought new attention to the field and catalyzed a paradigm shift, allowing rapid and semi-automatic design and optimization of drug-like molecules. This review explores the impact of de novo drug design, highlighting both traditional methodologies and the recently introduced generative algorithms, as well as the promising development of Active Learning (AL). It places special emphasis on their application in oncological drug development, where the need for novel therapeutic agents is urgent. The potential integration of these AI technologies with established computational and experimental methods heralds a new era in the rapid development of innovative drugs. Despite the promising developments and notable successes, these technologies are not without limitations, which require careful consideration and further advancement. This review, intended for professionals across related disciplines, provides a comprehensive introduction to AI-driven de novo drug design of small organic molecules. It aims to offer a clear understanding of the current state and future prospects of these innovative techniques in drug discovery

    Analysis of the impact of synaptic plasticity genes and Human Accelerated Regions on brain function and structure: from the healthy brain to schizophrenia

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    [eng] Schizophrenia is a severe psychiatric disorder affecting around 24 million people worldwide. While we begin to disentangle the biological actors implicated in the origin of the disorder, the precise aetiological mechanisms remain largely unknown. Therefore, psychiatry research efforts still need to focus on a better understanding of the complex biological foundations of the disorder to achieve more precise diagnoses and the development of novel therapeutic strategies improving the patients’ quality of life. The prevailing etiopathological hypothesis considers that schizophrenia originates from the interplay between subtle genetic and environmental insults that disrupt the perfectly orchestrated mechanisms guiding neurodevelopment. Additionally, from an evolutionary perspective, it is suggested that schizophrenia represents a costly trade-off in the evolution of human-specific ontogenic neurodevelopmental processes sustaining the inherent complexity and variability of brain functioning, cognition, and behaviour. Along the neurodevelopmental process, the synapse formation and the organisation and maturation of neural circuits anchor the emergence of distinctive human cortical brain functions. In turn, multidisciplinary evidence indicates that synaptic alterations participate in brain dysfunctions, eventually leading to the emergence of the symptoms and cognitive deficits of schizophrenia. Accordingly, it is suggested that synaptic plasticity impairments play a critical role in the pathophysiology of the disorder. Among genes converging in neurodevelopmental and synaptic plasticity pathways, there are genes mediating signalling pathways involved in neural homeostasis, dendritic spine development and neural excitability, such as KCNH2, DISC1, CACNA1C and ZNF804A, all of them previously associated with the risk for schizophrenia. Moreover, evolutionary approaches have identified regions that accumulated human-specific changes since the divergence from chimpanzees, like Human Accelerated Regions (HARs). These regions act as transcriptional regulatory elements that endow human neurodevelopment with unique characteristics and harbour schizophrenia genetic susceptibility variants. To facilitate the identification of the genetic and biological mechanisms involved in schizophrenia aetiology, the use of brain-based intermediate phenotypes is a valuable strategy. Following two approaches centred on the genetic-phenotypic correlates of synaptic plasticity candidate genes and HARs sequences in the brain-based alterations in schizophrenia, this thesis includes four original articles and one systematic review. In these articles, we report the effect of common polymorphisms in KCNH2, DISC1, CACNA1C and ZNF804A genes and the polygenic load of HARs-informative sets on the differences observed between healthy brains and brains with schizophrenia. Overall, the results validate the efficacy of neuroimaging phenotypes to identify the genetic determinants of schizophrenia and point out the complementarity of candidate genes and genome-wide approaches in the study of the genetic architecture of the disorder. First, we describe the role of KCNH2 and DISC1 genetic variability in modulating the attentional and working memory-related functional responses in a diagnosis- dependent manner. Furthermore, we identify that the epistasis between two schizophrenia GWAS-associated genes, CACNAC1C and ZNF804A, influence the functional ability to adapt to increased working memory difficulty euqally in healthy controls and patients with schizophrenia. Second, we present a review of how HARs underlie human neurodevelopmental signatures, brain configuration, functioning and susceptibility behind psychiatric disorders. Likewise, we report the modulatory effect of HARs polygenicity on brain cortical architectural differences in schizophrenia and provide evidence on the importance of foetal-active regulatory HARs in patients' cortical surface area variability. Globally, the findings exposed in this thesis point towards the fact that the aetiological foundations of schizophrenia are related to the individual genetic differences altering neurodevelopment and synaptic plasticity trajectories but also to the genomic make-up that defines us as a species. This thesis provides a drop in the ocean of knowledge on disorders inherently linked to the human condition and has sought to comprehend the unique characteristics of our brain to help unravel what it means to be human.[cat] L’esquizofrènia és un trastorn neuropsiquiàtric greu que afecta a 24 milions de persones a tot el món. Tot i que comencem a conèixer els mecanismes biològics implicats en l’origen del trastorn, els processos etiològics precisos continuen essent en gran part desconeguts. Per tant, els esforços en la recerca encara necessiten dirigir-se en millorar el coneixement dels fonaments biològics del trastorn, per tal d’aconseguir un diagnòstic més precís i el desenvolupament de noves estratègies terapèutiques que millorin la qualitat de vida dels pacients. La hipòtesi etiopatogènica predominant considera que el trastorn s’origina a partir de la interacció entre factors genètics i ambientals que pertorben els mecanismes perfectament orquestrats que guien el neurodesenvolupament. A més, des d’una perspectiva evolutiva, s’ha suggerit que l’esquizofrènia representaria el “preu a pagar” per evolució dels processos ontogènics específicament humans que sustenten la complexitat i la variabilitat inherent al funcionament del cervell, la cognició i el comportament de la nostra espècie. Al llarg del neurodevenvolupament, la formació de sinapsis i l’organització i maduració dels circuits neurals ancoren l’aparició de funcions cerebrals corticals distintivament humanes. Al seu torn, evidències multidisciplinàries indiquen que les alteracions sinàptiques participen en disfuncions cerebrals que tenen com a resultat l’aparició dels símptomes cognitius i clínics de l’esquizofrènia. En conseqüència, s’ha proposat que les alteracions de la plasticitat sinàptica tenen un paper crític en la fisiopatologia del trastorn. Entre els gens que conflueixen en vies del neurodesenvolupament i de plasticitat sinàptica, hi ha gens que participen en vies de senyalització implicades en l’homeòstasi neuronal, el desenvolupament de les espines dendrítiques i l’excitabilitat neuronal, com els gens KCNH2, el DISC1, el CACNA1C i el ZNF804A, tots prèviament associats amb el risc per a l’esquizofrènia. A més, aproximacions evolutives han identificat regions que han acumulat canvis específicament en humans des de la divergència amb els ximpanzés, com les Regions Humanes Accelerades (o Human Accelerated Regions, HARs en anglès). Aquestes regions actuen com a elements reguladors de la transcripció atorgant característiques úniques al neurodesenvolupament humà, i contenen variants genètiques de susceptibilitat per a l’esquizofrènia. Per tal de facilitar l’identificar els mecanismes genètics i biològics implicats en l’etiologia de l’esquizofrènia, la utilització de fenotips cerebrals intermedis, com mesures de neuroimatge funcional i estructural, representa una estratègia molt útil. Seguint dues aproximacions centrades en l’anàlisi dels correlats genètics-fenotípics entre gens candidats relacionats amb la plasticitat sinàptica i regions HARs i les alteracions cerebrals de l’esquizofrènia, aquesta tesi inclou quatre articles originals i una revisió sistemàtica. En aquests articles, exposem l’efecte de polimorfismes en els gens KCNH2, DISC1, CACNA1C i ZNF804A i la càrrega poligènica en conjunts informatius de HARs sobre les diferències observades entre cervells de persones sanes i persones amb esquizofrènia. En conjunt, els resultats validen l’efectivitat dels fenotips de neuroimatge per identificar els determinants genètics de l’esquizofrènia i posen de manifest la complementarietat de les aproximacions centrades tant en gens candidats com en la variabilitat global del genoma per a l’estudi de l’arquitectura genètica del trastorn. Primer, descrivim el paper de la variabilitat genètica dels genes KCNH2 i DISC1 en la modulació de la resposta funcional a l’atenció i la memòria de treball de manera condicionada al diagnòstic. També, identifiquem que l’epistasi entre dos gens associats amb l’esquizofrènia a nivell de GWAS, el CACNAC1C i el ZNF804A, influeix en la capacitat funcionalde cervell per adaptar-se a l’increment de requeriments cognitius en memòria de treball en controls sans i pacients amb esquizofrènia. En segon lloc, oferim una revisió sobre com les HARs sustenten les característiques del neurodesenvolupament humà, la configuració cerebral, el funcionament i la susceptibilitat per als trastorns psiquiàtrics Així mateix, informem de l'efecte modulador de la poligenicitat de les HARs sobre les diferències en l’arquitectura cortical en l'esquizofrènia i proporcionem evidències sobre l’especial rellevància de les HARs associades amb elements reguladors de la transcripció actius durant l’etapa fetal. De manera global, els resultats d’aquesta tesi indiquen que els fonaments etiològics de l’esquizofrènia estan relacionats amb diferències genètiques individuals que impacten en les trajectòries del neurodesenvolupament i les vies de plasticitat sinàptica, així com amb la composició genòmica que ens defineix com a espècie. Aquesta tesi aporta una gota en l’oceà del coneixement sobre els trastorns intrínsecament vinculats a la condició humana i ha pretès contribuir en la comprensió de les característiques úniques del nostre cervell per ajudar a entendre què vol dir ser humà.[spa] La esquizofrenia es un trastorno psiquiátrico que afecta a 24 millones de personas en todo el mundo. A pesar de que empezamos a conocer los mecanismos biológicos implicados en el origen del trastorno, los procesos etiológicos precisos continúan siendo en gran parte desconocidos. Por ello, los esfuerzos investigadores todavía necesitan dirigirse en mejorar el conocimiento de los fundamentos biológicos del trastorno, para así conseguir una mayor precisión en el diagnóstico y desarrollar nuevas estrategias terapéuticas que mejoren la calidad de vida de los pacientes. La hipótesis etiopatogénica predominante considera que el trastorno se origina de la interacción entre factores genéticos y ambientales que modifican los mecanismos perfectamente orquestados que guían el neurodesarrollo. Además, desde una perspectiva evolutiva, se sostiene que la esquizofrenia representa “el precio a pagar” por la evolución de los procesos ontogénicos específicamente humanos que sustentan la complejidad y la variabilidad inherente al funcionamiento del cerebro, así como la cognición y comportamiento de nuestra especie. A lo largo del neurodesarrollo, la formación de sinapsis y la organización y maduración de los circuitos neurales anclan la aparición de funciones cerebrales corticales distintivamente humanas. Por su parte, evidencias multidisciplinares indican que las alteraciones sinápticas participan en disfunciones cerebrales asociadas a la aparición de los síntomas cognitivos y clínicos de la esquizofrenia. En consecuencia, se ha propuesto que las alteraciones de la plasticidad sináptica tienen un papel crítico en la fisiopatología del trastorno. Entre los genes que confluyen en vías del neurodesarrollo y de plasticidad sináptica, hay genes que participan en vías de señalización implicadas en la homeostasis neuronal, el desarrollo de las espinas dendríticas y la excitabilidad neural, como el KCNH2, el DISC1, el CACNA1C y el ZNF804A, todos ellos previamente asociados con el riesgo para la esquizofrenia. Además, aproximaciones evolutivas han identificado regiones que han acumulado cambios específicamente humanos desde la divergencia con los chimpancés, como las Regiones Humanas Aceleradas (o Human Accelerated Regions, HARs en inglés). Estas regiones actúan como elementos reguladores de la transcripción otorgando características únicas al neurodesarrollo humano, y albergan variantes genéticas de susceptibilidad para la esquizofrenia. Para facilitar la identificación de los mecanismo genéticos y biológicos implicados en la etiología del trastorno, el uso de fenotipos cerebrales intermedios, como medidas de neuroimagen funcional y estructural, es una herramienta de gran valor. Siguiendo dos aproximaciones centradas en el análisis de los correlatos genético- fenotípicos entre genes candidatos relacionados con la plasticidad sináptica y secuencias HARs y las alteraciones cerebrales en la esquizofrenia, esta tesis incluye cuatro artículos originales y una revisión sistemática. En estos artículos, exponemos el efecto de polimorfismos en los genes KCNH2, DISC1, CACNA1C y ZNF804A y la carga poligénica en conjuntos informativos de HARs sobre las diferencias observadas entre cerebros sanos y cerebros con esquizofrenia. En su conjunto, los resultados validan la efectividad de los fenotipos de neuroimagen para identificar los mecanismos genéticos de la esquizofrenia y ponen de manifiesto la complementariedad de las aproximaciones centradas tanto en genes candidatos como en la variabilidad global del genoma para estudiar la arquitectura genética del trastorno. Primero describimos el papel de la variabilidad genética de los genes KCNH2 y DISC1 en la modulación de la respuesta funcional a la atención y la memoria de trabajo de manera condicional al diagnóstico. Además, identificamos que la epistasis entre dos genes asociados con la esquizofrenia a nivel de GWAS, el CACNAC1C y el ZNF804A, influye en la capacidad funcional de cerebro para adaptarse al incremento de requerimientos cognitivos en memoria de trabajo tanto en controles sanos como en pacientes con esquizofrenia. En segundo lugar, ofrecemos una revisión sobre cómo las HARs sustentan las características del neurodesarrollo humano, la configuración y el funcionamiento cerebral y la susceptibilidad para trastornos psiquiátricos. Así mismo, informamos del efecto modulador de la poligenicidad de las HARs sobre las diferencias en la arquitectura cortical en la esquizofrenia y proporcionamos evidencias sobre la especial relevancia de las HARs asociadas con elementos reguladores de la transcripción activos durante la etapa fetal. De manera global, los resultados de esta tesis indican que los fundamentos etiológicos de la esquizofrenia están relacionados con diferencias genéticas individuales que impactan en las trayectorias del neurodesarrollo y en las vías de plasticidad sináptica, así como en la composición genética que nos define como especie. Esta tesis aporta una gota en el océano del conocimiento sobre los trastornos intrínsicamente vinculados a la condición humana y ha pretendido contribuir en la comprensión de las características únicas de nuestro cerebro para ayudar a entender qué quiere decir ser humano

    Computational Approaches to Drug Profiling and Drug-Protein Interactions

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    Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster

    Machine Learning Approaches for the Prioritisation of Cardiovascular Disease Genes Following Genome- wide Association Study

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    Genome-wide association studies (GWAS) have revealed thousands of genetic loci, establishing itself as a valuable method for unravelling the complex biology of many diseases. As GWAS has grown in size and improved in study design to detect effects, identifying real causal signals, disentangling from other highly correlated markers associated by linkage disequilibrium (LD) remains challenging. This has severely limited GWAS findings and brought the method’s value into question. Although thousands of disease susceptibility loci have been reported, causal variants and genes at these loci remain elusive. Post-GWAS analysis aims to dissect the heterogeneity of variant and gene signals. In recent years, machine learning (ML) models have been developed for post-GWAS prioritisation. ML models have ranged from using logistic regression to more complex ensemble models such as random forests and gradient boosting, as well as deep learning models (i.e., neural networks). When combined with functional validation, these methods have shown important translational insights, providing a strong evidence-based approach to direct post-GWAS research. However, ML approaches are in their infancy across biological applications, and as they continue to evolve an evaluation of their robustness for GWAS prioritisation is needed. Here, I investigate the landscape of ML across: selected models, input features, bias risk, and output model performance, with a focus on building a prioritisation framework that is applied to blood pressure GWAS results and tested on re-application to blood lipid traits

    An innovative strategy to investigate microbial protein modifications in a reliable fast and sensitive way: A therapy oriented proof of concept based on UV-C irradiation of SARS-CoV-2 spike protein

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    : The characterization of modifications of microbial proteins is of primary importance to dissect pathogen lifecycle mechanisms and could be useful in identifying therapeutic targets. Attempts to solve this issue yielded only partial and non-exhaustive results. We developed a multidisciplinary approach by coupling in vitro infection assay, mass spectrometry (MS), protein 3D modelling, and surface plasma resonance (SPR). As a proof of concept, the effect of low UV-C (273 nm) irradiation on SARS-CoV-2 spike (S) protein was investigated. Following UV-C exposure, MS analysis identified, among other modifications, the disruption of a disulphide bond within the conserved S2 subunit of S protein. Computational analyses revealed that this bond breakage associates with an allosteric effect resulting in the generation of a closed conformation with a reduced ability to bind the ACE2 receptor. The UV-C-induced reduced affinity of S protein for ACE2 was further confirmed by SPR analyses and in vitro infection assays. This comprehensive approach pinpoints the S2 domain of S protein as a potential therapeutic target to prevent SARS-CoV-2 infection. Notably, this workflow could be used to screen a wide variety of microbial protein domains, resulting in a precise molecular fingerprint and providing new insights to adequately address future epidemics

    Pediatric diffuse midline glioma H3K27- altered: A complex clinical and biological landscape behind a neatly defined tumor type

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    The 2021 World Health Organization Classification of Tumors of the Central Nervous System, Fifth Edition (WHO-CNS5), has strengthened the concept of tumor grade as a combination of histologic features and molecular alterations. The WHO-CNS5 tumor type “Diffuse midline glioma, H3K27-altered,” classified within the family of “Pediatric-type diffuse high-grade gliomas,” incarnates an ideally perfect integrated diagnosis in which location, histology, and genetics clearly define a specific tumor entity. It tries to evenly characterize a group of neoplasms that occur primarily in children and midline structures and that have a dismal prognosis. Such a well-defined pathological categorization has strongly influenced the pediatric oncology community, leading to the uniform treatment of most cases of H3K27-altered diffuse midline gliomas (DMG), based on the simplification that the mutation overrides the histological, radiological, and clinical characteristics of such tumors. Indeed, multiple studies have described pediatric H3K27-altered DMG as incurable tumors. However, in biology and clinical practice, exceptions are frequent and complexity is the rule. First of all, H3K27 mutations have also been found in non-diffuse gliomas. On the other hand, a minority of DMGs are H3K27 wild-type but have a similarly poor prognosis. Furthermore, adult-type tumors may rarely occur in children, and differences in prognosis have emerged between adult and pediatric H3K27-altered DMGs. As well, tumor location can determine differences in the outcome: patients with thalamic and spinal DMG have significantly better survival. Finally, other concomitant molecular alterations in H3K27 gliomas have been shown to influence prognosis. So, when such additional mutations are found, which one should we focus on in order to make the correct clinical decision? Our review of the current literature on pediatric diffuse midline H3K27-altered DMG tries to address such questions. Indeed, H3K27 status has become a fundamental supplement to the histological grading of pediatric gliomas; however, it might not be sufficient alone to exhaustively define the complex biological behavior of DMG in children and might not represent an indication for a unique treatment strategy across all patients, irrespective of age, additional molecular alterations, and tumor location

    Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors

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    Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads
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