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BACKGROUND: Martinique shares with the other Caribbean countries specific public health issues, particularly in the diagnostic and therapeutic management of cancer patients. Mutualization of human and material resources by promoting cooperation is the most appropriate response to the challenges of the health systems of the Caribbean territories. Through the French PRPH-3 program, we propose to set up a collaborative digital platform adapted to the specificities of the Caribbean to strengthen professional links and skills in oncofertility and oncosexology and reduce inequalities in access to reproductive and sexual health care for cancer patients. METHODS: Within the context of this program, we have developed of an open-source platform based on a Learning Content Management System (LCMS), with an operating system developed by UNFM for low speed internet. LO libraries have been created and interaction between trainers and learners were done in asynchronous mode. This training management platform is based on: a TCC learning system (Training, Coaching, Communities); a web-hosting with pedagogical engineering appropriate to low bandwidth; a reporting system and a responsibility for processing. RESULTS: We have carried out a flexible, multilingual and accessible digital learning strategy functionality called e-MCPPO according to low-speed internet ecosystem. In close connection with the e-learning strategy we conceived (i) a multidisciplinary team; (ii) an appropriate training program for expert health professionals and (iii) a responsive design. DISCUSSION AND CONCLUSION: This low-speed web-based infrastructure allows communities of experts to cooperate in creating, validating, publishing and managing academic learning content. The self-learning modules provide the digital layer for each learner to extend their skills. Learners, as well as trainers, would gradually take ownership of this platform and encourage its promotion. Innovation in this context is both technological (low-speed Internet broadcasting, free interactive software) and organizational (moderating educational resources). This collaborative digital platform is unique in its form and content. This challenge could contribute to the digital transformation of the Caribbean ecosystem for capacity building in this specifics topics.
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Ecosistema , Neoplasias , Humanos , Martinica , Cuba , Hospitales Universitarios , Región del Caribe , Cooperación Internacional , InternetRESUMEN
Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild type and five variants that emerged in late 2020, focusing on the structure and dynamics of the spike protein interface with the human angiotensin-converting enzyme 2 (ACE2) receptor, by using crystallographic structures and extended analysis of microsecond molecular dynamics simulations. Dihedral angle principal component analysis (PCA) showed the strong similarities in the spike receptor binding domain (RBD) dynamics of the Alpha, Beta, Gamma, and Delta variants, in contrast with those of WT and Epsilon. Dynamical perturbation networks and contact PCA identified the peculiar interface dynamics of the Delta variant, which cannot be directly imputable to its specific L452R and T478K mutations since those residues are not in direct contact with the human ACE2 receptor. Our outcome shows that in the Delta variant the L452R and T478K mutations act synergistically on neighboring residues to provoke drastic changes in the spike/ACE2 interface; thus a singular mechanism of action eventually explains why it dominated over preceding variants.
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COVID-19 , SARS-CoV-2 , Enzima Convertidora de Angiotensina 2/genética , Humanos , Simulación de Dinámica Molecular , Mutación , Pandemias , Unión Proteica , SARS-CoV-2/genéticaRESUMEN
Aminopeptidase A (APA) is a membrane-bound monozinc aminopeptidase. In the brain, APA generates angiotensin III which exerts a tonic stimulatory effect on the control of blood pressure (BP) in hypertensive animals. The oral administration of RB150 renamed firibastat by WHO, an APA inhibitor prodrug, targeting only the S1 subsite, decreases BP in hypertensive patients from various ethnic origins. To identify new families of potent and selective APA inhibitors, we explored the organization of the APA active site, especially the S2' subsite. By molecular modeling, docking, molecular dynamics simulations and site-directed mutagenesis, we revealed that Arg368 and Arg386, in the S2' subsite of human APA established various types of interactions in major part with the P2' residue but also with the P1' residue of APA inhibitors, required for their nanomolar inhibitory potency. We also demonstrated an important role for Arg368 in APA catalysis, in maintaining the structural integrity of the GAMEN motif, a conserved sequence involved in exopeptidase specificity and optimal positioning of the substrate in monozinc aminopeptidases. This arginine together with the GAMEN motif are key players for the catalytic mechanism of these enzymes.
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Glutamil Aminopeptidasa/química , Glutamil Aminopeptidasa/metabolismo , Sitios de Unión , Catálisis , Disulfuros/farmacología , Glutamil Aminopeptidasa/antagonistas & inhibidores , Glutamil Aminopeptidasa/genética , Humanos , Simulación de Dinámica Molecular , Mutagénesis Sitio-Dirigida , Unión Proteica/efectos de los fármacos , Relación Estructura-Actividad , Especificidad por Sustrato , Ácidos Sulfónicos/farmacologíaRESUMEN
High average power high-intensity laser systems can suffer from a heat-induced deformation of the final compressor gratings, which introduces wavefront aberrations and spatio-temporal couplings to the pulse. Here, we use a simple numerical description, that was first introduced by Li et al. (Appl. Phys. Express, 10, 102702, 2017 and Optics Express, 26, 8453, 2018), to calculate the resulting degradation of the peak intensity and the 3-dimensional deformation of the laser pulse as a function of average power, and verify the results using experimental data. For a typical 100 TW-class laser we find that non-negligible pulse distortions can occur at an average power as low as 2.7 Watts. An open source implementation of our numerical description is available for researchers to estimate the effects of spatio-temporal couplings for their specific laser configuration.
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By using an ensemble-docking strategy, we undertook a large-scale virtual screening campaign in order to identify new putative hits against the MET kinase target. Following a large molecular dynamics sampling of its conformational space, a set of 45 conformers of the kinase was retained as docking targets to take into account the flexibility of the binding site moieties. Our screening funnel started from about 80,000 chemical compounds to be tested in silico for their potential affinities towards the kinase binding site. The top 100 molecules selected-thanks to the molecular docking results-were further analyzed for their interactions, and 25 of the most promising ligands were tested for their ability to inhibit MET activity in cells. F0514-4011 compound was the most efficient and impaired this scattering response to HGF (Hepatocyte Growth Factor) with an IC 50 of 7.2 µ M. Interestingly, careful docking analysis of this molecule with MET suggests a possible conformation halfway between classical type-I and type-II MET inhibitors, with an additional region of interaction. This compound could therefore be an innovative seed to be repositioned from its initial antiviral purpose towards the field of MET inhibitors. Altogether, these results validate our ensemble docking strategy as a cost-effective functional method for drug development.
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Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Inhibidores de Proteínas Quinasas/química , Proteínas Proto-Oncogénicas c-met/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-met/química , HumanosRESUMEN
Highly-efficient optical generation of narrowband terahertz radiation enables unexplored technologies and sciences from compact electron acceleration to charge manipulation in solids. State-of-the-art conversion efficiencies are currently achieved using difference-frequency generation driven by temporal beating of chirped pulses but remain, however, far lower than desired or predicted. Here we show that high-order spectral phase fundamentally limits the efficiency of narrowband difference-frequency generation using chirped-pulse beating and resolve this limitation by introducing a novel technique based on tuning the relative spectral phase of the pulses. For optical terahertz generation, we demonstrate a 13-fold enhancement in conversion efficiency for 1%-bandwidth, 0.361 THz pulses, yielding a record energy of 0.6 mJ and exceeding previous optically-generated energies by over an order of magnitude. Our results prove the feasibility of millijoule-scale applications like terahertz-based electron accelerators and light sources and solve the long-standing problem of temporal irregularities in the pulse trains generated by interfering chirped pulses.
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Background: The Food and Drug Administration (FDA) in the United States and the European Medicines Agency (EMA) have recognized social media as a new data source to strengthen their activities regarding drug safety. Objective: Our objective in the ADR-PRISM project was to provide text mining and visualization tools to explore a corpus of posts extracted from social media. We evaluated this approach on a corpus of 21 million posts from five patient forums, and conducted a qualitative analysis of the data available on methylphenidate in this corpus. Methods: We applied text mining methods based on named entity recognition and relation extraction in the corpus, followed by signal detection using proportional reporting ratio (PRR). We also used topic modeling based on the Correlated Topic Model to obtain the list of the matics in the corpus and classify the messages based on their topics. Results: We automatically identified 3443 posts about methylphenidate published between 2007 and 2016, among which 61 adverse drug reactions (ADR) were automatically detected. Two pharmacovigilance experts evaluated manually the quality of automatic identification, and a f-measure of 0.57 was reached. Patient's reports were mainly neuro-psychiatric effects. Applying PRR, 67% of the ADRs were signals, including most of the neuro-psychiatric symptoms but also palpitations. Topic modeling showed that the most represented topics were related to Childhood and Treatment initiation, but also Side effects. Cases of misuse were also identified in this corpus, including recreational use and abuse. Conclusion: Named entity recognition combined with signal detection and topic modeling have demonstrated their complementarity in mining social media data. An in-depth analysis focused on methylphenidate showed that this approach was able to detect potential signals and to provide better understanding of patients' behaviors regarding drugs, including misuse.
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High-repetition-rate high-power laser systems induce a high average power heat deposition into the gold-coated diffraction gratings. To study the effects of the thermal expansion of in-vacuum Pyrex gratings on the laser properties, we scan the pulse energy and repetition rate of a 200 TW laser system while monitoring the laser wavefront. Through the measured changes in laser divergence and focusability, we define an average power limit below which the in-vacuum compressor can be used with no degradation of the laser focus quality.
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BACKGROUND: Adverse drug reactions (ADRs) are an important cause of morbidity and mortality. Classical Pharmacovigilance process is limited by underreporting which justifies the current interest in new knowledge sources such as social media. The Adverse Drug Reactions from Patient Reports in Social Media (ADR-PRISM) project aims to extract ADRs reported by patients in these media. We identified 5 major challenges to overcome to operationalize the analysis of patient posts: (1) variable quality of information on social media, (2) guarantee of data privacy, (3) response to pharmacovigilance expert expectations, (4) identification of relevant information within Web pages, and (5) robust and evolutive architecture. OBJECTIVE: This article aims to describe the current state of advancement of the ADR-PRISM project by focusing on the solutions we have chosen to address these 5 major challenges. METHODS: In this article, we propose methods and describe the advancement of this project on several aspects: (1) a quality driven approach for selecting relevant social media for the extraction of knowledge on potential ADRs, (2) an assessment of ethical issues and French regulation for the analysis of data on social media, (3) an analysis of pharmacovigilance expert requirements when reviewing patient posts on the Internet, (4) an extraction method based on natural language processing, pattern based matching, and selection of relevant medical concepts in reference terminologies, and (5) specifications of a component-based architecture for the monitoring system. RESULTS: Considering the 5 major challenges, we (1) selected a set of 21 validated criteria for selecting social media to support the extraction of potential ADRs, (2) proposed solutions to guarantee data privacy of patients posting on Internet, (3) took into account pharmacovigilance expert requirements with use case diagrams and scenarios, (4) built domain-specific knowledge resources embeding a lexicon, morphological rules, context rules, semantic rules, syntactic rules, and post-analysis processing, and (5) proposed a component-based architecture that allows storage of big data and accessibility to third-party applications through Web services. CONCLUSIONS: We demonstrated the feasibility of implementing a component-based architecture that allows collection of patient posts on the Internet, near real-time processing of those posts including annotation, and storage in big data structures. In the next steps, we will evaluate the posts identified by the system in social media to clarify the interest and relevance of such approach to improve conventional pharmacovigilance processes based on spontaneous reporting.
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Chirped pulse amplification in optical lasers is a revolutionary technique, which allows the generation of extremely powerful femtosecond pulses in the infrared and visible spectral ranges. Such pulses are nowadays an indispensable tool for a myriad of applications, both in fundamental and applied research. In recent years, a strong need emerged for light sources producing ultra-short and intense laser-like X-ray pulses, to be used for experiments in a variety of disciplines, ranging from physics and chemistry to biology and material sciences. This demand was satisfied by the advent of short-wavelength free-electron lasers. However, for any given free-electron laser setup, a limit presently exists in the generation of ultra-short pulses carrying substantial energy. Here we present the experimental implementation of chirped pulse amplification on a seeded free-electron laser in the extreme-ultraviolet, paving the way to the generation of fully coherent sub-femtosecond gigawatt pulses in the water window (2.3-4.4 nm).
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We have previously demonstrated that the secreted prolyl oligopeptidase of Trypanosoma cruzi (POPTc80) is involved in the infection process by facilitating parasite migration through the extracellular matrix. We have built a 3D structural model where POPTc80 is formed by a catalytic α/ß-hydrolase domain and a ß-propeller domain, and in which the substrate docks at the inter-domain interface, suggesting a "jaw opening" gating access mechanism. This preliminary model was refined by molecular dynamics simulations and next used for a virtual screening campaign, whose predictions were tested by standard binding assays. This strategy was successful as all 13 tested molecules suggested from the in silico calculations were found out to be active POPTc80 inhibitors in the micromolar range (lowest K i at 667 nM). This work paves the way for future development of innovative drugs against Chagas disease.
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Simulación de Dinámica Molecular , Serina Endopeptidasas/química , Inhibidores de Serina Proteinasa/química , Tripanocidas/química , Trypanosoma cruzi/enzimología , Animales , Derivados del Benceno/química , Sitios de Unión , Dominio Catalítico , Bases de Datos de Compuestos Químicos , Humanos , Estructura Molecular , Prolil Oligopeptidasas , Unión Proteica , Pirimidinas/química , Homología de Secuencia de Aminoácido , Bibliotecas de Moléculas Pequeñas , Relación Estructura-Actividad , Sulfonamidas/química , Porcinos , Tiofenos/química , Triazoles/químicaRESUMEN
Coq6 is an enzyme involved in the biosynthesis of coenzyme Q, a polyisoprenylated benzoquinone lipid essential to the function of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, this putative flavin-dependent monooxygenase is proposed to hydroxylate the benzene ring of coenzyme Q (ubiquinone) precursor at position C5. We show here through biochemical studies that Coq6 is a flavoprotein using FAD as a cofactor. Homology models of the Coq6-FAD complex are constructed and studied through molecular dynamics and substrate docking calculations of 3-hexaprenyl-4-hydroxyphenol (4-HP6), a bulky hydrophobic model substrate. We identify a putative access channel for Coq6 in a wild type model and propose in silico mutations positioned at its entrance capable of partially (G248R and L382E single mutations) or completely (a G248R-L382E double-mutation) blocking access to the channel for the substrate. Further in vivo assays support the computational predictions, thus explaining the decreased activities or inactivation of the mutated enzymes. This work provides the first detailed structural information of an important and highly conserved enzyme of ubiquinone biosynthesis.
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Sitios de Unión/fisiología , Flavina-Adenina Dinucleótido/metabolismo , Oxigenasas de Función Mixta/química , Oxigenasas de Función Mixta/metabolismo , Ubiquinona/química , Ubiquinona/metabolismo , Secuencia de Aminoácidos , Sitios de Unión/genética , Biología Computacional , Simulación por Computador , Escherichia coli/genética , Flavina-Adenina Dinucleótido/química , Oxigenasas de Función Mixta/genética , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis , Conformación Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Alineación de Secuencia , Ubiquinona/genéticaRESUMEN
The prevalence of invasive fungal infections worldwide has increased in the last decades. The development of specific drugs targeting pathogenic fungi without producing collateral damage to mammalian cells is a daunting pharmacological challenge. Indeed, many of the toxicities and drug interactions observed with contemporary antifungal therapies can be attributed to "nonselective" interactions with enzymes or cell membrane systems found in mammalian host cells. A computer-aided screening strategy against the TRR1 protein of Paracoccidioides lutzii is presented here. Initially, a bank of commercially available compounds from Life Chemicals provider was docked to model by virtual screening simulations. The small molecules that interact with the model were ranked and, among the best hits, twelve compounds out of 3,000 commercially-available candidates were selected. These molecules were synthesized for validation and in vitro antifungal activity assays for Paracoccidioides lutzii and P. brasiliensis were performed. From 12 molecules tested, 3 harbor inhibitory activity in antifungal assays against the two pathogenic fungi. Corroborating these findings, the molecules have inhibitory activity against the purified recombinant enzyme TRR1 in biochemical assays. Therefore, a rational combination of molecular modeling simulations and virtual screening of new drugs has provided a cost-effective solution to an early-stage medicinal challenge. These results provide a promising technique to the development of new and innovative drugs.
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Antifúngicos/farmacología , Paracoccidioides/enzimología , Reductasa de Tiorredoxina-Disulfuro/antagonistas & inhibidores , Animales , Bioensayo , Muerte Celular/efectos de los fármacos , Línea Celular , Evaluación Preclínica de Medicamentos , Pruebas de Enzimas , Inhibidores Enzimáticos/análisis , Inhibidores Enzimáticos/farmacología , Ligandos , Ratones , Pruebas de Sensibilidad Microbiana , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Paracoccidioides/efectos de los fármacos , Paracoccidioides/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Bibliotecas de Moléculas Pequeñas/análisis , Bibliotecas de Moléculas Pequeñas/farmacología , Reductasa de Tiorredoxina-Disulfuro/aislamiento & purificación , Reductasa de Tiorredoxina-Disulfuro/metabolismoRESUMEN
Apelin is the endogenous ligand of the orphan 7-transmembrane domain GPCR APJ, now named the apelin receptor (ApelinR). Apelin plays a prominent role in body fluid and cardiovascular homeostasis. To better understand the structural organization of the ApelinR, we built 3 homology 3-dimensional (3D) models of the human ApelinR using the validated cholecystokinin receptor-1 3D model or the X-ray structures of the ß2-adrenergic and CXCR4 receptors as templates. Docking of the pyroglutamyl form of apelin 13 (pE13F) into these models revealed the conservation at the bottom of the binding site of a hydrophobic cavity in which the C-terminal Phe of pE13F was embedded. In contrast, at the top of the binding site, depending on the model, different interactions were visualized between acidic residues of the ApelinR and the basic residues of pE13F. Using site-directed mutagenesis, we showed that Asp 92, Glu 172, and Asp 282 of rat ApelinR are key residues in apelin binding by interacting with Lys 8, Arg 2, and Arg 4 of pE13F, respectively. These residues are only seen in the CXCR4-based ApelinR 3D model, further validating this model. These findings bring new insights into the structural organization of the ApelinR and the mode of apelin binding.
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Péptidos y Proteínas de Señalización Intercelular/metabolismo , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Animales , Apelina , Receptores de Apelina , Sitios de Unión/genética , Secuencia Conservada , AMP Cíclico/biosíntesis , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Complejos Multiproteicos/química , Mutagénesis Sitio-Dirigida , Conformación Proteica , Ratas , Receptores Acoplados a Proteínas G/genética , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Homología de Secuencia de Aminoácido , Homología Estructural de ProteínaRESUMEN
Hypertension affects one-third of the adult population and is a growing problem due to the increasing incidence of obesity and diabetes. Brain RAS (renin-angiotensin system) hyperactivity has been implicated in the development and maintenance of hypertension in several types of experimental and genetic hypertension animal models. We have identified in the brain RAS that APA (aminopeptidase A) and APN (aminopeptidase N), two membrane-bound zinc metalloproteases, are involved in the metabolism of AngII (angiotensin II) and AngIII (angiotensin III) respectively. The present review summarizes the main findings suggesting that AngIII plays a predominant role in the brain RAS in the control of BP (blood pressure). We first explored the organization of the APA active site by site-directed mutagenesis and molecular modelling. The development and the use in vivo of specific and selective APA and APN inhibitors EC33 and PC18 respectively, has allowed the demonstration that brain AngIII generated by APA is one of the main effector peptides of the brain RAS, exerting a tonic stimulatory control over BP in conscious hypertensive rats. This identified brain APA as a potential therapeutic target for the treatment of hypertension, which has led to the development of potent orally active APA inhibitors, such as RB150. RB150 administered orally in hypertensive DOCA (deoxycorticosteroneacetate)-salt rats or SHRs (spontaneously hypertensive rats) crosses the intestinal, hepatic and blood-brain barriers, enters the brain, generates two active molecules of EC33 which inhibit brain APA activity, block the formation of brain AngIII and normalize BP for several hours. The decrease in BP involves two different mechanisms: a decrease in vasopressin release into the bloodstream, which in turn increases diuresis resulting in a blood volume reduction that participates in the decrease in BP and/or a decrease in sympathetic tone, decreasing vascular resistance. RB150 constitutes the prototype of a new class of centrally acting antihypertensive agents and is currently being evaluated in a Phase Ib clinical trial.
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Disulfuros/uso terapéutico , Glutamil Aminopeptidasa/antagonistas & inhibidores , Hipertensión/tratamiento farmacológico , Inhibidores de Proteasas/uso terapéutico , Ácidos Sulfónicos/uso terapéutico , Angiotensina III/metabolismo , Angiotensina III/fisiología , Animales , Sitios de Unión , Presión Sanguínea , Barrera Hematoencefálica , Encéfalo/efectos de los fármacos , Ensayos Clínicos Fase I como Asunto , Diseño de Fármacos , Glutamil Aminopeptidasa/química , Humanos , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Inhibidores de Proteasas/farmacocinética , RatasRESUMEN
Tuberculosis (TB) is a devastating disease that claims millions of lives every year. Hindered access or non-compliance to medication, especially in developing countries, led to drug resistance, further aggravating the situation. With current standard therapies in use for over 50 years and only few new candidates in clinical trials, there is an urgent call for new TB drugs. A powerful tool for the development of new medication is structure-guided design, combined with virtual screening or docking studies. Here, we report the results of a drug-design project, which we based on a publication that claimed the structure-guided discovery of several promising and highly active inhibitors targeting the secreted chorismate mutase (*MtCM) from Mycobacterium tuberculosis. We set out to further improve on these compounds and synthesized a series of new derivatives. Thorough evaluation of these molecules in enzymatic assays revealed, to our dismay, that neither the claimed lead compounds, nor any of the synthesized derivatives, show any inhibitory effects against *MtCM.
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Antituberculosos/química , Antituberculosos/farmacología , Corismato Mutasa/antagonistas & inhibidores , Diseño de Fármacos , Mycobacterium tuberculosis/enzimología , Corismato Mutasa/metabolismo , Humanos , Simulación del Acoplamiento Molecular , Mycobacterium tuberculosis/efectos de los fármacos , Relación Estructura-Actividad , Tuberculosis/tratamiento farmacológico , Tuberculosis/microbiologíaRESUMEN
Virtual screening (VS) is becoming an increasingly important approach for identifying and selecting biologically active molecules against specific pharmaceutically relevant targets. Compared to conventional high throughput screening techniques, in silico screening is fast and inexpensive, and is increasing in popularity in early-stage drug discovery endeavours. This paper reviews and discusses recent trends and developments in three-dimensional (3D) receptor-based and ligand-based VS methodologies. First, we describe the concept of accessible chemical space and its exploration. We then describe 3D structural ligand-based VS techniques, hybrid approaches, and new approaches to exploit additional knowledge that can now be found in large chemogenomic databases. We also briefly discuss some potential issues relating to pharmacokinetics, toxicity profiling, target identification and validation, inverse docking, scaffold-hopping and drug re-purposing. We propose that the best way to advance the state of the art in 3D VS is to integrate complementary strategies in a single drug discovery pipeline, rather than to focus only on theoretical or computational improvements of individual techniques. Two recent 3D VS case studies concerning the LXR-ß receptor and the CCR5/CXCR4 HIV co-receptors are presented as examples which implement some of the complementary methods and strategies that are reviewed here.
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Ensayos Analíticos de Alto Rendimiento/métodos , Antagonistas de los Receptores CCR5 , Descubrimiento de Drogas , VIH/efectos de los fármacos , Ensayos Analíticos de Alto Rendimiento/tendencias , Humanos , Receptores X del Hígado , Estructura Molecular , Receptores Nucleares Huérfanos/antagonistas & inhibidores , Receptores CXCR4/antagonistas & inhibidoresRESUMEN
It is now widely recognized that the flexibility of both partners has to be considered in molecular docking studies. However, the question how to handle the best the huge computational complexity of exploring the protein binding site landscape is still a matter of debate. Here we investigate the flexibility of c-Met kinase as a test case for comparing several simulation methods. The c-Met kinase catalytic site is an interesting target for anticancer drug design. In particular, it harbors an unusual plasticity compared with other kinases ATP binding sites. Exploiting this feature may eventually lead to the discovery of new anticancer agents with exquisite specificity. We present in this article an extensive investigation of c-Met kinase conformational space using large-scale computational simulations in order to extend the knowledge already gathered from available X-ray structures. In the process, we compare the relevance of different strategies for modeling and injecting receptor flexibility information into early stage in silico structure-based drug discovery pipeline. The results presented here are currently being exploited in on-going virtual screening investigations on c-Met.
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Simulación de Dinámica Molecular , Fosfotransferasas/química , Proteínas Proto-Oncogénicas c-met/química , Adenosina Trifosfato/química , Algoritmos , Sitios de Unión , Análisis por Conglomerados , Cristalografía por Rayos X , Activación Enzimática , Humanos , Ligandos , Unión Proteica , Conformación ProteicaRESUMEN
The Met receptor tyrosine kinase is a promising target in anticancer therapies for its role during tumor evolution and resistance to treatment. It is characterized by an unusual structural plasticity as its active site accepts different inhibitor binding modes. Such feature can be exploited to identify distinct agents targeting tumor dependence and/or resistance by oncogenic Met. Here we report the identification of bioactive agents, featuring a new 4-(imidazo[2,1-b]benzothiazol-2-yl)phenyl moiety, targeting cancer cells dependent on oncogenic Met. One of these compounds (7c; Triflorcas) impairs survival, anchorage-independent growth, and in vivo tumorigenesis, without showing side effects. Our medicinal chemistry strategy was based on an in-house Met-focused library of aminoacid-amide derivatives enriched through structure-based computer modeling, taking into account the Met multiple-binding-mode feature. Altogether, our findings show how a rational structure-based drug design approach coupled to cell-based drug evaluation strategies can be applied in medicinal chemistry to identify new agents targeting a given oncogenic-dependency setting.
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Amidas/química , Amidas/farmacología , Aminoácidos/química , Imidazoles/química , Proteínas Proto-Oncogénicas c-met/metabolismo , Transducción de Señal/efectos de los fármacos , Animales , Antineoplásicos/química , Antineoplásicos/farmacología , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Supervivencia Celular/efectos de los fármacos , Perros , Diseño de Fármacos , Activación Enzimática/efectos de los fármacos , Humanos , Modelos Moleculares , Conformación Proteica , Proteínas Proto-Oncogénicas c-met/química , Interfaz Usuario-ComputadorRESUMEN
Apelin is the endogenous ligand of the orphan seven-transmembrane domain (TM) G protein-coupled receptor APJ. Apelin is involved in the regulation of body fluid homeostasis and cardiovascular functions. We previously showed the importance of the C-terminal Phe of apelin 17 (K17F) in the hypotensive activity of this peptide. Here, we show either by deleting the Phe residue (K16P) or by substituting it by an Ala (K17A), that it plays a crucial role in apelin receptor internalization but not in apelin binding or in Gα(i)-protein coupling. Then we built a homology three-dimensional model of the human apelin receptor using the cholecystokinin receptor-1 model as a template, and we subsequently docked K17F into the binding site. We visualized a hydrophobic cavity at the bottom of the binding pocket in which the C-terminal Phe of K17F was embedded by Trp(152) in TMIV and Trp(259) and Phe(255) in TMVI. Using molecular modeling and site-directed mutagenesis studies, we further showed that Phe(255) and Trp(259) are key residues in triggering receptor internalization without playing a role in apelin binding or in Gα(i)-protein coupling. These findings bring new insights into apelin receptor activation and show that Phe(255) and Trp(259), by interacting with the C-terminal Phe of the pyroglutamyl form of apelin 13 (pE13F) or K17F, are crucial for apelin receptor internalization.