Modified PNA design and synthesis: a novel approach using Molecular Dynamics and Metadynamics

Gli acidi peptido nucleici sono potenti strumenti utilizzati in ambito biotecnologico per colpire DNA o RNA. PNA contenenti basi o backbone modificati sono attualmente studiati per migliorarne le proprietà in ambito biologico. Bersagliare i micro RNA (anti-miR) è particolarmente interessante nell’ottica di future applicazioni terapeutiche, ma strumenti computazionali che aiutino nel design di nuovi PNA anti-miR non sono stati ancora completamente sviluppati. Le proprietà conformazionali del singolo filamento di PNA (non modificato o recante modificazioni in γ) e dei duplex PNA:RNA e i processi di re-annealing e melting sono stati studiati tramite Dinamica Molecolare e Metadinamica. L’approccio computazionale consolidato, assieme a un programma modificato per la generazione delle strutture dei duplex contenenti PNA, è stato utilizzato per il virtual screening di PNA contenenti basi modificate. Sono state inoltre sintetizzate le unità per l’ottenimento del composto più promettente e una funzione idrolitica da legare al monomero finale.

Design and synthesis of new multitarget inhibitors of dengue virus replication

Attraverso una combinazione di virtual screening/virtual library generation abbiamo identificato una nuova serie di inibitori della replicazione del virus Dengue, attivi sia su un target virale (NS5) sia su uno cellulare (Src chinasi)

Mapping the emergence of heart disease in a black, urban population in Africa: The Heart of Soweto Study

Background: There is increasing evidence that many populations in the developing world are in epidemiologic transition with the subsequent emergence of more affluent disease states. The Heart of Soweto Study will systematically investigate the emergence of heart disease (HD) in a large urban population in South Africa. Methods: Part of the conurbation of Johannesburg, South Africa, Soweto is a predominantly Black African community of I million individuals. During an initial two year period, all individuals presenting to the local Baragwanath Hospital (3500 beds) with any form of HD will be studied. Demographic and diagnostic coding data in those with pre-established HD will form an abbreviated clinical registry of > 12,000 prevalent cases. Similarly, socio-demographic, clinical and diagnostic data (e.g. echocardiography and ECG) in newly diagnosed patients will form a more detailed clinical registry of > 5000 incident cases. Sub-studies of the relationship between HIV status and H D and the optimal management of chronic heart failure will also be performed. Results: These data will provide a unique insight into the causes and consequences of a broad spectrum of HD-related conditions in a developing world community in epidemiologic transition. Initially documented Population rates, in addition to detailed examinations of the underlying risk factors and causes of HD-related morbidity/mortality will provide an important platform for future stages of the study: a community-based, population screening program and culturally specific primary and secondary programs of care. Conclusion: There is an urgent need to systematically track the emergence of HD in the developing world. Initially involving more than 15,000 individuals, the unique Heart of Soweto Study has the potential to provide a wealth of information in this regard. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

Susceptibility of source plants to Sugarcane Fiji disease virus influences the acquisition and transmission of the virus by the planthopper vector Perkinsiella saccharicida

Fiji leaf gall (FLG) caused by Sugarcane Fiji disease virus (SCFDV) is transmitted by the planthopper Perkinsiella saccharicida. FLG is managed through the identification and exploitation of plant resistance. The glasshouse-based resistance screening produced inconsistent transmission results and the factors responsible for that are not known. A series of glasshouse trials conducted over a 2-year period was compared to identify the factors responsible for the erratic transmission results. SCFDV transmission was greater when the virus was acquired by the vector from a cultivar that was susceptible to the virus than when the virus was acquired from a resistant cultivar. Virus acquisition by the vector was also greater when the vector was exposed to the susceptible cultivars than when exposed to the resistant cultivar. Results suggest that the variation in transmission levels is due to variation in susceptibility of sugarcane cultivars to SCFDV used for virus acquisition by the vector.

GABA-mediated changes in inter-hemispheric beta frequency activity in early-stage Parkinson's disease

In Parkinson's disease (PD), elevated beta (15-35Hz) power in subcortical motor networks is widely believed to promote aspects of PD symptomatology, moreover, a reduction in beta power and coherence accompanies symptomatic improvement following effective treatment with l-DOPA. Previous studies have reported symptomatic improvements that correlate with changes in cortical network activity following GABAA receptor modulation. In this study we have used whole-head magnetoencephalography to characterize neuronal network activity, at rest and during visually cued finger abductions, in unilaterally symptomatic PD and age-matched control participants. Recordings were then repeated following administration of sub-sedative doses of the hypnotic drug zolpidem (0.05mg/kg), which binds to the benzodiazepine site of the GABAA receptor. A beamforming based 'virtual electrode' approach was used to reconstruct oscillatory power in the primary motor cortex (M1), contralateral and ipsilateral to symptom presentation in PD patients or dominant hand in control participants. In PD patients, contralateral M1 showed significantly greater beta power than ipsilateral M1. Following zolpidem administration contralateral beta power was significantly reduced while ipsilateral beta power was significantly increased resulting in a hemispheric power ratio that approached parity. Furthermore, there was highly significant correlation between hemispheric beta power ratio and Unified Parkinson's Disease Rating Scale (UPDRS). The changes in contralateral and ipsilateral beta power were reflected in pre-movement beta desynchronization and the late post-movement beta rebound. However, the absolute level of movement-related beta desynchronization was not altered. These results show that low-dose zolpidem not only reduces contralateral beta but also increases ipsilateral beta, while rebalancing the dynamic range of M1 network oscillations between the two hemispheres. These changes appear to underlie the symptomatic improvements afforded by low-dose zolpidem.

Easy Creation of Semantics-Enhanced Digital Artwork Collections

In this paper we propose an approach for cost-effective employing of semantic technologies to improve the efficiency of searching and browsing of digital artwork collections. It is based on a semi-automatic creation of a Topic Map-based virtual art gallery portal by using existing Topic Maps tools. Such a ‘cheap’ solution could enable small art museums or art-related educational programs that lack sufficient funding for software development and publication infrastructure to take advantage of the emerging semantic technologies. The proposed approach has been used for creating the WSSU Diggs Gallery Portal.

Ampliando as ações educativas dos museus por meio da formação de comunidades virtuais de aprendizagem

Este artigo tem como objetivo mostrar que é possível incentivar a aprendizagem informal em museus através da construção de comunidades virtuais, com base em repositórios de objetos de aprendizagem, ferramentas comunicacionais e produção de OAs por parte dos visitantes. O enfoque é incentivar a aprendizagem no sentido de motivar a participação/envolvimento do visitante nas atividades da comunidade virtual. Nesta perspectiva, partimos do pressuposto de que a informação, a comunicação, a interação e a cooperação são essenciais para o processo de aprender no contexto informal dos museus. Acreditamos que a interação e a cooperação são partes integrantes do processo de aprendizagem proporcionado por comunidades virtuais e que o principal recurso de aprendizagem oferecido nessas comunidades são os objetos de aprendizagem. Diante do exposto, construímos a Comunidade Virtual do Muzar e realizamos uma experimentação do ambiente de modo a verificar o quanto os visitantes são incentivados a produzir novos conhecimentos.

La valeur prédictive et pronostique d’une faible expression des récepteurs d’oestrogènes en cancer du sein

L’objectif de ce projet fut d’évaluer le bénéfice associé à la thérapie antihormonale (TA) pour les cancers du sein avec des récepteurs d’estrogènes (ER) faiblement positifs (<10 fmol/mg de cytosol). Nous avons identifié 2221 patientes avec cancer du sein dont ER ont été évalués par méthode biochimique (Ligand-Based Assay ou LBA) de 1976 à 1995 et suivies jusqu’en 2008. Des modèles à risques proportionnels de Cox ont été utilisés pour évaluer l’impact des différents niveaux de ER sur la survie au cancer du sein chez les patientes ayant reçu ou non une TA. Parmi les 2221 patientes incluses dans l’étude, 661 (29,8%) ont reçu une TA. Chez celles avec TA, une diminution significative de la mortalité spécifique au cancer du sein n’a été démontrée que pour les niveaux de ER ≥10 fmol/mg de cytosol. Ainsi, ceci ne supporte pas une TA pour les cancers du sein faiblement positif pour ER testés en LBA.

Insight into the molecular and functional determinants of HP1043, the essential master regulator of Helicobacter pylori.

Helicobacter pylori is one of the most widespread and successful human pathogens, colonizing half of the population stomach mucosa and causing gastric malignancies in 1% of carriers. Due to the increasing number of antimicrobial-resistant strains, in 2017 the WHO included H. pylori among pathogens that pose a major threat for humankind. In this study, we propose as a molecular target for novel antimicrobial strategies HP1043, an orphan response regulator essential for the viability of H. pylori as it orchestrates all the most important cellular processes. Amino acids most relevant for HP1043 dimerization and target DNA recognition were identified and used to guide an in-silico protein-DNA docking and generate a high-resolution structural model of the interacting HP1043 dimer and its target DNA. The model was experimentally validated and exploited to carry out a virtual screening of small molecule libraries, identifying 8 compounds potentially able to interfere with HP1043 function and likely block H. pylori infection. A second line of research aimed at the characterization of the regulatory function of HP1043 and the tight mechanisms of regulation of hp1043 gene expression. In particular, we proved a direct interaction between HP1043 and the housekeeping sigma80 factor of the RNA polymerase. A conditional mutant H. pylori strain overexpressing a synthetic copy of the hp1043 gene altered in nucleotide sequence yet encoding the wild-type protein was generated, achieving increased intracellular levels of HP1043. However, overexpression of HP1043 did not result in an upregulation of target genes transcription nor modulation of hp1043 transcript levels, pinpointing the existence of multiple overlayed mechanisms of regulation that affect both protein levels and functionality as well as maintain steady the amount of hp1043 transcript. Finally, we proposed that a mechanism of post-transcriptional regulation could depend on an antisense transcript to the hp1043 gene which was validated in two different strains.

Synthesis and characterization of novel selective NKCC1 inhibitors for the treatment of down syndrome and brain disorders characterized by depolarizing GABAergic transmission.

Proper GABAergic transmission through Cl-permeable GABAA receptors is fundamental for physiological brain development and function. Indeed, defective GABAergic signaling – due to a high NKCC1/KCC2 expression ratio – has been implicated in several neurodevelopmental disorders (e.g., Down syndrome, DS, Autism spectrum disorders, ASD). Interestingly, NKCC1 inhibition by the FDA-approved diuretic drug bumetanide reverts cognitive deficits in the TS65Dn mouse models of DS and core symptoms in other models of brain disorders. However, the required chronic treatment with bumetanide is burdened by its diuretic side effects caused by the antagonization of the kidney Cl importer NKCC2. This may lead to hypokalemia, while jeopardizing drug compliance. Crucially, these issues would be solved by selective NKCC1 inhibitors, thus devoid of the diuretic effect of bumetanide. To this aim, starting from bumetanide’s structure, we applied a ligand-based computational approach to design new molecular entities that we tested in vitro for their capacity to selectively block NKCC1. Extensive synthetic efforts and structure-activity relationships analyses allowed us to improve in vitro potency and overall drug-like properties of the initially identified chemical hits. As a result, we identified a new highly potent NKCC1 inhibitor (ARN23746) that displayed excellent solubility, metabolic stability, and no significant effect on NKCC2 in vitro. Moreover, this novel and selective NKCC1 inhibitor was able to rescue cognitive deficits in DS mice and social/repetitive behaviors in ASD mice, with no diuretic effect and no overt toxicity upon chronic treatment in adult animals. Thus, ARN23746 a selective NKCC1 inhibitor devoid of the diuretic effect – represents a suitable and solid therapeutic strategy for the treatment of Down syndrome and all the brain neurological disorders characterized by depolarizing GABAergic transmission.

Sviluppo di un ambiente virtualizzato per la simulazione di attacchi a reti time-sensitive

Questo lavoro di tesi ha visto come obiettivo finale quello di realizzare una se- rie di attacchi, alcuni di questi totalmente originali, ai protocolli della famiglia Time-Sensitive Networking (TSN) attraverso lo sviluppo di un’infrastruttura virtualizzata. L’infrastruttura è stata costruita e progettata utilizzando mac- chine virtuali con Quick EMUlator (QEMU) come strato di virtualizzazione ed accelerate attraverso Kernel-based Virtual Machine (KVM). Il progetto è stato concepito come Infrastrucutre as Code (IaC), attraverso l’ausilio di Ansible e alcuni script shell utilizzati come collante per le varie parti del progetto.

Docking, virtual high throughput screening and in silico fragment-based drug design.

ABSTRACT The drug discovery process has been profoundly changed recently by the adoption of computational methods helping the design of new drug candidates more rapidly and at lower costs. In silico drug design consists of a collection of tools helping to make rational decisions at the different steps of the drug discovery process, such as the identification of a biomolecular target of therapeutical interest, the selection or the design of new lead compounds and their modification to obtain better affinities, as well as pharmacokinetic and pharmacodynamic properties. Among the different tools available, a particular emphasis is placed in this review on molecular docking, virtual high throughput screening and fragment-based ligand design.

Screening of highly modular sugar-based ligand libraries in the enantioselective C-C coupling reactions

Projecte de recerca elaborat a partir d’una estada a la University of Nottingham, Gran Bretanya, entre març i abril del 2007. Aquest treball s’ha centrat en l’aplicació de compostos derivats de la D-(+)-glucosa, de la D-(+)-fructosa i la D-galactosa com a lligands de catalitzadors homogenis quirals en dos reaccions asimètriques: addició 1,2 a aldehids catalitzada per níquel i addició 1,4 conjugada catalitzada per coure.(veure figura adjunta al final del document). En primer lloc, s’ha estudiat l’aplicació dels compostos L1-L6 a les reaccions d’addició 1,2 a aldehids catalitzades per níquel. S’ha observat que la selectivitat del procés depèn principalment del grup funcional unit a l’esquelet del lligand, de les propietats estèriques del substituent en la funció oxazolina i de l’estructura del substrat. S’ha obtingut fins a un 59% d’excés enantiomèric utilitzant el precursor de catalitzador que conté el lligand L3a. En segon lloc, aquest treball descriu l’aplicació de les tres famílies de compostos (L1-L11) com a lligands en la reacció d’addició 1,4 catalitzada per coure de compostos organometàl•lics a diferents enones amb diferents propietats estèriques. L’ús de les llibreries de compostos fosfit-oxazolina (L1-L5) i fosfit-fosforamidit (L6) han proporcionat bones enantioselectivitats (fins a 80%) en l’addició de reactius de trialquilalumini a diferents enones. En canvi, la llibreria de compostos monofosfit (L7-L11) ha mostrat bones activitats però enantioselectivitats fins a 57%.

Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

Protein-ligand docking has made important progress during the last decade and has become a powerful tool for drug development, opening the way to virtual high throughput screening and in silico structure-based ligand design. Despite the flattering picture that has been drawn, recent publications have shown that the docking problem is far from being solved, and that more developments are still needed to achieve high successful prediction rates and accuracy. Introducing an accurate description of the solvation effect upon binding is thought to be essential to achieve this goal. In particular, EADock uses the Generalized Born Molecular Volume 2 (GBMV2) solvent model, which has been shown to reproduce accurately the desolvation energies calculated by solving the Poisson equation. Here, the implementation of the Fast Analytical Continuum Treatment of Solvation (FACTS) as an implicit solvation model in small molecules docking calculations has been assessed using the EADock docking program. Our results strongly support the use of FACTS for docking. The success rates of EADock/FACTS and EADock/GBMV2 are similar, i.e. around 75% for local docking and 65% for blind docking. However, these results come at a much lower computational cost: FACTS is 10 times faster than GBMV2 in calculating the total electrostatic energy, and allows a speed up of EADock by a factor of 4. This study also supports the EADock development strategy relying on the CHARMM package for energy calculations, which enables straightforward implementation and testing of the latest developments in the field of Molecular Modeling.

Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain

Bromodomains are epigenetic reader domains that have recently become popular targets. In contrast to BET bromodomains, which have proven druggable, bromodomains from other regions of the phylogenetic tree have shallower pockets. We describe successful targeting of the challenging BAZ2B bromodomain using biophysical fragment screening and structure-based optimization of high ligand-efficiency fragments into a novel series of low-micromolar inhibitors. Our results provide attractive leads for development of BAZ2B chemical probes and indicate the whole family may be tractable.