EADock : design of a new molecular docking algorithm and some of its applications

3 Summary 3. 1 English The pharmaceutical industry has been facing several challenges during the last years, and the optimization of their drug discovery pipeline is believed to be the only viable solution. High-throughput techniques do participate actively to this optimization, especially when complemented by computational approaches aiming at rationalizing the enormous amount of information that they can produce. In siiico techniques, such as virtual screening or rational drug design, are now routinely used to guide drug discovery. Both heavily rely on the prediction of the molecular interaction (docking) occurring between drug-like molecules and a therapeutically relevant target. Several softwares are available to this end, but despite the very promising picture drawn in most benchmarks, they still hold several hidden weaknesses. As pointed out in several recent reviews, the docking problem is far from being solved, and there is now a need for methods able to identify binding modes with a high accuracy, which is essential to reliably compute the binding free energy of the ligand. This quantity is directly linked to its affinity and can be related to its biological activity. Accurate docking algorithms are thus critical for both the discovery and the rational optimization of new drugs. In this thesis, a new docking software aiming at this goal is presented, EADock. It uses a hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with .the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 R around the center of mass of the ligand position in the crystal structure, and conversely to other benchmarks, our algorithms was fed with optimized ligand positions up to 10 A root mean square deviation 2MSD) from the crystal structure. This validation illustrates the efficiency of our sampling heuristic, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best-ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures in this benchmark could be explained by the presence of crystal contacts in the experimental structure. EADock has been used to understand molecular interactions involved in the regulation of the Na,K ATPase, and in the activation of the nuclear hormone peroxisome proliferatoractivated receptors a (PPARa). It also helped to understand the action of common pollutants (phthalates) on PPARy, and the impact of biotransformations of the anticancer drug Imatinib (Gleevec®) on its binding mode to the Bcr-Abl tyrosine kinase. Finally, a fragment-based rational drug design approach using EADock was developed, and led to the successful design of new peptidic ligands for the a5ß1 integrin, and for the human PPARa. In both cases, the designed peptides presented activities comparable to that of well-established ligands such as the anticancer drug Cilengitide and Wy14,643, respectively. 3.2 French Les récentes difficultés de l'industrie pharmaceutique ne semblent pouvoir se résoudre que par l'optimisation de leur processus de développement de médicaments. Cette dernière implique de plus en plus. de techniques dites "haut-débit", particulièrement efficaces lorsqu'elles sont couplées aux outils informatiques permettant de gérer la masse de données produite. Désormais, les approches in silico telles que le criblage virtuel ou la conception rationnelle de nouvelles molécules sont utilisées couramment. Toutes deux reposent sur la capacité à prédire les détails de l'interaction moléculaire entre une molécule ressemblant à un principe actif (PA) et une protéine cible ayant un intérêt thérapeutique. Les comparatifs de logiciels s'attaquant à cette prédiction sont flatteurs, mais plusieurs problèmes subsistent. La littérature récente tend à remettre en cause leur fiabilité, affirmant l'émergence .d'un besoin pour des approches plus précises du mode d'interaction. Cette précision est essentielle au calcul de l'énergie libre de liaison, qui est directement liée à l'affinité du PA potentiel pour la protéine cible, et indirectement liée à son activité biologique. Une prédiction précise est d'une importance toute particulière pour la découverte et l'optimisation de nouvelles molécules actives. Cette thèse présente un nouveau logiciel, EADock, mettant en avant une telle précision. Cet algorithme évolutionnaire hybride utilise deux pressions de sélections, combinées à une gestion de la diversité sophistiquée. EADock repose sur CHARMM pour les calculs d'énergie et la gestion des coordonnées atomiques. Sa validation a été effectuée sur 37 complexes protéine-ligand cristallisés, incluant 11 protéines différentes. L'espace de recherche a été étendu à une sphère de 151 de rayon autour du centre de masse du ligand cristallisé, et contrairement aux comparatifs habituels, l'algorithme est parti de solutions optimisées présentant un RMSD jusqu'à 10 R par rapport à la structure cristalline. Cette validation a permis de mettre en évidence l'efficacité de notre heuristique de recherche car des modes d'interactions présentant un RMSD inférieur à 2 R par rapport à la structure cristalline ont été classés premier pour 68% des complexes. Lorsque les cinq meilleures solutions sont prises en compte, le taux de succès grimpe à 78%, et 92% lorsque la totalité de la dernière génération est prise en compte. La plupart des erreurs de prédiction sont imputables à la présence de contacts cristallins. Depuis, EADock a été utilisé pour comprendre les mécanismes moléculaires impliqués dans la régulation de la Na,K ATPase et dans l'activation du peroxisome proliferatoractivated receptor a (PPARa). Il a également permis de décrire l'interaction de polluants couramment rencontrés sur PPARy, ainsi que l'influence de la métabolisation de l'Imatinib (PA anticancéreux) sur la fixation à la kinase Bcr-Abl. Une approche basée sur la prédiction des interactions de fragments moléculaires avec protéine cible est également proposée. Elle a permis la découverte de nouveaux ligands peptidiques de PPARa et de l'intégrine a5ß1. Dans les deux cas, l'activité de ces nouveaux peptides est comparable à celles de ligands bien établis, comme le Wy14,643 pour le premier, et le Cilengitide (PA anticancéreux) pour la seconde.

Macular dystrophy associated with the mitochondrial DNA A3243G mutation: pericentral pigment deposits or atrophy? Report of two cases and review of the literature.

BACKGROUND: The A3243G point mutation in mitochondrial DNA (mtDNA) is associated with MELAS (mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes) and MIDD syndromes (maternally inherited diabetes and deafness). Both MELAS and MIDD patients can present with visual symptoms due to a retinopathy, sometimes before the genetic diagnosis is made. CASE PRESENTATION: Patient 1: 46 year-old woman with diabetes mellitus and hearing loss was referred for an unspecified maculopathy detected during screening evaluation for diabetic retinopathy. Visual acuity was 20/20 in both eyes. Fundus examination showed bilateral macular and peripapillary hyperpigmented/depigmented areas.Patient 2: 45 year-old woman was referred for recent vision loss in her left eye. History was remarkable for chronic fatigue, migraine and diffuse muscular pain. Visual acuity was 20/20 in her right eye and 20/30 in her left eye. Fundus exhibited several nummular perifoveal islands of retinal pigment epithelium atrophy and adjacent pale deposits in both eyes.Retinal anatomy was investigated with autofluorescence, retinal angiography and optical coherence tomography. Retinal function was assessed with automated static perimetry, full-field and multifocal electroretinography and electro-oculography. Genetic testing of mtDNA identified a point mutation at the locus 3243. CONCLUSION: Observation of RPE abnormalities in the context of suggestive systemic findings should prompt mtDNA testing.

Successful bilateral lung transplantation after previous pneumonectomy

Objective: To present the feasibility of bilateral lung transplantation after previously performed pneumonectomy.Methods: A 32 years old women underwent right pneumonectomy for bronchiectasis-related destroyed lung. Eight months later, she developed a vascular post-pneumonectomy syndrome and underwent realigning of the mediastinum by an intrathoracic expander that was complicated by an adult respiratory distress syndrome of the left lung requiring mechanical ventilation, arterio-venous CO2 removal (Novalung) and finally bilateral lung transplantation. Via clamshell incision, the post-pneumonectomy cavity was dissected and the superior vena cava (SVC) and carina were exposed. The pulmonary vessel stumps were dissected intrapericardically after realization of a right-sided hemi-pericardectomy. Extracorporeal circulation was started after central cannulation of the aorta and the inferior vena cava. A right upper lobe sleeve resection of the donor lung was performed. The intermediate bronchus was then implanted in the dissected recipient carina after realization of a hilar release maneuver. The right pulmonary artery was clamped between SVC andthe ascending aorta followed by end -to-end anastomosis of the donor and recipient artery and left atrial cuffs, respectively. Satisfactory graft function allowed decanulation and standard transplantation of the left lung without extracorporeal circulation.Results: Bronchoscopy and trans-esophageal echocardiography demonstrated a patent airway and vascular anastomoses without stenosis. Follow-up revealed excellent gas exchanges, no airway complications and well-functioning grafts on both sides with right-sided ventilation and perfusion two months after transplantation of 37% and 22%, respectively.Conclusion: This is to our knowledge the first report of successful bilateral lung transplantation after previous pneumonectomy unrelated to transplantation.

Communicating Highway Safety: What Works, 2002

Few topics in transportation are of greater significance, now and in the future, than making today’s roads safe for those who use them. This study aims to assist the formulation of policy by examining the empirical evidence currently available on the ability of several forms of communication efforts and activities to increase knowledge about and affect attitudes and behavior toward highway safety practices. The objective of this effort is to provide a comparative synthesis of what works and what does not in highway safety campaigns across a large number of topical areas that have a mass media component. This was accomplished by conducting an extensive literature review to determine the current state of knowledge concerning what works and what has significant potential for wide use in future highway safety campaigns. An analytic framework for investigating highway safety campaigns was created. The framework includes (1) the types of media components, (2) the types of collaborations, (3) the context in which the campaign is intended to have impact, (4) the structure or procedural steps into which campaigns are organized, (5) the principles for what works in a campaign, and (6) the desired impact of a campaign on its target audience. The report reveals 25 characteristics of successful communication campaigns, strategies that stand a chance of achieving changes in knowledge, attitude, and behavior. The actual impact of mass communication remains unproven because of a perceived lag in the development of adequate evaluation techniques. Education by itself has not generally resulted in significant changes in the behaviors targeted, but education of the public and advocacy groups has often helped enact necessary legislation, transmit knowledge about the provisions and penalties of laws in ways that increase their deterrent effect, and generate public support for law enforcement programs. Even in such cases, however, when enforcement is inconsistent, public compliance frequently decreases with time. Approaches to traffic safety that emphasize the need for long-term individual- and community-based measures are found to be especially crucial for addressing complex problems like drinking and driving that are determined by a myriad of lifestyle and psychosocial factors.

Endogenous ocular nocardiosis: an interventional case report with a review of the literature.

We present an illustrative case of endogenous ocular Nocardia (EON) infection in a man with Hodgkin disease treated by chemotherapy who underwent aggressive vitreoretinal surgery for diagnosis and treatment of a subretinal abscess. Visual acuity recovered from hand movements to 20/25. We review the 38 reported cases of EON published between 1967 and 2007, describe the clinical presentation from a systemic and ocular point of view, examine which ocular procedures were successful in identifying the bacterium, and analyze ocular morbidity and the factors affecting successful treatment.

Prurigo nodularis: retrospective study of 13 cases managed with methotrexate.

BACKGROUND: Prurigo nodularis (PN), or nodular prurigo, is a chronic, debilitating, inflammatory skin disease. It can be very difficult to manage, and represents a challenge for the physician. Methotrexate (MTX) is a safe folic acid antagonist widely used in the management of inflammatory skin diseases such as psoriasis. Weekly administration of 7.5-20 mg methotrexate (low-dose methotrexate, LD-MTX) represents an attractive treatment option, and could therefore find a place in the management of PN. AIM: To evaluate the efficacy of LD-MTX as a treatment option for PN. METHODS: Thirteen patients who had failed to respond to conventional therapies such as topical steroids, phototherapy and antipruritic agents were treated with LD-MTX. The mean age of the patients was 75.83. Objective symptoms (Prurigo Nodularis Area and Severity Index; PNASI) and subjective symptoms (Pruritus Numeric Rating Scale; PNRS) were recorded. Treatment consisted of one subcutaneous injection of MTX 7.5-20 mg once weekly for a minimum of 6 months. Adjuvant application of emollients and topical steroids was maintained where needed. RESULTS: There was remission or marked improvement (decrease in both PNRS or PNASI of > 75%) in 10 cases, a trend to improvement in 2 cases and relapse in 1 case after treatment discontinuation. CONCLUSIONS: LD-MTX may allow improvement of PN in some patients, with long-lasting remission.

Two cases of interferon-alpha-induced sarcoidosis koebnerized along venous drainage lines : new pathogenic insights and review of the literature of interferon-induced sarcoidosis

La sarcoïdose est une affection inflammatoire granuiomateuse systémique d'origine inconnue touchant le plus fréquemment les poumons, le système lymphoïde, le foie, les yeux et la peau. Dans cet article, nous rapportons deux cas de sarcoïdose cutanée touchant les avant-bras de deux patients anciens toxicomanes traités par interféron-a et ribavirine pour une hépatite C chronique. Nous procédons à une revue de la littérature de la sarcoïdose induite par l'interféron et élaborons une nouvelle hypothèse pathogénique de l'effet Koebner dans la sarcoïdose cutanée. Dans le cas des deux patients que nous décrivons, la distribution des lésions cutanées coïncide avec les anciens sites d'injection d'héroïne le long des trajets veineux des deux avant- bras. Cette distribution unique de l'atteinte cutanée suggère que les dommages tissulaires induits par la répétition d'injections percutanées puissent représenter un terrain favorisant au développement local d'une sarcoïdose cutanée. Fait intéressant, il a été récemment démontré que les cellules dendritiques plasmacytoïdes - sous-type de cellules dendritiques généralement absent de la peau - infiltrent rapidement les sites de peau lésée. Ces cellules sont la source d'une production endogène d'interféron-a, cytokine connue pour promouvoir le processus de cicatrisation, mais également pour favoriser le développement de sarcoïdose chez des individus prédisposés. Ainsi, nous postulons que les lésions de sarcoïdose cutanée limitées le long des trajets veineux - sites préalables d'injection percutanée de drogues - peuvent résulter d'une expression locale supplémentaire d'interféron-a. Celle-ci serait en outre favorisée par le traitement de ribavirine dans le cadre de l'hépatite C, connu pour renforcer la production endogène d'interféron-a. L'identification de nombreuses cellules dendritiques plasmacytoïdes circonscrivant l'inflammation granuiomateuse sur la biopsie cutanée de l'un de nos patients semble être un argument dans ce sens, conforté par l'absence de corps étranger détecté en microscopie par lumière polarisée. Cette observation semble pouvoir représenter un point crucial dans la compréhension des mécanismes physiopathologiques à la base de l'infiltration des cicatrices cutanées par la sarcoïdose. Des investigations supplémentaires doivent encore être effectuées afin de confirmer cette hypothèse.

Skull base chordomas: presentation of six cases and review of the literature.

Chordomas are uncommon tumours occuring from remnants of the notochord. They are mainly localized in the sacrococcygium, the spine and the skull base. We focused our study on skull base chordomas and reviewed 531 published cases and 6 cases diagnosed in our institution. The six cases diagnosed at our hospital are described with a special mention of a unique case presenting with meningitis. Clinical features, radiology, histopathology and survival with different treatments are reviewed. Skull base chordomas can occur at any age and are slightly more frequent in males. Patients complain most often of diplopia and headaches. Abducens nerve palsy is the commonest neurological finding. Radiological examination should include both CT-scan which shows extensive osteolysis, calcifications and contrast enhancement and MRI for topographical definition. Metastases rarely occur. Treatment remains controversial but combined surgery and radiotherapy is the best treatment with a 5 year survival rate of 75%.

Social factors related to the clinical severity of influenza cases in Spain during the A(H1N1)2009 virus pandemic

Background During the 2009 influenza pandemic, a change in the type of patients most often affected by influenza was observed. The objective of this study was to assess the role of individual and social determinants in hospitalizations due to influenza A (H1N1) 2009 infection. Methods We studied hospitalized patients (cases) and outpatients (controls) with confirmed influenza A (H1N1) 2009 infection. A standardized questionnaire was used to collect data. Variables that might be related to the hospitalization of influenza cases were compared by estimation of the odds ratio (OR) and 95% confidence intervals (CI) and the variables entered into binomial logistic regression models. Results Hospitalization due to pandemic A (H1N1) 2009 influenza virus infections was associated with non-Caucasian ethnicity (OR: 2.18, 95% CI 1.17 − 4.08), overcrowding (OR: 2.84, 95% CI 1.20 − 6.72), comorbidity and the lack of previous preventive information (OR: 2.69, 95% CI: 1.50 − 4.83). Secondary or higher education was associated with a lower risk of hospitalization (OR 0.56, 95% CI: 0.36 − 0.87) Conclusions In addition to individual factors such as comorbidity, other factors such as educational level, ethnicity or overcrowding were associated with hospitalization due to A (H1N1) 2009 influenza virus infections.

Inappropriate antidiuretic hormone secretion: long-term successful urea treatment.

Hyponatremia is the main complication of inappropriate antidiuretic hormone secretion (SIADH), sometimes fatal. Treatment strategy depends on the cause and the severity of the hyponatremia. Recent studies have shown the efficacy of urea in treating acute hyponatremia secondary to SIADH, by inducing an osmotic water drive. We describe an infant with chronic hyponatremia secondary to SIADH in which the long-term oral treatment with urea was successful and well tolerated. The aim of this paper is to highlight the potential benefits of urea treatment in case of chronic hyponatremia secondary to SIADH. CONCLUSION: Chronic oral urea treatment in children with SIADH allows an easy and safe water and sodium control and may permit a decrease in fluid restriction in this situation.

Stab wounds in a Swiss emergency department: a series of 80 consecutive cases.

Background: Interpersonal violence is a worldwide social reality which seems to increasingly affect even the safest of countries, such as Switzerland. In this country, road traffic accidents, as well as professional and recreational activities, are the main providers of trauma-related injuries. The incidence of penetrative trauma related to stab wounds seems to be regularly increasing in our ED. The question arises of whether our strategies in trauma management are adapted to deal efficiently with these injuries.Methods: To answer this question, the study analysed patients admitted for intentional penetrative injuries in a tertiary urban emergency department (ED) during a 23 month period. Demographics, conditions of the assault, injury type and treatments applied were analysed.Results: Eighty patients admitted due to an intentional penetrating trauma accounted for 0.2% of the surgical practice of our ED. The assault occurred equally in a public or a private context, mainly affecting young males during the night and the weekend. Sixty six patients (83%) were treated as out-patients. Only 10 patients needed surgery. None of them required damage control surgery. No patient died and the mean hospital stay was 5.5 days.Conclusions: The prevalence of stab wounds in Switzerland is low. These injuries rarely need complex, surgical procedures. Observational strategies should be considered according to the patient status.

Evaluation of Unbonded Ultrathin Whitetopping of Brick Streets, TR-466, Construction Report, 2002

Many cities in Iowa have retained the original brick street surfaces in downtown areas and in older residential areas as the base for modern driving surfaces. The original brick surfaces were not built to handle current and future traffic loadings. In recent years, these surfaces have tended to shift and become uneven, creating problems with safety. Asphaltic concrete overlays have been the typical rehabilitation technique in these situations. This has proven to be a successful rehabilitation technique in some cases; in other cases, the combination of movement of the brick and flexibility of the asphalt has proven to accentuate the original problems. Most of the existing literature on rehabilitation of brick streets shows the use of asphaltic concrete. Other rehabilitation methods include reconstruction of the brick surface and strengthening of the surface by placing asphaltic concrete or portland cement concrete, along with sand, underneath the brick layers. To date, little if anything has been done in the area of using portland cement concrete as an overlay of the brick surfaces. This final report documents the planning, construction, and performance of unbonded ultrathin whitetopping rehabilitation of a brick street in Oskaloosa, Iowa, in 2001. It also reports on a similar project in Des Moines that was constructed two years later in 2003.

Successful migration of three tracers without identification of sentinel nodes during intraoperative lymphatic mapping for non-small cell lung cancer.

Prospective comparative evaluation of patent V blue, fluorescein and (99m)TC-nanocolloids for intraoperative sentinel lymph node (SLN) mapping during surgery for non-small cell lung cancer (NSCLC). Ten patients with peripherally localised clinical stage I NSCLC underwent thoracotomy and peritumoral subpleural injection of 2 ml of patent V blue dye, 1 ml of 10% fluorescein and 1ml of (99m)Tc-nanocolloids (0.4 mCi). The migration and spatial distribution pattern of the tracers was assessed by direct visualisation (patent V blue), visualisation of fluorescence signalling by a lamp of Wood (fluorescein) and radioactivity counting with a hand held gamma-probe ((99m)Tc-nanocolloids). Lymph nodes at interlobar (ATS 11), hilar (ATS 10) and mediastinal (right ATS 2,4,7; left ATS 5,6,7) levels were systematically assessed every 10 min up to 60 min after injection, followed by lobectomy and formal lymph node dissection. Successful migration from the peritumoral area to the mediastinum was observed for all three tracers up to 60 min after injection. The interlobar lympho-fatty tissue (station ATS 11) revealed an early and preferential accumulation of all three tracers for all tumours assessed and irrespective of the tumour localisation. However, no preferential accumulation in one or two distinct lymph nodes was observed up to 60 min after injection for all three tracers assessed. Intraoperative SLN mapping revealed successful migration of the tracers from the site of peritumoral injection to the mediastinum, but in a diffuse pattern without preferential accumulation in sentinel lymph nodes.

OpenApp: experiencias y herramientas docentes y de gestión en abierto

La Universitat Oberta de Catalunya (UOC) es una universidad en línea que realiza un uso intensivo de las tecnologías de la información y la comunicación para proporcionar una educación y aprendizaje a lo largo de la vida. Des de sus inicios la universidad ha desarrollado y testeado metodologías y tecnologías con el objetivo de proporcionar soluciones a los retos de aprendizaje y docentes ofrecidos por la comunidad de estudiantes, académicos y personal de gestión.Fundamentado en este saber hacer, nace la plataforma OpenApps con la finalidad principal de poner a disposición de la comunidad la experiencia acumulada en la UOC durante más de 15 años en docencia, aprendizaje y gestión para que pueda ser aplicado, adaptado o evolucionado por terceros. En este artículo se presentan las características esenciales para que una innovación pueda formar parte de esta plataforma institucional, las especificaciones y usuarios de la plataforma, la finalidad del servicio y las futuras líneas de trabajo.