Exhaustive Search of Ligand Binding Pathways via Volume-based Metadynamics

Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics-based technique that addressed this issue and allows estimating affinities in the presence of multiple escape pathways. Our approach is shown on a Lysozyme T4 variant in complex with the benzene molecule. The calculated binding free energy is in agreement with experimental data. Remarkably, not only we were able to find all the previously identified ligand binding pathways, but also we uncovered 3 new ones. This results were obtained at a small computational cost, making this approach valuable for practical applications, such as screening of small compounds libraries

Electron paramagnetic resonance applications: from drug discovery to marine biology studies

El leitmotiv de la tesis es el uso de la técnica EPR, que implica el estudio de la dinámica de interacción de sistemas de interés con la ayuda de especies paramagnéticas apropiadas. El trabajo realizado en los tres años del doctorado se centró en el estudio químico-físico de moléculas de uso biomédico, más un trabajo extra sobre la interacción químico-física entre algunas formas de fitoplancton y microplásticos. La tesis se desarrolla en tres líneas de investigación: 1. El estudio de los glicodendrímeros para el tratamiento de la enfermedad de Wilson ocupó la mayor parte del primer año. Una nueva familia de glicodendrímeros, modificados con grupos DOTA, fue sintetizada el centro de investigación Leibniz-Intitute de Dresden, y analizada para evaluar su habilidad de quelar átomos de Cu(II). En particular, se puso bajo la lupa la interacción químico-física entre estas moléculas y los modelos de membrana, que confirmó su posible aplicación en campo biomédico. Este estudio condujo a la redacción de un artículo publicado en Langmuir. 2. Durante los tres años, se trabajó en la síntesis, caracterización y aplicación de metalodendrímeros para el tratamiento de diversas formas de neoplasia. La combinación de esta clase de polímeros e iones metálicos permite un control fino de los mecanismos anticancerígenos, que pueden moldearse según el sistema en estudio. Nuevas familias de metalodendrímeros de cobre y rutenio fueron sintetizadas en Alcalá y estudiadas bajo un punto de vista químico-físico en la universidad de Urbino. En este contexto, se han publicado 3 artículos y una reseña, además de un último artículo en proceso de peer review. 3. Un proyecto nacido y concluido en pocos meses con la publicación de un artículo en Chemosphere, se refiere a la demostración de la interacción física de algunos tipos de fitoplancton y microplásticos presentes en el Mediterráneo, para explicar un fenómeno particular de bio-contaminación que ha surgido en los últimos años. Dicha interacción fue estudiada en Urbino por medio de técnicas químico-físicas

The effect of morphology on poly(vinylidene fluoride-trifluoroethylene- chlorotrifluoroethylene)-based soft actuators: Films and electrospun aligned nanofiber mats

This paper analyzes soft actuators realized as unimorph cantilever beams, in which the active layer can have two different morphologies, i.e., either an extruded film or an aligned electrospun nanofiber mat of the poly (vinylidene fluoride-trifluoroethylene-chlorotrifluoroethylene). Six different soft actuators are fabricated, with active layers of varying thicknesses and morphologies, to study the electrostrictive effect of the polymer and to evaluate the stiffening properties, the mechanical work, and the blocking forces of the actuators when stimulated by different direct current electric fields. The comparison between the different actuators is performed by introducing weight specific properties, i.e., specific stiffness and specific work, showing improved specific properties for the nanofibers-based actuators. Moreover, the blocking forces, the tip deflections, and the leakage currents of the actuators are evaluated when stimulated by alternating current electric fields. The experiments show faster viscoelastic relaxation and lower electrical power consumption for the nanofibers-based actuators. This study concludes that, thank to its electro-mechanical properties, the poly(vinylidene fluoride-trifluoroethylene-chlorotrifluoroethylene) in the form of aligned electrospun nanofiber mat has high potential to be used as the active layer of electrostrictive unimorph beam soft actuators

Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors

We present an approach that, by integrating structural data with Direct Coupling Analysis, is able to pinpoint most of the interaction hotspots (i.e. key residues for the biological activity) across very sparse protein families in a single run. An application to the Class A G-protein coupled receptors (GPCRs), both in their active and inactive states, demonstrates the predictive power of our approach. The latter can be easily extended to any other kind of protein family, where it is expected to highlight most key sites involved in their functional activity

Soft composite actuators of poly(vinylidene fluoride-trifluoroethylene-chlorotrifluoroethylene)-based nanofibers and polydimethylsiloxane:Fabrication, electromechanical characterization, and dynamic modeling

Nanofibrous unimorph cantilever beam soft actuators offer remarkable advantages, such as rapid viscoelastic relaxation, low power consumption, and high weight-specific properties. However, the presence of high porosity in the nanofibrous active layer poses a challenge due to its low breakdown voltage, limiting the practical applications of this class of soft actuators. This study proposes an innovative solution to enhance the relative permittivity of the nanofibrous layer by redesigning it as a composite layer. By integrating electrospun aligned nanofibers of poly(vinylidene fluoride-trifluoroethylene-chlorotrifluoroethylene) into a polydimethylsiloxane elastomeric matrix, the composite active layer achieves a notable increase in relative permittivity (10.5 at 100 Hz), surpassing the individual materials' values (2.5 and 2.7 at 100 Hz for the nanofibers and polydimethylsiloxane, respectively). To realize novel soft actuators, the composite active layer is placed between carbon black electrodes, with Kapton® serving as the passive layer. Remarkably, aligning the nanofibers in the transversal direction of the actuator enhances its actuation capabilities significantly. When subjected to a 25 MVm−1 electric field, the tip deflection and blocking force exhibit a ∼400% improvement compared to polydimethylsiloxane-based actuators. To support these findings, a physics-based dynamic model is derived and validated through experimental tests in both static and transient time simulations

Self-sensing composite material based on piezoelectric nanofibers

Recently, efforts have been made to manufacture self-sensing smart composites by integrating piezoelectric sensors with laminates. However, the interleaving of pressure sensors, such as piezoelectric polymeric films, dramatically reduces the impact resistance of the hosting laminates, and consequently, delamination can occur. This study aimed to fabricate a self-sensing composite material by embedding piezoelectric nanofibers of poly(vinylidenefluoride-trifluoroethylene) (PVDF-TrFE) in a polymeric elastic matrix and carbon black-based electrodes to detect a piezoelectric signal. The mechanical and electrical properties of the self-sensing laminate were maintained after 106 fatigue test cycles. By appropriately tuning the parameters of the acquisition circuit, the sensor could measure not only impulsive loads but also low-frequency loads as low as 0.5 Hz. A piezoelectric model with lumped parameters for the polarization process and piezoelectric response of the nanofibers is proposed and validated by experimental results. As a proof of the model, the piezoelectric nanofiber sensors were embedded in a prosthetic carbon fiber sole, and the piezoelectric signal response closely followed the ground reaction force with a sensitivity of 0.14 mV/N

Appropriateness of Mini-Invasive Approaches for Nausea and Vomiting Refractory to Medical Therapy in Palliative Care Setting: A Case Report

Introduction: Nausea and vomiting are frequent multifactorial symptoms in oncological patients. These manifestations, mainly affecting the advanced disease stages, may lead to existential, psychological, and physical suffering, with a negative impact on the quality of life (QoL) of the individual and his family. The medical approach makes use of a wide range of drugs, with different antiemetic potency and various mechanisms of action, taking into account the etiology and the patient’s response to the different therapeutic strategies. In recent years, in addition to pharmacological treatments, some endoscopic procedures have been integrated into clinical practice as promising palliative approaches. Case Presentation: Herein, we describe and discuss a case of a 64-year-old female affected by advanced stage pancreatic adenocarcinoma, in which different techniques – both medical and endoscopic – have been used to approach a refractory symptomatology with a negative impact on the patient’s QoL. In the context of a multidisciplinary approach in primary palliative care, a tailored intervention encompassing invasive methods for palliative purposes, may be considered adequate and appropriate when the prognostic expectation and the physical functionality indices allow it. Conclusion: Minimally invasive palliative interventions should be offered to patients with advanced cancer when symptoms become refractory to standard medical therapies, as part of the holistic approach in modern treatments. Therefore, the integration of an early palliative approach into the patient’s therapeutic path becomes essential for the management of all the individual’s needs

Immunotherapy in Pancreatic Cancer: Why Do We Keep Failing? A Focus on Tumour Immune Microenvironment, Predictive Biomarkers and Treatment Outcomes

The advent of immunotherapy and targeted therapies has dramatically changed the outcomes of patients affected by many malignancies. Pancreatic cancer (PC) remains one the few tumors that is not treated with new generation therapies, as chemotherapy still represents the only effective therapeutic strategy in advanced-stage disease. Agents aiming to reactivate the host immune system against cancer cells, such as those targeting immune checkpoints, failed to demonstrate significant activity, despite the success of these treatments in other tumors. In many cases, the proportion of patients who derived benefits in early-phase trials was too small and unpredictable to justify larger studies. The population of PC patients with high microsatellite instability/mismatch repair deficiency is currently the only population that may benefit from immunotherapy; nevertheless, the prevalence of these alterations is too low to determine a real change in the treatment scenario of this tumor. The reasons for the unsuccess of immunotherapy may lie in the extremely peculiar tumor microenvironment, including distinctive immune composition and cross talk between different cells. These unique features may also explain why the biomarkers commonly used to predict immunotherapy efficacy in other tumors seem to be useless in PC. In the current paper, we provide a comprehensive and up-to-date review of immunotherapy in PC, from the analysis of the tumor immune microenvironment to immune biomarkers and treatment outcomes, with the aim to highlight that simply transferring the knowledge acquired on immunotherapy in other tumors might not be a successful strategy in patients affected by PC