1,720,971 research outputs found
In-silico methods applied on druggable proteins to identify transient pockets: new approaches for studying drug-target molecular mechanisms. A case study on CFTR.
No full textCystic Fibrosis is the most common genetical lethal disorder in Caucasians and it is caused by the mutation of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein. Up to now, for the treatment of cystic fibrosis patients carrying at least one copy of CFTR deleted of the phenylalanine 508 (F508del-CFTR), the worldwide most frequent mutation, only four drugs have been approved to be used in combination or alone. All the approved compounds have been developed, studied, and are currently commercialized by Vertex Pharmaceuticals. Despite the benefits of these marketed drugs, they are still too expensive for many countries, and they cannot be prescribed to all patients. Thus remains a pressing need to better understand the CFTR structure-function relationship, and the binding site and molecular mechanism of already approved drugs, to identify other CFTR modulators for the rescue of the mutated protein, in particular, F508del-CFTR.
On these bases my research activity has been focused on a deep study of the protein function, investigating its three-dimensional structure and dynamics in complex with the already approved CF drug lumacaftor and new possible CFTR modulators by means of drug repositioning. An optimized model, obtained before the starting of my PhD, of the F508del-CFTR protein and a library of pockets, in which an interesting large druggable pocket (DP1) was identified using lumacaftor as a template, has been used for the following drug repositioning strategy. An in-house database which included 846 drugs and nutraceuticals approved by AIFA (actually implemented to more than 10000 molecules from AIFA and Drugbank database) was built, drawing their 3D structure with the right protonation state of the drugs, and then screened by docking against F508del-CFTR. Among the best eleven repositioned compounds identified within this procedure, tadalafil was one that has been already taken into consideration for cystic fibrosis therapy, confirming the goodness of this approach. Quercetin emerged as the best ligand among the eleven selected, suggesting that small molecules could give a consistent contribution in the search for new CFTR modulators. Focusing on this concept, the several DP1 sub-pockets surrounding the lumacaftor binding region were explored, searching for the most druggable ones and in the meantime scouting small molecules able to fill the transient druggable DP1 sub-pockets and synergize with lumacaftor. At the end of this procedure, NAM was found as a possible hit.
Moreover, during my PhD project, my computational studies have been also focused on two proteins of therapeutical interest, which mutations are causative of rare genetical disorders: the Leucine-Rich and ImmunoGlobulin-like domains 2 (LRIG2) and the Nucleoporin 98 (NUP98), whose mutations lead to the Urofacial Syndrome and a phenotype resembling the Rothmund-Thomson syndrome, respectively.
The study of LRIG2 involved the investigation of the role of the first immunoglobulin-like domain (Ig1) of the LRIG2 protein, and its deletion and mutations, in the LRIG2 homodimerization. The LRIG2 homodimerization was predicted in silico and its dimerization interface was computationally characterized. Then, by means of accelerated molecular dynamic simulations, the central role of the Ig1 domain in the LRIG2 dimerization was furthermore validated by studying the impact of the Ig1 domain mutations, described in the literature as pathogenic, in the context of the monomeric LRIG2. This advanced molecular dynamic technique allowed to clarify the role of these mutations in the impairment of the LRIG2 homodimerization.
Eventually, regarding the study of NUP98, a novel germline alteration (G28D) located in the unstructured N-terminal of the NUP98, which is characterized by phenylalanine-glycine (FG) repeats, was computationally evaluated. Differences in the dynamic behavior between the wild type and G28D mutated protein were observed, which are produced from a dispersion of the intramolecular cohesion elements (FG repeats) leading to more elongated conformational states of the unstructured N-terminal of the NUP98 mutant in comparison to the wild type. Those differences may affect the role of NUP98 as a multi-docking station for RNA and proteins, and its folding process when a specific interaction is required
Teaching policymaking with games. Introduction to the special issue
No full textUnderstanding how policy decisions are made is a vital skill for students and practitioners in public administration. Yet policymaking remains a complex, dynamic, and often opaque process—where ideas compete, interests clash, and change is hard-won. This special issue examines how digital serious games can teach policymaking in a manner that is both theoretically grounded and experientially rich. This introductory article addresses the unique challenges of teaching policymaking—a subject that lies at the intersection of the technical and procedural aspects of public administration and the conceptual focus of policy process theories. Teaching policymaking carries both practical and democratic value. It helps students develop strategic agency by learning how actors frame problems, build coalitions, overcome opposition, and design pathways to policy reform. At the same time, it fosters democratic competence by encouraging students to recognise the pluralistic nature of public decisions, understand power asymmetries, and resist simplistic or populist narratives. The article also argues that addressing complex policy problems requires not only sound evidence but also knowledge of policymaking, i.e. a deep understanding of how evidence is framed, contested, and mobilised within the policy process. The introductory article discusses how serious games can effectively integrate these dimensions into the classroom. By simulating real-world dynamics, games allow students to experience policymaking first-hand. This experiential approach fosters critical thinking, soft skills, and a realistic understanding of the complexity of policy decisions. The articles in this special issue expand on these themes, presenting insights from the use of the P-CUBE digital game across diverse policy fields, including social inclusion, scientific decision-making, and urban policy, and offering practical guidance on game design, classroom strategies, and learning outcomes
Docking and Molecular dynamics protocol for ligand binding characterization of Nuclear Receptors
No full textHotspot residues involved in potency and selectivity of the ligand binding in Nuclear Receptors.
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Computational evaluation of the synergic effect of a small molecule on Lumacaftor F508del-CFTR rescue ability
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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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