Feed

Titolo: 3D Homology Model of Sigma1 Receptor
Abstract: This chapter presents the three-dimensional (3D) model of the Sigma1 receptor protein as obtained from homology modeling techniques. We show the applicability of this structure to docking-based virtual screening and discuss combined in silico/in vitro mutagenesis studies performed to validate the structural features of the Sigma1 receptor model and to qualify/quantify the prominent role of specific amino acid residues in ligand binding. The validation of the virtual 3D Sigma1 receptor model and its reliable applicability to docking-based virtual screening is of significance for rational ligand design, even in light of the recently reported crystal structure for the Sigma1 receptor.

Titolo: Design, synthesis and antitubercular activity of 4-alkoxy-triazoloquinolones able to inhibit the M. tuberculosis DNA gyrase
Abstract: A number of new F-triazolequinolones (FTQs) and alkoxy-triazolequinolones (ATQs) were designed, synthesized and evaluated for their activity against Mycobacterium tuberculosis H37Rv. Five out of 21 compounds exhibited interesting minimum inhibitory concentration (MIC) values (6.6-57.9 microM), ATQs generally being more potent than FTQs. Two ATQs, 21a and 30a, were endowed with the best anti-Mtb potency (MIC = 6.9 and 6.6 microM, respectively), and were not cytotoxic in a Vero cell line. Tested for activity against M. tuberculosis DNA gyrase in a DNA supercoiling activity assay, 21a and 30a showed IC50 values (27-28 microM) comparable to that of ciprofloxacin (10.6 microM). 21a was next selected for screening against several Mtb strains obtained from clinical isolates, including multi-drug-resistant (MDR) variants.
Importantly, this compound was effective in all cases, with very promising MIC values (4 microM) in the case of some isoniazid/rifampicin-resistant Mtb strains. Finally, computer-based simulations revealed that the binding mode of 21a in the Mtb gyrase cleavage core complexed with DNA and the relevant network of intermolecular interactions are utterly similar to those described for ciprofloxacin, yielding a molecular rationale for the comparable anti-mycobacterial and DNA gyrase inhibition activity of this quinolone.

Titolo: Molecular and functional characterization of a new 3′ end KIT juxtamembrane deletion in a duodenal GIST treated with neoadjuvant Imatinib
Abstract: Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. GISTs express the receptor tyrosine kinase KIT, and the majority of GISTs present KIT gain-of-function mutations that cluster in the 5' end of the receptor juxtamembrane domain. On the other hand, little information is known about GISTs carrying mutations in the 3′ end of the KIT juxtamembrane domain. Here we report and discuss a clinical case of localized duodenal GIST whose molecular characterization revealed the presence of a new 21 nucleotide/7 amino acid deletion in the 3′ end of KIT juxtamembrane domain (Δ574–580). The patient was treated with Imatinib at standard regimen dose (400 mg/day), and responded well as the original tumor mass reduced, ultimately allowing conservative surgery. In line with these clinical evidences computer simulations, biophysical techniques and in vitro experiments demonstrated that the receptor tyrosine kinase KIT carrying the Δ574–580 mutation displays constitutive phosphorylation, which can be switched-off upon Imatinib treatment. In addition, results from this study showed that a clinical useful procedure, neoadjuvant treatment, can occasionally be of value for the understanding of the molecular pathogenesis of GIST.

Titolo: Targeting Hsp27/eIF4E interaction with phenazine compound: A promising alternative for castration-resistant prostate cancer treatment
Abstract: The actual strategy to improve current therapies in advanced prostate cancer involves targeting genes activated by androgen withdrawal, either to delay or prevent the emergence of the castration-refractory phenotype. However, these genes are often implicated in several physiological processes, and long-term inhibition of survival proteins might be accompanied with cytotoxic effects. To avoid this problem, an alternative therapeutic strategy relies on the identification and use of compounds that disrupt specific protein-protein interactions involved in androgen withdrawal. Specifically, the interaction of the chaperone protein Hsp27 with the initiation factor eIF4E leads to the protection of protein synthesis initiation process and enhances cell survival during cell stress induced by castration or chemotherapy. Thus, in this work we aimed at i) identifying the interaction site of the Hsp27/eIF4E complex and ii) interfere with the relevant protein/protein association mechanism involved in castration-resistant progression of prostate cancer. By a combination of experimental and modeling techniques, we proved that eIF4E interacts with the C-terminal part of Hsp27, preferentially when Hsp27 is phosphorylated. We also observed that the loss of this interaction increased cell chemo-and hormone-sensitivity. In order to find a potential inhibitor of Hsp27/eIF4E interaction, BRET assays in combination with molecular simulations identified the phenazine derivative 14 as the compound able to efficiently interfere with this protein/protein interaction, thereby inhibiting cell viability and increasing cell death in chemo- and castration-resistant prostate cancer models in vitro and in vivo.

Titolo: Materials by design: multiscale molecular modeling for the design of nanostructured membranes
Abstract: The fast development of digitalization and computational science is opening new possibilities for a rapid design of new materials. Computational tools coupled with focused experiments can be successfully used for the design of new nanostructured materials in different sectors, including membrane engineering. Accordingly, in this Chapter, we present the application of a multiscale molecular simulation protocol for predicting gas transport properties in polymeric nanocomposite membranes constituted by titania (TiO2) nanoparticles dispersed in thermoplastic polyurethanes (TPUs). The Chapter starts with a general introduction on the future of computational tools for the design of new materials and introduces the paradigm underlying of multiscale molecular modelling. It then continues with the description of the multiscale (i.e., atomistic, mesoscale and finite element calculations) computational recipe developed ad hoc for the prediction of different gas permeation and diffusion in TPU/TiO2 nanocomposite membranes. Finally, the comparison of in silico and experimental results on these systems is reported and discussed. The quality of the agreement obtained between virtual and real data for such complex systems indeed confirms the validity of computational tools for the design and transport property prediction of nanocomposite membranes for gas treatment.

Titolo: Triazolopyridinyl-acrylonitrile derivatives as antimicrotubule agents: Synthesis, in vitro and in silico characterization of antiproliferative activity, inhibition of tubulin polymerization and binding thermodynamics
Abstract: In this paper we report the synthesis, in vitro anticancer activity, and the experimental/computational characterization of mechanism of action of a new series of E isomers of
triazolo[4,5-b/c]pyridin-acrylonitrile derivatives (6c-g, 7d-e, 8d-e, 9c-f, 10d-e, 11d-e). All new compounds are endowed with moderate to interesting antiproliferative activity against 9 different cancer cell lines derived from solid and hematological human tumors. Fluorescence-based assays prove that these molecules interfere with tubulin polymerization. Furthermore, isothermal titration calorimetry (ITC) provides full tubulin/compound binding thermodynamics, thereby ultimately qualifying and quantifying the interactions of these molecular series with the target protein. Lastly, the analysis based on the tight coupling of in vitro and in silico modelling of the interactions
between tubulin and the title compounds allows to propose a molecular rationale for their biological activity.

Titolo: Quinoxaline derivatives as new inhibitors of coxsackievirus B5
Abstract: Enteroviruses are among the most common and important human pathogens for which there are no specific antiviral agents approved by the US Food and Drug Administration so far. Particularly, coxsackievirus infections have a worldwide distribution and can cause many important diseases. We here report the synthesis of new 14 quinoxaline derivatives and the evaluation of their cytotoxicity and antiviral activity against representatives of ssRNA, dsRNA and dsDNA viruses. Promisingly, three compounds showed a very potent and selective antiviral activity against coxsackievirus B5, with EC50 in the sub-micromolar range (0.3 - 0.06 μM). A combination of experimental techniques (i.e. virucidal activity, time of drug addition and adsorption assays) and in silico modeling studies were further performed, aiming to understand the mode of action of the most active, selective and not cytotoxic compound, the ethyl 4-[(2,3-dimethoxyquinoxalin-6-yl)methylthio]benzoate (6).

Titolo: 9-Aminoacridine-based agents impair the bovine viral diarrhea virus (BVDV) replication targeting the RNA-dependent RNA polymerase (RdRp)
Abstract: Bovine viral diarrhea virus (BVDV) infection is still a plague that causes important livestock pandemics. Despite the availability of vaccines against BVDV, and the implementation of massive eradication or control programs, this virus still constitutes a serious agronomic burden. Therefore, the alternative approach to combat Pestivirus infections, based on the development of antiviral agents that specifically inhibit the replication of these viruses, is of preeminent actuality and importance.
Capitalizing from a long-standing experience in antiviral drug design and development, in this work we present and characterize a series of small molecules based on the 9-aminoacridine scaffold that exhibit potent anti-BVDV activity coupled with low cytotoxicity. The relevant viral protein target – the RNA-dependent RNA polymerase – the binding mode, and the mechanism of action of these new antivirals have been determined by a combination of in vitro (i.e., enzymatic inhibition,
isothermal titration calorimetry and site-directed mutagenesis assays) and computational experiments. The overall results obtained confirm that these acridine-based derivatives are promising compounds in the treatment of BVDV infections and, based on the reported structure-activity relationship, can be selected as a starting point for the design of a new generation of improved, safe and selective anti-BVDV agents.

Titolo: Development of a methodology for the sustainability evaluation of biodiesel production from vegetable oil
Abstract: Our work aims to extend the application field of a general framework for the evaluation of chemical continuous processes sustainability, i.e. Process Sustainability Prediction (PSP) Framework proposed by Fermeglia et al. [1], in order to perform a sustainability analysis of conventional processes of biotech industry, e.g. the biomass conversion to biofuel. The procedure proposed allows to choose the best operating parameters and inlet streams mass flow of the continuous process for the conversion of palm oil to biodiesel, employing a broad methodology that comprehends each aspect of sustainability, i.e. economy, environment and society. One indicator for each sustainability pillar has been adopted obtaining a global estimation of sustainability performances of process designs which will lead to the adoption of the most sustainable design among the different alternatives. The most relevant characteristics of our approach are the quickness of the sustainability evaluation as well as the opportunity of performing the analysis on a wide number of alternatives avoiding the need of new experimental data for each one. These benefits provided by our methodology give a considerable contribution to the wider context of sustainability assessment, reducing the number of possible alternatives to investigate using Life Cycle Assessment (LCA), a well-established but time-demanding methodology. The methodology proposed by Martins [2], based on four indicators, has been modified merging two indicators related to economic performances into a single one to reduce redundancy and considering the mass fraction of chemicals involved in the process instead of grouping them into quantity classes, aiming to avoid the imbalance generating by the adoption of various chemicals. The different process alternatives have been created performing a sensitivity analysis of the transformation process of palm oil into biodiesel [3] implemented in a process simulator (Aspen Plus), which includes transesterification, methanol recovery, water washing, fatty acid methyl ester (FAME) purification, catalyst removal and glycerol purification. Vegetable oil is the mixture of triglycerides (TG) as specified in [3], while the composition profile of palm oil feedstock is determined by Che Man[4]. The toxicity of compounds involved in the process has been estimated using quantum-mechanics property of molecular structures using COSMO-RS in order to calculate logKow, which is related to the hydro solubility of compounds and is adopted to evaluate whether a compound is more likely to reside in organic phase or in aquatic one. The scores obtained for each process alternative have been analysed using Data Envelopment Analyis (DEA) [6] in order to identify the optimal design and calculate the improvement needed for the others to become as efficient as the optimal one.

Titolo: β-catenin in Desmoid-Type Fibromatosis: deep insights on the role of T41A and S45F mutations on protein structure and gene expression
Abstract: Desmoid- type fibromatosis (DF) is a rare mesenchymal lesion with high risk of local recurrence. Specific β-catenin mutations (S45F) appeared to be related to this higher risk compared to T41A mutated or wild type (WT). We explored the influence of both mutations and WT on structure stability and affinity of β-catenin for α-catenin and the pattern of gene expression that may influence DF behavior. Using 33 surgically resected primary DFs harboring T41A (n=14), S45F (n=10) or WT (n=9), we performed a comparative molecular analysis by protein/protein interaction modeling, gene expression by DASL microarrays, human inflammation gene panel and assessment of immune system-based biomarkers by immunohistochemistry. Mutated proteins were more stable than WT and formed a weaker complex with α-catenin. Consensus unsupervised gene clustering revealed the presence of two DF group- mutated (T41A+S45F) and WT (p= 0.0047). The gene sets "Inflammatory- Defense- Humoral-Immune Response" and "Antigen Binding" were significantly enriched in T41A. The deregulation of 16 inflammation-related genes was confirmed. Low numbers of T- cells and TAM infiltrating the tumors and low/absent PD-1/PD-L1 expression were also identified. We demonstrated that mutated DFs (T41A or S45F) and WT are two distinct molecular subgroups with regard to β-catenin stability, α-catenin affinity and gene expression profiling. A different inflammation signature characterized the two mutated groups, suggesting a mediation either by T41A or S45F. Finally, all mutated cases showed a low number of TIL and TAM cells and a low or absent expression of PD-1 and PD-L1 consistent with β-catenin activation insensitive to check-point blockade.