Rational ligand-Based Virtual Screening and Structure-Activity Relationship Studies in the Ligand-Binding Domain of the Glucocorticoid Receptor-α.

The interest in developing synthetic glucocorticoids (GCs) arises from the utility of endogenous steroids as potent anti-inflammatory and immunosuppressant agents. The first GCs to be discovered, such as cortisol or dexamethasone, still represent the main treatment for conditions of the inflammatory process, despite the fact that they carry a significant risk of side effects. Hence, there is a continuing need to find drugs that preserve the immune effects of GCs without the side effects, such as those on metabolism (diabetes), bone tissue (osteoporosis), muscles (myopathy), eyes and skin. In this review, we focus on the recent use of ligand-based computational approaches in glucocorticoid receptor (GR) drug design efforts towards the determination of novel G R ligands. We examine a number of ligand­ based (similarity searches, pharmacophore screens, quantitative structure-activity relationships) approaches that have been implemented in recent years. A recent virtual high throughput screening similarity search was successful in developing a novel series of nonsteroidal GR antagonists. Additionally, there has been considerable success in ligand-based structure-analysis relationship generation and lead optimization studies for the GR. Future trends towards integrated GR ligand design incorporating ligand- and structure-based methodologies are inevitable

Rational ligand-based virtual screening and structure-activity relationship studies in the ligand-binding domain of the glucocorticoid receptor-α

The interest in developing synthetic glucocorticoids (GCs) arises from the utility of endogenous steroids as potent anti-inflammatory and immunosuppressant agents. The first GCs to be discovered, such as cortisol or dexamethasone, still represent the main treatment for conditions of the inflammatory process, despite the fact that they carry a significant risk of side effects. Hence, there is a continuing need to find drugs that preserve the immune effects of GCs without the side effects, such as those on metabolism (diabetes), bone tissue (osteoporosis), muscles (myopathy), eyes and skin. In this review, we focus on the recent use of ligand-based computational approaches in glucocorticoid receptor (GR) drug-design efforts for the determination of novel GR ligands. We examine a number of ligand-based (similarity searches, pharmacophore screens and quantitative structure-activity relationships) approaches that have been implemented in recent years. A recent virtual high-throughput screening similarity search was successful in developing a novel series of nonsteroidal GR antagonists. Additionally, there has been considerable success in ligand-based structure-analysis relationship generation and lead optimization studies for the GR. Future trends toward integrated GR ligand design incorporating ligand- and structure-based methodologies are inevitable.

Rational structure-based drug design and optimization in the ligand-binding domain of the glucocorticoid receptor-α

Conclusion : By the end of 2008, there had been limited achievements utilizing docking studies and no published successes in the area of virtual high-throughput screening. However, the availability of novel crystal structures and the use of induced-fit docking protocols are improving docking success rates and promising to aid the future delivery of nonsteroidal ligands.

Identification of tubulin as the molecular target of proapoptotic pyrrolo-1,5-benzoxazepines

We have demonstrated previously that certain members of a series of novel pyrrolo-1,5-benzoxazepine (PBOX) compounds potently induce apoptosis in a variety of human chemotherapy-resistant cancer cell lines and in primary ex vivo material derived from cancer patients. A better understanding of the molecular mechanisms underlying the apoptotic effects of these PBOX compounds is essential to their development as antineoplastic therapeutic agents. This study sought to test the hypothesis that proapoptotic PBOX compounds target the microtubules. We show that a representative proapoptotic PBOX compound, PBOX-6, induces apoptosis in both the MCF-7 and K562 cell lines. An accumulation of cells in G2/M precedes apoptosis in response to PBOX-6. PBOX-6 induces prometaphase arrest and causes an accumulation of cyclin B1 levels and activation of cyclin B1/CDK1 kinase in a manner similar to that of two representative antimicrotubule agents, nocodazole and paclitaxel. Indirect immunofluorescence demonstrates that both PBOX-6 and another pro-apoptotic PBOX compound, PBOX-15, cause microtubule depolymerization in MCF-7 cells. They also inhibit the assembly of purified tubulin in vitro, whereas a nonapoptotic PBOX compound (PBOX-21) has no effect on either the cellular microtubule network or on the assembly of purified tubulin. This suggests that the molecular target of the pro-apoptotic PBOX compounds is tubulin. PBOX-6 does not bind to either the vinblastine or the colchicine binding site on tubulin, suggesting that it binds to an as-yet-uncharacterised novel site on tubulin. The ability of PBOX-6 to bind tubulin and cause microtubule depolymerization confirms it as a novel candidate for antineoplastic therap

Ricerca è democrazia. Il ruolo dell’attività scientifica nella costruzione di un futuro equo e sostenibile

Il presente volume raccoglie gli atti della terza edizione del Convegno “Ricerca in Vetrina” che si è tenuto presso l’Aula Magna “Gaetano Cima” dell’Università degli Studi di Cagliari nelle giornate del 6 e 7 dicembre 2018. L’evento, promosso dalle sedi di Cagliari e Sassari dell’Associazione Dottorandi e Dottori di Ricerca Italiani (ADI), mette al centro il lavoro che dottorandi e dottori di ricerca non strutturati svolgono ogni giorno all’interno delle università italiane, con l’obiettivo di valorizzarne il contributo e creare una piattaforma conoscitiva e di dialogo tra accademia, istituzioni, imprese e società civile. “Ricerca è democrazia” è il tema proposto per questa edizione in cui sono state coinvolte alcune delle più importanti associazioni impegnate sul campo – Amnesty International, Libera, ASVIS, AISA, CSV Sardegna – al fine di riflettere, in questo momento storico di grave crisi delle democrazie mondiali, sul ruolo della ricerca come forma di “attivismo sociale” con forti implicazioni nella costruzione di un futuro equo e sostenibile. Come motore dell’innovazione, infatti, la ricerca può divenire uno strumento strategico per favorire il dialogo interculturale, incoraggiare la tolleranza, garantire pari opportunità, promuovere lo sviluppo di contesti svantaggiati e politiche di benessere per le generazioni presenti e future. Sono queste alcune delle questioni affrontate durante il convegno dai ricercatori esperti di diverse discipline, provenienti da nove università italiane: Cagliari, Sassari, Roma “La Sapienza”, Roma Tre, Firenze, Perugia, Verona, Bari e Catanzaro. Tutti i contributi presentati – suddivisi in tre sessioni tematiche interdisciplinari: Sviluppo, risorse e ambiente; Il passato e la sua eredità; Connessioni e reti – evidenziano, secondo molteplici approcci e prospettive, un articolato quadro di conoscenze teoriche e sperimentazioni empiriche che sottolineano la dimensione tecnico-applicativa e il valore etico della ricerca per la democrazia

Different binding thermodynamics of Ni+2, Cu+2 and Zn+2 to bacitracin A1 determined by capillary electrophoresis

Thermodynamics of the binding of Ni2+, Cu2+ and Zn2+ to bacitracin A(1) was studied by capillary electrophoresis measuring the peptide effective mobility at different pH in the presence of increasing concentration of the three ligands. The affinity follows the order Ni2+ > Cu2+ > Zn2+, with association constant values of (2.3+/- 0.1) X 10(4), (4.9+/-0.2) x 10(3), and (1.5 +/- 0.1) x 10(3) m(-1), respectively. The only model able to rationalize mobility data implies that metal ion binds to the P-O peptide form. Moreover, mobility values indicated a change of bacitracin A(1) acidic properties on Ni2+ and Cu2+ binding, with a shift of the pK(a), of N-terminal Ile-1 from 7.6 to about 5 and of the pK(a) of the delta-amino group Of D-Orn-7 from 9.7 to about 7. Even though on Zn2+ binding a shift of the N-terminal Ile-1 pK(a) was observed, restrictions in the pH range suitable for investigation, due to precipitation phenomena, did not allow establish if the shift Of D-Orn-7 lateral chain pK(a) also occurred. Nonetheless, if present, the shift should be limited to the 7.8-9.7 range. Mobility data indicated that the Stokes radius of the complexes is ca. 3 Angstrom lower than that of the free peptide. The present results indicate that metal-ion binding to bacitracin A(1) is more complex than previously assumed

Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes

Burkitt lymphoma (BL) is classified into 3 clinical subsets: endemic, sporadic, and immunodeficiency-associated BL. So far, possible differences in their gene expression profiles (GEPs) have not been investigated. We studied GEPs of BL subtypes, other B-cell lymphomas, and B lymphocytes; first, we found that BL is a unique molecular entity, distinct from other B-cell malignancies. Indeed, by unsupervised analysis all BLs clearly clustered apart of other lymphomas. Second, we found that BL subtypes presented slight differences in GEPs. Particularly, they differed for genes involved in cell cycle control, B-cell receptor signaling, and tumor necrosis factor/nuclear factor \u3baB pathways. Notably, by reverse engineering, we found that endemic and sporadic BLs diverged for genes dependent on RBL2 activity. Furthermore, we found that all BLs were intimately related to germinal center cells, differing from them for molecules involved in cell proliferation, immune response, and signal transduction. Finally, to validate GEP, we applied immunohistochemistry to a large panel of cases and showed that RBL2 can cooperate with MYC in inducing a neoplastic phenotype in vitro and in vivo. In conclusion, our study provided substantial insights on the pathobiology of BLs, by offering novel evidences that may be relevant for its classification and possibly future treatment